Sample records for include biological classification

  1. Functions in Biological Kind Classification (United States)

    Lombrozo, Tania; Rehder, Bob


    Biological traits that serve functions, such as a zebra's coloration (for camouflage) or a kangaroo's tail (for balance), seem to have a special role in conceptual representations for biological kinds. In five experiments, we investigate whether and why functional features are privileged in biological kind classification. Experiment 1…

  2. Biological signals classification and analysis

    CERN Document Server

    Kiasaleh, Kamran


    This authored monograph presents key aspects of signal processing analysis in the biomedical arena. Unlike wireless communication systems, biological entities produce signals with underlying nonlinear, chaotic nature that elude classification using the standard signal processing techniques, which have been developed over the past several decades for dealing primarily with standard communication systems. This book separates what is random from that which appears to be random, and yet is truly deterministic with random appearance. At its core, this work gives the reader a perspective on biomedical signals and the means to classify and process such signals. In particular, a review of random processes along with means to assess the behavior of random signals is also provided. The book also includes a general discussion of biological signals in order to demonstrate the inefficacy of the well-known techniques to correctly extract meaningful information from such signals. Finally, a thorough discussion of recently ...


    African Journals Online (AJOL)

    The biologic and economic effects of including three agro-industrial by-products as ingredients in turkey poult diets were investigated using 48 turkey poults in a completely randomised design experiment. Diets were formulated to contain the three by-products – wheat offal, rice husk and palm kernel meal, each at 20% level ...

  4. Rapid classification of biological components

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, Vicki S. (Idaho Falls, ID); Barrett, Karen B. (Meridian, ID); Key, Diane E. (Idaho Falls, ID)


    A method is disclosed for analyzing a biological sample by antibody profiling for identifying forensic samples or for detecting the presence of an analyte. In an illustrative embodiment of the invention, the analyte is a drug, such as marijuana, Cocaine (crystalline tropane alkaloid), methamphetamine, methyltestosterone, or mesterolone. The method involves attaching antigens of the surface of a solid support in a preselected pattern to form an array wherein the locations of the antigens are known; contacting the array with the biological sample such that a portion of antibodies in the sample reacts with and binds to antigens in the array, thereby forming immune complexes; washing away antibodies that do not form immune complexes; and detecting the immune complexes, thereby forming an antibody profile. Forensic samples are identified by comparing a sample from an unknown source with a sample from a known source. Further, an assay, such as a test for illegal drug use, can be coupled to a test for identity such that the results of the assay can be positively correlated to a subject's identity.

  5. Rapid classification of biological components

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, Vicki S.; Barrett, Karen B.; Key, Diane E.


    A method is disclosed for analyzing a biological sample by antibody profiling for identifying forensic samples or for detecting the presence of an analyte. In an illustrative embodiment of the invention, the analyte is a drug, such as marijuana, cocaine (crystalline tropane alkaloid), methamphetamine, methyltestosterone, or mesterolone. The method involves attaching antigens to a surface of a solid support in a preselected pattern to form an array wherein the locations of the antigens are known; contacting the array with the biological sample such that a portion of antibodies in the sample reacts with and binds to antigens in the array, thereby forming immune complexes; washing away antibodies that do not form immune complexes; and detecting the immune complexes, thereby forming an antibody profile. Forensic samples are identified by comparing a sample from an unknown source with a sample from a known source. Further, an assay, such as a test for illegal drug use, can be coupled to a test for identity such that the results of the assay can be positively correlated to a subject's identity.

  6. Rapid classification of biological components

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, Vicki S. (Idaho Falls, ID); Barrett, Karen B. (Meridian, ID); Key, Diane E. (Idaho Falls, ID)


    A method is disclosed for analyzing a biological sample by antibody profiling for identifying forensic samples or for detecting the presence of an analyte. In an illustrative embodiment of the invention, the analyte is a drug, such as marijuana, cocaine (crystalline tropane alkaloid), methamphetamine, methyltestosterone, or mesterolone. The method involves attaching antigens to a surface of a solid support in a preselected pattern to form an array wherein the locations of the antigens are known; contacting the array with the biological sample such that a portion of antibodies in the sample reacts with and binds to antigens in the array, thereby forming immune complexes; washing away antibodies that do not form immune complexes; and detecting the immune complexes, thereby forming an antibody profile. Forensic samples are identified by comparing a sample from an unknown source with a sample from a known source. Further, an assay, such as a test for illegal drug use, can be coupled to a test for identity such that the results of the assay can be positively correlated to a subject's identity.

  7. Rapid classification of biological components

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, Vicki S.; Barrett, Karen B.; Key, Diane E.


    A method is disclosed for analyzing a biological sample by antibody profiling for identifying forensic samples or for detecting the presence of an analyte. In an illustrative embodiment of the invention, the analyte is a drug, such as marijuana, cocaine, methamphetamine, methyltestosterone, or mesterolone. The method involves attaching antigens to the surface of a solid support in a preselected pattern to form an array wherein the locations of the antigens are known; contacting the array with the biological sample such that a portion of antibodies in the sample reacts with and binds to antigens in the array, thereby forming immune complexes; washing away antibodies that do form immune complexes; and detecting the immune complexes, thereby forming an antibody profile. Forensic samples are identified by comparing a sample from an unknown source with a sample from a known source. Further, an assay, such as a test for illegal drug use, can be coupled to a test for identity such that the results of the assay can be positively correlated to the subject's identity.

  8. Classification of Recombinant Biologics in the EU

    DEFF Research Database (Denmark)

    Klein, Kevin; De Bruin, Marie L; Broekmans, Andre W


    BACKGROUND AND OBJECTIVE: Biological medicinal products (biologics) are subject to specific pharmacovigilance requirements to ensure that biologics are identifiable by brand name and batch number in adverse drug reaction (ADR) reports. Since Member States collect ADR data at the national level...... before the data is aggregated at the European Union (EU) level, it is important that an unambiguous understanding of which medicinal products belong to the biological product category exists. This study aimed to identify the level of consistency between Member States regarding the classification...... of biologics by national authorities responsible for ADR reporting. METHODS: A sample list of recombinant biologics from the European Medicines Agency database of European Public Assessment Reports was created to analyze five Member States (Belgium, the Netherlands, Spain, Sweden, and the UK) according...

  9. Segmentation and classification of biological objects

    DEFF Research Database (Denmark)

    Schultz, Nette


    The present thesis is on segmentation and classification of biological objects using statistical methods. It is based on case studies dealing with different kinds of pork meat images, and we introduce appropriate statistical methods to solve the tasks in the case studies. The case studies concern...... classification of back bacon slices from images of back bacon, prediction of ham weight from images of the carcass, and estimation of meat percent from cross-sectional images of the carcass. The first case study investigates three different classifiers ability to classify the quality of back bacon slices....... The back bacon slices are classified into four ordered classes representing the quality, and we use the sizes of different meat and fat areas of the slices as variables. The classifiers are Bayesian discriminant functions, Classification and Regression Trees, and feed-forward neural networks with back...

  10. Saving our science from ourselves: the plight of biological classification

    Directory of Open Access Journals (Sweden)

    Malte C. Ebach


    Full Text Available Saving our science from ourselves: the plight of biological classification. Biological classification ( nomenclature, taxonomy, and systematics is being sold short. The desire for new technologies, faster and cheaper taxonomic descriptions, identifications, and revisions is symptomatic of a lack of appreciation and understanding of classification. The problem of gadget-driven science, a lack of best practice and the inability to accept classification as a descriptive and empirical science are discussed. The worst cases scenario is a future in which classifications are purely artificial and uninformative.

  11. How Many Kingdoms? Current Views of Biological Classification. (United States)

    Margulis, Lynn


    Argues for the acceptance and use of a five-kingdom classification system for biology comprised of monera, protoctista, fungi, animals, and plants. Justifies the new system based upon the difference between prokaryotes and eukaryotes. Outlines each kingdom and describes its members. (DC)

  12. A genetic and biologic classification of infantile spasms (United States)

    Paciorkowski, Alex R.; Thio, Liu Lin; Dobyns, William B.


    Infantile spasms are an age-dependent epilepsy that are highly associated with cognitive impairment, autism, and movement disorders. Previous classification systems have focused on a distinction between symptomatic and cryptogenic etiologies, and have not kept pace with the recent discoveries of mutations in genes in key pathways of central nervous system development in patients with infantile spasms. Children with certain genetic syndromes are much more likely to have infantile spasms, and we review the literature to propose a genetic classification of these disorders. Children with these genetic associations with infantile spasms also have phenotypes beyond epilepsy that may be explained by recent advances in the understanding of underlying biological mechanisms. We therefore also propose a biologic classification of the genes highly associated with infantile spasms, and articulate models for infantile spasms pathogenesis based on that data. The two best described pathways of pathogenesis are abnormalities in the gene regulatory network of GABAergic forebrain development, and abnormalities in molecules expressed at the synapse. We intend for these genetic and biologic classifications to be flexible, and hope that they will encourage much needed progress in syndrome recognition, clinical genetic testing, and ultimately the development of new therapies that target specific pathways of pathogenesis. PMID:22114996

  13. Literature classification for semi-automated updating of biological knowledgebases

    DEFF Research Database (Denmark)

    Olsen, Lars Rønn; Kudahl, Ulrich Johan; Winther, Ole


    abstracts yielded classification accuracy of 0.95, thus showing significant value in support of data extraction from the literature. Conclusion: We here propose a conceptual framework for semi-automated extraction of epitope data embedded in scientific literature using principles from text mining...... types of biological data, such as sequence data, are extensively stored in biological databases, functional annotations, such as immunological epitopes, are found primarily in semi-structured formats or free text embedded in primary scientific literature. Results: We defined and applied a machine...... learning approach for literature classification to support updating of TANTIGEN, a knowledgebase of tumor T-cell antigens. Abstracts from PubMed were downloaded and classified as either "relevant" or "irrelevant" for database update. Training and five-fold cross-validation of a k-NN classifier on 310...

  14. Histological image classification using biologically interpretable shape-based features

    International Nuclear Information System (INIS)

    Kothari, Sonal; Phan, John H; Young, Andrew N; Wang, May D


    Automatic cancer diagnostic systems based on histological image classification are important for improving therapeutic decisions. Previous studies propose textural and morphological features for such systems. These features capture patterns in histological images that are useful for both cancer grading and subtyping. However, because many of these features lack a clear biological interpretation, pathologists may be reluctant to adopt these features for clinical diagnosis. We examine the utility of biologically interpretable shape-based features for classification of histological renal tumor images. Using Fourier shape descriptors, we extract shape-based features that capture the distribution of stain-enhanced cellular and tissue structures in each image and evaluate these features using a multi-class prediction model. We compare the predictive performance of the shape-based diagnostic model to that of traditional models, i.e., using textural, morphological and topological features. The shape-based model, with an average accuracy of 77%, outperforms or complements traditional models. We identify the most informative shapes for each renal tumor subtype from the top-selected features. Results suggest that these shapes are not only accurate diagnostic features, but also correlate with known biological characteristics of renal tumors. Shape-based analysis of histological renal tumor images accurately classifies disease subtypes and reveals biologically insightful discriminatory features. This method for shape-based analysis can be extended to other histological datasets to aid pathologists in diagnostic and therapeutic decisions

  15. Molecular classification of pesticides including persistent organic pollutants, phenylurea and sulphonylurea herbicides. (United States)

    Torrens, Francisco; Castellano, Gloria


    Pesticide residues in wine were analyzed by liquid chromatography-tandem mass spectrometry. Retentions are modelled by structure-property relationships. Bioplastic evolution is an evolutionary perspective conjugating effect of acquired characters and evolutionary indeterminacy-morphological determination-natural selection principles; its application to design co-ordination index barely improves correlations. Fractal dimensions and partition coefficient differentiate pesticides. Classification algorithms are based on information entropy and its production. Pesticides allow a structural classification by nonplanarity, and number of O, S, N and Cl atoms and cycles; different behaviours depend on number of cycles. The novelty of the approach is that the structural parameters are related to retentions. Classification algorithms are based on information entropy. When applying procedures to moderate-sized sets, excessive results appear compatible with data suffering a combinatorial explosion. However, equipartition conjecture selects criterion resulting from classification between hierarchical trees. Information entropy permits classifying compounds agreeing with principal component analyses. Periodic classification shows that pesticides in the same group present similar properties; those also in equal period, maximum resemblance. The advantage of the classification is to predict the retentions for molecules not included in the categorization. Classification extends to phenyl/sulphonylureas and the application will be to predict their retentions.

  16. Molecular Classification of Pesticides Including Persistent Organic Pollutants, Phenylurea and Sulphonylurea Herbicides

    Directory of Open Access Journals (Sweden)

    Francisco Torrens


    Full Text Available Pesticide residues in wine were analyzed by liquid chromatography–tandem mass spectrometry. Retentions are modelled by structure–property relationships. Bioplastic evolution is an evolutionary perspective conjugating effect of acquired characters and evolutionary indeterminacy–morphological determination–natural selection principles; its application to design co-ordination index barely improves correlations. Fractal dimensions and partition coefficient differentiate pesticides. Classification algorithms are based on information entropy and its production. Pesticides allow a structural classification by nonplanarity, and number of O, S, N and Cl atoms and cycles; different behaviours depend on number of cycles. The novelty of the approach is that the structural parameters are related to retentions. Classification algorithms are based on information entropy. When applying procedures to moderate-sized sets, excessive results appear compatible with data suffering a combinatorial explosion. However, equipartition conjecture selects criterion resulting from classification between hierarchical trees. Information entropy permits classifying compounds agreeing with principal component analyses. Periodic classification shows that pesticides in the same group present similar properties; those also in equal period, maximum resemblance. The advantage of the classification is to predict the retentions for molecules not included in the categorization. Classification extends to phenyl/sulphonylureas and the application will be to predict their retentions.

  17. Conceptions of high school students on the theme Biological Classification

    Directory of Open Access Journals (Sweden)

    Leandro de Oliveira Costa


    Full Text Available The diversity of forms and behaviors by the biodiversity is found fascinating for the human mind since immemorial times generating hypotheses about the relationship between living organisms and extinct. Today a part of biology works from the standpoint of constructing phylogenies, which is based on assumptions of evolutionary relatedness, knowledge that is very important with regard to the teaching of biology. We intend in this work to know the evolutionary conceptions which high school students use to explain the origin of diversity and its current classification. Typological explanations are the most frequent, but a phylogenetic speech seems to appear at certain times, which opens the possibility of exploring it’s pedagogical aspects by teachers.

  18. SECLAF: A Webserver and Deep Neural Network Design Tool for Hierarchical Biological Sequence Classification. (United States)

    Szalkai, Balázs; Grolmusz, Vince


    Artificial intelligence (AI) tools are gaining more and more ground each year in bioinformatics. Learning algorithms can be taught for specific tasks by using the existing enormous biological databases, and the resulting models can be used for the high-quality classification of novel, un-categorized data in numerous areas, including biological sequence analysis. Here we introduce SECLAF, a webserver that uses deep neural networks for hierarchical biological sequence classification. By applying SECLAF for residue-sequences, we have reported (Methods (2018), the most accurate multi-label protein classifier to date (UniProt -into 698 classes- AUC 99.99%; Gene Ontology -into 983 classes- AUC 99.45%). Our framework SECLAF can be applied for other sequence classification tasks, as we describe in the present contribution. The program SECLAF is implemented in Python, and is available for download, with example datasets at the website For Gene Ontology and UniProt based classifications a webserver is also available at the address above. and

  19. Classification of biological signals using linear and nonlinear features. (United States)

    Balli, T; Palaniappan, R


    This paper investigates the characterization ability of linear and nonlinear features and proposes combining such features in order to improve the classification of biological signals, in particular single-trial electroencephalogram (EEG) and electrocardiogram (ECG) data. For this purpose, three data sets composed of ECG, epileptic EEG and finger-movement EEG were utilized. The characterization ability of seven nonlinear features namely the approximate entropy, largest Lyapunov exponents, correlation dimension, nonlinear prediction error, Hurst exponent, higher order autocovariance and asymmetry due to time reversal are compared with two linear features namely the autoregressive (AR) reflection coefficients and AR model coefficients. The features were tested by their ability to differentiate between different classes of data using a linear discriminant analysis (LDA) method with tenfold cross-validation. The class separability of combined linear and nonlinear features was assessed using sequential floating forward search with linear discriminant analysis method (SFFS-LDA). The results demonstrated that linear and nonlinear features on their own provided comparable results for the ECG data set and the finger-movement EEG data set whilst the linear features provided a better class separability compared to nonlinear features for the epileptic EEG data set. Combining linear and nonlinear features demonstrated a significant improvement in the class separability for all of the data sets where an average improvement of 20.56% was obtained with the ECG data set, 7.45% with finger-movement data set and 6.62% with the epileptic EEG data set. Overall results suggest that the use of combined linear and nonlinear feature sets would be a better approach for the characterization and classification of biological signals such as EEG and ECG.

  20. Biological treatment of inorganic ion contamination including radionuclides

    International Nuclear Information System (INIS)

    Cherry, R.S.


    Microorganisms and plants are capable of a broad range of activities useful in treating inorganic contaminants in soil, groundwater, and surface runoff water Among the advantages of biological processes for this purpose are relatively low costs (related to their mild conditions) and the practicality of letting them run unattended. This talk will review both kinds of treatment chemistry that can be done biologically as well as present data from INEEL projects on bioremediation of specific elements. Biological processes can either solubilize or immobilize metals and other ions depending on the need. Uranium ions are solubilized from soil by the local bioproduction of organic acids as chelating agents, allowing removal of this ion as part of an ex-situ treatment process. Further, the microbial production of sulfuric acid can be used to solubilize Cs contamination in concrete surfaces. More usual though is the need to control metal movement in soil or water. Various metals such as Se and Cd are taken up from soil by hyper-accumulating plants, where they can be harvested in concentrated form in the leaves and stems. Excess acidity and a broad variety of toxic metals in acid rock drainage, such as Hg, Cd, Zn and others, can be removed by the production of sulfide ion in an easily fielded biological reactor which may be useful on phosphate processing runoff water contaminated with naturally occuring radioactive materials. Soluble Co, Cu, and Cd can be treated by sorption onto immobilized algae. Inorganic ions can also be directly reduced by bacteria as part of treatment, for example the conversion of soluble selenate ion to insoluble elemental selenium and the conversion of highly toxic CR(VI) to the far less soluble and less toxic Cr(III)

  1. 77 FR 40090 - Proposed Collection of Information; Comment Request: Biological Sciences Proposal Classification... (United States)


    ... NATIONAL SCIENCE FOUNDATION Proposed Collection of Information; Comment Request: Biological Sciences Proposal Classification Form AGENCY: National Science Foundation. ACTION: Notice. SUMMARY: The... Biological Sciences has a continuing commitment to monitor its information collection in order to preserve...

  2. Aspen biology, community classification, and management in the Blue Mountains (United States)

    David K. Swanson; Craig L. Schmitt; Diane M. Shirley; Vicky Erickson; Kenneth J. Schuetz; Michael L. Tatum; David C. Powell


    Quaking aspen (Populus tremuloides Michx.) is a valuable species that is declining in the Blue Mountains of northeastern Oregon. This publication is a compilation of over 20 years of aspen management experience by USDA Forest Service workers in the Blue Mountains. It includes a summary of aspen biology and occurrence in the Blue Mountains, and a...


    Directory of Open Access Journals (Sweden)

    Spinello Antinori


    Full Text Available Malaria is a vector-borne infection caused by unicellular parasite of the genus Plasmodium. Plasmodia are obligate intracellular parasites that in humans after a clinically silent replication phase in the liver are able to infect and replicate within the erythrocytes. Four species (P.falciparum, P.malariae, P.ovale and P.vivax are traditionally recognized as responsible of natural infection in human beings but the recent upsurge of P.knowlesi malaria in South-East Asia has led clinicians to consider it as the fifth human malaria parasite. Recent studies in wild-living apes in Africa have revealed that P.falciparum, the most deadly form of human malaria, is not only human-host restricted as previously believed and its phylogenetic lineage is much more complex with new species identified in gorilla, bonobo and chimpanzee. Although less impressive, new data on biology of P.malariae, P.ovale and P.vivax are also emerging and will be briefly discussed in this review.

  4. A proposal for the classification of biological weapons sensu lato. (United States)

    Rozsa, Lajos


    Due to historical and legislation reasons, the category of bioweapons is rather poorly defined. Authors often disagree on involving or excluding agents like hormones, psychochemicals, certain plants and animals (such as weeds or pests) or synthetic organisms. Applying a wide definition apparently threatens by eroding the regime of international legislation, while narrow definitions abandon several important issues. Therefore, I propose a category of 'biological weapons sensu lato' (BWsl) that is defined here as any tool of human aggression whose acting principle is based on disciplines of biology including particularly microbiology, epidemiology, medical biology, physiology, psychology, pharmacology and ecology, but excluding those based on inorganic agents. Synthetically produced equivalents (not necessarily exact copies) and mock weapons are also included. This definition does not involve any claim to subject all these weapons to international legislation but serves a purely scholarly purpose. BWsl may be properly categorized on the base of the magnitude of the human population potentially targeted (4 levels: individuals, towns, countries, global) and the biological nature of the weapons' intended effects (4 levels: agricultural-ecological agents, and non-pathogenic, pathogenic, or lethal agents against humans).

  5. Classification

    DEFF Research Database (Denmark)

    Hjørland, Birger


    This article presents and discusses definitions of the term “classification” and the related concepts “Concept/conceptualization,”“categorization,” “ordering,” “taxonomy” and “typology.” It further presents and discusses theories of classification including the influences of Aristotle...... and Wittgenstein. It presents different views on forming classes, including logical division, numerical taxonomy, historical classification, hermeneutical and pragmatic/critical views. Finally, issues related to artificial versus natural classification and taxonomic monism versus taxonomic pluralism are briefly...

  6. Effective automated feature construction and selection for classification of biological sequences.

    Directory of Open Access Journals (Sweden)

    Uday Kamath

    Full Text Available Many open problems in bioinformatics involve elucidating underlying functional signals in biological sequences. DNA sequences, in particular, are characterized by rich architectures in which functional signals are increasingly found to combine local and distal interactions at the nucleotide level. Problems of interest include detection of regulatory regions, splice sites, exons, hypersensitive sites, and more. These problems naturally lend themselves to formulation as classification problems in machine learning. When classification is based on features extracted from the sequences under investigation, success is critically dependent on the chosen set of features.We present an algorithmic framework (EFFECT for automated detection of functional signals in biological sequences. We focus here on classification problems involving DNA sequences which state-of-the-art work in machine learning shows to be challenging and involve complex combinations of local and distal features. EFFECT uses a two-stage process to first construct a set of candidate sequence-based features and then select a most effective subset for the classification task at hand. Both stages make heavy use of evolutionary algorithms to efficiently guide the search towards informative features capable of discriminating between sequences that contain a particular functional signal and those that do not.To demonstrate its generality, EFFECT is applied to three separate problems of importance in DNA research: the recognition of hypersensitive sites, splice sites, and ALU sites. Comparisons with state-of-the-art algorithms show that the framework is both general and powerful. In addition, a detailed analysis of the constructed features shows that they contain valuable biological information about DNA architecture, allowing biologists and other researchers to directly inspect the features and potentially use the insights obtained to assist wet-laboratory studies on retainment or modification

  7. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes (United States)


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

  8. Ecological variables, including physiognomic-structural attributes, and classification of Indonesian coral reefs (United States)

    Bak, R. P. M.; Povel, G. D. E.

    Communities are distinguished by biological and physical features, such as size and shape of organisms and dead substrata, which are characteristic expressions of the organizing forces in the community. We measured 87 of such features in 39 transects on seaward-facing reef slopes in the eastern Indonesian archipelago, but did not identify coral species. We aimed to identify the basic variables that are indispensable to classify coral reef communities. This would give ecological information on variation in reef communities and show exactly which data must be recorded in the field. Principal Component Analysis (PCA) of the data matrix showed the following variables to be important in the ordination of transects along the axes: coral colony shape, loose fragments, bare bottom, coral tissue wounds, rubble, sediment/rubble, crustose coralline algae, excavating sponge, miscellaneous organisms, coral overgrowth, interaction coral/non-coral, Acanthaster, maximum size coral colonies, tabular Acropora, massive Porites, fungiids, angle slope, and crevices. We used the transect data to define four groups of environmental conditions: 'sheltered', 'exposed' (to water movement), 'biologically disturbed' and 'physically disturbed'. Discriminant Analysis was employed to classify additional transects. It appeared that a minimum of 9 variables has to be measured in the field (rubble, thick branching corals, fungiids, sediment/rubble, two largest-colonies diameters, massive Porites, angle slope, Acanthaster) to assign transects to one of those groups (P classification of transects was 100% correct. Two additional groups of environmental conditions are recognizable with, respectively, prominence of competitive interactions and Acanthaster predation. There were too few transect data to characterize these groups satisfactorily for Discriminant Analysis.

  9. Classification of Recombinant Biologics in the EU: Divergence Between National Pharmacovigilance Centers. (United States)

    Klein, Kevin; De Bruin, Marie L; Broekmans, Andre W; Stolk, Pieter


    Biological medicinal products (biologics) are subject to specific pharmacovigilance requirements to ensure that biologics are identifiable by brand name and batch number in adverse drug reaction (ADR) reports. Since Member States collect ADR data at the national level before the data is aggregated at the European Union (EU) level, it is important that an unambiguous understanding of which medicinal products belong to the biological product category exists. This study aimed to identify the level of consistency between Member States regarding the classification of biologics by national authorities responsible for ADR reporting. A sample list of recombinant biologics from the European Medicines Agency database of European Public Assessment Reports was created to analyze five Member States (Belgium, the Netherlands, Spain, Sweden, and the UK) according to which products were classified as biologics by each Member State. We calculated the Fleiss kappa value to analyze interrater reliability. A considerable divergence was identified regarding the classification of the 146 recombinant biologics from the sample list: one Member State classified 100 % of the recombinant biologics from the sample list as biologics, whereas the classification rates in the remaining four Member States ranged between 70 and 88 % for products available on the national market. The interrater reliability for 87 products available on the market in all five Member States was considered poor. Discrepancies exist between Member States in the classification of biologics; less divergence exists for common well-known biologics. These findings highlight the need to think about the best approaches to translate EU legislation into national practices. Additionally, we recommend a publicly available and frequently updated list of centrally authorized biologics.

  10. Integrative Chemical-Biological Read-Across Approach for Chemical Hazard Classification (United States)

    Low, Yen; Sedykh, Alexander; Fourches, Denis; Golbraikh, Alexander; Whelan, Maurice; Rusyn, Ivan; Tropsha, Alexander


    Traditional read-across approaches typically rely on the chemical similarity principle to predict chemical toxicity; however, the accuracy of such predictions is often inadequate due to the underlying complex mechanisms of toxicity. Here we report on the development of a hazard classification and visualization method that draws upon both chemical structural similarity and comparisons of biological responses to chemicals measured in multiple short-term assays (”biological” similarity). The Chemical-Biological Read-Across (CBRA) approach infers each compound's toxicity from those of both chemical and biological analogs whose similarities are determined by the Tanimoto coefficient. Classification accuracy of CBRA was compared to that of classical RA and other methods using chemical descriptors alone, or in combination with biological data. Different types of adverse effects (hepatotoxicity, hepatocarcinogenicity, mutagenicity, and acute lethality) were classified using several biological data types (gene expression profiling and cytotoxicity screening). CBRA-based hazard classification exhibited consistently high external classification accuracy and applicability to diverse chemicals. Transparency of the CBRA approach is aided by the use of radial plots that show the relative contribution of analogous chemical and biological neighbors. Identification of both chemical and biological features that give rise to the high accuracy of CBRA-based toxicity prediction facilitates mechanistic interpretation of the models. PMID:23848138

  11. Effect of Process-Oriented Guided-Inquiry Learning on Non-majors Biology Students' Understanding of Biological Classification (United States)

    Wozniak, Breann M.

    The purpose of this study was to examine the effect of process-oriented guided-inquiry learning (POGIL) on non-majors college biology students' understanding of biological classification. This study addressed an area of science instruction, POGIL in the non-majors college biology laboratory, which has yet to be qualitatively and quantitatively researched. A concurrent triangulation mixed methods approach was used. Students' understanding of biological classification was measured in two areas: scores on pre and posttests (consisting of 11 multiple choice questions), and conceptions of classification as elicited in pre and post interviews and instructor reflections. Participants were Minnesota State University, Mankato students enrolled in BIOL 100 Summer Session. One section was taught with the traditional curriculum (n = 6) and the other section in the POGIL curriculum (n = 10) developed by the researcher. Three students from each section were selected to take part in pre and post interviews. There were no significant differences within each teaching method (p group may have scored higher on the posttest (M = 8.830 +/- .477 vs. M = 7.330 +/- .330; z =-1.729, p = .084) and the traditional group may have scored higher on the pretest than the posttest (M = 8.333 +/- .333 vs M = 7.333 +/- .333; z = -1.650 , p = .099). Two themes emerged after the interviews and instructor reflections: 1) After instruction students had a more extensive understanding of classification in three areas: vocabulary terms, physical characteristics, and types of evidence used to classify. Both groups extended their understanding, but only POGIL students could explain how molecular evidence is used in classification. 2) The challenges preventing students from understanding classification were: familiar animal categories and aquatic habitats, unfamiliar organisms, combining and subdividing initial groupings, and the hierarchical nature of classification. The POGIL students were the only group to

  12. Antiphospholipid syndrome (APS) revisited: Would migraine headaches be included in future classification criteria? (United States)

    Noureldine, Mohammad Hassan A; Haydar, Ali A; Berjawi, Ahmad; Elnawar, Rody; Sweid, Ahmad; Khamashta, Munther A; Hughes, Graham R V; Uthman, Imad


    Headaches have been extensively reported in Antiphospholipid syndrome (APS)/Antiphospholipid antibodies (aPL)-positive patients. The aim of this study was to highlight the prevalence of headaches among APS/aPL-positive patients and discuss its association with laboratory, clinical and imaging findings. We searched the literature through Google Scholar and PubMed for publications on the epidemiology, pathogenesis, laboratory, imaging and clinical findings, and management of headaches in APS/aPL-positive patients. The following keywords were used: Antiphospholipid, Hughes syndrome, anticardiolipin, lupus anticoagulant, anti-β2 glycoprotein I, headache, migraine, tension, and cluster. All reports published between 1969 and 2015 were included. Migraine is the most commonly reported type of headache in APS/aPL-positive patients. Thrombotic and platelet dysfunction hypotheses have been studied to uncover the pathogenic role of aPL in the development of headaches. Several studies are reporting higher levels of aPL in primary and secondary APS migraineurs, but only few reached statistical significance. Migraine patients without clinical signs/symptoms of cerebral infarction rarely show positive imaging findings. Digital subtraction angiography shows promise in demonstrating small vascular lesions otherwise not detected on computed tomography, magnetic resonance imaging, or cerebral angiograms. Although it may be solitary and harmless in many cases, the deleterious effect of migraine on the quality of life of APS patients prompts rapid diagnosis and proper management. An anticoagulation trial is advisable in APS patients with migraine as many cases of severe, refractory migraine resolved with anticoagulation therapy. The profile of migraine headaches discussed in this study permits its candidacy for inclusion in future APS classification criteria.

  13. Molecular biology of glioblastoma: Classification and mutational locations. (United States)

    Soomro, Shahid Hussain; Ting, Li Rui; Qing, Yang Yi; Ren, Mingxin


    Glioblastomas are regarded as the most common malignant brain tumours with great morphological and genetical heterogeneity. They comprise 12% to 15% of all intracranial tumours, with its peak observed in the 8th decade of life. The five-year survival is only 5%. Primary glioblastomas are more common in elders while secondary glioblastomas mostly involve younger people. Based upon gene expression profile, researchers have classified glioblastomas into several subtypes. Genetic mutations provide an advanced standard platform essential for diagnosis, therapeutic remedies and prognosis of glioblastomas. Common mutations observed in glioblastomas are loss of heterozygosity at 10q followed by epidermal growth factor receptor amplification (34%) and others. Vascular occlusion model and tumour stem cell model can explain the possible mechanism in glioblastomas pathogenesis. This review highlights glioblastomas' classifications, genetic mutations, pathogenesis and prognosis of different sub-types.

  14. Application of Machine Learning to Proteomics Data: Classification and Biomarker Identification in Postgenomics Biology (United States)

    Swan, Anna Louise; Mobasheri, Ali; Allaway, David; Liddell, Susan


    Abstract Mass spectrometry is an analytical technique for the characterization of biological samples and is increasingly used in omics studies because of its targeted, nontargeted, and high throughput abilities. However, due to the large datasets generated, it requires informatics approaches such as machine learning techniques to analyze and interpret relevant data. Machine learning can be applied to MS-derived proteomics data in two ways. First, directly to mass spectral peaks and second, to proteins identified by sequence database searching, although relative protein quantification is required for the latter. Machine learning has been applied to mass spectrometry data from different biological disciplines, particularly for various cancers. The aims of such investigations have been to identify biomarkers and to aid in diagnosis, prognosis, and treatment of specific diseases. This review describes how machine learning has been applied to proteomics tandem mass spectrometry data. This includes how it can be used to identify proteins suitable for use as biomarkers of disease and for classification of samples into disease or treatment groups, which may be applicable for diagnostics. It also includes the challenges faced by such investigations, such as prediction of proteins present, protein quantification, planning for the use of machine learning, and small sample sizes. PMID:24116388

  15. BIOCAT: a pattern recognition platform for customizable biological image classification and annotation. (United States)

    Zhou, Jie; Lamichhane, Santosh; Sterne, Gabriella; Ye, Bing; Peng, Hanchuan


    Pattern recognition algorithms are useful in bioimage informatics applications such as quantifying cellular and subcellular objects, annotating gene expressions, and classifying phenotypes. To provide effective and efficient image classification and annotation for the ever-increasing microscopic images, it is desirable to have tools that can combine and compare various algorithms, and build customizable solution for different biological problems. However, current tools often offer a limited solution in generating user-friendly and extensible tools for annotating higher dimensional images that correspond to multiple complicated categories. We develop the BIOimage Classification and Annotation Tool (BIOCAT). It is able to apply pattern recognition algorithms to two- and three-dimensional biological image sets as well as regions of interest (ROIs) in individual images for automatic classification and annotation. We also propose a 3D anisotropic wavelet feature extractor for extracting textural features from 3D images with xy-z resolution disparity. The extractor is one of the about 20 built-in algorithms of feature extractors, selectors and classifiers in BIOCAT. The algorithms are modularized so that they can be "chained" in a customizable way to form adaptive solution for various problems, and the plugin-based extensibility gives the tool an open architecture to incorporate future algorithms. We have applied BIOCAT to classification and annotation of images and ROIs of different properties with applications in cell biology and neuroscience. BIOCAT provides a user-friendly, portable platform for pattern recognition based biological image classification of two- and three- dimensional images and ROIs. We show, via diverse case studies, that different algorithms and their combinations have different suitability for various problems. The customizability of BIOCAT is thus expected to be useful for providing effective and efficient solutions for a variety of biological

  16. iTools: a framework for classification, categorization and integration of computational biology resources. (United States)

    Dinov, Ivo D; Rubin, Daniel; Lorensen, William; Dugan, Jonathan; Ma, Jeff; Murphy, Shawn; Kirschner, Beth; Bug, William; Sherman, Michael; Floratos, Aris; Kennedy, David; Jagadish, H V; Schmidt, Jeanette; Athey, Brian; Califano, Andrea; Musen, Mark; Altman, Russ; Kikinis, Ron; Kohane, Isaac; Delp, Scott; Parker, D Stott; Toga, Arthur W


    The advancement of the computational biology field hinges on progress in three fundamental directions--the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources--data, software tools and web-services. The iTools design, implementation and resource meta-data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long-term resource management

  17. iTools: a framework for classification, categorization and integration of computational biology resources.

    Directory of Open Access Journals (Sweden)

    Ivo D Dinov


    Full Text Available The advancement of the computational biology field hinges on progress in three fundamental directions--the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources--data, software tools and web-services. The iTools design, implementation and resource meta-data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long

  18. A collection of annotated and harmonized human breast cancer transcriptome datasets, including immunologic classification. (United States)

    Roelands, Jessica; Decock, Julie; Boughorbel, Sabri; Rinchai, Darawan; Maccalli, Cristina; Ceccarelli, Michele; Black, Michael; Print, Cris; Chou, Jeff; Presnell, Scott; Quinn, Charlie; Jithesh, Puthen; Syed, Najeeb; Al Bader, Salha B J; Bedri, Shahinaz; Wang, Ena; Marincola, Francesco M; Chaussabel, Damien; Kuppen, Peter; Miller, Lance D; Bedognetti, Davide; Hendrickx, Wouter


    The increased application of high-throughput approaches in translational research has expanded the number of publicly available data repositories. Gathering additional valuable information contained in the datasets represents a crucial opportunity in the biomedical field. To facilitate and stimulate utilization of these datasets, we have recently developed an interactive data browsing and visualization web application, the Gene Expression Browser (GXB). In this note, we describe a curated compendium of 13 public datasets on human breast cancer, representing a total of 2142 transcriptome profiles. We classified the samples according to different immune based classification systems and integrated this information into the datasets. Annotated and harmonized datasets were uploaded to GXB. Study samples were categorized in different groups based on their immunologic tumor response profiles, intrinsic molecular subtypes and multiple clinical parameters. Ranked gene lists were generated based on relevant group comparisons. In this data note, we demonstrate the utility of GXB to evaluate the expression of a gene of interest, find differential gene expression between groups and investigate potential associations between variables with a specific focus on immunologic classification in breast cancer. This interactive resource is publicly available online at:

  19. A Biologically Inspired Approach to Frequency Domain Feature Extraction for EEG Classification

    Directory of Open Access Journals (Sweden)

    Nurhan Gursel Ozmen


    Full Text Available Classification of electroencephalogram (EEG signal is important in mental decoding for brain-computer interfaces (BCI. We introduced a feature extraction approach based on frequency domain analysis to improve the classification performance on different mental tasks using single-channel EEG. This biologically inspired method extracts the most discriminative spectral features from power spectral densities (PSDs of the EEG signals. We applied our method on a dataset of six subjects who performed five different imagination tasks: (i resting state, (ii mental arithmetic, (iii imagination of left hand movement, (iv imagination of right hand movement, and (v imagination of letter “A.” Pairwise and multiclass classifications were performed in single EEG channel using Linear Discriminant Analysis and Support Vector Machines. Our method produced results (mean classification accuracy of 83.06% for binary classification and 91.85% for multiclassification that are on par with the state-of-the-art methods, using single-channel EEG with low computational cost. Among all task pairs, mental arithmetic versus letter imagination yielded the best result (mean classification accuracy of 90.29%, indicating that this task pair could be the most suitable pair for a binary class BCI. This study contributes to the development of single-channel BCI, as well as finding the best task pair for user defined applications.

  20. An Evaluation of Peak Finding for DVR Classification of Biological Data

    KAUST Repository

    Knoll, Aaron


    In medicine and the life sciences, volume data are frequently entropic, containing numerous features at different scales as well as significant noise from the scan source. Conventional transfer function approaches for direct volume rendering have difficulty handling such data, resulting in poor classification or undersampled rendering. Peak finding addresses issues in classifying noisy data by explicitly solving for isosurfaces at desired peaks in a transfer function. As a result, one can achieve better classification and visualization with fewer samples and correspondingly higher performance. This paper applies peak finding to several medical and biological data sets, particularly examining its potential in directly rendering unfiltered and unsegmented data.

  1. Benthic indicators to use in Ecological Quality classification of Mediterranean soft bottom marine ecosystems, including a new Biotic Index

    Directory of Open Access Journals (Sweden)



    Full Text Available A general scheme for approaching the objective of Ecological Quality Status (EcoQ classification of zoobenthic marine ecosystems is presented. A system based on soft bottom benthic indicator species and related habitat types is suggested to be used for testing the typological definition of a given water body in the Mediterranean. Benthic indices including the Shannon-Wiener diversity index and the species richness are re-evaluated for use in classification. Ranges of values and of ecological quality categories are given for the diversity and species richness in different habitat types. A new biotic index (BENTIX is proposed based on the relative percentages of three ecological groups of species grouped according to their sensitivity or tolerance to disturbance factors and weighted proportionately to obtain a formula rendering a five step numerical scale of ecological quality classification. Its advantage against former biotic indices lies in the fact that it reduces the number of the ecological groups involved which makes it simpler and easier in its use. The Bentix index proposed is tested and validated with data from Greek and western Mediterranean ecosystems and examples are presented. Indicator species associated with specific habitat types and pollution indicator species, scored according to their degree of tolerance to pollution, are listed in a table. The Bentix index is compared and evaluated against the indices of diversity and species richness for use in classification. The advantages of the BENTIX index as a classification tool for ECoQ include independence from habitat type, sample size and taxonomic effort, high discriminative power and simplicity in its use which make it a robust, simple and effective tool for application in the Mediterranean Sea.

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

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


    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

  3. Integrative Biological Chemistry Program Includes the Use of Informatics Tools, GIS and SAS Software Applications (United States)

    D'Souza, Malcolm J.; Kashmar, Richard J.; Hurst, Kent; Fiedler, Frank; Gross, Catherine E.; Deol, Jasbir K.; Wilson, Alora


    Wesley College is a private, primarily undergraduate minority-serving institution located in the historic district of Dover, Delaware (DE). The College recently revised its baccalaureate biological chemistry program requirements to include a one-semester Physical Chemistry for the Life Sciences course and project-based experiential learning…

  4. Biologic basis of TCM syndromes and the standardization of syndrome classification

    Directory of Open Access Journals (Sweden)

    Fafeng Cheng


    Full Text Available Traditional Chinese medicine (TCM syndrome is an integral and essential component of TCM theory, and goes beyond philosophic concepts. This article reviews the concept of TCM syndromes and summarizes research findings on the biologic foundation of syndromes. In addition, insight is provided into the promotion of standardization of syndrome classification by enforcing uniformity of TCM terminology, applying standardized diagnostic criteria and operating procedures to minimize subjective effects. Also incorporating interdisciplinary approaches such as data mining and structure modeling, as well as integrating findings on biomarker research are discussed. Consideration is made of the fundamental TCM aspects of syndrome elements, symptoms, phenotypic features, as well as diseases, to form an integral process in the diagnostic path. We believe that better understanding of the biologic basis of the TCM syndrome and standardization of syndrome classification will improve diagnosis, which in turn will enhance therapeutic efficacy and disease prognosis.

  5. Fungal inhibitors of proteolytic enzymes: classification, properties, possible biological roles, and perspectives for practical use. (United States)

    Dunaevsky, Y E; Popova, V V; Semenova, T A; Beliakova, G A; Belozersky, M A


    Peptidase inhibitors are ubiquitous regulatory proteins controlling catalytic activity of proteolytic enzymes. Interest in these proteins increased substantially after it became clear that they can be used for therapy of various important diseases including cancer, malaria, and autoimmune and neurodegenerative diseases. In this review we summarize available data on peptidase inhibitors from fungi, emphasizing their properties, biological role, and possible practical applications of these proteins in the future. A number of fungal peptidase inhibitors with unique structure and specificity of action have no sequence homology with other classes of peptidase inhibitors, thus representing new and specific candidates for therapeutic use. The main classifications of inhibitors in current use are considered. Available data on structure, mechanisms and conditions of action, and diversity of functions of peptidase inhibitors of fungi are analyzed. It is mentioned that on one side the unique properties of some inhibitors can be used for selective inhibition of peptidases responsible for initiation and development of pathogenic processes. On the other side, general inhibitory activity of other inhibitors towards peptidases of various catalytic classes might be able to provide efficient defense of transgenic plants against insect pests by overcoming compensatory synthesis of new peptidases by these pests in response to introduction of a fungal inhibitor. Together, the data analyzed in this review reveal that fungal inhibitors extend the spectrum of known peptidase inhibitors potentially suitable for use in medicine and agriculture. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  6. Classification Framework and Chemical Biology of Tetracycline-Structure-Based Drugs

    Directory of Open Access Journals (Sweden)

    Domenico Fuoco


    Full Text Available By studying the literature about tetracyclines (TCs, it becomes clearly evident that TCs are very dynamic molecules. In some cases, their structure-activity-relationship (SAR are well known, especially against bacteria, while against other targets, they are virtually unknown. In other diverse fields of research—such as neurology, oncology and virology—the utility and activity of the tetracyclines are being discovered and are also emerging as new technological fronts. The first aim of this paper is to classify the compounds already used in therapy and prepare the schematic structure that includes the next generation of TCs. The second aim of this work is to introduce a new framework for the classification of old and new TCs, using a medicinal chemistry approach to the structure of those drugs. A fully documented Structure-Activity-Relationship (SAR is presented with the analysis data of antibacterial and nonantibacterial (antifungal, antiviral and anticancer tetracyclines. The lipophilicity and the conformational interchangeability of the functional groups are employed to develop the rules for TC biological activity.

  7. Classification (United States)

    Clary, Renee; Wandersee, James


    In this article, Renee Clary and James Wandersee describe the beginnings of "Classification," which lies at the very heart of science and depends upon pattern recognition. Clary and Wandersee approach patterns by first telling the story of the "Linnaean classification system," introduced by Carl Linnacus (1707-1778), who is…

  8. Mammographic quantitative image analysis and biologic image composition for breast lesion characterization and classification

    Energy Technology Data Exchange (ETDEWEB)

    Drukker, Karen, E-mail:; Giger, Maryellen L.; Li, Hui [Department of Radiology, University of Chicago, Chicago, Illinois 60637 (United States); Duewer, Fred; Malkov, Serghei; Joe, Bonnie; Kerlikowske, Karla; Shepherd, John A. [Radiology Department, University of California, San Francisco, California 94143 (United States); Flowers, Chris I. [Department of Radiology, University of South Florida, Tampa, Florida 33612 (United States); Drukteinis, Jennifer S. [Department of Radiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612 (United States)


    Purpose: To investigate whether biologic image composition of mammographic lesions can improve upon existing mammographic quantitative image analysis (QIA) in estimating the probability of malignancy. Methods: The study population consisted of 45 breast lesions imaged with dual-energy mammography prior to breast biopsy with final diagnosis resulting in 10 invasive ductal carcinomas, 5 ductal carcinomain situ, 11 fibroadenomas, and 19 other benign diagnoses. Analysis was threefold: (1) The raw low-energy mammographic images were analyzed with an established in-house QIA method, “QIA alone,” (2) the three-compartment breast (3CB) composition measure—derived from the dual-energy mammography—of water, lipid, and protein thickness were assessed, “3CB alone”, and (3) information from QIA and 3CB was combined, “QIA + 3CB.” Analysis was initiated from radiologist-indicated lesion centers and was otherwise fully automated. Steps of the QIA and 3CB methods were lesion segmentation, characterization, and subsequent classification for malignancy in leave-one-case-out cross-validation. Performance assessment included box plots, Bland–Altman plots, and Receiver Operating Characteristic (ROC) analysis. Results: The area under the ROC curve (AUC) for distinguishing between benign and malignant lesions (invasive and DCIS) was 0.81 (standard error 0.07) for the “QIA alone” method, 0.72 (0.07) for “3CB alone” method, and 0.86 (0.04) for “QIA+3CB” combined. The difference in AUC was 0.043 between “QIA + 3CB” and “QIA alone” but failed to reach statistical significance (95% confidence interval [–0.17 to + 0.26]). Conclusions: In this pilot study analyzing the new 3CB imaging modality, knowledge of the composition of breast lesions and their periphery appeared additive in combination with existing mammographic QIA methods for the distinction between different benign and malignant lesion types.

  9. Combining angular response classification and backscatter imagery segmentation for benthic biological habitat mapping (United States)

    Che Hasan, Rozaimi; Ierodiaconou, Daniel; Laurenson, Laurie


    Backscatter information from multibeam echosounders (MBES) have been shown to contain useful information for the characterisation of benthic habitats. Compared to backscatter imagery, angular response of backscatter has shown advantages for feature discrimination. However its low spatial resolution inhibits the generation of fine scale habitat maps. In this study, angular backscatter response was combined with image segmentation of backscatter imagery to characterise benthic biological habitats in Discovery Bay Marine National Park, Victoria, Australia. Angular response of backscatter data from a Reson Seabat 8101 MBES (240 kHz) was integrated with georeferenced underwater video observations for constructing training data. To produce benthic habitat maps, decision tree supervised classification results were combined with mean shift image segmentation for class assignment. The results from mean angular response characteristics show effects of incidence angle at the outer angle for invertebrates (INV) and mixed red and invertebrates (MRI) classes, whilst mixed brown algae (MB) and mixed brown algae and invertebrates (MBI) showed similar responses independent from incidence angle. Automatic segmentation processing produce over segmented results but showed good discrimination between heterogeneous regions. Accuracy assessment from habitat maps produced overall accuracies of 79.6% (Kappa coefficient = 0.66) and 80.2% (Kappa coefficient = 0.67) for biota and substratum classifications respectively. MRI and MBI produced the lowest average accuracy while INV the highest. The ability to combine angular response and backscatter imagery provides an alternative approach for investigating biological information from acoustic backscatter data.

  10. WHO standards for biotherapeutics, including biosimilars: an example of the evaluation of complex biological products. (United States)

    Knezevic, Ivana; Griffiths, Elwyn


    The most advanced regulatory processes for complex biological products have been put in place in many countries to provide appropriate regulatory oversight of biotherapeutic products in general, and similar biotherapeutics in particular. This process is still ongoing and requires regular updates to national regulatory requirements in line with scientific developments and up-to-date standards. For this purpose, strong knowledge of and expertise in evaluating biotherapeutics in general and similar biotherapeutic products, also called biosimilars, in particular is essential. Here, we discuss the World Health Organization's international standard-setting role in the regulatory evaluation of recombinant DNA-derived biotherapeutic products, including biosimilars, and provide examples that may serve as models for moving forward with nonbiological complex medicinal products. A number of scientific challenges and regulatory considerations imposed by the advent of biosimilars are described, together with the lessons learned, to stimulate future discussions on this topic. In addition, the experiences of facilitating the implementation of guiding principles for evaluation of similar biotherapeutic products into regulatory and manufacturers' practices in various countries over the past 10 years are briefly explained, with the aim of promoting further developments and regulatory convergence of complex biological and nonbiological products. © 2017 The Authors. Annals of the New York Academy of Sciences. The World Health Organization retains copyright and all other rights in the manuscript of this article as submitted for publication.

  11. Safety aspects in biotechnology. Classifications and safety precautions for handling of biological agents. (United States)

    Frommer, W; Krämer, P


    The term "biotechnology" is today used much more widely than 10 years ago. According to the modern definition, biotechnology represents the "conveyor belt" which brings advances in the fields of molecular biology, cell biology, molecular genetics, microbiology, biochemistry and process engineering, etc., into the areas of application. It is attempted to indicate the development of safety standards concerning biotechnology. This development is in a state of flux, and the finding that the risks in handling r-DNA organisms are not larger than those arising when handling the known pathogens is becoming more accepted. Accordingly, these r-DNA organisms can also be classified into the known risk groups I-IV and handled under the corresponding safety conditions according to this classification: In the laboratory under the laboratory safety measures L1-L4 described in the BMFT-Guidelines or guidelines for occupational health and hygiene (UVV Biotechnologie) and on a process scale under the process safety measures described in the OECD report. The discussion of aspects on waste disposal, education/training and public perception in the field of biological safety completes the report.

  12. Availability of MudPIT data for classification of biological samples. (United States)

    Silvestre, Dario Di; Zoppis, Italo; Brambilla, Francesca; Bellettato, Valeria; Mauri, Giancarlo; Mauri, Pierluigi


    Mass spectrometry is an important analytical tool for clinical proteomics. Primarily employed for biomarker discovery, it is increasingly used for developing methods which may help to provide unambiguous diagnosis of biological samples. In this context, we investigated the classification of phenotypes by applying support vector machine (SVM) on experimental data obtained by MudPIT approach. In particular, we compared the performance capabilities of SVM by using two independent collection of complex samples and different data-types, such as mass spectra (m/z), peptides and proteins. Globally, protein and peptide data allowed a better discriminant informative content than experimental mass spectra (overall accuracy higher than 87% in both collection 1 and 2). These results indicate that sequencing of peptides and proteins reduces the experimental noise affecting the raw mass spectra, and allows the extraction of more informative features available for the effective classification of samples. In addition, proteins and peptides features selected by SVM matched for 80% with the differentially expressed proteins identified by the MAProMa software. These findings confirm the availability of the most label-free quantitative methods based on processing of spectral count and SEQUEST-based SCORE values. On the other hand, it stresses the usefulness of MudPIT data for a correct grouping of sample phenotypes, by applying both supervised and unsupervised learning algorithms. This capacity permit the evaluation of actual samples and it is a good starting point to translate proteomic methodology to clinical application.

  13. Classification (United States)

    Oza, Nikunj C.


    A supervised learning task involves constructing a mapping from input data (normally described by several features) to the appropriate outputs. Within supervised learning, one type of task is a classification learning task, in which each output is one or more classes to which the input belongs. In supervised learning, a set of training examples---examples with known output values---is used by a learning algorithm to generate a model. This model is intended to approximate the mapping between the inputs and outputs. This model can be used to generate predicted outputs for inputs that have not been seen before. For example, we may have data consisting of observations of sunspots. In a classification learning task, our goal may be to learn to classify sunspots into one of several types. Each example may correspond to one candidate sunspot with various measurements or just an image. A learning algorithm would use the supplied examples to generate a model that approximates the mapping between each supplied set of measurements and the type of sunspot. This model can then be used to classify previously unseen sunspots based on the candidate's measurements. This chapter discusses methods to perform machine learning, with examples involving astronomy.

  14. Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment

    Directory of Open Access Journals (Sweden)

    Manzini Giovanni


    Full Text Available Abstract Background Similarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. It is currently primarily handled using alignments. However, the alignment methods seem inadequate for post-genomic studies since they do not scale well with data set size and they seem to be confined only to genomic and proteomic sequences. Therefore, alignment-free similarity measures are actively pursued. Among those, USM (Universal Similarity Metric has gained prominence. It is based on the deep theory of Kolmogorov Complexity and universality is its most novel striking feature. Since it can only be approximated via data compression, USM is a methodology rather than a formula quantifying the similarity of two strings. Three approximations of USM are available, namely UCD (Universal Compression Dissimilarity, NCD (Normalized Compression Dissimilarity and CD (Compression Dissimilarity. Their applicability and robustness is tested on various data sets yielding a first massive quantitative estimate that the USM methodology and its approximations are of value. Despite the rich theory developed around USM, its experimental assessment has limitations: only a few data compressors have been tested in conjunction with USM and mostly at a qualitative level, no comparison among UCD, NCD and CD is available and no comparison of USM with existing methods, both based on alignments and not, seems to be available. Results We experimentally test the USM methodology by using 25 compressors, all three of its known approximations and six data sets of relevance to Molecular Biology. This offers the first systematic and quantitative experimental assessment of this methodology, that naturally complements the many theoretical and the preliminary experimental results available. Moreover, we compare the USM methodology both with methods based on alignments and not. We may group our experiments into two sets. The first one, performed via ROC

  15. Using Variable Precision Rough Set for Selection and Classification of Biological Knowledge Integrated in DNA Gene Expression

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    Calvo-Dmgz D.


    Full Text Available DNA microarrays have contributed to the exponential growth of genomic and experimental data in the last decade. This large amount of gene expression data has been used by researchers seeking diagnosis of diseases like cancer using machine learning methods. In turn, explicit biological knowledge about gene functions has also grown tremendously over the last decade. This work integrates explicit biological knowledge, provided as gene sets, into the classication process by means of Variable Precision Rough Set Theory (VPRS. The proposed model is able to highlight which part of the provided biological knowledge has been important for classification. This paper presents a novel model for microarray data classification which is able to incorporate prior biological knowledge in the form of gene sets. Based on this knowledge, we transform the input microarray data into supergenes, and then we apply rough set theory to select the most promising supergenes and to derive a set of easy interpretable classification rules. The proposed model is evaluated over three breast cancer microarrays datasets obtaining successful results compared to classical classification techniques. The experimental results shows that there are not significat differences between our model and classical techniques but it is able to provide a biological-interpretable explanation of how it classifies new samples.

  16. Molecular and morphological data supporting phylogenetic reconstruction of the genus Goniothalamus (Annonaceae), including a reassessment of previous infrageneric classifications. (United States)

    Tang, Chin Cheung; Thomas, Daniel C; Saunders, Richard M K


    Data is presented in support of a phylogenetic reconstruction of the species-rich early-divergent angiosperm genus Goniothalamus (Annonaceae) (Tang et al., Mol. Phylogenetic Evol., 2015) [1], inferred using chloroplast DNA (cpDNA) sequences. The data includes a list of primers for amplification and sequencing for nine cpDNA regions: atpB-rbcL, matK, ndhF, psbA-trnH, psbM-trnD, rbcL, trnL-F, trnS-G, and ycf1, the voucher information and molecular data (GenBank accession numbers) of 67 ingroup Goniothalamus accessions and 14 outgroup accessions selected from across the tribe Annoneae, and aligned data matrices for each gene region. We also present our Bayesian phylogenetic reconstructions for Goniothalamus, with information on previous infrageneric classifications superimposed to enable an evaluation of monophyly, together with a taxon-character data matrix (with 15 morphological characters scored for 66 Goniothalamus species and seven other species from the tribe Annoneae that are shown to be phylogenetically correlated).

  17. Molecular and morphological data supporting phylogenetic reconstruction of the genus Goniothalamus (Annonaceae, including a reassessment of previous infrageneric classifications

    Directory of Open Access Journals (Sweden)

    Chin Cheung Tang


    Full Text Available Data is presented in support of a phylogenetic reconstruction of the species-rich early-divergent angiosperm genus Goniothalamus (Annonaceae (Tang et al., Mol. Phylogenetic Evol., 2015 [1], inferred using chloroplast DNA (cpDNA sequences. The data includes a list of primers for amplification and sequencing for nine cpDNA regions: atpB-rbcL, matK, ndhF, psbA-trnH, psbM-trnD, rbcL, trnL-F, trnS-G, and ycf1, the voucher information and molecular data (GenBank accession numbers of 67 ingroup Goniothalamus accessions and 14 outgroup accessions selected from across the tribe Annoneae, and aligned data matrices for each gene region. We also present our Bayesian phylogenetic reconstructions for Goniothalamus, with information on previous infrageneric classifications superimposed to enable an evaluation of monophyly, together with a taxon-character data matrix (with 15 morphological characters scored for 66 Goniothalamus species and seven other species from the tribe Annoneae that are shown to be phylogenetically correlated.

  18. Teaching Methods in Biology Education and Sustainability Education Including Outdoor Education for Promoting Sustainability--A Literature Review (United States)

    Jeronen, Eila; Palmberg, Irmeli; Yli-Panula, Eija


    There are very few studies concerning the importance of teaching methods in biology education and environmental education including outdoor education for promoting sustainability at the levels of primary and secondary schools and pre-service teacher education. The material was selected using special keywords from biology and sustainable education…

  19. Linking Biological Responses of Terrestrial N Eutrophication to the Final Ecosystem Goods and Services Classification System (United States)

    Bell, M. D.; Clark, C.; Blett, T.


    The response of a biological indicator to N deposition can indicate that an ecosystem has surpassed a critical load and is at risk of significant change. The importance of this exceedance is often difficult to digest by policy makers and public audiences if the change is not linked to a familiar ecosystem endpoint. A workshop was held to bring together scientists, resource managers, and policy makers with expertise in ecosystem functioning, critical loads, and economics in an effort to identify the ecosystem services impacted by air pollution. This was completed within the framework of the Final Ecosystem Goods and Services (FEGS) Classification System to produce a product that identified distinct interactions between society and the effects of nitrogen pollution. From each change in a biological indicator, we created multiple ecological production functions to identify the cascading effects of the change to a measureable ecosystem service that a user interacts with either by enjoying, consuming, or appreciating the good or service, or using it as an input in the human economy. This FEGS metric was then linked to a beneficiary group that interacts with the service. Chains detailing the links from the biological indicator to the beneficiary group were created for aquatic and terrestrial acidification and eutrophication at the workshop, and here we present a subset of the workshop results by highlighting for 9 different ecosystems affected by terrestrial eutrophication. A total of 213 chains that linked to 37 unique FEGS metrics and impacted 15 beneficiary groups were identified based on nitrogen deposition mediated changes to biological indicators. The chains within each ecosystem were combined in flow charts to show the complex, overlapping relationships among biological indicators, ecosystem services, and beneficiary groups. Strength of relationship values were calculated for each chain based on support for the link in the scientific literature. We produced the

  20. Revealing Significant Relations between Chemical/Biological Features and Activity: Associative Classification Mining for Drug Discovery (United States)

    Yu, Pulan


    Classification, clustering and association mining are major tasks of data mining and have been widely used for knowledge discovery. Associative classification mining, the combination of both association rule mining and classification, has emerged as an indispensable way to support decision making and scientific research. In particular, it offers a…

  1. Mechanical–biological treatment: Performance and potentials. An LCA of 8 MBT plants including waste characterization

    DEFF Research Database (Denmark)

    Montejo, Cristina; Tonini, Davide; Márquez, María del Carmen


    In the endeavour of avoiding presence of biodegradable waste in landfills and increasing recycling, mechanical–biological treatment (MBT) plants have seen a significant increase in number and capacity in the last two decades. The aim of these plants is separating and stabilizing the quickly...... of the MBT plants. These widely differed in type of biological treatment and recovery efficiencies. The results indicated that the performance is strongly connected with energy and materials recovery efficiency. The recommendation for upgrading and/or commissioning of future plants is to optimize materials...... recovery through increased automation of the selection and to prioritize biogas-electricity production from the organic fraction over direct composting. The optimal strategy for refuse derived fuel (RDF) management depends upon the environmental compartment to be prioritized and the type of marginal...

  2. BClass: A Bayesian Approach Based on Mixture Models for Clustering and Classification of Heterogeneous Biological Data

    Directory of Open Access Journals (Sweden)

    Arturo Medrano-Soto


    Full Text Available Based on mixture models, we present a Bayesian method (called BClass to classify biological entities (e.g. genes when variables of quite heterogeneous nature are analyzed. Various statistical distributions are used to model the continuous/categorical data commonly produced by genetic experiments and large-scale genomic projects. We calculate the posterior probability of each entry to belong to each element (group in the mixture. In this way, an original set of heterogeneous variables is transformed into a set of purely homogeneous characteristics represented by the probabilities of each entry to belong to the groups. The number of groups in the analysis is controlled dynamically by rendering the groups as 'alive' and 'dormant' depending upon the number of entities classified within them. Using standard Metropolis-Hastings and Gibbs sampling algorithms, we constructed a sampler to approximate posterior moments and grouping probabilities. Since this method does not require the definition of similarity measures, it is especially suitable for data mining and knowledge discovery in biological databases. We applied BClass to classify genes in RegulonDB, a database specialized in information about the transcriptional regulation of gene expression in the bacterium Escherichia coli. The classification obtained is consistent with current knowledge and allowed prediction of missing values for a number of genes. BClass is object-oriented and fully programmed in Lisp-Stat. The output grouping probabilities are analyzed and interpreted using graphical (dynamically linked plots and query-based approaches. We discuss the advantages of using Lisp-Stat as a programming language as well as the problems we faced when the data volume increased exponentially due to the ever-growing number of genomic projects.

  3. CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets. (United States)

    Dao, David; Fraser, Adam N; Hung, Jane; Ljosa, Vebjorn; Singh, Shantanu; Carpenter, Anne E


    CellProfiler Analyst allows the exploration and visualization of image-based data, together with the classification of complex biological phenotypes, via an interactive user interface designed for biologists and data scientists. CellProfiler Analyst 2.0, completely rewritten in Python, builds on these features and adds enhanced supervised machine learning capabilities (Classifier), as well as visualization tools to overview an experiment (Plate Viewer and Image Gallery). CellProfiler Analyst 2.0 is free and open source, available at and from GitHub ( under the BSD license. It is available as a packaged application for Mac OS X and Microsoft Windows and can be compiled for Linux. We implemented an automatic build process that supports nightly updates and regular release cycles for the software. anne@broadinstitute.orgSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  4. Artificial intelligence in label-free microscopy biological cell classification by time stretch

    CERN Document Server

    Mahjoubfar, Ata; Jalali, Bahram


    This book introduces time-stretch quantitative phase imaging (TS-QPI), a high-throughput label-free imaging flow cytometer developed for big data acquisition and analysis in phenotypic screening. TS-QPI is able to capture quantitative optical phase and intensity images simultaneously, enabling high-content cell analysis, cancer diagnostics, personalized genomics, and drug development. The authors also demonstrate a complete machine learning pipeline that performs optical phase measurement, image processing, feature extraction, and classification, enabling high-throughput quantitative imaging that achieves record high accuracy in label -free cellular phenotypic screening and opens up a new path to data-driven diagnosis. • Demonstrates how machine learning is used in high-speed microscopy imaging to facilitate medical diagnosis; • Provides a systematic and comprehensive illustration of time stretch technology; • Enables multidisciplinary application, including industrial, biomedical, and artificial intell...

  5. Biological review of 82 species of coral petitioned to be included in the Endangered Species Act (United States)

    Brainard, Russell E.; Birkeland, Charles; Eakin, C. Mark; McElhany, Paul; Miller, Margaret W.; Patterson, Matt; Piniak, G.A.


    list 83 coral species as threatened or endangered under the U.S. Endangered Species Act. The petition was based on a predicted decline in available habitat for the species, citing anthropogenic climate change and ocean acidification as the lead factors among the various stressors responsible for the potential decline. The NMFS identified 82 of the corals as candidate species, finding that the petition provided substantive information for a potential listing of these species. The NMFS established a Biological Review Team (BRT) to prepare this Status Review Report that examines the status of these 82 candidate coral species and evaluates extinction risk for each of them. This document makes no recommendations for listing, as that is a separate evaluation to be conducted by the NMFS.

  6. A collection of annotated and harmonized human breast cancer transcriptome datasets, including immunologic classification [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Jessica Roelands


    Full Text Available The increased application of high-throughput approaches in translational research has expanded the number of publicly available data repositories. Gathering additional valuable information contained in the datasets represents a crucial opportunity in the biomedical field. To facilitate and stimulate utilization of these datasets, we have recently developed an interactive data browsing and visualization web application, the Gene Expression Browser (GXB. In this note, we describe a curated compendium of 13 public datasets on human breast cancer, representing a total of 2142 transcriptome profiles. We classified the samples according to different immune based classification systems and integrated this information into the datasets. Annotated and harmonized datasets were uploaded to GXB. Study samples were categorized in different groups based on their immunologic tumor response profiles, intrinsic molecular subtypes and multiple clinical parameters. Ranked gene lists were generated based on relevant group comparisons. In this data note, we demonstrate the utility of GXB to evaluate the expression of a gene of interest, find differential gene expression between groups and investigate potential associations between variables with a specific focus on immunologic classification in breast cancer. This interactive resource is publicly available online at:

  7. Deliverable 4.2: Methodology for including specific biological effects and pathogen aspects into LCA

    DEFF Research Database (Denmark)

    Larsen, Henrik Fred; Olsen, Stig Irving; Hauschild, Michael Zwicky


    .e. endocrine disruptors) and the possibilities and relevance of including impact categories on land use and site-specific assessments have been addressed. Further, the special problems on how to deal with land fill and how to do normalization and weighting of impact potentials are also dealt with. The problem...

  8. Controlled Carbon Source Addition to an Alternating Nitrification-Denitrification Wastewater Treatment Process Including Biological P Removal

    DEFF Research Database (Denmark)

    Isaacs, Steven Howard; Henze, Mogens


    The paper investigates the effect of adding an external carbon source on the rate of denitrification in an alternating activated sludge process including biological P removal. Two carbon sources were examined, acetate and hydrolysate derived from biologically hydrolyzed sludge. Preliminary batch...... that external carbon source addition may serve as a suitable control variable to improve process performance....... process, the addition of either carbon source to the anoxic zone also resulted in an instantaneous and fairly reproducible increase in the denitrification rate. Some release of phosphate associated with the carbon source addition was observed. With respect to nitrogen removal, these results indicate...

  9. MO-DE-207B-03: Improved Cancer Classification Using Patient-Specific Biological Pathway Information Via Gene Expression Data

    Energy Technology Data Exchange (ETDEWEB)

    Young, M; Craft, D [Massachusetts General Hospital and Harvard Medical School, Boston, MA (United States)


    Purpose: To develop an efficient, pathway-based classification system using network biology statistics to assist in patient-specific response predictions to radiation and drug therapies across multiple cancer types. Methods: We developed PICS (Pathway Informed Classification System), a novel two-step cancer classification algorithm. In PICS, a matrix m of mRNA expression values for a patient cohort is collapsed into a matrix p of biological pathways. The entries of p, which we term pathway scores, are obtained from either principal component analysis (PCA), normal tissue centroid (NTC), or gene expression deviation (GED). The pathway score matrix is clustered using both k-means and hierarchical clustering, and a clustering is judged by how well it groups patients into distinct survival classes. The most effective pathway scoring/clustering combination, per clustering p-value, thus generates various ‘signatures’ for conventional and functional cancer classification. Results: PICS successfully regularized large dimension gene data, separated normal and cancerous tissues, and clustered a large patient cohort spanning six cancer types. Furthermore, PICS clustered patient cohorts into distinct, statistically-significant survival groups. For a suboptimally-debulked ovarian cancer set, the pathway-classified Kaplan-Meier survival curve (p = .00127) showed significant improvement over that of a prior gene expression-classified study (p = .0179). For a pancreatic cancer set, the pathway-classified Kaplan-Meier survival curve (p = .00141) showed significant improvement over that of a prior gene expression-classified study (p = .04). Pathway-based classification confirmed biomarkers for the pyrimidine, WNT-signaling, glycerophosphoglycerol, beta-alanine, and panthothenic acid pathways for ovarian cancer. Despite its robust nature, PICS requires significantly less run time than current pathway scoring methods. Conclusion: This work validates the PICS method to improve

  10. Burke-Fahn-Marsden dystonia severity, Gross Motor, Manual Ability, and Communication Function Classification scales in childhood hyperkinetic movement disorders including cerebral palsy: a 'Rosetta Stone' study. (United States)

    Elze, Markus C; Gimeno, Hortensia; Tustin, Kylee; Baker, Lesley; Lumsden, Daniel E; Hutton, Jane L; Lin, Jean-Pierre S-M


    Hyperkinetic movement disorders (HMDs) can be assessed using impairment-based scales or functional classifications. The Burke-Fahn-Marsden Dystonia Rating Scale-movement (BFM-M) evaluates dystonia impairment, but may not reflect functional ability. The Gross Motor Function Classification System (GMFCS), Manual Ability Classification System (MACS), and Communication Function Classification System (CFCS) are widely used in the literature on cerebral palsy to classify functional ability, but not in childhood movement disorders. We explore the concordance of these three functional scales in a large sample of paediatric HMDs and the impact of dystonia severity on these scales. Children with HMDs (n=161; median age 10y 3mo, range 2y 6mo-21y) were assessed using the BFM-M, GMFCS, MACS, and CFCS from 2007 to 2013. This cross-sectional study contrasts the information provided by these scales. All four scales were strongly associated (all Spearman's rank correlation coefficient rs >0.72, pdisorders including cerebral palsy can be effectively evaluated using these scales. © 2015 Mac Keith Press.

  11. Multi trace element analysis of dry biological materials by neutron activation analysis including a chemical group separation

    International Nuclear Information System (INIS)

    Weers, C.A.


    Multi-element analysis of dry biological material by neutron activation analysis has to include radiochemical separation. The evaporation process is described in terms of the half-volume. The pretreatment of the samples and the development of the destruction-evaporation apparatus are described. The successive adsorption steps with active charcoal, Al 2 O 3 and coprecipitation with Fe(OH) 3 are described. Results obtained for standard reference materials are summarized. (G.T.H.)

  12. Controlled Carbon Source Addition to an Alternating Nitrification-Denitrification Wastewater Treatment Process Including Biological P Removal

    DEFF Research Database (Denmark)

    Isaacs, Steven Howard; Henze, Mogens


    The paper investigates the effect of adding an external carbon source on the rate of denitrification in an alternating activated sludge process including biological P removal. Two carbon sources were examined, acetate and hydrolysate derived from biologically hydrolyzed sludge. Preliminary batch...... experiments performed in 5 liter bottles indicated that the denitrification rate can be instantaneously increased through the addition of either carbon source. The amount by which the rate was increased depended on the amount of carbon added. In the main experiments performed in a pilot scale alternating...... process, the addition of either carbon source to the anoxic zone also resulted in an instantaneous and fairly reproducible increase in the denitrification rate. Some release of phosphate associated with the carbon source addition was observed. With respect to nitrogen removal, these results indicate...

  13. Classification in conservation biology: A comparison of five machine-learning methods

    NARCIS (Netherlands)

    Kampichler, C.; Wieland, R.; Calmé, S.; Weissenberger, H.; Arriaga-Weiss, S.


    Classification is one of the most widely applied tasks in ecology. Ecologists have to deal with noisy, highdimensional data that often are non-linear and do not meet the assumptions of conventional statistical procedures. To overcome this problem, machine-learning methods have been adopted as

  14. Evaluation of machine learning algorithms for classification of primary biological aerosol using a new UV-LIF spectrometer (United States)

    Ruske, Simon; Topping, David O.; Foot, Virginia E.; Kaye, Paul H.; Stanley, Warren R.; Crawford, Ian; Morse, Andrew P.; Gallagher, Martin W.


    Characterisation of bioaerosols has important implications within environment and public health sectors. Recent developments in ultraviolet light-induced fluorescence (UV-LIF) detectors such as the Wideband Integrated Bioaerosol Spectrometer (WIBS) and the newly introduced Multiparameter Bioaerosol Spectrometer (MBS) have allowed for the real-time collection of fluorescence, size and morphology measurements for the purpose of discriminating between bacteria, fungal spores and pollen.This new generation of instruments has enabled ever larger data sets to be compiled with the aim of studying more complex environments. In real world data sets, particularly those from an urban environment, the population may be dominated by non-biological fluorescent interferents, bringing into question the accuracy of measurements of quantities such as concentrations. It is therefore imperative that we validate the performance of different algorithms which can be used for the task of classification.For unsupervised learning we tested hierarchical agglomerative clustering with various different linkages. For supervised learning, 11 methods were tested, including decision trees, ensemble methods (random forests, gradient boosting and AdaBoost), two implementations for support vector machines (libsvm and liblinear) and Gaussian methods (Gaussian naïve Bayesian, quadratic and linear discriminant analysis, the k-nearest neighbours algorithm and artificial neural networks).The methods were applied to two different data sets produced using the new MBS, which provides multichannel UV-LIF fluorescence signatures for single airborne biological particles. The first data set contained mixed PSLs and the second contained a variety of laboratory-generated aerosol.Clustering in general performs slightly worse than the supervised learning methods, correctly classifying, at best, only 67. 6 and 91. 1 % for the two data sets respectively. For supervised learning the gradient boosting algorithm was

  15. Automated Processing of Imaging Data through Multi-tiered Classification of Biological Structures Illustrated Using Caenorhabditis elegans.

    Directory of Open Access Journals (Sweden)

    Mei Zhan


    Full Text Available Quantitative imaging has become a vital technique in biological discovery and clinical diagnostics; a plethora of tools have recently been developed to enable new and accelerated forms of biological investigation. Increasingly, the capacity for high-throughput experimentation provided by new imaging modalities, contrast techniques, microscopy tools, microfluidics and computer controlled systems shifts the experimental bottleneck from the level of physical manipulation and raw data collection to automated recognition and data processing. Yet, despite their broad importance, image analysis solutions to address these needs have been narrowly tailored. Here, we present a generalizable formulation for autonomous identification of specific biological structures that is applicable for many problems. The process flow architecture we present here utilizes standard image processing techniques and the multi-tiered application of classification models such as support vector machines (SVM. These low-level functions are readily available in a large array of image processing software packages and programming languages. Our framework is thus both easy to implement at the modular level and provides specific high-level architecture to guide the solution of more complicated image-processing problems. We demonstrate the utility of the classification routine by developing two specific classifiers as a toolset for automation and cell identification in the model organism Caenorhabditis elegans. To serve a common need for automated high-resolution imaging and behavior applications in the C. elegans research community, we contribute a ready-to-use classifier for the identification of the head of the animal under bright field imaging. Furthermore, we extend our framework to address the pervasive problem of cell-specific identification under fluorescent imaging, which is critical for biological investigation in multicellular organisms or tissues. Using these examples as a

  16. Physical urticaria: Review on classification, triggers and management with special focus on prevalence including a meta-analysis. (United States)

    Trevisonno, Jordan; Balram, Bhairavi; Netchiporouk, Elena; Ben-Shoshan, Moshe


    Physical urticaria (PU) is a subset of chronic urticaria (CU) induced by physical stimuli. To date, there is no consensus in the literature on the prevalence of PU among patients with CU. Our objective was to review the clinical presentation, diagnosis and management of PU and to estimate the prevalence of PU in CU patients. We performed a narrative review of PU and conducted a systemic review and meta-analysis to determine the pooled estimates of the prevalence of PU among patients with CU in the literature up to September 2014. We searched four databases (PubMed, Ovid MEDLINE and Web of Science) of published work for which full text was available in English or French. Studies were eligible if they measured the prevalence of PU in adults or children with CU worldwide and ineligible if CU cases were not differentiated from total urticaria cases. Meta-analysis was conducted using Stata, version 12.0 (StataCorp, College Station, TX). In addition, the quality and validity of the articles included in the meta-analysis was assessed. Ten studies were included in our meta-analysis. Sample sizes ranged from 202 to 4157 patients. The pooled prevalence estimate of PU including and excluding cholinergic forms among all cases of CU were 13.1% (95% CI: 12.5, 13.6) and 14.9% (95% CI: 14.3, 15.7), respectively. Our results must be viewed with circumspection because of the small number of eligible articles and heterogeneity among studies. Even so, the results suggest that PU is an important subset of CU and that physicians should be aware of this important condition in order to manage patients appropriately.

  17. Classification of the micro and nanoparticles and biological agents by neural network analysis of the parameters of optical resonance of whispering gallery mode in dielectric microspheres (United States)

    Saetchnikov, Vladimir A.; Tcherniavskaia, Elina A.; Schweiger, Gustav; Ostendorf, Andreas


    A novel technique for the label-free analysis of micro and nanoparticles including biomolecules using optical micro cavity resonance of whispering-gallery-type modes is being developed. Various schemes of the method using both standard and specially produced microspheres have been investigated to make further development for microbial application. It was demonstrated that optical resonance under optimal geometry could be detected under the laser power of less 1 microwatt. The sensitivity of developed schemes has been tested by monitoring the spectral shift of the whispering gallery modes. Water solutions of ethanol, ascorbic acid, blood phantoms including albumin and HCl, glucose, biotin, biomarker like C reactive protein so as bacteria and virus phantoms (gels of silica micro and nanoparticles) have been used. Structure of resonance spectra of the solutions was a specific subject of investigation. Probabilistic neural network classifier for biological agents and micro/nano particles classification has been developed. Several parameters of resonance spectra as spectral shift, broadening, diffuseness and others have been used as input parameters to develop a network classifier for micro and nanoparticles and biological agents in solution. Classification probability of approximately 98% for probes under investigation have been achieved. Developed approach have been demonstrated to be a promising technology platform for sensitive, lab-on-chip type sensor which can be used for development of diagnostic tools for different biological molecules, e.g. proteins, oligonucleotides, oligosaccharides, lipids, small molecules, viral particles, cells as well as in different experimental contexts e.g. proteomics, genomics, drug discovery, and membrane studies.

  18. Comparison of Principal Component Analysis and Linear Discriminant Analysis applied to classification of excitation-emission matrices of the selected biological material

    Directory of Open Access Journals (Sweden)

    Maciej Leśkiewicz


    Full Text Available Quality of two linear methods (PCA and LDA applied to reduce dimensionality of feature analysis is compared and efficiency of their algorithms in classification of the selected biological materials according to their excitation-emission fluorescence matrices is examined. It has been found that LDA method reduces the dimensions (or a number of significant variables more effectively than PCA method. A relatively good discrimination within the examined biological material has been obtained with the use of LDA algorithm.[b]Keywords[/b]: Feature Analysis, Fluorescence Spectroscopy, Biological Material Classification

  19. Objective classification of latent behavioral states in bio-logging data using multivariate-normal hidden Markov models. (United States)

    Phillips, Joe Scutt; Patterson, Toby A; Leroy, Bruno; Pilling, Graham M; Nicol, Simon J


    many different types of noisy autocorrelated data, as typically found across a range of ecological systems. Summarizing time-series data into a multivariate assemblage of dimensions relevant to the desired classification provides a means to examine these data in an appropriate behavioral space. We discuss how outputs of these models can be applied to bio-logging and other imperfect behavioral data, providing easily interpretable models for hypothesis testing.

  20. Teaching Methods in Biology Education and Sustainability Education Including Outdoor Education for Promoting Sustainability—A Literature Review

    Directory of Open Access Journals (Sweden)

    Eila Jeronen


    Full Text Available There are very few studies concerning the importance of teaching methods in biology education and environmental education including outdoor education for promoting sustainability at the levels of primary and secondary schools and pre-service teacher education. The material was selected using special keywords from biology and sustainable education in several scientific databases. The article provides an overview of 24 selected articles published in peer-reviewed scientific journals from 2006–2016. The data was analyzed using qualitative content analysis. Altogether, 16 journals were selected and 24 articles were analyzed in detail. The foci of the analyses were teaching methods, learning environments, knowledge and thinking skills, psychomotor skills, emotions and attitudes, and evaluation methods. Additionally, features of good methods were investigated and their implications for teaching were emphasized. In total, 22 different teaching methods were found to improve sustainability education in different ways. The most emphasized teaching methods were those in which students worked in groups and participated actively in learning processes. Research points toward the value of teaching methods that provide a good introduction and supportive guidelines and include active participation and interactivity.

  1. Planar optical waveguide based sandwich assay sensors and processes for the detection of biological targets including early detection of cancers

    Energy Technology Data Exchange (ETDEWEB)

    Martinez, Jennifer S [Santa Fe, NM; Swanson, Basil I [Los Alamos, NM; Shively, John E [Arcadia, CA; Li, Lin [Monrovia, CA


    An assay element is described including recognition ligands adapted for binding to carcinoembryonic antigen (CEA) bound to a film on a single mode planar optical waveguide, the film from the group of a membrane, a polymerized bilayer membrane, and a self-assembled monolayer containing polyethylene glycol or polypropylene glycol groups therein and an assay process for detecting the presence of CEA is described including injecting a possible CEA-containing sample into a sensor cell including the assay element, maintaining the sample within the sensor cell for time sufficient for binding to occur between CEA present within the sample and the recognition ligands, injecting a solution including a reporter ligand into the sensor cell; and, interrogating the sample within the sensor cell with excitation light from the waveguide, the excitation light provided by an evanescent field of the single mode penetrating into the biological target-containing sample to a distance of less than about 200 nanometers from the waveguide thereby exciting any bound reporter ligand within a distance of less than about 200 nanometers from the waveguide and resulting in a detectable signal.

  2. Combining biological gene expression signatures in predicting outcome in breast cancer: An alternative to supervised classification

    NARCIS (Netherlands)

    Nuyten, Dimitry S. A.; Hastie, Trevor; Chi, Jen-Tsan Ashley; Chang, Howard Y.; van de Vijver, Marc J.


    INTRODUCTION: Gene expression profiling has been extensively used to predict outcome in breast cancer patients. We have previously reported on biological hypothesis-driven analysis of gene expression profiling data and we wished to extend this approach through the combinations of various gene

  3. Biological characteristics that influence the SEUROP system classification for Czech fleckvieh and Holstein bull carcasses

    Directory of Open Access Journals (Sweden)

    Radek Filipčík


    Full Text Available The aim of this work was to analyse the influence of certain characteristics (aptitude, age, carcass weight, net daily gain, feeding on the final carcass classification in the SEUROP system. 703 Czech Fleckvieh bulls and 642 Holstein bulls were studied. The animals were slaughtered and evaluated at a designated beef processing company. Combine aptitude carcasses shown significant differences between characteristics. Remarkable differences of group averages (P>0, 01 were established between farms and they were due to various rearing conditions. Also the levels of net daily gain between aptitudes were proved significantly. Holstein breed showed significant difference among The net daily gain < 500–1 and levels 551–600; 601–650 and above 651–1. The SEUROP system is influenced the most by the feeding regime, which is described by a net daily gain in this work, and farm impact.

  4. The 'antisocial' person: an insight in to biology, classification and current evidence on treatment

    Directory of Open Access Journals (Sweden)

    Rajapakse Senaka


    Full Text Available Abstract Background This review analyses and summarises the recent advances in understanding the neurobiology of violence and empathy, taxonomical issues on defining personality disorders characterised by disregard for social norms, evidence for efficacy of different treatment modalities and ethical implications in defining 'at-risk' individuals for preventive interventions. Methods PubMed was searched with the keywords 'antisocial personality disorder', 'dissocial personality disorder' and 'psychopathy'. The search was limited to articles published in English over the last 10 years (1999 to 2009 Results Both diagnostic manuals used in modern psychiatry, the Diagnostic and Statistical Manual published by the American Psychiatric Association and the International Classification of Diseases published by the World Health Organization, identify a personality disorder sharing similar traits. It is termed antisocial personality disorder in the diagnostic and statistical manual and dissocial personality disorder in the International Classification of Diseases. However, some authors query the ability of the existing manuals to identify a special category termed 'psychopathy', which in their opinion deserves special attention. On treatment-related issues, many psychological and behavioural therapies have shown success rates ranging from 25% to 62% in different cohorts. Multisystemic therapy and cognitive behaviour therapy have been proven efficacious in many trials. There is no substantial evidence for the efficacy of pharmacological therapy. Currently, the emphasis is on early identification and prevention of antisocial behaviour despite the ethical implications of defining at-risk children. Conclusions Further research is needed in the areas of neuroendocrinological associations of violent behaviour, taxonomic existence of psychopathy and efficacy of treatment modalities.

  5. Application of multivariate analysis and vibrational spectroscopy in classification of biological systems (United States)

    Salman, A.; Shufan, E.; Lapidot, I.; Tsror, L.; Zeiri, L.; Sahu, R. K.; Moreh, R.; Mordechai, S.; Huleihel, M.


    Fourier Transform Infrared (FTIR) and Raman spectroscopies have emerged as powerful tools for chemical analysis. This is due to their ability to provide detailed information about the spatial distribution of chemical composition at the molecular level. A biological sample, i.e. bacteria or fungi, has a typical spectrum. This spectral fingerprint, characterizes the sample and can therefore be used for differentiating between biology samples which belong to different groups, i.e., several different isolates of a given fungi. When the spectral differences between the groups are minute, multivariate analysis should be used to provide a good differentiation. We hereby review several results which demonstrate the differentiation success obtained by combining spectroscopy measurements and multivariate analysis.

  6. Classification of biological cells using a sound wave based flow cytometer (United States)

    Strohm, Eric M.; Gnyawali, Vaskar; Van De Vondervoort, Mia; Daghighi, Yasaman; Tsai, Scott S. H.; Kolios, Michael C.


    A flow cytometer that uses sound waves to determine the size of biological cells is presented. In this system, a microfluidic device made of polydimethylsiloxane (PDMS) was developed to hydrodynamically flow focus cells in a single file through a target area. Integrated into the microfluidic device was an ultrasound transducer with a 375 MHz center frequency, aligned opposite the transducer was a pulsed 532 nm laser focused into the device by a 10x objective. Each passing cell was insonfied with a high frequency ultrasound pulse, and irradiated with the laser. The resulting ultrasound and photoacoustic waves from each cell were analyzed using signal processing methods, where features in the power spectra were compared to theoretical models to calculate the cell size. Two cell lines with different size distributions were used to test the system: acute myeloid leukemia cells (AML) and melanoma cells. Over 200 cells were measured using this system. The average calculated diameter of the AML cells was 10.4 +/- 2.5 μm using ultrasound, and 11.4 +/- 2.3 μm using photoacoustics. The average diameter of the melanoma cells was 16.2 +/- 2.9 μm using ultrasound, and 18.9 +/- 3.5 μm using photoacoustics. The cell sizes calculated using ultrasound and photoacoustic methods agreed with measurements using a Coulter Counter, where the AML cells were 9.8 +/- 1.8 μm and the melanoma cells were 16.0 +/- 2.5 μm. These results demonstrate a high speed method of assessing cell size using sound waves, which is an alternative method to traditional flow cytometry techniques.

  7. Phylogenetic Classification of Seed Plants of Taiwan. (United States)

    Lin, Cheng-Tao; Chung, Kuo-Fang


    Biological classification, the hierarchical arrangement of scientific names of organisms, constitutes the core infrastructure of biological databases. For an efficient management of biological databases, adopting a stable and universal biological classification system is crucial. Currently in Taiwan Biodiversity Information Facility (TaiBIF; ), the national portal website that integrates Taiwan's biodiversity information databases, angiosperms are arranged according to Cronquist's System of Classification, which is not compatible with current trend of the Angiosperm Phylogeny Group (APG) classification. To consolidate the function and management of the database, TaiBIF is moving to adopt the APG IV classification and Christenhusz et al. (Phytotaxa 19:55-70, 2011)'s classification of gymnosperms, which we summarize as the Phylogenetic Classification of Seed Plants of Taiwan. The Phylogenetic Classification of Seed Plants of Taiwan places gymnosperms in five families [vs. eight families in the Flora of Taiwan (FOT)] and angiosperms in 210 families (vs. 193 families in FOT). Three FOT gymnosperm families are synonymized in current treatment. Of the 210 APG IV families, familial circumscriptions of 114 families are identical with FOT and 50 families are recircumscription of FOT, with 46 families newly added. Of the 29 FOT families not included in current classification, two families are excluded and 27 families are synonymized. The adoption of the Phylogenetic Classification of Seed Plants of Taiwan in TaiBIF will provide better service and efficient management of the nation's biodiversity information databases.

  8. Extended automated separation techniques in destructive neutron activation analysis; application to various biological materials, including human tissues and blood

    International Nuclear Information System (INIS)

    Tjioe, P.S.; Goeij, J.J.M. de; Houtman, J.P.W.


    Neutron activation analysis may be performed as a multi-element and low-level technique for many important trace elements in biological materials, provided that post-irradiation chemical separations are applied. This paper describes a chemical separation consisting of automated procedures for destruction, distillation, and anion-chromatography. The system developed enables the determination of 14 trace elements in biological materials, viz. antimony, arsenic, bromine, cadmium, chromium, cobalt, copper, gold, iron, mercury, molybdenum, nickel, selenium, and zinc. The aspects of sample preparation, neutron irradiation, gamma-spectrum evaluation, and blank-value contribution are also discussed

  9. Including a Service Learning Educational Research Project in a Biology Course-I: Assessing Community Awareness of Childhood Lead Poisoning (United States)

    Abu-Shakra, Amal; Saliim, Eric


    A university course project was developed and implemented in a biology course, focusing on environmental problems, to assess community awareness of childhood lead poisoning. A set of 385 questionnaires was generated and distributed in an urban community in North Carolina, USA. The completed questionnaires were sorted first into yes and no sets…



    Stolуarova M. A.; Shcherbina I. D.


    The article describes the innovations in the classification and measurement of biological assets according to IFRS (IAS) 41 "Agriculture". The difficulties faced by agricultural producers using standard, set out in article. The classification based on the adopted amendments, according to which the fruit-bearing plants, previously accounted for as biological assets are measured at fair value are included in the category of fixed assets. The structure of biological assets and main means has bee...

  11. Including a service learning educational research project in a biology course-I: Assessing community awareness of childhood lead poisoning


    Abu-Shakra, Amal; Saliim, Eric


    A university course project was developed and implemented in a biology course, focusing on environmental problems, to assess community awareness of childhood lead poisoning. A set of 385 questionnaires was generated and distributed in an urban community in North Carolina, USA. The completed questionnaires were sorted fırst into yes and no sets based on the responses obtained for the fırst question, which gauged the participants' awareness of lead as an indoor pollutant at 71% (n=273)...

  12. Classification of biological agents

    NARCIS (Netherlands)

    Klein MR; LIS; cib


    Deze rapportage omvat een inventarisatie van de problematiek rond de classificatie van biologische agentia, die ziekte bij de mens kunnen veroorzaken.

    De constatering is dat de Europese lijst met classificaties verouderd is en geactualiseerd en uitgebreid zou moeten worden. De lijst bevat

  13. An updated check list of the Cochylina (Tortricidae, Tortricinae, Euliini) of North America north of Mexico including Greenland, with comments on classification and identification (United States)

    We present an updated list of the members of the subtribe Cochylina (Tortricidae) in North America north of Mexico. We summarize the proposed changes in the classification since about 1983. We propose revised status for two genera, Rolandylis Gibeaux, 1985 and Thyraylia Walsingham, 1897. We propose ...

  14. Planar optical waveguide based sandwich assay sensors and processes for the detection of biological targets including protein markers, pathogens and cellular debris (United States)

    Martinez, Jennifer S [Santa Fe, NM; Swanson, Basil I [Los Alamos, NM; Grace, Karen M [Los Alamos, NM; Grace, Wynne K [Los Alamos, NM; Shreve, Andrew P [Santa Fe, NM


    An assay element is described including recognition ligands bound to a film on a single mode planar optical waveguide, the film from the group of a membrane, a polymerized bilayer membrane, and a self-assembled monolayer containing polyethylene glycol or polypropylene glycol groups therein and an assay process for detecting the presence of a biological target is described including injecting a biological target-containing sample into a sensor cell including the assay element, with the recognition ligands adapted for binding to selected biological targets, maintaining the sample within the sensor cell for time sufficient for binding to occur between selected biological targets within the sample and the recognition ligands, injecting a solution including a reporter ligand into the sensor cell; and, interrogating the sample within the sensor cell with excitation light from the waveguide, the excitation light provided by an evanescent field of the single mode penetrating into the biological target-containing sample to a distance of less than about 200 nanometers from the waveguide thereby exciting the fluorescent-label in any bound reporter ligand within a distance of less than about 200 nanometers from the waveguide and resulting in a detectable signal.

  15. Convex reformulation of biologically-based multi-criteria intensity-modulated radiation therapy optimization including fractionation effects. (United States)

    Hoffmann, Aswin L; den Hertog, Dick; Siem, Alex Y D; Kaanders, Johannes H A M; Huizenga, Henk


    Finding fluence maps for intensity-modulated radiation therapy (IMRT) can be formulated as a multi-criteria optimization problem for which Pareto optimal treatment plans exist. To account for the dose-per-fraction effect of fractionated IMRT, it is desirable to exploit radiobiological treatment plan evaluation criteria based on the linear-quadratic (LQ) cell survival model as a means to balance the radiation benefits and risks in terms of biologic response. Unfortunately, the LQ-model-based radiobiological criteria are nonconvex functions, which make the optimization problem hard to solve. We apply the framework proposed by Romeijn et al (2004 Phys. Med. Biol. 49 1991-2013) to find transformations of LQ-model-based radiobiological functions and establish conditions under which transformed functions result in equivalent convex criteria that do not change the set of Pareto optimal treatment plans. The functions analysed are: the LQ-Poisson-based model for tumour control probability (TCP) with and without inter-patient heterogeneity in radiation sensitivity, the LQ-Poisson-based relative seriality s-model for normal tissue complication probability (NTCP), the equivalent uniform dose (EUD) under the LQ-Poisson model and the fractionation-corrected Probit-based model for NTCP according to Lyman, Kutcher and Burman. These functions differ from those analysed before in that they cannot be decomposed into elementary EUD or generalized-EUD functions. In addition, we show that applying increasing and concave transformations to the convexified functions is beneficial for the piecewise approximation of the Pareto efficient frontier.

  16. Biology

    Indian Academy of Sciences (India)

    I am particularly happy that the Academy is bringing out this document by Professor M S. Valiathan on Ayurvedic Biology. It is an effort to place before the scientific community, especially that of India, the unique scientific opportunities that arise out of viewing Ayurveda from the perspective of contemporary science, its tools ...

  17. The Frontlines of Medicine Project: a proposal for the standardized communication of emergency department data for public health uses including syndromic surveillance for biological and chemical terrorism. (United States)

    Barthell, Edward N; Cordell, William H; Moorhead, John C; Handler, Jonathan; Feied, Craig; Smith, Mark S; Cochrane, Dennis G; Felton, Christopher W; Collins, Michael A


    The Frontlines of Medicine Project is a collaborative effort of emergency medicine (including emergency medical services and clinical toxicology), public health, emergency government, law enforcement, and informatics. This collaboration proposes to develop a nonproprietary, "open systems" approach for reporting emergency department patient data. The common element is a standard approach to sending messages from individual EDs to regional oversight entities that could then analyze the data received. ED encounter data could be used for various public health initiatives, including syndromic surveillance for chemical and biological terrorism. The interlinking of these regional systems could also permit public health surveillance at a national level based on ED patient encounter data. Advancements in the Internet and Web-based technologies could allow the deployment of these standardized tools in a rapid time frame.

  18. [Myelodysplastic syndrome classification]. (United States)

    Ghariani, Ines; Braham, Najia; Hassine, Mohsen; Kortas, Mondher


    Myelodysplastic syndromes (MDS) are myeloid disorders with various clinical and biological presentations. The French-American-British (FAB-1982) classification included five categories basing on morphology and bone marrow blast count. Three criteria are taken into account: 1) the percentage of blasts in peripheral blood and bone marrow, 2) the percentage of ringed sideroblasts, and 3) the number of monocytes in peripheral blood. The World Health Organization classification (WHO 2001, 2008) modifies the FAB system by also taking cytogenetic characteristics and molecular biology into consideration. The last classification (WHO-2008) takes into account: 1) the number of peripheral cytopenia, 2) the percentage of blasts in peripheral blood and bone marrow, 3) the percentage of ringed sideroblasts, 4) the possible presence of Auer Rods, and 5) the detection of a cytogenetic abnormality (the isolated 5q deletion). The following subgroups are defined: refractory cytopenia with unilineage dysplasia, refractory anemia with ringed sideroblasts, refractory cytopenia with multilineage dysplasia, refractory anemia with excess blasts, myelodysplastic syndrome unclassifiable and myelodysplastic syndrome with isolated del(5q).

  19. Classification of planctonema-like algae, including a new genus Planctonemopsis gen. nov., a new species Planctonema gelatinosum sp. nov. and a reinstated genus Psephonema (Trebouxiophyceae, Chlorophyta). (United States)

    Liu, Xudong; Zhu, Huan; Liu, Benwen; Liu, Guoxiang; Hu, Zhengyu


    Planctonema-like species consist of planktonic green algae and are found throughout the world. Their characteristic morphology, which includes short and slender filaments consisting of side-by-side or distant cylindrical cells enclosed in a fine and hyaline sheath, makes them easily distinguishable. To date, Planctonema lauterbornii was the only taxon accepted for this group. However, descriptions from different materials have revealed notable morphological differences, including the presence/absence of a pyrenoid, a mucilage sheath and an apical thickening of the cell wall. In this study, six strains of Planctonema-like species were identified and successfully cultured in the laboratory. We used a molecular approach to determine their taxonomic relationships and phylogenetic positions. The molecular analysis resolved them to at least three genera. The genus Planctonema was positioned in Trebouxiophyceae as an incertae sedis taxon that is closely related to Oocystaceae and was divided into two species. Planctonema gelatinosum was determined to be a new species with approximately twice the width and a thicker mucilage sheath, which differentiated it from the type species Planctonema lauterbornii. The genus Psephonema was reinstated based on 1.5-2 times length-width ratio than Planctonema and the big difference on the rbcL cpDNA gene marker and an intron insertion in the 18S rDNA. A new genus, Planctonemopsis, which represents the pyrenoid-present strains among the Planctonema-like species, was established. Planctonemopsis was positioned within Oocystaceae as a new clade and is distantly related to the other two genera. Taxonomic diversity was proven by distinctive morphological differences and phylogenetic divergence in the Planctonema-like group identified herein. © 2017 Phycological Society of America.

  20. Nematodes that associate with terrestrial molluscs as definitive hosts, including Phasmarhabditis hermaphrodita (Rhabditida: Rhabditidae) and its development as a biological molluscicide. (United States)

    Pieterse, A; Malan, A P; Ross, J L


    Terrestrial molluscs (Mollusca: Gastropoda) are important economic pests worldwide, causing extensive damage to a variety of crop types, and posing a health risk to both humans and wildlife. Current knowledge indicates that there are eight nematode families that associate with molluscs as definitive hosts, including Agfidae, Alaninematidae, Alloionematidae, Angiostomatidae, Cosmocercidae, Diplogastridae, Mermithidae and Rhabditidae. To date, Phasmarhabditis hermaphrodita (Schneider, 1859) Andrássy, 1983 (Rhabditida: Rhabditidae) is the only nematode that has been developed as a biological molluscicide. The nematode, which was commercially released in 1994 by MicroBio Ltd, Littlehampton, UK (formally Becker Underwood, now BASF) under the tradename Nemaslug®, is now sold in 15 different European countries. This paper reviews nematodes isolated from molluscs, with specially detailed information on the life cycle, host range, commercialization, natural distribution, mass production and field application of P. hermaphrodita.

  1. PredHSP: Sequence Based Proteome-Wide Heat Shock Protein Prediction and Classification Tool to Unlock the Stress Biology.

    Directory of Open Access Journals (Sweden)

    Ravindra Kumar

    Full Text Available Heat shock proteins are chaperonic proteins, which are present in every domain of life. They play a crucial role in folding/unfolding of proteins, their sorting and assembly into multi-protein complex, cell cycle control and also protect the cell during stress. Considering the fact that no web-based predictor is available for simultaneous prediction and classification of HSPs, it is imperative to develop a method, which can predict and classify them efficiently. In this study, we have developed coupled amino acid composition and support vector machine based two-tier method, PredHSP that identifies heat shock proteins (1st tier and classifies it to different families (at 2nd tier. At 1st tier, we achieved maximum accuracy 76.66% with MCC 0.43, while at 2nd tier we achieved maximum accuracy 96.36% with MCC 0.87 for HSP20, 91.91% with MCC 0.83 for HSP40, 95.96% with MCC 0.72 for HSP60, 91.87% with MCC 0.71 for HSP70, 98.43% with MCC 0.70 for HSP90 and 97.48% with MCC 0.71 for HSP100. We have also developed a webserver, as well as standalone package for the use of scientific community, which can be accessed at

  2. Biological warfare warriors, secrecy and pure science in the Cold War: how to understand dialogue and the classifications of science. (United States)

    Bud, Robert


    This paper uses a case study from the Cold War to reflect on the meaning at the time of the term 'Pure Science'. In 1961, four senior scientists from Britain's biological warfare centre at Porton Down visited Moscow both attending an International Congress and visiting Russian microbiological and biochemical laboratories. The reports of the British scientists in talking about a limited range of topics encountered in the Soviet Union expressed qualities of openness, sociologists of the time associated with pure science. The paper reflects on the discourses of "Pure Science", secrecy and security in the Cold War. Using Bakhtin's approach, I suggest the cordial communication between scientists from opposing sides can be seen in terms of the performance, or speaking, of one language among several at their disposal. Pure science was the language they were allowed to share outside their institutions, and indeed political blocs.

  3. Optimization of biological and instrumental detection of explosives and ignitable liquid residues including canines, SPME/ITMS and GC/MSn (United States)

    Furton, Kenneth G.; Harper, Ross J.; Perr, Jeannette M.; Almirall, Jose R.


    A comprehensive study and comparison is underway using biological detectors and instrumental methods for the rapid detection of ignitable liquid residues (ILR) and high explosives. Headspace solid phase microextraction (SPME) has been demonstrated to be an effective sampling method helping to identify active odor signature chemicals used by detector dogs to locate forensic specimens as well as a rapid pre-concentration technique prior to instrumental detection. Common ignitable liquids and common military and industrial explosives have been studied including trinitrotoluene, tetryl, RDX, HMX, EGDN, PETN and nitroglycerine. This study focuses on identifying volatile odor signature chemicals present, which can be used to enhance the level and reliability of detection of ILR and explosives by canines and instrumental methods. While most instrumental methods currently in use focus on particles and on parent organic compounds, which are often involatile, characteristic volatile organics are generally also present and can be exploited to enhance detection particularly for well-concealed devices. Specific examples include the volatile odor chemicals 2-ethyl-1-hexanol and cyclohexanone, which are readily available in the headspace of the high explosive composition C-4; whereas, the active chemical cyclo-1,3,5-trimethylene-2,4,6-trinitramine (RDX) is not. The analysis and identification of these headspace 'fingerprint' organics is followed by double-blind dog trials of the individual components using certified teams in an attempt to isolate and understand the target compounds to which dogs are sensitive. Studies to compare commonly used training aids with the actual target explosive have also been undertaken to determine their suitability and effectiveness. The optimization of solid phase microextraction (SPME) combined with ion trap mobility spectrometry (ITMS) and gas chromatography/mass spectrometry/mass spectrometry (GC/MSn) is detailed including interface development

  4. Hypoxia in tumors: pathogenesis-related classification, characterization of hypoxia subtypes, and associated biological and clinical implications. (United States)

    Vaupel, Peter; Mayer, Arnulf


    Hypoxia is a hallmark of tumors leading to (mal-)adaptive processes, development of aggressive phenotypes and treatment resistance. Based on underlying mechanisms and their duration, two main types of hypoxia have been identified, coexisting with complex spatial and temporal heterogeneities. Chronic hypoxia is mainly caused by diffusion limitations due to enlarged diffusion distances and adverse diffusion geometries (e.g., concurrent vs. countercurrent microvessels, Krogh- vs. Hill-type diffusion geometry) and, to a lesser extent, by hypoxemia (e.g., in anemic patients, HbCO formation in heavy smokers), and a compromised perfusion or flow stop (e.g., due to disturbed Starling forces or intratumor solid stress). Acute hypoxia mainly results from transient disruptions in perfusion (e.g., vascular occlusion by cell aggregates), fluctuating red blood cell fluxes or short-term contractions of the interstitial matrix. In each of these hypoxia subtypes oxygen supply is critically reduced, but perfusion-dependent nutrient supply, waste removal, delivery of anticancer or diagnostic agents, and repair competence can be impaired or may not be affected. This detailed differentiation of tumor hypoxia may impact on our understanding of tumor biology and may aid in the development of novel treatment strategies, tumor detection by imaging and tumor targeting, and is thus of great clinical relevance.

  5. Wetland Biomass Production: emergent aquatic management options and evaluations. A final subcontract report. [Includes a bibliography containing 686 references on Typha from biological abstracts

    Energy Technology Data Exchange (ETDEWEB)

    Pratt, D.C.; Dubbe, D.R.; Garver, E.G.; Linton, P.J.


    The high yield potential and attractive chemical composition of Typha make it a particularly viable energy crop. The Minnesota research effort has demonstrated that total annual biomass yields equivalent to 30 dry tonnes/ha (13 tons/acre) are possible in planted stands. This compares with yields of total plant material between 9 and 16 dry tonnes/ha (4 to 7 tons/acre) in a typical Minnesota corn field. At least 50% of the Typha plant is comprised of a belowground rhizome system containing 40% starch and sugar. This high level of easily fermentable carbohydrate makes rhizomes an attractive feedstock for alcohol production. The aboveground portion of the plant is largely cellulose, and although it is not easily fermentable, it can be gasified or burned. This report is organized in a manner that focuses on the evaluation of the management options task. Results from stand management research performed at the University of Minnesota during 1982 and 1983 are integrated with findings from an extensive survey of relevant emergent aquatic plant research and utilization. These results and findings are then arranged in sections dealing with key steps and issues that need to be dealt with in the development of a managed emergent aquatic bio-energy system. A brief section evaluating the current status of rhizome harvesting is also included along with an indexed bibliography of the biology, ecology, and utilization of Typha which was completed with support from this SERI subcontract. 686 references, 11 figures, 17 tables.

  6. Biologically relevant oxidants and terminology, classification and nomenclature of oxidatively generated damage to nucleobases and 2-deoxyribose in nucleic acids

    DEFF Research Database (Denmark)

    Cadet, Jean; Loft, Steffen; Olinski, Ryszard


    of the oxidized bases including 8-oxo-7,8-dihydroguanine (8-oxoGua), a ubiquitous marker of almost every type of oxidative stress in cells. Efforts to standardize the nomenclature and abbreviations of the main DNA degradation products that arise from oxidative pathways are reported. Information is also provided...

  7. Classifications of track structures

    International Nuclear Information System (INIS)

    Paretzke, H.G.


    When ionizing particles interact with matter they produce random topological structures of primary activations which represent the initial boundary conditions for all subsequent physical, chemical and/or biological reactions. There are two important aspects of research on such track structures, namely their experimental or theoretical determination on one hand and the quantitative classification of these complex structures which is a basic pre-requisite for the understanding of mechanisms of radiation actions. This paper deals only with the latter topic, i.e. the problems encountered in and possible approaches to quantitative ordering and grouping of these multidimensional objects by their degrees of similarity with respect to their efficiency in producing certain final radiation effects, i.e. to their ''radiation quality.'' Various attempts of taxonometric classification with respect to radiation efficiency have been made in basic and applied radiation research including macro- and microdosimetric concepts as well as track entities and stopping power based theories. In this paper no review of those well-known approaches is given but rather an outline and discussion of alternative methods new to this field of radiation research which have some very promising features and which could possibly solve at least some major classification problems

  8. Classifying Classifications

    DEFF Research Database (Denmark)

    Debus, Michael S.


    al. 2013). The analysis aims at three goals: The classifications’ internal consistency, the abstraction of classification criteria and the identification of differences in classification across fields and/or time. Especially the abstraction of classification criteria can be used in future endeavors......This paper critically analyzes seventeen game classifications. The classifications were chosen on the basis of diversity, ranging from pre-digital classification (e.g. Murray 1952), over game studies classifications (e.g. Elverdam & Aarseth 2007) to classifications of drinking games (e.g. LaBrie et...... into the topic of game classifications....

  9. Xenolog classification. (United States)

    Darby, Charlotte A; Stolzer, Maureen; Ropp, Patrick J; Barker, Daniel; Durand, Dannie


    Orthology analysis is a fundamental tool in comparative genomics. Sophisticated methods have been developed to distinguish between orthologs and paralogs and to classify paralogs into subtypes depending on the duplication mechanism and timing, relative to speciation. However, no comparable framework exists for xenologs: gene pairs whose history, since their divergence, includes a horizontal transfer. Further, the diversity of gene pairs that meet this broad definition calls for classification of xenologs with similar properties into subtypes. We present a xenolog classification that uses phylogenetic reconciliation to assign each pair of genes to a class based on the event responsible for their divergence and the historical association between genes and species. Our classes distinguish between genes related through transfer alone and genes related through duplication and transfer. Further, they separate closely-related genes in distantly-related species from distantly-related genes in closely-related species. We present formal rules that assign gene pairs to specific xenolog classes, given a reconciled gene tree with an arbitrary number of duplications and transfers. These xenology classification rules have been implemented in software and tested on a collection of ∼13 000 prokaryotic gene families. In addition, we present a case study demonstrating the connection between xenolog classification and gene function prediction. The xenolog classification rules have been implemented in N otung 2.9, a freely available phylogenetic reconciliation software package. . Gene trees are available at . Supplementary data are available at Bioinformatics online.

  10. A comprehensive assessment protocol including patient reported outcomes, physical tests, and biological sampling in newly diagnosed patients with head and neck cancer: is it feasible?

    NARCIS (Netherlands)

    van Nieuwenhuizen, A.J.; Buffart, L.M.; Smit, J.H.; Brakenhoff, R.H.; Braakhuis, B.J.; de Bree, R.; Leemans, C.; Verdonck-de Leeuw, I.M.


    Purpose Large cohort studies are needed taking into account cancer-related, personal, biological, psychobehavioral, and lifestyle-related factors, to guide future research to improve treatment and supportive care. We aimed to evaluate the feasibility of a comprehensive baseline assessment of a

  11. Estimation of biological chromophores using diffuse optical spectroscopy: benefit of extending the UV-VIS wavelength range to include 1000 to 1600 nm

    NARCIS (Netherlands)

    Nachabé, Rami; Hendriks, Benno H. W.; van der Voort, Marjolein; Desjardins, Adrien E.; Sterenborg, Henricus J. C. M.


    With an optical fiber probe, we acquired spectra from swine tissue between 500 and 1600 nm by combining a silicon and an InGaAs spectrometer. The concentrations of the biological chromophores were estimated by fitting a mathematical model derived from diffusion theory. The advantage of our technique

  12. Estimation of biological chromophores using diffuse optical spectroscopy: Benefit of extending the UV-VIS wavelength range to include 1000 to 1600 nm

    NARCIS (Netherlands)

    R. Nachabé (Rami); B.H.W. Hendriks (Benno); M. van der Voort (Marjolein); A.E. Desjardins (Adrien); H.J.C.M. Sterenborg (Dick)


    textabstractWith an optical fiber probe, we acquired spectra from swine tissue between 500 and 1600 nm by combining a silicon and an InGaAs spectrometer. The concentrations of the biological chromophores were estimated by fitting a mathematical model derived from diffusion theory. The advantage of

  13. Tissue Classification

    DEFF Research Database (Denmark)

    Van Leemput, Koen; Puonti, Oula


    Computational methods for automatically segmenting magnetic resonance images of the brain have seen tremendous advances in recent years. So-called tissue classification techniques, aimed at extracting the three main brain tissue classes (white matter, gray matter, and cerebrospinal fluid), are now...... well established. In their simplest form, these methods classify voxels independently based on their intensity alone, although much more sophisticated models are typically used in practice. This article aims to give an overview of often-used computational techniques for brain tissue classification....... Although other methods exist, we concentrate on Bayesian modeling approaches, in which generative image models are constructed and subsequently ‘inverted’ to obtain automated segmentations. This general framework encompasses a large number of segmentation methods, including those implemented in widely used...

  14. Lie Group Classification of a Generalized Lane-Emden Type System in Two Dimensions

    Directory of Open Access Journals (Sweden)

    Motlatsi Molati


    Full Text Available The aim of this work is to perform a complete Lie symmetry classification of a generalized Lane-Emden type system in two dimensions which models many physical phenomena in biological and physical sciences. The classical approach of group classification is employed for classification. We show that several cases arise in classifying the arbitrary parameters, the forms of which include amongst others the power law nonlinearity, and exponential and quadratic forms.

  15. Biological effects of radiation

    International Nuclear Information System (INIS)


    This fourth chapter presents: cell structure and metabolism; radiation interaction with biological tissues; steps of the production of biological effect of radiation; radiosensitivity of tissues; classification of biological effects; reversibility, transmissivity and influence factors; pre-natal biological effects; biological effects in therapy and syndrome of acute irradiation

  16. Studies of the reproductive biology of deep-sea megabenthos. 7: The Porcellanasteridae (Asteroidea: Echinodermata) including material collected at Great Meteor East, during Discovery cruise 156

    International Nuclear Information System (INIS)

    Tyler, P.A.; Muirhead, A.


    The reproductive biology of Porcellanaster ceruleus, Hyphalaster inermis and Styrachaster horridus is described. P. ceruleus was collected as part of the time series study in the rockall Trough, N.E. Atlantic. This species had a maximum size of 7.0mm arm radius although maximum size known is 36.0mm arm radius. Relatively few eggs are produced and in these samples grow to a maximum size of 230μm. There was no evidence of reproductive seasonality. In Hyphalaster inermis and Styrachaster horridus the eggs grow to 600μm diameter. At this size the cytoplasm is reticulate and filled with neutral fat whilst the periphery is an amorphous layer. Development of the testes in all three species appears typical of deep-sea asteroids. (author)

  17. Information gathering for CLP classification

    Directory of Open Access Journals (Sweden)

    Ida Marcello


    Full Text Available Regulation 1272/2008 includes provisions for two types of classification: harmonised classification and self-classification. The harmonised classification of substances is decided at Community level and a list of harmonised classifications is included in the Annex VI of the classification, labelling and packaging Regulation (CLP. If a chemical substance is not included in the harmonised classification list it must be self-classified, based on available information, according to the requirements of Annex I of the CLP Regulation. CLP appoints that the harmonised classification will be performed for carcinogenic, mutagenic or toxic to reproduction substances (CMR substances and for respiratory sensitisers category 1 and for other hazard classes on a case-by-case basis. The first step of classification is the gathering of available and relevant information. This paper presents the procedure for gathering information and to obtain data. The data quality is also discussed.

  18. Security classification of information

    Energy Technology Data Exchange (ETDEWEB)

    Quist, A.S.


    This document is the second of a planned four-volume work that comprehensively discusses the security classification of information. The main focus of Volume 2 is on the principles for classification of information. Included herein are descriptions of the two major types of information that governments classify for national security reasons (subjective and objective information), guidance to use when determining whether information under consideration for classification is controlled by the government (a necessary requirement for classification to be effective), information disclosure risks and benefits (the benefits and costs of classification), standards to use when balancing information disclosure risks and benefits, guidance for assigning classification levels (Top Secret, Secret, or Confidential) to classified information, guidance for determining how long information should be classified (classification duration), classification of associations of information, classification of compilations of information, and principles for declassifying and downgrading information. Rules or principles of certain areas of our legal system (e.g., trade secret law) are sometimes mentioned to .provide added support to some of those classification principles.

  19. Radiation biology in Canada 1962-63

    International Nuclear Information System (INIS)

    Thacker, D.G.


    A survey of the research projects in radiation biology being carried out in Canada during the fiscal year 1962-63. The report includes the names of the investigators, their location, a brief description of the projects and information on the financial support being provided. A classification of the projects into areas of specific interest is also included. (author)

  20. Endothelin-2/Vasoactive Intestinal Contractor: Regulation of Expression via Reactive Oxygen Species Induced by CoCl22, and Biological Activities Including Neurite Outgrowth in PC12 Cells

    Directory of Open Access Journals (Sweden)

    Eiichi Kotake-Nara


    Full Text Available This paper reviews the local hormone endothelin-2 (ET-2, or vasoactive intestinal contractor (VIC, a member of the vasoconstrictor ET peptide family, where ET-2 is the human orthologous peptide of the murine VIC. While ET-2/VIC gene expression has been observed in some normal tissues, ET-2 recently has been reported to act as a tumor marker and as a hypoxia-induced autocrine survival factor in tumor cells. A recently published study reported that the hypoxic mimetic agent CoCl2 at 200 µM increased expression of the ET-2/VIC gene, decreased expression of the ET-1 gene, and induced intracellular reactive oxygen species (ROS increase and neurite outgrowth in neuronal model PC12 cells. The ROS was generated by addition of CoCl2 to the culture medium, and the CoCl2-induced effects were completely inhibited by the antioxidant N-acetyl cysteine. Furthermore, interleukin-6 (IL-6 gene expression was up-regulated upon the differentiation induced by CoCl2. These results suggest that expression of ET-2/VIC and ET-1 mediated by CoCl2-induced ROS may be associated with neuronal differentiation through the regulation of IL-6 expression. CoCl2 acts as a pro-oxidant, as do Fe(II, III and Cu(II. However, some biological activities have been reported for CoCl2 that have not been observed for other metal salts such as FeCl3, CuSO4, and NiCl2. The characteristic actions of CoCl2 may be associated with the differentiation of PC12 cells. Further elucidation of the mechanism of neurite outgrowth and regulation of ET-2/VIC expression by CoCl2 may lead to the development of treatments for neuronal disorders.

  1. Text classification


    Deveikis, Karolis


    This paper investigates the problem of text classification. The task of text classification is to assign a piece of text to one of several categories based on its content. Text classification is one of the tasks of natural language processing. Like the others, it is often solved using machine learning algorithms. There are many algorithms suitable for text classification. As a result, a problem of choice arises. In an effort to solve this problem, this paper analyzes various feature extractio...

  2. Classification of cell signalling in tissue development. (United States)

    Platt, Craig Charles; Nicholls, Clare; Brookes, Chris; Wood, Ian


    The traditional classification of signalling in biological systems is insufficient and outdated and novel efforts must take into account advances in systems theory, information theory and linguistics. We present some of the classification systems currently used both within and outside of the biological field and discuss some specific aspects of the nature of signalling in tissue development. The analytical methods used in understanding non-biological networks provide a valuable vocabulary, which requires integration and a system of classification to further facilitate development.

  3. An Ecological Diagnostic Classification Plan. (United States)

    Hurst, James C.; McKinley, Donna L.


    Discusses the value of diagnostic classification systems to counseling professionals. Describes the Ecological Diagnostic Classification Plan, an approach to diagnosis that includes the environment as a possible cause of pathology and target of intervention. (Author/KS)

  4. 32 CFR 2001.14 - Classification challenges. (United States)


    ... 32 National Defense 6 2010-07-01 2010-07-01 false Classification challenges. 2001.14 Section 2001... Classification § 2001.14 Classification challenges. (a) Challenging classification. Authorized holders, including authorized holders outside the classifying agency, who want to challenge the classification status of...

  5. Examination of the regulatory frameworks applicable to biologic drugs (including stem cells and their progeny) in Europe, the U.S., and Australia: part I--a method of manual documentary analysis. (United States)

    Ilic, Nina; Savic, Snezana; Siegel, Evan; Atkinson, Kerry; Tasic, Ljiljana


    Recent development of a wide range of regulatory standards applicable to production and use of tissues, cells, and other biologics (or biologicals), as advanced therapies, indicates considerable interest in the regulation of these products. The objective of this study was to analyze and compare high-tier documents within the Australian, European, and U.S. biologic drug regulatory environments using qualitative methodology. Cohort 1 of the selected 18 high-tier regulatory documents from the European Medicines Agency (EMA), the U.S. Food and Drug Administration (FDA), and the Therapeutic Goods Administration (TGA) regulatory frameworks were subject to a manual documentary analysis. These documents were consistent with the legal requirements for manufacturing and use of biologic drugs in humans and fall into six different categories. Manual analysis included a terminology search. The occurrence, frequency, and interchangeable use of different terms and phrases were recorded in the manual documentary analysis. Despite obvious differences, manual documentary analysis revealed certain consistency in use of terminology across analyzed frameworks. Phrase search frequencies have shown less uniformity than the search of terms. Overall, the EMA framework's documents referred to "medicinal products" and "marketing authorization(s)," the FDA documents discussed "drug(s)" or "biologic(s)," and the TGA documents referred to "biological(s)." Although high-tier documents often use different terminology they share concepts and themes. Documents originating from the same source have more conjunction in their terminology although they belong to different frameworks (i.e., Good Clinical Practice requirements based on the Declaration of Helsinki, 1964). Automated (software-based) documentary analysis should be obtained for the conceptual and relational analysis.

  6. Routing, Disjoint Paths, and Classification

    National Research Council Canada - National Science Library

    Zhou, Shuheng


    .... The third part of this thesis concerns a type of classification problem that is motivated by a computational biology problem, where it is desirable that a small amount of genotype data from each...

  7. Genetic Classification of Infantile Spasms


    J Gordon Millichap


    Researchers from University of Washington, Seattle, WA, and Washington University, St Louis, MO propose a genetic and biologic classification of infantile spasms. Infantile spasms are of 2 main groups: those with known or unknown predisposing genotypes.

  8. [Biogeography: geography or biology?]. (United States)

    Kafanov, A I


    General biogeography is an interdisciplinary science, which combines geographic and biological aspects constituting two distinct research fields: biological geography and geographic biology. These fields differ in the nature of their objects of study, employ different methods and represent Earth sciences and biological sciences, respectively. It is suggested therefore that the classification codes for research fields and the state professional education standard should be revised.

  9. Investigating the use of support vector machine classification on structural brain images of preterm-born teenagers as a biological marker.

    Directory of Open Access Journals (Sweden)

    Carlton Chu

    Full Text Available Preterm birth has been shown to induce an altered developmental trajectory of brain structure and function. With the aid support vector machine (SVM classification methods we aimed to investigate whether MRI data, collected in adolescence, could be used to predict whether an individual had been born preterm or at term. To this end we collected T1-weighted anatomical MRI data from 143 individuals (69 controls, mean age 14.6y. The inclusion criteria for those born preterm were birth weight ≤ 1500g and gestational age < 37w. A linear SVM was trained on the grey matter segment of MR images in two different ways. First, all the individuals were used for training and classification was performed by the leave-one-out method, yielding 93% correct classification (sensitivity = 0.905, specificity = 0.942. Separately, a random half of the available data were used for training twice and each time the other, unseen, half of the data was classified, resulting 86% and 91% accurate classifications. Both gestational age (R = -0.24, p<0.04 and birth weight (R = -0.51, p < 0.001 correlated with the distance to decision boundary within the group of individuals born preterm. Statistically significant correlations were also found between IQ (R = -0.30, p < 0.001 and the distance to decision boundary. Those born small for gestational age did not form a separate subgroup in these analyses. The high rate of correct classification by the SVM motivates further investigation. The long-term goal is to automatically and non-invasively predict the outcome of preterm-born individuals on an individual basis using as early a scan as possible.

  10. A biological method of including mineralized human liquid and solid wastes into the mass exchange of bio-technical life support systems (United States)

    Ushakova, S. A.; Tikhomirov, A. A.; Tikhomirova, N. A.; Kudenko, Yu. A.; Litovka, Yu. A.; Anishchenko, O. V.


    The main obstacle to using mineralized human solid and liquid wastes as a source of mineral elements for plants cultivated in bio-technical life support systems (BLSS) is that they contain NaCl. The purpose of this study is to determine whether mineralized human wastes can be used to prepare the nutrient solution for long-duration conveyor cultivation of uneven-aged wheat and Salicornia europaea L. plant community. Human solid and liquid wastes were mineralized by the method of "wet incineration" developed by Yu. Kudenko. They served as a basis for preparing the solutions that were used for conveyor-type cultivation of wheat community represented by 5 age groups, planted with a time interval of 14 days. Wheat was cultivated hydroponically on expanded clay particles. To reduce salt content of the nutrient solution, every two weeks, after wheat was harvested, 12 L of solution was removed from the wheat irrigation tank and used for Salicornia europaea cultivation in water culture in a conveyor mode. The Salicornia community was represented by 2 age groups, planted with a time interval of 14 days. As some portion of the nutrient solution used for wheat cultivation was regularly removed, sodium concentration in the wheat irrigation solution did not exceed 400 mg/L, and mineral elements contained in the removed portion were used for Salicornia cultivation. The experiment lasted 4 months. The total wheat biomass productivity averaged 30.1 g · m-2 · day-1, and the harvest index amounted to 36.8%. The average productivity of Salicornia edible biomass on a dry weight basis was 39.3 g · m-2 · day-1, and its aboveground mass contained at least 20% of NaCl. Thus, the proposed technology of cultivation of wheat and halophyte plant community enables using mineralized human wastes as a basis for preparing nutrient solutions and including NaCl in the mass exchange of the BLSS; moreover, humans are supplied with additional amounts of leafy vegetables.

  11. Short Time Exposure (STE) test in conjunction with Bovine Corneal Opacity and Permeability (BCOP) assay including histopathology to evaluate correspondence with the Globally Harmonized System (GHS) eye irritation classification of textile dyes. (United States)

    Oliveira, Gisele Augusto Rodrigues; Ducas, Rafael do Nascimento; Teixeira, Gabriel Campos; Batista, Aline Carvalho; Oliveira, Danielle Palma; Valadares, Marize Campos


    Eye irritation evaluation is mandatory for predicting health risks in consumers exposed to textile dyes. The two dyes, Reactive Orange 16 (RO16) and Reactive Green 19 (RG19) are classified as Category 2A (irritating to eyes) based on the UN Globally Harmonized System for classification (UN GHS), according to the Draize test. On the other hand, animal welfare considerations and the enforcement of a new regulation in the EU are drawing much attention in reducing or replacing animal experiments with alternative methods. This study evaluated the eye irritation of the two dyes RO16 and RG19 by combining the Short Time Exposure (STE) and the Bovine Corneal Opacity and Permeability (BCOP) assays and then comparing them with in vivo data from the GHS classification. The STE test (first level screening) categorized both dyes as GHS Category 1 (severe irritant). In the BCOP, dye RG19 was also classified as GHS Category 1 while dye RO16 was classified as GHS no prediction can be made. Both dyes caused damage to the corneal tissue as confirmed by histopathological analysis. Our findings demonstrated that the STE test did not contribute to arriving at a better conclusion about the eye irritation potential of the dyes when used in conjunction with the BCOP test. Adding the histopathology to the BCOP test could be an appropriate tool for a more meaningful prediction of the eye irritation potential of dyes. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Study about quantification and classification of biological tissues in tomographic images from histograms; Estudo sobre quantificacao e classificacao dos tecidos biologicos em imagens tomograficas a partir de histogramas

    Energy Technology Data Exchange (ETDEWEB)

    Souza, Rafael T.F.; Lemke, Ney; Hormaza, Joel Mesa; Alvarez, Matheus, E-mail: rafael@ibb.unesp.b [Universidade Estadual Paulista Julio de Mesquisa Filho (DFB/IB/UNESP), Botucatu, SP (Brazil). Inst. de Biociencias. Dept. de Fisica e Biofisica; Pina, Diana R.; Teixeira, Altamir S. [Universidade Estadual Paulista Julio de Mesquisa Filho (HC/FM/UNESP), Botucatu, SP (Brazil). Hospital de Clinicas. Dept. de Doencas Tropicais e Diagnostico por Imagem


    An algorithm for determining the equivalent thickness of biological tissue by the removal of Gaussian from the histograms was proposed. This algorithm classifies the different biological tissues using histograms, constructed from CT scans in DICOM format and calculates the average thickness of these tissues. The founded results show to be coherent with literature, with discrepancies of up to 21.6% on the bone, and analyzed for the anthropomorphic phantom (RANDO). These results allow the use of this method in living tissues for the construction of chest homogeneous phantoms of newborn and suckling patients, which are subsequently used in the optimization process of pediatric radiographic images. (author)

  13. Population Genomics and the Statistical Values of Race: An Interdisciplinary Perspective on the Biological Classification of Human Populations and Implications for Clinical Genetic Epidemiological Research (United States)

    Maglo, Koffi N.; Mersha, Tesfaye B.; Martin, Lisa J.


    The biological status and biomedical significance of the concept of race as applied to humans continue to be contentious issues despite the use of advanced statistical and clustering methods to determine continental ancestry. It is thus imperative for researchers to understand the limitations as well as potential uses of the concept of race in biology and biomedicine. This paper deals with the theoretical assumptions behind cluster analysis in human population genomics. Adopting an interdisciplinary approach, it demonstrates that the hypothesis that attributes the clustering of human populations to “frictional” effects of landform barriers at continental boundaries is empirically incoherent. It then contrasts the scientific status of the “cluster” and “cline” constructs in human population genomics, and shows how cluster may be instrumentally produced. It also shows how statistical values of race vindicate Darwin's argument that race is evolutionarily meaningless. Finally, the paper explains why, due to spatiotemporal parameters, evolutionary forces, and socio-cultural factors influencing population structure, continental ancestry may be pragmatically relevant to global and public health genomics. Overall, this work demonstrates that, from a biological systematic and evolutionary taxonomical perspective, human races/continental groups or clusters have no natural meaning or objective biological reality. In fact, the utility of racial categorizations in research and in clinics can be explained by spatiotemporal parameters, socio-cultural factors, and evolutionary forces affecting disease causation and treatment response. PMID:26925096

  14. Population Genomics and the Statistical Values of Race: An Interdisciplinary Perspective on the Biological Classification of Human Populations and Implications for Clinical Genetic Epidemiological Research. (United States)

    Maglo, Koffi N; Mersha, Tesfaye B; Martin, Lisa J


    The biological status and biomedical significance of the concept of race as applied to humans continue to be contentious issues despite the use of advanced statistical and clustering methods to determine continental ancestry. It is thus imperative for researchers to understand the limitations as well as potential uses of the concept of race in biology and biomedicine. This paper deals with the theoretical assumptions behind cluster analysis in human population genomics. Adopting an interdisciplinary approach, it demonstrates that the hypothesis that attributes the clustering of human populations to "frictional" effects of landform barriers at continental boundaries is empirically incoherent. It then contrasts the scientific status of the "cluster" and "cline" constructs in human population genomics, and shows how cluster may be instrumentally produced. It also shows how statistical values of race vindicate Darwin's argument that race is evolutionarily meaningless. Finally, the paper explains why, due to spatiotemporal parameters, evolutionary forces, and socio-cultural factors influencing population structure, continental ancestry may be pragmatically relevant to global and public health genomics. Overall, this work demonstrates that, from a biological systematic and evolutionary taxonomical perspective, human races/continental groups or clusters have no natural meaning or objective biological reality. In fact, the utility of racial categorizations in research and in clinics can be explained by spatiotemporal parameters, socio-cultural factors, and evolutionary forces affecting disease causation and treatment response.


    Directory of Open Access Journals (Sweden)

    I. P. Prokopenko


    Full Text Available Correctly organized nutritive and pharmacological support is an important component of an athlete's preparation for competitions, an optimal shape maintenance, fast recovery and rehabilitation after traumas and defatigation. Special products of enhanced biological value (BAS for athletes nutrition are used with this purpose. Easy-to-use energy sources are administered into athlete's organism, yielded materials and biologically active substances which regulate and activate exchange reactions which proceed with difficulties during certain physical trainings. The article presents sport supplements classification which can be used before warm-up and trainings, after trainings and in competitions breaks.

  16. Biological rhythms (United States)

    Halberg, F.


    An overview is given of basic features of biological rhythms. The classification of periodic behavior of physical and psychological characteristics as circadian, circannual, diurnal, and ultradian is discussed, and the notion of relativistic time as it applies in biology is examined. Special attention is given to circadian rhythms which are dependent on the adrenocortical cycle. The need for adequate understanding of circadian variations in the basic physiological indicators of an individual (heart rate, body temperature, systolic and diastolic blood pressure, etc.) to ensure the effectiveness of prophylactic and therapeutic measures is stressed.

  17. 22 CFR 9.4 - Original classification. (United States)


    ... classification. (a) Definition. Original classification is the initial determination that certain information... the national security; which includes defense against transnational terrorism; (vi) United States... national security, which includes defense against transnational terrorism; or (viii) Weapons of mass...

  18. Biological therapeutics

    National Research Council Canada - National Science Library

    Greenstein, Ben; Brook, Daniel A


    This introductory textbook covers all the main categories of biological medicines, including vaccines, hormonal preparations, drugs for rheumatoid arthritis and other connective tissue diseases, drugs...

  19. Using ethnicity as a classification variable in health research: perpetuating the myth of biological determinism, serving socio-political agendas, or making valuable contributions to medical sciences? (United States)

    Anand, S S


    There is a need for a valid way to classify the human species consistently and reliably, be it to highlight similarities between human populations such as intelligence or physical capacity, to dispel myths about group differences, or to discover 'novel' risk factors for diseases. In contrast to racial divisions, which are usually based on differences in skin colour and physical features, ethnicity is a complex concept which has both socio-cultural and biological components. However, because of the relative vagueness of the term, the interpretation of the 'Ethnicity' construct is not simple, and its definition is often unique to the research project at hand. Therefore conducting ethnicity-research necessitates being aware of the differences between the concept of ethnicity and race, acknowledgement of the complexity of the ethnicity construct, and requires that a clear definition of the use of this term be made explicit by the researcher.

  20. Transporter Classification Database (TCDB) (United States)

    U.S. Department of Health & Human Services — The Transporter Classification Database details a comprehensive classification system for membrane transport proteins known as the Transporter Classification (TC)...

  1. Revised description and classification of atypical isolates of Pasteurella multocida from bovine lungs based on genotypic characterization to include variants previously classified as biovar 2 of Pasteurella canis and Pasteurella avium

    DEFF Research Database (Denmark)

    Christensen, Henrik; Angen, Øystein; Olsen, John E.


    Strains deviating in key phenotypic characters, mainly isolated from cases of bovine pneumonia in five European countries, were genotyped in order to examine their genotypic relationship with Pasteurella multocida. Twenty-two strains of Pasteurella avium biovar 2, including variants in indole......, xylose and mannitol, 18 strains of Pasteurella canis biovar 2 and variants of this taxon, five strains of P multocida subsp. septica showing variations in indole and ornithine decarboxylase, nine strains of P. multocida subsp. multocida showing variation in ornithine decarboxylase and mannitol, and type...... strains of the subspecies of P. multocida were included. Ribotyping was used to examine the relationship of the strains, and 13 types, each containing between one and 20 isolates, were observed. Identical ribotypes; were observed in some cases for P. avium biovar 2 and either P. canis biovar 2 or P...

  2. Biomarker Selection and Classification of “-Omics” Data Using a Two-Step Bayes Classification Framework

    Directory of Open Access Journals (Sweden)

    Anunchai Assawamakin


    Full Text Available Identification of suitable biomarkers for accurate prediction of phenotypic outcomes is a goal for personalized medicine. However, current machine learning approaches are either too complex or perform poorly. Here, a novel two-step machine-learning framework is presented to address this need. First, a Naïve Bayes estimator is used to rank features from which the top-ranked will most likely contain the most informative features for prediction of the underlying biological classes. The top-ranked features are then used in a Hidden Naïve Bayes classifier to construct a classification prediction model from these filtered attributes. In order to obtain the minimum set of the most informative biomarkers, the bottom-ranked features are successively removed from the Naïve Bayes-filtered feature list one at a time, and the classification accuracy of the Hidden Naïve Bayes classifier is checked for each pruned feature set. The performance of the proposed two-step Bayes classification framework was tested on different types of -omics datasets including gene expression microarray, single nucleotide polymorphism microarray (SNParray, and surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF proteomic data. The proposed two-step Bayes classification framework was equal to and, in some cases, outperformed other classification methods in terms of prediction accuracy, minimum number of classification markers, and computational time.

  3. Faculty Assignment Classification System. (United States)

    Whatcom Community Coll., Ferndale, WA.

    This document outlines the point-based faculty assignment classification system in effect at Whatcom Community College (Washington). The purpose of the point system is to provide an equitable and flexible means of compensating faculty members based on a system of assigning quantitative values to tasks. Teaching, which includes classroom…

  4. Ecosystem classification, Chapter 2 (United States)

    M.J. Robin-Abbott; L.H. Pardo


    The ecosystem classification in this report is based on the ecoregions developed through the Commission for Environmental Cooperation (CEC) for North America (CEC 1997). Only ecosystems that occur in the United States are included. CEC ecoregions are described, with slight modifications, below (CEC 1997) and shown in Figures 2.1 and 2.2. We chose this ecosystem...

  5. Minimum Error Entropy Classification

    CERN Document Server

    Marques de Sá, Joaquim P; Santos, Jorge M F; Alexandre, Luís A


    This book explains the minimum error entropy (MEE) concept applied to data classification machines. Theoretical results on the inner workings of the MEE concept, in its application to solving a variety of classification problems, are presented in the wider realm of risk functionals. Researchers and practitioners also find in the book a detailed presentation of practical data classifiers using MEE. These include multi‐layer perceptrons, recurrent neural networks, complexvalued neural networks, modular neural networks, and decision trees. A clustering algorithm using a MEE‐like concept is also presented. Examples, tests, evaluation experiments and comparison with similar machines using classic approaches, complement the descriptions.

  6. Molecular Classification and Correlates in Colorectal Cancer


    Ogino, Shuji; Goel, Ajay


    Molecular classification of colorectal cancer is evolving. As our understanding of colorectal carcinogenesis improves, we are incorporating new knowledge into the classification system. In particular, global genomic status [microsatellite instability (MSI) status and chromosomal instability (CIN) status] and epigenomic status [CpG island methylator phenotype (CIMP) status] play a significant role in determining clinical, pathological and biological characteristics of colorectal cancer. In thi...

  7. River Pollution: Part II. Biological Methods for Assessing Water Quality. (United States)

    Openshaw, Peter


    Discusses methods used in the biological assessment of river quality and such indicators of clean and polluted waters as the Trent Biotic Index, Chandler Score System, and species diversity indexes. Includes a summary of a river classification scheme based on quality criteria related to water use. (JN)

  8. Similar effects of disease-modifying antirheumatic drugs, glucocorticoids, and biologic agents on radiographic progression in rheumatoid arthritis: meta-analysis of 70 randomized placebo-controlled or drug-controlled studies, including 112 comparisons

    DEFF Research Database (Denmark)

    Graudal, Niels; Jürgens, Gesche


    To define the differences in effects on joint destruction in rheumatoid arthritis (RA) patients between therapy with single and combination disease-modifying antirheumatic drugs (DMARDs), glucocorticoids, and biologic agents.......To define the differences in effects on joint destruction in rheumatoid arthritis (RA) patients between therapy with single and combination disease-modifying antirheumatic drugs (DMARDs), glucocorticoids, and biologic agents....

  9. Accurate vehicle classification including motorcycles using piezoelectric sensors. (United States)


    State and federal departments of transportation are charged with classifying vehicles and monitoring mileage traveled. Accurate data reporting enables suitable roadway design for safety and capacity. Vehicle classifiers currently employ inductive loo...

  10. Classification of high resolution satellite images


    Karlsson, Anders


    In this thesis the Support Vector Machine (SVM)is applied on classification of high resolution satellite images. Sveral different measures for classification, including texture mesasures, 1st order statistics, and simple contextual information were evaluated. Additionnally, the image was segmented, using an enhanced watershed method, in order to improve the classification accuracy.

  11. 17 CFR 200.506 - Derivative classification. (United States)


    ... 17 Commodity and Securities Exchanges 2 2010-04-01 2010-04-01 false Derivative classification. 200...; CONDUCT AND ETHICS; AND INFORMATION AND REQUESTS Classification and Declassification of National Security Information and Material § 200.506 Derivative classification. Any document that includes paraphrases...

  12. Stellar Spectral Classification with Locality Preserving Projections ...

    Indian Academy of Sciences (India)

    With the help of computer tools and algorithms, automatic stellar spectral classification has become an area of current interest. The process of stellar spectral classification mainly includes two steps: dimension reduction and classification. As a popular dimensionality reduction technique, Principal Component Analysis (PCA) ...

  13. [Definition, etiology, classification and presentation forms]. (United States)

    Mas Garriga, Xavier


    Osteoarthritis is defined as a degenerative process affecting the joints as a result of mechanical and biological disorders that destabilize the balance between the synthesis and degradation of joint cartilage, stimulating the growth of subchondral bone; chronic synovitis is also present. Currently, the joint is considered as a functional unit that includes distinct tissues, mainly cartilage, the synovial membrane, and subchondral bone, all of which are involved in the pathogenesis of the disease. Distinct risk factors for the development of osteoarthritis have been described: general, unmodifiable risk factors (age, sex, and genetic makeup), general, modifiable risk factors (obesity and hormonal factors) and local risk factors (prior joint anomalies and joint overload). Notable among the main factors related to disease progression are joint alignment defects and generalized osteoarthritis. Several classifications of osteoarthritis have been proposed but none is particularly important for the primary care management of the disease. These classifications include etiological (primary or idiopathic forms and secondary forms) and topographical (typical and atypical localizations) classifications, the Kellgren and Lawrence classification (radiological repercussions) and that of the American College of Rheumatology for osteoarthritis of the hand, hip and knee. The prevalence of knee osteoarthritis is 10.2% in Spain and shows a marked discrepancy between clinical and radiological findings. Hand osteoarthritis, with a prevalence of symptomatic involvement of around 6.2%, has several forms of presentation (nodal osteoarthritis, generalized osteoarthritis, rhizarthrosis, and erosive osteoarthritis). Symptomatic osteoarthritis of the hip affects between 3.5% and 5.6% of persons older than 50 years and has different radiological patterns depending on femoral head migration. Copyright © 2014 Elsevier España, S.L. All rights reserved.

  14. Optimal classification of standoff bioaerosol measurements using evolutionary algorithms (United States)

    Nyhavn, Ragnhild; Moen, Hans J. F.; Farsund, Øystein; Rustad, Gunnar


    Early warning systems based on standoff detection of biological aerosols require real-time signal processing of a large quantity of high-dimensional data, challenging the systems efficiency in terms of both computational complexity and classification accuracy. Hence, optimal feature selection is essential in forming a stable and efficient classification system. This involves finding optimal signal processing parameters, characteristic spectral frequencies and other data transformations in large magnitude variable space, stating the need for an efficient and smart search algorithm. Evolutionary algorithms are population-based optimization methods inspired by Darwinian evolutionary theory. These methods focus on application of selection, mutation and recombination on a population of competing solutions and optimize this set by evolving the population of solutions for each generation. We have employed genetic algorithms in the search for optimal feature selection and signal processing parameters for classification of biological agents. The experimental data were achieved with a spectrally resolved lidar based on ultraviolet laser induced fluorescence, and included several releases of 5 common simulants. The genetic algorithm outperform benchmark methods involving analytic, sequential and random methods like support vector machines, Fisher's linear discriminant and principal component analysis, with significantly improved classification accuracy compared to the best classical method.

  15. Linking the biological underpinnings of depression: Role of mitochondria interactions with melatonin, inflammation, sirtuins, tryptophan catabolites, DNA repair and oxidative and nitrosative stress, with consequences for classification and cognition. (United States)

    Anderson, George


    The pathophysiological underpinnings of neuroprogressive processes in recurrent major depressive disorder (rMDD) are reviewed. A wide array of biochemical processes underlie MDD presentations and their shift to a recurrent, neuroprogressive course, including: increased immune-inflammation, tryptophan catabolites (TRYCATs), mitochondrial dysfunction, aryl hydrocarbonn receptor activation, and oxidative and nitrosative stress (O&NS), as well as decreased sirtuins and melatonergic pathway activity. These biochemical changes may have their roots in central, systemic and/or peripheral sites, including in the gut, as well as in developmental processes, such as prenatal stressors and breastfeeding consequences. Consequently, conceptualizations of MDD have dramatically moved from simple psychological and central biochemical models, such as lowered brain serotonin, to a conceptualization that incorporates whole body processes over a lifespan developmental timescale. However, important hubs are proposed, including the gut-brain axis, and mitochondrial functioning, which may provide achievable common treatment targets despite considerable inter-individual variability in biochemical changes. This provides a more realistic model of the complexity of MDD and the pathophysiological processes that underpin the shift to rMDD and consequent cognitive deficits. Such accumulating data on the pathophysiological processes underpinning MDD highlights the need in psychiatry to shift to a classification system that is based on biochemical processes, rather than subjective phenomenology. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Classification in context

    DEFF Research Database (Denmark)

    Mai, Jens Erik


    This paper surveys classification research literature, discusses various classification theories, and shows that the focus has traditionally been on establishing a scientific foundation for classification research. This paper argues that a shift has taken place, and suggests that contemporary...... classification research focus on contextual information as the guide for the design and construction of classification schemes....

  17. BIRADS classification in mammography. (United States)

    Balleyguier, Corinne; Ayadi, Salma; Van Nguyen, Kim; Vanel, Daniel; Dromain, Clarisse; Sigal, Robert


    The Breast Imaging Report and Data System (BIRADS) of the American College of Radiology (ACR) is today largely used in most of the countries where breast cancer screening is implemented. It is a tool defined to reduce variability between radiologists when creating the reports in mammography, ultrasonography or MRI. Some changes in the last version of the BIRADStrade mark have been included to reduce the inaccuracy of some categories, especially for category 4. The BIRADStrade mark includes a lexicon and descriptive diagrams of the anomalies, recommendations for the mammographic report as well as councils and examples of mammographic cases. This review describes the mammographic items of the BIRADS classification with its more recent developments, while detailing the advantages and limits of this classification.

  18. Genetic Bio-Ancestry and Social Construction of Racial Classification in Social Surveys in the Contemporary United States (United States)

    Guo, Guang; Fu, Yilan; Lee, Hedwig; Cai, Tianji; Harris, Kathleen Mullan; Li, Yi


    Self-reported race is generally considered the basis for racial classification in social surveys, including the U.S. census. Drawing on recent advances in human molecular genetics and social science perspectives of socially constructed race, our study takes into account both genetic bio-ancestry and social context in understanding racial classification. This article accomplishes two objectives. First, our research establishes geographic genetic bio-ancestry as a component of racial classification. Second, it shows how social forces trump biology in racial classification and/or how social context interacts with bio-ancestry in shaping racial classification. The findings were replicated in two racially and ethnically diverse data sets: the College Roommate Study (N = 2,065) and the National Longitudinal Study of Adolescent Health (N = 2,281). PMID:24019100

  19. CP-CHARM: segmentation-free image classification made accessible. (United States)

    Uhlmann, Virginie; Singh, Shantanu; Carpenter, Anne E


    Automated classification using machine learning often relies on features derived from segmenting individual objects, which can be difficult to automate. WND-CHARM is a previously developed classification algorithm in which features are computed on the whole image, thereby avoiding the need for segmentation. The algorithm obtained encouraging results but requires considerable computational expertise to execute. Furthermore, some benchmark sets have been shown to be subject to confounding artifacts that overestimate classification accuracy. We developed CP-CHARM, a user-friendly image-based classification algorithm inspired by WND-CHARM in (i) its ability to capture a wide variety of morphological aspects of the image, and (ii) the absence of requirement for segmentation. In order to make such an image-based classification method easily accessible to the biological research community, CP-CHARM relies on the widely-used open-source image analysis software CellProfiler for feature extraction. To validate our method, we reproduced WND-CHARM's results and ensured that CP-CHARM obtained comparable performance. We then successfully applied our approach on cell-based assay data and on tissue images. We designed these new training and test sets to reduce the effect of batch-related artifacts. The proposed method preserves the strengths of WND-CHARM - it extracts a wide variety of morphological features directly on whole images thereby avoiding the need for cell segmentation, but additionally, it makes the methods easily accessible for researchers without computational expertise by implementing them as a CellProfiler pipeline. It has been demonstrated to perform well on a wide range of bioimage classification problems, including on new datasets that have been carefully selected and annotated to minimize batch effects. This provides for the first time a realistic and reliable assessment of the whole image classification strategy.

  20. Regularized binormal ROC method in disease classification using microarray data

    Directory of Open Access Journals (Sweden)

    Huang Jian


    Full Text Available Abstract Background An important application of microarrays is to discover genomic biomarkers, among tens of thousands of genes assayed, for disease diagnosis and prognosis. Thus it is of interest to develop efficient statistical methods that can simultaneously identify important biomarkers from such high-throughput genomic data and construct appropriate classification rules. It is also of interest to develop methods for evaluation of classification performance and ranking of identified biomarkers. Results The ROC (receiver operating characteristic technique has been widely used in disease classification with low dimensional biomarkers. Compared with the empirical ROC approach, the binormal ROC is computationally more affordable and robust in small sample size cases. We propose using the binormal AUC (area under the ROC curve as the objective function for two-sample classification, and the scaled threshold gradient directed regularization method for regularized estimation and biomarker selection. Tuning parameter selection is based on V-fold cross validation. We develop Monte Carlo based methods for evaluating the stability of individual biomarkers and overall prediction performance. Extensive simulation studies show that the proposed approach can generate parsimonious models with excellent classification and prediction performance, under most simulated scenarios including model mis-specification. Application of the method to two cancer studies shows that the identified genes are reasonably stable with satisfactory prediction performance and biologically sound implications. The overall classification performance is satisfactory, with small classification errors and large AUCs. Conclusion In comparison to existing methods, the proposed approach is computationally more affordable without losing the optimality possessed by the standard ROC method.



    Natalia Romanova


    New types of criminal groups are emerging in modern society.  These types have their special criminal subculture. The research objective is to develop new parameters of classification of modern criminal groups, create a new typology of criminal groups and identify some features of their subculture. Research methodology is based on the system approach that includes using the method of analysis of documentary sources (materials of a criminal case), method of conversations with themembers of the...


    Directory of Open Access Journals (Sweden)



    Full Text Available Problem statement. Ecopolices are the newest stage of the urban planning. They have to be consideredsuchas material and energy informational structures, included to the dynamic-evolutionary matrix netsofex change processes in the ecosystems. However, there are not made the ecopolice classifications, developing on suchapproaches basis. And this determined the topicality of the article. Analysis of publications on theoretical and applied aspects of the ecopolices formation showed, that the work on them is managed mainly in the context of the latest scientific and technological achievements in the various knowledge fields. These settlements are technocratic. They are connected with the morphology of space, network structures of regional and local natural ecosystems, without independent stability, can not exist without continuous man support. Another words, they do not work in with an ecopolices idea. It is come to a head for objective, symbiotic searching of ecopolices concept with the development of their classifications. Purpose statement is to develop the objective evidence for ecopolices and to propose their new classification. Conclusion. On the base of the ecopolices classification have to lie an elements correlation idea of their general plans and men activity type according with natural mechanism of accepting, reworking and transmission of material, energy and information between geo-ecosystems, planet, man, ecopolices material part and Cosmos. New ecopolices classification should be based on the principles of multi-dimensional, time-spaced symbiotic clarity with exchange ecosystem networks. The ecopolice function with this approach comes not from the subjective anthropocentric economy but from the holistic objective of Genesis paradigm. Or, otherwise - not from the Consequence, but from the Cause.

  3. Hazard classification methodology

    International Nuclear Information System (INIS)

    Brereton, S.J.


    This document outlines the hazard classification methodology used to determine the hazard classification of the NIF LTAB, OAB, and the support facilities on the basis of radionuclides and chemicals. The hazard classification determines the safety analysis requirements for a facility

  4. DTI measurements for Alzheimer's classification. (United States)

    Maggipinto, Tommaso; Bellotti, Roberto; Amoroso, Nicola; Diacono, Domenico; Donvito, Giacinto; Lella, Eufemia; Monaco, Alfonso; Antonella Scelsi, Marzia; Tangaro, Sabina


    Diffusion tensor imaging (DTI) is a promising imaging technique that provides insight into white matter microstructure integrity and it has greatly helped identifying white matter regions affected by Alzheimer's disease (AD) in its early stages. DTI can therefore be a valuable source of information when designing machine-learning strategies to discriminate between healthy control (HC) subjects, AD patients and subjects with mild cognitive impairment (MCI). Nonetheless, several studies have reported so far conflicting results, especially because of the adoption of biased feature selection strategies. In this paper we firstly analyzed DTI scans of 150 subjects from the Alzheimer's disease neuroimaging initiative (ADNI) database. We measured a significant effect of the feature selection bias on the classification performance (p-value  content provided by DTI measurements for AD classification. Classification performances and biological insight, concerning brain regions related to the disease, provided by cross-validation analysis were both confirmed on the independent test.

  5. Interagency Security Classification Appeals Panel (ISCAP) Decisions (United States)

    National Archives and Records Administration — This online collection includes documents decided upon by the Interagency Security Classification Appeals Panel (ISCAP) starting in Fiscal Year 2012. The documents...

  6. Marine biology

    International Nuclear Information System (INIS)

    Thurman, H.V.; Webber, H.H.


    This book discusses both taxonomic and ecological topics on marine biology. Full coverage of marine organisms of all five kingdoms is provided, along with interesting and thorough discussion of all major marine habitats. Organization into six major parts allows flexibility. It also provides insight into important topics such as disposal of nuclear waste at sea, the idea that life began on the ocean floor, and how whales, krill, and people interact. A full-color photo chapter reviews questions, and exercises. The contents are: an overview marine biology: fundamental concepts/investigating life in the ocean; the physical ocean, the ocean floor, the nature of water, the nature and motion of ocean water; general ecology, conditions for life in the sea, biological productivity and energy transfer; marine organisms; monera, protista, mycota and metaphyta; the smaller marine animals, the large animals marine habitats, the intertidal zone/benthos of the continental shelf, the photic zone, the deep ocean, the ocean under stress, marine pollution, appendix a: the metric system and conversion factors/ appendix b: prefixes and suffixes/ appendix c: taxonomic classification of common marine organisms, and glossary, and index

  7. The development of a classification system for inland aquatic ...

    African Journals Online (AJOL)

    A classification system is described that was developed for inland aquatic ecosystems in South Africa, including wetlands. The six-tiered classification system is based on a top-down, hierarchical classification of aquatic ecosystems, following the functionally-oriented hydrogeomorphic (HGM) approach to classification but ...

  8. Biological Oceanography (United States)

    Dyhrman, Sonya


    The ocean is arguably the largest habitat on the planet, and it houses an astounding array of life, from microbes to whales. As a testament to this diversity and its importance, the discipline of biological oceanography spans studies of all levels of biological organization, from that of single genes, to organisms, to their population dynamics. Biological oceanography also includes studies on how organisms interact with, and contribute to, essential global processes. Students of biological oceanography are often as comfortable looking at satellite images as they are electron micrographs. This diversity of perspective begins the textbook Biological Oceanography, with cover graphics including a Coastal Zone Color Scanner image representing chlorophyll concentration, an electron micrograph of a dinoflagellate, and a photograph of a copepod. These images instantly capture the reader's attention and illustrate some of the different scales on which budding oceanographers are required to think. Having taught a core graduate course in biological oceanography for many years, Charlie Miller has used his lecture notes as the genesis for this book. The text covers the subject of biological oceanography in a manner that is targeted to introductory graduate students, but it would also be appropriate for advanced undergraduates.

  9. Classification of the web

    DEFF Research Database (Denmark)

    Mai, Jens Erik


    This paper discusses the challenges faced by investigations into the classification of the Web and outlines inquiries that are needed to use principles for bibliographic classification to construct classifications of the Web. This paper suggests that the classification of the Web meets challenges...

  10. Protist classification and the kingdoms of organisms. (United States)

    Whittaker, R H; Margulis, L


    Traditional classification imposed a division into plant-like and animal-like forms on the unicellular eukaryotes, or protists; in a current view the protists are a diverse assemblage of plant-, animal- and fungus-like groups. Classification of these into phyla is difficult because of their relatively simple structure and limited geological record, but study of ultrastructure and other characteristics is providing new insight on protist classification. Possible classifications are discussed, and a summary classification of the living world into kingdoms (Monera, Protista, Fungi, Animalia, Plantae) and phyla is suggested. This classification also suggests groupings of phyla into superphyla and form-superphyla, and a broadened kingdom Protista (including green algae, oomycotes and slime molds but excluding red and brown algae). The classification thus seeks to offer a compromise between the protist and protoctist kingdoms of Whittaker and Margulis and to combine a full listing of phyla with grouping of these for synoptic treatment.

  11. Classifying Life, Reconstructing History and Teaching Diversity: Philosophical Issues in the Teaching of Biological Systematics and Biodiversity (United States)

    Reydon, Thomas A. C.


    Classification is a central endeavor in every scientific field of work. Classification in biology, however, is distinct from classification in other fields of science in a number of ways. Thus, understanding how biological classification works is an important element in understanding the nature of biological science. In the present paper, I…

  12. Product Classification (United States)

    U.S. Department of Health & Human Services — This database contains medical device names and associated information developed by the Center. It includes a three letter device product code and a Device Class...

  13. Whewell on classification and consilience. (United States)

    Quinn, Aleta


    In this paper I sketch William Whewell's attempts to impose order on classificatory mineralogy, which was in Whewell's day (1794-1866) a confused science of uncertain prospects. Whewell argued that progress was impeded by the crude reductionist assumption that all macroproperties of crystals could be straightforwardly explained by reference to the crystals' chemical constituents. By comparison with biological classification, Whewell proposed methodological reforms that he claimed would lead to a natural classification of minerals, which in turn would support advances in causal understanding of the properties of minerals. Whewell's comparison to successful biological classification is particularly striking given that classificatory biologists did not share an understanding of the causal structure underlying the natural classification of life (the common descent with modification of all organisms). Whewell's key proposed methodological reform is consideration of multiple, distinct principles of classification. The most powerful evidence in support of a natural classificatory claim is the consilience of claims arrived at through distinct lines of reasoning, rooted in distinct conceptual approaches to the target objects. Mineralogists must consider not only elemental composition and chemical affinities, but also symmetry and polarity. Geometrical properties are central to what makes an individual mineral the type of mineral that it is. In Whewell's view, function and organization jointly define life, and so are the keys to understanding what makes an organism the type of organism that it is. I explain the relationship between Whewell's teleological account of life and his natural theology. I conclude with brief comments about the importance of Whewell's classificatory theory for the further development of his philosophy of science and in particular his account of consilience. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Quantum Biology

    Directory of Open Access Journals (Sweden)

    Alessandro Sergi


    Full Text Available A critical assessment of the recent developmentsof molecular biology is presented.The thesis that they do not lead to a conceptualunderstanding of life and biological systems is defended.Maturana and Varela's concept of autopoiesis is briefly sketchedand its logical circularity avoided by postulatingthe existence of underlying living processes,entailing amplification from the microscopic to the macroscopic scale,with increasing complexity in the passage from one scale to the other.Following such a line of thought, the currently accepted model of condensed matter, which is based on electrostatics and short-ranged forces,is criticized. It is suggested that the correct interpretationof quantum dispersion forces (van der Waals, hydrogen bonding, and so onas quantum coherence effects hints at the necessity of includinglong-ranged forces (or mechanisms for them incondensed matter theories of biological processes.Some quantum effects in biology are reviewedand quantum mechanics is acknowledged as conceptually important to biology since withoutit most (if not all of the biological structuresand signalling processes would not even exist. Moreover, it is suggested that long-rangequantum coherent dynamics, including electron polarization,may be invoked to explain signal amplificationprocess in biological systems in general.

  15. SAW Classification Algorithm for Chinese Text Classification


    Xiaoli Guo; Huiyu Sun; Tiehua Zhou; Ling Wang; Zhaoyang Qu; Jiannan Zang


    Considering the explosive growth of data, the increased amount of text data’s effect on the performance of text categorization forward the need for higher requirements, such that the existing classification method cannot be satisfied. Based on the study of existing text classification technology and semantics, this paper puts forward a kind of Chinese text classification oriented SAW (Structural Auxiliary Word) algorithm. The algorithm uses the special space effect of Chinese text where words...

  16. 5th Conference of the International Federation of Classification Societies

    CERN Document Server

    Yajima, Keiji; Bock, Hans-Hermann; Ohsumi, Noboru; Tanaka, Yutaka; Baba, Yasumasa


    This volume, Data Science, Classification, and Related Methods, contains a selection of papers presented at the Fifth Conference of the International Federation of Oassification Societies (IFCS-96), which was held in Kobe, Japan, from March 27 to 30,1996. The volume covers a wide range of topics and perspectives in the growing field of data science, including theoretical and methodological advances in domains relating to data gathering, classification and clustering, exploratory and multivariate data analysis, and knowledge discovery and seeking. It gives a broad view of the state of the art and is intended for those in the scientific community who either develop new data analysis methods or gather data and use search tools for analyzing and interpreting large and complex data sets. Presenting a wide field of applications, this book is of interest not only to data analysts, mathematicians, and statisticians but also to scientists from many areas and disciplines concerned with complex data: medicine, biology, ...

  17. Phylogenetic classification of bony fishes. (United States)

    Betancur-R, Ricardo; Wiley, Edward O; Arratia, Gloria; Acero, Arturo; Bailly, Nicolas; Miya, Masaki; Lecointre, Guillaume; Ortí, Guillermo


    Fish classifications, as those of most other taxonomic groups, are being transformed drastically as new molecular phylogenies provide support for natural groups that were unanticipated by previous studies. A brief review of the main criteria used by ichthyologists to define their classifications during the last 50 years, however, reveals slow progress towards using an explicit phylogenetic framework. Instead, the trend has been to rely, in varying degrees, on deep-rooted anatomical concepts and authority, often mixing taxa with explicit phylogenetic support with arbitrary groupings. Two leading sources in ichthyology frequently used for fish classifications (JS Nelson's volumes of Fishes of the World and W. Eschmeyer's Catalog of Fishes) fail to adopt a global phylogenetic framework despite much recent progress made towards the resolution of the fish Tree of Life. The first explicit phylogenetic classification of bony fishes was published in 2013, based on a comprehensive molecular phylogeny ( ). We here update the first version of that classification by incorporating the most recent phylogenetic results. The updated classification presented here is based on phylogenies inferred using molecular and genomic data for nearly 2000 fishes. A total of 72 orders (and 79 suborders) are recognized in this version, compared with 66 orders in version 1. The phylogeny resolves placement of 410 families, or ~80% of the total of 514 families of bony fishes currently recognized. The ordinal status of 30 percomorph families included in this study, however, remains uncertain (incertae sedis in the series Carangaria, Ovalentaria, or Eupercaria). Comments to support taxonomic decisions and comparisons with conflicting taxonomic groups proposed by others are presented. We also highlight cases were morphological support exist for the groups being classified. This version of the phylogenetic classification of bony fishes is substantially improved, providing resolution

  18. Pattern classification

    CERN Document Server

    Duda, Richard O; Stork, David G


    The first edition, published in 1973, has become a classic reference in the field. Now with the second edition, readers will find information on key new topics such as neural networks and statistical pattern recognition, the theory of machine learning, and the theory of invariances. Also included are worked examples, comparisons between different methods, extensive graphics, expanded exercises and computer project topics. An Instructor's Manual presenting detailed solutions to all the problems in the book is available from the Wiley editorial department.

  19. Proteomic classification of breast cancer.

    LENUS (Irish Health Repository)

    Kamel, Dalia


    Being a significant health problem that affects patients in various age groups, breast cancer has been extensively studied to date. Recently, molecular breast cancer classification has advanced significantly with the availability of genomic profiling technologies. Proteomic technologies have also advanced from traditional protein assays including enzyme-linked immunosorbent assay, immunoblotting and immunohistochemistry to more comprehensive approaches including mass spectrometry and reverse phase protein lysate arrays (RPPA). The purpose of this manuscript is to review the current protein markers that influence breast cancer prediction and prognosis and to focus on novel advances in proteomic classification of breast cancer.

  20. Lipid classification, structures and tools☆ (United States)

    Fahy, Eoin; Cotter, Dawn; Sud, Manish; Subramaniam, Shankar


    The study of lipids has developed into a research field of increasing importance as their multiple biological roles in cell biology, physiology and pathology are becoming better understood. The Lipid Metabolites and Pathways Strategy (LIPID MAPS) consortium is actively involved in an integrated approach for the detection, quantitation and pathway reconstruction of lipids and related genes and proteins at a systems-biology level. A key component of this approach is a bioinformatics infrastructure involving a clearly defined classification of lipids, a state-of-the-art database system for molecular species and experimental data and a suite of user-friendly tools to assist lipidomics researchers. Herein, we discuss a number of recent developments by the LIPID MAPS bioinformatics core in pursuit of these objectives. This article is part of a Special Issue entitled Lipodomics and Imaging Mass Spectrometry. PMID:21704189

  1. Lipid classification, structures and tools. (United States)

    Fahy, Eoin; Cotter, Dawn; Sud, Manish; Subramaniam, Shankar


    The study of lipids has developed into a research field of increasing importance as their multiple biological roles in cell biology, physiology and pathology are becoming better understood. The Lipid Metabolites and Pathways Strategy (LIPID MAPS) consortium is actively involved in an integrated approach for the detection, quantitation and pathway reconstruction of lipids and related genes and proteins at a systems-biology level. A key component of this approach is a bioinformatics infrastructure involving a clearly defined classification of lipids, a state-of-the-art database system for molecular species and experimental data and a suite of user-friendly tools to assist lipidomics researchers. Herein, we discuss a number of recent developments by the LIPID MAPS bioinformatics core in pursuit of these objectives. Copyright © 2011 Elsevier B.V. All rights reserved.

  2. Analysis and classification of human error (United States)

    Rouse, W. B.; Rouse, S. H.


    The literature on human error is reviewed with emphasis on theories of error and classification schemes. A methodology for analysis and classification of human error is then proposed which includes a general approach to classification. Identification of possible causes and factors that contribute to the occurrence of errors is also considered. An application of the methodology to the use of checklists in the aviation domain is presented for illustrative purposes.

  3. Computational aspects of systematic biology. (United States)

    Lilburn, Timothy G; Harrison, Scott H; Cole, James R; Garrity, George M


    We review the resources available to systematic biologists who wish to use computers to build classifications. Algorithm development is in an early stage, and only a few examples of integrated applications for systematic biology are available. The availability of data is crucial if systematic biology is to enter the computer age.

  4. Phytochemical and biological studies of bryophytes. (United States)

    Asakawa, Yoshinori; Ludwiczuk, Agnieszka; Nagashima, Fumihiro


    The bryophytes contain the Marchantiophyta (liverworts), Bryophyta (mosses) and Anthocerotophyta (hornworts). Of these, the Marchantiophyta have a cellular oil body which produce a number of mono-, sesqui- and di-terpenoids, aromatic compounds like bibenzyl, bis-bibenzyls and acetogenins. Most sesqui- and di-terpenoids obtained from liverworts are enantiomers of those found in higher plants. Many of these compounds display a characteristic odor, and can have interesting biological activities. These include: allergenic contact dermatitis, antimicrobial, antifungal and antiviral, cytotoxic, insecticidal, insect antifeedant, superoxide anion radical release, 5-lipoxygenase, calmodulin, hyaluronidase, cyclooxygenase, DNA polymerase β, and α-glucosidase and NO production inhibitory, antioxidant, piscicidal, neurotrophic and muscle relaxing activities among others. Each liverwort biosynthesizes unique components, which are valuable for their chemotaxonomic classification. Typical chemical structures and biological activity of the selected liverwort constituents as well as the hemi- and total synthesis of some biologically active compounds are summarized. Copyright © 2012 Elsevier Ltd. All rights reserved.

  5. Kankerrisico van biologicals vaststellen?

    DEFF Research Database (Denmark)

    Vermeer, Niels S; De Bruin, Marie L


    Safety meta-analyses could play an important role in capturing fragmented safety data from underpowered clinical studies. Their utility, however, is hampered by the same constraints surrounding clinical studies, including limited external validity, inconsistent classification and the underreporting...

  6. Kankerrisico van biologicals vaststellen?

    DEFF Research Database (Denmark)

    Vermeer, Niels S; De Bruin, Marie L


    Safety meta-analyses could play an important role in capturing fragmented safety data from underpowered clinical studies. Their utility, however, is hampered by the same constraints surrounding clinical studies, including limited external validity, inconsistent classification and the underreporti...

  7. Biology Notes. (United States)

    School Science Review, 1981


    Outlines a variety of laboratory procedures, techniques, and materials including construction of a survey frame for field biology, a simple tidal system, isolation and applications of plant protoplasts, tropisms, teaching lung structure, and a key to statistical methods for biologists. (DS)

  8. Classification of cultivated plants.

    NARCIS (Netherlands)

    Brandenburg, W.A.


    Agricultural practice demands principles for classification, starting from the basal entity in cultivated plants: the cultivar. In establishing biosystematic relationships between wild, weedy and cultivated plants, the species concept needs re-examination. Combining of botanic classification, based

  9. Objects Classification by Learning-Based Visual Saliency Model and Convolutional Neural Network

    Directory of Open Access Journals (Sweden)

    Na Li


    Full Text Available Humans can easily classify different kinds of objects whereas it is quite difficult for computers. As a hot and difficult problem, objects classification has been receiving extensive interests with broad prospects. Inspired by neuroscience, deep learning concept is proposed. Convolutional neural network (CNN as one of the methods of deep learning can be used to solve classification problem. But most of deep learning methods, including CNN, all ignore the human visual information processing mechanism when a person is classifying objects. Therefore, in this paper, inspiring the completed processing that humans classify different kinds of objects, we bring forth a new classification method which combines visual attention model and CNN. Firstly, we use the visual attention model to simulate the processing of human visual selection mechanism. Secondly, we use CNN to simulate the processing of how humans select features and extract the local features of those selected areas. Finally, not only does our classification method depend on those local features, but also it adds the human semantic features to classify objects. Our classification method has apparently advantages in biology. Experimental results demonstrated that our method made the efficiency of classification improve significantly.

  10. Classification of EEG Signals using adaptive weighted distance nearest neighbor algorithm

    Directory of Open Access Journals (Sweden)

    E. Parvinnia


    Full Text Available Electroencephalogram (EEG signals are often used to diagnose diseases such as seizure, alzheimer, and schizophrenia. One main problem with the recorded EEG samples is that they are not equally reliable due to the artifacts at the time of recording. EEG signal classification algorithms should have a mechanism to handle this issue. It seems that using adaptive classifiers can be useful for the biological signals such as EEG. In this paper, a general adaptive method named weighted distance nearest neighbor (WDNN is applied for EEG signal classification to tackle this problem. This classification algorithm assigns a weight to each training sample to control its influence in classifying test samples. The weights of training samples are used to find the nearest neighbor of an input query pattern. To assess the performance of this scheme, EEG signals of thirteen schizophrenic patients and eighteen normal subjects are analyzed for the classification of these two groups. Several features including, fractal dimension, band power and autoregressive (AR model are extracted from EEG signals. The classification results are evaluated using Leave one (subject out cross validation for reliable estimation. The results indicate that combination of WDNN and selected features can significantly outperform the basic nearest-neighbor and the other methods proposed in the past for the classification of these two groups. Therefore, this method can be a complementary tool for specialists to distinguish schizophrenia disorder.

  11. Classification of Pemphigus

    Directory of Open Access Journals (Sweden)

    Ayşe Akman


    Full Text Available Clinical classification of pemphigus is not yet complete. The classic classification based on clinical and histologic features. Because of the progress in the pathogenesis of pemphigus, the current classifications based on accumulating analyses of antigen molecules and subclasses of immunoglobulins and etiologic aspects of pemphigus as weel as the clinical, histologic features. The aim of this paper is to review classification of pemphigus.

  12. A comprehensive classification system for lipids


    Fahy, E.; Subramaniam, S.; Brown, H.A.; Glass, C.K.; Merrill, A.H.; Murphy, R.C.; Raetz, C.R.H.; Russell, D.W.; Seyama, Y.; Shaw, W.; Shimizu, T.; Spener, F.; van Meer, G.; VanNieuwenhze, M.S.; White, S.H.


    Lipids are produced, transported, and recognized by the concerted actions of numerous enzymes, binding proteins, and receptors. A comprehensive analysis of lipid molecules, “lipidomics,” in the context of genomics and proteomics is crucial to understanding cellular physiology and pathology; consequently, lipid biology has become a major research target of the postgenomic revolution and systems biology. To facilitate international communication about lipids, a comprehensive classification of l...

  13. Classification of soft tissues using laser-induced breakdown spectroscopy (United States)

    Li, Xiaohui; An, Xiaokang; Fan, Rongwei; Yu, Xin; Chen, Deying


    Classification of pork soft tissues, including skin, fat, loin, tenderloin and ham muscles, was achieved using combination of laser-induced breakdown spectroscopy, principal component analysis and k nearest neighbors classification.

  14. Nonlinear estimation and classification

    CERN Document Server

    Hansen, Mark; Holmes, Christopher; Mallick, Bani; Yu, Bin


    Researchers in many disciplines face the formidable task of analyzing massive amounts of high-dimensional and highly-structured data This is due in part to recent advances in data collection and computing technologies As a result, fundamental statistical research is being undertaken in a variety of different fields Driven by the complexity of these new problems, and fueled by the explosion of available computer power, highly adaptive, non-linear procedures are now essential components of modern "data analysis," a term that we liberally interpret to include speech and pattern recognition, classification, data compression and signal processing The development of new, flexible methods combines advances from many sources, including approximation theory, numerical analysis, machine learning, signal processing and statistics The proposed workshop intends to bring together eminent experts from these fields in order to exchange ideas and forge directions for the future

  15. Linear Classification of Dairy Cattle. Slide Script. (United States)

    Sipiorski, James; Spike, Peter

    This slide script, part of a series of slide scripts designed for use in vocational agriculture classes, deals with principles of the linear classification of dairy cattle. Included in the guide are narrations for use with 63 slides, which illustrate the following areas that are considered in the linear classification system: stature, strength,…

  16. Computational Intelligence Paradigms in Advanced Pattern Classification

    CERN Document Server

    Jain, Lakhmi


    This monograph presents selected areas of application of pattern recognition and classification approaches including handwriting recognition, medical image analysis and interpretation, development of cognitive systems for image computer understanding, moving object detection, advanced image filtration and intelligent multi-object labelling and classification. It is directed to the scientists, application engineers, professors, professors and students will find this book useful.

  17. Deep learning for image classification (United States)

    McCoppin, Ryan; Rizki, Mateen


    This paper provides an overview of deep learning and introduces the several subfields of deep learning including a specific tutorial of convolutional neural networks. Traditional methods for learning image features are compared to deep learning techniques. In addition, we present our preliminary classification results, our basic implementation of a convolutional restricted Boltzmann machine on the Mixed National Institute of Standards and Technology database (MNIST), and we explain how to use deep learning networks to assist in our development of a robust gender classification system.

  18. Classification, disease, and diagnosis. (United States)

    Jutel, Annemarie


    Classification shapes medicine and guides its practice. Understanding classification must be part of the quest to better understand the social context and implications of diagnosis. Classifications are part of the human work that provides a foundation for the recognition and study of illness: deciding how the vast expanse of nature can be partitioned into meaningful chunks, stabilizing and structuring what is otherwise disordered. This article explores the aims of classification, their embodiment in medical diagnosis, and the historical traditions of medical classification. It provides a brief overview of the aims and principles of classification and their relevance to contemporary medicine. It also demonstrates how classifications operate as social framing devices that enable and disable communication, assert and refute authority, and are important items for sociological study.

  19. Green nanotechnology - a new hope for medical biology. (United States)

    Nath, Debjani; Banerjee, Pratyusha


    The development of eco-friendly technologies in material synthesis is of considerable importance to expand their biological applications. Nowadays, a variety of green nanoparticles with well-defined chemical composition, size, and morphology have been synthesized by different methods and their applications in many cutting-edge technological areas have been explored. This review highlights the classification of nanoparticles giving special emphasis on biosynthesis of metal nanoparticle by viable organisms. It also focuses on the applications of these biosynthesized nanoparticles in a wide spectrum of potential areas of medical biology including catalysis, targeted drug delivery, cancer treatment, antibacterial agents and as biosensors. Copyright © 2013 Elsevier B.V. All rights reserved.

  20. Advances in Biological Science. (United States)

    Oppenheimer, Steven B.; And Others


    Reviews major developments in areas that are at the cutting edge of biological research. Areas include: human anti-cancer gene, recombinant DNA techniques for the detection of Huntington disease carriers, and marine biology. (CW)

  1. The survey of large-scale query classification (United States)

    Zhou, Sanduo; Cheng, Kefei; Men, Lijun


    In recent years, a lot of researches have been done on query classification. The paper introduces the recent researches on query classification in detail, mainly including the source of query log, the category systems, the feature extraction methods, classification methods and the evaluation methodology. Then it discusses the issues of large-scale query classification and the solved methods combined with big data analysis systems. The research result shows there still are several problems and challenges, such as lack of authoritative classification system and evaluation methodology, efficiency of the feature extraction method, uncertainty of the performance on large-scale query log and the further query classification on the big data platform, etc.

  2. Recursive heuristic classification (United States)

    Wilkins, David C.


    The author will describe a new problem-solving approach called recursive heuristic classification, whereby a subproblem of heuristic classification is itself formulated and solved by heuristic classification. This allows the construction of more knowledge-intensive classification programs in a way that yields a clean organization. Further, standard knowledge acquisition and learning techniques for heuristic classification can be used to create, refine, and maintain the knowledge base associated with the recursively called classification expert system. The method of recursive heuristic classification was used in the Minerva blackboard shell for heuristic classification. Minerva recursively calls itself every problem-solving cycle to solve the important blackboard scheduler task, which involves assigning a desirability rating to alternative problem-solving actions. Knowing these ratings is critical to the use of an expert system as a component of a critiquing or apprenticeship tutoring system. One innovation of this research is a method called dynamic heuristic classification, which allows selection among dynamically generated classification categories instead of requiring them to be prenumerated.

  3. Cutaneous hidradenocarcinoma: a clinicopathological, immunohistochemical, and molecular biologic study of 14 cases, including Her2/neu gene expression/amplification, TP53 gene mutation analysis, and t(11;19) translocation. (United States)

    Kazakov, Dmitry V; Ivan, Doina; Kutzner, Heinz; Spagnolo, Dominic V; Grossmann, Petr; Vanecek, Tomas; Sima, Radek; Kacerovska, Denisa; Shelekhova, Ksenia V; Denisjuk, Natalja; Hillen, Uwe; Kuroda, Naoto; Mukensnabl, Petr; Danis, Dusan; Michal, Michal


    We present a series of 14 cases of cutaneous hidradenocarcinomas. The patients included 6 women and 8 men ranging in age at diagnosis from 34 to 93 years. All but 1 patient presented with a solitary nodule. There was no predilection site. One patient presented with multiple lesions representing metastatic nodules. Of 12 patients with available follow-up, 2 died of disease, whereas the remaining 10 patients were alive but 3 of them experienced a local recurrence in the course of the disease. Grossly, the tumors ranged in size from 1.2 to 6 cm. Microscopically, of the 14 primary tumors, 9 showed low-grade cytomorphology, whereas the remaining 5 neoplasms were high-grade lesions. The residuum of a hidradenoma was present in 5 of the 14 primaries. The mitotic rate was highly variable, ranging from 2 to 64 mitoses per 10 high-power field. The cellular composition of the tumors varied slightly, with clear cells, epidermoid cells, and transitional forms being present in each case. In 1 case, there was metaplastic transformation into sarcomatoid carcinoma. Glandular differentiation varied from case to case and appeared most commonly as simple round glands or as cells with intracytoplasmic lumens. Necrosis en masse was detected in 8 specimens. One specimen represented a reexcision and was unusual as it showed a well-demarcated intradermal proliferation of relatively bland clear cells accompanied by an overlying intraepidermal growth of clear cells resembling hidradenoacanthoma simplex. Despite the bland appearance, the tumor metastasized to a lymph node. Immunohistochemically, 5 of the 8 specimens studied for Her2/neu expression were negative, whereas 3 specimens from 2 cases yielded score +2, but all the 3 specimens with score 2+ subsequently proved negative for Her2/neu gene amplification by fluorescence in situ hybridization. Of 10 primaries studied, 4 tumors showed positive p53 immunoreaction in more than 25% of the cells comprising the malignant portion of the lesions

  4. Classification of Flotation Frothers

    Directory of Open Access Journals (Sweden)

    Jan Drzymala


    Full Text Available In this paper, a scheme of flotation frothers classification is presented. The scheme first indicates the physical system in which a frother is present and four of them i.e., pure state, aqueous solution, aqueous solution/gas system and aqueous solution/gas/solid system are distinguished. As a result, there are numerous classifications of flotation frothers. The classifications can be organized into a scheme described in detail in this paper. The frother can be present in one of four physical systems, that is pure state, aqueous solution, aqueous solution/gas and aqueous solution/gas/solid system. It results from the paper that a meaningful classification of frothers relies on choosing the physical system and next feature, trend, parameter or parameters according to which the classification is performed. The proposed classification can play a useful role in characterizing and evaluation of flotation frothers.

  5. New classification efforts in epilepsy: Opportunities for clinical neurosciences. (United States)

    Berg, Anne T


    Classification is truly a scientific endeavor. In recent years, the use of the term in clinical epilepsy has diverged from the purpose of the intellectual process of classification in the sciences. As genetics and molecular biology come into their own, scientific classification may finally come to epilepsy and begin to shed light on the many aspects of brain disorders that are characterized by seizures but which are truly multifaceted disorders and deserve more comprehensive, multidisciplinary approaches than they have received previously. This article is part of a Special Issue entitled "The new approach to classification: Rethinking cognition and behavior in epilepsy". Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Definition and classification of epilepsy. Classification of epileptic seizures 2016

    Directory of Open Access Journals (Sweden)

    K. Yu. Mukhin


    Full Text Available Epilepsy is one of the most common neurological diseases, especially in childhood and adolescence. The incidence varies from 15 to 113 cases per 100 000 population with the maximum among children under 1 year old. The prevalence of epilepsy is high, ranging from 5 to 8 cases (in some regions – 10 cases per 1000 children under 15 years old. Classification of the disease has great importance for diagnosis, treatment and prognosis. The article presents a novel strategy for classification of epileptic seizures, developed in 2016. It contains a number of brand new concepts, including a very important one, saying that some seizures, previously considered as generalized or focal only, can be, in fact, both focal and generalized. They include tonic, atonic, myoclonic seizures and epileptic spasms. The term “secondarily generalized seizure” is replace by the term “bilateral tonic-clonic seizure” (as soon as it is not a separate type of epileptic seizures, and the term reflects the spread of discharge from any area of cerebral cortex and evolution of any types of focal seizures. International League Against Epilepsy recommends to abandon the term “pseudo-epileptic seizures” and replace it by the term “psychogenic non-epileptic seizures”. If a doctor is not sure that seizures have epileptic nature, the term “paroxysmal event” should be used without specifying the disease. The conception of childhood epileptic encephalopathies, developed within this novel classification project, is one of the most significant achievements, since in this case not only the seizures, but even epileptiform activity can induce severe disorders of higher mental functions. In addition to detailed description of the new strategy for classification of epileptic seizures, the article contains a comprehensive review of the existing principles of epilepsy and epileptic seizures classification.

  7. The top-scoring ‘N’ algorithm: a generalized relative expression classification method from small numbers of biomolecules (United States)


    Background Relative expression algorithms such as the top-scoring pair (TSP) and the top-scoring triplet (TST) have several strengths that distinguish them from other classification methods, including resistance to overfitting, invariance to most data normalization methods, and biological interpretability. The top-scoring ‘N’ (TSN) algorithm is a generalized form of other relative expression algorithms which uses generic permutations and a dynamic classifier size to control both the permutation and combination space available for classification. Results TSN was tested on nine cancer datasets, showing statistically significant differences in classification accuracy between different classifier sizes (choices of N). TSN also performed competitively against a wide variety of different classification methods, including artificial neural networks, classification trees, discriminant analysis, k-Nearest neighbor, naïve Bayes, and support vector machines, when tested on the Microarray Quality Control II datasets. Furthermore, TSN exhibits low levels of overfitting on training data compared to other methods, giving confidence that results obtained during cross validation will be more generally applicable to external validation sets. Conclusions TSN preserves the strengths of other relative expression algorithms while allowing a much larger permutation and combination space to be explored, potentially improving classification accuracies when fewer numbers of measured features are available. PMID:22966958

  8. The top-scoring 'N' algorithm: a generalized relative expression classification method from small numbers of biomolecules. (United States)

    Magis, Andrew T; Price, Nathan D


    Relative expression algorithms such as the top-scoring pair (TSP) and the top-scoring triplet (TST) have several strengths that distinguish them from other classification methods, including resistance to overfitting, invariance to most data normalization methods, and biological interpretability. The top-scoring 'N' (TSN) algorithm is a generalized form of other relative expression algorithms which uses generic permutations and a dynamic classifier size to control both the permutation and combination space available for classification. TSN was tested on nine cancer datasets, showing statistically significant differences in classification accuracy between different classifier sizes (choices of N). TSN also performed competitively against a wide variety of different classification methods, including artificial neural networks, classification trees, discriminant analysis, k-Nearest neighbor, naïve Bayes, and support vector machines, when tested on the Microarray Quality Control II datasets. Furthermore, TSN exhibits low levels of overfitting on training data compared to other methods, giving confidence that results obtained during cross validation will be more generally applicable to external validation sets. TSN preserves the strengths of other relative expression algorithms while allowing a much larger permutation and combination space to be explored, potentially improving classification accuracies when fewer numbers of measured features are available.

  9. The top-scoring ‘N’ algorithm: a generalized relative expression classification method from small numbers of biomolecules

    Directory of Open Access Journals (Sweden)

    Magis Andrew T


    Full Text Available Abstract Background Relative expression algorithms such as the top-scoring pair (TSP and the top-scoring triplet (TST have several strengths that distinguish them from other classification methods, including resistance to overfitting, invariance to most data normalization methods, and biological interpretability. The top-scoring ‘N’ (TSN algorithm is a generalized form of other relative expression algorithms which uses generic permutations and a dynamic classifier size to control both the permutation and combination space available for classification. Results TSN was tested on nine cancer datasets, showing statistically significant differences in classification accuracy between different classifier sizes (choices of N. TSN also performed competitively against a wide variety of different classification methods, including artificial neural networks, classification trees, discriminant analysis, k-Nearest neighbor, naïve Bayes, and support vector machines, when tested on the Microarray Quality Control II datasets. Furthermore, TSN exhibits low levels of overfitting on training data compared to other methods, giving confidence that results obtained during cross validation will be more generally applicable to external validation sets. Conclusions TSN preserves the strengths of other relative expression algorithms while allowing a much larger permutation and combination space to be explored, potentially improving classification accuracies when fewer numbers of measured features are available.

  10. Ontologies vs. Classification Systems

    DEFF Research Database (Denmark)

    Madsen, Bodil Nistrup; Erdman Thomsen, Hanne


    What is an ontology compared to a classification system? Is a taxonomy a kind of classification system or a kind of ontology? These are questions that we meet when working with people from industry and public authorities, who need methods and tools for concept clarification, for developing meta...... data sets or for obtaining advanced search facilities. In this paper we will present an attempt at answering these questions. We will give a presentation of various types of ontologies and briefly introduce terminological ontologies. Furthermore we will argue that classification systems, e.g. product...... classification systems and meta data taxonomies, should be based on ontologies....

  11. Pump apparatus including deconsolidator

    Energy Technology Data Exchange (ETDEWEB)

    Sonwane, Chandrashekhar; Saunders, Timothy; Fitzsimmons, Mark Andrew


    A pump apparatus includes a particulate pump that defines a passage that extends from an inlet to an outlet. A duct is in flow communication with the outlet. The duct includes a deconsolidator configured to fragment particle agglomerates received from the passage.

  12. Marine habitat classification for ecosystem-based management: a proposed hierarchical framework. (United States)

    Guarinello, Marisa L; Shumchenia, Emily J; King, John W


    Creating a habitat classification and mapping system for marine and coastal ecosystems is a daunting challenge due to the complex array of habitats that shift on various spatial and temporal scales. To meet this challenge, several countries have, or are developing, national classification systems and mapping protocols for marine habitats. To be effectively applied by scientists and managers it is essential that classification systems be comprehensive and incorporate pertinent physical, geological, biological, and anthropogenic habitat characteristics. Current systems tend to provide over-simplified conceptual structures that do not capture biological habitat complexity, marginalize anthropogenic features, and remain largely untested at finer scales. We propose a multi-scale hierarchical framework with a particular focus on finer scale habitat classification levels and conceptual schematics to guide habitat studies and management decisions. A case study using published data is included to compare the proposed framework with existing schemes. The example demonstrates how the proposed framework's inclusion of user-defined variables, a combined top-down and bottom-up approach, and multi-scale hierarchical organization can facilitate examination of marine habitats and inform management decisions.

  13. The surgery of peripheral nerves (including tumors)

    DEFF Research Database (Denmark)

    Fugleholm, Kåre


    Surgical pathology of the peripheral nervous system includes traumatic injury, entrapment syndromes, and tumors. The recent significant advances in the understanding of the pathophysiology and cellular biology of peripheral nerve degeneration and regeneration has yet to be translated into improved...

  14. Chemometric and Statistical Analyses of ToF-SIMS Spectra of Increasingly Complex Biological Samples

    Energy Technology Data Exchange (ETDEWEB)

    Berman, E S; Wu, L; Fortson, S L; Nelson, D O; Kulp, K S; Wu, K J


    Characterizing and classifying molecular variation within biological samples is critical for determining fundamental mechanisms of biological processes that will lead to new insights including improved disease understanding. Towards these ends, time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used to examine increasingly complex samples of biological relevance, including monosaccharide isomers, pure proteins, complex protein mixtures, and mouse embryo tissues. The complex mass spectral data sets produced were analyzed using five common statistical and chemometric multivariate analysis techniques: principal component analysis (PCA), linear discriminant analysis (LDA), partial least squares discriminant analysis (PLSDA), soft independent modeling of class analogy (SIMCA), and decision tree analysis by recursive partitioning. PCA was found to be a valuable first step in multivariate analysis, providing insight both into the relative groupings of samples and into the molecular basis for those groupings. For the monosaccharides, pure proteins and protein mixture samples, all of LDA, PLSDA, and SIMCA were found to produce excellent classification given a sufficient number of compound variables calculated. For the mouse embryo tissues, however, SIMCA did not produce as accurate a classification. The decision tree analysis was found to be the least successful for all the data sets, providing neither as accurate a classification nor chemical insight for any of the tested samples. Based on these results we conclude that as the complexity of the sample increases, so must the sophistication of the multivariate technique used to classify the samples. PCA is a preferred first step for understanding ToF-SIMS data that can be followed by either LDA or PLSDA for effective classification analysis. This study demonstrates the strength of ToF-SIMS combined with multivariate statistical and chemometric techniques to classify increasingly complex biological samples

  15. The Classification and Indexing of Imaginative Literature

    DEFF Research Database (Denmark)

    Eriksson, Rune


    With the indexing of imaginative literature included in an expanding number of bibliographic databases, the overall representation of this kind of literature has definitely been improved. Still, in terms of information retrieval and being able to judge the relevance of the titles, it seems...... that the usefulness of classification and indexing alike are still being restricted by some old romantic and objectivistic, or even positivistic, ideas and ideals. In order to argue that point the paper firstly re-examines the classification of imaginative literature in early editions of the Dewey Decimal...... Classification, then analyzes the main structures in the modern classification and indexing in the Library of Congress and in the Danish Bibliographic Centre. It is concluded that the classification of imaginative literature not has changed very much since the days of Dewey and that the indexing largely reflects...

  16. Classification of Radioactive Waste. General Safety Guide

    International Nuclear Information System (INIS)


    This publication is a revision of an earlier Safety Guide of the same title issued in 1994. It recommends revised waste management strategies that reflect changes in practices and approaches since then. It sets out a classification system for the management of waste prior to disposal and for disposal, driven by long term safety considerations. It includes a number of schemes for classifying radioactive waste that can be used to assist with planning overall national approaches to radioactive waste management and to assist with operational management at facilities. Contents: 1. Introduction; 2. The radioactive waste classification scheme; Appendix: The classification of radioactive waste; Annex I: Evolution of IAEA standards on radioactive waste classification; Annex II: Methods of classification; Annex III: Origin and types of radioactive waste

  17. Support Vector Machines for Pattern Classification

    CERN Document Server

    Abe, Shigeo


    A guide on the use of SVMs in pattern classification, including a rigorous performance comparison of classifiers and regressors. The book presents architectures for multiclass classification and function approximation problems, as well as evaluation criteria for classifiers and regressors. Features: Clarifies the characteristics of two-class SVMs; Discusses kernel methods for improving the generalization ability of neural networks and fuzzy systems; Contains ample illustrations and examples; Includes performance evaluation using publicly available data sets; Examines Mahalanobis kernels, empir

  18. Optical modulator including grapene (United States)

    Liu, Ming; Yin, Xiaobo; Zhang, Xiang


    The present invention provides for a one or more layer graphene optical modulator. In a first exemplary embodiment the optical modulator includes an optical waveguide, a nanoscale oxide spacer adjacent to a working region of the waveguide, and a monolayer graphene sheet adjacent to the spacer. In a second exemplary embodiment, the optical modulator includes at least one pair of active media, where the pair includes an oxide spacer, a first monolayer graphene sheet adjacent to a first side of the spacer, and a second monolayer graphene sheet adjacent to a second side of the spacer, and at least one optical waveguide adjacent to the pair.

  19. Phenotype classification of zebrafish embryos by supervised learning.

    Directory of Open Access Journals (Sweden)

    Nathalie Jeanray

    Full Text Available Zebrafish is increasingly used to assess biological properties of chemical substances and thus is becoming a specific tool for toxicological and pharmacological studies. The effects of chemical substances on embryo survival and development are generally evaluated manually through microscopic observation by an expert and documented by several typical photographs. Here, we present a methodology to automatically classify brightfield images of wildtype zebrafish embryos according to their defects by using an image analysis approach based on supervised machine learning. We show that, compared to manual classification, automatic classification results in 90 to 100% agreement with consensus voting of biological experts in nine out of eleven considered defects in 3 days old zebrafish larvae. Automation of the analysis and classification of zebrafish embryo pictures reduces the workload and time required for the biological expert and increases the reproducibility and objectivity of this classification.

  20. Phenotype classification of zebrafish embryos by supervised learning. (United States)

    Jeanray, Nathalie; Marée, Raphaël; Pruvot, Benoist; Stern, Olivier; Geurts, Pierre; Wehenkel, Louis; Muller, Marc


    Zebrafish is increasingly used to assess biological properties of chemical substances and thus is becoming a specific tool for toxicological and pharmacological studies. The effects of chemical substances on embryo survival and development are generally evaluated manually through microscopic observation by an expert and documented by several typical photographs. Here, we present a methodology to automatically classify brightfield images of wildtype zebrafish embryos according to their defects by using an image analysis approach based on supervised machine learning. We show that, compared to manual classification, automatic classification results in 90 to 100% agreement with consensus voting of biological experts in nine out of eleven considered defects in 3 days old zebrafish larvae. Automation of the analysis and classification of zebrafish embryo pictures reduces the workload and time required for the biological expert and increases the reproducibility and objectivity of this classification.

  1. Optimization models for cancer classification: extracting gene interaction information from microarray expression data. (United States)

    Antonov, Alexey V; Tetko, Igor V; Mader, Michael T; Budczies, Jan; Mewes, Hans W


    Microarray data appear particularly useful to investigate mechanisms in cancer biology and represent one of the most powerful tools to uncover the genetic mechanisms causing loss of cell cycle control. Recently, several different methods to employ microarray data as a diagnostic tool in cancer classification have been proposed. These procedures take changes in the expression of particular genes into account but do not consider disruptions in certain gene interactions caused by the tumor. It is probable that some genes participating in tumor development do not change their expression level dramatically. Thus, they cannot be detected by simple classification approaches used previously. For these reasons, a classification procedure exploiting information related to changes in gene interactions is needed. We propose a MAximal MArgin Linear Programming (MAMA) method for the classification of tumor samples based on microarray data. This procedure detects groups of genes and constructs models (features) that strongly correlate with particular tumor types. The detected features include genes whose functional relations are changed for particular cancer types. The proposed method was tested on two publicly available datasets and demonstrated a prediction ability superior to previously employed classification schemes. The MAMA system was developed using the linear programming system LINDO A Perl script that specifies the optimization problem for this software is available upon request from the authors.

  2. Gynecomastia Classification for Surgical Management: A Systematic Review and Novel Classification System. (United States)

    Waltho, Daniel; Hatchell, Alexandra; Thoma, Achilleas


    Gynecomastia is a common deformity of the male breast, where certain cases warrant surgical management. There are several surgical options, which vary depending on the breast characteristics. To guide surgical management, several classification systems for gynecomastia have been proposed. A systematic review was performed to (1) identify all classification systems for the surgical management of gynecomastia, and (2) determine the adequacy of these classification systems to appropriately categorize the condition for surgical decision-making. The search yielded 1012 articles, and 11 articles were included in the review. Eleven classification systems in total were ascertained, and a total of 10 unique features were identified: (1) breast size, (2) skin redundancy, (3) breast ptosis, (4) tissue predominance, (5) upper abdominal laxity, (6) breast tuberosity, (7) nipple malposition, (8) chest shape, (9) absence of sternal notch, and (10) breast skin elasticity. On average, classification systems included two or three of these features. Breast size and ptosis were the most commonly included features. Based on their review of the current classification systems, the authors believe the ideal classification system should be universal and cater to all causes of gynecomastia; be surgically useful and easy to use; and should include a comprehensive set of clinically appropriate patient-related features, such as breast size, breast ptosis, tissue predominance, and skin redundancy. None of the current classification systems appears to fulfill these criteria.

  3. Biologic Scaffolds. (United States)

    Costa, Alessandra; Naranjo, Juan Diego; Londono, Ricardo; Badylak, Stephen F


    Biologic scaffold materials composed of allogeneic or xenogeneic extracellular matrix are commonly used for the repair and functional reconstruction of injured and missing tissues. These naturally occurring bioscaffolds are manufactured by the removal of the cellular content from source tissues while preserving the structural and functional molecular units of the remaining extracellular matrix (ECM). The mechanisms by which these bioscaffolds facilitate constructive remodeling and favorable clinical outcomes include release or creation of effector molecules that recruit endogenous stem/progenitor cells to the site of scaffold placement and modulation of the innate immune response, specifically the activation of an anti-inflammatory macrophage phenotype. The methods by which ECM biologic scaffolds are prepared, the current understanding of in vivo scaffold remodeling, and the associated clinical outcomes are discussed in this article. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

  4. Linear Classification Functions. (United States)

    Huberty, Carl J.; Smith, Jerry D.

    Linear classification functions (LCFs) arise in a predictive discriminant analysis for the purpose of classifying experimental units into criterion groups. The relative contribution of the response variables to classification accuracy may be based on LCF-variable correlations for each group. It is proved that, if the raw response measures are…

  5. Classification, confusion and misclassification

    African Journals Online (AJOL)

    Classifications change and in that process, we can see that someone or some group has recognise that a previous classification hindered understanding or moulded ... to a pathologist's ability to distinguish, had led to confusion and mismanagement by gynaecologists. What is worrying if not the word. 'complex'? But this is ...

  6. Spectroscopic classification of transients

    DEFF Research Database (Denmark)

    Stritzinger, M. D.; Fraser, M.; Hummelmose, N. N.


    We report the spectroscopic classification of several transients based on observations taken with the Nordic Optical Telescope (NOT) equipped with ALFOSC, over the nights 23-25 August 2017.......We report the spectroscopic classification of several transients based on observations taken with the Nordic Optical Telescope (NOT) equipped with ALFOSC, over the nights 23-25 August 2017....

  7. Library Classification 2020 (United States)

    Harris, Christopher


    In this article the author explores how a new library classification system might be designed using some aspects of the Dewey Decimal Classification (DDC) and ideas from other systems to create something that works for school libraries in the year 2020. By examining what works well with the Dewey Decimal System, what features should be carried…

  8. Colombia: Territorial classification

    International Nuclear Information System (INIS)

    Mendoza Morales, Alberto


    The article is about the approaches of territorial classification, thematic axes, handling principles and territorial occupation, politician and administrative units and administration regions among other topics. Understanding as Territorial Classification the space distribution on the territory of the country, of the geographical configurations, the human communities, the political-administrative units and the uses of the soil, urban and rural, existent and proposed

  9. DOE LLW classification rationale

    International Nuclear Information System (INIS)

    Flores, A.Y.


    This report was about the rationale which the US Department of Energy had with low-level radioactive waste (LLW) classification. It is based on the Nuclear Regulatory Commission's classification system. DOE site operators met to review the qualifications and characteristics of the classification systems. They evaluated performance objectives, developed waste classification tables, and compiled dose limits on the waste. A goal of the LLW classification system was to allow each disposal site the freedom to develop limits to radionuclide inventories and concentrations according to its own site-specific characteristics. This goal was achieved with the adoption of a performance objectives system based on a performance assessment, with site-specific environmental conditions and engineered disposal systems

  10. Comparison of feature selection and classification for MALDI-MS data

    Directory of Open Access Journals (Sweden)

    Yang Mary


    Full Text Available Abstract Introduction In the classification of Mass Spectrometry (MS proteomics data, peak detection, feature selection, and learning classifiers are critical to classification accuracy. To better understand which methods are more accurate when classifying data, some publicly available peak detection algorithms for Matrix assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS data were recently compared; however, the issue of different feature selection methods and different classification models as they relate to classification performance has not been addressed. With the application of intelligent computing, much progress has been made in the development of feature selection methods and learning classifiers for the analysis of high-throughput biological data. The main objective of this paper is to compare the methods of feature selection and different learning classifiers when applied to MALDI-MS data and to provide a subsequent reference for the analysis of MS proteomics data. Results We compared a well-known method of feature selection, Support Vector Machine Recursive Feature Elimination (SVMRFE, and a recently developed method, Gradient based Leave-one-out Gene Selection (GLGS that effectively performs microarray data analysis. We also compared several learning classifiers including K-Nearest Neighbor Classifier (KNNC, Naïve Bayes Classifier (NBC, Nearest Mean Scaled Classifier (NMSC, uncorrelated normal based quadratic Bayes Classifier recorded as UDC, Support Vector Machines, and a distance metric learning for Large Margin Nearest Neighbor classifier (LMNN based on Mahanalobis distance. To compare, we conducted a comprehensive experimental study using three types of MALDI-MS data. Conclusion Regarding feature selection, SVMRFE outperformed GLGS in classification. As for the learning classifiers, when classification models derived from the best training were compared, SVMs performed the best with respect to the expected testing

  11. Biological Water Quality Criteria (United States)

    Page contains links to Technical Documents pertaining to Biological Water Quality Criteria, including, technical assistance documents for states, tribes and territories, program overviews, and case studies.

  12. Classification of anemia for gastroenterologists. (United States)

    Moreno Chulilla, Jose Antonio; Romero Colás, Maria Soledad; Gutiérrez Martín, Martín


    Most anemia is related to the digestive system by dietary deficiency, malabsorption, or chronic bleeding. We review the World Health Organization definition of anemia, its morphological classification (microcytic, macrocytic and normocytic) and pathogenic classification (regenerative and hypo regenerative), and integration of these classifications. Interpretation of laboratory tests is included, from the simplest (blood count, routine biochemistry) to the more specific (iron metabolism, vitamin B12, folic acid, reticulocytes, erythropoietin, bone marrow examination and Schilling test). In the text and various algorithms, we propose a hierarchical and logical way to reach a diagnosis as quickly as possible, by properly managing the medical interview, physical examination, appropriate laboratory tests, bone marrow examination, and other complementary tests. The prevalence is emphasized in all sections so that the gastroenterologist can direct the diagnosis to the most common diseases, although the tables also include rare diseases. Digestive diseases potentially causing anemia have been studied in preference, but other causes of anemia have been included in the text and tables. Primitive hematological diseases that cause anemia are only listed, but are not discussed in depth. The last section is dedicated to simplifying all items discussed above, using practical rules to guide diagnosis and medical care with the greatest economy of resources and time.

  13. Using EUNIS habitat classification for benthic mapping in European seas: present concerns and future needs. (United States)

    Galparsoro, Ibon; Connor, David W; Borja, Angel; Aish, Annabelle; Amorim, Patricia; Bajjouk, Touria; Chambers, Caroline; Coggan, Roger; Dirberg, Guillaume; Ellwood, Helen; Evans, Douglas; Goodin, Kathleen L; Grehan, Anthony; Haldin, Jannica; Howell, Kerry; Jenkins, Chris; Michez, Noëmie; Mo, Giulia; Buhl-Mortensen, Pål; Pearce, Bryony; Populus, Jacques; Salomidi, Maria; Sánchez, Francisco; Serrano, Alberto; Shumchenia, Emily; Tempera, Fernando; Vasquez, Mickaël


    ) biology; (3) terminology; (4) mapping; and (5) future development. The workshop ended with a declaration from the attendees, with recommendations to the EEA and European Topic Centre on Biological Diversity, to take into account the outputs of the workshop, which identify weaknesses in the current classification and include proposals for its modification, and to devise a process to further develop the marine component of the EUNIS habitat classification. Copyright © 2012 Elsevier Ltd. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Franziska Althaus

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

  15. [Terminological and classification aspects of laparoscopic hysterectomies]. (United States)

    Tomov, S; Gorchev, G; Tzvetkov, Ch; Iliev, S; Gincheva, D


    There is a great variety of terms and concepts describing laparoscopic hysterectomy in scientific literature. The term "laparoscopic hysterectomy" includes different operations where the laparoscope is used as an aid for a hysterectomy. The first classifications related to hysterectomy laparoscopic procedures were suggested by Munro and Parker (1993) Johns and Diamonds (1994) and Garry et al. (1994). Based on them is the American Association of Gynecologic Laparoscopists (AAGL) classification of 2000. Reich defined basic terms easy to use in clinical practice. The elaboration of a suitable classification system describing the size of laparoscopic intervention in hysterectomy is a prerequisite for an adequate comparison of the results of scientific researches.

  16. Kappa Coefficients for Circular Classifications

    NARCIS (Netherlands)

    Warrens, Matthijs J.; Pratiwi, Bunga C.


    Circular classifications are classification scales with categories that exhibit a certain periodicity. Since linear scales have endpoints, the standard weighted kappas used for linear scales are not appropriate for analyzing agreement between two circular classifications. A family of kappa

  17. Oral epithelial dysplasia classification systems

    DEFF Research Database (Denmark)

    Warnakulasuriya, S; Reibel, J; Bouquot, J


    . In this report, we review the oral epithelial dysplasia classification systems. The three classification schemes [oral epithelial dysplasia scoring system, squamous intraepithelial neoplasia and Ljubljana classification] were presented and the Working Group recommended epithelial dysplasia grading for routine...

  18. [Endoscopic classification of colon and rectal neoplasias]. (United States)

    Zavoral, Miroslav; Vojtěchová, Gabriela; Suchánek, Stěpán


    Along with the dynamic evolution of the new field of digestive endoscopy, the need of unified and unambiguous terms for endoscopic findings arose in the second half of the 20th century. In collaboration with the OMED members, professor Zdeněk Mařatka drew up the first internationally acknowledged terminology for digestive endoscopy which was used in the full range for a period of almost 20 years. The technical progress later brought with it endoscopes which made it possible to view flat lesions, frequently overlooked until then. The classification of the surface lesions was further specified by the Paris Classification which drew from the experience of Japanese endoscopists. Thanks to the new endoscopic methods of imaging mucosa in vivo and the pit-pattern and vascular-pattern classification, we can currently estimate the biological nature of lesion with great accuracy and therefore choose the best therapeutic procedure.

  19. DTI measurements for Alzheimer’s classification (United States)

    Maggipinto, Tommaso; Bellotti, Roberto; Amoroso, Nicola; Diacono, Domenico; Donvito, Giacinto; Lella, Eufemia; Monaco, Alfonso; Antonella Scelsi, Marzia; Tangaro, Sabina; Disease Neuroimaging Initiative, Alzheimer's.


    Diffusion tensor imaging (DTI) is a promising imaging technique that provides insight into white matter microstructure integrity and it has greatly helped identifying white matter regions affected by Alzheimer’s disease (AD) in its early stages. DTI can therefore be a valuable source of information when designing machine-learning strategies to discriminate between healthy control (HC) subjects, AD patients and subjects with mild cognitive impairment (MCI). Nonetheless, several studies have reported so far conflicting results, especially because of the adoption of biased feature selection strategies. In this paper we firstly analyzed DTI scans of 150 subjects from the Alzheimer’s disease neuroimaging initiative (ADNI) database. We measured a significant effect of the feature selection bias on the classification performance (p-value  content provided by DTI measurements for AD classification. Classification performances and biological insight, concerning brain regions related to the disease, provided by cross-validation analysis were both confirmed on the independent test.

  20. Cluster Based Text Classification Model

    DEFF Research Database (Denmark)

    Nizamani, Sarwat; Memon, Nasrullah; Wiil, Uffe Kock


    We propose a cluster based classification model for suspicious email detection and other text classification tasks. The text classification tasks comprise many training examples that require a complex classification model. Using clusters for classification makes the model simpler and increases......, the classifier is trained on each cluster having reduced dimensionality and less number of examples. The experimental results show that the proposed model outperforms the existing classification models for the task of suspicious email detection and topic categorization on the Reuters-21578 and 20 Newsgroups...... datasets. Our model also outperforms A Decision Cluster Classification (ADCC) and the Decision Cluster Forest Classification (DCFC) models on the Reuters-21578 dataset....

  1. Classification of hand eczema

    DEFF Research Database (Denmark)

    Agner, T; Aalto-Korte, K; Andersen, K E


    BACKGROUND: Classification of hand eczema (HE) is mandatory in epidemiological and clinical studies, and also important in clinical work. OBJECTIVES: The aim was to test a recently proposed classification system of HE in clinical practice in a prospective multicentre study. METHODS: Patients were......%) could not be classified. 38% had one additional diagnosis and 26% had two or more additional diagnoses. Eczema on feet was found in 30% of the patients, statistically significantly more frequently associated with hyperkeratotic and vesicular endogenous eczema. CONCLUSION: We find that the classification...

  2. Pitch Based Sound Classification

    DEFF Research Database (Denmark)

    Nielsen, Andreas Brinch; Hansen, Lars Kai; Kjems, U


    A sound classification model is presented that can classify signals into music, noise and speech. The model extracts the pitch of the signal using the harmonic product spectrum. Based on the pitch estimate and a pitch error measure, features are created and used in a probabilistic model with soft......-max output function. Both linear and quadratic inputs are used. The model is trained on 2 hours of sound and tested on publicly available data. A test classification error below 0.05 with 1 s classification windows is achieved. Further more it is shown that linear input performs as well as a quadratic...

  3. Breast radiological cases: training with BIRADS classification. (United States)

    Balleyguier, C; Vanel, D; Athanasiou, A; Mathieu, M C; Sigal, R


    The American College of Radiology has established guidelines for outcomes monitoring known as the Breast Imaging Reporting and Data System. The last edition of the BIRADS classification includes mammography, but also ultrasonography and MRI. Radiologists must be used to the BIRADS lexicon and the BIRADS assessment, in order to clarify mammography reports and to facilitate communication with the other physicians. This work is a training on 20 mammography cases to be familiar with the BIRADS classification.

  4. FAB classification of leukemia: a cytochemical study. (United States)

    Sharma, Jai Shree; Mohindroo, Shobha


    The reproducibility of FAB classification for acute leukemia was assessed using the modified criteria of the FAB classification. Peripheral smears and bone marrow smears from 36 cases of acute leukemia stained with May-Graunwald-Giemsa were used for this purpose. Cytochemical stains used for this purpose were myeloperoxidase (MPO), Sudan Black B (SBB), Periodic acid Schiff's (PAS) and Alpha-naphthyl acetate esterase (ANAE). The concordance with morphology alone was 75% which improved to 92% when cytochemistry was included.

  5. A method to incorporate uncertainty in the classification of remote sensing images


    Gonçalves, Luísa M. S.; Fonte, Cidália C.; Júlio, Eduardo N. B. S.; Caetano, Mario


    The aim of this paper is to investigate if the incorporation of the uncertainty associated with the classification of surface elements into the classification of landscape units (LUs) increases the results accuracy. To this end, a hybrid classification method is developed, including uncertainty information in the classification of very high spatial resolution multi-spectral satellite images, to obtain a map of LUs. The developed classification methodology includes the following...

  6. Towards a unified classification of the ectodermal dysplasias: opportunities outweigh challenges.

    LENUS (Irish Health Repository)

    Irvine, Alan D


    The ectodermal dysplasias include a complex and highly diverse group of heritable disorders that share in common developmental abnormalities of ectodermal derivatives. The broader definition of ectodermal dysplasias (as heritable disorders involving at least two of the ectodermal derivatives nails, teeth, hair, and eccrine sweat glands) encompasses 170-200 conditions. Some conditions included by this definition are relatively common; others are rare and, in some cases, family-specific. Classification of the ectodermal dysplasias has largely been approached by categorizing patterns of clinical findings (phenotypic grouping). In the last 2 decades great progress has been made in understanding the molecular pathogenesis and inter-relatedness of some of these conditions and a new consensus approach to classification that incorporates this new information is needed. A comprehensive and definitive classification of these disorders would be highly valuable for the many stakeholders in ED. As disease-specific molecular treatments are developed, accurate classification will assume greater importance in designing registries to enable rapid identification of those with rare disorders who may wish to participate in clinical trials. Ideally a working classification of such a disparate collection of conditions would have a design and architecture that would facilitate easy accessibility by each of the key stakeholder groups and would encourage enhanced interaction between these parties. Attaining this objective is a major challenge but is achievable. This article reviews the historical-clinical perspective and the impact of recent developments in molecular biology in the field. Reflections are offered as to the future direction of classification systems in these disorders.

  7. Odor Classification using Agent Technology

    Directory of Open Access Journals (Sweden)

    Sigeru OMATU


    Full Text Available In order to measure and classify odors, Quartz Crystal Microbalance (QCM can be used. In the present study, seven QCM sensors and three different odors are used. The system has been developed as a virtual organization of agents using an agent platform called PANGEA (Platform for Automatic coNstruction of orGanizations of intElligent Agents. This is a platform for developing open multi-agent systems, specifically those including organizational aspects. The main reason for the use of agents is the scalability of the platform, i.e. the way in which it models the services. The system models functionalities as services inside the agents, or as Service Oriented Approach (SOA architecture compliant services using Web Services. This way the adaptation of the odor classification systems with new algorithms, tools and classification techniques is allowed.

  8. ACCUWIND - Methods for classification of cup anemometers

    Energy Technology Data Exchange (ETDEWEB)

    Dahlberg, J.Aa.; Friis Pedersen, T.; Busche, P.


    Errors associated with the measurement of wind speed are the major sources of uncertainties in power performance testing of wind turbines. Field comparisons of well-calibrated anemometers show significant and not acceptable difference. The European CLASSCUP project posed the objectives to quantify the errors associated with the use of cup anemometers, and to develop a classification system for quantification of systematic errors of cup anemometers. This classification system has now been implemented in the IEC 61400-12-1 standard on power performance measurements in annex I and J. The classification of cup anemometers requires general external climatic operational ranges to be applied for the analysis of systematic errors. A Class A category classification is connected to reasonably flat sites, and another Class B category is connected to complex terrain, General classification indices are the result of assessment of systematic deviations. The present report focuses on methods that can be applied for assessment of such systematic deviations. A new alternative method for torque coefficient measurements at inclined flow have been developed, which have then been applied and compared to the existing methods developed in the CLASSCUP project and earlier. A number of approaches including the use of two cup anemometer models, two methods of torque coefficient measurement, two angular response measurements, and inclusion and exclusion of influence of friction have been implemented in the classification process in order to assess the robustness of methods. The results of the analysis are presented as classification indices, which are compared and discussed. (au)

  9. Classifications of patterned hair loss: a review

    Directory of Open Access Journals (Sweden)

    Mrinal Gupta


    Full Text Available Patterned hair loss is the most common cause of hair loss seen in both the sexes after puberty. Numerous classification systems have been proposed by various researchers for grading purposes. These systems vary from the simpler systems based on recession of the hairline to the more advanced multifactorial systems based on the morphological and dynamic parameters that affect the scalp and the hair itself. Most of these preexisting systems have certain limitations. Currently, the Hamilton-Norwood classification system for males and the Ludwig system for females are most commonly used to describe patterns of hair loss. In this article, we review the various classification systems for patterned hair loss in both the sexes. Relevant articles were identified through searches of MEDLINE and EMBASE. Search terms included but were not limited to androgenic alopecia classification, patterned hair loss classification, male pattern baldness classification, and female pattern hair loss classification. Further publications were identified from the reference lists of the reviewed articles.

  10. Graph-based semi-supervised learning with genomic data integration using condition-responsive genes applied to phenotype classification. (United States)

    Doostparast Torshizi, Abolfazl; Petzold, Linda R


    Data integration methods that combine data from different molecular levels such as genome, epigenome, transcriptome, etc., have received a great deal of interest in the past few years. It has been demonstrated that the synergistic effects of different biological data types can boost learning capabilities and lead to a better understanding of the underlying interactions among molecular levels. In this paper we present a graph-based semi-supervised classification algorithm that incorporates latent biological knowledge in the form of biological pathways with gene expression and DNA methylation data. The process of graph construction from biological pathways is based on detecting condition-responsive genes, where 3 sets of genes are finally extracted: all condition responsive genes, high-frequency condition-responsive genes, and P-value-filtered genes. The proposed approach is applied to ovarian cancer data downloaded from the Human Genome Atlas. Extensive numerical experiments demonstrate superior performance of the proposed approach compared to other state-of-the-art algorithms, including the latest graph-based classification techniques. Simulation results demonstrate that integrating various data types enhances classification performance and leads to a better understanding of interrelations between diverse omics data types. The proposed approach outperforms many of the state-of-the-art data integration algorithms. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email:

  11. Systems Biology

    Indian Academy of Sciences (India)

    IAS Admin

    Systems biology seeks to study biological systems as a whole, contrary to the reductionist approach that has dominated biology. Such a view of biological systems emanating from strong foundations of molecular level understanding of the individual components in terms of their form, function and interactions is promising to ...


    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. CLASSIFICATION OF VIRUSES. On basis of morphology. On basis of chemical composition. On basis of structure of genome. On basis of mode of replication. Notes:

  13. Update on diabetes classification. (United States)

    Thomas, Celeste C; Philipson, Louis H


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

  14. Learning Apache Mahout classification

    CERN Document Server

    Gupta, Ashish


    If you are a data scientist who has some experience with the Hadoop ecosystem and machine learning methods and want to try out classification on large datasets using Mahout, this book is ideal for you. Knowledge of Java is essential.

  15. Latent classification models

    DEFF Research Database (Denmark)

    Langseth, Helge; Nielsen, Thomas Dyhre


    parametric family ofdistributions.  In this paper we propose a new set of models forclassification in continuous domains, termed latent classificationmodels. The latent classification model can roughly be seen ascombining the \\NB model with a mixture of factor analyzers,thereby relaxing the assumptions...... classification model, and wedemonstrate empirically that the accuracy of the proposed model issignificantly higher than the accuracy of other probabilisticclassifiers....

  16. Multilingual News Article Classification


    Skjennum, Patrick L


    News is an ever-growing and global resource, reliant on robust distribution networks to spread information. This thesis investigates how exploiting semantic, contextual and ontological information may form a basis for a language independent news article classification system. In light of the above, a scalable multi-label news article classification system, based exclusively on extracted DBpedia entities, and a predetermined standardized set of fixed-size IPTC Media Topic categories, is p...

  17. Classification of age-related changes in lumbar intervertebral discs: 2002 Volvo Award in basic science. (United States)

    Boos, Norbert; Weissbach, Sabine; Rohrbach, Helmut; Weiler, Christoph; Spratt, Kevin F; Nerlich, Andreas G


    A histologic study on age-related changes of the human lumbar intervertebral disc was conducted. To investigate comprehensively age-related temporospatial histologic changes in human lumbar intervertebral disc, and to develop a practicable and reliable classification system for age-related histologic disc alteration. No comprehensive microscopic analysis of age-related disc changes is available. There is no conceptual morphologic framework for classifying age-related disc changes as a reference basis for more sophisticated molecular biologic analyses of the causative factors of disc aging or premature aging (degeneration). A total of 180 complete sagittal lumbar motion segment slices obtained from 44 deceased individuals (fetal to 88 years of age) were analyzed with regard to 11 histologic variables for the intervertebral disc and endplate, respectively. In addition, 30 surgical specimens (3 regions each) were investigated with regard to five histologic variables. Based on the semiquantitative analyses of 20,250 histologic variable assessments, a classification system was developed and tested in terms of validity, practicability, and reliability. The classification system was applied to cadaveric and surgical disc specimens not included in the development of the classification system, and the scores were assessed by two additional independent raters. A semiquantitative analyses provided clear histologic evidence for the detrimental effect of a diminished blood supply on the endplate, resulting in the tissue breakdown beginning in the nucleus pulposus and starting in the second life decade. Significant temporospatial variations in the presence and abundance of histologic disc alterations were observed across levels, regions, macroscopic degeneration grades, and age groups. A practicable classification system for age-related histologic disc alterations was developed, resulting in moderate to excellent reliability (kappa values, 0.49-0.98) depending on the histologic

  18. Pathological classification of brain tumors. (United States)

    Pollo, B


    The tumors of the central nervous system are classified according to the last international classification published by World Health Organization. The Classification of Tumors of the Central Nervous System was done on 2007, based on morphological features, growth pattern and molecular profile of neoplastic cells, defining malignancy grade. The neuropathological diagnosis and the grading of each histotype are based on identification of histopathological criteria and immunohistochemical data. The histopathology, also consisting of findings with prognostic or predictive relevance, plays a critical role in the diagnosis and treatment of brain tumors. The recent progresses on radiological, pathological, immunohistochemical, molecular and genetic diagnosis improved the characterization of brain tumors. Molecular and genetic profiles may identify different tumor subtypes varying in biological and clinical behavior. To investigate new therapeutic approaches is important to study the molecular pathways that lead the processes of proliferation, invasion, angiogenesis, anaplastic transformation. Different molecular biomarkers were identified by genetic studies and some of these are used in neuro-oncology for the evaluation of glioma patients, in particular combined deletions of the chromosome arms 1p and 19q in oligodendroglial tumors, methylation status of the O-6 methylguanine- DNA methyltransferase gene promoter and alterations in the epidermal growth factor receptor pathway in adult malignant gliomas, isocitrate dehydrogenase 1 (IDH1) and IDH2 gene mutations in diffuse gliomas, as well as BRAF status in pilocytic astrocytomas. The prognostic evaluation and the therapeutic strategies for patients depend on synthesis of clinical, pathological and biological data: histological diagnosis, malignancy grade, gene-molecular profile, radiological pictures, surgical resection and clinical findings (age, tumor location, "performance status").

  19. Branching processes in biology

    CERN Document Server

    Kimmel, Marek


    This book provides a theoretical background of branching processes and discusses their biological applications. Branching processes are a well-developed and powerful set of tools in the field of applied probability. The range of applications considered includes molecular biology, cellular biology, human evolution and medicine. The branching processes discussed include Galton-Watson, Markov, Bellman-Harris, Multitype, and General Processes. As an aid to understanding specific examples, two introductory chapters, and two glossaries are included that provide background material in mathematics and in biology. The book will be of interest to scientists who work in quantitative modeling of biological systems, particularly probabilists, mathematical biologists, biostatisticians, cell biologists, molecular biologists, and bioinformaticians. The authors are a mathematician and cell biologist who have collaborated for more than a decade in the field of branching processes in biology for this new edition. This second ex...


    Directory of Open Access Journals (Sweden)

    Volodymyr Lushchak


    Full Text Available In living organisms, production of reactive oxygen species (ROS is counterbalanced by their elimination and/or prevention of formation which in concert can typically maintain a steady-state (stationary ROS level. However, this balance may be disturbed and lead to elevated ROS levels and enhanced damage to biomolecules. Since 1985, when H. Sies first introduced the definition of oxidative stress, this area has become one of the hot topics in biology and, to date, many details related to ROS-induced damage to cellular components, ROS-based signaling, cellular responses and adaptation have been disclosed. However, some basal oxidative damage always occurs under unstressed conditions, and in many experimental studies it is difficult to show definitely that oxidative stress is indeed induced by the stressor. Therefore, usually researchers experience substantial difficulties in the correct interpretation of oxidative stress development. For example, in many cases an increase or decrease in the activity of antioxidant and related enzymes are interpreted as evidences of oxidative stress. Careful selection of specific biomarkers (ROS-modified targets may be very helpful. To avoid these sorts of problems, I propose several classifications of oxidative stress based on its time-course and intensity. The time-course classification includes acute and chronic stresses. In the intensity based classification, I propose to discriminate four zones of function in the relationship between “Dose/concentration of inducer” and the measured “Endpoint”: I – basal oxidative stress zone (BOS; II – low intensity oxidative stress (LOS; III – intermediate intensity oxidative stress (IOS; IV – high intensity oxidative stress (HOS. The proposed classifications may be helpful to describe experimental data where oxidative stress is induced and systematize it based on its time course and intensity. Perspective directions of investigations in the field include

  1. Developmental biology, the stem cell of biological disciplines. (United States)

    Gilbert, Scott F


    Developmental biology (including embryology) is proposed as "the stem cell of biological disciplines." Genetics, cell biology, oncology, immunology, evolutionary mechanisms, neurobiology, and systems biology each has its ancestry in developmental biology. Moreover, developmental biology continues to roll on, budding off more disciplines, while retaining its own identity. While its descendant disciplines differentiate into sciences with a restricted set of paradigms, examples, and techniques, developmental biology remains vigorous, pluripotent, and relatively undifferentiated. In many disciplines, especially in evolutionary biology and oncology, the developmental perspective is being reasserted as an important research program.

  2. A New Classification Approach Based on Multiple Classification Rules


    Zhongmei Zhou


    A good classifier can correctly predict new data for which the class label is unknown, so it is important to construct a high accuracy classifier. Hence, classification techniques are much useful in ubiquitous computing. Associative classification achieves higher classification accuracy than some traditional rule-based classification approaches. However, the approach also has two major deficiencies. First, it generates a very large number of association classification rules, especially when t...

  3. [Definition and classification of pulmonary arterial hypertension]. (United States)

    Nakanishi, Norifumi


    Pulmonary hypertension(PH) is a disorder that may occur either in the setting of a variety of underlying medical conditions or as a disease that uniquely affects the pulmonary vasculature. Because an accurate diagnosis of PH in a patient is essential to establish an effective treatment, a classification of PH has been helpful. The first classification, established at WHO Symposium in 1973, classified PH into groups based on the known cause and defined primary pulmonary hypertension (PPH) as a separate entity of unknown cause. In 1998, the second World Symposium on PPH was held in Evian. Evian classification introduced the concept of conditions that directly affected the pulmonary vasculature (i.e., PAH), which included PPH. In 2003, the third World Symposium on PAH convened in Venice. In Venice classification, the term 'PPH' was abandoned in favor of 'idiopathic' within the group of disease known as 'PAH'.

  4. Biological computation

    CERN Document Server

    Lamm, Ehud


    Introduction and Biological BackgroundBiological ComputationThe Influence of Biology on Mathematics-Historical ExamplesBiological IntroductionModels and Simulations Cellular Automata Biological BackgroundThe Game of Life General Definition of Cellular Automata One-Dimensional AutomataExamples of Cellular AutomataComparison with a Continuous Mathematical Model Computational UniversalitySelf-Replication Pseudo Code Evolutionary ComputationEvolutionary Biology and Evolutionary ComputationGenetic AlgorithmsExample ApplicationsAnalysis of the Behavior of Genetic AlgorithmsLamarckian Evolution Genet

  5. Mathematical classification and clustering

    CERN Document Server

    Mirkin, Boris


    I am very happy to have this opportunity to present the work of Boris Mirkin, a distinguished Russian scholar in the areas of data analysis and decision making methodologies. The monograph is devoted entirely to clustering, a discipline dispersed through many theoretical and application areas, from mathematical statistics and combina­ torial optimization to biology, sociology and organizational structures. It compiles an immense amount of research done to date, including many original Russian de­ velopments never presented to the international community before (for instance, cluster-by-cluster versions of the K-Means method in Chapter 4 or uniform par­ titioning in Chapter 5). The author's approach, approximation clustering, allows him both to systematize a great part of the discipline and to develop many in­ novative methods in the framework of optimization problems. The optimization methods considered are proved to be meaningful in the contexts of data analysis and clustering. The material presented in ...

  6. Quantum biological information theory

    CERN Document Server

    Djordjevic, Ivan B


    This book is a self-contained, tutorial-based introduction to quantum information theory and quantum biology. It serves as a single-source reference to the topic for researchers in bioengineering, communications engineering, electrical engineering, applied mathematics, biology, computer science, and physics. The book provides all the essential principles of the quantum biological information theory required to describe the quantum information transfer from DNA to proteins, the sources of genetic noise and genetic errors as well as their effects. Integrates quantum information and quantum biology concepts; Assumes only knowledge of basic concepts of vector algebra at undergraduate level; Provides a thorough introduction to basic concepts of quantum information processing, quantum information theory, and quantum biology; Includes in-depth discussion of the quantum biological channel modelling, quantum biological channel capacity calculation, quantum models of aging, quantum models of evolution, quantum models o...

  7. Comparison of Classification Algorithms and Training Sample Sizes in Urban Land Classification with Landsat Thematic Mapper Imagery

    Directory of Open Access Journals (Sweden)

    Congcong Li


    Full Text Available Although a large number of new image classification algorithms have been developed, they are rarely tested with the same classification task. In this research, with the same Landsat Thematic Mapper (TM data set and the same classification scheme over Guangzhou City, China, we tested two unsupervised and 13 supervised classification algorithms, including a number of machine learning algorithms that became popular in remote sensing during the past 20 years. Our analysis focused primarily on the spectral information provided by the TM data. We assessed all algorithms in a per-pixel classification decision experiment and all supervised algorithms in a segment-based experiment. We found that when sufficiently representative training samples were used, most algorithms performed reasonably well. Lack of training samples led to greater classification accuracy discrepancies than classification algorithms themselves. Some algorithms were more tolerable to insufficient (less representative training samples than others. Many algorithms improved the overall accuracy marginally with per-segment decision making.

  8. Clinical classification of syncope. (United States)

    Sutton, Richard


    Syncope is a presenting symptom, and in itself is not a diagnosis. An etiology or a mechanism must be sought in all cases. Currently, most clinicians classify syncope on clinical grounds by attempting to ascertain its etiology. They then use this classification to guide further management. Using this approach, reflex syncope is the most common form of syncope, occurring in approximately 60% of syncope presentations. Orthostatic hypotension presents in around 15% with arrhythmic syncope in 10% and structural heart disease as the cause of syncope in 5%; in 10% of patients no diagnosis is made. An alternative classification system uses the mechanism of syncope derived from an implanted ECG loop recorder (ILR). While this approach may be of value for optimizing therapy, it cannot be considered as the primary classification since ILRs are not typically implanted early in the evaluation process of most patients. ILRs are usually placed after "risk stratification" in those deemed not to be at high risk but remain in the uncertain etiology category. Furthermore, there exists, in current ILR technology, lack of ambulatory blood pressure monitoring capability. Thus, vasodilation leading to hypotension, the main trigger of cerebral hypoperfusion other than bradycardia, cannot be detected and is currently unavailable for use in a mechanistic-based classification. Thus, the etiological classification remains the basis for both risk stratification and subsequent clinical management. Copyright © 2013 Elsevier Inc. All rights reserved.

  9. Ovarian Cancer Classification based on Mass Spectrometry Analysis of Sera

    Directory of Open Access Journals (Sweden)

    Baolin Wu


    Full Text Available In our previous study [1], we have compared the performance of a number of widely used discrimination methods for classifying ovarian cancer using Matrix Assisted Laser Desorption Ionization (MALDI mass spectrometry data on serum samples obtained from Reflectron mode. Our results demonstrate good performance with a random forest classifier. In this follow-up study, to improve the molecular classification power of the MALDI platform for ovarian cancer disease, we expanded the mass range of the MS data by adding data acquired in Linear mode and evaluated the resultant decrease in classification error. A general statistical framework is proposed to obtain unbiased classification error estimates and to analyze the effects of sample size and number of selected m/z features on classification errors. We also emphasize the importance of combining biological knowledge and statistical analysis to obtain both biologically and statistically sound results. Our study shows improvement in classification accuracy upon expanding the mass range of the analysis. In order to obtain the best classification accuracies possible, we found that a relatively large training sample size is needed to obviate the sample variations. For the ovarian MS dataset that is the focus of the current study, our results show that approximately 20-40 m/z features are needed to achieve the best classification accuracy from MALDI-MS analysis of sera. Supplementary information can be found at

  10. Cirrhosis Classification Based on Texture Classification of Random Features

    Directory of Open Access Journals (Sweden)

    Hui Liu


    Full Text Available Accurate staging of hepatic cirrhosis is important in investigating the cause and slowing down the effects of cirrhosis. Computer-aided diagnosis (CAD can provide doctors with an alternative second opinion and assist them to make a specific treatment with accurate cirrhosis stage. MRI has many advantages, including high resolution for soft tissue, no radiation, and multiparameters imaging modalities. So in this paper, multisequences MRIs, including T1-weighted, T2-weighted, arterial, portal venous, and equilibrium phase, are applied. However, CAD does not meet the clinical needs of cirrhosis and few researchers are concerned with it at present. Cirrhosis is characterized by the presence of widespread fibrosis and regenerative nodules in the hepatic, leading to different texture patterns of different stages. So, extracting texture feature is the primary task. Compared with typical gray level cooccurrence matrix (GLCM features, texture classification from random features provides an effective way, and we adopt it and propose CCTCRF for triple classification (normal, early, and middle and advanced stage. CCTCRF does not need strong assumptions except the sparse character of image, contains sufficient texture information, includes concise and effective process, and makes case decision with high accuracy. Experimental results also illustrate the satisfying performance and they are also compared with typical NN with GLCM.

  11. Transportation Modes Classification Using Sensors on Smartphones

    Directory of Open Access Journals (Sweden)

    Shih-Hau Fang


    Full Text Available This paper investigates the transportation and vehicular modes classification by using big data from smartphone sensors. The three types of sensors used in this paper include the accelerometer, magnetometer, and gyroscope. This study proposes improved features and uses three machine learning algorithms including decision trees, K-nearest neighbor, and support vector machine to classify the user’s transportation and vehicular modes. In the experiments, we discussed and compared the performance from different perspectives including the accuracy for both modes, the executive time, and the model size. Results show that the proposed features enhance the accuracy, in which the support vector machine provides the best performance in classification accuracy whereas it consumes the largest prediction time. This paper also investigates the vehicle classification mode and compares the results with that of the transportation modes.

  12. Cellular image classification

    CERN Document Server

    Xu, Xiang; Lin, Feng


    This book introduces new techniques for cellular image feature extraction, pattern recognition and classification. The authors use the antinuclear antibodies (ANAs) in patient serum as the subjects and the Indirect Immunofluorescence (IIF) technique as the imaging protocol to illustrate the applications of the described methods. Throughout the book, the authors provide evaluations for the proposed methods on two publicly available human epithelial (HEp-2) cell datasets: ICPR2012 dataset from the ICPR'12 HEp-2 cell classification contest and ICIP2013 training dataset from the ICIP'13 Competition on cells classification by fluorescent image analysis. First, the reading of imaging results is significantly influenced by one’s qualification and reading systems, causing high intra- and inter-laboratory variance. The authors present a low-order LP21 fiber mode for optical single cell manipulation and imaging staining patterns of HEp-2 cells. A focused four-lobed mode distribution is stable and effective in optical...

  13. Bosniak classification system

    DEFF Research Database (Denmark)

    Graumann, Ole; Osther, Susanne Sloth; Karstoft, Jens


    BACKGROUND: The Bosniak classification was originally based on computed tomographic (CT) findings. Magnetic resonance (MR) and contrast-enhanced ultrasonography (CEUS) imaging may demonstrate findings that are not depicted at CT, and there may not always be a clear correlation between the findings...... at MR and CEUS imaging and those at CT. PURPOSE: To compare diagnostic accuracy of MR, CEUS, and CT when categorizing complex renal cystic masses according to the Bosniak classification. MATERIAL AND METHODS: From February 2011 to June 2012, 46 complex renal cysts were prospectively evaluated by three...... readers. Each mass was categorized according to the Bosniak classification and CT was chosen as gold standard. Kappa was calculated for diagnostic accuracy and data was compared with pathological results. RESULTS: CT images found 27 BII, six BIIF, seven BIII, and six BIV. Forty-three cysts could...

  14. Medical imbalanced data classification

    Directory of Open Access Journals (Sweden)

    Sara Belarouci


    Full Text Available In general, the imbalanced dataset is a problem often found in health applications. In medical data classification, we often face the imbalanced number of data samples where at least one of the classes constitutes only a very small minority of the data. In the same time, it represent a difficult problem in most of machine learning algorithms. There have been many works dealing with classification of imbalanced dataset. In this paper, we proposed a learning method based on a cost sensitive extension of Least Mean Square (LMS algorithm that penalizes errors of different samples with different weights and some rules of thumb to determine those weights. After the balancing phase, we apply the different techniques (Support Vector Machine [SVM], K- Nearest Neighbor [K-NN] and Multilayer perceptron [MLP] for the balanced datasets. We have also compared the obtained results before and after balancing method. We have obtained best results compared to literature with a classification accuracy of 100%.

  15. Acoustic classification of dwellings

    DEFF Research Database (Denmark)

    Berardi, Umberto; Rasmussen, Birgit


    Schemes for the classification of dwellings according to different building performances have been proposed in the last years worldwide. The general idea behind these schemes relates to the positive impact a higher label, and thus a better performance, should have. In particular, focusing on sound...... insulation performance, national schemes for sound classification of dwellings have been developed in several European countries. These schemes define acoustic classes according to different levels of sound insulation. Due to the lack of coordination among countries, a significant diversity in terms...... of descriptors, number of classes, and class intervals occurred between national schemes. However, a proposal “acoustic classification scheme for dwellings” has been developed recently in the European COST Action TU0901 with 32 member countries. This proposal has been accepted as an ISO work item. This paper...

  16. Biological detector and method (United States)

    Sillerud, Laurel; Alam, Todd M; McDowell, Andrew F


    A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

  17. Classification of iconic images


    Zrianina, Mariia; Kopf, Stephan


    Iconic images represent an abstract topic and use a presentation that is intuitively understood within a certain cultural context. For example, the abstract topic “global warming” may be represented by a polar bear standing alone on an ice floe. Such images are widely used in media and their automatic classification can help to identify high-level semantic concepts. This paper presents a system for the classification of iconic images. It uses a variation of the Bag of Visual Words approach wi...

  18. Latent Classification Models for Binary Data

    DEFF Research Database (Denmark)

    Langseth, Helge; Nielsen, Thomas Dyhre


    the class of that instance. To relax this independence assumption, we have in previous work proposed a family of models, called latent classification models (LCMs). LCMs are defined for continuous domains and generalize the naive Bayes model by using latent variables to model class-conditional dependencies...... between the attributes. In addition to providing good classification accuracy, the LCM model has several appealing properties, including a relatively small parameter space making it less susceptible to over-fitting. In this paper we take a first-step towards generalizing LCMs to hybrid domains...... of different domains, including the problem of recognizing symbols in black and white images....

  19. [Biology molecular of glioblastomas]. (United States)

    Franco-Hernández, C; Martínez-Glez, V; Rey, J A


    Glioblastomas, the most frequent and malignant human brain tumors, may develop de novo (primary glioblastoma) or by progression from low-grade or anapalsic astrocytoma (secondary glioblastoma). The molecular alteration most frequent in these tumor-like types is the loss of heterozygosity on chromosome 10, in which several genes have been identified as tumors suppressor. The TP53/MDM2/P14arf and CDK4/RB1/ P16ink4 genetic pathways involved in cycle control are deregulated in the majority of gliomas as well as genes that promote the cellular division, EGFR. Finally the increase of growth and angiogenics factors is also involved in the development of glioblastomas. One of the objectives of molecular biology in tumors of glial ancestry is to try to find the genetic alterations that allow to approach better the classification of glioblastomas, its evolution prediction and treatment. The new pathmolecular classification of gliomas should improve the old one, especially being concerned about the oncogenesis and heterogeneity of these tumors. It is desirable that this classification had clinical applicability and integrates new molecular findings with some known histological features with pronostic value. In this paper we review the most frequent molecular mechanisms involved in the patogenesis of glioblastomas.

  20. [Psychiatry of the future: multidimensionality of the problems of modern psychiatry and development of classification systems]. (United States)

    Makushkin, E V; Oskolkova, S N; Fastovtsov, G A

    The success and achievements in the area of neurosciences due to the development of neuroimaging, neurochemical and genome studies provide tasks for psychiatry determined by the necessity to develop new classifications of mental diseases, primarily ICD-11, specify clinical diagnostic criteria and rethink the essence of some mental disorders. In spite of the multiple direction of scientific opinions on the discussed issues, the development of modern psychiatry is characterized by intensive search of biological background of psychiatric disorders and elaboration of effective approaches to the diagnosis and treatment of mental diseases, including medical rehabilitation of patients.

  1. Radiological classification of mandibular fractures

    International Nuclear Information System (INIS)

    Mihailova, H.


    Mandibular fractures present the biggest part (up to 97%) of the facial bone fractures. Method of choice for diagnosing of mandibular fractures is conventional radiography. The aim of the issue is to present an unified radiological classification of mandibular fractures for the clinical practice. This classification includes only those clinical symptoms of mandibular fracture which could be radiologically objectified: exact anatomical localization (F1-F6), teeth in fracture line (Ta,Tb), grade of dislocation (D I, D II), occlusal disturbances (O(+), O(-)). Radiological symptoms expressed by letter and number symbols are systematized in a formula - FTDO of mandibular fractures similar to TNM formula for tumours. FTDO formula expresses radiological diagnose of each mandibular fracture but it doesn't include neither the site (left or right) of the fracture, nor the kind and number of fractures. In order to express topography and number of fractures the radiological formula is transformed into a decimal fraction. The symbols (FTD) of right mandible fracture are written in the numerator and those of the left site - in the denominator. For double and multiple fractures between the symbols for each fracture we put '+'. Symbols for occlusal disturbances are put down opposite, the fractional line. So topographo-anatomical formula (FTD/FTD)xO is formed. In this way the whole radiological information for unilateral, bilateral, single or multiple fractures of the mandible is expressed. The information in the radiological topography anatomic formula, resp. from the unified topography-anatomic classification ensures a quick and exact X-ray diagnose of mandibular fracture. In this way contributes to get better, make easier and faster X-ray diagnostic process concerning mandibular fractures. And all these is a precondition for prevention of retardation of the diagnosis mandibular fracture. (author)

  2. Advances in radiation biology

    International Nuclear Information System (INIS)

    Lett, J.T.; Ehmann, U.K.; Cox, A.B.


    The classical period of radiation biology is coming to a close. Such change always occurs at a time when the ideas and concepts that promoted the burgeoning of an infant science are no longer adequate. This volume covers a number of areas in which new ideas and research are playing a vital role, including cellular radiation sensitivity, radioactive waste disposal, and space radiation biology

  3. Experimenting with Mathematical Biology (United States)

    Sanft, Rebecca; Walter, Anne


    St. Olaf College recently added a Mathematical Biology concentration to its curriculum. The core course, Mathematics of Biology, was redesigned to include a wet laboratory. The lab classes required students to collect data and implement the essential modeling techniques of formulation, implementation, validation, and analysis. The four labs…

  4. Extended Abstracts from BioGeo99: Applications of Geospatial Technology to Biological Sciences

    National Research Council Canada - National Science Library

    Handley, Lawrence


    ... of Global Positioning System (GPS), aquatic and terrestrial telemetry, national classification systems, remote sensing, metadata, and other geospatial technologies used in biological science applications...

  5. Event Classification using Concepts

    NARCIS (Netherlands)

    Boer, M.H.T. de; Schutte, K.; Kraaij, W.


    The semantic gap is one of the challenges in the GOOSE project. In this paper a Semantic Event Classification (SEC) system is proposed as an initial step in tackling the semantic gap challenge in the GOOSE project. This system uses semantic text analysis, multiple feature detectors using the BoW

  6. Shark Teeth Classification (United States)

    Brown, Tom; Creel, Sally; Lee, Velda


    On a recent autumn afternoon at Harmony Leland Elementary in Mableton, Georgia, students in a fifth-grade science class investigated the essential process of classification--the act of putting things into groups according to some common characteristics or attributes. While they may have honed these skills earlier in the week by grouping their own…

  7. Classification system: Netherlands

    NARCIS (Netherlands)

    Hartemink, A.E.


    Although people have always classified soils, it is only since the mid 19th century that soil classification emerged as an important topic within soil science. It forced soil scientists to think systematically about soils and its genesis and developed to facilitate communication between soil

  8. Text document classification

    Czech Academy of Sciences Publication Activity Database

    Novovičová, Jana

    č. 62 (2005), s. 53-54 ISSN 0926-4981 R&D Projects: GA AV ČR IAA2075302; GA AV ČR KSK1019101; GA MŠk 1M0572 Institutional research plan: CEZ:AV0Z10750506 Keywords : document representation * categorization * classification Subject RIV: BD - Theory of Information

  9. Classifications in popular music

    NARCIS (Netherlands)

    van Venrooij, A.; Schmutz, V.; Wright, J.D.


    The categorical system of popular music, such as genre categories, is a highly differentiated and dynamic classification system. In this article we present work that studies different aspects of these categorical systems in popular music. Following the work of Paul DiMaggio, we focus on four

  10. Mimicking human texture classification

    NARCIS (Netherlands)

    Rogowitz, B.E.; van Rikxoort, Eva M.; van den Broek, Egon; Pappas, T.N.; Schouten, Theo E.; Daly, S.J.


    In an attempt to mimic human (colorful) texture classification by a clustering algorithm three lines of research have been encountered, in which as test set 180 texture images (both their color and gray-scale equivalent) were drawn from the OuTex and VisTex databases. First, a k-means algorithm was

  11. Classification of myocardial infarction

    DEFF Research Database (Denmark)

    Saaby, Lotte; Poulsen, Tina Svenstrup; Hosbond, Susanne


    The classification of myocardial infarction into 5 types was introduced in 2007 as an important component of the universal definition. In contrast to the plaque rupture-related type 1 myocardial infarction, type 2 myocardial infarction is considered to be caused by an imbalance between demand...

  12. Steel column base classification


    Jaspart, J.P.; Wald, F.; Weynand, K.; Gresnigt, A.M.


    The influence of the rotational characteristics of the column bases on the structural frame response is discussed and specific design criteria for stiffness classification into semi-rigid and rigid joints are derived. The particular case of an industrial portal frame is then considered. Peer reviewed

  13. Principles for ecological classification (United States)

    Dennis H. Grossman; Patrick Bourgeron; Wolf-Dieter N. Busch; David T. Cleland; William Platts; G. Ray; C. Robins; Gary Roloff


    The principal purpose of any classification is to relate common properties among different entities to facilitate understanding of evolutionary and adaptive processes. In the context of this volume, it is to facilitate ecosystem stewardship, i.e., to help support ecosystem conservation and management objectives.

  14. Ontologies vs. Classification Systems

    DEFF Research Database (Denmark)

    Madsen, Bodil Nistrup; Erdman Thomsen, Hanne


    data sets or for obtaining advanced search facilities. In this paper we will present an attempt at answering these questions. We will give a presentation of various types of ontologies and briefly introduce terminological ontologies. Furthermore we will argue that classification systems, e.g. product...

  15. Bosniak classification system

    DEFF Research Database (Denmark)

    Graumann, Ole; Osther, Susanne S; Karstoft, Jens


    BACKGROUND: The Bosniak classification is a diagnostic tool for the differentiation of cystic changes in the kidney. The process of categorizing renal cysts may be challenging, involving a series of decisions that may affect the final diagnosis and clinical outcome such as surgical management. PU...

  16. An automated cirrus classification (United States)

    Gryspeerdt, Edward; Quaas, Johannes; Sourdeval, Odran; Goren, Tom


    Cirrus clouds play an important role in determining the radiation budget of the earth, but our understanding of the lifecycle and controls on cirrus clouds remains incomplete. Cirrus clouds can have very different properties and development depending on their environment, particularly during their formation. However, the relevant factors often cannot be distinguished using commonly retrieved satellite data products (such as cloud optical depth). In particular, the initial cloud phase has been identified as an important factor in cloud development, but although back-trajectory based methods can provide information on the initial cloud phase, they are computationally expensive and depend on the cloud parametrisations used in re-analysis products. In this work, a classification system (Identification and Classification of Cirrus, IC-CIR) is introduced. Using re-analysis and satellite data, cirrus clouds are separated in four main types: frontal, convective, orographic and in-situ. The properties of these classes show that this classification is able to provide useful information on the properties and initial phase of cirrus clouds, information that could not be provided by instantaneous satellite retrieved cloud properties alone. This classification is designed to be easily implemented in global climate models, helping to improve future comparisons between observations and models and reducing the uncertainty in cirrus clouds properties, leading to improved cloud parametrisations.

  17. Systems Biology of Metabolism. (United States)

    Nielsen, Jens


    Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology are described, and two different types of mathematical models used for studying metabolism are discussed: kinetic models and genome-scale metabolic models. The use of different omics technologies, including transcriptomics, proteomics, metabolomics, and fluxomics, for studying metabolism is presented. Finally, the application of systems biology for analyzing global regulatory structures, engineering the metabolism of cell factories, and analyzing human diseases is discussed.

  18. Multiple Sparse Representations Classification (United States)

    Plenge, Esben; Klein, Stefan S.; Niessen, Wiro J.; Meijering, Erik


    Sparse representations classification (SRC) is a powerful technique for pixelwise classification of images and it is increasingly being used for a wide variety of image analysis tasks. The method uses sparse representation and learned redundant dictionaries to classify image pixels. In this empirical study we propose to further leverage the redundancy of the learned dictionaries to achieve a more accurate classifier. In conventional SRC, each image pixel is associated with a small patch surrounding it. Using these patches, a dictionary is trained for each class in a supervised fashion. Commonly, redundant/overcomplete dictionaries are trained and image patches are sparsely represented by a linear combination of only a few of the dictionary elements. Given a set of trained dictionaries, a new patch is sparse coded using each of them, and subsequently assigned to the class whose dictionary yields the minimum residual energy. We propose a generalization of this scheme. The method, which we call multiple sparse representations classification (mSRC), is based on the observation that an overcomplete, class specific dictionary is capable of generating multiple accurate and independent estimates of a patch belonging to the class. So instead of finding a single sparse representation of a patch for each dictionary, we find multiple, and the corresponding residual energies provides an enhanced statistic which is used to improve classification. We demonstrate the efficacy of mSRC for three example applications: pixelwise classification of texture images, lumen segmentation in carotid artery magnetic resonance imaging (MRI), and bifurcation point detection in carotid artery MRI. We compare our method with conventional SRC, K-nearest neighbor, and support vector machine classifiers. The results show that mSRC outperforms SRC and the other reference methods. In addition, we present an extensive evaluation of the effect of the main mSRC parameters: patch size, dictionary size, and

  19. Gene-ontology enrichment analysis in two independent family-based samples highlights biologically plausible processes for autism spectrum disorders.

    LENUS (Irish Health Repository)

    Anney, Richard J L


    Recent genome-wide association studies (GWAS) have implicated a range of genes from discrete biological pathways in the aetiology of autism. However, despite the strong influence of genetic factors, association studies have yet to identify statistically robust, replicated major effect genes or SNPs. We apply the principle of the SNP ratio test methodology described by O\\'Dushlaine et al to over 2100 families from the Autism Genome Project (AGP). Using a two-stage design we examine association enrichment in 5955 unique gene-ontology classifications across four groupings based on two phenotypic and two ancestral classifications. Based on estimates from simulation we identify excess of association enrichment across all analyses. We observe enrichment in association for sets of genes involved in diverse biological processes, including pyruvate metabolism, transcription factor activation, cell-signalling and cell-cycle regulation. Both genes and processes that show enrichment have previously been examined in autistic disorders and offer biologically plausibility to these findings.

  20. Standard biological parts knowledgebase. (United States)

    Galdzicki, Michal; Rodriguez, Cesar; Chandran, Deepak; Sauro, Herbert M; Gennari, John H


    We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology ( The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts ( SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate "promoter" parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.

  1. Standard biological parts knowledgebase.

    Directory of Open Access Journals (Sweden)

    Michal Galdzicki


    Full Text Available We have created the Knowledgebase of Standard Biological Parts (SBPkb as a publically accessible Semantic Web resource for synthetic biology ( The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts ( SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL, a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate "promoter" parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.

  2. Plant synthetic biology. (United States)

    Liu, Wusheng; Stewart, C Neal


    Plant synthetic biology is an emerging field that combines engineering principles with plant biology toward the design and production of new devices. This emerging field should play an important role in future agriculture for traditional crop improvement, but also in enabling novel bioproduction in plants. In this review we discuss the design cycles of synthetic biology as well as key engineering principles, genetic parts, and computational tools that can be utilized in plant synthetic biology. Some pioneering examples are offered as a demonstration of how synthetic biology can be used to modify plants for specific purposes. These include synthetic sensors, synthetic metabolic pathways, and synthetic genomes. We also speculate about the future of synthetic biology of plants. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. 78 FR 54970 - Cotton Futures Classification: Optional Classification Procedure (United States)


    ... industry and ICE, AMS proposes to offer a futures classification option whereby cotton bales may be... contract month. It is anticipated that AMS would make the futures classification option available December... Sec. 121.201). Establishing the registration option for cotton futures classification will not...

  4. 78 FR 68983 - Cotton Futures Classification: Optional Classification Procedure (United States)


    ... response to requests from the U.S. cotton industry and ICE, AMS will offer a futures classification option... parameters established by that exchange. AMS anticipates that the futures classification option will be... competition in the marketplace; (5) The futures classification option is expected to streamline marketing and...

  5. Biological treatment of polluted lands

    International Nuclear Information System (INIS)

    Le Brun, S.


    Several techniques of lands cleansing exist; they include the thermal techniques, the biological treatment or the disposal. The Biogenie firm is specialized in the biological cleansing of soils on and outside site. (O.M.)

  6. Computational intelligence techniques for biological data mining: An overview (United States)

    Faye, Ibrahima; Iqbal, Muhammad Javed; Said, Abas Md; Samir, Brahim Belhaouari


    Computational techniques have been successfully utilized for a highly accurate analysis and modeling of multifaceted and raw biological data gathered from various genome sequencing projects. These techniques are proving much more effective to overcome the limitations of the traditional in-vitro experiments on the constantly increasing sequence data. However, most critical problems that caught the attention of the researchers may include, but not limited to these: accurate structure and function prediction of unknown proteins, protein subcellular localization prediction, finding protein-protein interactions, protein fold recognition, analysis of microarray gene expression data, etc. To solve these problems, various classification and clustering techniques using machine learning have been extensively used in the published literature. These techniques include neural network algorithms, genetic algorithms, fuzzy ARTMAP, K-Means, K-NN, SVM, Rough set classifiers, decision tree and HMM based algorithms. Major difficulties in applying the above algorithms include the limitations found in the previous feature encoding and selection methods while extracting the best features, increasing classification accuracy and decreasing the running time overheads of the learning algorithms. The application of this research would be potentially useful in the drug design and in the diagnosis of some diseases. This paper presents a concise overview of the well-known protein classification techniques.

  7. Machine Learning Based Classification of Microsatellite Variation: An Effective Approach for Phylogeographic Characterization of Olive Populations. (United States)

    Torkzaban, Bahareh; Kayvanjoo, Amir Hossein; Ardalan, Arman; Mousavi, Soraya; Mariotti, Roberto; Baldoni, Luciana; Ebrahimie, Esmaeil; Ebrahimi, Mansour; Hosseini-Mazinani, Mehdi


    Finding efficient analytical techniques is overwhelmingly turning into a bottleneck for the effectiveness of large biological data. Machine learning offers a novel and powerful tool to advance classification and modeling solutions in molecular biology. However, these methods have been less frequently used with empirical population genetics data. In this study, we developed a new combined approach of data analysis using microsatellite marker data from our previous studies of olive populations using machine learning algorithms. Herein, 267 olive accessions of various origins including 21 reference cultivars, 132 local ecotypes, and 37 wild olive specimens from the Iranian plateau, together with 77 of the most represented Mediterranean varieties were investigated using a finely selected panel of 11 microsatellite markers. We organized data in two '4-targeted' and '16-targeted' experiments. A strategy of assaying different machine based analyses (i.e. data cleaning, feature selection, and machine learning classification) was devised to identify the most informative loci and the most diagnostic alleles to represent the population and the geography of each olive accession. These analyses revealed microsatellite markers with the highest differentiating capacity and proved efficiency for our method of clustering olive accessions to reflect upon their regions of origin. A distinguished highlight of this study was the discovery of the best combination of markers for better differentiating of populations via machine learning models, which can be exploited to distinguish among other biological populations.

  8. ERLN Biological Focus Area (United States)

    The Environmental Response Laboratory Network supports the goal to increase national capacity for biological analysis of environmental samples. This includes methods development and verification, technology transfer, and collaboration with USDA, FERN, CDC.

  9. The Biology of Behaviour. (United States)

    Broom, D. M.


    Discusses topics to aid in understanding animal behavior, including the value of the biological approach to psychology, functional systems, optimality and fitness, universality of environmental effects on behavior, and evolution of social behavior. (DS)

  10. Fishery Biology Database (AGDBS) (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Basic biological data are the foundation on which all assessments of fisheries resources are built. These include parameters such as the size and age composition of...

  11. Quality-Oriented Classification of Aircraft Material Based on SVM

    Directory of Open Access Journals (Sweden)

    Hongxia Cai


    Full Text Available The existing material classification is proposed to improve the inventory management. However, different materials have the different quality-related attributes, especially in the aircraft industry. In order to reduce the cost without sacrificing the quality, we propose a quality-oriented material classification system considering the material quality character, Quality cost, and Quality influence. Analytic Hierarchy Process helps to make feature selection and classification decision. We use the improved Kraljic Portfolio Matrix to establish the three-dimensional classification model. The aircraft materials can be divided into eight types, including general type, key type, risk type, and leveraged type. Aiming to improve the classification accuracy of various materials, the algorithm of Support Vector Machine is introduced. Finally, we compare the SVM and BP neural network in the application. The results prove that the SVM algorithm is more efficient and accurate and the quality-oriented material classification is valuable.

  12. Biologic mesh in ventral hernia repair: Outcomes, recurrence, and charge analysis. (United States)

    Huntington, Ciara R; Cox, Tiffany C; Blair, Laurel J; Schell, Samuel; Randolph, David; Prasad, Tanushree; Lincourt, Amy; Heniford, B Todd; Augenstein, Vedra A


    Biologic mesh choice in ventral hernia repair is challenging due to lack of prospective data. This study examines long-term, single-center biologic mesh outcomes. Prospective operative outcomes data was queried for open ventral hernia repair with biologic mesh. Univariate and multivariate analysis were used to compare mesh outcomes. In the study, 223 patients underwent open ventral hernia repair with biologic mesh, including 40 with Alloderm, 23 AlloMax, 70 FlexHD, 68 Strattice, and 22 Xenmatrix. Overall, 9.8% had an American Society of Anesthesiology classification of 4, 54.6% with a classification of 3, and 35.6% with a classification of 1 or 2. Operative time averaged 241 minutes with estimated blood loss of 202 mL. Hernia defects averaged 257 ± 245 cm 2 with mesh size 384 cm 2 . Biologic mesh was used as a fascial bridge in 19.6%, component separation was performed in 47.5%, and 82% had concomitant procedure. Inpatient mortality was 1.4%. Hernia recurrence varied significantly by mesh type: 35% Alloderm, 34.5% AlloMax, 37.1% FlexHD, 14.7% Strattice, and 59.1% Xenmatrix (P = .001). The mean follow-up was 18.2 months. After multivariate analysis comparing to Strattice, AlloMax had a 3.4 higher odds ratio for recurrence, FlexHD a 2.9 odds ratio, and Xenmatrix a 7.8 odds ratio. The rate of mesh infections requiring explantation was biologic mesh at a tertiary care institution, Strattice, a porcine acellular dermal mesh, had significantly lower odds of hernia recurrence compared with AlloMax, FlexHD, and Xenmatrix. Choice of biologic mesh affects long-term postoperative outcomes in ventral hernia repair. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. Systems Biology

    Energy Technology Data Exchange (ETDEWEB)

    Wiley, H S.


    The biology revolution over the last 50 years has been driven by the ascendancy of molecular biology. This was enthusiastically embraced by most biologists because it took us into increasingly familiar territory. It took mysterious processes, such as the replication of genetic material and assigned them parts that could be readily understood by the human mind. When we think of ''molecular machines'' as being the underlying basis of life, we are using a paradigm derived from everyday experience. However, the price that we paid was a relentless drive towards reductionism and the attendant balkanization of biology. Now along comes ''systems biology'' that promises us a solution to the problem of ''knowing more and more about less and less''. Unlike molecular biology, systems biology appears to be taking us into unfamiliar intellectual territory, such as statistics, mathematics and computer modeling. Not surprisingly, systems biology has met with widespread skepticism and resistance. Why do we need systems biology anyway and how does this new area of research promise to change the face of biology in the next couple of decades?

  14. Applications of intelligent optimization in biology and medicine current trends and open problems

    CERN Document Server

    Grosan, Crina; Tolba, Mohamed


    This volume provides updated, in-depth material on the application of intelligent optimization in biology and medicine. The aim of the book is to present solutions to the challenges and problems facing biology and medicine applications. This Volume comprises of 13 chapters, including an overview chapter, providing an up-to-date and state-of-the research on the application of intelligent optimization for bioinformatics applications, DNA based Steganography, a modified Particle Swarm Optimization Algorithm for Solving Capacitated Maximal Covering Location Problem in Healthcare Systems, Optimization Methods for Medical Image Super Resolution Reconstruction and breast cancer classification. Moreover, some chapters that describe several bio-inspired approaches in MEDLINE Text Mining, DNA-Binding Proteins and Classes, Optimized Tumor Breast Cancer Classification using Combining Random Subspace and Static Classifiers Selection Paradigms, and Dental Image Registration. The book will be a useful compendium for a broad...

  15. Classification of Osteogenesis Imperfecta revisited

    NARCIS (Netherlands)

    van Dijk, F. S.; Pals, G.; van Rijn, R. R.; Nikkels, P. G. J.; Cobben, J. M.


    In 1979 Sillence proposed a classification of Osteogenesis Imperfecta (OI) in OI types I, II, III and IV. In 2004 and 2007 this classification was expanded with OI types V-VIII because of distinct clinical features and/or different causative gene mutations. We propose a revised classification of OI

  16. IAEA Classification of Uranium Deposits

    International Nuclear Information System (INIS)

    Bruneton, Patrice


    Classifications of uranium deposits follow two general approaches, focusing on: • descriptive features such as the geotectonic position, the host rock type, the orebody morphology, …… : « geologic classification »; • or on genetic aspects: « genetic classification »

  17. A comprehensive classification system for lipids. (United States)

    Fahy, Eoin; Subramaniam, Shankar; Brown, H Alex; Glass, Christopher K; Merrill, Alfred H; Murphy, Robert C; Raetz, Christian R H; Russell, David W; Seyama, Yousuke; Shaw, Walter; Shimizu, Takao; Spener, Friedrich; van Meer, Gerrit; VanNieuwenhze, Michael S; White, Stephen H; Witztum, Joseph L; Dennis, Edward A


    Lipids are produced, transported, and recognized by the concerted actions of numerous enzymes, binding proteins, and receptors. A comprehensive analysis of lipid molecules, "lipidomics," in the context of genomics and proteomics is crucial to understanding cellular physiology and pathology; consequently, lipid biology has become a major research target of the postgenomic revolution and systems biology. To facilitate international communication about lipids, a comprehensive classification of lipids with a common platform that is compatible with informatics requirements has been developed to deal with the massive amounts of data that will be generated by our lipid community. As an initial step in this development, we divide lipids into eight categories (fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, sterol lipids, prenol lipids, saccharolipids, and polyketides) containing distinct classes and subclasses of molecules, devise a common manner of representing the chemical structures of individual lipids and their derivatives, and provide a 12 digit identifier for each unique lipid molecule. The lipid classification scheme is chemically based and driven by the distinct hydrophobic and hydrophilic elements that compose the lipid. This structured vocabulary will facilitate the systematization of lipid biology and enable the cataloging of lipids and their properties in a way that is compatible with other macromolecular databases.

  18. Molecular Biology Database List. (United States)

    Burks, C


    Molecular Biology Database List (MBDL) includes brief descriptions and pointers to Web sites for the various databases described in this issue as well as other Web sites presenting data sets relevant to molecular biology. This information is compiled into a list ( gkc105_gml.html) which includes links both to source Web sites and to on-line versions of articles describing the databases. PMID:9847130


    International Nuclear Information System (INIS)

    Lochner, Michelle; Peiris, Hiranya V.; Lahav, Ofer; Winter, Max K.; McEwen, Jason D.


    Automated photometric supernova classification has become an active area of research in recent years in light of current and upcoming imaging surveys such as the Dark Energy Survey (DES) and the Large Synoptic Survey Telescope, given that spectroscopic confirmation of type for all supernovae discovered will be impossible. Here, we develop a multi-faceted classification pipeline, combining existing and new approaches. Our pipeline consists of two stages: extracting descriptive features from the light curves and classification using a machine learning algorithm. Our feature extraction methods vary from model-dependent techniques, namely SALT2 fits, to more independent techniques that fit parametric models to curves, to a completely model-independent wavelet approach. We cover a range of representative machine learning algorithms, including naive Bayes, k -nearest neighbors, support vector machines, artificial neural networks, and boosted decision trees (BDTs). We test the pipeline on simulated multi-band DES light curves from the Supernova Photometric Classification Challenge. Using the commonly used area under the curve (AUC) of the Receiver Operating Characteristic as a metric, we find that the SALT2 fits and the wavelet approach, with the BDTs algorithm, each achieve an AUC of 0.98, where 1 represents perfect classification. We find that a representative training set is essential for good classification, whatever the feature set or algorithm, with implications for spectroscopic follow-up. Importantly, we find that by using either the SALT2 or the wavelet feature sets with a BDT algorithm, accurate classification is possible purely from light curve data, without the need for any redshift information.

  20. The Influence of Hindu Epistemology on Ranganathan's Colon Classification. (United States)

    Maurer, Bradley Gerald

    This study attempted to determine the influence of Hindu epistemology on Ranganathan's Colon Classification. Only the epistemological schools of Hindu philosophy and the Idea Plane element of Colon Classification were included. A literature search revealed that, although there is significant literature on each side of the problem, no bridges exist…

  1. Fatigue classification of welded joints in orthotropic steel bridge decks

    NARCIS (Netherlands)

    Kolstein, M.H.


    This dissertation presents the research into fatigue classifications of welded joints in orthotropic steel bridge decks. These classifications are needed to calculate the fatigue life of these joints and should be included in the design codes. For years bridge design was mainly based on static

  2. Classification of marine Ascomycota, Basidiomycota, Blastocladiomycota and Chytridiomycota

    NARCIS (Netherlands)

    Jones, E. B. Gareth; Suetrong, Satinee; Sakayaroj, Jariya; Bahkali, Ali H.; Abdel-Wahab, Mohamed A.; Boekhout, Teun; Pang, Ka-Lai

    This paper lists the accepted names and classification of marine fungi, updating the scheme presented in 2009. The classification includes 1,112 species (in 472 genera): Ascomycota 805 (in 352 genera), Basidiomycota 21 species (in 17 genera), Chytridiomycota and related phyla 26 species (in 13

  3. A higher-level phylogenetic classification of the Fungi

    NARCIS (Netherlands)

    Hibbett, David S; Binder, Manfred; Bischoff, Joseph F; Blackwell, Meredith; Cannon, Paul F; Eriksson, Ove E; Huhndorf, Sabine; James, Timothy; Kirk, Paul M; Lücking, Robert; Thorsten Lumbsch, H; Lutzoni, François; Matheny, P Brandon; McLaughlin, David J; Powell, Martha J; Redhead, Scott; Schoch, Conrad L; Spatafora, Joseph W; Stalpers, Joost A; Vilgalys, Rytas; Aime, M Catherine; Aptroot, André; Bauer, Robert; Begerow, Dominik; Benny, Gerald L; Castlebury, Lisa A; Crous, Pedro W; Dai, Yu-Cheng; Gams, Walter; Geiser, David M; Griffith, Gareth W; Gueidan, Cécile; Hawksworth, David L; Hestmark, Geir; Hosaka, Kentaro; Humber, Richard A; Hyde, Kevin D; Ironside, Joseph E; Kõljalg, Urmas; Kurtzman, Cletus P; Larsson, Karl-Henrik; Lichtwardt, Robert; Longcore, Joyce; Miadlikowska, Jolanta; Miller, Andrew; Moncalvo, Jean-Marc; Mozley-Standridge, Sharon; Oberwinkler, Franz; Parmasto, Erast; Reeb, Valérie; Rogers, Jack D; Roux, Claude; Ryvarden, Leif; Sampaio, José Paulo; Schüssler, Arthur; Sugiyama, Junta; Thorn, R Greg; Tibell, Leif; Untereiner, Wendy A; Walker, Christopher; Wang, Zheng; Weir, Alex; Weiss, Michael; White, Merlin M; Winka, Katarina; Yao, Yi-Jian; Zhang, Ning


    A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 16 are described

  4. Establishment of water quality classification scheme: a case study of ...

    African Journals Online (AJOL)

    A water quality classification scheme based on 11 routinely measured physicochemical variables has been developed for the Calabar River Estuary. The variables considered include water temperature, pH. Eh, DO, DO saturation, BOD5, COD, TSS, turbidity, NH4-N and electrical conductivity. Classification of water source ...

  5. Sound classification of dwellings

    DEFF Research Database (Denmark)

    Rasmussen, Birgit


    National schemes for sound classification of dwellings exist in more than ten countries in Europe, typically published as national standards. The schemes define quality classes reflecting different levels of acoustical comfort. Main criteria concern airborne and impact sound insulation between...... dwellings, facade sound insulation and installation noise. The schemes have been developed, implemented and revised gradually since the early 1990s. However, due to lack of coordination between countries, there are significant discrepancies, and new standards and revisions continue to increase the diversity...... is needed, and a European COST Action TU0901 "Integrating and Harmonizing Sound Insulation Aspects in Sustainable Urban Housing Constructions", has been established and runs 2009-2013, one of the main objectives being to prepare a proposal for a European sound classification scheme with a number of quality...

  6. [Headache: classification and diagnosis]. (United States)

    Carbaat, P A T; Couturier, E G M


    There are many types of headache and, moreover, many people have different types of headache at the same time. Adequate treatment is possible only on the basis of the correct diagnosis. Technically and in terms of content the current diagnostics process for headache is based on the 'International Classification of Headache Disorders' (ICHD-3-beta) that was produced under the auspices of the International Headache Society. This classification is based on a distinction between primary and secondary headaches. The most common primary headache types are the tension type headache, migraine and the cluster headache. Application of uniform diagnostic concepts is essential to come to the most appropriate treatment of the various types of headache.

  7. Comparison Between Revised Atlanta Classification and Determinant-Based Classification for Acute Pancreatitis in Intensive Care Medicine. Why Do Not Use a Modified Determinant-Based Classification? (United States)

    Zubia-Olaskoaga, Felix; Maraví-Poma, Enrique; Urreta-Barallobre, Iratxe; Ramírez-Puerta, María-Rosario; Mourelo-Fariña, Mónica; Marcos-Neira, María-Pilar


    To compare the classification performance of the Revised Atlanta Classification, the Determinant-Based Classification, and a new modified Determinant-Based Classification according to observed mortality and morbidity. A prospective multicenter observational study conducted in 1-year period. Forty-six international ICUs (Epidemiology of Acute Pancreatitis in Intensive Care Medicine study). Admitted to an ICU with acute pancreatitis and at least one organ failure. Modified Determinant-Based Classification included four categories: In group 1, patients with transient organ failure and without local complications; in group 2, patients with transient organ failure and local complications; in group 3, patients with persistent organ failure and without local complications; and in group 4, patients with persistent organ failure and local complications. A total of 374 patients were included (mortality rate of 28.9%). When modified Determinant-Based Classification was applied, patients in group 1 presented low mortality (2.26%) and morbidity (5.38%), patients in group 2 presented low mortality (6.67%) and high morbidity (60.71%), patients in group 3 presented high mortality (41.46%) and low morbidity (8.33%), and patients in group 4 presented high mortality (59.09%) and morbidity (88.89%). The area under the receiver operator characteristics curve of modified Determinant-Based Classification for mortality was 0.81 (95% CI, 0.77-0.85), with significant differences in comparison to Revised Atlanta Classification (0.77; 95% CI, 0.73-0.81; p Determinant-Based Classification (0.77; 95% CI, 0.72-0.81; p Determinant-Based Classification was 0.80 (95% CI, 0.73-0.86), with significant differences in comparison to Revised Atlanta Classification (0.63, 95% CI, 0.57-0.70; p Determinant-Based Classification (0.81, 95% CI, 0.74-0.88; nonsignificant). Modified Determinant-Based Classification identified four groups with different clinical presentation in patients with acute pancreatitis in

  8. Classification, Properties, and Management of Aridisols. (United States)

    Mack, C. B.; And Others


    Described is a slide set which is designed to illustrate the entire range of soils found in the arid regions of the earth's surface. Information on physical and chemical soil properties, soil classification, and related soil management considerations for agricultural development are included. (CW)

  9. Dynamic Time Warping for Vehicle Classification


    Halachkin, A.


    This work focuses on the dynamic time warping for vehicle classification. The theoretical part includes the dynamic time warping algorithm description. The DTW module in Python, that was created during this work, is subsequently applied for the recognition of vehicle types by their side profiles based on the DTW.

  10. Oriented Shape Index Histograms for Cell Classification

    DEFF Research Database (Denmark)

    Larsen, Anders Boesen Lindbo; Dahl, Anders Bjorholm; Larsen, Rasmus


    evaluate our new feature descriptor using a public dataset consisting of HEp-2 cell images from indirect immunoflourescence lighting. Our results show that we can improve classification performance significantly when including the shape index orientation. Notably, we show that shape index orientation...

  11. Is synthetic biology mechanical biology? (United States)

    Holm, Sune


    A widespread and influential characterization of synthetic biology emphasizes that synthetic biology is the application of engineering principles to living systems. Furthermore, there is a strong tendency to express the engineering approach to organisms in terms of what seems to be an ontological claim: organisms are machines. In the paper I investigate the ontological and heuristic significance of the machine analogy in synthetic biology. I argue that the use of the machine analogy and the aim of producing rationally designed organisms does not necessarily imply a commitment to mechanical biology. The ideal of applying engineering principles to biology is best understood as expressing recognition of the machine-unlikeness of natural organisms and the limits of human cognition. The paper suggests an interpretation of the identification of organisms with machines in synthetic biology according to which it expresses a strategy for representing, understanding, and constructing living systems that are more machine-like than natural organisms.

  12. Classification and regression trees

    CERN Document Server

    Breiman, Leo; Olshen, Richard A; Stone, Charles J


    The methodology used to construct tree structured rules is the focus of this monograph. Unlike many other statistical procedures, which moved from pencil and paper to calculators, this text's use of trees was unthinkable before computers. Both the practical and theoretical sides have been developed in the authors' study of tree methods. Classification and Regression Trees reflects these two sides, covering the use of trees as a data analysis method, and in a more mathematical framework, proving some of their fundamental properties.

  13. Classification Constrained Dimensionality Reduction


    Raich, Raviv; Costa, Jose A.; Damelin, Steven B.; Hero III, Alfred O.


    Dimensionality reduction is a topic of recent interest. In this paper, we present the classification constrained dimensionality reduction (CCDR) algorithm to account for label information. The algorithm can account for multiple classes as well as the semi-supervised setting. We present an out-of-sample expressions for both labeled and unlabeled data. For unlabeled data, we introduce a method of embedding a new point as preprocessing to a classifier. For labeled data, we introduce a method tha...

  14. Classification of nanopolymers

    Energy Technology Data Exchange (ETDEWEB)

    Larena, A; Tur, A [Department of Chemical Industrial Engineering and Environment, Universidad Politecnica de Madrid, E.T.S. Ingenieros Industriales, C/ Jose Gutierrez Abascal, Madrid (Spain); Baranauskas, V [Faculdade de Engenharia Eletrica e Computacao, Departamento de Semicondutores, Instrumentos e Fotonica, Universidade Estadual de Campinas, UNICAMP, Av. Albert Einstein N.400, 13 083-852 Campinas SP Brasil (Brazil)], E-mail:


    Nanopolymers with different structures, shapes, and functional forms have recently been prepared using several techniques. Nanopolymers are the most promising basic building blocks for mounting complex and simple hierarchical nanosystems. The applications of nanopolymers are extremely broad and polymer-based nanotechnologies are fast emerging. We propose a nanopolymer classification scheme based on self-assembled structures, non self-assembled structures, and on the number of dimensions in the nanometer range (nD)

  15. Decimal Classification Editions

    Directory of Open Access Journals (Sweden)

    Zenovia Niculescu


    Full Text Available The study approaches the evolution of Dewey Decimal Classification editions from the perspective of updating the terminology, reallocating and expanding the main and auxilary structure of Dewey indexing language. The comparative analysis of DDC editions emphasizes the efficiency of Dewey scheme from the point of view of improving the informational offer, through basic index terms, revised and developed, as well as valuing the auxilary notations.

  16. Diagnosis and classification of autoimmune hemolytic anemia. (United States)

    Bass, Garrett F; Tuscano, Emily T; Tuscano, Joseph M


    Uncompensated autoantibody-mediated red blood cell (RBC) consumption is the hallmark of autoimmune hemolytic anemia (AIHA). Classification of AIHA is pathophysiologically based and divides AIHA into warm, mixed or cold-reactive subtypes. This thermal-based classification is based on the optimal autoantibody-RBC reactivity temperatures. AIHA is further subcategorized into idiopathic and secondary with the later being associated with a number of underlying infectious, neoplastic and autoimmune disorders. In most cases AIHA is confirmed by a positive direct antiglobulin test (DAT). The standard therapeutic approaches to treatment of AIHA include corticosteroids, splenectomy, immunosuppressive agents and monoclonal antibodies. Published by Elsevier B.V.

  17. Mesoscopic biology

    Indian Academy of Sciences (India)

    Abstract. In this paper we present a qualitative outlook of mesoscopic biology where the typical length scale is of the order of nanometers and the energy scales comparable to thermal energy. ... National Center for Biological Sciences, Tata Institute of Fundamental Research, UAS-GKVK Campus, Bangalore 560 065, India ...

  18. Computational biology

    DEFF Research Database (Denmark)

    Hartmann, Lars Røeboe; Jones, Neil; Simonsen, Jakob Grue


    Computation via biological devices has been the subject of close scrutiny since von Neumann’s early work some 60 years ago. In spite of the many relevant works in this field, the notion of programming biological devices seems to be, at best, ill-defined. While many devices are claimed or proved t...

  19. Mesoscopic biology

    Indian Academy of Sciences (India)

    In this paper we present a qualitative outlook of mesoscopic biology where the typical length scale is of the order of nanometers and the energy scales comparable to thermal energy. Novel biomolecular machines, governed by coded information at the level of DNA and proteins, operate at these length scales in biological ...

  20. Neuromuscular disease classification system (United States)

    Sáez, Aurora; Acha, Begoña; Montero-Sánchez, Adoración; Rivas, Eloy; Escudero, Luis M.; Serrano, Carmen


    Diagnosis of neuromuscular diseases is based on subjective visual assessment of biopsies from patients by the pathologist specialist. A system for objective analysis and classification of muscular dystrophies and neurogenic atrophies through muscle biopsy images of fluorescence microscopy is presented. The procedure starts with an accurate segmentation of the muscle fibers using mathematical morphology and a watershed transform. A feature extraction step is carried out in two parts: 24 features that pathologists take into account to diagnose the diseases and 58 structural features that the human eye cannot see, based on the assumption that the biopsy is considered as a graph, where the nodes are represented by each fiber, and two nodes are connected if two fibers are adjacent. A feature selection using sequential forward selection and sequential backward selection methods, a classification using a Fuzzy ARTMAP neural network, and a study of grading the severity are performed on these two sets of features. A database consisting of 91 images was used: 71 images for the training step and 20 as the test. A classification error of 0% was obtained. It is concluded that the addition of features undetectable by the human visual inspection improves the categorization of atrophic patterns.

  1. Trends and concepts in fern classification (United States)

    Christenhusz, Maarten J. M.; Chase, Mark W.


    sister to all other vascular plants, whereas the whisk ferns (Psilotaceae), often included in the lycopods or believed to be associated with the first vascular plants, are sister to Ophioglossaceae and thus belong to the fern clade. The horsetails (Equisetaceae) are also members of the fern clade (sometimes inappropriately called ‘monilophytes’), but, within that clade, their placement is still uncertain. Leptosporangiate ferns are better understood, although deep relationships within this group are still unresolved. Earlier, almost all leptosporangiate ferns were placed in a single family (Polypodiaceae or Dennstaedtiaceae), but these families have been redefined to narrower more natural entities. Conclusions Concluding this paper, a classification is presented based on our current understanding of relationships of fern and lycopod clades. Major changes in our understanding of these families are highlighted, illustrating issues of classification in relation to convergent evolution and false homologies. Problems with the current classification and groups that still need study are pointed out. A summary phylogenetic tree is also presented. A new classification in which Aspleniaceae, Cyatheaceae, Polypodiaceae and Schizaeaceae are expanded in comparison with the most recent classifications is presented, which is a modification of those proposed by Smith et al. (2006, 2008) and Christenhusz et al. (2011). These classifications are now finding a wider acceptance and use, and even though a few amendments are made based on recently published results from molecular analyses, we have aimed for a stable family and generic classification of ferns. PMID:24532607

  2. Integrated Biological Control

    International Nuclear Information System (INIS)



    Biological control is any activity taken to prevent, limit, clean up, or remediate potential environmental, health and safety, or workplace quality impacts from plants, animals, or microorganisms. At Hanford the principal emphasis of biological control is to prevent the transport of radioactive contamination by biological vectors (plants, animals, or microorganisms), and where necessary, control and clean up resulting contamination. Other aspects of biological control at Hanford include industrial weed control (e.g.; tumbleweeds), noxious weed control (invasive, non-native plant species), and pest control (undesirable animals such as rodents and stinging insects; and microorganisms such as molds that adversely affect the quality of the workplace environment). Biological control activities may be either preventive (apriori) or in response to existing contamination spread (aposteriori). Surveillance activities, including ground, vegetation, flying insect, and other surveys, and apriori control actions, such as herbicide spraying and placing biological barriers, are important in preventing radioactive contamination spread. If surveillance discovers that biological vectors have spread radioactive contamination, aposteriori control measures, such as fixing contamination, followed by cleanup and removal of the contamination to an approved disposal location are typical response functions. In some cases remediation following the contamination cleanup and removal is necessary. Biological control activities for industrial weeds, noxious weeds and pests have similar modes of prevention and response

  3. The paradox of atheoretical classification

    DEFF Research Database (Denmark)

    Hjørland, Birger


    be very successful. The best example of a successful “atheoretical” classification is probably the prestigious Diagnostic and Statistical Manual of Mental Disorders (DSM) since its third edition from 1980. Based on such successes one may ask: Should the claim that classifications ideally are natural......A distinction can be made between “artificial classifications” and “natural classifications,” where artificial classifications may adequately serve some limited purposes, but natural classifications are overall most fruitful by allowing inference and thus many different purposes. There is strong...

  4. New international classification of functioning, disability and health

    Directory of Open Access Journals (Sweden)

    Stucki Gerold


    Full Text Available The WHO International Classification of Functioning, Disability and Health (ICF provides a coherent view of health from a biological, individual and social perspective. This view may be defined both as multi- and interdisciplinary management of one’s functioning and health. This new classification is currently being assessed in multiple centers in 32 countries, on 12 health conditions. The Institute of Hygiene and Medical Ecology, School of Medicine, University of Belgrade, is one of them, serving as the centre where the classification is being tested in obese population. The objective of this paper is to provide information needed for further development and practical application of this classification in various health conditions. The new language of ICF is an exciting landmark event for preventive medicine and rehabilitation. It may lead to a stronger position of rehabilitation within the medical community, change multiprofessional communication and improve communication between patients and health professionals. .

  5. Automatic Classification Using Supervised Learning in a Medical Document Filtering Application. (United States)

    Mostafa, J.; Lam, W.


    Presents a multilevel model of the information filtering process that permits document classification. Evaluates a document classification approach based on a supervised learning algorithm, measures the accuracy of the algorithm in a neural network that was trained to classify medical documents on cell biology, and discusses filtering…

  6. Decomposition and classification of electroencephalography data

    DEFF Research Database (Denmark)

    Frølich, Laura

    _MARC was also used to inspect effects of artefacts on motor imagery based Brain-Computer Interfaces (BCIs) in two studies, where removing artefactual ICs had little performance impact. Finally, we investigated multi-linear classification on single trials of EEG data, proposing a rigorous optimisation approach......This thesis is about linear and multi-linear analyses of electroencephalography (EEG) data and classification of estimated EEG sources. One contribution consists of an automatic classification method for independent components (ICs) of EEG data and a freely available implementation as an EEGLab...... of six linear decomposition methods. This study showed that high-pass filtering data at high cut-off frequencies improved artefact removal performances in an Event-Related Desynchronisation setting, providing similar performances of the three included Independent Component Analysis variants. IC...

  7. Automated source classification of new transient sources (United States)

    Oertel, M.; Kreikenbohm, A.; Wilms, J.; DeLuca, A.


    The EXTraS project harvests the hitherto unexplored temporal domain information buried in the serendipitous data collected by the European Photon Imaging Camera (EPIC) onboard the ESA XMM-Newton mission since its launch. This includes a search for fast transients, missed by standard image analysis, and a search and characterization of variability in hundreds of thousands of sources. We present an automated classification scheme for new transient sources in the EXTraS project. The method is as follows: source classification features of a training sample are used to train machine learning algorithms (performed in R; randomForest (Breiman, 2001) in supervised mode) which are then tested on a sample of known source classes and used for classification.

  8. Dense Iterative Contextual Pixel Classification using Kriging

    DEFF Research Database (Denmark)

    Ganz, Melanie; Loog, Marco; Brandt, Sami


    have been proposed to this end, e.g., iterative contextual pixel classification, iterated conditional modes, and other approaches related to Markov random fields. A problem of these methods, however, is their computational complexity, especially when dealing with high-resolution images in which......In medical applications, segmentation has become an ever more important task. One of the competitive schemes to perform such segmentation is by means of pixel classification. Simple pixel-based classification schemes can be improved by incorporating contextual label information. Various methods...... relatively long range interactions may play a role. We propose a new method based on Kriging that makes it possible to include such long range interactions, while keeping the computations manageable when dealing with large medical images....

  9. Automatic workflow for the classification of local DNA conformations

    Czech Academy of Sciences Publication Activity Database

    Čech, P.; Kukal, J.; Černý, Jiří; Schneider, Bohdan; Svozil, D.


    Roč. 14, č. 205 (2013) ISSN 1471-2105 R&D Projects: GA ČR GAP305/12/1801 Institutional research plan: CEZ:AV0Z50520701 Keywords : DNA * Dinucleotide conformation * Classification * Machine learning * Neural network * k-NN * Cluster analysis Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.672, year: 2013

  10. 10 CFR 1045.15 - Classification and declassification presumptions. (United States)


    ... experimental physics, engineering, materials science, biology and medicine; (2) Magnetic confinement fusion... Section 1045.15 Energy DEPARTMENT OF ENERGY (GENERAL PROVISIONS) NUCLEAR CLASSIFICATION AND... before applying the criteria in § 1045.16. (b) Not all areas of nuclear-related information are covered...

  11. Classification of mitocans, anti-cancer drugs acting on mitochondria

    Czech Academy of Sciences Publication Activity Database

    Neužil, Jiří; Dong, L. F.; Rohlena, Jakub; Truksa, Jaroslav; Ralph, S. J.


    Roč. 13, č. 3 (2013), s. 199-208 ISSN 1567-7249 Institutional research plan: CEZ:AV0Z50520701 Keywords : Mitocans * Anti-cancer therapeutics * Classification Subject RIV: EB - Gene tics ; Molecular Biology Impact factor: 3.524, year: 2013

  12. Classification of mitocans, anti-cancer drugs acting on mitochondria

    Czech Academy of Sciences Publication Activity Database

    Neužil, Jiří; Dong, L. F.; Rohlena, Jakub; Truksa, Jaroslav; Ralph, S. J.


    Roč. 13, č. 3 (2013), s. 199-208 ISSN 1567-7249 Institutional research plan: CEZ:AV0Z50520701 Keywords : Mitocans * Anti-cancer therapeutics * Classification Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.524, year: 2013

  13. Systema naturae or the outline of living world classification


    Shipunov, Alexey


    Here we present the short outline of the classification of living things (to the level of classes), given with two main goals: to provide a compact, synthetic overview of the biological diversity; and to supply users with up-todate information of latest taxonomic achievements. The latter is especially important in the recent epoch of molecular revolution in the taxonomy.

  14. Deep learning for tumor classification in imaging mass spectrometry. (United States)

    Behrmann, Jens; Etmann, Christian; Boskamp, Tobias; Casadonte, Rita; Kriegsmann, Jörg; Maaß, Peter


    Tumor classification using imaging mass spectrometry (IMS) data has a high potential for future applications in pathology. Due to the complexity and size of the data, automated feature extraction and classification steps are required to fully process the data. Since mass spectra exhibit certain structural similarities to image data, deep learning may offer a promising strategy for classification of IMS data as it has been successfully applied to image classification. Methodologically, we propose an adapted architecture based on deep convolutional networks to handle the characteristics of mass spectrometry data, as well as a strategy to interpret the learned model in the spectral domain based on a sensitivity analysis. The proposed methods are evaluated on two algorithmically challenging tumor classification tasks and compared to a baseline approach. Competitiveness of the proposed methods is shown on both tasks by studying the performance via cross-validation. Moreover, the learned models are analyzed by the proposed sensitivity analysis revealing biologically plausible effects as well as confounding factors of the considered tasks. Thus, this study may serve as a starting point for further development of deep learning approaches in IMS classification tasks. or Supplementary data are available at Bioinformatics online.

  15. Maximum mutual information regularized classification

    KAUST Repository

    Wang, Jim Jing-Yan


    In this paper, a novel pattern classification approach is proposed by regularizing the classifier learning to maximize mutual information between the classification response and the true class label. We argue that, with the learned classifier, the uncertainty of the true class label of a data sample should be reduced by knowing its classification response as much as possible. The reduced uncertainty is measured by the mutual information between the classification response and the true class label. To this end, when learning a linear classifier, we propose to maximize the mutual information between classification responses and true class labels of training samples, besides minimizing the classification error and reducing the classifier complexity. An objective function is constructed by modeling mutual information with entropy estimation, and it is optimized by a gradient descend method in an iterative algorithm. Experiments on two real world pattern classification problems show the significant improvements achieved by maximum mutual information regularization.

  16. Information theory applications for biological sequence analysis. (United States)

    Vinga, Susana


    Information theory (IT) addresses the analysis of communication systems and has been widely applied in molecular biology. In particular, alignment-free sequence analysis and comparison greatly benefited from concepts derived from IT, such as entropy and mutual information. This review covers several aspects of IT applications, ranging from genome global analysis and comparison, including block-entropy estimation and resolution-free metrics based on iterative maps, to local analysis, comprising the classification of motifs, prediction of transcription factor binding sites and sequence characterization based on linguistic complexity and entropic profiles. IT has also been applied to high-level correlations that combine DNA, RNA or protein features with sequence-independent properties, such as gene mapping and phenotype analysis, and has also provided models based on communication systems theory to describe information transmission channels at the cell level and also during evolutionary processes. While not exhaustive, this review attempts to categorize existing methods and to indicate their relation with broader transversal topics such as genomic signatures, data compression and complexity, time series analysis and phylogenetic classification, providing a resource for future developments in this promising area.

  17. The role of classification of chronic low back pain. (United States)

    Fairbank, Jeremy; Gwilym, Stephen E; France, John C; Daffner, Scott D; Dettori, Joseph; Hermsmeyer, Jeff; Andersson, Gunnar


    Systematic review. To describe the various ways chronic low back pain (CLBP) is classified, to determine if the classification systems are reliable and to assess whether classification-specific interventions have been shown to be effective in treating CLBP. A classification system by which individual patients with CLBP could be identified and directed to an effective treatment protocol would be beneficial. Those systems that direct treatment have the greatest potential influence on patient outcomes. A systematic search was conducted in MEDLINE and the Cochrane Collaboration Library for English language literature published through January 2011. We included articles that specifically described a clinical classification system for CLBP, reported on the reliability of a classification system, or evaluated the effectiveness of classification-specific interventions. A total of 60 articles were initially reviewed. We identified 28 classification systems that met inclusion criteria: 16 diagnostic systems, 7 prognostic systems, and 5 treatment-based systems. In addition, we found 10 randomized controlled trials of CLBP treatment from which we compared inclusion and exclusion criteria. Treatment-based systems were all directed at nonoperative management. Four of the 5 treatment-based systems underwent reliability testing and were found to have interobserver agreement of 70% to 100%. Reliability increased with training and familiarity with a given classification. As the number of subgroups within a classification increased, interobserver agreement decreased. Function and pain were similar between patients treated with the McKenzie classification system and those treated with dynamic strengthening training after 8 months of follow-up in one randomized controlled trial. One prospective cohort study reported better pain and function using the Canadian Back Institute Classification system than with standard rehabilitation. An analysis of the admission criteria to recent

  18. Preliminary classification criteria for the cryoglobulinaemic vasculitis (United States)

    De Vita, S; Soldano, F; Isola, M; Monti, G; Gabrielli, A; Tzioufas, A; Ferri, C; Ferraccioli, G F; Quartuccio, L; Corazza, L; De Marchi, G; Casals, M Ramos; Voulgarelis, M; Lenzi, M; Saccardo, F; Fraticelli, P; Mascia, M T; Sansonno, D; Cacoub, P; Tomsic, M; Tavoni, A; Pietrogrande, M; Zignego, A L; Scarpato, S; Mazzaro, C; Pioltelli, P; Steinfeld, S; Lamprecht, P; Bombardieri, S; Galli, M


    Background To develop preliminary classification criteria for the cryoglobulinaemic syndrome or cryoglobulinaemic vasculitis (CV). Methods Study part I developed a questionnaire for CV to be included in the formal, second part (study part II). Positivity of serum cryoglobulins was defined by experts as an essential condition for CV classification. In study part II, a core set of classification items (questionnaire, clinical and laboratory items, as agreed) was tested in three groups of patients and controls—that is, group A (new patients with the CV), group B (controls with serum cryoglobulins but lacking CV) and group C (controls without serum cryoglobulins but with features which can be observed in CV). Results In study part I (188 cases, 284 controls), a positive response to at least two of three selected questions showed a sensitivity of 81.9% and a specificity of 83.5% for CV. This questionnaire was employed and validated in study part II, which included 272 patients in group A and 228 controls in group B. The final classification criteria for CV, by pooling data from group A and group B, required the positivity of questionnaire plus clinical, questionnaire plus laboratory, or clinical plus laboratory items, or all the three, providing a sensitivity of 88.5% and a specificity of 93.6% for CV. By comparing data in group A versus group C (425 controls), the same classification criteria showed a sensitivity 88.5% and a specificity 97.0% for CV. Conclusion Classification criteria for CV were developed, and now need validation. PMID:21571735

  19. Risk factors and classifications of hilar cholangiocarcinoma. (United States)

    Suarez-Munoz, Miguel Angel; Fernandez-Aguilar, Jose Luis; Sanchez-Perez, Belinda; Perez-Daga, Jose Antonio; Garcia-Albiach, Beatriz; Pulido-Roa, Ysabel; Marin-Camero, Naiara; Santoyo-Santoyo, Julio


    Cholangiocarcinoma is the second most common primary malignant tumor of the liver. Perihilar cholangiocarcinoma or Klatskin tumor represents more than 50% of all biliary tract cholangiocarcinomas. A wide range of risk factors have been identified among patients with Perihilar cholangiocarcinoma including advanced age, male gender, primary sclerosing cholangitis, choledochal cysts, cholelithiasis, cholecystitis, parasitic infection (Opisthorchis viverrini and Clonorchis sinensis), inflammatory bowel disease, alcoholic cirrhosis, nonalcoholic cirrhosis, chronic pancreatitis and metabolic syndrome. Various classifications have been used to describe the pathologic and radiologic appearance of cholangiocarcinoma. The three systems most commonly used to evaluate Perihilar cholangiocarcinoma are the Bismuth-Corlette (BC) system, the Memorial Sloan-Kettering Cancer Center and the TNM classification. The BC classification provides preoperative assessment of local spread. The Memorial Sloan-Kettering cancer center proposes a staging system according to three factors related to local tumor extent: the location and extent of bile duct involvement, the presence or absence of portal venous invasion, and the presence or absence of hepatic lobar atrophy. The TNM classification, besides the usual descriptors, tumor, node and metastases, provides additional information concerning the possibility for the residual tumor (R) and the histological grade (G). Recently, in 2011, a new consensus classification for the Perihilar cholangiocarcinoma had been published. The consensus was organised by the European Hepato-Pancreato-Biliary Association which identified the need for a new staging system for this type of tumors. The classification includes information concerning biliary or vascular (portal or arterial) involvement, lymph node status or metastases, but also other essential aspects related to the surgical risk, such as remnant hepatic volume or the possibility of underlying disease.

  20. Cameroon Journal of Experimental Biology: Submissions

    African Journals Online (AJOL)

    Author Guidelines. Instructions to Authors The Cameroon Journal of Experimental Biology (Cameroon J. Exp. Biol.) welcomes contributions in all fields of experimental biology including biochemistry, physiology, pharmacology, toxicology, pathology, environmental biology, microbiology, parasitology, phytochemistry, food ...

  1. Building the United States National Vegetation Classification (United States)

    Franklin, S.B.; Faber-Langendoen, D.; Jennings, M.; Keeler-Wolf, T.; Loucks, O.; Peet, R.; Roberts, D.; McKerrow, A.


    The Federal Geographic Data Committee (FGDC) Vegetation Subcommittee, the Ecological Society of America Panel on Vegetation Classification, and NatureServe have worked together to develop the United States National Vegetation Classification (USNVC). The current standard was accepted in 2008 and fosters consistency across Federal agencies and non-federal partners for the description of each vegetation concept and its hierarchical classification. The USNVC is structured as a dynamic standard, where changes to types at any level may be proposed at any time as new information comes in. But, because much information already exists from previous work, the NVC partners first established methods for screening existing types to determine their acceptability with respect to the 2008 standard. Current efforts include a screening process to assign confidence to Association and Group level descriptions, and a review of the upper three levels of the classification. For the upper levels especially, the expectation is that the review process includes international scientists. Immediate future efforts include the review of remaining levels and the development of a proposal review process.

  2. 14 CFR 1203.412 - Classification guides. (United States)


    ... 14 Aeronautics and Space 5 2010-01-01 2010-01-01 false Classification guides. 1203.412 Section... PROGRAM Guides for Original Classification § 1203.412 Classification guides. (a) General. A classification guide, based upon classification determinations made by appropriate program and classification...

  3. Agricultural Land Use classification from Envisat MERIS (United States)

    Brodsky, L.; Kodesova, R.


    This study focuses on evaluation of a crop classification from middle-resolution images (Envisat MERIS) at national level. The main goal of such Land Use product is to provid spatial data for optimisation of monitoring of surface and groundwater pollution in the Czech Republic caused by pesticides use in agriculture. As there is a lack of spatial data on the pesticide use and their distribution, the localisation can be done according to the crop cover on arable land derived from the remote sensing images. Often high resolution data are used for agricultural Land Use classification but only at regional or local level. Envisat MERIS data, due to the wide satellite swath, can be used also at national level. The high temporal and also spectral resolution of MERIS data has indisputable advantage for crop classification. Methodology of a pixel-based MERIS classification applying an artificial neural-network (ANN) technique was proposed and performed at a national level, the Czech Republic. Five crop groups were finally selected - winter crops, spring crops, summer crops and other crops to be classified. Classification models included a linear, radial basis function (RBF) and a multi-layer percepton (MLP) ANN with 50 networks tested in training. The training data set consisted of about 200 samples per class, on which bootstrap resampling was applied. Selection of a subset of independent variables (Meris spectral channels) was used in the procedure. The best selected ANN model (MLP: 3 in, 13 hidden, 3 out) resulted in very good performance (correct classification rate 0.974, error 0.103) applying three crop types data set. In the next step data set with five crop types was evaluated. The ANN model (MLP: 5 in, 12 hidden, 5 out) performance was also very good (correct classification rate 0.930, error 0.370). The study showed, that while accuracy of about 80 % was achieved at pixel level when classifying only three crops, accuracy of about 70 % was achieved for five crop

  4. Using the biological literature a practical guide

    CERN Document Server

    Schmidt, Diane


    IntroductionSearching the Biological LiteratureGeneral SourcesAssociationsBibliographiesClassification, Nomenclature, and SystematicsDictionaries and EncyclopediasDirectoriesField GuidesSeriesFull-Text SourcesGeneral WorksGuides for young ScientistsGuides to the LiteratureHandbooksHistoriesMathematics and StatisticsMethods and TechniquesTextbooks and TreatisesWriting GuidesPeriodicalsReviews of the LiteratureAbstracts and IndexesBiochemistry and BiophysicsMolecular and Cellular BiologyGenetics, Biotechnology, and Developmental BiologyMicrobiology and ImmunologyEcology, Evolution, and Animal BehaviorPlant BiologyAnatomy and PhysiologyEntomologyZoologyIndex.

  5. Learning Biology with Plant Pathology. (United States)

    Carroll, Juliet E.

    This monograph contains 10 plant pathology experiments that were written to correspond to portions of a biology curriculum. Each experiment is suitable to a biology topic and designed to encourage exploration of those biological concepts being taught. Experiments include: (1) The Symptoms and Signs of Disease; (2) Koch's Postulates; (3)…

  6. Cameroon Journal of Experimental Biology

    African Journals Online (AJOL)

    The Cameroon Journal of Experimental Biology is the official journal of the Cameroon Forum for Biological Sciences (CAFOBIOS). It is an interdisciplinary journal for the publication of original research papers, short communications and review articles in all fields of experimental biology including biochemistry, physiology, ...

  7. Biological Pathways (United States)

    Skip to main content Biological Pathways Fact Sheet Enter Search Term(s): Español Research Funding An Overview Bioinformatics Current Grants Education and Training Funding Extramural Research News Features ...

  8. Classification and identification of rhodococci. (United States)

    Goodfellow, M; Thomas, E G; Ward, A C; James, A L


    Ninety-nine representative strains of Rhodococcus were compared through 129 unit characters and the data examined using the simple matching, Jaccard and pattern coefficients. Clustering was achieved using the unweighted pair group method with arithmetic averages algorithm. The numerical classification was not affected by the statistics used or by test error, estimated at 1.95%. Sixteen multimembered and 23 single member clusters were defined by the simple matching coefficient at or above the 89% similarity level. The numerical phenetic data support the taxonomic integrity of all 13 validly described species of Rhodococcus, including Rhodococcus aichiensis. Rapid enzymic tests based upon fluorophores 7-amino-4-methylcoumarin and 4-methylumbelliferone provide valuable data for rhodococcal systematics.

  9. Megaureter: classification, pathophysiology, and management. (United States)

    Simoni, F; Vino, L; Pizzini, C; Benini, D; Fanos, V


    The term megaureter does not define a specific pathological condition, because it can be due to different underlying abnormalities. The most used classification includes three groups: refluxing megaureter, associated with vesicoureteral reflux (VUR); obstructive megaureter, associated with urine flow impairment at the vesicoureteral junction; non-refluxing non-obstructive megaureter, if neither obstruction nor reflux can be identified. Each group can be divided into two subgroups: primary megaureter; secondary megaureter. With the advent of antenatal ultrasound an increased number of cases are identified prior to the onset of symptoms. The common used investigation are: urinary tract ultrasound, voiding cystourethrography, urography, serial diuretic renography and pressure-perfusion studies (Whitaker test). The advent of prenatal and neonatal echography has modified the natural history of megaureter. Nowadays non operative management is preferred. Operative intervention is indicated only in these cases: significant impairment to urine flow; worsening renal function during the observation time; recurrent UTI in spite of adequate antibiotic prophylaxis.

  10. Physics and biology

    International Nuclear Information System (INIS)

    Frauenfelder, H.


    The author points out that the coupling between physics and biology is becoming closer as time goes on. He tries to show that physical studies on biological systems not only yield insight into biology but also provide results of interest to physics. Biological systems are extremly complex system. Ideally one would like to understand the behavior of such systems in terms of the behavior of its constituent atoms. Since in small organisms this may be 10 20 atoms, it is clear these are not simple many-body systems. He reviews the basic elements of cells and then considers the broader questions of structure, complexity, and function, which must be looked at on levels from the cell to the organism. Despite the vast amount of observational material already in existence, biophysics and biological physics are only at a beginning. We can expect that physics will continue to interact strongly with biology. Actually, the connection also includes chemistry and mathematics. New tools that become available in physics will continue to be applied to biological problems. We can expect that the flow of information will not be one way; biological systems will provide new information on many old and new parts of physics, from reaction theory and transport phenomena to complexity, cooperativity, and nonlinear processes

  11. Classification in Medical Imaging

    DEFF Research Database (Denmark)

    Chen, Chen

    Classification is extensively used in the context of medical image analysis for the purpose of diagnosis or prognosis. In order to classify image content correctly, one needs to extract efficient features with discriminative properties and build classifiers based on these features. In addition...... to segment breast tissue and pectoral muscle area from the background in mammogram. The second focus is the choices of metric and its influence to the feasibility of a classifier, especially on k-nearest neighbors (k-NN) algorithm, with medical applications on breast cancer prediction and calcification...

  12. Dynamic Latent Classification Model

    DEFF Research Database (Denmark)

    Zhong, Shengtong; Martínez, Ana M.; Nielsen, Thomas Dyhre

    Monitoring a complex process often involves keeping an eye on hundreds or thousands of sensors to determine whether or not the process is under control. We have been working with dynamic data from an oil production facility in the North sea, where unstable situations should be identified as soon...... as possible. Motivated by this problem setting, we propose a generative model for dynamic classification in continuous domains. At each time point the model can be seen as combining a naive Bayes model with a mixture of factor analyzers (FA). The latent variables of the FA are used to capture the dynamics...... in the process as well as modeling dependences between attributes....

  13. Constructing criticality by classification

    DEFF Research Database (Denmark)

    Machacek, Erika


    " in the bureaucratic practice of classification: Experts construct material criticality in assessments as they allot information on the materials to the parameters of the assessment framework. In so doing, they ascribe a new set of connotations to the materials, namely supply risk, and their importance to clean energy......This paper explores the role of expertise, the nature of criticality, and their relationship to securitisation as mineral raw materials are classified. It works with the construction of risk along the liberal logic of security to explore how "key materials" are turned into "critical materials...

  14. Gene expression classification of colon cancer into molecular subtypes: characterization, validation, and prognostic value.

    Directory of Open Access Journals (Sweden)

    Laetitia Marisa

    Full Text Available Colon cancer (CC pathological staging fails to accurately predict recurrence, and to date, no gene expression signature has proven reliable for prognosis stratification in clinical practice, perhaps because CC is a heterogeneous disease. The aim of this study was to establish a comprehensive molecular classification of CC based on mRNA expression profile analyses.Fresh-frozen primary tumor samples from a large multicenter cohort of 750 patients with stage I to IV CC who underwent surgery between 1987 and 2007 in seven centers were characterized for common DNA alterations, including BRAF, KRAS, and TP53 mutations, CpG island methylator phenotype, mismatch repair status, and chromosomal instability status, and were screened with whole genome and transcriptome arrays. 566 samples fulfilled RNA quality requirements. Unsupervised consensus hierarchical clustering applied to gene expression data from a discovery subset of 443 CC samples identified six molecular subtypes. These subtypes were associated with distinct clinicopathological characteristics, molecular alterations, specific enrichments of supervised gene expression signatures (stem cell phenotype-like, normal-like, serrated CC phenotype-like, and deregulated signaling pathways. Based on their main biological characteristics, we distinguished a deficient mismatch repair subtype, a KRAS mutant subtype, a cancer stem cell subtype, and three chromosomal instability subtypes, including one associated with down-regulated immune pathways, one with up-regulation of the Wnt pathway, and one displaying a normal-like gene expression profile. The classification was validated in the remaining 123 samples plus an independent set of 1,058 CC samples, including eight public datasets. Furthermore, prognosis was analyzed in the subset of stage II-III CC samples. The subtypes C4 and C6, but not the subtypes C1, C2, C3, and C5, were independently associated with shorter relapse-free survival, even after

  15. Regulatory Biology: Depressed Metabolic States (United States)

    Holton, E. M. (Editor)


    Exobiological aspects of depressed metabolism and thermoregulation are discussed for subsequent development of biological space flight experiments. Included is a brief description of differential hypothermia in cancer chemotherapy.

  16. Constructions and classifications of projective Poisson varieties (United States)

    Pym, Brent


    This paper is intended both as an introduction to the algebraic geometry of holomorphic Poisson brackets, and as a survey of results on the classification of projective Poisson manifolds that have been obtained in the past 20 years. It is based on the lecture series delivered by the author at the Poisson 2016 Summer School in Geneva. The paper begins with a detailed treatment of Poisson surfaces, including adjunction, ruled surfaces and blowups, and leading to a statement of the full birational classification. We then describe several constructions of Poisson threefolds, outlining the classification in the regular case, and the case of rank-one Fano threefolds (such as projective space). Following a brief introduction to the notion of Poisson subspaces, we discuss Bondal's conjecture on the dimensions of degeneracy loci on Poisson Fano manifolds. We close with a discussion of log symplectic manifolds with simple normal crossings degeneracy divisor, including a new proof of the classification in the case of rank-one Fano manifolds.

  17. A Unique Model Platform for C4 Plant Systems and Synthetic Biology (United States)


    mediated transformation of Setaria viridis. Agrobacterium tumefaciens strain GV3101 was transformed by electroporation with pBI 121. Agrobacterium ... agrobacterium mediated transformation 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT Same as Report (SAR) 18. NUMBER OF...successful agrobacterium mediated transformation 15. SUBJECT TERMS synthetic biology, Systems Biology 16. SECURITY CLASSIFICATION OF

  18. Human papillomavirus molecular biology. (United States)

    Harden, Mallory E; Munger, Karl

    Human papillomaviruses are small DNA viruses with a tropism for squamous epithelia. A unique aspect of human papillomavirus molecular biology involves dependence on the differentiation status of the host epithelial cell to complete the viral lifecycle. A small group of these viruses are the etiologic agents of several types of human cancers, including oral and anogenital tract carcinomas. This review focuses on the basic molecular biology of human papillomaviruses. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Revue bibliographique: les méthodes chimiques d'identification et de classification des champignons

    Directory of Open Access Journals (Sweden)

    Verscheure M.


    Full Text Available Chemotaxonomy of fungi : a review. For few years, advancements of molecular methods and analytical techniques enabled scientists to realise a classification of microorganisms based on biochemical characteristics. This classification, called chemotaxonomy, includes molecular methods and chemical methods which provide additional data and lead to a better identification and/or classification.

  20. Pattern classification for incomplete data


    Gabrys, Bogdan


    The problem of pattern classification for inputs with missing values is considered. A general fuzzy min-max (GFMM) neural network utilising hyperbox fuzzy sets as a representation of data cluster prototypes is used. It is shown how a classification decisions can be carried out on a subspace of high dimensional input data. No substitution scheme for missing values is utilised. The result is a classification procedure that reduces a number of viable class alternatives on the basis of available ...

  1. Unsupervised Classification Using Immune Algorithm


    Al-Muallim, M. T.; El-Kouatly, R.


    Unsupervised classification algorithm based on clonal selection principle named Unsupervised Clonal Selection Classification (UCSC) is proposed in this paper. The new proposed algorithm is data driven and self-adaptive, it adjusts its parameters to the data to make the classification operation as fast as possible. The performance of UCSC is evaluated by comparing it with the well known K-means algorithm using several artificial and real-life data sets. The experiments show that the proposed U...

  2. Search techniques in intelligent classification systems

    CERN Document Server

    Savchenko, Andrey V


    A unified methodology for categorizing various complex objects is presented in this book. Through probability theory, novel asymptotically minimax criteria suitable for practical applications in imaging and data analysis are examined including the special cases such as the Jensen-Shannon divergence and the probabilistic neural network. An optimal approximate nearest neighbor search algorithm, which allows faster classification of databases is featured. Rough set theory, sequential analysis and granular computing are used to improve performance of the hierarchical classifiers. Practical examples in face identification (including deep neural networks), isolated commands recognition in voice control system and classification of visemes captured by the Kinect depth camera are included. This approach creates fast and accurate search procedures by using exact probability densities of applied dissimilarity measures. This book can be used as a guide for independent study and as supplementary material for a technicall...

  3. Classification of Chronic Pain at a Multidisciplinary Pain Rehabilitation Clinic

    Directory of Open Access Journals (Sweden)

    Jan Lidbeck


    Full Text Available OBJECTIVE: To make a detailed diagnostic analysis of patients with chronic pain syndromes, including classification according to the International Association for the Study of Pain (IASP.

  4. Maps of Geocryological Regions and Classifications in China, Version 1 (United States)

    National Aeronautics and Space Administration — This data set includes digital versions of 'The Map of Geocryological Regionalization and Classification in China' from Geocryology in China by Y. Zhou, D. Guo, G....

  5. Mining vehicle classifications from the Columbus Metropolitan Freeway Management System. (United States)


    Vehicle classification data are used in many transportation applications, including: pavement design, : environmental impact studies, traffic control, and traffic safety. Ohio has over 200 permanent count stations, : supplemented by many more short-t...

  6. The Theoretical Construction of a Classification of Clinical Somatic Symptoms in Psychosomatic Medicine Theory. (United States)

    Zeng, Fanmin; Sun, Xueli; Yang, Bangxiang; Shen, Hong; Liu, Ling


    This article adopts the perspective of psychosomatic medicine to present and test a theoretical model of the classification of clinical somatic symptoms. The theoretical model consists of four dimensions: emotional somatic symptoms, biological somatic symptoms, imaginative somatic symptoms, and cognitive somatic symptoms. A clinical somatic symptom classification scale was developed according to the theoretical model. A total of 542 participants completed the clinical somatic symptoms classification scale. The data were analyzed using exploratory and confirmatory factor analyses. The results confirmed the theoretical model. The analyses found that the proposed theoretical structure of the scale was good, as indicated by factor loadings and fit indices, and that the scale had good reliability and construct validity. Based on the interpretation of the clinical symptoms of psychosomatic medicine, the treatment of chronic non-infectious diseases includes at least three dimensions: the first is the etiological treatment, the second is the pathophysiological and pathopsychological dimension, and the third is symptomatic treatment. The unified psychosomatic point of view and diverse clinical thinking modes are aimed at identifying different classes of somatic symptoms and important prerequisites for the treatment of these symptoms. We registered the study with the Chinese Clinical Trial Registry and it was approved by the West China Hospital, Sichuan University ethics committee. The registration number is ChiCTR-OCS-14004632 (time: 2014-05-12).

  7. Automated compound classification using a chemical ontology

    Directory of Open Access Journals (Sweden)

    Bobach Claudia


    Full Text Available Abstract Background Classification of chemical compounds into compound classes by using structure derived descriptors is a well-established method to aid the evaluation and abstraction of compound properties in chemical compound databases. MeSH and recently ChEBI are examples of chemical ontologies that provide a hierarchical classification of compounds into general compound classes of biological interest based on their structural as well as property or use features. In these ontologies, compounds have been assigned manually to their respective classes. However, with the ever increasing possibilities to extract new compounds from text documents using name-to-structure tools and considering the large number of compounds deposited in databases, automated and comprehensive chemical classification methods are needed to avoid the error prone and time consuming manual classification of compounds. Results In the present work we implement principles and methods to construct a chemical ontology of classes that shall support the automated, high-quality compound classification in chemical databases or text documents. While SMARTS expressions have already been used to define chemical structure class concepts, in the present work we have extended the expressive power of such class definitions by expanding their structure-based reasoning logic. Thus, to achieve the required precision and granularity of chemical class definitions, sets of SMARTS class definitions are connected by OR and NOT logical operators. In addition, AND logic has been implemented to allow the concomitant use of flexible atom lists and stereochemistry definitions. The resulting chemical ontology is a multi-hierarchical taxonomy of concept nodes connected by directed, transitive relationships. Conclusions A proposal for a rule based definition of chemical classes has been made that allows to define chemical compound classes more precisely than before. The proposed structure-based reasoning

  8. Automated compound classification using a chemical ontology. (United States)

    Bobach, Claudia; Böhme, Timo; Laube, Ulf; Püschel, Anett; Weber, Lutz


    Classification of chemical compounds into compound classes by using structure derived descriptors is a well-established method to aid the evaluation and abstraction of compound properties in chemical compound databases. MeSH and recently ChEBI are examples of chemical ontologies that provide a hierarchical classification of compounds into general compound classes of biological interest based on their structural as well as property or use features. In these ontologies, compounds have been assigned manually to their respective classes. However, with the ever increasing possibilities to extract new compounds from text documents using name-to-structure tools and considering the large number of compounds deposited in databases, automated and comprehensive chemical classification methods are needed to avoid the error prone and time consuming manual classification of compounds. In the present work we implement principles and methods to construct a chemical ontology of classes that shall support the automated, high-quality compound classification in chemical databases or text documents. While SMARTS expressions have already been used to define chemical structure class concepts, in the present work we have extended the expressive power of such class definitions by expanding their structure-based reasoning logic. Thus, to achieve the required precision and granularity of chemical class definitions, sets of SMARTS class definitions are connected by OR and NOT logical operators. In addition, AND logic has been implemented to allow the concomitant use of flexible atom lists and stereochemistry definitions. The resulting chemical ontology is a multi-hierarchical taxonomy of concept nodes connected by directed, transitive relationships. A proposal for a rule based definition of chemical classes has been made that allows to define chemical compound classes more precisely than before. The proposed structure-based reasoning logic allows to translate chemistry expert knowledge into a


    Directory of Open Access Journals (Sweden)

    R. Müller


    Full Text Available In this paper a new classification technique for hyperspectral data based on synergetics theory is presented. Synergetics – originally introduced by the physicist H. Haken – is an interdisciplinary theory to find general rules for pattern formation through selforganization and has been successfully applied in fields ranging from biology to ecology, chemistry, cosmology, and thermodynamics up to sociology. Although this theory describes general rules for pattern formation it was linked also to pattern recognition. Pattern recognition algorithms based on synergetics theory have been applied to images in the spatial domain with limited success in the past, given their dependence on the rotation, shifting, and scaling of the images. These drawbacks can be discarded if such methods are applied to data acquired by a hyperspectral sensor in the spectral domain, as each single spectrum, related to an image element in the hyperspectral scene, can be analysed independently. The classification scheme based on synergetics introduces also methods for spatial regularization to get rid of "salt and pepper" classification results and for iterative parameter tuning to optimize class weights. The paper reports an experiment on a benchmark data set frequently used for method comparisons. This data set consists of a hyperspectral scene acquired by the Airborne Visible Infrared Imaging Spectrometer AVIRIS sensor of the Jet Propulsion Laboratory acquired over the Salinas Valley in CA, USA, with 15 vegetation classes. The results are compared to state-of-the-art methodologies like Support Vector Machines (SVM, Spectral Information Divergence (SID, Neural Networks, Logistic Regression, Factor Graphs or Spectral Angle Mapper (SAM. The outcomes are promising and often outperform state-of-the-art classification methodologies.

  10. Reliability of Oronasal Fistula Classification. (United States)

    Sitzman, Thomas J; Allori, Alexander C; Matic, Damir B; Beals, Stephen P; Fisher, David M; Samson, Thomas D; Marcus, Jeffrey R; Tse, Raymond W


    Objective Oronasal fistula is an important complication of cleft palate repair that is frequently used to evaluate surgical quality, yet reliability of fistula classification has never been examined. The objective of this study was to determine the reliability of oronasal fistula classification both within individual surgeons and between multiple surgeons. Design Using intraoral photographs of children with repaired cleft palate, surgeons rated the location of palatal fistulae using the Pittsburgh Fistula Classification System. Intrarater and interrater reliability scores were calculated for each region of the palate. Participants Eight cleft surgeons rated photographs obtained from 29 children. Results Within individual surgeons reliability for each region of the Pittsburgh classification ranged from moderate to almost perfect (κ = .60-.96). By contrast, reliability between surgeons was lower, ranging from fair to substantial (κ = .23-.70). Between-surgeon reliability was lowest for the junction of the soft and hard palates (κ = .23). Within-surgeon and between-surgeon reliability were almost perfect for the more general classification of fistula in the secondary palate (κ = .95 and κ = .83, respectively). Conclusions This is the first reliability study of fistula classification. We show that the Pittsburgh Fistula Classification System is reliable when used by an individual surgeon, but less reliable when used among multiple surgeons. Comparisons of fistula occurrence among surgeons may be subject to less bias if they use the more general classification of "presence or absence of fistula of the secondary palate" rather than the Pittsburgh Fistula Classification System.

  11. Safety classification of nuclear power plant systems, structures and components

    International Nuclear Information System (INIS)


    The Safety Classification principles used for the systems, structures and components of a nuclear power plant are detailed in the guide. For classification, the nuclear power plant is divided into structural and operational units called systems. Every structure and component under control is included into some system. The Safety Classes are 1, 2 and 3 and the Class EYT (non-nuclear). Instructions how to assign each system, structure and component to an appropriate safety class are given in the guide. The guide applies to new nuclear power plants and to the safety classification of systems, structures and components designed for the refitting of old nuclear power plants. The classification principles and procedures applying to the classification document are also given

  12. Asynchronous data-driven classification of weapon systems

    International Nuclear Information System (INIS)

    Jin, Xin; Mukherjee, Kushal; Gupta, Shalabh; Ray, Asok; Phoha, Shashi; Damarla, Thyagaraju


    This communication addresses real-time weapon classification by analysis of asynchronous acoustic data, collected from microphones on a sensor network. The weapon classification algorithm consists of two parts: (i) feature extraction from time-series data using symbolic dynamic filtering (SDF), and (ii) pattern classification based on the extracted features using the language measure (LM) and support vector machine (SVM). The proposed algorithm has been tested on field data, generated by firing of two types of rifles. The results of analysis demonstrate high accuracy and fast execution of the pattern classification algorithm with low memory requirements. Potential applications include simultaneous shooter localization and weapon classification with soldier-wearable networked sensors. (rapid communication)

  13. a Curvature Based Adaptive Neighborhood for Individual Point Cloud Classification (United States)

    He, E.; Chen, Q.; Wang, H.; Liu, X.


    As a key step in 3D scene analysis, point cloud classification has gained a great deal of concerns in the past few years. Due to the uneven density, noise and data missing in point cloud, how to automatically classify the point cloud with a high precision is a very challenging task. The point cloud classification process typically includes the extraction of neighborhood based statistical information and machine learning algorithms. However, the robustness of neighborhood is limited to the density and curvature of the point cloud which lead to a label noise behavior in classification results. In this paper, we proposed a curvature based adaptive neighborhood for individual point cloud classification. Our main improvement is the curvature based adaptive neighborhood method, which could derive ideal 3D point local neighborhood and enhance the separability of features. The experiment result on Oakland benchmark dataset shows that the proposed method can effectively improve the classification accuracy of point cloud.

  14. Methods for data classification (United States)

    Garrity, George [Okemos, MI; Lilburn, Timothy G [Front Royal, VA


    The present invention provides methods for classifying data and uncovering and correcting annotation errors. In particular, the present invention provides a self-organizing, self-correcting algorithm for use in classifying data. Additionally, the present invention provides a method for classifying biological taxa.

  15. Biological preconcentrator (United States)

    Manginell, Ronald P [Albuquerque, NM; Bunker, Bruce C [Albuquerque, NM; Huber, Dale L [Albuquerque, NM


    A biological preconcentrator comprises a stimulus-responsive active film on a stimulus-producing microfabricated platform. The active film can comprise a thermally switchable polymer film that can be used to selectively absorb and desorb proteins from a protein mixture. The biological microfabricated platform can comprise a thin membrane suspended on a substrate with an integral resistive heater and/or thermoelectric cooler for thermal switching of the active polymer film disposed on the membrane. The active polymer film can comprise hydrogel-like polymers, such as poly(ethylene oxide) or poly(n-isopropylacrylamide), that are tethered to the membrane. The biological preconcentrator can be fabricated with semiconductor materials and technologies.

  16. a structural biology perspective TANWEER HUSSAIN

    Indian Academy of Sciences (India)



    Jul 1, 2017 ... Structural biology of Molecular machines. Determine the three-dimensional structure of the macromolecular complexes. X-ray crystallography. Crystals. X-ray diffraction. Electron density. Model. Cryo-electron microscopy (cryo-EM). Image. Particle picking. 2D class averages. 3D classification. 3D autorefine ...

  17. Simple Calculation Programs for Biology Other Methods

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. Simple Calculation Programs for Biology Other Methods. Hemolytic potency of drugs. Raghava et al., (1994) Biotechniques 17: 1148. FPMAP: methods for classification and identification of microorganisms 16SrRNA. graphical display of restriction and fragment map of ...

  18. Multispectral Image classification using the theories of neural networks

    International Nuclear Information System (INIS)

    Ardisasmita, M.S.; Subki, M.I.R.


    Image classification is the one of the important part of digital image analysis. the objective of image classification is to identify and regroup the features occurring in an image into one or several classes in terms of the object. basic to the understanding of multispectral classification is the concept of the spectral response of an object as a function of the electromagnetic radiation and the wavelength of the spectrum. new approaches to classification has been developed to improve the result of analysis, these state-of-the-art classifiers are based upon the theories of neural networks. Neural network classifiers are algorithmes which mimic the computational abilities of the human brain. Artificial neurons are simple emulation's of biological neurons; they take in information from sensors or other artificial neurons, perform very simple operations on this data, and pass the result to other recognize the spectral signature of each image pixel. Neural network image classification has been divided into supervised and unsupervised training procedures. In the supervised approach, examples of each cover type can be located and the computer can compute spectral signatures to categorize all pixels in a digital image into several land cover classes. In supervised classification, spectral signatures are generated by mathematically grouping and it does not require analyst-specified training data. Thus, in the supervised approach we define useful information categories and then examine their spectral reparability; in the unsupervised approach the computer determines spectrally sapable classes and then we define thei information value

  19. Probing spermiogenesis: a digital strategy for mouse acrosome classification. (United States)

    Taloni, Alessandro; Font-Clos, Francesc; Guidetti, Luca; Milan, Simone; Ascagni, Miriam; Vasco, Chiara; Pasini, Maria Enrica; Gioria, Maria Rosa; Ciusani, Emilio; Zapperi, Stefano; La Porta, Caterina A M


    Classification of morphological features in biological samples is usually performed by a trained eye but the increasing amount of available digital images calls for semi-automatic classification techniques. Here we explore this possibility in the context of acrosome morphological analysis during spermiogenesis. Our method combines feature extraction from three dimensional reconstruction of confocal images with principal component analysis and machine learning. The method could be particularly useful in cases where the amount of data does not allow for a direct inspection by trained eye.

  20. HEp-2 Cell Image Classification With Deep Convolutional Neural Networks. (United States)

    Gao, Zhimin; Wang, Lei; Zhou, Luping; Zhang, Jianjia


    Efficient Human Epithelial-2 cell image classification can facilitate the diagnosis of many autoimmune diseases. This paper proposes an automatic framework for this classification task, by utilizing the deep convolutional neural networks (CNNs) which have recently attracted intensive attention in visual recognition. In addition to describing the proposed classification framework, this paper elaborates several interesting observations and findings obtained by our investigation. They include the important factors that impact network design and training, the role of rotation-based data augmentation for cell images, the effectiveness of cell image masks for classification, and the adaptability of the CNN-based classification system across different datasets. Extensive experimental study is conducted to verify the above findings and compares the proposed framework with the well-established image classification models in the literature. The results on benchmark datasets demonstrate that 1) the proposed framework can effectively outperform existing models by properly applying data augmentation, 2) our CNN-based framework has excellent adaptability across different datasets, which is highly desirable for cell image classification under varying laboratory settings. Our system is ranked high in the cell image classification competition hosted by ICPR 2014.

  1. Classification of radioactive waste

    International Nuclear Information System (INIS)


    Radioactive wastes are generated in a number of different kinds of facilities and arise in a wide range of concentrations of radioactive materials and in a variety of physical and chemical forms. To simplify their management, a number of schemes have evolved for classifying radioactive waste according to the physical, chemical and radiological properties of significance to those facilities managing this waste. These schemes have led to a variety of terminologies, differing from country to country and even between facilities in the same country. This situation makes it difficult for those concerned to communicate with one another regarding waste management practices. This document revises and updates earlier IAEA references on radioactive waste classification systems given in IAEA Technical Reports Series and Safety Series. Guidance regarding exemption of materials from regulatory control is consistent with IAEA Safety Series and the RADWASS documents published under IAEA Safety Series. 11 refs, 2 figs, 2 tab

  2. Automatic diabetic retinopathy classification (United States)

    Bravo, María. A.; Arbeláez, Pablo A.


    Diabetic retinopathy (DR) is a disease in which the retina is damaged due to augmentation in the blood pressure of small vessels. DR is the major cause of blindness for diabetics. It has been shown that early diagnosis can play a major role in prevention of visual loss and blindness. This work proposes a computer based approach for the detection of DR in back-of-the-eye images based on the use of convolutional neural networks (CNNs). Our CNN uses deep architectures to classify Back-of-the-eye Retinal Photographs (BRP) in 5 stages of DR. Our method combines several preprocessing images of BRP to obtain an ACA score of 50.5%. Furthermore, we explore subproblems by training a larger CNN of our main classification task.

  3. A New Classification for the Varus Knee. (United States)

    Thienpont, Emmanuel; Parvizi, Javad


    A new classification for osteoarthritis of the knee associated with varus deformity is presented. This classification is derived from the combination of conventional radiographs, stress radiographs (when needed), and clinical examination. This study included the analysis of coronal alignment on full-leg standing radiographs of 526 patients awaiting knee arthroplasty for varus deformity in a single institution. Various mechanical and anatomic angles were measured, and these findings were combined with a basic clinical examination of patients. The radiographs were measured on 2 separate occasions to determine the intraobserver reliability. Cross-sectional studies such as computed tomography or magnetic resonance imaging were used to further refine observations about different wear patterns. Varus deformity can either be intra-articular or extra-articular. Intra-articular deformities can be correctable or fixed. In fixed deformities, the status of the lateral ligament is taken into account. Extra-articular deformity can be metaphyseal or diaphyseal, and the possibility for intra-articular correction will depend on the degree of deformity and its distance from the joint. This new classification allows for better definition of varus deformity, which can help surgeons during preoperative planning, particularly with their choice of implant and potentially the degree of constraint. The classification can also be a tool for further prospective studies about varus deformity. Copyright © 2016 Elsevier Inc. All rights reserved.

  4. Pulmonary nodule classification with deep residual networks. (United States)

    Nibali, Aiden; He, Zhen; Wollersheim, Dennis


    PURPOSE  : Lung cancer has the highest death rate among all cancers in the USA. In this work we focus on improving the ability of computer-aided diagnosis (CAD) systems to predict the malignancy of nodules from cropped CT images of lung nodules. We evaluate the effectiveness of very deep convolutional neural networks at the task of expert-level lung nodule malignancy classification. Using the state-of-the-art ResNet architecture as our basis, we explore the effect of curriculum learning, transfer learning, and varying network depth on the accuracy of malignancy classification. Due to a lack of public datasets with standardized problem definitions and train/test splits, studies in this area tend to not compare directly against other existing work. This makes it hard to know the relative improvement in the new solution. In contrast, we directly compare our system against two state-of-the-art deep learning systems for nodule classification on the LIDC/IDRI dataset using the same experimental setup and data set. The results show that our system achieves the highest performance in terms of all metrics measured including sensitivity, specificity, precision, AUROC, and accuracy. The proposed method of combining deep residual learning, curriculum learning, and transfer learning translates to high nodule classification accuracy. This reveals a promising new direction for effective pulmonary nodule CAD systems that mirrors the success of recent deep learning advances in other image-based application domains.

  5. Semantic Shot Classification in Sports Video (United States)

    Duan, Ling-Yu; Xu, Min; Tian, Qi


    In this paper, we present a unified framework for semantic shot classification in sports videos. Unlike previous approaches, which focus on clustering by aggregating shots with similar low-level features, the proposed scheme makes use of domain knowledge of a specific sport to perform a top-down video shot classification, including identification of video shot classes for each sport, and supervised learning and classification of the given sports video with low-level and middle-level features extracted from the sports video. It is observed that for each sport we can predefine a small number of semantic shot classes, about 5~10, which covers 90~95% of sports broadcasting video. With the supervised learning method, we can map the low-level features to middle-level semantic video shot attributes such as dominant object motion (a player), camera motion patterns, and court shape, etc. On the basis of the appropriate fusion of those middle-level shot classes, we classify video shots into the predefined video shot classes, each of which has a clear semantic meaning. The proposed method has been tested over 4 types of sports videos: tennis, basketball, volleyball and soccer. Good classification accuracy of 85~95% has been achieved. With correctly classified sports video shots, further structural and temporal analysis, such as event detection, video skimming, table of content, etc, will be greatly facilitated.

  6. Mathematical modeling of biological processes

    CERN Document Server

    Friedman, Avner


    This book on mathematical modeling of biological processes includes a wide selection of biological topics that demonstrate the power of mathematics and computational codes in setting up biological processes with a rigorous and predictive framework. Topics include: enzyme dynamics, spread of disease, harvesting bacteria, competition among live species, neuronal oscillations, transport of neurofilaments in axon, cancer and cancer therapy, and granulomas. Complete with a description of the biological background and biological question that requires the use of mathematics, this book is developed for graduate students and advanced undergraduate students with only basic knowledge of ordinary differential equations and partial differential equations; background in biology is not required. Students will gain knowledge on how to program with MATLAB without previous programming experience and how to use codes in order to test biological hypothesis.

  7. Marine Biology (United States)

    Dewees, Christopher M.; Hooper, Jon K.


    A variety of informational material for a course in marine biology or oceanology at the secondary level is presented. Among the topics discussed are: food webs and pyramids, planktonic blooms, marine life, plankton nets, food chains, phytoplankton, zooplankton, larval plankton and filter feeders. (BT)

  8. Mesoscopic biology

    Indian Academy of Sciences (India)

    Abstract. In this paper we present a qualitative outlook of mesoscopic biology where the typical length scale is of the order of nanometers and the energy scales comparable to thermal energy. Novel biomolecular machines, governed by coded information at the level of DNA and proteins, operate at these length scales in ...

  9. Scaffolded biology. (United States)

    Minelli, Alessandro


    Descriptions and interpretations of the natural world are dominated by dichotomies such as organism vs. environment, nature vs. nurture, genetic vs. epigenetic, but in the last couple of decades strong dissatisfaction with those partitions has been repeatedly voiced and a number of alternative perspectives have been suggested, from perspectives such as Dawkins' extended phenotype, Turner's extended organism, Oyama's Developmental Systems Theory and Odling-Smee's niche construction theory. Last in time is the description of biological phenomena in terms of hybrids between an organism (scaffolded system) and a living or non-living scaffold, forming unit systems to study processes such as reproduction and development. As scaffold, eventually, we can define any resource used by the biological system, especially in development and reproduction, without incorporating it as happens in the case of resources fueling metabolism. Addressing biological systems as functionally scaffolded systems may help pointing to functional relationships that can impart temporal marking to the developmental process and thus explain its irreversibility; revisiting the boundary between development and metabolism and also regeneration phenomena, by suggesting a conceptual framework within which to investigate phenomena of regular hypermorphic regeneration such as characteristic of deer antlers; fixing a periodization of development in terms of the times at which a scaffolding relationship begins or is terminated; and promoting plant galls to legitimate study objects of developmental biology.

  10. Biological digestion

    International Nuclear Information System (INIS)

    Rosevear, A.


    This paper discusses the biological degradation of non-radioactive organic material occurring in radioactive wastes. The biochemical steps are often performed using microbes or isolated enzymes in combination with chemical steps and the aim is to oxidise the carbon, hydrogen, nitrogen and sulphur to their respective oxides. (U.K.)

  11. 10 CFR 1045.17 - Classification levels. (United States)


    ... Confidential classification are the amount of high explosives used in nuclear weapons, gaseous diffusion design... Classification, jointly with the DoD, shall assign one of the classification levels in paragraph (a) of this.... The Director of Classification shall assign one of the following classification levels to RD...

  12. 49 CFR 8.17 - Classification challenges. (United States)


    ... 49 Transportation 1 2010-10-01 2010-10-01 false Classification challenges. 8.17 Section 8.17.../ACCESS Classification/Declassification of Information § 8.17 Classification challenges. (a) Authorized... classification status is improper are encouraged and expected to challenge the classification status of the...

  13. 40 CFR 152.164 - Classification procedures. (United States)


    ... PESTICIDE REGISTRATION AND CLASSIFICATION PROCEDURES Classification of Pesticides § 152.164 Classification... Agency normally will conduct classification reviews of all uses of a currently registered pesticide at... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Classification procedures. 152.164...

  14. 32 CFR 2400.15 - Classification guides. (United States)


    ... 32 National Defense 6 2010-07-01 2010-07-01 false Classification guides. 2400.15 Section 2400.15... Derivative Classification § 2400.15 Classification guides. (a) OSTP shall issue and maintain classification guides to facilitate the proper and uniform derivative classification of information. These guides shall...

  15. 32 CFR 2001.15 - Classification guides. (United States)


    ... 32 National Defense 6 2010-07-01 2010-07-01 false Classification guides. 2001.15 Section 2001.15..., NATIONAL ARCHIVES AND RECORDS ADMINISTRATION CLASSIFIED NATIONAL SECURITY INFORMATION Classification § 2001.15 Classification guides. (a) Preparation of classification guides. Originators of classification...

  16. 37 CFR 2.85 - Classification schedules. (United States)


    ... classification, where appropriate. (f) Classification schedules shall not limit or extend the applicant's rights.... (a) International classification system. Section 6.1 of this chapter sets forth the international... international classification pursuant to § 2.85(e)(3). (b) Prior United States classification system. Section 6...

  17. Possibilistic approach to target classification

    NARCIS (Netherlands)

    Huizing, A.G.; Groen, F.C.A.


    Abstract: This chapter describes an alternative to the Bayesian approach to target classification that is based on possibility theory. A possibilistic classifier minimizes the maximum cost of the classification decision taking into account the a posteriori possibilities of the target classes given

  18. Forensic Classification of Digital Information

    Directory of Open Access Journals (Sweden)

    Ivanov N. A.


    Full Text Available Several classification schemes for digital information that could be used as sources of evidence in criminal proceedings are offered. In terms of application the proposed classification is very important for the development of forensic tools, means, methods, techniques for the detection, capture, inspection, seizure, investigation of digital information, as well as for the detection and investigation of crimes

  19. Seismic texture classification. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Vinther, R.


    The seismic texture classification method, is a seismic attribute that can both recognize the general reflectivity styles and locate variations from these. The seismic texture classification performs a statistic analysis for the seismic section (or volume) aiming at describing the reflectivity. Based on a set of reference reflectivities the seismic textures are classified. The result of the seismic texture classification is a display of seismic texture categories showing both the styles of reflectivity from the reference set and interpolations and extrapolations from these. The display is interpreted as statistical variations in the seismic data. The seismic texture classification is applied to seismic sections and volumes from the Danish North Sea representing both horizontal stratifications and salt diapers. The attribute succeeded in recognizing both general structure of successions and variations from these. Also, the seismic texture classification is not only able to display variations in prospective areas (1-7 sec. TWT) but can also be applied to deep seismic sections. The seismic texture classification is tested on a deep reflection seismic section (13-18 sec. TWT) from the Baltic Sea. Applied to this section the seismic texture classification succeeded in locating the Moho, which could not be located using conventional interpretation tools. The seismic texture classification is a seismic attribute which can display general reflectivity styles and deviations from these and enhance variations not found by conventional interpretation tools. (LN)

  20. Vegetation classification and distribution mapping report Mesa Verde National Park (United States)

    Thomas, Kathryn A.; McTeague, Monica L.; Ogden, Lindsay; Floyd, M. Lisa; Schulz, Keith; Friesen, Beverly A.; Fancher, Tammy; Waltermire, Robert G.; Cully, Anne


    The classification and distribution mapping of the vegetation of Mesa Verde National Park (MEVE) and surrounding environment was achieved through a multi-agency effort between 2004 and 2007. The National Park Service’s Southern Colorado Plateau Network facilitated the team that conducted the work, which comprised the U.S. Geological Survey’s Southwest Biological Science Center, Fort Collins Research Center, and Rocky Mountain Geographic Science Center; Northern Arizona University; Prescott College; and NatureServe. The project team described 47 plant communities for MEVE, 34 of which were described from quantitative classification based on f eld-relevé data collected in 1993 and 2004. The team derived 13 additional plant communities from field observations during the photointerpretation phase of the project. The National Vegetation Classification Standard served as a framework for classifying these plant communities to the alliance and association level. Eleven of the 47 plant communities were classified as “park specials;” that is, plant communities with insufficient data to describe them as new alliances or associations. The project team also developed a spatial vegetation map database representing MEVE, with three different map-class schemas: base, group, and management map classes. The base map classes represent the fi nest level of spatial detail. Initial polygons were developed using Definiens Professional (at the time of our use, this software was called eCognition), assisted by interpretation of 1:12,000 true-color digital orthophoto quarter quadrangles (DOQQs). These polygons (base map classes) were labeled using manual photo interpretation of the DOQQs and 1:12,000 true-color aerial photography. Field visits verified interpretation concepts. The vegetation map database includes 46 base map classes, which consist of associations, alliances, and park specials classified with quantitative analysis, additional associations and park specials noted

  1. Geological-genetic classification for uranium deposits

    International Nuclear Information System (INIS)

    Terentiev, V.M.; Naumov, S.S.


    The paper describes a system for classification uranium deposits based on geological and genetic characteristics. The system is based on the interrelation and interdependence of uranium ore formation processes and other geological phenomena including sedimentation, magmatism and tectonics, as well as the evolution of geotectonic structures. Using these aspects, deposits are classified in three categories: endogenic - predominately hydrothermal and hydrothermal-metasomatic; exogenic - sedimentary diagenetic, biogenic sorption, and infiltrational; and polygenetic or composite types. The latter complex types includes: sedimentary/metamorphic and metamorphic and sedimentary/hydrothermal, where different ore generating processes have prevailed over a rock unit at different times. The 3 page classification is given in both the English and Russian languages. (author). 3 tabs

  2. BIRADS{sup TM} classification in mammography

    Energy Technology Data Exchange (ETDEWEB)

    Balleyguier, Corinne [Department of Radiology, Institut de Cancerologie Gustave-Roussy, 39 rue Camille Desmoulins, 94805 Villejuif (France)]. E-mail:; Ayadi, Salma [Department of Radiology, Institut de Cancerologie Gustave-Roussy, 39 rue Camille Desmoulins, 94805 Villejuif (France); Van Nguyen, Kim [Department of Radiology, Institut de Cancerologie Gustave-Roussy, 39 rue Camille Desmoulins, 94805 Villejuif (France); Vanel, Daniel [Department of Radiology, Institut de Cancerologie Gustave-Roussy, 39 rue Camille Desmoulins, 94805 Villejuif (France); Dromain, Clarisse [Department of Radiology, Institut de Cancerologie Gustave-Roussy, 39 rue Camille Desmoulins, 94805 Villejuif (France); Sigal, Robert [Department of Radiology, Institut de Cancerologie Gustave-Roussy, 39 rue Camille Desmoulins, 94805 Villejuif (France)


    The Breast Imaging Report and Data System (BIRADS) of the American College of Radiology (ACR) is today largely used in most of the countries where breast cancer screening is implemented. It is a tool defined to reduce variability between radiologists when creating the reports in mammography, ultrasonography or MRI. Some changes in the last version of the BIRADS{sup TM} have been included to reduce the inaccuracy of some categories, especially for category 4. The BIRADS{sup TM} includes a lexicon and descriptive diagrams of the anomalies, recommendations for the mammographic report as well as councils and examples of mammographic cases. This review describes the mammographic items of the BIRADS classification with its more recent developments, while detailing the advantages and limits of this classification.

  3. PRN 2001-2: Acute Toxicity Data Requirements For Granular Pesticide Products, Including Those With Granular Fertilizers in the Product. (United States)

    This PR Notice announces guidance intended to streamline the acute toxicity review and classification process for certain granular pesticide products, including those products that contain granular fertilizers.

  4. Information Classification on University Websites

    DEFF Research Database (Denmark)

    Nawaz, Ather; Clemmensen, Torkil; Hertzum, Morten


    Websites are increasingly used as a medium for providing information to university students. The quality of a university website depends on how well the students’ information classification fits with the structure of the information on the website. This paper investigates the information...... classification of 14 Danish and 14 Pakistani students and compares it with the information classification of their university website. Brainstorming, card sorting, and task exploration activities were used to discover similarities and differences in the participating students’ classification of website...... information and their ability to navigate the websites. The results of the study indicate group differences in user classification and related task-performance differences. The main implications of the study are that (a) the edit distance appears a useful measure in cross-country HCI research and practice...

  5. Vietnamese Document Representation and Classification (United States)

    Nguyen, Giang-Son; Gao, Xiaoying; Andreae, Peter

    Vietnamese is very different from English and little research has been done on Vietnamese document classification, or indeed, on any kind of Vietnamese language processing, and only a few small corpora are available for research. We created a large Vietnamese text corpus with about 18000 documents, and manually classified them based on different criteria such as topics and styles, giving several classification tasks of different difficulty levels. This paper introduces a new syllable-based document representation at the morphological level of the language for efficient classification. We tested the representation on our corpus with different classification tasks using six classification algorithms and two feature selection techniques. Our experiments show that the new representation is effective for Vietnamese categorization, and suggest that best performance can be achieved using syllable-pair document representation, an SVM with a polynomial kernel as the learning algorithm, and using Information gain and an external dictionary for feature selection.

  6. Sequence-based classification and identification of Fungi. (United States)

    Hibbett, David; Abarenkov, Kessy; Kõljalg, Urmas; Öpik, Maarja; Chai, Benli; Cole, James; Wang, Qiong; Crous, Pedro; Robert, Vincent; Helgason, Thorunn; Herr, Joshua R; Kirk, Paul; Lueschow, Shiloh; O'Donnell, Kerry; Nilsson, R Henrik; Oono, Ryoko; Schoch, Conrad; Smyth, Christopher; Walker, Donald M; Porras-Alfaro, Andrea; Taylor, John W; Geiser, David M

    Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes. To realize the full potential of fungal SBCI it will be necessary to make advances in multiple areas. Improvements in sequencing methods, including long-read and single-cell technologies, will empower fungal molecular ecologists to look beyond ITS and current shotgun metagenomics approaches. Data quality and accessibility will be enhanced by attention to data and metadata standards and rigorous enforcement of policies for deposition of data and workflows. Taxonomic communities will need to develop best practices for molecular characterization in their focal clades, while also contributing to globally useful datasets including ITS. Changes to nomenclatural rules are needed to enable validPUBLICation of sequence-based taxon descriptions. Finally, cultural shifts are necessary to promote adoption of SBCI and to accord professional credit to individuals who contribute to community resources.

  7. A new classification scheme of European cold-water coral habitats: Implications for ecosystem-based management of the deep sea (United States)

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


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

  8. Cirse Quality Assurance Document and Standards for Classification of Complications: The Cirse Classification System. (United States)

    Filippiadis, D K; Binkert, C; Pellerin, O; Hoffmann, R T; Krajina, A; Pereira, P L


    Interventional radiology provides a wide variety of vascular, nonvascular, musculoskeletal, and oncologic minimally invasive techniques aimed at therapy or palliation of a broad spectrum of pathologic conditions. Outcome data for these techniques are globally evaluated by hospitals, insurance companies, and government agencies targeting in a high-quality health care policy, including reimbursement strategies. To analyze effectively the outcome of a technique, accurate reporting of complications is necessary. Throughout the literature, numerous classification systems for complications grading and classification have been reported. Until now, there has been no method for uniform reporting of complications both in terms of definition and grading. The purpose of this CIRSE guideline is to provide a classification system of complications based on combining outcome and severity of sequelae. The ultimate challenge will be the adoption of this system by practitioners in different countries and health economies within the European Union and beyond.

  9. A uniform residual tumor (R) classification: integration of the R classification and the circumferential margin status. (United States)

    Wittekind, Christian; Compton, Carolyn; Quirke, Phil; Nagtegaal, Iris; Merkel, Susanne; Hermanek, Paul; Sobin, Leslie H


    Since the introduction of the TNM residual tumor (R) classification, the involvement of resection margins has been defined either as a microscopic (R1) or a macroscopic (R2) demonstration of tumor directly at the resection margin ("tumor transected"). The recognition of the importance of the circumferential resection margin (CRM) in patients with rectal cancer patients raises the need for an alternative definition of resection margin involvement, namely, the importance of delineating tumor with a minimal distance from the CRM of CRM-positive) from tumor directly at the resection margin. The different use of both definitions of resection margin involvement prevents valid comparisons between reports on treatment results. To avoid confusion by different definitions, the authors proposed including the minimal distance between tumor and resection margin into the current R classification. By using the proposed expanded classification, comparisons of new data with previous publications will be possible. Copyright (c) 2009 American Cancer Society.

  10. The radiology of abdominal calcification including demonstration of a readily useful and comprehensive classification scheme

    International Nuclear Information System (INIS)

    Baker, S.R.


    The analysis of abdominal calcifications and other radiopacities on plain radiographs is often a diagnostic challenge. Occasionally, historical information will be a value; at times, physical examination will contribute important clues. Laboratory date such as the presence of microscopic hematuria will sometimes be helpful. Yet, very frequently, the appearance of the opacity is unexpected. The contents are morphology; concretions; conduit wall, cyst wall, solid mass calcification; mobility; effect of respiration; effect of peristalsis, growth of masses

  11. Sex Classification Using the Three-Dimensional Tibia Form or Shape Including Population Specificity Approach

    Czech Academy of Sciences Publication Activity Database

    Brzobohatá, Hana; Krajíček, V.; Horák, Z.; Velemínská, J.


    Roč. 60, č. 1 (2015), s. 29-40 ISSN 0022-1198 Grant - others:GA UK(CZ) 613012 Institutional support: RVO:67985912 Keywords : forensic science * geometric morphometrics * sexual dimorphism * optical scanning * computed tomography-derived models * tibia Subject RIV: AC - Archeology, Anthropology, Ethnology Impact factor: 1.322, year: 2015

  12. Fold classification based on secondary structure – how much is gained by including loop topology?

    Directory of Open Access Journals (Sweden)

    Przytycka Teresa


    Full Text Available Abstract Background It has been proposed that secondary structure information can be used to classify (to some extend protein folds. Since this method utilizes very limited information about the protein structure, it is not surprising that it has a higher error rate than the approaches that use full 3D fold description. On the other hand, the comparing of 3D protein structures is computing intensive. This raises the question to what extend the error rate can be decreased with each new source of information, especially if the new information can still be used with simple alignment algorithms. We consider the question whether the information about closed loops can improve the accuracy of this approach. While the answer appears to be obvious, we had to overcome two challenges. First, how to code and to compare topological information in such a way that local alignment of strings will properly identify similar structures. Second, how to properly measure the effect of new information in a large data sample. We investigate alternative ways of computing and presenting this information. Results We used the set of beta proteins with at most 30% pairwise identity to test the approach; local alignment scores were used to build a tree of clusters which was evaluated using a new log-odd cluster scoring function. In particular, we derive a closed formula for the probability of obtaining a given score by chance.Parameters of local alignment function were optimized using a genetic algorithm. Of 81 folds that had more than one representative in our data set, log-odds scores registered significantly better clustering in 27 cases and significantly worse in 6 cases, and small differences in the remaining cases. Various notions of the significant change or average change were considered and tried, and the results were all pointing in the same direction. Conclusion We found that, on average, properly presented information about the loop topology improves noticeably the accuracy of the method but the benefits vary between fold families as measured by log-odds cluster score.

  13. Cardiac Arrhythmia Classification by Wavelet Transform


    Hadji Salah; Ellouze Noureddine


    Cardiovascular diseases are the major public health parameter; they are the leading causes of mortality in the world. In fact many studies have been implemented to reduce the risk, including promoting education, prevention, and monitoring of patients at risk. In this paper we propose to develop classification system heartbeats. This system is based mainly on Wavelet Transform to extract features and Kohonen self-organization map the arrhythmias are considered in this study: N,(Normal), V(Prem...

  14. ABC Inventory classification application: Özdemirler


    Duru, Mehmet


    Ankara : The Department of Management and the Institute of Management Sciences of Bilkent Univ. , 1989. Thesis (Master's) -- Bilkent University, 1989. Includes bibliographical references leaves 37. ABC inventory classification can result in more effective control of business. In this work, ABC method is applied to Ozdemirler to examine the inventory profile of the store, and to be able to aid the management in allocating control effort among items more effectively. Dur...

  15. Enhanced Twitter Sentiment Classification Using Contextual Information


    Vosoughi, Soroush; Zhou, Helen L.; Roy, Deb K.


    The rise in popularity and ubiquity of Twitter has made sentiment analysis of tweets an important and well-covered area of research. However, the 140 character limit imposed on tweets makes it hard to use standard linguistic methods for sentiment classification. On the other hand, what tweets lack in structure they make up with sheer volume and rich metadata. This metadata includes geolocation, temporal and author information. We hypothesize that sentiment is d...

  16. Neuroendocrine tumours of the pancreas: a clinicopathological study of nine cases including six insulinomas. (United States)

    Limaiem, F; Arfa, N; Ben Hassen, E; Lahmar, A; Bouraoui, S


    Pancreatic neuroendocrine tumours (pNET) are relatively uncommon, accounting for 1-2% of all pancreatic neoplasms. They are characterised by varying clinical presentation, tumour biology and prognosis. To provide an updated overview on clinicopathological features, treatment and outcome of pNET. In our retrospective study, we reviewed 9 cases of pNET that were diagnosed at the Pathology Department of Mongi Slim Hospital over an 11-year period (2003- 2013). Relevant clinical information and microscopic slides were available in all cases and were retrospectively reviewed. The latest WHO classification (2010) was adopted. Our study group included 3 men and 6 women (M/F ratio 0.5) with an age between 20 and 75 years (mean = 52 years). Pancreatic neuroendocrine tumours ranged in size from 0.5 to 10 cm (mean 4 cm). The sites of pNET were the head of the pancreas (n = 4), the body of the pancreas (n = 3) and the tail of the pancreas (n = 2). Enucleation of the tumour was performed in five cases, Three patients underwent distal pancreatectomy and splenectomy, whereas only one patient had central pancreatectomy. Histopathological examination of the surgical specimen coupled with immunohistochemical study established a diagnosis of pNET grade 1 (G1) in seven cases and grade 2 (G2) in two cases. Pancreatic neuroendocrine tumours are a heterogeneous group of neoplasms with distinct tumour genetics, biology and clinicopathological features. Accurate clinical and pathologic diagnosis is an important first step in developing an appropriate management plan.

  17. Classification of multiple sclerosis lesions using adaptive dictionary learning. (United States)

    Deshpande, Hrishikesh; Maurel, Pierre; Barillot, Christian


    This paper presents a sparse representation and an adaptive dictionary learning based method for automated classification of multiple sclerosis (MS) lesions in magnetic resonance (MR) images. Manual delineation of MS lesions is a time-consuming task, requiring neuroradiology experts to analyze huge volume of MR data. This, in addition to the high intra- and inter-observer variability necessitates the requirement of automated MS lesion classification methods. Among many image representation models and classification methods that can be used for such purpose, we investigate the use of sparse modeling. In the recent years, sparse representation has evolved as a tool in modeling data using a few basis elements of an over-complete dictionary and has found applications in many image processing tasks including classification. We propose a supervised classification approach by learning dictionaries specific to the lesions and individual healthy brain tissues, which include white matter (WM), gray matter (GM) and cerebrospinal fluid (CSF). The size of the dictionaries learned for each class plays a major role in data representation but it is an even more crucial element in the case of competitive classification. Our approach adapts the size of the dictionary for each class, depending on the complexity of the underlying data. The algorithm is validated using 52 multi-sequence MR images acquired from 13 MS patients. The results demonstrate the effectiveness of our approach in MS lesion classification. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Classifications for Proliferative Vitreoretinopathy (PVR: An Analysis of Their Use in Publications over the Last 15 Years

    Directory of Open Access Journals (Sweden)

    Salvatore Di Lauro


    Full Text Available Purpose. To evaluate the current and suitable use of current proliferative vitreoretinopathy (PVR classifications in clinical publications related to treatment. Methods. A PubMed search was undertaken using the term “proliferative vitreoretinopathy therapy”. Outcome parameters were the reported PVR classification and PVR grades. The way the classifications were used in comparison to the original description was analyzed. Classification errors were also included. It was also noted whether classifications were used for comparison before and after pharmacological or surgical treatment. Results. 138 papers were included. 35 of them (25.4% presented no classification reference or did not use any one. 103 publications (74.6% used a standardized classification. The updated Retina Society Classification, the first Retina Society Classification, and the Silicone Study Classification were cited in 56.3%, 33.9%, and 3.8% papers, respectively. Furthermore, 3 authors (2.9% used modified-customized classifications and 4 (3.8% classification errors were identified. When the updated Retina Society Classification was used, only 10.4% of authors used a full C grade description. Finally, only 2 authors reported PVR grade before and after treatment. Conclusions. Our findings suggest that current classifications are of limited value in clinical practice due to the inconsistent and limited use and that it may be of benefit to produce a revised classification.

  19. Operationalising UN security council resolution 1540: an overview of select practical activities in the chemical and biological weapon-related areas

    International Nuclear Information System (INIS)

    Hart, J.


    The UN member states are continuing to take measures to inter alia establish and effectively implement controls to prevent the proliferation of nuclear, biological and chemical weapons and their means of delivery in accordance with United Nations Security Council Resolution 1540 (2004). The resolution also encourages enhanced international cooperation on such efforts, including by working through the 1540 Committee. Most analyses on the implementation of the resolution have focused on nuclear issues. This presentation provides an overview of select practical activities in the chemical and biological weapon-related areas, including chemical product classification and identification, biosafety and biosecurity practices and criminal prosecutions for unauthorised chemical transfers.(author)

  20. Binary Classification Method of Social Network Users

    Directory of Open Access Journals (Sweden)

    I. A. Poryadin


    Full Text Available The subject of research is a binary classification method of social network users based on the data analysis they have placed. Relevance of the task to gain information about a person by examining the content of his/her pages in social networks is exemplified. The most common approach to its solution is a visual browsing. The order of the regional authority in our country illustrates that its using in school education is needed. The article shows restrictions on the visual browsing of pupil’s pages in social networks as a tool for the teacher and the school psychologist and justifies that a process of social network users’ data analysis should be automated. Explores publications, which describe such data acquisition, processing, and analysis methods and considers their advantages and disadvantages. The article also gives arguments to support a proposal to study the classification method of social network users. One such method is credit scoring, which is used in banks and credit institutions to assess the solvency of clients. Based on the high efficiency of the method there is a proposal for significant expansion of its using in other areas of society. The possibility to use logistic regression as the mathematical apparatus of the proposed method of binary classification has been justified. Such an approach enables taking into account the different types of data extracted from social networks. Among them: the personal user data, information about hobbies, friends, graphic and text information, behaviour characteristics. The article describes a number of existing methods of data transformation that can be applied to solve the problem. An experiment of binary gender-based classification of social network users is described. A logistic model obtained for this example includes multiple logical variables obtained by transforming the user surnames. This experiment confirms the feasibility of the proposed method. Further work is to define a system

  1. Deep Recurrent Neural Networks for Supernovae Classification (United States)

    Charnock, Tom; Moss, Adam


    We apply deep recurrent neural networks, which are capable of learning complex sequential information, to classify supernovae (code available at The observational time and filter fluxes are used as inputs to the network, but since the inputs are agnostic, additional data such as host galaxy information can also be included. Using the Supernovae Photometric Classification Challenge (SPCC) data, we find that deep networks are capable of learning about light curves, however the performance of the network is highly sensitive to the amount of training data. For a training size of 50% of the representational SPCC data set (around 104 supernovae) we obtain a type-Ia versus non-type-Ia classification accuracy of 94.7%, an area under the Receiver Operating Characteristic curve AUC of 0.986 and an SPCC figure-of-merit F 1 = 0.64. When using only the data for the early-epoch challenge defined by the SPCC, we achieve a classification accuracy of 93.1%, AUC of 0.977, and F 1 = 0.58, results almost as good as with the whole light curve. By employing bidirectional neural networks, we can acquire impressive classification results between supernovae types I, II and III at an accuracy of 90.4% and AUC of 0.974. We also apply a pre-trained model to obtain classification probabilities as a function of time and show that it can give early indications of supernovae type. Our method is competitive with existing algorithms and has applications for future large-scale photometric surveys.

  2. [New molecular classification of colorectal cancer, pancreatic cancer and stomach cancer: Towards "à la carte" treatment?]. (United States)

    Dreyer, Chantal; Afchain, Pauline; Trouilloud, Isabelle; André, Thierry


    This review reports 3 of recently published molecular classifications of the 3 main gastro-intestinal cancers: gastric, pancreatic and colorectal adenocarcinoma. In colorectal adenocarcinoma, 6 independent classifications were combined to finally hold 4 molecular sub-groups, Consensus Molecular Subtypes (CMS 1-4), linked to various clinical, molecular and survival data. CMS1 (14% MSI with immune activation); CMS2 (37%: canonical with epithelial differentiation and activation of the WNT/MYC pathway); CMS3 (13% metabolic with epithelial differentiation and RAS mutation); CMS4 (23%: mesenchymal with activation of TGFβ pathway and angiogenesis with stromal invasion). In gastric adenocarcinoma, 4 groups were established: subtype "EBV" (9%, high frequency of PIK3CA mutations, hypermetylation and amplification of JAK2, PD-L1 and PD-L2), subtype "MSI" (22%, high rate of mutation), subtype "genomically stable tumor" (20%, diffuse histology type and mutations of RAS and genes encoding integrins and adhesion proteins including CDH1) and subtype "tumors with chromosomal instability" (50%, intestinal type, aneuploidy and receptor tyrosine kinase amplification). In pancreatic adenocarcinomas, a classification in four sub-groups has been proposed, stable subtype (20%, aneuploidy), locally rearranged subtype (30%, focal event on one or two chromosoms), scattered subtype (36%,200 structural variation events, defects in DNA maintenance). Although currently away from the care of patients, these classifications open the way to "à la carte" treatment depending on molecular biology. Copyright © 2016 Société Française du Cancer. Published by Elsevier Masson SAS. All rights reserved.

  3. TFOS DEWS II Definition and Classification Report. (United States)

    Craig, Jennifer P; Nichols, Kelly K; Akpek, Esen K; Caffery, Barbara; Dua, Harminder S; Joo, Choun-Ki; Liu, Zuguo; Nelson, J Daniel; Nichols, Jason J; Tsubota, Kazuo; Stapleton, Fiona


    The goals of the TFOS DEWS II Definition and Classification Subcommittee were to create an evidence-based definition and a contemporary classification system for dry eye disease (DED). The new definition recognizes the multifactorial nature of dry eye as a disease where loss of homeostasis of the tear film is the central pathophysiological concept. Ocular symptoms, as a broader term that encompasses reports of discomfort or visual disturbance, feature in the definition and the key etiologies of tear film instability, hyperosmolarity, and ocular surface inflammation and damage were determined to be important for inclusion in the definition. In the light of new data, neurosensory abnormalities were also included in the definition for the first time. In the classification of DED, recent evidence supports a scheme based on the pathophysiology where aqueous deficient and evaporative dry eye exist as a continuum, such that elements of each are considered in diagnosis and management. Central to the scheme is a positive diagnosis of DED with signs and symptoms, and this is directed towards management to restore homeostasis. The scheme also allows consideration of various related manifestations, such as non-obvious disease involving ocular surface signs without related symptoms, including neurotrophic conditions where dysfunctional sensation exists, and cases where symptoms exist without demonstrable ocular surface signs, including neuropathic pain. This approach is not intended to override clinical assessment and judgment but should prove helpful in guiding clinical management and research. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Development of a classification system for periodontal diseases and conditions. (United States)

    Armitage, G C


    Classification systems are necessary in order to provide a framework in which to scientifically study the etiology, pathogenesis, and treatment of diseases in an orderly fashion. In addition, such systems give clinicians a way to organize the health care needs of their patients. The last time scientists and clinicians in the field of periodontology and related areas agreed upon a classification system for periodontal diseases was in 1989 at the World Workshop in Clinical Periodontics. Subsequently, a simpler classification was agreed upon at the 1st European Workshop in Periodontology. These classification systems have been widely used by clinicians and research scientists throughout the world. Unfortunately, the 1989 classification had many shortcomings, including: (1) considerable overlap in disease categories, (2) absence of a gingival disease component, (3) inappropriate emphasis on age of onset of disease and rates of progression, and (4) inadequate or unclear classification criteria. The 1993 European classification lacked the detail necessary for adequate characterization of the broad spectrum of periodontal diseases encountered in clinical practice. The need for a revised classification system for periodontal diseases was emphasized during the 1996 World Workshop in Periodontics. In 1997 the American Academy of Periodontology responded to this need and formed a committee to plan and organize an international workshop to revise the classification system for periodontal diseases. The proceedings in this volume are the result of this reclassification effort. The process involved development by the Organizing Committee of an outline for a new classification and identification of individuals to write state-of-the-science reviews for each of the items on the outline. The reviewers were encouraged to depart from the preliminary outline if there were data to support any modifications. On October 30-November 2, 1999, the International Workshop for a Classification

  5. Automatic Classification of Marine Mammals with Speaker Classification Methods. (United States)

    Kreimeyer, Roman; Ludwig, Stefan


    We present an automatic acoustic classifier for marine mammals based on human speaker classification methods as an element of a passive acoustic monitoring (PAM) tool. This work is part of the Protection of Marine Mammals (PoMM) project under the framework of the European Defense Agency (EDA) and joined by the Research Department for Underwater Acoustics and Geophysics (FWG), Bundeswehr Technical Centre (WTD 71) and Kiel University. The automatic classification should support sonar operators in the risk mitigation process before and during sonar exercises with a reliable automatic classification result.

  6. ALHAMBRA survey: morphological classification (United States)

    Pović, M.; Huertas-Company, M.; Márquez, I.; Masegosa, J.; Aguerri, J. A. López; Husillos, C.; Molino, A.; Cristóbal-Hornillos, D.


    The Advanced Large Homogeneous Area Medium Band Redshift Astronomical (ALHAMBRA) survey is a photometric survey designed to study systematically cosmic evolution and cosmic variance (Moles et al. 2008). It employs 20 continuous medium-band filters (3500 - 9700 Å), plus JHK near-infrared (NIR) bands, which enable measurements of photometric redshifts with good accuracy. ALHAMBRA covers > 4 deg2 in eight discontinuous regions (~ 0.5 deg2 per region), of theseseven fields overlap with other extragalactic, multiwavelength surveys (DEEP2, SDSS, COSMOS, HDF-N, Groth, ELAIS-N1). We detect > 600.000 sources, reaching the depth of R(AB) ~ 25.0, and photometric accuracy of 2-4% (Husillos et al., in prep.). Photometric redshifts are measured using the Bayesian Photometric Redshift (BPZ) code (Benítez et al. 2000), reaching one of the best accuracies up to date of δz/z Huertas-Company 2008, 2009), one of the new non-parametric methods for morphological classification, specially useful when dealing with low resolution and high-redshift data. To test the accuracy of our morphological classification we used a sample of 3000 local, visually classified galaxies (Nair & Abraham 2010), moving them to conditions typical of our ALHAMBRA data (taking into account the background, redshift and magnitude distributions, etc.), and measuring their morphology using galSVM. Finally, we measured the morphology of ALHAMBRA galaxies, obtaining for each source seven morphological parameters (two concentration indexes, asymmetry, Gini, M20 moment of light, smoothness, and elongation), probability if the source belongs to early- or late-type, and its error. Comparing ALHAMBRA morph COSMOS/ACS morphology (obtained with the same method) we expect to have qualitative separation in two main morphological types for ~ 20.000 sources in 8 ALHAMBRA fields. For early-type galaxies we expect to recover ~ 70% and 30-40% up to magnitudes 20.0 and 21.5, respectively, having the contamination of late-types of

  7. 15th Conference of the International Federation of Classification Societies

    CERN Document Server

    Montanari, Angela; Vichi, Maurizio


    This edited volume on the latest advances in data science covers a wide range of topics in the context of data analysis and classification. In particular, it includes contributions on classification methods for high-dimensional data, clustering methods, multivariate statistical methods, and various applications. The book gathers a selection of peer-reviewed contributions presented at the Fifteenth Conference of the International Federation of Classification Societies (IFCS2015), which was hosted by the Alma Mater Studiorum, University of Bologna, from July 5 to 8, 2015.

  8. Application of pattern classification in the diagnosis of Alzheimer's disease

    Directory of Open Access Journals (Sweden)

    Min-yue CHI


    Full Text Available Alzheimer's disease (AD is a common neurodegenerative disease in the elderly. Early diagnosis and prediction plays an important role in early intervention and delaying disease progression of AD. This paper focused on the principles and process of pattern classification method, and its application in the clinical study and auxiliary diagnosis of AD. The biomarkers, neuroimaging and cognitive ability scales are important features for pattern classification. Various classification algorithms including Bayesian networks, decision trees, support vector machines (SVM and multilayer perception have been adopted to distinguish AD, mild cognitive impairment (MCI and normal aging subjects. Besides, they can effectively trace and analyze MCI patients.

  9. Formalization of the classification pattern: survey of classification modeling in information systems engineering. (United States)

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


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

  10. A microarray gene expressions with classification using extreme learning machine

    Directory of Open Access Journals (Sweden)

    Yasodha M.


    Full Text Available In the present scenario, one of the dangerous disease is cancer. It spreads through blood or lymph to other location of the body, it is a set of cells display uncontrolled growth, attack and destroy nearby tissues, and occasionally metastasis. In cancer diagnosis and molecular biology, a utilized effective tool is DNA microarrays. The dominance of this technique is recognized, so several open doubt arise regarding proper examination of microarray data. In the field of medical sciences, multicategory cancer classification plays very important role. The need for cancer classification has become essential because the number of cancer sufferers is increasing. In this research work, to overcome problems of multicategory cancer classification an improved Extreme Learning Machine (ELM classifier is used. It rectify problems faced by iterative learning methods such as local minima, improper learning rate and over fitting and the training completes with high speed.

  11. A supervised learning rule for classification of spatiotemporal spike patterns. (United States)

    Lilin Guo; Zhenzhong Wang; Adjouadi, Malek


    This study introduces a novel supervised algorithm for spiking neurons that take into consideration synapse delays and axonal delays associated with weights. It can be utilized for both classification and association and uses several biologically influenced properties, such as axonal and synaptic delays. This algorithm also takes into consideration spike-timing-dependent plasticity as in Remote Supervised Method (ReSuMe). This paper focuses on the classification aspect alone. Spiked neurons trained according to this proposed learning rule are capable of classifying different categories by the associated sequences of precisely timed spikes. Simulation results have shown that the proposed learning method greatly improves classification accuracy when compared to the Spike Pattern Association Neuron (SPAN) and the Tempotron learning rule.

  12. [Diagnostics, classification and prognostic criteria of acute myeloid leukemia]. (United States)

    Heilmeier, Bernhard; Buske, Christian; Spiekermann, Karsten; Bohlander, Stefan; Feuring-Buske, Michaela; Hiddemann, Wolfgang; Braess, Jan


    The continuously growing knowledge about criteria important for biology, pathogenesis, prognosis and treatment of acute myeloid leukemia (AML) necessitates a broad spectrum of diagnostic methods for first diagnosis and for the further course of the disease. Relevant diagnostic techniques (cytomorphology with cytochemistry, immunophenotyping, cytogenetics and molecular genetics, DNA array) are described - with a focus on their mode of operation as well on their clinical significance. Due to the high clinical relevance and growing complexity, AML diagnostics should be performed in specialized laboratories. Compared to the FAB classification which is based primarily on morphological criteria, the classification recommended in 2001 by the WHO additionally takes cytogenetics, molecular genetics and further clinical factors into consideration. Both classifications are described. A wide range of prognostic criteria of AML is discussed on the basis of currently available clinical data. The most important criteria are the karyotype of the leukemic clone and the patient's age.

  13. Topics in mathematical biology

    CERN Document Server

    Hadeler, Karl Peter


    This book analyzes the impact of quiescent phases on biological models. Quiescence arises, for example, when moving individuals stop moving, hunting predators take a rest, infected individuals are isolated, or cells enter the quiescent compartment of the cell cycle. In the first chapter of Topics in Mathematical Biology general principles about coupled and quiescent systems are derived, including results on shrinking periodic orbits and stabilization of oscillations via quiescence. In subsequent chapters classical biological models are presented in detail and challenged by the introduction of quiescence. These models include delay equations, demographic models, age structured models, Lotka-Volterra systems, replicator systems, genetic models, game theory, Nash equilibria, evolutionary stable strategies, ecological models, epidemiological models, random walks and reaction-diffusion models. In each case we find new and interesting results such as stability of fixed points and/or periodic orbits, excitability...

  14. Biological radioprotector

    International Nuclear Information System (INIS)

    Stefanescu, Ioan; Titescu, Gheorghe; Tamaian, Radu; Haulica, Ion; Bild, Walther


    According to the patent description, the biological radioprotector is deuterium depleted water, DDW, produced by vacuum distillation with an isotopic content lower than natural value. It appears as such or in a mixture with natural water and carbon dioxide. It can be used for preventing and reducing the ionizing radiation effects upon humans or animal organisms, exposed therapeutically, professionally or accidentally to radiation. The most significant advantage of using DDW as biological radioprotector results from its way of administration. Indeed no one of the radioprotectors currently used today can be orally administrated, what reduces the patients' compliance to prophylactic administrations. The biological radioprotector is an unnoxious product obtained from natural water, which can be administrated as food additive instead of drinking water. Dose modification factor is according to initial estimates around 1.9, what is a remarkable feature when one takes into account that the product is toxicity-free and side effect-free and can be administrated prophylactically as a food additive. A net radioprotective action of the deuterium depletion was evidenced experimentally in laboratory animals (rats) hydrated with DDW of 30 ppm D/(D+H) concentration as compared with normally hydrated control animals. Knowing the effects of irradiation and mechanisms of the acute radiation disease as well as the effects of administration of radiomimetic chemicals upon cellular lines of fast cell division, it appears that the effects of administrating DDW result from stimulation of the immunity system. In conclusion, the biological radioprotector DDW presents the following advantages: - it is obtained from natural products without toxicity; - it is easy to be administrated as a food additive, replacing the drinking water; - besides radioprotective effects, the product has also immunostimulative and antitumoral effects

  15. Crusts: biological (United States)

    Belnap, Jayne; Elias, Scott A.


    Biological soil crusts, a community of cyanobacteria, lichens, mosses, and fungi, are an essential part of dryland ecosystems. They are critical in the stabilization of soils, protecting them from wind and water erosion. Similarly, these soil surface communities also stabilized soils on early Earth, allowing vascular plants to establish. They contribute nitrogen and carbon to otherwise relatively infertile dryland soils, and have a strong influence on hydrologic cycles. Their presence can also influence vascular plant establishment and nutrition.


    Directory of Open Access Journals (Sweden)

    T. V. Korotaeva


    Full Text Available The lecture gives basic information about psoriatic arthritis (PsA, a chronic inflammatory disease of the joints, spine, and enthesises from a group of spondyloarthritis. It describes the epidemiology of the disease and considers current ideas on its pathogenesis and factors influencing the development of PsA in psoriatic patients. The classification and clinical forms of PsA are presented. The major clinical manifestations of the disease are indicated to include peripheral arthritis, enthesitis, dactylitis, and spondylitis. The diagnosis of the disease is noted to be established on the basis of its detected typical clinical and radiological signs, by applying the CASPAR criteria. A dermatologist, rheumatologist, and general practitioner screen PsA, by actively detecting complaints, characteristic clinical and radiological signs of damage to the joints, and/or spine, and/or enthesises and by using screening questionnaires. There are data that patients with PsA are observed to be at higher risk for a number of diseases type 2 diabetes mellitus hypertension, coronary heart disease, obesity, metabolic syndrome, inflammatory bowel diseases, etc. The aim of current pharmacotherapy for PsA is to achieve remission or minimal activity of clinical manifestations of the disease, to delay or prevent its X-ray progression, to increase survival, to improve quality of life in patients, and to reduce the risk of comorbidities. The paper considers groups of medicines used to treat the disease, among other issues, information about biological agents (BA registered in the Russian Federation for the treatment of PsA. Most patients are mentioned to show a good response to this therapy option just 3–6 months after treatment initiation; however, some of them develop primary inefficiency. In this case, switching one BA to another is recommended. Some patients using a BA develop secondary treatment inefficiency, which is firstly due to the appearance of

  17. EDITORIAL: Physical Biology (United States)

    Roscoe, Jane


    Physical Biology is a new peer-reviewed publication from Institute of Physics Publishing. Launched in 2004, the journal will foster the integration of biology with the traditionally more quantitative fields of physics, chemistry, computer science and other math-based disciplines. Its primary aim is to further the understanding of biological systems at all levels of complexity, ranging from the role of structure and dynamics of a single molecule to cellular networks and organisms. The journal encourages the development of a new biology-driven physics based on the extraordinary and increasingly rich data arising in biology, and provides research directions for those involved in the creation of novel bio-engineered systems. Physical Biology will publish a stimulating combination of full length research articles, communications, perspectives, reviews and tutorials from a wide range of disciplines covering topics such as: Single-molecule studies and nanobiotechnology Molecular interactions and protein folding Charge transfer and photobiology Ion channels; structure, function and ion regulation Molecular motors and force generation Subcellular processes Biological networks and neural systems Modeling aspects of molecular and cell biology Cell-cell signaling and interaction Biological patterns and development Evolutionary processes Novel tools and methods in physical biology Experts in the areas encompassed by the journal's scope have been appointed to the Editorial Scientific Committee and the composition of the Committee will be updated regularly to reflect the developments in this new and exciting field. Physical Biology is free online to everyone in 2004; you are invited to take advantage of this offer by visiting the journal homepage at This special print edition of Physical Biology is a combination of issues 1 and 2 of this electronic-only journal and it brings together an impressive range of articles in the fields covered, including a popular

  18. Teaching systems biology. (United States)

    Alves, R; Vilaprinyo, E; Sorribas, A


    Advances in systems biology are increasingly dependent upon the integration of various types of data and different methodologies to reconstruct how cells work at the systemic level. Thus, teams with a varied array of expertise and people with interdisciplinary training are needed. So far this training was thought to be more productive if aimed at the Masters or PhD level. At this level, multiple specialised and in-depth courses on the different subject matters of systems biology are taught to already well-prepared students. This approach is mostly based on the recognition that systems biology requires a wide background that is hard to find in undergraduate students. Nevertheless, and given the importance of the field, the authors argue that exposition of undergraduate students to the methods and paradigms of systems biology would be advantageous. Here they present and discuss a successful experiment in teaching systems biology to third year undergraduate biotechnology students at the University of Lleida in Spain. The authors' experience, together with that from others, argues for the adequateness of teaching systems biology at the undergraduate level. [Includes supplementary material].

  19. Classification of titanium dioxide

    International Nuclear Information System (INIS)

    Macias B, L.R.; Garcia C, R.M.; Maya M, M.E.; Ita T, A. De; Palacios G, J.


    In this work the X-ray diffraction (XRD), Scanning Electron Microscopy (Sem) and the X-ray Dispersive Energy Spectroscopy techniques are used with the purpose to achieve a complete identification of phases and mixture of phases of a crystalline material as titanium dioxide. The problem for solving consists of being able to distinguish a sample of titanium dioxide being different than a titanium dioxide pigment. A standard sample of titanium dioxide with NIST certificate is used, which indicates a purity of 99.74% for the TiO 2 . The following way is recommended to proceed: a)To make an analysis by means of X-ray diffraction technique to the sample of titanium dioxide pigment and on the standard of titanium dioxide waiting not find differences. b) To make a chemical analysis by the X-ray Dispersive Energy Spectroscopy via in a microscope, taking advantage of the high vacuum since it is oxygen which is analysed and if it is concluded that the aluminium oxide appears in a greater proportion to 1% it is established that is a titanium dioxide pigment, but if it is lesser then it will be only titanium dioxide. This type of analysis is an application of the nuclear techniques useful for the tariff classification of merchandise which is considered as of difficult recognition. (Author)

  20. Infrared Spectral Classification with Artificial Neural Networks and Classical Pattern Recognition

    National Research Council Canada - National Science Library

    Mayfield, Howard


    .... Computer-assisted classification tools, including pattern recognition and artificial neural network techniques, have been applied to a collection of infrared spectra of organophosphorus compounds...

  1. [The importance of classifications in psychiatry]. (United States)

    Lempérière, T


    The classifications currently used in psychiatry have different aims: to facilitate communication between researchers and clinicians at national and international levels through the use of a common language, or at least a clearly and precisely defined nomenclature; to provide a nosographical reference system which can be used in practice (diagnosis, prognosis, treatment); to optimize research by ensuring that sample cases are as homogeneous as possible; to facilitate statistical records for public health institutions. A classification is of practical interest only if it is reliable, valid and acceptable to all potential users. In recent decades, there has been a considerable systematic and coordinated effort to improve the methodological approach to classification and categorization in the field of psychiatry, including attempts to create operational definitions, field trials of inter-assessor reliability, attempts to validate the selected nosological categories by analysis of correlation between progression, treatment response, family history and additional examinations. The introduction of glossaries, and particularly of diagnostic criteria, marked a decisive step in this new approach. The key problem remains that of the validity of diagnostic criteria. Ideally, these should be based on demonstrable etiologic or pathogenic data, but such information is rarely available in psychiatry. Current classifications rely on the use of extremely diverse elements in differing degrees: descriptive criteria, evolutive criteria, etiopathogenic criteria, psychopathogenic criteria, etc. Certain syndrome-based classifications such as DSM III and its successors aim to be atheoretical and pragmatic. Others, such as ICD-10, while more eclectic than the different versions of DSM, follow suit by abandoning the terms "disease" and "illness" in favor of the more consensual "disorder". The legitimacy of classifications in the field of psychiatry has been fiercely contested, being

  2. Substantial accuracy of fracture classification in the Swedish Fracture Register: Evaluation of AO/OTA-classification in 152 ankle fractures. (United States)

    Juto, Hans; Möller, Michael; Wennergren, David; Edin, Klas; Apelqvist, Ida; Morberg, Per


    Since 2011 the Swedish Fracture Register (SFR) has collected information on fracture epidemiology, treatment and outcome. More than 112 000 fractures, including 11 600 ankle fractures, have been registered so far. The accuracy of the classification is crucial when using the register in future research and quality improvement of care. In this study we examine the degree of accuracy of the AO/OTA-classification in which ankle fractures are recorded in the SFR. 152 randomly selected ankle fractures registered in the SFR were classified independently by a reference group of three orthopedic surgeons on two occasions. The agreed AO/OTA-classification of the reference group was regarded as the gold standard classification for each case. The originally recorded classification in the SFR was subsequently compared with the classification of the reference group and accuracy calculated. The agreement between the classification in the SFR and of the reference group was 74%, corresponding to kappa 0.67, 95% CI (0.58-0.76) for AO/OTA group level. An agreement of 88% equivalent to kappa 0.77, 95% CI (0.67-0.87) was noted for AO/OTA type level. The agreement corresponds to substantial according to Landis and Koch. The kappa value of inter- and intraobserver agreement ranged from 0.67 to 0.93. The study results show substantial agreement between classifications made in the SFR and gold standard classification. The finding is equivalent to or higher than in previous studies. Consequently, we conclude that classifications of ankle fractures in the SFR are accurate and valid. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  3. Standardised classification of pre-release development in male-brooding pipefish, seahorses, and seadragons (Family Syngnathidae

    Directory of Open Access Journals (Sweden)

    Sommer Stefan


    Full Text Available Abstract Background Members of the family Syngnathidae share a unique reproductive mode termed male pregnancy. Males carry eggs in specialised brooding structures for several weeks and release free-swimming offspring. Here we describe a systematic investigation of pre-release development in syngnathid fishes, reviewing available data for 17 species distributed across the family. This work is complemented by in-depth examinations of the straight-nosed pipefish Nerophis ophidion, the black-striped pipefish Syngnathus abaster, and the potbellied seahorse Hippocampus abdominalis. Results We propose a standardised classification of early syngnathid development that extends from the activation of the egg to the release of newborn. The classification consists of four developmental periods – early embryogenesis, eye development, snout formation, and juvenile – which are further divided into 11 stages. Stages are characterised by morphological traits that are easily visible in live and preserved specimens using incident-light microscopy. Conclusions Our classification is derived from examinations of species representing the full range of brooding-structure complexity found in the Syngnathidae, including tail-brooding as well as trunk-brooding species, which represent independent evolutionary lineages. We chose conspicuous common traits as diagnostic features of stages to allow for rapid and consistent staging of embryos and larvae across the entire family. In view of the growing interest in the biology of the Syngnathidae, we believe that the classification proposed here will prove useful for a wide range of studies on the unique reproductive biology of these male-brooding fish.

  4. Dual Causality and the Autonomy of Biology. (United States)

    Bock, Walter J


    Ernst Mayr's concept of dual causality in biology with the two forms of causes (proximate and ultimate) continues to provide an essential foundation for the philosophy of biology. They are equivalent to functional (=proximate) and evolutionary (=ultimate) causes with both required for full biological explanations. The natural sciences can be classified into nomological, historical nomological and historical dual causality, the last including only biology. Because evolutionary causality is unique to biology and must be included for all complete biological explanations, biology is autonomous from the physical sciences.

  5. Comparison between different papillary recession classification systems

    Directory of Open Access Journals (Sweden)

    Li-Ching Chang


    Conclusion: This study confirmed a significant correlation between the two existing classification methods. The proposed PR classification system characterizes open embrasures in greater detail than previous systems.

  6. Systema Naturae. Classification of living things.


    Alexey Shipunov


    Original classification of living organisms containing four kingdoms (Monera, Protista, Vegetabilia and Animalia), 60 phyla and 254 classes, is presented. The classification is based on latest available information.

  7. Music classification with MPEG-7 (United States)

    Crysandt, Holger; Wellhausen, Jens


    Driven by increasing amount of music available electronically the need and possibility of automatic classification systems for music becomes more and more important. Currently most search engines for music are based on textual descriptions like artist or/and title. This paper presents a system for automatic music description, classification and visualization for a set of songs. The system is designed to extract significant features of a piece of music in order to find songs of similar genre or a similar sound characteristics. The description is done with the help of MPEG-7 only. The classification and visualization is done with the self organizing map algorithm.

  8. Next-generation biology

    DEFF Research Database (Denmark)

    Rodrigues da Fonseca, Rute Andreia; Albrechtsen, Anders; Themudo, Goncalo Espregueira Cruz


    we present an overview of the current sequencing technologies and the methods used in typical high-throughput data analysis pipelines. Subsequently, we contextualize high-throughput DNA sequencing technologies within their applications in non-model organism biology. We include tips regarding managing...

  9. Water pollution biology

    Energy Technology Data Exchange (ETDEWEB)

    Mason, C.F. [University of Essex, Colchester (United Kingdom). Dept. of Biology


    Chapter 4 of this book describes the effects of major types of pollutants on aquatic life. These are: organic pollution, eutrophication, acidification, toxic chemicals, oil, and radioactivity. The review includes an description of some of the methods of assessing the biological impacts of pollution. 50 refs., 8 figs., 3 tabs.

  10. Data Pipeline Development for Grain Boundary Structures Classification


    Li, Bingxi


    Grain Boundaries govern many properties of polycrystalline materials, including the vast majority of engineering materials. Evolutionary algorithm can be applied to predict the grain boundary structures in different systems. However, the recognition and classification of thousands of predicted structures is a very challenging work for eye detection in terms of efficiency and accuracy. A data pipeline is developed to accelerate the classification and recognition of grain boundary structures pr...

  11. Improved Automated Classification of Alcoholics and Non-alcoholics


    Ramaswamy Palaniappan


    In this paper, several improvements are proposed to previous work of automated classification of alcoholics and nonalcoholics. In the previous paper, multiplayer-perceptron neural network classifying energy of gamma band Visual Evoked Potential (VEP) signals gave the best classification performance using 800 VEP signals from 10 alcoholics and 10 non-alcoholics. Here, the dataset is extended to include 3560 VEP signals from 102 subjects: 62 alcoholics and 40 non-alcoholics...

  12. Marine molecular biology: an emerging field of biological sciences. (United States)

    Thakur, Narsinh L; Jain, Roopesh; Natalio, Filipe; Hamer, Bojan; Thakur, Archana N; Müller, Werner E G


    An appreciation of the potential applications of molecular biology is of growing importance in many areas of life sciences, including marine biology. During the past two decades, the development of sophisticated molecular technologies and instruments for biomedical research has resulted in significant advances in the biological sciences. However, the value of molecular techniques for addressing problems in marine biology has only recently begun to be cherished. It has been proven that the exploitation of molecular biological techniques will allow difficult research questions about marine organisms and ocean processes to be addressed. Marine molecular biology is a discipline, which strives to define and solve the problems regarding the sustainable exploration of marine life for human health and welfare, through the cooperation between scientists working in marine biology, molecular biology, microbiology and chemistry disciplines. Several success stories of the applications of molecular techniques in the field of marine biology are guiding further research in this area. In this review different molecular techniques are discussed, which have application in marine microbiology, marine invertebrate biology, marine ecology, marine natural products, material sciences, fisheries, conservation and bio-invasion etc. In summary, if marine biologists and molecular biologists continue to work towards strong partnership during the next decade and recognize intellectual and technological advantages and benefits of such partnership, an exciting new frontier of marine molecular biology will emerge in the future.

  13. Characteristics and application study of AP1000 NPPs equipment reliability classification method

    International Nuclear Information System (INIS)

    Guan Gao


    AP1000 nuclear power plant applies an integrated approach to establish equipment reliability classification, which includes probabilistic risk assessment technique, maintenance rule administrative, power production reliability classification and functional equipment group bounding method, and eventually classify equipment reliability into 4 levels. This classification process and result are very different from classical RCM and streamlined RCM. It studied the characteristic of AP1000 equipment reliability classification approach, considered that equipment reliability classification should effectively support maintenance strategy development and work process control, recommended to use a combined RCM method to establish the future equipment reliability program of AP1000 nuclear power plants. (authors)

  14. Intelligent Computer Vision System for Automated Classification

    International Nuclear Information System (INIS)

    Jordanov, Ivan; Georgieva, Antoniya


    In this paper we investigate an Intelligent Computer Vision System applied for recognition and classification of commercially available cork tiles. The system is capable of acquiring and processing gray images using several feature generation and analysis techniques. Its functionality includes image acquisition, feature extraction and preprocessing, and feature classification with neural networks (NN). We also discuss system test and validation results from the recognition and classification tasks. The system investigation also includes statistical feature processing (features number and dimensionality reduction techniques) and classifier design (NN architecture, target coding, learning complexity and performance, and training with our own metaheuristic optimization method). The NNs trained with our genetic low-discrepancy search method (GLPτS) for global optimisation demonstrated very good generalisation abilities. In our view, the reported testing success rate of up to 95% is due to several factors: combination of feature generation techniques; application of Analysis of Variance (ANOVA) and Principal Component Analysis (PCA), which appeared to be very efficient for preprocessing the data; and use of suitable NN design and learning method.

  15. mritc: A Package for MRI Tissue Classification

    Directory of Open Access Journals (Sweden)

    Luke Tierney


    Full Text Available This paper presents an R package for magnetic resonance imaging (MRI tissue classification. The methods include using normal mixture models, hidden Markov normal mixture models, and a higher resolution hidden Markov normal mixture model fitted by various optimization algorithms and by a Bayesian Markov chain Monte Carlo (MCMC method. Functions to obtain initial values of parameters of normal mixture models and spatial parameters are provided. Supported input formats are ANALYZE, NIfTI, and a raw byte format. The function slices3d in misc3d is used for visualizing data and results. Various performance evaluation indices are provided to evaluate classification results. To improve performance, table lookup methods are used in several places, and vectorized computation taking advantage of conditional independence properties are used. Some computations are performed by C code, and OpenMP is used to parallelize key loops in the C code.

  16. Classification of human leukocyte antigen (HLA) supertypes

    DEFF Research Database (Denmark)

    Wang, Mingjun; Claesson, Mogens H


    Identification of new antigenic peptides, derived from infectious agents or cancer cells, which bind to human leukocyte antigen (HLA) class I and II molecules, is of importance for the development of new effective vaccines capable of activating the cellular arm of the immune response. However......, the barrier to the development of peptide-based vaccines with maximum population coverage is that the restricting HLA genes are extremely polymorphic resulting in a vast diversity of peptide-binding HLA specificities and a low population coverage for any given peptide-HLA specificity. One way to reduce...... this complexity is to group thousands of different HLA molecules into several so-called HLA supertypes: a classification that refers to a group of HLA alleles with largely overlapping peptide binding specificities. In this chapter, we focus on the state-of-the-art classification of HLA supertypes including HLA...

  17. Prediction and classification of respiratory motion

    CERN Document Server

    Lee, Suk Jin


    This book describes recent radiotherapy technologies including tools for measuring target position during radiotherapy and tracking-based delivery systems. This book presents a customized prediction of respiratory motion with clustering from multiple patient interactions. The proposed method contributes to the improvement of patient treatments by considering breathing pattern for the accurate dose calculation in radiotherapy systems. Real-time tumor-tracking, where the prediction of irregularities becomes relevant, has yet to be clinically established. The statistical quantitative modeling for irregular breathing classification, in which commercial respiration traces are retrospectively categorized into several classes based on breathing pattern are discussed as well. The proposed statistical classification may provide clinical advantages to adjust the dose rate before and during the external beam radiotherapy for minimizing the safety margin. In the first chapter following the Introduction  to this book, we...

  18. Classification, (big) data analysis and statistical learning

    CERN Document Server

    Conversano, Claudio; Vichi, Maurizio


    This edited book focuses on the latest developments in classification, statistical learning, data analysis and related areas of data science, including statistical analysis of large datasets, big data analytics, time series clustering, integration of data from different sources, as well as social networks. It covers both methodological aspects as well as applications to a wide range of areas such as economics, marketing, education, social sciences, medicine, environmental sciences and the pharmaceutical industry. In addition, it describes the basic features of the software behind the data analysis results, and provides links to the corresponding codes and data sets where necessary. This book is intended for researchers and practitioners who are interested in the latest developments and applications in the field. The peer-reviewed contributions were presented at the 10th Scientific Meeting of the Classification and Data Analysis Group (CLADAG) of the Italian Statistical Society, held in Santa Margherita di Pul...

  19. Attribute Learning for SAR Image Classification

    Directory of Open Access Journals (Sweden)

    Chu He


    Full Text Available This paper presents a classification approach based on attribute learning for high spatial resolution Synthetic Aperture Radar (SAR images. To explore the representative and discriminative attributes of SAR images, first, an iterative unsupervised algorithm is designed to cluster in the low-level feature space, where the maximum edge response and the ratio of mean-to-variance are included; a cross-validation step is applied to prevent overfitting. Second, the most discriminative clustering centers are sorted out to construct an attribute dictionary. By resorting to the attribute dictionary, a representation vector describing certain categories in the SAR image can be generated, which in turn is used to perform the classifying task. The experiments conducted on TerraSAR-X images indicate that those learned attributes have strong visual semantics, which are characterized by bright and dark spots, stripes, or their combinations. The classification method based on these learned attributes achieves better results.

  20. ILAE Classification of the Epilepsies Position Paper of the ILAE Commission for Classification and Terminology (United States)

    Scheffer, Ingrid E; Berkovic, Samuel; Capovilla, Giuseppe; Connolly, Mary B; French, Jacqueline; Guilhoto, Laura; Hirsch, Edouard; Jain, Satish; Mathern, Gary W.; Moshé, Solomon L; Nordli, Douglas R; Perucca, Emilio; Tomson, Torbjörn; Wiebe, Samuel; Zhang, Yue-Hua; Zuberi, Sameer M


    Summary The ILAE Classification of the Epilepsies has been updated to reflect our gain in understanding of the epilepsies and their underlying mechanisms following the major scientific advances which have taken place since the last ratified classification in 1989. As a critical tool for the practising clinician, epilepsy classification must be relevant and dynamic to changes in thinking, yet robust and translatable to all areas of the globe. Its primary purpose is for diagnosis of patients, but it is also critical for epilepsy research, development of antiepileptic therapies and communication around the world. The new classification originates from a draft document submitted for public comments in 2013 which was revised to incorporate extensive feedback from the international epilepsy community over several rounds of consultation. It presents three levels, starting with seizure type where it assumes that the patient is having epileptic seizures as defined by the new 2017 ILAE Seizure Classification. After diagnosis of the seizure type, the next step is diagnosis of epilepsy type, including focal epilepsy, generalized epilepsy, combined generalized and focal epilepsy, and also an unknown epilepsy group. The third level is that of epilepsy syndrome where a specific syndromic diagnosis can be made. The new classification incorporates etiology along each stage, emphasizing the need to consider etiology at each step of diagnosis as it often carries significant treatment implications. Etiology is broken into six subgroups, selected because of their potential therapeutic consequences. New terminology is introduced such as developmental and epileptic encephalopathy. The term benign is replaced by the terms self-limited and pharmacoresponsive, to be used where appropriate. It is hoped that this new framework will assist in improving epilepsy care and research in the 21st century. PMID:28276062

  1. Supervised nonlinear dimensionality reduction for visualization and classification. (United States)

    Geng, Xin; Zhan, De-Chuan; Zhou, Zhi-Hua


    When performing visualization and classification, people often confront the problem of dimensionality reduction. Isomap is one of the most promising nonlinear dimensionality reduction techniques. However, when Isomap is applied to real-world data, it shows some limitations, such as being sensitive to noise. In this paper, an improved version of Isomap, namely S-Isomap, is proposed. S-Isomap utilizes class information to guide the procedure of nonlinear dimensionality reduction. Such a kind of procedure is called supervised nonlinear dimensionality reduction. In S-Isomap, the neighborhood graph of the input data is constructed according to a certain kind of dissimilarity between data points, which is specially designed to integrate the class information. The dissimilarity has several good properties which help to discover the true neighborhood of the data and, thus, makes S-Isomap a robust technique for both visualization and classification, especially for real-world problems. In the visualization experiments, S-Isomap is compared with Isomap, LLE, and WeightedIso. The results show that S-Isomap performs the best. In the classification experiments, S-Isomap is used as a preprocess of classification and compared with Isomap, WeightedIso, as well as some other well-established classification methods, including the K-nearest neighbor classifier, BP neural network, J4.8 decision tree, and SVM. The results reveal that S-Isomap excels compared to Isomap and WeightedIso in classification, and it is highly competitive with those well-known classification methods.


    Directory of Open Access Journals (Sweden)

    A. Diederichs


    Full Text Available Advertising plays a distinct role in economies around the world. Previous studieshave not resolved the question related to the classification of advertising as anexpense or capital asset. Understanding the principles set out in TheIncome TaxAct 58 of 1962, with regard to the classification of advertising cost as capital orrevenue of nature is important, since the incorrect interpretation of principles willhave a direct impact on tax liability. The focus of this study is the classification ofadvertising costs for tax purposes. Research questions posed in this paper areanswered through the development of a classification process that may assist withthe classification of advertising costs for the purpose of taxation. Guidelines forthe classification of advertising costs as capital or revenue of nature are needed tocorrectly classify advertising costs for tax purposes. Furthermore, thedetermination of when advertising costs will be regarded as capital of nature isalso determined. A qualitative research approach is applied, including a literaturereview of case law and income tax acts. The contribution of this study is found inthe guidelines set for the classification of advertising costs for tax purposes byusing principles from national and international case law.

  3. PAI-1 and EGFR expression in adult glioma tumors: toward a molecular prognostic classification

    International Nuclear Information System (INIS)

    Muracciole, Xavier; Romain, Sylvie; Dufour, Henri; Palmari, Jacqueline; Chinot, Olivier; Ouafik, L'Houcine; Grisoli, Francois; Figarella-Branger, Dominique; Martin, Pierre-Marie


    Purpose: Molecular classification of gliomas is a major challenge in the effort to improve therapeutic decisions. The plasminogen activator system, including plasminogen activator inhibitor type 1 (PAI-1), plays a key role in tumor invasion and neoangiogenesis. Epidermal growth factor receptor (EGFR) is involved in the control of proliferation. The contribution of PAI-1 and EGFR to the survival of gliomas was retrospectively investigated. Methods and Materials: Fifty-nine adult gliomas treated by neurosurgery and conventional irradiation were analyzed, including 9 low-grade (2) and 50 high-grade (3-4) tumors (WHO classification). PAI-1 was measured on cytosols and EGFR on solubilized membranes using ELISA methods. Results: High PAI-1 levels were strongly associated with high histologic grade (p<0.001) and histologic necrosis (p<0.001). PAI-1 also correlated positively with patient age (p=0.05) and negatively with Karnofsky index (p=0.01). By univariate analysis of the high-grade population, higher PAI-1 (p<0.0001) and EGFR values (p=0.02) were associated with shorter overall survival. Only PAI-1 was an independent factor in multivariate analysis. Grade 3 tumors with low PAI-1 (100% 3-year overall survival rate) presented the same clinical outcome as the low-grade tumors. Conclusions: In this prognostic study, PAI-1 and EGFR expression revealed similarities and differences between high-grade gliomas that were not apparent by traditional clinical criteria. These data strongly support that biologic factors should be included in glioma classification and the design of clinical trials to treat more homogeneous populations

  4. Buried penis: classification surgical approach. (United States)

    Hadidi, Ahmed T


    The purpose of this study was to describe morphological classification of congenital buried penis (BP) and present a versatile surgical approach for correction. Sixty-one patients referred with BP were classified into 3 grades according to morphological findings: Grade 1-29 patients with Longer Inner Prepuce (LIP) only, Grade II-20 patients who presented with LIP associated with indrawn penis that required division of the fundiform and suspensory ligaments, and Grade III-12 patients who had in addition to the above, excess supra-pubic fat. A ventral midline penile incision extending from the tip of prepuce down to the penoscrotal junction was used in all patients. The operation was tailored according to the BP Grade. All patients underwent circumcision. Mean follow up was 3 years (range 1 to 10). All 61 patients had an abnormally long inner prepuce (LIP). Forty-seven patients had a short penile shaft. Early improvement was noted in all cases. Satisfactory results were achieved in all 29 patients in grade I and in 27 patients in grades II and III. Five children (Grades II and III) required further surgery (9%). Congenital buried penis is a spectrum characterized by LIP and may include in addition; short penile shaft, abnormal attachment of fundiform, and suspensory ligaments and excess supra-pubic fat. Congenital Mega Prepuce (CMP) is a variant of Grade I BP, with LIP characterized by intermittent ballooning of the genital area. Copyright © 2014 Elsevier Inc. All rights reserved.

  5. The classification of easement

    Directory of Open Access Journals (Sweden)

    Popov Danica D.


    Full Text Available Easement means, a right enjoyed by the owner of land over the lands of another: such as rights of way, right of light, rights of support, rights to a flow of air or water etc. The dominant tenement is the land owned by the possessor of the easement, and the servient tenement is the land over which the right is enjoyed. An easement must exist for the accommodation and better enjoyment to which it is annexed, otherwise it may amount to mere licence. An easement benefits and binds the land itself and therefore countinious despite any change of ownership of either dominant or servient tenement, although it will be extinguished if the two tenemants come into common ownership. An easement can only be enjoyed in respect of land. This means two parcels of land. First there must be a 'dominant tenement' and a 'servient tenement'. Dominant tenement to which the benefit of the easement attaches, and another (servient tenement which bears the burden of the easement. A positive easement consist of a right to do something on the land of another; a negative easement restrict the use of owner of the serviant tenement may make of his land. An easement may be on land or on the house made on land. The next classification is on easement on the ground, and the other one under the ground. An easement shall be done in accordance with the principle of restrictions. This means that the less burden the servient tenement. When there is doubt about the extent of the actual easement shall take what easier the servient tenement. The new needs of the dominant estate does not result in the expansion of servitude. In the article is made comparison between The Draft Code of property and other real estate, and The Draft of Civil Code of Serbia.

  6. Classification and clinical assessment

    Directory of Open Access Journals (Sweden)

    F. Cantini


    Full Text Available There are at least nine classification criteria for psoriatic arthritis (PsA that have been proposed and used in clinical studies. With the exception of the ESSG and Bennett rules, all of the other criteria sets have a good performance in identifying PsA patients. As the CASPAR criteria are based on a robust study methodology, they are considered the current reference standard. However, if there seems to be no doubt that they are very good to classify PsA patients (very high specificity, they might be not sensitive enough to diagnose patients with unknown early PsA. The vast clinical heterogeneity of PsA makes its assessment very challenging. Peripheral joint involvement is measured by 78/76 joint counts, spine involvement by the instruments used for ankylosing spondylitis (AS, dactylitis by involved digit count or by the Leeds dactylitis index, enthesitis by the number of affected entheses (several indices available and psoriasis by the Psoriasis Area and Severity Index (PASI. Peripheral joint damage can be assessed by a modified van der Heijde-Sharp scoring system and axial damage by the methods used for AS or by the Psoriatic Arthritis Spondylitis Radiology Index (PASRI. As in other arthritides, global evaluation of disease activity and severity by patient and physician and assessment of disability and quality of life are widely used. Finally, composite indices that capture several clinical manifestations of PsA have been proposed and a new instrument, the Psoriatic ARthritis Disease Activity Score (PASDAS, is currently being developed.

  7. Progression in nuclear classification

    International Nuclear Information System (INIS)

    Wang Yuying


    In this book, summarize the author's achievements of nuclear classification by new method in latest 30 years, new foundational law of nuclear layer in matter world is found. It is explained with a hypothesis of a nucleus which it is made up of two nucleon's clusters with deuteron and triton. Its concrete content is: to advance a new method which analyze data of nuclei with natural abundance using relationship between the numbers of proton and neutron. The relationship of each nucleus increases to 4 sets: S+H=Z H+Z=N Z+N=A and S-H=K. To expand the similarity between proton and neutron to the similarity among p,n, deuteron, triton, and He-5 clusters. According to the distribution law of same kind of nuclei, it obtains that the upper limits of stable region both should be '44s'. New foundational law of nuclear system is 1,2,4,8,16,8,4,2,1. In order to explain new law, a hypothesis which nucleus is made up of deuteron and triton is developing and nuclear field of whole number is built up. And it relates that unity of matter motion, which is the most foundational form atomic nuclear systematic is similar to the most first-class form chromosome numbers of mankind. These achievements will shake the foundations of traditional nuclear science. These achievements will supply new tasks in developing nuclear theory. And shake the ground of which magic number is the basic of nuclear science. It opens up a new field on foundational research. The book will supply new knowledge for researcher, teachers and students in universities and polytechnic schools. Scientific workers read in works of research and technical exploit. It can be stored up for library and laboratory of society and universities. In nowadays of prosperity our nation by science and education, the book is readable for workers of scientific technology and amateurs of natural science

  8. (including travel dates) Proposed itinerary

    Indian Academy of Sciences (India)


    31 July to 22 August 2012 (including travel dates). Proposed itinerary: Arrival in Bangalore on 1 August. 1-5 August: Bangalore, Karnataka. Suggested institutions: Indian Institute of Science, Bangalore. St Johns Medical College & Hospital, Bangalore. Jawaharlal Nehru Centre, Bangalore. 6-8 August: Chennai, TN.

  9. VT Biodiversity Project - Bedrock Classification (United States)

    Vermont Center for Geographic Information — (Link to Metadata) This dataset is a five category, nine sub-category classification of the bedrock units appearing on the Centennial Geologic Map of Vermont. The...

  10. The last classification of vasculitis

    NARCIS (Netherlands)

    Kallenberg, Cees G. M.


    Systemic vasculitides are a group of diverse conditions characterized by inflammation of the blood vessels. To obtain homogeneity in clinical characteristics, prognosis, and response to treatment, patients with vasculitis should be classified into defined disease categories. Many classification

  11. Deep Learning for ECG Classification (United States)

    Pyakillya, B.; Kazachenko, N.; Mikhailovsky, N.


    The importance of ECG classification is very high now due to many current medical applications where this problem can be stated. Currently, there are many machine learning (ML) solutions which can be used for analyzing and classifying ECG data. However, the main disadvantages of these ML results is use of heuristic hand-crafted or engineered features with shallow feature learning architectures. The problem relies in the possibility not to find most appropriate features which will give high classification accuracy in this ECG problem. One of the proposing solution is to use deep learning architectures where first layers of convolutional neurons behave as feature extractors and in the end some fully-connected (FCN) layers are used for making final decision about ECG classes. In this work the deep learning architecture with 1D convolutional layers and FCN layers for ECG classification is presented and some classification results are showed.

  12. Vehicle classification using mobile sensors. (United States)


    In this research, the feasibility of using mobile traffic sensors for binary vehicle classification on arterial roads is investigated. Features (e.g. : speed related, acceleration/deceleration related, etc.) are extracted from vehicle traces (passeng...

  13. [Definition and classification of epilepsy]. (United States)

    Jibiki, Itsuki


    The concept or definition of epilepsy was mentioned as a chronic disease of the brain consisting of repetitions of EEG paroxysm and clinical seizures caused by excessive discharges of the cerebral neurons, in reference with Gastaut's opinion and the other statements. Further, we referred to diseases to be excluded from epilepsy such as isolated, occasional and subclinical seizures and so on. Next, new classifications of seizures and epilepsies were explained on the basis of revised terminology and concepts for organization of seizures and epilepsies in Report of the ILAE Communication in Classification and Terminology, 2005-09, in comparison with the Classification of Epileptic Seizures in 1981 and the Classification of Epilepsies and Epileptic Syndromes in 1989.

  14. Classification of remotely sensed images

    CSIR Research Space (South Africa)

    Dudeni, N


    Full Text Available For this research, the researchers examine various existing image classification algorithms with the aim of demonstrating how these algorithms can be applied to remote sensing images. These algorithms are broadly divided into supervised...

  15. Critical Evaluation of Headache Classifications. (United States)

    Özge, Aynur


    Transforming a subjective sense like headache into an objective state and establishing a common language for this complaint which can be both a symptom and a disease all by itself have kept the investigators busy for years. Each recommendation proposed has brought along a set of patients who do not meet the criteria. While almost the most ideal and most comprehensive classification studies continued at this point, this time criticisims about withdrawing from daily practice came to the fore. In this article, the classification adventure of scientists who work in the area of headache will be summarized. More specifically, 2 classifications made by the International Headache Society (IHS) and the point reached in relation with the 3rd classification which is still being worked on will be discussed together with headache subtypes. It has been presented with the wish and belief that it will contribute to the readers and young investigators who are interested in this subject.

  16. A machine learning approach for viral genome classification. (United States)

    Remita, Mohamed Amine; Halioui, Ahmed; Malick Diouara, Abou Abdallah; Daigle, Bruno; Kiani, Golrokh; Diallo, Abdoulaye Baniré


    Advances in cloning and sequencing technology are yielding a massive number of viral genomes. The classification and annotation of these genomes constitute important assets in the discovery of genomic variability, taxonomic characteristics and disease mechanisms. Existing classification methods are often designed for specific well-studied family of viruses. Thus, the viral comparative genomic studies could benefit from more generic, fast and accurate tools for classifying and typing newly sequenced strains of diverse virus families. Here, we introduce a virus classification platform, CASTOR, based on machine learning methods. CASTOR is inspired by a well-known technique in molecular biology: restriction fragment length polymorphism (RFLP). It simulates, in silico, the restriction digestion of genomic material by different enzymes into fragments. It uses two metrics to construct feature vectors for machine learning algorithms in the classification step. We benchmark CASTOR for the classification of distinct datasets of human papillomaviruses (HPV), hepatitis B viruses (HBV) and human immunodeficiency viruses type 1 (HIV-1). Results reveal true positive rates of 99%, 99% and 98% for HPV Alpha species, HBV genotyping and HIV-1 M subtyping, respectively. Furthermore, CASTOR shows a competitive performance compared to well-known HIV-1 specific classifiers (REGA and COMET) on whole genomes and pol fragments. The performance of CASTOR, its genericity and robustness could permit to perform novel and accurate large scale virus studies. The CASTOR web platform provides an open access, collaborative and reproducible machine learning classifiers. CASTOR can be accessed at .

  17. Automated Diatom Classification (Part B: A Deep Learning Approach

    Directory of Open Access Journals (Sweden)

    Anibal Pedraza


    Full Text Available Diatoms, a kind of algae microorganisms with several species, are quite useful for water quality determination, one of the hottest topics in applied biology nowadays. At the same time, deep learning and convolutional neural networks (CNN are becoming an extensively used technique for image classification in a variety of problems. This paper approaches diatom classification with this technique, in order to demonstrate whether it is suitable for solving the classification problem. An extensive dataset was specifically collected (80 types, 100 samples/type for this study. The dataset covers different illumination conditions and it was computationally augmented to more than 160,000 samples. After that, CNNs were applied over datasets pre-processed with different image processing techniques. An overall accuracy of 99% is obtained for the 80-class problem and different kinds of images (brightfield, normalized. Results were compared to previous presented classification techniques with different number of samples. As far as the authors know, this is the first time that CNNs are applied to diatom classification.

  18. Comparing multilabel classification methods for provisional biopharmaceutics class prediction. (United States)

    Newby, Danielle; Freitas, Alex A; Ghafourian, Taravat


    The biopharmaceutical classification system (BCS) is now well established and utilized for the development and biowaivers of immediate oral dosage forms. The prediction of BCS class can be carried out using multilabel classification. Unlike single label classification, multilabel classification methods predict more than one class label at the same time. This paper compares two multilabel methods, binary relevance and classifier chain, for provisional BCS class prediction. Large data sets of permeability and solubility of drug and drug-like compounds were obtained from the literature and were used to build models using decision trees. The separate permeability and solubility models were validated, and a BCS validation set of 127 compounds where both permeability and solubility were known was used to compare the two aforementioned multilabel classification methods for provisional BCS class prediction. Overall, the results indicate that the classifier chain method, which takes into account label interactions, performed better compared to the binary relevance method. This work offers a comparison of multilabel methods and shows the potential of the classifier chain multilabel method for improved biological property predictions for use in drug discovery and development.

  19. Synthetic biology and occupational risk. (United States)

    Howard, John; Murashov, Vladimir; Schulte, Paul


    Synthetic biology is an emerging interdisciplinary field of biotechnology that involves applying the principles of engineering and chemical design to biological systems. Biosafety professionals have done an excellent job in addressing research laboratory safety as synthetic biology and gene editing have emerged from the larger field of biotechnology. Despite these efforts, risks posed by synthetic biology are of increasing concern as research procedures scale up to industrial processes in the larger bioeconomy. A greater number and variety of workers will be exposed to commercial synthetic biology risks in the future, including risks to a variety of workers from the use of lentiviral vectors as gene transfer devices. There is a need to review and enhance current protection measures in the field of synthetic biology, whether in experimental laboratories where new advances are being researched, in health care settings where treatments using viral vectors as gene delivery systems are increasingly being used, or in the industrial bioeconomy. Enhanced worker protection measures should include increased injury and illness surveillance of the synthetic biology workforce; proactive risk assessment and management of synthetic biology products; research on the relative effectiveness of extrinsic and intrinsic biocontainment methods; specific safety guidance for synthetic biology industrial processes; determination of appropriate medical mitigation measures for lentiviral vector exposure incidents; and greater awareness and involvement in synthetic biology safety by the general occupational safety and health community as well as by government occupational safety and health research and regulatory agencies.

  20. Restriction endonucleases: classification, properties, and applications. (United States)

    Williams, Raymond J


    Restriction endonucleases have become a fundamental tool of molecular biology with many commercial vendors and extensive product lines. While a significant amount has been learned about restriction enzyme diversity, genomic organization, and mechanism, these continue to be active areas of research and assist in classification efforts. More recently, one focus has been their exquisite specificity for the proper recognition sequence and the lack of homology among enzymes recognizing the same DNA sequence. Some questions also remain regarding in vivo function. Site-directed mutagenesis and fusion proteins based on known endonucleases show promise for custom-designed cleavage. An understanding of the enzymes and their properties can improve their productive application by maintaining critical digest parameters and enhancing or avoiding alternative activities.