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Sample records for accurate molecular classification

  1. Accurate molecular classification of cancer using simple rules

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    Gotoh Osamu

    2009-10-01

    Full Text Available Abstract Background One intractable problem with using microarray data analysis for cancer classification is how to reduce the extremely high-dimensionality gene feature data to remove the effects of noise. Feature selection is often used to address this problem by selecting informative genes from among thousands or tens of thousands of genes. However, most of the existing methods of microarray-based cancer classification utilize too many genes to achieve accurate classification, which often hampers the interpretability of the models. For a better understanding of the classification results, it is desirable to develop simpler rule-based models with as few marker genes as possible. Methods We screened a small number of informative single genes and gene pairs on the basis of their depended degrees proposed in rough sets. Applying the decision rules induced by the selected genes or gene pairs, we constructed cancer classifiers. We tested the efficacy of the classifiers by leave-one-out cross-validation (LOOCV of training sets and classification of independent test sets. Results We applied our methods to five cancerous gene expression datasets: leukemia (acute lymphoblastic leukemia [ALL] vs. acute myeloid leukemia [AML], lung cancer, prostate cancer, breast cancer, and leukemia (ALL vs. mixed-lineage leukemia [MLL] vs. AML. Accurate classification outcomes were obtained by utilizing just one or two genes. Some genes that correlated closely with the pathogenesis of relevant cancers were identified. In terms of both classification performance and algorithm simplicity, our approach outperformed or at least matched existing methods. Conclusion In cancerous gene expression datasets, a small number of genes, even one or two if selected correctly, is capable of achieving an ideal cancer classification effect. This finding also means that very simple rules may perform well for cancerous class prediction.

  2. The molecular genetics and morphometry-based Endometrial Intraepithelial Neoplasia classification system predicts disease progression in Endometrial hyperplasia more accurately than the 1994 World Health Organization classification system

    NARCIS (Netherlands)

    Baak, JP; Mutter, GL; Robboy, S; van Diest, PJ; Uyterlinde, AM; Orbo, A; Palazzo, J; Fiane, B; Lovslett, K; Burger, C; Voorhorst, F; Verheijen, RH

    2005-01-01

    BACKGROUND. The objective of this study was to compare the accuracy of disease progression prediction of the molecular genetics and morphometry-based Endometrial Intraepithelial Neoplasia (EIN) and World Health Organization 1994 (WHO94) classification systems in patients with endometrial hyperplasia

  3. Molecular Classification of Medulloblastoma

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    KIJIMA, Noriyuki; KANEMURA, Yonehiro

    2016-01-01

    Medulloblastoma (MB) is one of the most frequent malignant brain tumors in children. The current standard treatment regimen consists of surgical resection, craniospinal irradiation, and adjuvant chemotherapy. Although these treatments have the potential to increase the survival of 70–80% of patients with MB, they are also associated with serious treatment-induced morbidity. The current risk stratification of MB is based on clinical factors, including age at presentation, metastatic status, and the presence of residual tumor following resection. In addition, recent genomic studies indicate that MB consists of at least four distinct molecular subgroups: WNT, sonic hedgehog (SHH), Group 3, and Group 4. WNT and SHH MBs are characterized by aberrations in the WNT and SHH signaling pathways, respectively. WNT MB has the best prognosis compared to the other MBs, while SHH MB has an intermediate prognosis. The underlying signaling pathways associated with Group 3 and 4 MBs have not been identified. Group 3 MB is frequently associated with metastasis, resulting in a poor prognosis, while Group 4 is sometimes associated with metastasis and has an intermediate prognosis. Group 4 is the most frequent MB and represents 35% of all MBs. These findings suggest that MB is a heterogeneous disease, and that MB subgroups have distinct molecular, demographic, and clinical characteristics. The molecular classification of MBs is redefining the risk stratification of patients with MB, and has the potential to identify new therapeutic strategies for the treatment of MB. PMID:27238212

  4. Redundancy-Free, Accurate Analytical Center Machine for Classification

    Institute of Scientific and Technical Information of China (English)

    ZHENGFanzi; QIUZhengding; LengYonggang; YueJianhai

    2005-01-01

    Analytical center machine (ACM) has remarkable generalization performance based on analytical center of version space and outperforms SVM. From the analysis of geometry of machine learning and principle of ACM, it is showed that some training patterns are redundant to the definition of version space. Redundant patterns push ACM classifier away from analytical center of the prime version space so that the generalization performance degrades, at the same time redundant patterns slow down the classifier and reduce the efficiency of storage. Thus, an incremental algorithm is proposed to remove redundant patterns and embed into the frame of ACM that yields a Redundancy free accurate-Analytical center machine (RFA-ACM) for classification. Experiments with Heart, Thyroid, Banana datasets demonstrate the validity of RFA-ACM.

  5. Automatic classification and accurate size measurement of blank mask defects

    Science.gov (United States)

    Bhamidipati, Samir; Paninjath, Sankaranarayanan; Pereira, Mark; Buck, Peter

    2015-07-01

    complexity of defects encountered. The variety arises due to factors such as defect nature, size, shape and composition; and the optical phenomena occurring around the defect. This paper focuses on preliminary characterization results, in terms of classification and size estimation, obtained by Calibre MDPAutoClassify tool on a variety of mask blank defects. It primarily highlights the challenges faced in achieving the results with reference to the variety of defects observed on blank mask substrates and the underlying complexities which make accurate defect size measurement an important and challenging task.

  6. Accurate mobile malware detection and classification in the cloud.

    Science.gov (United States)

    Wang, Xiaolei; Yang, Yuexiang; Zeng, Yingzhi

    2015-01-01

    As the dominator of the Smartphone operating system market, consequently android has attracted the attention of s malware authors and researcher alike. The number of types of android malware is increasing rapidly regardless of the considerable number of proposed malware analysis systems. In this paper, by taking advantages of low false-positive rate of misuse detection and the ability of anomaly detection to detect zero-day malware, we propose a novel hybrid detection system based on a new open-source framework CuckooDroid, which enables the use of Cuckoo Sandbox's features to analyze Android malware through dynamic and static analysis. Our proposed system mainly consists of two parts: anomaly detection engine performing abnormal apps detection through dynamic analysis; signature detection engine performing known malware detection and classification with the combination of static and dynamic analysis. We evaluate our system using 5560 malware samples and 6000 benign samples. Experiments show that our anomaly detection engine with dynamic analysis is capable of detecting zero-day malware with a low false negative rate (1.16 %) and acceptable false positive rate (1.30 %); it is worth noting that our signature detection engine with hybrid analysis can accurately classify malware samples with an average positive rate 98.94 %. Considering the intensive computing resources required by the static and dynamic analysis, our proposed detection system should be deployed off-device, such as in the Cloud. The app store markets and the ordinary users can access our detection system for malware detection through cloud service.

  7. How accurate are the European Union's classifications of chemical substances.

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    Rudén, Christina; Hansson, Sven Ove

    2003-09-30

    The European Commission has decided on harmonized classifications for a large number of individual chemicals according to its own directive for classification and labeling of dangerous substances. We have compared the harmonized classifications for acute oral toxicity to the acute oral toxicity data available in the RTECS database. Of the 992 substances eligible for this comparison, 15% were assigned a too low danger class and 8% a too high danger class according to the RTECS data. Due to insufficient transparency-scientific documentations of the classification decisions are not available-the causes of this discrepancy can only be hypothesized. We propose that the scientific motivations of future classifications be published and that the apparent over- and underclassifications in the present system be either explained or rectified, according to what are the facts in the matter.

  8. Accurate phylogenetic classification of DNA fragments based onsequence composition

    Energy Technology Data Exchange (ETDEWEB)

    McHardy, Alice C.; Garcia Martin, Hector; Tsirigos, Aristotelis; Hugenholtz, Philip; Rigoutsos, Isidore

    2006-05-01

    Metagenome studies have retrieved vast amounts of sequenceout of a variety of environments, leading to novel discoveries and greatinsights into the uncultured microbial world. Except for very simplecommunities, diversity makes sequence assembly and analysis a verychallenging problem. To understand the structure a 5 nd function ofmicrobial communities, a taxonomic characterization of the obtainedsequence fragments is highly desirable, yet currently limited mostly tothose sequences that contain phylogenetic marker genes. We show that forclades at the rank of domain down to genus, sequence composition allowsthe very accurate phylogenetic 10 characterization of genomic sequence.We developed a composition-based classifier, PhyloPythia, for de novophylogenetic sequence characterization and have trained it on adata setof 340 genomes. By extensive evaluation experiments we show that themethodis accurate across all taxonomic ranks considered, even forsequences that originate fromnovel organisms and are as short as 1kb.Application to two metagenome datasets 15 obtained from samples ofphosphorus-removing sludge showed that the method allows the accurateclassification at genus level of most sequence fragments from thedominant populations, while at the same time correctly characterizingeven larger parts of the samples at higher taxonomic levels.

  9. HIPPI: highly accurate protein family classification with ensembles of HMMs

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    Nam-phuong Nguyen

    2016-11-01

    Full Text Available Abstract Background Given a new biological sequence, detecting membership in a known family is a basic step in many bioinformatics analyses, with applications to protein structure and function prediction and metagenomic taxon identification and abundance profiling, among others. Yet family identification of sequences that are distantly related to sequences in public databases or that are fragmentary remains one of the more difficult analytical problems in bioinformatics. Results We present a new technique for family identification called HIPPI (Hierarchical Profile Hidden Markov Models for Protein family Identification. HIPPI uses a novel technique to represent a multiple sequence alignment for a given protein family or superfamily by an ensemble of profile hidden Markov models computed using HMMER. An evaluation of HIPPI on the Pfam database shows that HIPPI has better overall precision and recall than blastp, HMMER, and pipelines based on HHsearch, and maintains good accuracy even for fragmentary query sequences and for protein families with low average pairwise sequence identity, both conditions where other methods degrade in accuracy. Conclusion HIPPI provides accurate protein family identification and is robust to difficult model conditions. Our results, combined with observations from previous studies, show that ensembles of profile Hidden Markov models can better represent multiple sequence alignments than a single profile Hidden Markov model, and thus can improve downstream analyses for various bioinformatic tasks. Further research is needed to determine the best practices for building the ensemble of profile Hidden Markov models. HIPPI is available on GitHub at https://github.com/smirarab/sepp .

  10. Accurate Classification of RNA Structures Using Topological Fingerprints

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    Li, Kejie; Gribskov, Michael

    2016-01-01

    While RNAs are well known to possess complex structures, functionally similar RNAs often have little sequence similarity. While the exact size and spacing of base-paired regions vary, functionally similar RNAs have pronounced similarity in the arrangement, or topology, of base-paired stems. Furthermore, predicted RNA structures often lack pseudoknots (a crucial aspect of biological activity), and are only partially correct, or incomplete. A topological approach addresses all of these difficulties. In this work we describe each RNA structure as a graph that can be converted to a topological spectrum (RNA fingerprint). The set of subgraphs in an RNA structure, its RNA fingerprint, can be compared with the fingerprints of other RNA structures to identify and correctly classify functionally related RNAs. Topologically similar RNAs can be identified even when a large fraction, up to 30%, of the stems are omitted, indicating that highly accurate structures are not necessary. We investigate the performance of the RNA fingerprint approach on a set of eight highly curated RNA families, with diverse sizes and functions, containing pseudoknots, and with little sequence similarity–an especially difficult test set. In spite of the difficult test set, the RNA fingerprint approach is very successful (ROC AUC > 0.95). Due to the inclusion of pseudoknots, the RNA fingerprint approach both covers a wider range of possible structures than methods based only on secondary structure, and its tolerance for incomplete structures suggests that it can be applied even to predicted structures. Source code is freely available at https://github.rcac.purdue.edu/mgribsko/XIOS_RNA_fingerprint. PMID:27755571

  11. Machine Learning of Accurate Energy-Conserving Molecular Force Fields

    CERN Document Server

    Chmiela, Stefan; Sauceda, Huziel E; Poltavsky, Igor; Schütt, Kristof; Müller, Klaus-Robert

    2016-01-01

    Using conservation of energy -- a fundamental property of closed classical and quantum mechanical systems -- we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential-energy surfaces of intermediate-size molecules with an accuracy of 0.3 kcal/mol for energies and 1 kcal/mol/{\\AA} for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations...

  12. Accurate and interpretable classification of microspectroscopy pixels using artificial neural networks.

    Science.gov (United States)

    Manescu, Petru; Jong Lee, Young; Camp, Charles; Cicerone, Marcus; Brady, Mary; Bajcsy, Peter

    2017-04-01

    This paper addresses the problem of classifying materials from microspectroscopy at a pixel level. The challenges lie in identifying discriminatory spectral features and obtaining accurate and interpretable models relating spectra and class labels. We approach the problem by designing a supervised classifier from a tandem of Artificial Neural Network (ANN) models that identify relevant features in raw spectra and achieve high classification accuracy. The tandem of ANN models is meshed with classification rule extraction methods to lower the model complexity and to achieve interpretability of the resulting model. The contribution of the work is in designing each ANN model based on the microspectroscopy hypothesis about a discriminatory feature of a certain target class being composed of a linear combination of spectra. The novelty lies in meshing ANN and decision rule models into a tandem configuration to achieve accurate and interpretable classification results. The proposed method was evaluated using a set of broadband coherent anti-Stokes Raman scattering (BCARS) microscopy cell images (600 000  pixel-level spectra) and a reference four-class rule-based model previously created by biochemical experts. The generated classification rule-based model was on average 85% accurate measured by the DICE pixel label similarity metric, and on average 96% similar to the reference rules measured by the vector cosine metric.

  13. Accurate crop classification using hierarchical genetic fuzzy rule-based systems

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    Topaloglou, Charalampos A.; Mylonas, Stelios K.; Stavrakoudis, Dimitris G.; Mastorocostas, Paris A.; Theocharis, John B.

    2014-10-01

    This paper investigates the effectiveness of an advanced classification system for accurate crop classification using very high resolution (VHR) satellite imagery. Specifically, a recently proposed genetic fuzzy rule-based classification system (GFRBCS) is employed, namely, the Hierarchical Rule-based Linguistic Classifier (HiRLiC). HiRLiC's model comprises a small set of simple IF-THEN fuzzy rules, easily interpretable by humans. One of its most important attributes is that its learning algorithm requires minimum user interaction, since the most important learning parameters affecting the classification accuracy are determined by the learning algorithm automatically. HiRLiC is applied in a challenging crop classification task, using a SPOT5 satellite image over an intensively cultivated area in a lake-wetland ecosystem in northern Greece. A rich set of higher-order spectral and textural features is derived from the initial bands of the (pan-sharpened) image, resulting in an input space comprising 119 features. The experimental analysis proves that HiRLiC compares favorably to other interpretable classifiers of the literature, both in terms of structural complexity and classification accuracy. Its testing accuracy was very close to that obtained by complex state-of-the-art classification systems, such as the support vector machines (SVM) and random forest (RF) classifiers. Nevertheless, visual inspection of the derived classification maps shows that HiRLiC is characterized by higher generalization properties, providing more homogeneous classifications that the competitors. Moreover, the runtime requirements for producing the thematic map was orders of magnitude lower than the respective for the competitors.

  14. Transcriptome classification reveals molecular subtypes in psoriasis

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    Ainali Chrysanthi

    2012-09-01

    Full Text Available Abstract Background Psoriasis is an immune-mediated disease characterised by chronically elevated pro-inflammatory cytokine levels, leading to aberrant keratinocyte proliferation and differentiation. Although certain clinical phenotypes, such as plaque psoriasis, are well defined, it is currently unclear whether there are molecular subtypes that might impact on prognosis or treatment outcomes. Results We present a pipeline for patient stratification through a comprehensive analysis of gene expression in paired lesional and non-lesional psoriatic tissue samples, compared with controls, to establish differences in RNA expression patterns across all tissue types. Ensembles of decision tree predictors were employed to cluster psoriatic samples on the basis of gene expression patterns and reveal gene expression signatures that best discriminate molecular disease subtypes. This multi-stage procedure was applied to several published psoriasis studies and a comparison of gene expression patterns across datasets was performed. Conclusion Overall, classification of psoriasis gene expression patterns revealed distinct molecular sub-groups within the clinical phenotype of plaque psoriasis. Enrichment for TGFb and ErbB signaling pathways, noted in one of the two psoriasis subgroups, suggested that this group may be more amenable to therapies targeting these pathways. Our study highlights the potential biological relevance of using ensemble decision tree predictors to determine molecular disease subtypes, in what may initially appear to be a homogenous clinical group. The R code used in this paper is available upon request.

  15. HMM-FRAME: accurate protein domain classification for metagenomic sequences containing frameshift errors

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    Sun Yanni

    2011-05-01

    Full Text Available Abstract Background Protein domain classification is an important step in metagenomic annotation. The state-of-the-art method for protein domain classification is profile HMM-based alignment. However, the relatively high rates of insertions and deletions in homopolymer regions of pyrosequencing reads create frameshifts, causing conventional profile HMM alignment tools to generate alignments with marginal scores. This makes error-containing gene fragments unclassifiable with conventional tools. Thus, there is a need for an accurate domain classification tool that can detect and correct sequencing errors. Results We introduce HMM-FRAME, a protein domain classification tool based on an augmented Viterbi algorithm that can incorporate error models from different sequencing platforms. HMM-FRAME corrects sequencing errors and classifies putative gene fragments into domain families. It achieved high error detection sensitivity and specificity in a data set with annotated errors. We applied HMM-FRAME in Targeted Metagenomics and a published metagenomic data set. The results showed that our tool can correct frameshifts in error-containing sequences, generate much longer alignments with significantly smaller E-values, and classify more sequences into their native families. Conclusions HMM-FRAME provides a complementary protein domain classification tool to conventional profile HMM-based methods for data sets containing frameshifts. Its current implementation is best used for small-scale metagenomic data sets. The source code of HMM-FRAME can be downloaded at http://www.cse.msu.edu/~zhangy72/hmmframe/ and at https://sourceforge.net/projects/hmm-frame/.

  16. Molecular classification of Maize cytoplasms in a breeding program

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    Colombo. N * , Presello, D.A. , Kandus M. , G.E. Eyherabide and J.C. Salerno

    2012-06-01

    Full Text Available Cytoplasmic male sterility (CMS is maternally inherited in most of higher plants species. Together with nuclear restorer genes (Rf, CMS cytoplasms contribute significantly to the efficient production of hybrid seed. Three main types of male sterile cytoplasms are known in maize: T, S and C, which can be distinguished by crossing with specific restorer lines. Recently, PCR markers have been developed allowing the identification of different cytoplasms quickly and accurately. Our objective was to classify the cytoplasm type of maize inbred lines used in our breeding program and F1s obtained from crosses between CMS lines and elite maize lines using PCR multiplex. A multiplex PCR protocol was optimized for our conditions. We obtained the molecular classification of the analyzed cytoplasms. The optimized protocol is a valuable tool to trace male sterile cytoplasms and determine hybrid seed purity in our maize breeding program.

  17. Accurate and reliable cancer classification based on probabilistic inference of pathway activity.

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    Junjie Su

    Full Text Available With the advent of high-throughput technologies for measuring genome-wide expression profiles, a large number of methods have been proposed for discovering diagnostic markers that can accurately discriminate between different classes of a disease. However, factors such as the small sample size of typical clinical data, the inherent noise in high-throughput measurements, and the heterogeneity across different samples, often make it difficult to find reliable gene markers. To overcome this problem, several studies have proposed the use of pathway-based markers, instead of individual gene markers, for building the classifier. Given a set of known pathways, these methods estimate the activity level of each pathway by summarizing the expression values of its member genes, and use the pathway activities for classification. It has been shown that pathway-based classifiers typically yield more reliable results compared to traditional gene-based classifiers. In this paper, we propose a new classification method based on probabilistic inference of pathway activities. For a given sample, we compute the log-likelihood ratio between different disease phenotypes based on the expression level of each gene. The activity of a given pathway is then inferred by combining the log-likelihood ratios of the constituent genes. We apply the proposed method to the classification of breast cancer metastasis, and show that it achieves higher accuracy and identifies more reproducible pathway markers compared to several existing pathway activity inference methods.

  18. On the accurate molecular dynamics analysis of biological molecules

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    Yamashita, Takefumi

    2016-12-01

    As the evolution of computational technology has now enabled long molecular dynamics (MD) simulation, the evaluation of many physical properties shows improved convergence. Therefore, we can examine the detailed conditions of MD simulations and perform quantitative MD analyses. In this study, we address the quantitative and accuracy aspects of MD simulations using two example systems. First, it is found that several conditions of the MD simulations influence the area/lipid of the lipid bilayer. Second, we successfully detect the small but important differences in antibody motion between the antigen-bound and unbound states.

  19. Quantitatively accurate calculations of conductance and thermopower of molecular junctions

    DEFF Research Database (Denmark)

    Markussen, Troels; Jin, Chengjun; Thygesen, Kristian Sommer

    2013-01-01

    ) connected to gold electrodes using first‐principles calculations. We find excellent agreement with experiments for both molecules when exchange–correlation effects are described by the many‐body GW approximation. In contrast, results from standard density functional theory (DFT) deviate from experiments......‐interaction errors and image charge effects. Finally, we show that the conductance and thermopower of the considered junctions are relatively insensitive to the metal–molecule bonding geometry. Our results demonstrate that electronic and thermoelectric properties of molecular junctions can be predicted from first‐principles...... calculations when exchange–correlation effects are taken properly into account....

  20. Photometric brown-dwarf classification. I. A method to identify and accurately classify large samples of brown dwarfs without spectroscopy

    Science.gov (United States)

    Skrzypek, N.; Warren, S. J.; Faherty, J. K.; Mortlock, D. J.; Burgasser, A. J.; Hewett, P. C.

    2015-02-01

    Aims: We present a method, named photo-type, to identify and accurately classify L and T dwarfs onto the standard spectral classification system using photometry alone. This enables the creation of large and deep homogeneous samples of these objects efficiently, without the need for spectroscopy. Methods: We created a catalogue of point sources with photometry in 8 bands, ranging from 0.75 to 4.6 μm, selected from an area of 3344 deg2, by combining SDSS, UKIDSS LAS, and WISE data. Sources with 13.0 0.8, were then classified by comparison against template colours of quasars, stars, and brown dwarfs. The L and T templates, spectral types L0 to T8, were created by identifying previously known sources with spectroscopic classifications, and fitting polynomial relations between colour and spectral type. Results: Of the 192 known L and T dwarfs with reliable photometry in the surveyed area and magnitude range, 189 are recovered by our selection and classification method. We have quantified the accuracy of the classification method both externally, with spectroscopy, and internally, by creating synthetic catalogues and accounting for the uncertainties. We find that, brighter than J = 17.5, photo-type classifications are accurate to one spectral sub-type, and are therefore competitive with spectroscopic classifications. The resultant catalogue of 1157 L and T dwarfs will be presented in a companion paper.

  1. Clinical and molecular classification of cardiomyopathies

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    Franco Cecchi

    2012-07-01

    Full Text Available The term “cardiomyopathies” was used for the first time 55 years ago, in 1957. Since then awareness and knowledge of this important and complex group of heart muscle diseases have improved substantially. Over these past five decades a large number of definitions, nomenclature and schemes, have been advanced by experts and consensus panel, which reflect the fast and continued advance of the scientific understanding in the field. Cardiomyopathies are a heterogeneous group of inherited myocardial diseases, which represent an important cause of disability and adverse outcome. Although considered rare diseases, the overall estimated prevalence of all cardiomyopathies is at least 3% in the general population worldwide. Furthermore, their recognition is increasing due to advances in imaging techniques and greater awareness in both the public and medical community. Cardiomyopathies represent an ideal translational model of integration between basic and clinical sciences. A multidisciplinary approach is therefore essential in order to ensure their correct diagnosis and management. In the present work, we aim to provide a concise overview of the historical background, genetic and phenotypic spectrum and evolving concepts leading to the various attempts of cardiomyopathy classifications produced over the decades.

  2. Pathological Bases for a Robust Application of Cancer Molecular Classification

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    Salvador J. Diaz-Cano

    2015-04-01

    Full Text Available Any robust classification system depends on its purpose and must refer to accepted standards, its strength relying on predictive values and a careful consideration of known factors that can affect its reliability. In this context, a molecular classification of human cancer must refer to the current gold standard (histological classification and try to improve it with key prognosticators for metastatic potential, staging and grading. Although organ-specific examples have been published based on proteomics, transcriptomics and genomics evaluations, the most popular approach uses gene expression analysis as a direct correlate of cellular differentiation, which represents the key feature of the histological classification. RNA is a labile molecule that varies significantly according with the preservation protocol, its transcription reflect the adaptation of the tumor cells to the microenvironment, it can be passed through mechanisms of intercellular transference of genetic information (exosomes, and it is exposed to epigenetic modifications. More robust classifications should be based on stable molecules, at the genetic level represented by DNA to improve reliability, and its analysis must deal with the concept of intratumoral heterogeneity, which is at the origin of tumor progression and is the byproduct of the selection process during the clonal expansion and progression of neoplasms. The simultaneous analysis of multiple DNA targets and next generation sequencing offer the best practical approach for an analytical genomic classification of tumors.

  3. Molecular Pathology of Hepatic Neoplasms: Classification and Clinical Significance

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    Zenta Walther

    2011-01-01

    Full Text Available Recent technological advances have enabled investigators to characterize the molecular genetics and genomics of hepatic neoplasia in remarkable detail. From these studies, an increasing number of molecular markers are being identified that correlate with clinically important tumor phenotypes. This paper discusses current knowledge relevant to the molecular classification of epithelial primary hepatic tumors that arise in adults, including focal nodular hyperplasia (FNH, hepatocellular adenoma (HCA, hepatocellular carcinoma (HCC, cholangiocarcinoma (CC, and combined HCC-CC. Genetic analysis has defined molecular subtypes of HCA that are clinicopathologically distinct and can be distinguished through immunohistochemistry. Gene expression studies have identified molecular signatures of progression from dysplastic nodules (DNs to early HCC in cirrhosis. Analyses of the mutational spectra, chromosomal aberrations and instability, transcriptomics, and microRNA profiles of HCC have revealed the existence of biologically distinct subtypes of this common malignancy, with prognostic implications. Molecular characterization of biliary and hepatic progenitor cell phenotypes in liver cancer has shed new light on the histogenesis of these tumors and has focused attention on novel therapeutic targets. In coming years, the molecular classification of hepatic neoplasms will be increasingly valuable for guiding patient care, as targeted therapies for liver cancer are developed and brought into clinical practice.

  4. MOLECULAR (RE-)CLASSIFICATION OF CNS-PRIMITIVE NEUROECTODERMAL TUMORS

    OpenAIRE

    Kool, Marcel; Sturm, Dominik; Northcott, Paul A.; Jones, David T. W.; Korshunov, Andrey; Lichter, Peter; Pfister, Stefan

    2014-01-01

    BACKGROUND: According to the current WHO classification of CNS tumors, childhood CNS primitive neuro-ectodermal tumors (CNS-PNETs; WHO °IV) are poorly differentiated embryonal tumors with early onset and aggressive clinical behavior. Histological diagnosis can be complicated by morphological heterogeneity and divergent differentiation. Recent studies suggest the existence of molecular subgroups of CNS-PNETs sharing biological characteristics with other childhood CNS tumors. Here, we aimed at ...

  5. A practical approach to accurate classification and staging of mycosis fungoides and Sézary syndrome.

    Science.gov (United States)

    Thomas, Bjorn Rhys; Whittaker, Sean

    2012-12-01

    Cutaneous T-cell lymphomas are rare, distinct forms of non-Hodgkin's lymphomas. Of which, mycosis fungoides (MF) and Sézary syndrome (SS) are two of the most common forms. Careful, clear classification and staging of these lymphomas allow dermatologists to commence appropriate therapy and allow correct prognostic stratification for those patients affected. Of note, patients with more advanced disease will require multi-disciplinary input in determining specialist therapy. Literature has been summarized into an outline for classification/staging of MF and SS with the aim to provide clinical dermatologists with a concise review.

  6. Current Trends in the Molecular Classification of Renal Neoplasms

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    Andrew N. Young

    2006-01-01

    Full Text Available Renal cell carcinoma (RCC is the most common form of kidney cancer in adults. RCC is a significant challenge for pathologic diagnosis and clinical management. The primary approach to diagnosis is by light microscopy, using the World Health Organization (WHO classification system, which defines histopathologic tumor subtypes with distinct clinical behavior and underlying genetic mutations. However, light microscopic diagnosis of RCC subtypes is often difficult due to variable histology. In addition, the clinical behavior of RCC is highly variable and therapeutic response rates are poor. Few clinical assays are available to predict outcome in RCC or correlate behavior with histology. Therefore, novel RCC classification systems based on gene expression should be useful for diagnosis, prognosis, and treatment. Recent microarray studies have shown that renal tumors are characterized by distinct gene expression profiles, which can be used to discover novel diagnostic and prognostic biomarkers. Here, we review clinical features of kidney cancer, the WHO classification system, and the growing role of molecular classification for diagnosis, prognosis, and therapy of this disease.

  7. Genetic classification and molecular mechanisms of primary dystonia

    Institute of Scientific and Technical Information of China (English)

    Xueping Chen; Huifang Shang; Zuming Luo

    2008-01-01

    BACKGROUND: Primary dystonia is a heterogeneous disease, with a complex genetic basis. In previous studies, primary dystonia was classified according to age of onset, involved regions, and other clinical characteristics. With the development of molecular genetics, new virulence genes and sites have been discovered. Therefore, there is a gradual understanding of the various forms of dystonia, based on new viewpoints. There are 15 subtypes of dystonia, based on the molecular level, i.e., DYT1 to DYT15. OBJECTIVE: To analyze the genetic development of dystonia in detail, and to further investigate molecular mechanisms of dystonia. RETRIEVAL STRATEGY: A computer-based online search was conducted in PubMed for English language publications containing the keywords "dystonia and genetic" from January 1980 to March 2007. There were 105 articles in total. Inclusion criteria: ① the contents of the articles should closely address genetic classification and molecular mechanisms of primary dystonia; ② the articles published in recent years or in high-impact journals took preference. Exclusion criteria: duplicated articles. LITERATURE EVALUATION: The selected articles were on genetic classification and molecular genetics mechanism of primary dystonia. Of those, 27 were basic or clinical studies. DATA SYNTHESIS: ① Dystonia is a heterogeneous disease, with a complex genetic basis. According to the classification of the Human Genome Organization, there are 15 dystonia subtypes, based on genetics, i.e., DYT1-DYT15,including primary dystonia, dystonia plus syndrome, degeneration plus dystonia, and paroxysmal dyskinesia plus dystonia. ② To date, the chromosomes of 13 subtypes have been localized; however, DYT2 and DYT4 remain unclear. Six subtypes have been located within virulence genes. Specifically, torsinA gene expression results in the DYT1 genotype; autosomal dominant GTP cyclohydrolase I gene expression and recessive tyrosine hydroxylase expression result in the DYT5

  8. Classification algorithms with multi-modal data fusion could accurately distinguish neuromyelitis optica from multiple sclerosis.

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    Eshaghi, Arman; Riyahi-Alam, Sadjad; Saeedi, Roghayyeh; Roostaei, Tina; Nazeri, Arash; Aghsaei, Aida; Doosti, Rozita; Ganjgahi, Habib; Bodini, Benedetta; Shakourirad, Ali; Pakravan, Manijeh; Ghana'ati, Hossein; Firouznia, Kavous; Zarei, Mojtaba; Azimi, Amir Reza; Sahraian, Mohammad Ali

    2015-01-01

    Neuromyelitis optica (NMO) exhibits substantial similarities to multiple sclerosis (MS) in clinical manifestations and imaging results and has long been considered a variant of MS. With the advent of a specific biomarker in NMO, known as anti-aquaporin 4, this assumption has changed; however, the differential diagnosis remains challenging and it is still not clear whether a combination of neuroimaging and clinical data could be used to aid clinical decision-making. Computer-aided diagnosis is a rapidly evolving process that holds great promise to facilitate objective differential diagnoses of disorders that show similar presentations. In this study, we aimed to use a powerful method for multi-modal data fusion, known as a multi-kernel learning and performed automatic diagnosis of subjects. We included 30 patients with NMO, 25 patients with MS and 35 healthy volunteers and performed multi-modal imaging with T1-weighted high resolution scans, diffusion tensor imaging (DTI) and resting-state functional MRI (fMRI). In addition, subjects underwent clinical examinations and cognitive assessments. We included 18 a priori predictors from neuroimaging, clinical and cognitive measures in the initial model. We used 10-fold cross-validation to learn the importance of each modality, train and finally test the model performance. The mean accuracy in differentiating between MS and NMO was 88%, where visible white matter lesion load, normal appearing white matter (DTI) and functional connectivity had the most important contributions to the final classification. In a multi-class classification problem we distinguished between all of 3 groups (MS, NMO and healthy controls) with an average accuracy of 84%. In this classification, visible white matter lesion load, functional connectivity, and cognitive scores were the 3 most important modalities. Our work provides preliminary evidence that computational tools can be used to help make an objective differential diagnosis of NMO and MS.

  9. Classification algorithms with multi-modal data fusion could accurately distinguish neuromyelitis optica from multiple sclerosis

    Directory of Open Access Journals (Sweden)

    Arman Eshaghi

    2015-01-01

    Full Text Available Neuromyelitis optica (NMO exhibits substantial similarities to multiple sclerosis (MS in clinical manifestations and imaging results and has long been considered a variant of MS. With the advent of a specific biomarker in NMO, known as anti-aquaporin 4, this assumption has changed; however, the differential diagnosis remains challenging and it is still not clear whether a combination of neuroimaging and clinical data could be used to aid clinical decision-making. Computer-aided diagnosis is a rapidly evolving process that holds great promise to facilitate objective differential diagnoses of disorders that show similar presentations. In this study, we aimed to use a powerful method for multi-modal data fusion, known as a multi-kernel learning and performed automatic diagnosis of subjects. We included 30 patients with NMO, 25 patients with MS and 35 healthy volunteers and performed multi-modal imaging with T1-weighted high resolution scans, diffusion tensor imaging (DTI and resting-state functional MRI (fMRI. In addition, subjects underwent clinical examinations and cognitive assessments. We included 18 a priori predictors from neuroimaging, clinical and cognitive measures in the initial model. We used 10-fold cross-validation to learn the importance of each modality, train and finally test the model performance. The mean accuracy in differentiating between MS and NMO was 88%, where visible white matter lesion load, normal appearing white matter (DTI and functional connectivity had the most important contributions to the final classification. In a multi-class classification problem we distinguished between all of 3 groups (MS, NMO and healthy controls with an average accuracy of 84%. In this classification, visible white matter lesion load, functional connectivity, and cognitive scores were the 3 most important modalities. Our work provides preliminary evidence that computational tools can be used to help make an objective differential diagnosis

  10. Molecular Classification of Lobular Carcinoma of the Breast

    Science.gov (United States)

    Fu, Denggang; Zuo, Qi; Huang, Qi; Su, Li; Ring, Huijun Z.; Ring, Brian Z.

    2017-01-01

    The morphology of breast tumors is complicated and diagnosis can be difficult. We present here a novel diagnostic model which we validate on both array-based and RNA sequencing platforms which reliably distinguishes this tumor type across multiple cohorts. We also examine how this molecular classification predicts sensitivity to common chemotherapeutics in cell-line based assays. A total of 1845 invasive breast cancer cases in six cohorts were collected, split into discovery and validation cohorts, and a classifier was created and compared to pathological diagnosis, grade and survival. In the validation cohorts the concordance of predicted diagnosis with a pathological diagnosis was 92%, and 97% when inconclusively classified cases were excluded. Tumor-derived cell lines were classified with the model as having predominantly ductal or lobular-like molecular physiologies, and sensitivity of these lines to relevant compounds was analyzed. A diagnostic tool can be created that reliably distinguishes lobular from ductal carcinoma and allows the classification of cell lines on the basis of molecular profiles associated with these tumor types. This tool may assist in improved diagnosis and aid in explorations of the response of lobular type breast tumor models to different compounds. PMID:28303886

  11. Molecular voting for glioma classification reflecting heterogeneity in the continuum of cancer progression.

    Science.gov (United States)

    Fuller, Gregory N; Mircean, Cristian; Tabus, Ioan; Taylor, Ellen; Sawaya, Raymond; Bruner, Janet M; Shmulevich, Ilya; Zhang, Wei

    2005-09-01

    Gliomas, the most common brain tumors, are generally categorized into two lineages (astrocytic and oligodendrocytic) and further classified as low-grade (astrocytoma and oligodendroglioma), mid-grade (anaplastic astrocytoma and anaplastic oligodendroglioma), and high-grade (glioblastoma multiforme) based on morphological features. A strict classification scheme has limitations because a specific glioma can be at any stage of the continuum of cancer progression and may contain mixed features. Thus, a more comprehensive classification based on molecular signatures may reflect the biological nature of specific tumors more accurately. In this study, we used microarray technology to profile the gene expression of 49 human brain tumors and applied the k-nearest neighbor algorithm for classification. We first trained the classification gene set with 19 of the most typical glioma cases and selected a set of genes that provide the lowest cross-validation classification error with k=5. We then applied this gene set to the 30 remaining cases, including several that do not belong to gliomas such as atypical meningioma. The results showed that not only does the algorithm correctly classify most of the gliomas, but the detailed voting results also provide more subtle information regarding the molecular similarities to neighboring classes. For atypical meningioma, the voting was equally split among the four classes, indicating a difficulty in placement of meningioma into the four classes of gliomas. Thus, the actual voting results, which are typically used only to decide the winning class label in k-nearest neighbor algorithms, provide a useful method for gaining deeper insight into the stage of a tumor in the continuum of cancer development.

  12. The International Classification of Headache Disorders: accurate diagnosis of orofacial pain?

    Science.gov (United States)

    Benoliel, R; Birman, N; Eliav, E; Sharav, Y

    2008-07-01

    The aim was to apply diagnostic criteria, as published by the International Headache Society (IHS), to the diagnosis of orofacial pain. A total of 328 consecutive patients with orofacial pain were collected over a period of 2 years. The orofacial pain clinic routinely employs criteria published by the IHS, the American Academy of Orofacial Pain (AAOP) and the Research Diagnostic Criteria for Temporomandibular Disorders (RDCTMD). Employing IHS criteria, 184 patients were successfully diagnosed (56%), including 34 with persistent idiopathic facial pain. In the remaining 144 we applied AAOP/RDCTMD criteria and diagnosed 120 as masticatory myofascial pain (MMP) resulting in a diagnostic efficiency of 92.7% (304/328) when applying the three classifications (IHS, AAOP, RDCTMD). Employing further published criteria, 23 patients were diagnosed as neurovascular orofacial pain (NVOP, facial migraine) and one as a neuropathy secondary to connective tissue disease. All the patients were therefore allocated to predefined diagnoses. MMP is clearly defined by AAOP and the RDCTMD. However, NVOP is not defined by any of the above classification systems. The features of MMP and NVOP are presented and analysed with calculations for positive (PPV) and negative predictive values (NPV). In MMP the combination of facial pain aggravated by jaw movement, and the presence of three or more tender muscles resulted in a PPV = 0.82 and a NPV = 0.86. For NVOP the combination of facial pain, throbbing quality, autonomic and/or systemic features and attack duration of > 60 min gave a PPV = 0.71 and a NPV = 0.95. Expansion of the IHS system is needed so as to integrate more orofacial pain syndromes.

  13. Photometric brown-dwarf classification. I. A method to identify and accurately classify large samples of brown dwarfs without spectroscopy

    CERN Document Server

    Skrzypek, Nathalie; Faherty, Jacqueline K; Mortlock, Daniel J; Burgasser, Adam J; Hewett, Paul C

    2014-01-01

    Aims. We present a method, named photo-type, to identify and accurately classify L and T dwarfs onto the standard spectral classification system using photometry alone. This enables the creation of large and deep homogeneous samples of these objects efficiently, without the need for spectroscopy. Methods. We created a catalogue of point sources with photometry in 8 bands, ranging from 0.75 to 4.6 microns, selected from an area of 3344 deg^2, by combining SDSS, UKIDSS LAS, and WISE data. Sources with 13.0 0.8, were then classified by comparison against template colours of quasars, stars, and brown dwarfs. The L and T templates, spectral types L0 to T8, were created by identifying previously known sources with spectroscopic classifications, and fitting polynomial relations between colour and spectral type. Results. Of the 192 known L and T dwarfs with reliable photometry in the surveyed area and magnitude range, 189 are recovered by our selection and classification method. We have quantified the accuracy of th...

  14. Treatment response classification of liver metastatic disease evaluated on imaging. Are RECIST unidimensional measurements accurate?

    Science.gov (United States)

    Mantatzis, Michael; Kakolyris, Stylianos; Amarantidis, Kyriakos; Karayiannakis, Anastasios; Prassopoulos, Panos

    2009-07-01

    The purpose of this study was to evaluate the accuracy of unidimensional measurements (response evaluation criteria in solid tumors, RECIST) compared with volumetric measurements in patients with liver metastases undergoing chemotherapy. Forty-four patients with newly diagnosed liver lesions underwent three MRI examinations at treatment initiation, during chemotherapy, and immediately post-treatment. Measurements based on RECIST guidelines and volume calculations were performed on the "target" lesions (TLs). The two methods were in agreement in 64/77 of patients and 253/301 of individual lesions classification in response categories ("good" agreement, Cohen kappa = 0.735 and 0.741, respectively). In 16.88% of the comparisons the two methods stratified patients to a different response category; 27.6% of TLs did not follow the response category of the patient in whom lesions were located. The actual volume of TLs differs from the calculated volume of a sphere with the same diameter. Our study supports the use of volumetric techniques that may overcome certain disadvantages of unidimensional measurements.

  15. On the errors in molecular dipole moments derived from accurate diffraction data.

    Science.gov (United States)

    Coppens; Volkov; Abramov; Koritsanszky

    1999-09-01

    The error in the molecular dipole moment as derived from accurate X-ray diffraction data is shown to be origin dependent in the general case. It is independent of the choice of origin if an electroneutrality constraint is introduced, even when additional constraints are applied to the monopole populations. If a constraint is not applied to individual moieties, as is appropriate for multicomponent crystals or crystals containing molecular ions, the geometric center of the entity considered is a suitable choice of origin for the error treatment.

  16. Enabling Computational Technologies for the Accurate Prediction/Description of Molecular Interactions in Condensed Phases

    Science.gov (United States)

    2014-10-08

    models to compute accurately the molecular interactions between a mobile or stationary phase and a target substrate or analyte , which are fundamental...mobile or stationary phase and a target substrate or analyte , which are fundamental to diverse technologies, e.g., sensor or separation design. With...D. G., New Orleans, LA, April 9, 2013. 223rd Electrochemical Society Meeting, Continuum Solvation Models for Computational Electrochemistry

  17. A Void Reference Sensor-Multiple Signal Classification Algorithm for More Accurate Direction of Arrival Estimation of Low Altitude Target

    Institute of Scientific and Technical Information of China (English)

    XIAO Hui; SUN Jin-cai; YUAN Jun; NIU Yi-long

    2007-01-01

    There exists MUSIC (multiple signal classification) algorithm for direction of arrival (DOA) estimation. This paper is to present a different MUSIC algorithm for more accurate estimation of low altitude target. The possibility of better performance is analyzed using a void reference sensor (VRS) in MUSIC algorithm. The following two topics are discussed: 1) the time delay formula and VRS-MUSIC algorithm with VRS located on the minus of z-axes; 2) the DOA estimation results of VRS-MUSIC and MUSIC algorithms. The simulation results show VRS-MUSIC algorithm has three advantages compared with MUSIC: 1 ) When the signal to noise ratio (SNR) is more than - 5 dB, the direction estimation error is 1/2 as much as that obtained by MUSIC; 2) The side lobe is more lower and the stability is better; 3) The size of array that the algorithm requires is smaller.

  18. Novel approaches for the molecular classification of prostate cancer

    Institute of Scientific and Technical Information of China (English)

    Robert H. Getzenberg

    2010-01-01

    @@ Among the urologic cancers, prostate cancer is by far the most common, and it appears to have the potential to affect almost all men throughout the world as they age. A number of studies have shown that many men with prostate cancer will not die from their disease, but rather with the disease but from other causes. These men have a form of prostate cancer that is de-scribed as "very low risk" and has often been called indolent. There are however a group of men that have a form of prostate cancer that is much more aggressive and life threatening. Unlike other cancer types, we have few tools to provide for the molecular classification of prostate cancer.

  19. Molecular observations of HH34 - Does NH3 accurately trace dense molecular gas near young stars?

    Science.gov (United States)

    Davis, C. J.; Dent, W. R. F.

    1993-03-01

    Single-dish observations in HCO(+) J = 4-3 are presented of the regions around HH34 and around HH34IRS. The former is one of the best examples of the association between Herbig-Haro shocks, optical jets, and young stellar objects. The HCO(+) and CS maps peak toward the outflow source HH34IRS and suggest the presence of a hot dense molecular core. The NH3 is confined to a peak about 4-0 arcsec east of HH34IRS and to a ridge which extends in a north-south direction and peaks about 20 arcsec south of the end of the optical jet. Thus, the NH3 observations do not trace the underlying gas density and temperature in this outflow source. Toward HH34IRS the NH3 column density is less by a factor of about 10 than toward the NH3 peak position is the HH34 region, providing evidence that the NH3 is underabundant towards the central exciting stars. This underabundance may explain the toroidal structures often seen in NH3 observations of other outflow sources.

  20. 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 BACKGROUND: 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. METHODS AND FINDINGS: 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

  1. CAST: a new program package for the accurate characterization of large and flexible molecular systems.

    Science.gov (United States)

    Grebner, Christoph; Becker, Johannes; Weber, Daniel; Bellinger, Daniel; Tafipolski, Maxim; Brückner, Charlotte; Engels, Bernd

    2014-09-15

    The presented program package, Conformational Analysis and Search Tool (CAST) allows the accurate treatment of large and flexible (macro) molecular systems. For the determination of thermally accessible minima CAST offers the newly developed TabuSearch algorithm, but algorithms such as Monte Carlo (MC), MC with minimization, and molecular dynamics are implemented as well. For the determination of reaction paths, CAST provides the PathOpt, the Nudge Elastic band, and the umbrella sampling approach. Access to free energies is possible through the free energy perturbation approach. Along with a number of standard force fields, a newly developed symmetry-adapted perturbation theory-based force field is included. Semiempirical computations are possible through DFTB+ and MOPAC interfaces. For calculations based on density functional theory, a Message Passing Interface (MPI) interface to the Graphics Processing Unit (GPU)-accelerated TeraChem program is available. The program is available on request.

  2. A simplified approach for the molecular classification of glioblastomas.

    Directory of Open Access Journals (Sweden)

    Marie Le Mercier

    Full Text Available Glioblastoma (GBM is the most common malignant primary brain tumors in adults and exhibit striking aggressiveness. Although GBM constitute a single histological entity, they exhibit considerable variability in biological behavior, resulting in significant differences in terms of prognosis and response to treatment. In an attempt to better understand the biology of GBM, many groups have performed high-scale profiling studies based on gene or protein expression. These studies have revealed the existence of several GBM subtypes. Although there remains to be a clear consensus, two to four major subtypes have been identified. Interestingly, these different subtypes are associated with both differential prognoses and responses to therapy. In the present study, we investigated an alternative immunohistochemistry (IHC-based approach to achieve a molecular classification for GBM. For this purpose, a cohort of 100 surgical GBM samples was retrospectively evaluated by immunohistochemical analysis of EGFR, PDGFRA and p53. The quantitative analysis of these immunostainings allowed us to identify the following two GBM subtypes: the "Classical-like" (CL subtype, characterized by EGFR-positive and p53- and PDGFRA-negative staining and the "Proneural-like" (PNL subtype, characterized by p53- and/or PDGFRA-positive staining. This classification represents an independent prognostic factor in terms of overall survival compared to age, extent of resection and adjuvant treatment, with a significantly longer survival associated with the PNL subtype. Moreover, these two GBM subtypes exhibited different responses to chemotherapy. The addition of temozolomide to conventional radiotherapy significantly improved the survival of patients belonging to the CL subtype, but it did not affect the survival of patients belonging to the PNL subtype. We have thus shown that it is possible to differentiate between different clinically relevant subtypes of GBM by using IHC

  3. Accurate studies on the full vibrational energy spectra and molecular dissociation energies for some electronic states of N2 molecule

    Institute of Scientific and Technical Information of China (English)

    REN; Weiyi; SUN; Weiguo; HOU; Shilin; FENG; Hao

    2005-01-01

    It is usually very difficult to directly obtain molecular dissociation energy De and all accurate high-lying vibrational energies for most diatomic electronic states using modern experimental techniques or quantum theories, and it is also very difficult to give accurate analytical expression for diatomic molecular dissociation energy. This study proposes a new analytical formula for obtaining accurate molecular dissociation energy based on the LeRoy and Bernstein's energy expression in dissociation limit. A set of full vibrational energy spectra for some electronic states of N2 molecule are studied using the algebraic method (AM) suggested recently, and the corresponding accurate molecular dissociation energies are evaluated using the proposed new formula and high-lying AM vibrational energies. The results show that the AM spectra and the new theoretical dissociation energies agree excellently with experimental data, and thereby providing a new physical approach to generating accurate dissociation energies for electronic states of diatomic molecules.

  4. Simple, rapid and accurate molecular diagnosis of acute promyelocytic leukemia by loop mediated amplification technology.

    Science.gov (United States)

    Spinelli, Orietta; Rambaldi, Alessandro; Rigo, Francesca; Zanghì, Pamela; D'Agostini, Elena; Amicarelli, Giulia; Colotta, Francesco; Divona, Mariadomenica; Ciardi, Claudia; Coco, Francesco Lo; Minnucci, Giulia

    2015-01-01

    The diagnostic work-up of acute promyelocytic leukemia (APL) includes the cytogenetic demonstration of the t(15;17) translocation and/or the PML-RARA chimeric transcript by RQ-PCR or RT-PCR. This latter assays provide suitable results in 3-6 hours. We describe here two new, rapid and specific assays that detect PML-RARA transcripts, based on the RT-QLAMP (Reverse Transcription-Quenching Loop-mediated Isothermal Amplification) technology in which RNA retrotranscription and cDNA amplification are carried out in a single tube with one enzyme at one temperature, in fluorescence and real time format. A single tube triplex assay detects bcr1 and bcr3 PML-RARA transcripts along with GUS housekeeping gene. A single tube duplex assay detects bcr2 and GUSB. In 73 APL cases, these assays detected in 16 minutes bcr1, bcr2 and bcr3 transcripts. All 81 non-APL samples were negative by RT-QLAMP for chimeric transcripts whereas GUSB was detectable. In 11 APL patients in which RT-PCR yielded equivocal breakpoint type results, RT-QLAMP assays unequivocally and accurately defined the breakpoint type (as confirmed by sequencing). Furthermore, RT-QLAMP could amplify two bcr2 transcripts with particularly extended PML exon 6 deletions not amplified by RQ-PCR. RT-QLAMP reproducible sensitivity is 10(-3) for bcr1 and bcr3 and 10(-)2 for bcr2 thus making this assay particularly attractive at diagnosis and leaving RQ-PCR for the molecular monitoring of minimal residual disease during the follow up. In conclusion, PML-RARA RT-QLAMP compared to RT-PCR or RQ-PCR is a valid improvement to perform rapid, simple and accurate molecular diagnosis of APL.

  5. PyVCI: A flexible open-source code for calculating accurate molecular infrared spectra

    Science.gov (United States)

    Sibaev, Marat; Crittenden, Deborah L.

    2016-06-01

    The PyVCI program package is a general purpose open-source code for simulating accurate molecular spectra, based upon force field expansions of the potential energy surface in normal mode coordinates. It includes harmonic normal coordinate analysis and vibrational configuration interaction (VCI) algorithms, implemented primarily in Python for accessibility but with time-consuming routines written in C. Coriolis coupling terms may be optionally included in the vibrational Hamiltonian. Non-negligible VCI matrix elements are stored in sparse matrix format to alleviate the diagonalization problem. CPU and memory requirements may be further controlled by algorithmic choices and/or numerical screening procedures, and recommended values are established by benchmarking using a test set of 44 molecules for which accurate analytical potential energy surfaces are available. Force fields in normal mode coordinates are obtained from the PyPES library of high quality analytical potential energy surfaces (to 6th order) or by numerical differentiation of analytic second derivatives generated using the GAMESS quantum chemical program package (to 4th order).

  6. Exchange-Hole Dipole Dispersion Model for Accurate Energy Ranking in Molecular Crystal Structure Prediction.

    Science.gov (United States)

    Whittleton, Sarah R; Otero-de-la-Roza, A; Johnson, Erin R

    2017-02-14

    Accurate energy ranking is a key facet to the problem of first-principles crystal-structure prediction (CSP) of molecular crystals. This work presents a systematic assessment of B86bPBE-XDM, a semilocal density functional combined with the exchange-hole dipole moment (XDM) dispersion model, for energy ranking using 14 compounds from the first five CSP blind tests. Specifically, the set of crystals studied comprises 11 rigid, planar compounds and 3 co-crystals. The experimental structure was correctly identified as the lowest in lattice energy for 12 of the 14 total crystals. One of the exceptions is 4-hydroxythiophene-2-carbonitrile, for which the experimental structure was correctly identified once a quasi-harmonic estimate of the vibrational free-energy contribution was included, evidencing the occasional importance of thermal corrections for accurate energy ranking. The other exception is an organic salt, where charge-transfer error (also called delocalization error) is expected to cause the base density functional to be unreliable. Provided the choice of base density functional is appropriate and an estimate of temperature effects is used, XDM-corrected density-functional theory is highly reliable for the energetic ranking of competing crystal structures.

  7. Molecular Classification of Gastric Cancer: A new paradigm

    Science.gov (United States)

    Shah, Manish A.; Khanin, Raya; Tang, Laura; Janjigian, Yelena Y.; Klimstra, David S.; Gerdes, Hans; Kelsen, David P.

    2011-01-01

    Purpose Gastric cancer may be subdivided into three distinct subtypes –proximal, diffuse, and distal gastric cancer– based on histopathologic and anatomic criteria. Each subtype is associated with unique epidemiology. Our aim is to test the hypothesis that these distinct gastric cancer subtypes may also be distinguished by gene expression analysis. Experimental Design Patients with localized gastric adenocarcinoma being screened for a phase II preoperative clinical trial (NCI 5917) underwent endoscopic biopsy for fresh tumor procurement. 4–6 targeted biopsies of the primary tumor were obtained. Macrodissection was performed to ensure >80% carcinoma in the sample. HG-U133A GeneChip (Affymetrix) was used for cDNA expression analysis, and all arrays were processed and analyzed using the Bioconductor R-package. Results Between November 2003 and January 2006, 57 patients were screened to identify 36 patients with localized gastric cancer who had adequate RNA for expression analysis. Using supervised analysis, we built a classifier to distinguish the three gastric cancer subtypes, successfully classifying each into tightly grouped clusters. Leave-one-out cross validation error was 0.14, suggesting that >85% of samples were classified correctly. Gene set analysis with the False Discovery Rate set at 0.25 identified several pathways that were differentially regulated when comparing each gastric cancer subtype to adjacent normal stomach. Conclusions Subtypes of gastric cancer that have epidemiologic and histologic distinction are also distinguished by gene expression data. These preliminary data suggest a new classification of gastric cancer with implications for improving our understanding of disease biology and identification of unique molecular drivers for each gastric cancer subtype. PMID:21430069

  8. Warm gas in the rotating disk of the Red Rectangle: accurate models of molecular line emission

    CERN Document Server

    Bujarrabal, V

    2013-01-01

    We aim to study the excitation conditions of the molecular gas in the rotating disk of the Red Rectangle, the only post-Asymptotic-Giant-Branch object in which the existence of an equatorial rotating disk has been demonstrated. For this purpose, we developed a complex numerical code that accurately treats radiative transfer in 2-D, adapted to the study of molecular lines from rotating disks. We present far-infrared Herschel/HIFI observations of the 12CO and 13CO J=6-5, J=10-9, and J=16-15 transitions in the Red Rectangle. We also present our code in detail and discuss the accuracy of its predictions, from comparison with well-tested codes. Theoretical line profiles are compared with the empirical data to deduce the physical conditions in the disk by means of model fitting. We conclude that our code is very efficient and produces reliable results. The comparison of the theoretical predictions with our observations reveals that the temperature of the Red Rectangle disk is typically ~ 100-150 K, about twice as h...

  9. Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields

    Science.gov (United States)

    Lee, M.W.; Meuwly, M.

    2013-01-01

    The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.

  10. Accurate molecular structure and spectroscopic properties for nucleobases: A combined computational - microwave investigation of 2-thiouracil as a case study

    Science.gov (United States)

    Puzzarini, Cristina; Biczysko, Malgorzata; Barone, Vincenzo; Peña, Isabel; Cabezas, Carlos; Alonso, José L.

    2015-01-01

    The computational composite scheme purposely set up for accurately describing the electronic structure and spectroscopic properties of small biomolecules has been applied to the first study of the rotational spectrum of 2-thiouracil. The experimental investigation was made possible thanks to the combination of the laser ablation technique with Fourier Transform Microwave spectrometers. The joint experimental – computational study allowed us to determine accurate molecular structure and spectroscopic properties for the title molecule, but more important, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules. PMID:24002739

  11. Review of current classification, molecular alterations, and tyrosine kinase inhibitor therapies in myeloproliferative disorders with hypereosinophilia

    Directory of Open Access Journals (Sweden)

    Havelange V

    2013-08-01

    Full Text Available Violaine Havelange,1,2 Jean-Baptiste Demoulin1 1de Duve Institute, Université catholique de Louvain, Brussels, Belgium; 2Department of Hematology, Cliniques universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium Abstract: Recent advances in our understanding of the molecular mechanisms underlying hypereosinophilia have led to the development of a 'molecular' classification of myeloproliferative disorders with eosinophilia. The revised 2008 World Health Organization classification of myeloid neoplasms included a new category called “myeloid and lymphoid neoplasms with eosinophilia and abnormalities of PDGFRA, PDGFRB or FGFR1.” Despite the molecular heterogeneity of PDGFR (platelet-derived growth factor receptor rearrangements, tyrosine kinase inhibitors at low dose induce rapid and complete hematological remission in the majority of these patients. Other kinase inhibitors are promising. Further discoveries of new molecular alterations will direct the development of new specific inhibitors. In this review, an update of the classifications of myeloproliferative disorders associated with hypereosinophilia is discussed together with open and controversial questions. Molecular mechanisms and promising results of tyrosine kinase inhibitor treatments are reviewed. Keywords: hypereosinophilia, classification, myeloproliferative disorders, molecular alterations, tyrosine kinase inhibitor

  12. Classification

    Science.gov (United States)

    Clary, Renee; Wandersee, James

    2013-01-01

    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…

  13. [New molecular classification of colorectal cancer, pancreatic cancer and stomach cancer: Towards "à la carte" treatment?].

    Science.gov (United States)

    Dreyer, Chantal; Afchain, Pauline; Trouilloud, Isabelle; André, Thierry

    2016-01-01

    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.

  14. Molecular and Translational Classifications of DAMPs in Immunogenic Cell Death

    Directory of Open Access Journals (Sweden)

    Abhishek D Garg

    2015-11-01

    Full Text Available The immunogenicity of malignant cells has recently been acknowledged as a critical determinant of efficacy in cancer therapy. Thus, besides developing direct immunostimulatory regimens including dendritic cell-based vaccines, checkpoint-blocking therapies, and adoptive T-cell transfer, researchers have started to focus on the overall immunobiology of neoplastic cells. It is now clear that cancer cells can succumb to some anticancer therapies by undergoing a peculiar form of cell death that is characterized by an increased immunogenic potential, owing to the emission of so-called damage-associated molecular patterns (DAMPs. The emission of DAMPs and other immunostimulatory factors by cells succumbing to immunogenic cell death (ICD favors the establishment of a productive interface with the immune system. This results in the elicitation of tumor-targeting immune responses associated with the elimination of residual, treatment-resistant cancer cells, as well as with the establishment of immunological memory. Although ICD has been characterized with increased precision since its discovery, several questions remain to be addressed. Here, we summarize and tabulate the main molecular, immunological, preclinical and clinical aspects of ICD, in an attempt to capture the essence of this clinically relevant phenomenon, and identify future challenges for this rapidly expanding field of investigation.

  15. Fast and Accurate Modeling of Molecular Atomization Energies with Machine Learning

    CERN Document Server

    Rupp, Matthias; Müller, Klaus-Robert; von Lilienfeld, O Anatole

    2011-01-01

    We introduce a machine learning model to predict atomization energies of a diverse set of organic molecules, based on nuclear charges and atomic positions only. The problem of solving the molecular Schr\\"odinger equation is mapped onto a non-linear statistical regression problem of reduced complexity. Regression models are trained on and compared to atomization energies computed with hybrid density-functional theory. Cross-validation over more than seven thousand small organic molecules yields a mean absolute error of ~10 kcal/mol. Applicability is demonstrated for the prediction of molecular atomization potential energy curves.

  16. Molecular and biochemical classification of plant-derived food allergens.

    Science.gov (United States)

    Breiteneder, H; Ebner, C

    2000-07-01

    Molecular biology and biochemical techniques have significantly advanced the knowledge of allergens derived from plant foods. Surprisingly, many of the known plant food allergens are homologous to pathogenesis-related proteins (PRs), proteins that are induced by pathogens, wounding, or certain environmental stresses. PRs have been classified into 14 families. Examples of allergens homologous to PRs include chitinases (PR-3 family) from avocado, banana, and chestnut; antifungal proteins such as the thaumatin-like proteins (PR-5) from cherry and apple; proteins homologous to the major birch pollen allergen Bet v 1 (PR-10) from vegetables and fruits; and lipid transfer proteins (PR-14) from fruits and cereals. Allergens other than PR homologs can be allotted to other well-known protein families such as inhibitors of alpha-amylases and trypsin from cereal seeds, profilins from fruits and vegetables, seed storage proteins from nuts and mustard seeds, and proteases from fruits. As more clinical data and structural information on allergenic molecules becomes available, we may finally be able to answer what characteristics of a molecule are responsible for its allergenicity.

  17. A Large Catalog of Accurate Distances to Molecular Clouds from PS1 Photometry

    CERN Document Server

    Schlafly, E F; Finkbeiner, D P; Rix, H -W; Bell, E F; Burgett, W S; Chambers, K C; Draper, P W; Hodapp, K W; Kaiser, N; Magnier, E A; Martin, N F; Metcalfe, N; Price, P A; Tonry, J L

    2014-01-01

    Distance measurements to molecular clouds are important, but are often made separately for each cloud of interest, employing very different different data and techniques. We present a large, homogeneous catalog of distances to molecular clouds, most of which are of unprecedented accuracy. We determine distances using optical photometry of stars along lines of sight toward these clouds, obtained from PanSTARRS-1. We simultaneously infer the reddenings and distances to these stars, tracking the full probability distribution function using a technique presented in Green et al. (2014). We fit these star-by-star measurements using a simple dust screen model to find the distance to each cloud. We thus estimate the distances to almost all of the clouds in the Magnani et al. (1985) catalog, as well as many other well-studied clouds, including Orion, Perseus, Taurus, Cepheus, Polaris, California, and Monoceros R2, avoiding only the inner Galaxy. Typical statistical uncertainties in the distances are 5%, though the sys...

  18. Utilizing fast multipole expansions for efficient and accurate quantum-classical molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Schwörer, Magnus; Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul, E-mail: paul.tavan@physik.uni-muenchen.de [Lehrstuhl für BioMolekulare Optik, Ludwig–Maximilians Universität München, Oettingenstr. 67, 80538 München (Germany)

    2015-03-14

    Recently, a novel approach to hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations has been suggested [Schwörer et al., J. Chem. Phys. 138, 244103 (2013)]. Here, the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 10{sup 3}-10{sup 5} molecules as negative gradients of a DFT/PMM hybrid Hamiltonian. The electrostatic interactions are efficiently described by a hierarchical fast multipole method (FMM). Adopting recent progress of this FMM technique [Lorenzen et al., J. Chem. Theory Comput. 10, 3244 (2014)], which particularly entails a strictly linear scaling of the computational effort with the system size, and adapting this revised FMM approach to the computation of the interactions between the DFT and PMM fragments of a simulation system, here, we show how one can further enhance the efficiency and accuracy of such DFT/PMM-MD simulations. The resulting gain of total performance, as measured for alanine dipeptide (DFT) embedded in water (PMM) by the product of the gains in efficiency and accuracy, amounts to about one order of magnitude. We also demonstrate that the jointly parallelized implementation of the DFT and PMM-MD parts of the computation enables the efficient use of high-performance computing systems. The associated software is available online.

  19. Fast, Simple and Accurate Handwritten Digit Classification by Training Shallow Neural Network Classifiers with the 'Extreme Learning Machine' Algorithm.

    Science.gov (United States)

    McDonnell, Mark D; Tissera, Migel D; Vladusich, Tony; van Schaik, André; Tapson, Jonathan

    2015-01-01

    Recent advances in training deep (multi-layer) architectures have inspired a renaissance in neural network use. For example, deep convolutional networks are becoming the default option for difficult tasks on large datasets, such as image and speech recognition. However, here we show that error rates below 1% on the MNIST handwritten digit benchmark can be replicated with shallow non-convolutional neural networks. This is achieved by training such networks using the 'Extreme Learning Machine' (ELM) approach, which also enables a very rapid training time (∼ 10 minutes). Adding distortions, as is common practise for MNIST, reduces error rates even further. Our methods are also shown to be capable of achieving less than 5.5% error rates on the NORB image database. To achieve these results, we introduce several enhancements to the standard ELM algorithm, which individually and in combination can significantly improve performance. The main innovation is to ensure each hidden-unit operates only on a randomly sized and positioned patch of each image. This form of random 'receptive field' sampling of the input ensures the input weight matrix is sparse, with about 90% of weights equal to zero. Furthermore, combining our methods with a small number of iterations of a single-batch backpropagation method can significantly reduce the number of hidden-units required to achieve a particular performance. Our close to state-of-the-art results for MNIST and NORB suggest that the ease of use and accuracy of the ELM algorithm for designing a single-hidden-layer neural network classifier should cause it to be given greater consideration either as a standalone method for simpler problems, or as the final classification stage in deep neural networks applied to more difficult problems.

  20. Fast, Simple and Accurate Handwritten Digit Classification by Training Shallow Neural Network Classifiers with the 'Extreme Learning Machine' Algorithm.

    Directory of Open Access Journals (Sweden)

    Mark D McDonnell

    Full Text Available Recent advances in training deep (multi-layer architectures have inspired a renaissance in neural network use. For example, deep convolutional networks are becoming the default option for difficult tasks on large datasets, such as image and speech recognition. However, here we show that error rates below 1% on the MNIST handwritten digit benchmark can be replicated with shallow non-convolutional neural networks. This is achieved by training such networks using the 'Extreme Learning Machine' (ELM approach, which also enables a very rapid training time (∼ 10 minutes. Adding distortions, as is common practise for MNIST, reduces error rates even further. Our methods are also shown to be capable of achieving less than 5.5% error rates on the NORB image database. To achieve these results, we introduce several enhancements to the standard ELM algorithm, which individually and in combination can significantly improve performance. The main innovation is to ensure each hidden-unit operates only on a randomly sized and positioned patch of each image. This form of random 'receptive field' sampling of the input ensures the input weight matrix is sparse, with about 90% of weights equal to zero. Furthermore, combining our methods with a small number of iterations of a single-batch backpropagation method can significantly reduce the number of hidden-units required to achieve a particular performance. Our close to state-of-the-art results for MNIST and NORB suggest that the ease of use and accuracy of the ELM algorithm for designing a single-hidden-layer neural network classifier should cause it to be given greater consideration either as a standalone method for simpler problems, or as the final classification stage in deep neural networks applied to more difficult problems.

  1. From molecular classification to targeted therapeutics: the changing face of systemic therapy in metastatic gastroesophageal cancer.

    Science.gov (United States)

    Murphy, Adrian; Kelly, Ronan J

    2015-01-01

    Histological classification of adenocarcinoma or squamous cell carcinoma for esophageal cancer or using the Lauren classification for intestinal and diffuse type gastric cancer has limited clinical utility in the management of advanced disease. Germline mutations in E-cadherin (CDH1) or mismatch repair genes (Lynch syndrome) were identified many years ago but given their rarity, the identification of these molecular alterations does not substantially impact treatment in the advanced setting. Recent molecular profiling studies of upper GI tumors have added to our knowledge of the underlying biology but have not led to an alternative classification system which can guide clinician's therapeutic decisions. Recently the Cancer Genome Atlas Research Network has proposed four subtypes of gastric cancer dividing tumors into those positive for Epstein-Barr virus, microsatellite unstable tumors, genomically stable tumors, and tumors with chromosomal instability. Unfortunately to date, many phase III clinical trials involving molecularly targeted agents have failed to meet their survival endpoints due to their use in unselected populations. Future clinical trials should utilize molecular profiling of individual tumors in order to determine the optimal use of targeted therapies in preselected patients.

  2. From Molecular Classification to Targeted Therapeutics: The Changing Face of Systemic Therapy in Metastatic Gastroesophageal Cancer

    Directory of Open Access Journals (Sweden)

    Adrian Murphy

    2015-01-01

    Full Text Available Histological classification of adenocarcinoma or squamous cell carcinoma for esophageal cancer or using the Lauren classification for intestinal and diffuse type gastric cancer has limited clinical utility in the management of advanced disease. Germline mutations in E-cadherin (CDH1 or mismatch repair genes (Lynch syndrome were identified many years ago but given their rarity, the identification of these molecular alterations does not substantially impact treatment in the advanced setting. Recent molecular profiling studies of upper GI tumors have added to our knowledge of the underlying biology but have not led to an alternative classification system which can guide clinician’s therapeutic decisions. Recently the Cancer Genome Atlas Research Network has proposed four subtypes of gastric cancer dividing tumors into those positive for Epstein-Barr virus, microsatellite unstable tumors, genomically stable tumors, and tumors with chromosomal instability. Unfortunately to date, many phase III clinical trials involving molecularly targeted agents have failed to meet their survival endpoints due to their use in unselected populations. Future clinical trials should utilize molecular profiling of individual tumors in order to determine the optimal use of targeted therapies in preselected patients.

  3. Cluster Analysis and Significance of Novel Genes Related to Molecular Classification of Glioma

    Institute of Scientific and Technical Information of China (English)

    Juxiang Chen; Yicheng Lu; Guohan Hu; Kehua Sun; Chun Luo; Meiqing Lou; Kang Ying; Yao Li

    2005-01-01

    OBJECTIVE To screen differentially expressed genes in the development of human glioma and establish a primary molecular classification of glioma based on gene expression using cDNA microarrays.METHODS Brain specimens were obtained from 18 patients with glioma, 10males and 8 females, ages 14~62 with an average age of 44.4. The total RNAs of these glioma specimens and two specimens of donated brain of normal adults were extracted. BioStarH140S microarrays (including 8,347old genes and 5,592 novel genes) were adopted and hybridized with probes which were prepared from the total RNAs. Differentially expressed genes between normal tissues and glioma tissues were assayed after scanning cDNA microarrays with ScanArray4000. Northern hybridization and in situ hybridization (ISH) were used to identify functions of novel genes. Those differentially expressed genes were studied with a Hierarchical method and molecular classification of glioma was preliminary carried out.RESULTS Among the 13,939 target genes, there were 1,200 (8.61%)differentially expressed genes, of which 395 (2.83%) were novel genes. A total of 348 genes were up-regulated and 852 genes were down-regulated in the gliomas. The results of bioinformatical analysis, Northern hybridization and ISH revealed that those novel genes were highly associated with gliomas. There were multiple genes, such as the MAP gene、cytoskeleton & matrix motility genes, etc, which were of relevance to classification by the Hierarchical method. Molecular classification of glioma using a Hierarchical cluster was in accordance with pathology and suggested a molecular process of tumorigenesis and development.CONCLUSION Multiple genes play important roles in development of glioma. cDNA microarray technology is a powerful technique in screening for differentially expressed genes between two different kinds of tissues. Further analysis of gene expression and novel genes would be helpful to understand the molecular mechanism of glioma

  4. Accurate Modeling of Organic Molecular Crystals by Dispersion-Corrected Density Functional Tight Binding (DFTB).

    Science.gov (United States)

    Brandenburg, Jan Gerit; Grimme, Stefan

    2014-06-05

    The ambitious goal of organic crystal structure prediction challenges theoretical methods regarding their accuracy and efficiency. Dispersion-corrected density functional theory (DFT-D) in principle is applicable, but the computational demands, for example, to compute a huge number of polymorphs, are too high. Here, we demonstrate that this task can be carried out by a dispersion-corrected density functional tight binding (DFTB) method. The semiempirical Hamiltonian with the D3 correction can accurately and efficiently model both solid- and gas-phase inter- and intramolecular interactions at a speed up of 2 orders of magnitude compared to DFT-D. The mean absolute deviations for interaction (lattice) energies for various databases are typically 2-3 kcal/mol (10-20%), that is, only about two times larger than those for DFT-D. For zero-point phonon energies, small deviations of <0.5 kcal/mol compared to DFT-D are obtained.

  5. [Pathological anatomical characteristics of Klatskin tumors. Classification, current molecular biological aspects, prognosis factors].

    Science.gov (United States)

    Munding, J; Tannapfel, A

    2012-03-01

    Klatskin tumors are a distinct subgroup of cholangiocarcinomas which are a surgical challenge due to their special localization. Different localizations do not show great differences concerning histomorphology and precursor lesions. With respect to molecular alterations there are only small differences. Accurate clinical and histomorphological diagnosis is important for therapy and especially the prediction of prognosis as well as standardized processing of the resection specimen if the carcinoma is resectable. Additionally, accurate lymph node dissection is necessary. Concerning molecular markers further investigations are needed to develop individualized therapy regimes.

  6. Molecular Detection of Foodborne Pathogens: A Rapid and Accurate Answer to Food Safety.

    Science.gov (United States)

    Mangal, Manisha; Bansal, Sangita; Sharma, Satish K; Gupta, Ram K

    2016-07-03

    Food safety is a global health concern. For the prevention and recognition of problems related to health and safety, detection of foodborne pathogen is of utmost importance at all levels of food production chain. For several decades, a lot of research has been targeted at the development of rapid methodology as reducing the time needed to complete pathogen detection tests has been the primary goal of food microbiologists. With the result, food microbiology laboratories now have a wide array of detection methods and automated technologies such as enzyme immunoassay, polymerase chain reaction, and microarrays, which can cut test times considerably. Nucleic acid amplification strategies and advances in amplicon detection methodologies have been the key factors in the progress of molecular microbiology. A comprehensive literature survey has been carried out to give an overview in the field of foodborne pathogen detection. In this paper, we describe the conventional methods, as well as recent developments in food pathogen detection, identification, and quantification, with a major emphasis on molecular detection methods.

  7. Coupling density functional theory to polarizable force fields for efficient and accurate Hamiltonian molecular dynamics simulations.

    Science.gov (United States)

    Schwörer, Magnus; Breitenfeld, Benedikt; Tröster, Philipp; Bauer, Sebastian; Lorenzen, Konstantin; Tavan, Paul; Mathias, Gerald

    2013-06-28

    Hybrid molecular dynamics (MD) simulations, in which the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 10(3)-10(5) molecules, pose a challenge. A corresponding computational approach should guarantee energy conservation, exclude artificial distortions of the electron density at the interface between the DFT and PMM fragments, and should treat the long-range electrostatic interactions within the hybrid simulation system in a linearly scaling fashion. Here we describe a corresponding Hamiltonian DFT/(P)MM implementation, which accounts for inducible atomic dipoles of a PMM environment in a joint DFT/PMM self-consistency iteration. The long-range parts of the electrostatics are treated by hierarchically nested fast multipole expansions up to a maximum distance dictated by the minimum image convention of toroidal boundary conditions and, beyond that distance, by a reaction field approach such that the computation scales linearly with the number of PMM atoms. Short-range over-polarization artifacts are excluded by using Gaussian inducible dipoles throughout the system and Gaussian partial charges in the PMM region close to the DFT fragment. The Hamiltonian character, the stability, and efficiency of the implementation are investigated by hybrid DFT/PMM-MD simulations treating one molecule of the water dimer and of bulk water by DFT and the respective remainder by PMM.

  8. A simple and accurate algorithm for path integral molecular dynamics with the Langevin thermostat.

    Science.gov (United States)

    Liu, Jian; Li, Dezhang; Liu, Xinzijian

    2016-07-14

    We introduce a novel simple algorithm for thermostatting path integral molecular dynamics (PIMD) with the Langevin equation. The staging transformation of path integral beads is employed for demonstration. The optimum friction coefficients for the staging modes in the free particle limit are used for all systems. In comparison to the path integral Langevin equation thermostat, the new algorithm exploits a different order of splitting for the phase space propagator associated to the Langevin equation. While the error analysis is made for both algorithms, they are also employed in the PIMD simulations of three realistic systems (the H2O molecule, liquid para-hydrogen, and liquid water) for comparison. It is shown that the new thermostat increases the time interval of PIMD by a factor of 4-6 or more for achieving the same accuracy. In addition, the supplementary material shows the error analysis made for the algorithms when the normal-mode transformation of path integral beads is used.

  9. Accurate reaction-diffusion operator splitting on tetrahedral meshes for parallel stochastic molecular simulations

    Science.gov (United States)

    Hepburn, I.; Chen, W.; De Schutter, E.

    2016-08-01

    Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, which has led to the development of parallel methods that can take advantage of the power of modern supercomputers in recent years. We systematically test suggested components of stochastic reaction-diffusion operator splitting in the literature and discuss their effects on accuracy. We introduce an operator splitting implementation for irregular meshes that enhances accuracy with minimal performance cost. We test a range of models in small-scale MPI simulations from simple diffusion models to realistic biological models and find that multi-dimensional geometry partitioning is an important consideration for optimum performance. We demonstrate performance gains of 1-3 orders of magnitude in the parallel implementation, with peak performance strongly dependent on model specification.

  10. A simple and accurate algorithm for path integral molecular dynamics with the Langevin thermostat

    Science.gov (United States)

    Liu, Jian; Li, Dezhang; Liu, Xinzijian

    2016-07-01

    We introduce a novel simple algorithm for thermostatting path integral molecular dynamics (PIMD) with the Langevin equation. The staging transformation of path integral beads is employed for demonstration. The optimum friction coefficients for the staging modes in the free particle limit are used for all systems. In comparison to the path integral Langevin equation thermostat, the new algorithm exploits a different order of splitting for the phase space propagator associated to the Langevin equation. While the error analysis is made for both algorithms, they are also employed in the PIMD simulations of three realistic systems (the H2O molecule, liquid para-hydrogen, and liquid water) for comparison. It is shown that the new thermostat increases the time interval of PIMD by a factor of 4-6 or more for achieving the same accuracy. In addition, the supplementary material shows the error analysis made for the algorithms when the normal-mode transformation of path integral beads is used.

  11. Accurate molecular diagnosis of phenylketonuria and tetrahydrobiopterin-deficient hyperphenylalaninemias using high-throughput targeted sequencing

    Science.gov (United States)

    Trujillano, Daniel; Perez, Belén; González, Justo; Tornador, Cristian; Navarrete, Rosa; Escaramis, Georgia; Ossowski, Stephan; Armengol, Lluís; Cornejo, Verónica; Desviat, Lourdes R; Ugarte, Magdalena; Estivill, Xavier

    2014-01-01

    Genetic diagnostics of phenylketonuria (PKU) and tetrahydrobiopterin (BH4) deficient hyperphenylalaninemia (BH4DH) rely on methods that scan for known mutations or on laborious molecular tools that use Sanger sequencing. We have implemented a novel and much more efficient strategy based on high-throughput multiplex-targeted resequencing of four genes (PAH, GCH1, PTS, and QDPR) that, when affected by loss-of-function mutations, cause PKU and BH4DH. We have validated this approach in a cohort of 95 samples with the previously known PAH, GCH1, PTS, and QDPR mutations and one control sample. Pooled barcoded DNA libraries were enriched using a custom NimbleGen SeqCap EZ Choice array and sequenced using a HiSeq2000 sequencer. The combination of several robust bioinformatics tools allowed us to detect all known pathogenic mutations (point mutations, short insertions/deletions, and large genomic rearrangements) in the 95 samples, without detecting spurious calls in these genes in the control sample. We then used the same capture assay in a discovery cohort of 11 uncharacterized HPA patients using a MiSeq sequencer. In addition, we report the precise characterization of the breakpoints of four genomic rearrangements in PAH, including a novel deletion of 899 bp in intron 3. Our study is a proof-of-principle that high-throughput-targeted resequencing is ready to substitute classical molecular methods to perform differential genetic diagnosis of hyperphenylalaninemias, allowing the establishment of specifically tailored treatments a few days after birth. PMID:23942198

  12. Predicting accurate fluorescent spectra for high molecular weight polycyclic aromatic hydrocarbons using density functional theory

    Science.gov (United States)

    Powell, Jacob; Heider, Emily C.; Campiglia, Andres; Harper, James K.

    2016-10-01

    The ability of density functional theory (DFT) methods to predict accurate fluorescence spectra for polycyclic aromatic hydrocarbons (PAHs) is explored. Two methods, PBE0 and CAM-B3LYP, are evaluated both in the gas phase and in solution. Spectra for several of the most toxic PAHs are predicted and compared to experiment, including three isomers of C24H14 and a PAH containing heteroatoms. Unusually high-resolution experimental spectra are obtained for comparison by analyzing each PAH at 4.2 K in an n-alkane matrix. All theoretical spectra visually conform to the profiles of the experimental data but are systematically offset by a small amount. Specifically, when solvent is included the PBE0 functional overestimates peaks by 16.1 ± 6.6 nm while CAM-B3LYP underestimates the same transitions by 14.5 ± 7.6 nm. These calculated spectra can be empirically corrected to decrease the uncertainties to 6.5 ± 5.1 and 5.7 ± 5.1 nm for the PBE0 and CAM-B3LYP methods, respectively. A comparison of computed spectra in the gas phase indicates that the inclusion of n-octane shifts peaks by +11 nm on average and this change is roughly equivalent for PBE0 and CAM-B3LYP. An automated approach for comparing spectra is also described that minimizes residuals between a given theoretical spectrum and all available experimental spectra. This approach identifies the correct spectrum in all cases and excludes approximately 80% of the incorrect spectra, demonstrating that an automated search of theoretical libraries of spectra may eventually become feasible.

  13. Immunohistochemical characterization of molecular classification of breast carcinoma and its relation with Ki-67

    Directory of Open Access Journals (Sweden)

    Shabnam Karangadan

    2016-01-01

    Full Text Available Background: Breast carcinoma is the leading cause of cancer deaths in women. Molecular classification of breast carcinoma along with Ki-67 index is considered a better predictive factor for prognosis and treatment than routine histopathology. Aims: To classify breast carcinoma into the four molecular subtypes defined by immunohistochemical expression of triple markers: Luminal A (estrogen receptor/progesterone receptor-positive [ER/PR+] and human epidermal growth factor receptor 2 HER2/neu, luminal B (ER/PR + and HER2/neu+, triple negative (ER/PR − and HER2/neu−, and HER2 positive (ER/PR−, HER2/neu+, and to correlate the expression of ER, PR, HER2/neu, and classification with Ki-67. Materials and Methods: The present study includes sixty breast carcinoma cases studied over a 3-year period. The expression patterns of ER, PR, HER2/neu, and Ki-67 were studied. Clinical features, pathologic features such as size, grade, and lymph node status, and correlation with Ki-67 of the four subtypes were compared. Results: Out of sixty cases, most common molecular subtype was triple negative (40.00% followed by luminal B (23.33%. Most of the tumors showed low proliferative index (low Ki-67; however, triple negative and HER2 positive subtype showed high proliferative index. Most common histological subtype was ductal carcinoma which was mainly triple negative. All medullary carcinoma cases were triple negative. One case of lobular carcinoma and mucinous carcinoma each was HER2 positive and luminal B, respectively. Single case of carcinoma of male breast was luminal B subtype. Conclusion: Correlation of molecular classification with age, histological grade, and Ki-67 was statistically significant (P < 0.05. ER/PR also correlated with histological grade and Ki-67 (P < 0.01. These results emphasize the fact that molecular subtypes correlate with prognosis and aid in targeted therapy.

  14. Molecular phylogenetic perspectives for character classification and convergence: Framing some issues with nematode vulval appendages and telotylenchid tail termini

    Science.gov (United States)

    Characters flagged as convergent based on newer molecular phylogenetic trees inform both practical identification and more esoteric classification. Nematode morphological characters such as lateral lines, bullae and laciniae are quite independent structures from those similarly named in other organi...

  15. Quantification and classification of substituent effects in organic chemistry: a theoretical molecular electrostatic potential study.

    Science.gov (United States)

    Remya, Geetha S; Suresh, Cherumuttathu H

    2016-07-27

    Substituent effects in organic chemistry are generally described in terms of experimentally derived Hammett parameters whereas a convenient theoretical tool to study these effects in π-conjugated molecular systems is molecular electrostatic potential (MESP) analysis. The present study shows that the difference between MESP at the nucleus of the para carbon of substituted benzene and a carbon atom in benzene, designated as ΔVC, is very useful to quantify and classify substituent effects. On the basis of positive and negative ΔVC values, a broad classification of around 381 substituents into electron withdrawing and donating categories is made. Each category is again sorted based on the magnitude of ΔVC into subcategories such as very strong, strong, medium, and weak electron donating/withdrawing. Furthermore, the data are used to show the transferability and additivity of substituent effects in π-conjugated organic molecules such as condensed aromatic, olefinic, acetylenic, and heterocyclic systems. The transferability properties hold good for ΔVC in all these molecular systems. The additive properties of substituent effects are strongly reflected on ΔVC and the predictive power of the data to assign the total substituent effects of multi-substituted systems is verified. The ΔVC data and the present classification of substituents are very useful to design π-conjugated organic molecular systems with desired electron rich/poor character.

  16. Use of multivariate analysis to suggest a new molecular classification of colorectal cancer

    Science.gov (United States)

    Domingo, Enric; Ramamoorthy, Rajarajan; Oukrif, Dahmane; Rosmarin, Daniel; Presz, Michal; Wang, Haitao; Pulker, Hannah; Lockstone, Helen; Hveem, Tarjei; Cranston, Treena; Danielsen, Havard; Novelli, Marco; Davidson, Brian; Xu, Zheng-Zhou; Molloy, Peter; Johnstone, Elaine; Holmes, Christopher; Midgley, Rachel; Kerr, David; Sieber, Oliver; Tomlinson, Ian

    2013-01-01

    Abstract Molecular classification of colorectal cancer (CRC) is currently based on microsatellite instability (MSI), KRAS or BRAF mutation and, occasionally, chromosomal instability (CIN). Whilst useful, these categories may not fully represent the underlying molecular subgroups. We screened 906 stage II/III CRCs from the VICTOR clinical trial for somatic mutations. Multivariate analyses (logistic regression, clustering, Bayesian networks) identified the primary molecular associations. Positive associations occurred between: CIN and TP53 mutation; MSI and BRAF mutation; and KRAS and PIK3CA mutations. Negative associations occurred between: MSI and CIN; MSI and NRAS mutation; and KRAS mutation, and each of NRAS, TP53 and BRAF mutations. Some complex relationships were elucidated: KRAS and TP53 mutations had both a direct negative association and a weaker, confounding, positive association via TP53–CIN–MSI–BRAF–KRAS. Our results suggested a new molecular classification of CRCs: (1) MSI+ and/or BRAF-mutant; (2) CIN+ and/or TP53– mutant, with wild-type KRAS and PIK3CA; (3) KRAS- and/or PIK3CA-mutant, CIN+, TP53-wild-type; (4) KRAS– and/or PIK3CA-mutant, CIN–, TP53-wild-type; (5) NRAS-mutant; (6) no mutations; (7) others. As expected, group 1 cancers were mostly proximal and poorly differentiated, usually occurring in women. Unexpectedly, two different types of CIN+ CRC were found: group 2 cancers were usually distal and occurred in men, whereas group 3 showed neither of these associations but were of higher stage. CIN+ cancers have conventionally been associated with all three of these variables, because they have been tested en masse. Our classification also showed potentially improved prognostic capabilities, with group 3, and possibly group 1, independently predicting disease-free survival. Copyright © 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. PMID:23165447

  17. Automated Analysis and Classification of Histological Tissue Features by Multi-Dimensional Microscopic Molecular Profiling.

    Directory of Open Access Journals (Sweden)

    Daniel P Riordan

    Full Text Available Characterization of the molecular attributes and spatial arrangements of cells and features within complex human tissues provides a critical basis for understanding processes involved in development and disease. Moreover, the ability to automate steps in the analysis and interpretation of histological images that currently require manual inspection by pathologists could revolutionize medical diagnostics. Toward this end, we developed a new imaging approach called multidimensional microscopic molecular profiling (MMMP that can measure several independent molecular properties in situ at subcellular resolution for the same tissue specimen. MMMP involves repeated cycles of antibody or histochemical staining, imaging, and signal removal, which ultimately can generate information analogous to a multidimensional flow cytometry analysis on intact tissue sections. We performed a MMMP analysis on a tissue microarray containing a diverse set of 102 human tissues using a panel of 15 informative antibody and 5 histochemical stains plus DAPI. Large-scale unsupervised analysis of MMMP data, and visualization of the resulting classifications, identified molecular profiles that were associated with functional tissue features. We then directly annotated H&E images from this MMMP series such that canonical histological features of interest (e.g. blood vessels, epithelium, red blood cells were individually labeled. By integrating image annotation data, we identified molecular signatures that were associated with specific histological annotations and we developed statistical models for automatically classifying these features. The classification accuracy for automated histology labeling was objectively evaluated using a cross-validation strategy, and significant accuracy (with a median per-pixel rate of 77% per feature from 15 annotated samples for de novo feature prediction was obtained. These results suggest that high-dimensional profiling may advance the

  18. Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids

    Energy Technology Data Exchange (ETDEWEB)

    Dunn, Nicholas J. H.; Noid, W. G., E-mail: wnoid@chem.psu.edu [Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802 (United States)

    2015-12-28

    The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed “pressure-matching” variational principle to determine a volume-dependent contribution to the potential, U{sub V}(V), that approximates the volume-dependence of the PMF. We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing U{sub V}, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that U{sub V} accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the “simplicity” of the model.

  19. Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids

    Science.gov (United States)

    Dunn, Nicholas J. H.; Noid, W. G.

    2015-12-01

    The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed "pressure-matching" variational principle to determine a volume-dependent contribution to the potential, UV(V), that approximates the volume-dependence of the PMF. We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing UV, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that UV accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the "simplicity" of the model.

  20. The molecular subtype classification is a determinant of sentinel node positivity in early breast carcinoma.

    Directory of Open Access Journals (Sweden)

    Fabien Reyal

    Full Text Available INTRODUCTION: Several authors have underscored a strong relation between the molecular subtypes and the axillary status of breast cancer patients. The aim of our work was to decipher the interaction between this classification and the probability of a positive sentinel node biopsy. MATERIALS AND METHODS: Our dataset consisted of a total number of 2654 early-stage breast cancer patients. Patients treated at first by conservative breast surgery plus sentinel node biopsies were selected. A multivariate logistic regression model was trained and validated. Interaction covariate between ER and HER2 markers was a forced input of this model. The performance of the multivariate model in the training and the two validation sets was analyzed in terms of discrimination and calibration. Probability of axillary metastasis was detailed for each molecular subtype. RESULTS: The interaction covariate between ER and HER2 status was a stronger predictor (p = 0.0031 of positive sentinel node biopsy than the ER status by itself (p = 0.016. A multivariate model to determine the probability of sentinel node positivity was defined with the following variables; tumour size, lympho-vascular invasion, molecular subtypes and age at diagnosis. This model showed similar results in terms of discrimination (AUC = 0.72/0.73/0.72 and calibration (HL p = 0.28/0.05/0.11 in the training and validation sets. The interaction between molecular subtypes, tumour size and sentinel nodes status was approximated. DISCUSSION: We showed that biologically-driven analyses are able to build new models with higher performance in terms of breast cancer axillary status prediction. The molecular subtype classification strongly interacts with the axillary and distant metastasis process.

  1. History, Classification, Molecular Structure and Properties of Dendrimers which are a New Concept in Textile

    Directory of Open Access Journals (Sweden)

    Osman NAMIRTI

    2011-02-01

    Full Text Available Over the last 20 years polymer chemistry has created a number of non-lineer structures and introduction of a large number of branches during the polymer synthesis leads to obtain molecules with many end groups. Two types of these polymers are regularly branched "dendrimers" and "hyperbranched polymers" where branching is formed randomly. In this article knowledge about history, classification, molecular structure and properties of dendrimers which have found various application areas also in textile due to their special structures is given.

  2. Accurate path integral molecular dynamics simulation of ab-initio water at near-zero added cost

    Science.gov (United States)

    Elton, Daniel; Fritz, Michelle; Soler, José; Fernandez-Serra, Marivi

    It is now established that nuclear quantum motion plays an important role in determining water's structure and dynamics. These effects are important to consider when evaluating DFT functionals and attempting to develop better ones for water. The standard way of treating nuclear quantum effects, path integral molecular dynamics (PIMD), multiplies the number of energy/force calculations by the number of beads, which is typically 32. Here we introduce a method whereby PIMD can be incorporated into a DFT molecular dynamics simulation at virtually zero cost. The method is based on the cluster (many body) expansion of the energy. We first subtract the DFT monomer energies, using a custom DFT-based monomer potential energy surface. The evolution of the PIMD beads is then performed using only the more-accurate Partridge-Schwenke monomer energy surface. The DFT calculations are done using the centroid positions. Various bead thermostats can be employed to speed up the sampling of the quantum ensemble. The method bears some resemblance to multiple timestep algorithms and other schemes used to speed up PIMD with classical force fields. We show that our method correctly captures some of key effects of nuclear quantum motion on both the structure and dynamics of water. We acknowledge support from DOE Award No. DE-FG02-09ER16052 (D.E.) and DOE Early Career Award No. DE-SC0003871 (M.V.F.S.).

  3. Appraisal of progenitor markers in the context of molecular classification of breast cancers.

    Science.gov (United States)

    Haviv, Izhak

    2011-01-25

    Clinical management of breast cancer relies on case stratification, which increasingly employs molecular markers. The motivation behind delineating breast epithelial differentiation is to better target cancer cases through innate sensitivities bequeathed to the cancer from its normal progenitor state. A combination of histopathological and molecular classification of breast cancer cases suggests a role for progenitors in particular breast cancer cases. Although a remarkable fraction of the real tissue repertoire is maintained within a population of independent cell line cultures, some steps that are closer to the terminal differentiation state and that form a majority of primary human breast tissues are missing in the cell line cultures. This raises concerns about current breast cancer models.

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

    Science.gov (United States)

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

    2016-06-17

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

  5. Molecular classification of basal cell carcinoma of skin by gene expression profiling.

    Science.gov (United States)

    Jee, Byul A; Lim, Hyoseob; Kwon, So Mee; Jo, Yuna; Park, Myong Chul; Lee, Il Jae; Woo, Hyun Goo

    2015-12-01

    Non-melanoma skin cancers (NMSC) including basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) are more common kinds of skin cancer. Although these tumors share common pathological and clinical features, their similarity and heterogeneity at molecular levels are not fully elaborated yet. Here, by performing comparative analysis of gene expression profiling of BCC, SCC, and normal skin tissues, we could classify the BCC into three subtypes of classical, SCC-like, and normal-like BCCs. Functional enrichment and pathway analyses revealed the molecular characteristics of each subtype. The classical BCC showed the enriched expression and transcription signature with the activation of Wnt and Hedgehog signaling pathways, which were well known key features of BCC. By contrast, the SCC-like BCC was enriched with immune-response genes and oxidative stress-related genes. Network analysis revealed the PLAU/PLAUR as a key regulator of SCC-like BCC. The normal-like BCC showed prominent activation of metabolic processes particularly the fatty acid metabolism. The existence of these molecular subtypes could be validated in an independent dataset, which demonstrated the three subgroups of BCC with distinct functional enrichment. In conclusion, we suggest a novel molecular classification of BCC providing insights on the heterogeneous progression of BCC.

  6. An accurate metalloprotein-specific scoring function and molecular docking program devised by a dynamic sampling and iteration optimization strategy.

    Science.gov (United States)

    Bai, Fang; Liao, Sha; Gu, Junfeng; Jiang, Hualiang; Wang, Xicheng; Li, Honglin

    2015-04-27

    Metalloproteins, particularly zinc metalloproteins, are promising therapeutic targets, and recent efforts have focused on the identification of potent and selective inhibitors of these proteins. However, the ability of current drug discovery and design technologies, such as molecular docking and molecular dynamics simulations, to probe metal-ligand interactions remains limited because of their complicated coordination geometries and rough treatment in current force fields. Herein we introduce a robust, multiobjective optimization algorithm-driven metalloprotein-specific docking program named MpSDock, which runs on a scheme similar to consensus scoring consisting of a force-field-based scoring function and a knowledge-based scoring function. For this purpose, in this study, an effective knowledge-based zinc metalloprotein-specific scoring function based on the inverse Boltzmann law was designed and optimized using a dynamic sampling and iteration optimization strategy. This optimization strategy can dynamically sample and regenerate decoy poses used in each iteration step of refining the scoring function, thus dramatically improving both the effectiveness of the exploration of the binding conformational space and the sensitivity of the ranking of the native binding poses. To validate the zinc metalloprotein-specific scoring function and its special built-in docking program, denoted MpSDockZn, an extensive comparison was performed against six universal, popular docking programs: Glide XP mode, Glide SP mode, Gold, AutoDock, AutoDock4Zn, and EADock DSS. The zinc metalloprotein-specific knowledge-based scoring function exhibited prominent performance in accurately describing the geometries and interactions of the coordination bonds between the zinc ions and chelating agents of the ligands. In addition, MpSDockZn had a competitive ability to sample and identify native binding poses with a higher success rate than the other six docking programs.

  7. A High Resolution/Accurate Mass (HRAM) Data-Dependent MS3 Neutral Loss Screening, Classification, and Relative Quantitation Methodology for Carbonyl Compounds in Saliva

    Science.gov (United States)

    Dator, Romel; Carrà, Andrea; Maertens, Laura; Guidolin, Valeria; Villalta, Peter W.; Balbo, Silvia

    2016-10-01

    Reactive carbonyl compounds (RCCs) are ubiquitous in the environment and are generated endogenously as a result of various physiological and pathological processes. These compounds can react with biological molecules inducing deleterious processes believed to be at the basis of their toxic effects. Several of these compounds are implicated in neurotoxic processes, aging disorders, and cancer. Therefore, a method characterizing exposures to these chemicals will provide insights into how they may influence overall health and contribute to disease pathogenesis. Here, we have developed a high resolution accurate mass (HRAM) screening strategy allowing simultaneous identification and relative quantitation of DNPH-derivatized carbonyls in human biological fluids. The screening strategy involves the diagnostic neutral loss of hydroxyl radical triggering MS3 fragmentation, which is only observed in positive ionization mode of DNPH-derivatized carbonyls. Unique fragmentation pathways were used to develop a classification scheme for characterizing known and unanticipated/unknown carbonyl compounds present in saliva. Furthermore, a relative quantitation strategy was implemented to assess variations in the levels of carbonyl compounds before and after exposure using deuterated d 3 -DNPH. This relative quantitation method was tested on human samples before and after exposure to specific amounts of alcohol. The nano-electrospray ionization (nano-ESI) in positive mode afforded excellent sensitivity with detection limits on-column in the high-attomole levels. To the best of our knowledge, this is the first report of a method using HRAM neutral loss screening of carbonyl compounds. In addition, the method allows simultaneous characterization and relative quantitation of DNPH-derivatized compounds using nano-ESI in positive mode.

  8. Accurate molecular structures and infrared spectra of trans-2,3-dideuterooxirane, methyloxirane, and trans-2,3-dimethyloxirane

    Energy Technology Data Exchange (ETDEWEB)

    Barone, Vincenzo [Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa (Italy); Biczysko, Malgorzata, E-mail: malgorzata.biczysko@sns.it; Bloino, Julien [Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa (Italy); Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa (Italy); Puzzarini, Cristina [Dipartimento di Chimica “Giacomo Ciamician,” Università di Bologna, Via F. Selmi 2, I-40126 Bologna (Italy)

    2014-07-21

    Oxirane derivatives are the most used benchmarks for chiroptical spectroscopies in view of their small size and relative rigidity. The molecular structure, vibrational harmonic and anharmonic frequencies, and infrared intensities of the ground electronic states are analyzed in this paper. Equilibrium structure and harmonic force fields have been evaluated by means of high-level quantum-chemical calculations at the coupled-cluster level including single and double excitations together with a perturbative treatment of triples (CCSD(T)). Extrapolation to the complete basis-set limit as well as core-correlation effects have also been taken into account. Anharmonic contributions have been computed at the CCSD(T)/cc-pVTZ level for trans-2,3-dideuterooxirane. These data can serve as references to evaluate the accuracy of less expensive computational approaches rooted in the density functional theory (DFT). The latter have been used within hybrid CC/DFT approaches, which have been applied to simulate fully anharmonic infrared (IR) spectra. Finally, the best theoretical estimates of the equilibrium structures and vibrational wavenumbers are compared to the most accurate experimental data and show in all cases very good agreement, i.e., within 0.001 Å, 0.1 deg, 10 cm{sup −1}, and 0.5 km mol{sup −1}, for bond lengths, angles, wavenumbers, and IR intensities, respectively.

  9. Nuclear Quantum Effects in Liquid Water: A Highly Accurate ab initio Path-Integral Molecular Dynamics Study

    Science.gov (United States)

    Distasio, Robert A., Jr.; Santra, Biswajit; Ko, Hsin-Yu; Car, Roberto

    2014-03-01

    In this work, we report highly accurate ab initio path-integral molecular dynamics (AI-PIMD) simulations on liquid water at ambient conditions utilizing the recently developed PBE0+vdW(SC) exchange-correlation functional, which accounts for exact exchange and a self-consistent pairwise treatment of van der Waals (vdW) or dispersion interactions, combined with nuclear quantum effects (via the colored-noise generalized Langevin equation). The importance of each of these effects in the theoretical prediction of the structure of liquid water will be demonstrated by a detailed comparative analysis of the predicted and experimental oxygen-oxygen (O-O), oxygen-hydrogen (O-H), and hydrogen-hydrogen (H-H) radial distribution functions as well as other structural properties. In addition, we will discuss the theoretically obtained proton momentum distribution, computed using the recently developed Feynman path formulation, in light of the experimental deep inelastic neutron scattering (DINS) measurements. DOE: DE-SC0008626, DOE: DE-SC0005180.

  10. Integrated classification of inflammatory myopathies.

    Science.gov (United States)

    Allenbach, Y; Benveniste, O; Goebel, H-H; Stenzel, W

    2017-02-01

    Inflammatory myopathies comprise a multitude of diverse diseases, most often occurring in complex clinical settings. To ensure accurate diagnosis, multidisciplinary expertise is required. Here, we propose a comprehensive myositis classification that incorporates clinical, morphological and molecular data as well as autoantibody profile. This review focuses on recent advances in myositis research, in particular, the correlation between autoantibodies and morphological or clinical phenotypes that can be used as the basis for an 'integrated' classification system.

  11. Quantitative structure-activity relationship modeling of polycyclic aromatic hydrocarbon mutagenicity by classification methods based on holistic theoretical molecular descriptors.

    Science.gov (United States)

    Gramatica, Paola; Papa, Ester; Marrocchi, Assunta; Minuti, Lucio; Taticchi, Aldo

    2007-03-01

    Various polycyclic aromatic hydrocarbons (PAHs), ubiquitous environmental pollutants, are recognized mutagens and carcinogens. A homogeneous set of mutagenicity data (TA98 and TA100,+S9) for 32 benzocyclopentaphenanthrenes/chrysenes was modeled by the quantitative structure-activity relationship classification methods k-nearest neighbor and classification and regression tree, using theoretical holistic molecular descriptors. Genetic algorithm provided the selection of the best subset of variables for modeling mutagenicity. The models were validated by leave-one-out and leave-50%-out approaches and have good performance, with sensitivity and specificity ranges of 90-100%. Mutagenicity assessment for these PAHs requires only a few theoretical descriptors of their molecular structure.

  12. 乳腺癌的分子分型%Molecular classification of breast cancer

    Institute of Scientific and Technical Information of China (English)

    张百红; 岳红云

    2014-01-01

    乳腺癌是一种分子水平异质性很高的疾病,分子分型可为乳腺癌的个体化治疗提供一个新视野.在分子病理学、分子生物学和系统生物学指导下,乳腺癌经历了4类分型、70种和21种基因蛋白谱以及基因组整合分类等不同分型.这些分型将为乳腺癌的精确治疗提供指导.%Breast cancer is a group of heterogeneous diseases.Molecular portraits provide a new insight for personalized cancer management in breast cancer.According to the molecular pathology,molecular biology and system biology,breast cancer goes through different typing methods,including four subclasses,geneexpression signature and integrated genomic classification.These major subtypes of breast cancer may provide guidance for precise therapeutics.

  13. Molecular phylogenetic evaluation of classification and scenarios of character evolution in calcareous sponges (Porifera, Class Calcarea.

    Directory of Open Access Journals (Sweden)

    Oliver Voigt

    Full Text Available Calcareous sponges (Phylum Porifera, Class Calcarea are known to be taxonomically difficult. Previous molecular studies have revealed many discrepancies between classically recognized taxa and the observed relationships at the order, family and genus levels; these inconsistencies question underlying hypotheses regarding the evolution of certain morphological characters. Therefore, we extended the available taxa and character set by sequencing the complete small subunit (SSU rDNA and the almost complete large subunit (LSU rDNA of additional key species and complemented this dataset by substantially increasing the length of available LSU sequences. Phylogenetic analyses provided new hypotheses about the relationships of Calcarea and about the evolution of certain morphological characters. We tested our phylogeny against competing phylogenetic hypotheses presented by previous classification systems. Our data reject the current order-level classification by again finding non-monophyletic Leucosolenida, Clathrinida and Murrayonida. In the subclass Calcinea, we recovered a clade that includes all species with a cortex, which is largely consistent with the previously proposed order Leucettida. Other orders that had been rejected in the current system were not found, but could not be rejected in our tests either. We found several additional families and genera polyphyletic: the families Leucascidae and Leucaltidae and the genus Leucetta in Calcinea, and in Calcaronea the family Amphoriscidae and the genus Ute. Our phylogeny also provided support for the vaguely suspected close relationship of several members of Grantiidae with giantortical diactines to members of Heteropiidae. Similarly, our analyses revealed several unexpected affinities, such as a sister group relationship between Leucettusa (Leucaltidae and Leucettidae and between Leucascandra (Jenkinidae and Sycon carteri (Sycettidae. According to our results, the taxonomy of Calcarea is in

  14. Molecular phylogenetic evaluation of classification and scenarios of character evolution in calcareous sponges (Porifera, Class Calcarea).

    Science.gov (United States)

    Voigt, Oliver; Wülfing, Eilika; Wörheide, Gert

    2012-01-01

    Calcareous sponges (Phylum Porifera, Class Calcarea) are known to be taxonomically difficult. Previous molecular studies have revealed many discrepancies between classically recognized taxa and the observed relationships at the order, family and genus levels; these inconsistencies question underlying hypotheses regarding the evolution of certain morphological characters. Therefore, we extended the available taxa and character set by sequencing the complete small subunit (SSU) rDNA and the almost complete large subunit (LSU) rDNA of additional key species and complemented this dataset by substantially increasing the length of available LSU sequences. Phylogenetic analyses provided new hypotheses about the relationships of Calcarea and about the evolution of certain morphological characters. We tested our phylogeny against competing phylogenetic hypotheses presented by previous classification systems. Our data reject the current order-level classification by again finding non-monophyletic Leucosolenida, Clathrinida and Murrayonida. In the subclass Calcinea, we recovered a clade that includes all species with a cortex, which is largely consistent with the previously proposed order Leucettida. Other orders that had been rejected in the current system were not found, but could not be rejected in our tests either. We found several additional families and genera polyphyletic: the families Leucascidae and Leucaltidae and the genus Leucetta in Calcinea, and in Calcaronea the family Amphoriscidae and the genus Ute. Our phylogeny also provided support for the vaguely suspected close relationship of several members of Grantiidae with giantortical diactines to members of Heteropiidae. Similarly, our analyses revealed several unexpected affinities, such as a sister group relationship between Leucettusa (Leucaltidae) and Leucettidae and between Leucascandra (Jenkinidae) and Sycon carteri (Sycettidae). According to our results, the taxonomy of Calcarea is in desperate need of a

  15. Gene expression profiling for molecular classification of multiple myeloma in newly diagnosed patients.

    Science.gov (United States)

    Broyl, Annemiek; Hose, Dirk; Lokhorst, Henk; de Knegt, Yvonne; Peeters, Justine; Jauch, Anna; Bertsch, Uta; Buijs, Arjan; Stevens-Kroef, Marian; Beverloo, H Berna; Vellenga, Edo; Zweegman, Sonja; Kersten, Marie-Josée; van der Holt, Bronno; el Jarari, Laila; Mulligan, George; Goldschmidt, Hartmut; van Duin, Mark; Sonneveld, Pieter

    2010-10-07

    To identify molecularly defined subgroups in multiple myeloma, gene expression profiling was performed on purified CD138(+) plasma cells of 320 newly diagnosed myeloma patients included in the Dutch-Belgian/German HOVON-65/GMMG-HD4 trial. Hierarchical clustering identified 10 subgroups; 6 corresponded to clusters described in the University of Arkansas for Medical Science (UAMS) classification, CD-1 (n = 13, 4.1%), CD-2 (n = 34, 1.6%), MF (n = 32, 1.0%), MS (n = 33, 1.3%), proliferation-associated genes (n = 15, 4.7%), and hyperdiploid (n = 77, 24.1%). Moreover, the UAMS low percentage of bone disease cluster was identified as a subcluster of the MF cluster (n = 15, 4.7%). One subgroup (n = 39, 12.2%) showed a myeloid signature. Three novel subgroups were defined, including a subgroup of 37 patients (11.6%) characterized by high expression of genes involved in the nuclear factor kappa light-chain-enhancer of activated B cells pathway, which include TNFAIP3 and CD40. Another subgroup of 22 patients (6.9%) was characterized by distinct overexpression of cancer testis antigens without overexpression of proliferation genes. The third novel cluster of 9 patients (2.8%) showed up-regulation of protein tyrosine phosphatases PRL-3 and PTPRZ1 as well as SOCS3. To conclude, in addition to 7 clusters described in the UAMS classification, we identified 3 novel subsets of multiple myeloma that may represent unique diagnostic entities.

  16. Traditional taxonomic groupings mask evolutionary history: a molecular phylogeny and new classification of the chromodorid nudibranchs.

    Science.gov (United States)

    Johnson, Rebecca Fay; Gosliner, Terrence M

    2012-01-01

    Chromodorid nudibranchs (16 genera, 300+ species) are beautiful, brightly colored sea slugs found primarily in tropical coral reef habitats and subtropical coastal waters. The chromodorids are the most speciose family of opisthobranchs and one of the most diverse heterobranch clades. Chromodorids have the potential to be a model group with which to study diversification, color pattern evolution, are important source organisms in natural products chemistry and represent a stunning and widely compelling example of marine biodiversity. Here, we present the most complete molecular phylogeny of the chromodorid nudibranchs to date, with a broad sample of 244 specimens (142 new), representing 157 (106 new) chromodorid species, four actinocylcid species and four additional dorid species utilizing two mitochondrial markers (16s and COI). We confirmed the monophyly of the Chromodorididae and its sister group relationship with the Actinocyclidae. We were also able to, for the first time, test generic monophyly by including more than one member of all 14 of the non-monotypic chromodorid genera. Every one of these 14 traditional chromodorid genera are either non-monophyletic, or render another genus paraphyletic. Additionally, both the monotypic genera Verconia and Diversidoris are nested within clades. Based on data shown here, there are three individual species and five clades limited to the eastern Pacific and Atlantic Oceans (or just one of these ocean regions), while the majority of chromodorid clades and species are strictly Indo-Pacific in distribution. We present a new classification of the chromodorid nudibranchs. We use molecular data to untangle evolutionary relationships and retain a historical connection to traditional systematics by using generic names attached to type species as clade names.

  17. Traditional taxonomic groupings mask evolutionary history: a molecular phylogeny and new classification of the chromodorid nudibranchs.

    Directory of Open Access Journals (Sweden)

    Rebecca Fay Johnson

    Full Text Available Chromodorid nudibranchs (16 genera, 300+ species are beautiful, brightly colored sea slugs found primarily in tropical coral reef habitats and subtropical coastal waters. The chromodorids are the most speciose family of opisthobranchs and one of the most diverse heterobranch clades. Chromodorids have the potential to be a model group with which to study diversification, color pattern evolution, are important source organisms in natural products chemistry and represent a stunning and widely compelling example of marine biodiversity. Here, we present the most complete molecular phylogeny of the chromodorid nudibranchs to date, with a broad sample of 244 specimens (142 new, representing 157 (106 new chromodorid species, four actinocylcid species and four additional dorid species utilizing two mitochondrial markers (16s and COI. We confirmed the monophyly of the Chromodorididae and its sister group relationship with the Actinocyclidae. We were also able to, for the first time, test generic monophyly by including more than one member of all 14 of the non-monotypic chromodorid genera. Every one of these 14 traditional chromodorid genera are either non-monophyletic, or render another genus paraphyletic. Additionally, both the monotypic genera Verconia and Diversidoris are nested within clades. Based on data shown here, there are three individual species and five clades limited to the eastern Pacific and Atlantic Oceans (or just one of these ocean regions, while the majority of chromodorid clades and species are strictly Indo-Pacific in distribution. We present a new classification of the chromodorid nudibranchs. We use molecular data to untangle evolutionary relationships and retain a historical connection to traditional systematics by using generic names attached to type species as clade names.

  18. Molecular Phylogeny of the Cliff Ferns (Woodsiaceae: Polypodiales) with a Proposed Infrageneric Classification.

    Science.gov (United States)

    Shao, Yizhen; Wei, Ran; Zhang, Xianchun; Xiang, Qiaoping

    2015-01-01

    The cliff fern family Woodsiaceae has experienced frequent taxonomic changes at the familial and generic ranks since its establishment. The bulk of its species were placed in Woodsia, while Cheilanthopsis, Hymenocystis, Physematium, and Protowoodsia are segregates recognized by some authors. Phylogenetic relationships among the genera of Woodsiaceae remain unclear because of the extreme morphological diversity and inadequate taxon sampling in phylogenetic studies to date. In this study, we carry out comprehensive phylogenetic analyses of Woodsiaceae using molecular evidence from four chloroplast DNA markers (atpA, matK, rbcL and trnL-F) and covering over half the currently recognized species. Our results show three main clades in Woodsiaceae corresponding to Physematium (clade I), Cheilanthopsis-Protowoodsia (clade II) and Woodsia s.s. (clade III). In the interest of preserving monophyly and taxonomic stability, a broadly defined Woodsia including the other segregates is proposed, which is characterized by the distinctive indument and inferior indusia. Therefore, we present a new subgeneric classification of the redefined Woodsia based on phylogenetic and ancestral state reconstructions to better reflect the morphological variation, geographic distribution pattern, and evolutionary history of the genus. Our analyses of the cytological character evolution support multiple aneuploidy events that have resulted in the reduction of chromosome base number from 41 to 33, 37, 38, 39 and 40 during the evolutionary history of the cliff ferns.

  19. Molecular Phylogeny of the Cliff Ferns (Woodsiaceae: Polypodiales with a Proposed Infrageneric Classification.

    Directory of Open Access Journals (Sweden)

    Yizhen Shao

    Full Text Available The cliff fern family Woodsiaceae has experienced frequent taxonomic changes at the familial and generic ranks since its establishment. The bulk of its species were placed in Woodsia, while Cheilanthopsis, Hymenocystis, Physematium, and Protowoodsia are segregates recognized by some authors. Phylogenetic relationships among the genera of Woodsiaceae remain unclear because of the extreme morphological diversity and inadequate taxon sampling in phylogenetic studies to date. In this study, we carry out comprehensive phylogenetic analyses of Woodsiaceae using molecular evidence from four chloroplast DNA markers (atpA, matK, rbcL and trnL-F and covering over half the currently recognized species. Our results show three main clades in Woodsiaceae corresponding to Physematium (clade I, Cheilanthopsis-Protowoodsia (clade II and Woodsia s.s. (clade III. In the interest of preserving monophyly and taxonomic stability, a broadly defined Woodsia including the other segregates is proposed, which is characterized by the distinctive indument and inferior indusia. Therefore, we present a new subgeneric classification of the redefined Woodsia based on phylogenetic and ancestral state reconstructions to better reflect the morphological variation, geographic distribution pattern, and evolutionary history of the genus. Our analyses of the cytological character evolution support multiple aneuploidy events that have resulted in the reduction of chromosome base number from 41 to 33, 37, 38, 39 and 40 during the evolutionary history of the cliff ferns.

  20. Molecular phylogeny and revised classification of the haplotilapiine cichlid fishes formerly referred to as "Tilapia".

    Science.gov (United States)

    Dunz, Andreas R; Schliewen, Ulrich K

    2013-07-01

    African cichlids formerly referred to as "Tilapia" represent a paraphyletic species assemblage belonging to the so called haplotilapiine lineage which gave rise to the spectacular East African cichlid radiations (EARs) as well as to globally important aquaculture species. We present a comprehensive molecular phylogeny of representative haplotilapiine cichlids, combining in one data set four mitochondrial and five nuclear loci for 76 species, and compare it with phylogenetic information of a second data set of 378 mitochondrial ND2 haplotypes representing almost all important "Tilapia" or Tilapia-related lineages as well as most EAR lineages. The monophyly of haplotilapiines is supported, as is the nested sister group relationship of Etia and mouthbrooding tilapiines with the remaining haplotilapiines. The latter are consistently placed in eight monophyletic clades over all datasets and analyses, but several dichotomous phylogenetic relationships appear compromised by cytonuclear discordant phylogenetic signal. Based on these results as well as on extensive morphological evidence we propose a novel generic and suprageneric classification including a (re-)diagnosis of 20 haplotilapiine cichlid genera and nine tribes. New tribes are provided for the former subgenera Coptodon Gervais, 1853, HeterotilapiaRegan, 1920 and PelmatolapiaThys van den Audenaerde, 1969, in addition for "Tilapia" joka, Tilapia sensu stricto and Chilochromis, Etia, Steatocranus sensu stricto, the mouthbrooding tilapiines and for a clade of West African tilapiines.

  1. Molecular phylogeny of the families Pleuronectidae and Poecilopsettidae (PISCES, Pleuronectiformes) from Korea, with a Proposal for a new classification

    Science.gov (United States)

    Ji, Hwan-Sung; Kim, Jin-Koo; Kim, Byung-Jik

    2016-03-01

    A new classification of the Korean pleuronectids was proposed based on a molecular phylogeny using specimens collected from Korea (including some Japanese specimens) between 2008 and 2013. A molecular phylogeny based on partial sequences of the two mitochondrial DNA regions (COI and 16S rRNA) supported the reciprocal monophyly of the three genera, Cleisthenes, Pleuronectes and Pseudopleuronectes. We also found that the genus Poecilopsetta is clearly distinct from Pleuronectidae at the family level. Therefore, the previous classification of the Korean pleuronectids should be changed as follows; two families (Pleuronectidae and Poecilopsettidae), 18 genera, and 26 species. Further research is required to resolve the taxonomic uncertainty of the five species in the genus Limanda, which clustered into two clades in our analysis.

  2. The Significance of Molecular Classification in Breast Cancer for Prognosis%乳腺癌分子分型对乳腺癌预后的意义

    Institute of Scientific and Technical Information of China (English)

    王会东

    2013-01-01

    Objective To investigate the molecular classification and prognosis of breast cancer and the relationship between . Methods Retrospective analysis of 316 cases of female primary breast cancer patients with the clinical pathological ,average age 54.5 years.According to estrogen receptor (ER),pregnancy hormone receptor (PR) and human epidermal growth factor receptor 2(HER2) immu-nohistochemical findings,breast cancer types as type Luminal A ,type Luminal B,triple-negative and HER2 positive type,differences in mo-lecular classification of breast cancer prognosis were observed ,various types of patients with postoperative disease -free survival were com-pared.Results The patients were followed up for 5~124 months,a median follow-up time of 58 months,32 patients had recurrence of metas-tasis or death,the single factor analysis showed that the breast cancer disease free survival and molecular types had relation .Conclusion The molecular classification of breast cancer accurately reflects the prognosis of breast cancer .Type Luminal has the best prognosis ,while triple-negative has the worst prognosis .%  目的 探讨乳腺癌分子分型与预后之间的关系。方法 回顾性分析316例原发性乳腺癌患者的临床病理资料,患者均为女性,平均年龄54.5岁。根据雌激素受体(ER)、孕激素受体(PR)及人类表皮生长因子受体2(HER2)的免疫组织化学结果,乳腺癌分型为Luminal A型、Luminal B型、三阴型及 HER2阳性型,观察不同分子分型乳腺癌的预后,比较各型患者术后的无病生存期。结果 随访5~124个月,中位随访时间58个月,32例患者复发转移或死亡,单因素分析示乳腺癌无病生存期与分子分型有关。结论 乳腺癌的分子分型能够准确反映乳腺癌的预后,Luminal型预后最好,而三阴型预后最差。

  3. Quantitative LC-MS of polymers: determining accurate molecular weight distributions by combined size exclusion chromatography and electrospray mass spectrometry with maximum entropy data processing.

    Science.gov (United States)

    Gruendling, Till; Guilhaus, Michael; Barner-Kowollik, Christopher

    2008-09-15

    We report on the successful application of size exclusion chromatography (SEC) combined with electrospray ionization mass spectrometry (ESI-MS) and refractive index (RI) detection for the determination of accurate molecular weight distributions of synthetic polymers, corrected for chromatographic band broadening. The presented method makes use of the ability of ESI-MS to accurately depict the peak profiles and retention volumes of individual oligomers eluting from the SEC column, whereas quantitative information on the absolute concentration of oligomers is obtained from the RI-detector only. A sophisticated computational algorithm based on the maximum entropy principle is used to process the data gained by both detectors, yielding an accurate molecular weight distribution, corrected for chromatographic band broadening. Poly(methyl methacrylate) standards with molecular weights up to 10 kDa serve as model compounds. Molecular weight distributions (MWDs) obtained by the maximum entropy procedure are compared to MWDs, which were calculated by a conventional calibration of the SEC-retention time axis with peak retention data obtained from the mass spectrometer. Comparison showed that for the employed chromatographic system, distributions below 7 kDa were only weakly influenced by chromatographic band broadening. However, the maximum entropy algorithm could successfully correct the MWD of a 10 kDa standard for band broadening effects. Molecular weight averages were between 5 and 14% lower than the manufacturer stated data obtained by classical means of calibration. The presented method demonstrates a consistent approach for analyzing data obtained by coupling mass spectrometric detectors and concentration sensitive detectors to polymer liquid chromatography.

  4. Establishment of an accurate and fast detection method using molecular beacons in loop-mediated isothermal amplification assay

    Science.gov (United States)

    Liu, Wei; Huang, Simo; Liu, Ningwei; Dong, Derong; Yang, Zhan; Tang, Yue; Ma, Wen; He, Xiaoming; Ao, Da; Xu, Yaqing; Zou, Dayang; Huang, Liuyu

    2017-01-01

    This study established a constant-temperature fluorescence quantitative detection method, combining loop-mediated isothermal amplification (LAMP) with molecular beacons. The advantages of LAMP are its convenience and efficiency, as it does not require a thermocycler and results are easily visualized by the naked eye. However, a major disadvantage of current LAMP techniques is the use of indirect evaluation methods (e.g., electrophoresis, SYBR Green I dye, precipitation, hydroxynaphthol blue dye, the turbidimetric method, calcein/Mn2+ dye, and the composite probe method), which cannot distinguish between the desired products and products of nonspecific amplification, thereby leading to false positives. Use of molecular beacons avoids this problem because molecular beacons produce fluorescence signals only when binding to target DNA, thus acting as a direct indicator of amplification products. Our analyses determined the optimal conditions for molecular beacons as an evaluation tool in LAMP: beacon length of 25–45 bp, beacon concentration of 0.6–1 pmol/μL, and reaction temperature of 60–65 °C. In conclusion, we validated a novel molecular beacon loop-mediated isothermal amplification method (MB-LAMP), realizing the direct detection of LAMP product. PMID:28059137

  5. Morphological and molecular characteristics do not confirm popular classification of the Brazil nut tree in Acre, Brazil.

    Science.gov (United States)

    Sujii, P S; Fernandes, E T M B; Azevedo, V C R; Ciampi, A Y; Martins, K; de O Wadt, L H

    2013-01-01

    In the State of Acre, the Brazil nut tree, Bertholletia excelsa (Lecythidaceae), is classified by the local population into two types according to morphological characteristics, including color and quality of wood, shape of the trunk and crown, and fruit production. We examined the reliability of this classification by comparing morphological and molecular data of four populations of Brazil nut trees from Vale do Rio Acre in the Brazilian Amazon. For the morphological analysis, we evaluated qualitative and quantitative information of the trees, fruits, and seeds. The molecular analysis was performed using RAPD and ISSR markers, with cluster analysis. Significant differences were found between the two types of Brazil nut trees for the characters diameter at breast height, fruit yield, fruit size, and number of seeds per fruit. Despite the significant correlation between the morphological characteristics and the popular classification, we observed all possible combinations of morphological characteristics in both types of Brazil nut trees. In some individuals, the classification did not correspond to any of the characteristics. The results obtained with molecular markers showed that the two locally classified types of Brazil nut trees did not differ genetically, indicating that there is no consistent separation between them.

  6. Molecular and biochemical taxonomic tools for the identification and classification of plant-pathogenic Penicillium species

    Directory of Open Access Journals (Sweden)

    Mohamed A. Mahmoud

    2016-11-01

    Full Text Available Five species of Penicillium (Penicillium chrysogenum, P. funiculosum, P. griseofulvum, P. implicatum and P. oxalicum are implicated in seed-borne diseases. Here, we report the discovery of molecular markers based on the internal transcribed spacer regions of fungal ribosomal DNA (rDNA, which are described as primary DNA barcode markers of fungi, for rapid diagnosis and early detection of Penicillium spp. The present markers are expected to be useful for the prevention of seedling and systemic plant diseases associated with Penicillium spp. Our findings, which provide valuable insights into the taxonomy of Penicillium spp., should contribute to improve safety of agricultural produce, thereby protecting both humans and animals from harmful food contaminants such as mycotoxins. In addition, we examined the cellular fatty acid composition of five species of Penicillium. The species studied were found to possess similar fatty acid composition; however, they differed in terms of relative concentration. The principal fatty acids were oleic acid (C18:1 and linoleic acid (C18:2, comprising 80% or more of the total fatty acid composition of these species. These fatty acid profiles may be useful for characterization and identification of fungi. Data derived from the present study highlight the importance of using polyphasic methods for accurate species-level identification of Penicillium.

  7. Toward Accurate Reaction Energetics for Molecular Line Growth at Surface: Quantum Monte Carlo and Density Functional Theory Calculations

    Energy Technology Data Exchange (ETDEWEB)

    Kanai, Y; Takeuchi, N

    2009-10-14

    We revisit the molecular line growth mechanism of styrene on the hydrogenated Si(001) 2x1 surface. In particular, we investigate the energetics of the radical chain reaction mechanism by means of diffusion quantum Monte Carlo (QMC) and density functional theory (DFT) calculations. For the exchange correlation (XC) functional we use the non-empirical generalized-gradient approximation (GGA) and meta-GGA. We find that the QMC result also predicts the intra dimer-row growth of the molecular line over the inter dimer-row growth, supporting the conclusion based on DFT results. However, the absolute magnitudes of the adsorption and reaction energies, and the heights of the energy barriers differ considerably between the QMC and DFT with the GGA/meta-GGA XC functionals.

  8. Accurate and Scalable O(N) Algorithm for First-Principles Molecular-Dynamics Computations on Large Parallel Computers

    Energy Technology Data Exchange (ETDEWEB)

    Osei-Kuffuor, Daniel [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Fattebert, Jean-Luc [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2014-01-01

    We present the first truly scalable first-principles molecular dynamics algorithm with O(N) complexity and controllable accuracy, capable of simulating systems with finite band gaps of sizes that were previously impossible with this degree of accuracy. By avoiding global communications, we provide a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wave functions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 101 952 atoms on 23 328 processors, with a wall-clock time of the order of 1 min per molecular dynamics time step and numerical error on the forces of less than 7x10-4 Ha/Bohr.

  9. Accurate and scalable O(N) algorithm for first-principles molecular-dynamics computations on large parallel computers.

    Science.gov (United States)

    Osei-Kuffuor, Daniel; Fattebert, Jean-Luc

    2014-01-31

    We present the first truly scalable first-principles molecular dynamics algorithm with O(N) complexity and controllable accuracy, capable of simulating systems with finite band gaps of sizes that were previously impossible with this degree of accuracy. By avoiding global communications, we provide a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wave functions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 101,952 atoms on 23,328 processors, with a wall-clock time of the order of 1 min per molecular dynamics time step and numerical error on the forces of less than 7×10(-4)  Ha/Bohr.

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

    Directory of Open Access Journals (Sweden)

    Francisco Torrens

    2014-06-01

    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.

  11. Development of an accurate molecular mechanics model for buckling behavior of multi-walled carbon nanotubes under axial compression.

    Science.gov (United States)

    Safaei, B; Naseradinmousavi, P; Rahmani, A

    2016-04-01

    In the present paper, an analytical solution based on a molecular mechanics model is developed to evaluate the elastic critical axial buckling strain of chiral multi-walled carbon nanotubes (MWCNTs). To this end, the total potential energy of the system is calculated with the consideration of the both bond stretching and bond angular variations. Density functional theory (DFT) in the form of generalized gradient approximation (GGA) is implemented to evaluate force constants used in the molecular mechanics model. After that, based on the principle of molecular mechanics, explicit expressions are proposed to obtain elastic surface Young's modulus and Poisson's ratio of the single-walled carbon nanotubes corresponding to different types of chirality. Selected numerical results are presented to indicate the influence of the type of chirality, tube diameter, and number of tube walls in detailed. An excellent agreement is found between the present numerical results and those found in the literature which confirms the validity as well as the accuracy of the present closed-form solution. It is found that the value of critical axial buckling strain exhibit significant dependency on the type of chirality and number of tube walls.

  12. Accurate determination of genetic identity for a single cacao bean, using molecular markers with a nanofluidic system, ensures cocoa authentication.

    Science.gov (United States)

    Fang, Wanping; Meinhardt, Lyndel W; Mischke, Sue; Bellato, Cláudia M; Motilal, Lambert; Zhang, Dapeng

    2014-01-15

    Cacao (Theobroma cacao L.), the source of cocoa, is an economically important tropical crop. One problem with the premium cacao market is contamination with off-types adulterating raw premium material. Accurate determination of the genetic identity of single cacao beans is essential for ensuring cocoa authentication. Using nanofluidic single nucleotide polymorphism (SNP) genotyping with 48 SNP markers, we generated SNP fingerprints for small quantities of DNA extracted from the seed coat of single cacao beans. On the basis of the SNP profiles, we identified an assumed adulterant variety, which was unambiguously distinguished from the authentic beans by multilocus matching. Assignment tests based on both Bayesian clustering analysis and allele frequency clearly separated all 30 authentic samples from the non-authentic samples. Distance-based principle coordinate analysis further supported these results. The nanofluidic SNP protocol, together with forensic statistical tools, is sufficiently robust to establish authentication and to verify gourmet cacao varieties. This method shows significant potential for practical application.

  13. Laryngeal Squamous Intraepithelial Lesions: An Updated Review on Etiology, Classification, Molecular Changes, and Treatment.

    Science.gov (United States)

    Gale, Nina; Gnepp, Douglas R; Poljak, Mario; Strojan, Primož; Cardesa, Antonio; Helliwell, Tim; Šifrer, Robert; Volavšek, Metka; Sandison, Ann; Zidar, Nina

    2016-03-01

    Laryngeal carcinogenesis is a multistep process, characterized by an accumulation of genetic changes associated with architectural and cytologic alterations, ranging from squamous hyperplasia to carcinoma in situ and encompassed by the terminology of squamous intraepithelial lesions (SILs). The etiology, classification, genetic changes, and malignant progression of these lesions are reviewed. Tobacco remains the principal etiological factor with gastroesophageal reflux disease recently considered as a possible factor. In contrast, there is little evidence that microbiological agents, especially human papillomavirus infection, are frequently involved in laryngeal carcinogenesis and probably treatment. The currently used classifications, the dysplasia system, squamous intraepithelial neoplasia, and the Ljubljana classification, reflect different standpoints on this important topic. The modified Ljubljana classification, with good interobserver agreement, could be considered as a proposal for a unified classification of laryngeal SILs. This review also briefly discusses recently discovered genetic changes, such as CDKN2A and CTNNB1 genes, and chromosome instability of chromosomes 1 and 7; however, none of these can at present improve histologic diagnosis. Malignant progression of precursor lesions varies from 2% to 74%, according to different studies. Cold-steel microinstruments, CO2 laser, and radiotherapy are used to treat the different grades of precursor lesions. There is as yet no worldwide agreement on the treatment of high-grade lesions and carcinoma in situ.

  14. Accurate Treatment of Electrostatics during Molecular Adsorption in Nanoporous Crystals without Assigning Point Charges to Framework Atoms

    Energy Technology Data Exchange (ETDEWEB)

    Watanabe, T; Manz, TA; Sholl, DS

    2011-03-24

    Molecular simulations have become an important complement to experiments for studying gas adsorption and separation in crystalline nanoporous materials. Conventionally, these simulations use force fields that model adsorbate-pore interactions by assigning point charges to the atoms of the adsorbent. The assignment of framework charges always introduces ambiguity because there are many different choices for defining point charges, even when the true electron density of a material is known. We show how to completely avoid such ambiguity by using the electrostatic potential energy surface (EPES) calculated from plane wave density functional theory (DFT). We illustrate this approach by simulating CO(2) adsorption in four metal-organic frameworks (MOFs): IRMOF-1, ZIE-8, ZIE-90, and Zn(nicotinate)(2). The resulting CO(2) adsorption isotherms are insensitive to the exchange-correlation functional used in the DFT calculation of the EPES but are sensitive to changes in the crystal structure and lattice parameters. Isotherms computed from the DFT EPES are compared to those computed from several point charge models. This comparison makes possible, for the first time, an unbiased assessment of the accuracy of these point charge models for describing adsorption in MOFs. We find an unusually high Henry's constant (109 mmol/g.bar) and intermediate isosteric heat of adsorption (34.9 kJ/mol) for Zn(nicotinate)(2), which makes it a potentially attractive mateiial for CO(2) adsorption applications.

  15. Accurate Treatment of Electrostatics during Molecular Adsorption in Nanoporous Crystals without Assigning Point Charges to Framework Atoms

    Energy Technology Data Exchange (ETDEWEB)

    Watanabe, Taku [Georgia Inst. of Technology, Atlanta, GA (United States); Manz, Thomas A. [Georgia Inst. of Technology, Atlanta, GA (United States); Sholl, David S. [Georgia Inst. of Technology, Atlanta, GA (United States)

    2011-02-28

    Molecular simulations have become an important complement to experiments for studying gas adsorption and separation in crystalline nanoporous materials. Conventionally, these simulations use force fields that model adsorbate-pore interactions by assigning point charges to the atoms of the adsorbent. The assignment of framework charges always introduces ambiguity because there are many different choices for defining point charges, even when the true electron density of a material is known. We show how to completely avoid such ambiguity by using the electrostatic potential energy surface (EPES) calculated from plane wave density functional theory (DFT). We illustrate this approach by simulating CO2 adsorption in four metal-organic frameworks (MOFs): IRMOF-1, ZIF-8, ZIF-90, and Zn(nicotinate)2. The resulting CO2 adsorption isotherms are insensitive to the exchange-correlation functional used in the DFT calculation of the EPES but are sensitive to changes in the crystal structure and lattice parameters. Isotherms computed from the DFT EPES are compared to those computed from several point charge models. This comparison makes possible, for the first time, an unbiased assessment of the accuracy of these point charge models for describing adsorption in MOFs. We find an unusually high Henry’s constant (109 mmol/g·bar) and intermediate isosteric heat of adsorption (34.9 kJ/mol) for Zn(nicotinate)2, which makes it a potentially attractive material for CO2 adsorption applications.

  16. Olfaction-Inspired Sensing Using a Sensor System with Molecular Recognition and Optimal Classification Ability for Comprehensive Detection of Gases

    Directory of Open Access Journals (Sweden)

    Masahiro Imahashi

    2014-03-01

    Full Text Available In this study, we examined the comprehensive detection of numerous volatile molecules based on the olfactory information constructed by using olfaction-inspired sensor technology. The sensor system can simultaneously detect multiple odors by the separation and condensation ability of molecularly imprinted filtering adsorbents (MIFAs, where a MIP filter with a molecular sieve was deposited on a polydimethylsiloxane (PDMS substrate. The adsorption properties of MIFAs were evaluated using the solid-phase microextraction (SPME and gas chromatography-mass spectrometry (GC-MS. The results demonstrated that the system embedded with MIFAs possesses high sensitivity and specific selectivity. The digitization and comprehensive classification of odors were accomplished by using artificial odor maps constructed through this system.

  17. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin

    DEFF Research Database (Denmark)

    Hoadley, Katherine A; Yau, Christina; Wolf, Denise M

    2014-01-01

    Recent genomic analyses of pathologically defined tumor types identify "within-a-tissue" disease subtypes. However, the extent to which genomic signatures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform...... on 3,527 specimens from 12 cancer types, revealing a unified classification into 11 major subtypes. Five subtypes were nearly identical to their tissue-of-origin counterparts, but several distinct cancer types were found to converge into common subtypes. Lung squamous, head and neck, and a subset...... of bladder cancers coalesced into one subtype typified by TP53 alterations, TP63 amplifications, and high expression of immune and proliferation pathway genes. Of note, bladder cancers split into three pan-cancer subtypes. The multiplatform classification, while correlated with tissue-of-origin, provides...

  18. Taxonomic position of Eunapius subterraneus (Porifera, Spongillidae) inferred from molecular data--a revised classification needed?

    Science.gov (United States)

    Harcet, Matija; Bilandzija, Helena; Bruvo-Madarić, Branka; Cetković, Helena

    2010-03-01

    The freshwater sponge Eunapius subterraneus was described in 1984 on the basis of its morphology and unique ecological features. It inhabits caves in the Ogulin karst area as the only known stygobitic sponge, and an endangered karst species. We used three genetic markers with different evolutionary rates in phylogenetic analyses of E. subterraneus. All of the markers exclude this sponge from the genus Eunapius. Based on our results, we emphasize the need for revision of the taxonomic classification of E. subterraneus as well as the need for a thorough re-evaluation of freshwater sponge systematics.

  19. A Molecular Predictor Reassesses Classification of Human Grade II/III Gliomas.

    Directory of Open Access Journals (Sweden)

    Thierry Rème

    Full Text Available Diffuse gliomas are incurable brain tumors divided in 3 WHO grades (II; III; IV based on histological criteria. Grade II/III gliomas are clinically very heterogeneous and their prognosis somewhat unpredictable, preventing definition of appropriate treatment. On a cohort of 65 grade II/III glioma patients, a QPCR-based approach allowed selection of a biologically relevant gene list from which a gene signature significantly correlated to overall survival was extracted. This signature clustered the training cohort into two classes of low and high risk of progression and death, and similarly clustered two external independent test cohorts of 104 and 73 grade II/III patients. A 22-gene class predictor of the training clusters optimally distinguished poor from good prognosis patients (median survival of 13-20 months versus over 6 years in the validation cohorts. This classification was stronger at predicting outcome than the WHO grade II/III classification (P≤2.8E-10 versus 0.018. When compared to other prognosis factors (histological subtype and genetic abnormalities in a multivariate analysis, the 22-gene predictor remained significantly associated with overall survival. Early prediction of high risk patients (3% of WHO grade II, and low risk patients (29% of WHO grade III in clinical routine will allow the development of more appropriate follow-up and treatments.

  20. Radiolabelled nanoparticles: novel classification of radiopharmaceuticals for molecular imaging of cancer.

    Science.gov (United States)

    Mirshojaei, Seyedeh Fatemeh; Ahmadi, Amirhossein; Morales-Avila, Enrique; Ortiz-Reynoso, Mariana; Reyes-Perez, Horacio

    2016-01-01

    Nanotechnology has been used for every single modality in the molecular imaging arena for imaging purposes. Synergic advantages can be explored when multiple molecular imaging modalities are combined with respect to single imaging modalities. Multifunctional nanoparticles have large surface areas, where multiple functional moieties can be incorporated, including ligands for site-specific targeting and radionuclides, which can be detected to create 3D images. Recently, radiolabeled nanoparticles with individual properties have attracted great interest regarding their use in multimodality tumor imaging. Multifunctional nanoparticles can combine diagnostic and therapeutic capabilities for both target-specific diagnosis and the treatment of a given disease. The future of nanomedicine lies in multifunctional nanoplatforms that combine the diagnostic ability and therapeutic effects using appropriate ligands, drugs, responses and technological devices, which together are collectively called theranostic drugs. Co-delivery of radiolabeled nanoparticles is useful in multifunctional molecular imaging areas because it comprises several advantages based on nanoparticles architecture, pharmacokinetics and pharmacodynamic properties.

  1. Accurate Arabic Script Language/Dialect Classification

    Science.gov (United States)

    2014-01-01

    dialects. language identification, Arabic, dialect, natural language processing, machine learning 30 Stephen C. Tratz 301-394-1057Unclassified...Arabic, Farsi, Urdu), Cyrillic script (Bulgarian, Russian, Ukrainian), and Devanagari script ( Hindi , Marathi, Nepali). They use Mechanical Turk to...to 1, which can be a useful feature. The Java port of the LIBLINEAR (Fan et al., 2008) machine learning software package1 is used to train all our

  2. Self Organizing Map-Based Classification of Cathepsin k and S Inhibitors with Different Selectivity Profiles Using Different Structural Molecular Fingerprints: Design and Application for Discovery of Novel Hits.

    Science.gov (United States)

    Ihmaid, Saleh K; Ahmed, Hany E A; Zayed, Mohamed F; Abadleh, Mohammed M

    2016-01-30

    The main step in a successful drug discovery pipeline is the identification of small potent compounds that selectively bind to the target of interest with high affinity. However, there is still a shortage of efficient and accurate computational methods with powerful capability to study and hence predict compound selectivity properties. In this work, we propose an affordable machine learning method to perform compound selectivity classification and prediction. For this purpose, we have collected compounds with reported activity and built a selectivity database formed of 153 cathepsin K and S inhibitors that are considered of medicinal interest. This database has three compound sets, two K/S and S/K selective ones and one non-selective KS one. We have subjected this database to the selectivity classification tool 'Emergent Self-Organizing Maps' for exploring its capability to differentiate selective cathepsin inhibitors for one target over the other. The method exhibited good clustering performance for selective ligands with high accuracy (up to 100 %). Among the possibilites, BAPs and MACCS molecular structural fingerprints were used for such a classification. The results exhibited the ability of the method for structure-selectivity relationship interpretation and selectivity markers were identified for the design of further novel inhibitors with high activity and target selectivity.

  3. New Brain Tumor Entities Emerge from Molecular Classification of CNS-PNETs

    DEFF Research Database (Denmark)

    Sturm, Dominik; Orr, Brent A; Toprak, Umut H

    2016-01-01

    with a recurrent genetic alteration and distinct histopathological and clinical features. These new molecular entities, designated "CNS neuroblastoma with FOXR2 activation (CNS NB-FOXR2)," "CNS Ewing sarcoma family tumor with CIC alteration (CNS EFT-CIC)," "CNS high-grade neuroepithelial tumor with MN1 alteration...

  4. Beyond laminar fate: toward a molecular classification of cortical projection/pyramidal neurons.

    NARCIS (Netherlands)

    Hevner, R.F.; Daza, R.A.; Rubenstein, J.L.; Stunnenberg, H.G.; Olavarria, J.F.; Englund, C.

    2003-01-01

    Cortical projection neurons exhibit diverse morphological, physiological, and molecular phenotypes, but it is unknown how many distinct types exist. Many projection cell phenotypes are associated with laminar fate (radial position), but each layer may also contain multiple types of projection cells.

  5. Consensus classification of human prion disease histotypes allows reliable identification of molecular subtypes: an inter-rater study among surveillance centres in Europe and USA

    Science.gov (United States)

    de Boni, Laura; Saverioni, Daniela; Cohen, Mark L.; Ferrer, Isidro; Gambetti, Pierluigi; Gelpi, Ellen; Giaccone, Giorgio; Hauw, Jean-Jacques; Höftberger, Romana; Ironside, James W.; Jansen, Casper; Kovacs, Gabor G.; Rozemuller, Annemieke; Seilhean, Danielle; Tagliavini, Fabrizio; Giese, Armin

    2013-01-01

    The current classification of human sporadic prion diseases recognizes six major phenotypic subtypes with distinctive clinicopathological features, which largely correlate at the molecular level with the genotype at the polymorphic codon 129 (methionine, M, or valine, V) in the prion protein gene and with the size of the protease-resistant core of the abnormal prion protein, PrPSc (i.e. type 1 migrating at 21 kDa and type 2 at 19 kDa). We previously demonstrated that PrPSc typing by Western blotting is a reliable means of strain typing and disease classification. Limitations of this approach, however, particularly in the interlaboratory setting, are the association of PrPSc types 1 or 2 with more than one clinicopathological phenotype, which precludes definitive case classification if not supported by further analysis, and the difficulty of fully recognizing cases with mixed phenotypic features. In this study, we tested the inter-rater reliability of disease classification based only on histopathological criteria. Slides from 21 cases covering the whole phenotypic spectrum of human sporadic prion diseases, and also including two cases of variant Creutzfeldt–Jakob disease (CJD), were distributed blindly to 13 assessors for classification according to given instructions. The results showed good-to-excellent agreement between assessors in the classification of cases. In particular, there was full agreement (100 %) for the two most common sporadic CJD subtypes and variant CJD, and very high concordance in general for all pure phenotypes and the most common subtype with mixed phenotypic features. The present data fully support the basis for the current classification of sporadic human prion diseases and indicate that, besides molecular PrPSc typing, histopathological analysis permits reliable disease classification with high interlaboratory accuracy. PMID:22744790

  6. Molecular classification of familial non-BRCA1/BRCA2 breast cancer.

    Science.gov (United States)

    Hedenfalk, Ingrid; Ringner, Markus; Ben-Dor, Amir; Yakhini, Zohar; Chen, Yidong; Chebil, Gunilla; Ach, Robert; Loman, Niklas; Olsson, Håkan; Meltzer, Paul; Borg, Ake; Trent, Jeffrey

    2003-03-01

    In the decade since their discovery, the two major breast cancer susceptibility genes BRCA1 and BRCA2, have been shown conclusively to be involved in a significant fraction of families segregating breast and ovarian cancer. However, it has become equally clear that a large proportion of families segregating breast cancer alone are not caused by mutations in BRCA1 or BRCA2. Unfortunately, despite intensive effort, the identification of additional breast cancer predisposition genes has so far been unsuccessful, presumably because of genetic heterogeneity, low penetrance, or recessive/polygenic mechanisms. These non-BRCA1/2 breast cancer families (termed BRCAx families) comprise a histopathologically heterogeneous group, further supporting their origin from multiple genetic events. Accordingly, the identification of a method to successfully subdivide BRCAx families into recognizable groups could be of considerable value to further genetic analysis. We have previously shown that global gene expression analysis can identify unique and distinct expression profiles in breast tumors from BRCA1 and BRCA2 mutation carriers. Here we show that gene expression profiling can discover novel classes among BRCAx tumors, and differentiate them from BRCA1 and BRCA2 tumors. Moreover, microarray-based comparative genomic hybridization (CGH) to cDNA arrays revealed specific somatic genetic alterations within the BRCAx subgroups. These findings illustrate that, when gene expression-based classifications are used, BRCAx families can be grouped into homogeneous subsets, thereby potentially increasing the power of conventional genetic analysis.

  7. Risk-based classification of leukemia by cytogenetic and multiplex molecular methods: results from a multicenter validation study.

    Science.gov (United States)

    Gocke, C D; Mason, J; Brusca, L; Laosinchai-Wolf, W; Higgs, C; Newell, H; Masters, A; Friar, L; Karp, J; Griffiths, M; Wei, Q; Labourier, E

    2012-07-01

    Modern management of leukemia and selection of optimal treatment approaches entails the analysis of multiple recurrent cytogenetic abnormalities with independent diagnostic or prognostic value. We report the first multicenter validation of a multiplex molecular assay for 12 relevant fusion transcripts relative to cytogenetic methods. Performance was evaluated using a set of 280 adult and pediatric acute or chronic leukemias representative of the variety of presentations and pre-analytical parameters encountered in the clinical setting. The positive, negative and overall agreements were >98.5% with high concordance at each of the four sites. Positive detection of cases with low blast count or at relapse was consistent with a method sensitivity of 1%. There was 98.7% qualitative agreement with independent reference molecular tests. Apparent false negatives corresponded to rare alternative splicing isoforms not included in the panel. We further demonstrate that clinical sensitivity can be increased by adding those rare variants and other relevant transcripts or submicroscopic abnormalities. We conclude that multiplex RT-PCR followed by liquid bead array detection is a rapid and flexible method attuned to the clinical laboratory workflow, complementing standard cytogenetic methods and generating additional information valuable for the accurate diagnosis, prognosis and subsequent molecular monitoring of leukemia.

  8. Deceptive desmas: molecular phylogenetics suggests a new classification and uncovers convergent evolution of lithistid demosponges.

    Directory of Open Access Journals (Sweden)

    Astrid Schuster

    Full Text Available Reconciling the fossil record with molecular phylogenies to enhance the understanding of animal evolution is a challenging task, especially for taxa with a mostly poor fossil record, such as sponges (Porifera. 'Lithistida', a polyphyletic group of recent and fossil sponges, are an exception as they provide the richest fossil record among demosponges. Lithistids, currently encompassing 13 families, 41 genera and >300 recent species, are defined by the common possession of peculiar siliceous spicules (desmas that characteristically form rigid articulated skeletons. Their phylogenetic relationships are to a large extent unresolved and there has been no (taxonomically comprehensive analysis to formally reallocate lithistid taxa to their closest relatives. This study, based on the most comprehensive molecular and morphological investigation of 'lithistid' demosponges to date, corroborates some previous weakly-supported hypotheses, and provides novel insights into the evolutionary relationships of the previous 'order Lithistida'. Based on molecular data (partial mtDNA CO1 and 28S rDNA sequences, we show that 8 out of 13 'Lithistida' families belong to the order Astrophorida, whereas Scleritodermidae and Siphonidiidae form a separate monophyletic clade within Tetractinellida. Most lithistid astrophorids are dispersed between different clades of the Astrophorida and we propose to formally reallocate them, respectively. Corallistidae, Theonellidae and Phymatellidae are monophyletic, whereas the families Pleromidae and Scleritodermidae are polyphyletic. Family Desmanthidae is polyphyletic and groups within Halichondriidae--we formally propose a reallocation. The sister group relationship of the family Vetulinidae to Spongillida is confirmed and we propose here for the first time to include Vetulina into a new Order Sphaerocladina. Megascleres and microscleres possibly evolved and/or were lost several times independently in different 'lithistid' taxa, and

  9. Large cell carcinoma of the lung: clinically oriented classification integrating immunohistochemistry and molecular biology.

    Science.gov (United States)

    Rossi, G; Mengoli, M C; Cavazza, A; Nicoli, D; Barbareschi, M; Cantaloni, C; Papotti, M; Tironi, A; Graziano, P; Paci, M; Stefani, A; Migaldi, M; Sartori, G; Pelosi, G

    2014-01-01

    This study aimed at challenging pulmonary large cell carcinoma (LLC) as tumor entity and defining different subgroups according to immunohistochemical and molecular features. Expression of markers specific for glandular (TTF-1, napsin A, cytokeratin 7), squamous cell (p40, p63, cytokeratins 5/6, desmocollin-3), and neuroendocrine (chromogranin, synaptophysin, CD56) differentiation was studied in 121 LCC across their entire histological spectrum also using direct sequencing for epidermal growth factor receptor (EGFR) and v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations and FISH analysis for ALK gene translocation. Survival was not investigated. All 47 large cell neuroendocrine carcinomas demonstrated a true neuroendocrine cell lineage, whereas all 24 basaloid and both 2 lymphoepithelioma-like carcinomas showed squamous cell markers. Eighteen out of 22 clear cell carcinomas had glandular differentiation, with KRAS mutations being present in 39 % of cases, whereas squamous cell differentiation was present in four cases. Eighteen out of 20 large cell carcinomas, not otherwise specified, had glandular differentiation upon immunohistochemistry, with an exon 21 L858R EGFR mutation in one (5 %) tumor, an exon 2 KRAS mutation in eight (40 %) tumors, and an ALK translocation in one (5 %) tumor, whereas two tumors positive for CK7 and CK5/6 and negative for all other markers were considered adenocarcinoma. All six LCC of rhabdoid type expressed TTF-1 and/or CK7, three of which also harbored KRAS mutations. When positive and negative immunohistochemical staining for these markers was combined, three subsets of LCC emerged exhibiting glandular, squamous, and neuroendocrine differentiation. Molecular alterations were restricted to tumors classified as adenocarcinoma. Stratifying LCC into specific categories using immunohistochemistry and molecular analysis may significantly impact on the choice of therapy.

  10. New Brain Tumor Entities Emerge from Molecular Classification of CNS-PNETs.

    Science.gov (United States)

    Sturm, Dominik; Orr, Brent A; Toprak, Umut H; Hovestadt, Volker; Jones, David T W; Capper, David; Sill, Martin; Buchhalter, Ivo; Northcott, Paul A; Leis, Irina; Ryzhova, Marina; Koelsche, Christian; Pfaff, Elke; Allen, Sariah J; Balasubramanian, Gnanaprakash; Worst, Barbara C; Pajtler, Kristian W; Brabetz, Sebastian; Johann, Pascal D; Sahm, Felix; Reimand, Jüri; Mackay, Alan; Carvalho, Diana M; Remke, Marc; Phillips, Joanna J; Perry, Arie; Cowdrey, Cynthia; Drissi, Rachid; Fouladi, Maryam; Giangaspero, Felice; Łastowska, Maria; Grajkowska, Wiesława; Scheurlen, Wolfram; Pietsch, Torsten; Hagel, Christian; Gojo, Johannes; Lötsch, Daniela; Berger, Walter; Slavc, Irene; Haberler, Christine; Jouvet, Anne; Holm, Stefan; Hofer, Silvia; Prinz, Marco; Keohane, Catherine; Fried, Iris; Mawrin, Christian; Scheie, David; Mobley, Bret C; Schniederjan, Matthew J; Santi, Mariarita; Buccoliero, Anna M; Dahiya, Sonika; Kramm, Christof M; von Bueren, André O; von Hoff, Katja; Rutkowski, Stefan; Herold-Mende, Christel; Frühwald, Michael C; Milde, Till; Hasselblatt, Martin; Wesseling, Pieter; Rößler, Jochen; Schüller, Ulrich; Ebinger, Martin; Schittenhelm, Jens; Frank, Stephan; Grobholz, Rainer; Vajtai, Istvan; Hans, Volkmar; Schneppenheim, Reinhard; Zitterbart, Karel; Collins, V Peter; Aronica, Eleonora; Varlet, Pascale; Puget, Stephanie; Dufour, Christelle; Grill, Jacques; Figarella-Branger, Dominique; Wolter, Marietta; Schuhmann, Martin U; Shalaby, Tarek; Grotzer, Michael; van Meter, Timothy; Monoranu, Camelia-Maria; Felsberg, Jörg; Reifenberger, Guido; Snuderl, Matija; Forrester, Lynn Ann; Koster, Jan; Versteeg, Rogier; Volckmann, Richard; van Sluis, Peter; Wolf, Stephan; Mikkelsen, Tom; Gajjar, Amar; Aldape, Kenneth; Moore, Andrew S; Taylor, Michael D; Jones, Chris; Jabado, Nada; Karajannis, Matthias A; Eils, Roland; Schlesner, Matthias; Lichter, Peter; von Deimling, Andreas; Pfister, Stefan M; Ellison, David W; Korshunov, Andrey; Kool, Marcel

    2016-02-25

    Primitive neuroectodermal tumors of the central nervous system (CNS-PNETs) are highly aggressive, poorly differentiated embryonal tumors occurring predominantly in young children but also affecting adolescents and adults. Herein, we demonstrate that a significant proportion of institutionally diagnosed CNS-PNETs display molecular profiles indistinguishable from those of various other well-defined CNS tumor entities, facilitating diagnosis and appropriate therapy for patients with these tumors. From the remaining fraction of CNS-PNETs, we identify four new CNS tumor entities, each associated with a recurrent genetic alteration and distinct histopathological and clinical features. These new molecular entities, designated "CNS neuroblastoma with FOXR2 activation (CNS NB-FOXR2)," "CNS Ewing sarcoma family tumor with CIC alteration (CNS EFT-CIC)," "CNS high-grade neuroepithelial tumor with MN1 alteration (CNS HGNET-MN1)," and "CNS high-grade neuroepithelial tumor with BCOR alteration (CNS HGNET-BCOR)," will enable meaningful clinical trials and the development of therapeutic strategies for patients affected by poorly differentiated CNS tumors.

  11. Using molecular classification to predict gains in maximal aerobic capacity following endurance exercise training in humans

    DEFF Research Database (Denmark)

    Timmons, James A; Knudsen, Steen; Rankinen, Tuomo

    2010-01-01

    A low maximal oxygen consumption (VO2max) is a strong risk factor for premature mortality. Supervised endurance exercise training increases VO2max with a very wide range of effectiveness in humans. Discovering the DNA variants that contribute to this heterogeneity typically requires substantial s...... of genetic biomarkers, sufficiently discrete for diagnostic purposes, for a range of physiological and pharmacological phenotypes in humans.......A low maximal oxygen consumption (VO2max) is a strong risk factor for premature mortality. Supervised endurance exercise training increases VO2max with a very wide range of effectiveness in humans. Discovering the DNA variants that contribute to this heterogeneity typically requires substantial...... association analysis yields a strongly validated molecular predictor with meaningful explanatory power. VO2max responses to endurance training can be predicted by measuring a approximately 30-gene RNA expression signature in muscle prior to training. The general approach taken could accelerate the discovery...

  12. Molecular Classification and Pharmacogenetics of Primary Plasma Cell Leukemia: An Initial Approach toward Precision Medicine.

    Science.gov (United States)

    Simeon, Vittorio; Todoerti, Katia; La Rocca, Francesco; Caivano, Antonella; Trino, Stefania; Lionetti, Marta; Agnelli, Luca; De Luca, Luciana; Laurenzana, Ilaria; Neri, Antonino; Musto, Pellegrino

    2015-07-30

    Primary plasma cell leukemia (pPCL) is a rare and aggressive variant of multiple myeloma (MM) which may represent a valid model for high-risk MM. This disease is associated with a very poor prognosis, and unfortunately, it has not significantly improved during the last three decades. New high-throughput technologies have allowed a better understanding of the molecular basis of this disease and moved toward risk stratification, providing insights for targeted therapy studies. This knowledge, added to the pharmacogenetic profile of new and old agents in the analysis of efficacy and safety, could contribute to help clinical decisions move toward a precision medicine and a better clinical outcome for these patients. In this review, we describe the available literature concerning the genomic characterization and pharmacogenetics of plasma cell leukemia (PCL).

  13. Rapid Classification of Imaged Objects Using Molecular Factor and Multivariate Optical Computing

    Science.gov (United States)

    Pearl, Megan Renee

    Unique algorithm development is vital for the success of novel instrumentation. Our lab has focused on the design of imaging systems based on molecular factor and multivariate optical computing. A simulation-driven design approach was utilized to develop a multimode infrared imaging system for chemical contrast enhancement. This infrared thermal imaging system is based on molecular factor (MFC) and lockin computing methods. MFC was accomplished with filter elements made of thin organic films deposited on IR-transparent substrates and allows a system response to be tuned to a specific analyte. Unique algorithms were written in-house using MatLabRTM (The Mathworks, Natick, MA). The algorithms used a lock-in computing technique to amplify the diffuse re ectance signal, which is only a few percent of the total signal. Intensive thin film studies were conducted to understand the effects of films on fabric to improve our simulation-driven design approach. A prototype instrument has been validated through the production of a real setup. We have shown that it is able to detect trace amounts of blood diluted in water (as small as 1:100) on fabric as well as differentiate blood from common false positives of other blood detection methods (i.e., luminol). The second imaging system was designed for the differentiation of phytoplankton species in the ocean. Multivariate optical computing (MOC) was applied to the uorescence excitation spectra of individual phytoplankton cells to design multivariate optical elements (MOEs). MOEs are filters fabricated to mimic linear discriminants analysis (LDA) results based on plankton spectroscopy. The imaging system uses these MOEs housed in a filter wheel to produce "streak" images of phytoplankton as they flow past a CCD camera, with each streak having the appearance of a barcode whose intensities are related to scores of the plankton spectra on linear discriminant functions. Algorithms for this system have been designed to automatically

  14. Molecular and metabolic pattern classification for detection of brain glioma progression

    Energy Technology Data Exchange (ETDEWEB)

    Imani, Farzin, E-mail: imanif@upmc.edu [Department of Radiology, University of Pittsburgh Medical Center, PA (United States); Boada, Fernando E. [Department of Radiology, University of Pittsburgh Medical Center, PA (United States); Lieberman, Frank S. [Department of Neurology, University of Pittsburgh Medical Center, PA (United States); Davis, Denise K.; Mountz, James M. [Department of Radiology, University of Pittsburgh Medical Center, PA (United States)

    2014-02-15

    %. Conclusion: This study suggests that SVM models may improve detection of glioma progression more accurately than single parametric imaging methods. Research support: National Cancer Institute, Cancer Center Support Grant Supplement Award, Imaging Response Assessment Teams.

  15. Focal Gains of Vascular Endothelial Growth Factor A and Molecular Classification of Hepatocellular Carcinoma

    Science.gov (United States)

    Chiang, Derek Y.; Villanueva, Augusto; Hoshida, Yujin; Peix, Judit; Newell, Philippa; Minguez, Beatriz; LeBlanc, Amanda C.; Donovan, Diana J.; Thung, Swan N.; Sole, Manel; Tovar, Victoria; Alsinet, Clara; Ramos, Alex H.; Barretina, Jordi; Roayaie, Sasan; Schwartz, Myron; Waxman, Samuel; Bruix, Jordi; Mazzaferro, Vincenzo; Ligon, Azra H.; Najfeld, Vesna; Friedman, Scott L.; Sellers, William R.; Meyerson, Matthew; Llovet, Josep M.

    2008-01-01

    Hepatocellular carcinomas (HCC) represent the third-leading cause of cancer-related deaths worldwide. The vast majority of cases arise in the context of chronic liver injury due to hepatitis B virus or hepatitis C virus infection. In order to identify genetic mechanisms of hepatocarcinogenesis, we characterized copy number alterations and gene expression profiles from the same set of tumors associated with hepatitis C virus. Most tumors harbored 1q gain, 8q gain or 8p loss, with occasional alterations in 13 additional chromosome arms. In addition to amplifications at 11q13 in 6 of 103 tumors, 4 tumors harbored focal gains at 6p21 incorporating VEGFA. Fluorescence in situ hybridization on an independent validation set of 210 tumors found 6p21 high-level gains in 14 tumors, as well as 2 tumors with 6p21 amplifications. Strikingly, this locus overlapped with copy gains in 4 of 371 lung adenocarcinomas. Overexpression of VEGFA via 6p21 gain in hepatocellular carcinomas suggested a novel, cell-nonautonomous mechanism of oncogene activation. Hierarchical clustering of gene expression among 91 of these tumors identified 5 classes, including ‘CTNNB1’, ‘proliferation’, ‘interferon-related’, and a novel class defined by polysomy of chromosome 7. These class labels were further supported by molecular data: mutations in CTNNB1 were enriched in the ‘CTNNB1’ class, while IGF1R and RPS6 phosphorylation were enriched in the ‘proliferation’ class. The enrichment of signaling pathway alterations in gene expression classes provides insights on HCC pathogenesis. Furthermore, the prevalence of VEGFA high-level gains in multiple tumor types suggests indications for clinical trials of anti-angiogenic therapies. PMID:18701503

  16. Clinical utility of reverse phase protein array for molecular classification of breast cancer.

    Science.gov (United States)

    Negm, Ola H; Muftah, Abir A; Aleskandarany, Mohammed A; Hamed, Mohamed R; Ahmad, Dena A J; Nolan, Christopher C; Diez-Rodriguez, Maria; Tighe, Patrick J; Ellis, Ian O; Rakha, Emad A; Green, Andrew R

    2016-01-01

    Reverse Phase Protein Array (RPPA) represents a sensitive and high-throughput technique allowing simultaneous quantitation of protein expression levels in biological samples. This study aimed to confirm the ability of RPPA to classify archival formalin-fixed paraffin-embedded (FFPE) breast cancer tissues into molecular classes used in the Nottingham prognostic index plus (NPI+) determined by immunohistochemistry (IHC). Proteins were extracted from FFPE breast cancer tissues using three extraction protocols: the Q-proteome FFPE Tissue Kit (Qiagen, Hilden, Germany) and two in-house methods using Laemmli buffer with either incubation for 20 min or 2 h at 105 °C. Two preparation methods, full-face sections and macrodissection, were used to assess the yield and quality of protein extracts. Ten biomarkers used for the NPI+ (ER, PgR, HER2, Cytokeratins 5/6 and 7/8, EGFR, HER3, HER4, p53 and Mucin 1) were quantified using RPPA and compared to results determined by IHC. The Q-proteome FFPE Tissue Kit produced significantly higher protein concentration and signal intensities. The intra- and inter-array reproducibility assessment indicated that RPPA using FFPE lysates was a highly reproducible and robust technique. Expression of the biomarkers individually and in combination using RPPA was highly consistent with IHC results. Macrodissection of the invasive tumour component gave more reliable results with the majority of biomarkers determined by IHC, (80 % concordance) compared with full-face sections (60 % concordance). Our results provide evidence for the technical feasibility of RPPA for high-throughput protein expression profiling of FFPE breast cancer tissues. The sensitivity of the technique is related to the quality of extracted protein and purity of tumour tissue. RPPA could provide a quantitative technique alternative to IHC for the biomarkers used in the NPI+.

  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

    2015-09-01

    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. Diffuse low-grade glioma: a review on the new molecular classification, natural history and current management strategies.

    Science.gov (United States)

    Delgado-López, P D; Corrales-García, E M; Martino, J; Lastra-Aras, E; Dueñas-Polo, M T

    2017-03-02

    The management of diffuse supratentorial WHO grade II glioma remains a challenge because of the infiltrative nature of the tumor, which precludes curative therapy after total or even supratotal resection. When possible, functional-guided resection is the preferred initial treatment. Total and subtotal resections correlate with increased overall survival. High-risk patients (age >40, partial resection), especially IDH-mutated and 1p19q-codeleted oligodendroglial lesions, benefit from surgery plus adjuvant chemoradiation. Under the new 2016 WHO brain tumor classification, which now incorporates molecular parameters, all diffusely infiltrating gliomas are grouped together since they share specific genetic mutations and prognostic factors. Although low-grade gliomas cannot be regarded as benign tumors, large observational studies have shown that median survival can actually be doubled if an early, aggressive, multi-stage and personalized therapy is applied, as compared to prior wait-and-see policy series. Patients need an honest long-term therapeutic strategy that should ideally anticipate neurological, cognitive and histopathologic worsening.

  19. Molecular Classification of Melanoma

    Science.gov (United States)

    Tissue-based analyses of precursors, melanoma tumors and metastases within existing study populations to further understanding of the heterogeneity of melanoma and determine a predictive pattern of progression for dysplastic nevi.

  20. Binary classification of chalcone derivatives with LDA or KNN based on their antileishmanial activity and molecular descriptors selected using the Successive Projections Algorithm feature-selection technique.

    Science.gov (United States)

    Goodarzi, Mohammad; Saeys, Wouter; de Araujo, Mario Cesar Ugulino; Galvão, Roberto Kawakami Harrop; Vander Heyden, Yvan

    2014-01-23

    Chalcones are naturally occurring aromatic ketones, which consist of an α-, β-unsaturated carbonyl system joining two aryl rings. These compounds are reported to exhibit several pharmacological activities, including antiparasitic, antibacterial, antifungal, anticancer, immunomodulatory, nitric oxide inhibition and anti-inflammatory effects. In the present work, a Quantitative Structure-Activity Relationship (QSAR) study is carried out to classify chalcone derivatives with respect to their antileishmanial activity (active/inactive) on the basis of molecular descriptors. For this purpose, two techniques to select descriptors are employed, the Successive Projections Algorithm (SPA) and the Genetic Algorithm (GA). The selected descriptors are initially employed to build Linear Discriminant Analysis (LDA) models. An additional investigation is then carried out to determine whether the results can be improved by using a non-parametric classification technique (One Nearest Neighbour, 1NN). In a case study involving 100 chalcone derivatives, the 1NN models were found to provide better rates of correct classification than LDA, both in the training and test sets. The best result was achieved by a SPA-1NN model with six molecular descriptors, which provided correct classification rates of 97% and 84% for the training and test sets, respectively.

  1. The accurate calculation of the band gap of liquid water by means of GW corrections applied to plane-wave density functional theory molecular dynamics simulations

    NARCIS (Netherlands)

    Fang, Changming; Li, Wun Fan; Koster, Rik S.; Klimeš, Jiří; Van Blaaderen, Alfons; Van Huis, Marijn A.

    2015-01-01

    Knowledge about the intrinsic electronic properties of water is imperative for understanding the behaviour of aqueous solutions that are used throughout biology, chemistry, physics, and industry. The calculation of the electronic band gap of liquids is challenging, because the most accurate ab initi

  2. Comprehensive gene expression profiling and immunohistochemical studies support application of immunophenotypic algorithm for molecular subtype classification in diffuse large B-cell lymphoma

    DEFF Research Database (Denmark)

    Visco, C; Xu-Monette, Z Y; Miranda, R N

    2012-01-01

    Gene expression profiling (GEP) has stratified diffuse large B-cell lymphoma (DLBCL) into molecular subgroups that correspond to different stages of lymphocyte development-namely germinal center B-cell like and activated B-cell like. This classification has prognostic significance, but GEP...... on formalin-fixed, paraffin-embedded tissue samples. Sections were stained with antibodies reactive with CD10, GCET1, FOXP1, MUM1 and BCL6 and cases were classified following a rationale of sequential steps of differentiation of B cells. Cutoffs for each marker were obtained using receiver...

  3. Accurate calculation of chemical shifts in highly dynamic H2@C60 through an integrated quantum mechanics/molecular dynamics scheme.

    Science.gov (United States)

    Jiménez-Osés, Gonzalo; García, José I; Corzana, Francisco; Elguero, José

    2011-05-20

    A new protocol combining classical MD simulations and DFT calculations is presented to accurately estimate the (1)H NMR chemical shifts of highly mobile guest-host systems and their thermal dependence. This strategy has been successfully applied for the hydrogen molecule trapped into C(60) fullerene, an unresolved and challenging prototypical case for which experimental values have never been reproduced. The dependence of the final values on the theoretical method and their implications to avoid over interpretation of the obtained results are carefully described.

  4. Tissue-specific gene expression templates for accurate molecular characterization of the normal physiological states of multiple human tissues with implication in development and cancer studies

    Directory of Open Access Journals (Sweden)

    Yuan Shinsheng

    2011-09-01

    Full Text Available Abstract Background To elucidate the molecular complications in many complex diseases, we argue for the priority to construct a model representing the normal physiological state of a cell/tissue. Results By analyzing three independent microarray datasets on normal human tissues, we established a quantitative molecular model GET, which consists of 24 tissue-specific Gene Expression Templates constructed from a set of 56 genes, for predicting 24 distinct tissue types under disease-free condition. 99.2% correctness was reached when a large-scale validation was performed on 61 new datasets to test the tissue-prediction power of GET. Network analysis based on molecular interactions suggests a potential role of these 56 genes in tissue differentiation and carcinogenesis. Applying GET to transcriptomic datasets produced from tissue development studies the results correlated well with developmental stages. Cancerous tissues and cell lines yielded significantly lower correlation with GET than the normal tissues. GET distinguished melanoma from normal skin tissue or benign skin tumor with 96% sensitivity and 89% specificity. Conclusions These results strongly suggest that a normal tissue or cell may uphold its normal functioning and morphology by maintaining specific chemical stoichiometry among genes. The state of stoichiometry can be depicted by a compact set of representative genes such as the 56 genes obtained here. A significant deviation from normal stoichiometry may result in malfunction or abnormal growth of the cells.

  5. Pharmacological Classification and Activity Evaluation of Furan and Thiophene Amide Derivatives Applying Semi-Empirical ab initio Molecular Modeling Methods

    Directory of Open Access Journals (Sweden)

    Leszek Bober

    2012-05-01

    Full Text Available Pharmacological and physicochemical classification of the furan and thiophene amide derivatives by multiple regression analysis and partial least square (PLS based on semi-empirical ab initio molecular modeling studies and high-performance liquid chromatography (HPLC retention data is proposed. Structural parameters obtained from the PCM (Polarizable Continuum Model method and the literature values of biological activity (antiproliferative for the A431 cells expressed as LD50 of the examined furan and thiophene derivatives was used to search for relationships. It was tested how variable molecular modeling conditions considered together, with or without HPLC retention data, allow evaluation of the structural recognition of furan and thiophene derivatives with respect to their pharmacological properties.

  6. Accurate molecular dynamics and nuclear quantum effects at low cost by multiple steps in real and imaginary time: Using density functional theory to accelerate wavefunction methods

    Energy Technology Data Exchange (ETDEWEB)

    Kapil, V.; Ceriotti, M., E-mail: michele.ceriotti@epfl.ch [Laboratory of Computational Science and Modelling, Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, Lausanne (Switzerland); VandeVondele, J., E-mail: joost.vandevondele@mat.ethz.ch [Department of Materials, ETH Zurich, Wolfgang-Pauli-Strasse 27, CH-8093 Zurich (Switzerland)

    2016-02-07

    The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious approximations. Even though recent developments have significantly reduced the overhead for modeling the quantum nature of the nuclei, the cost is still prohibitive when combined with advanced electronic structure methods. Here we present how multiple time step integrators can be combined with ring-polymer contraction techniques (effectively, multiple time stepping in imaginary time) to reduce virtually to zero the overhead of modelling nuclear quantum effects, while describing inter-atomic forces at high levels of electronic structure theory. This is demonstrated for a combination of MP2 and semi-local DFT applied to the Zundel cation. The approach can be seamlessly combined with other methods to reduce the computational cost of path integral calculations, such as high-order factorizations of the Boltzmann operator or generalized Langevin equation thermostats.

  7. Simple and accurate scheme to compute electrostatic interaction: Zero-dipole summation technique for molecular system and application to bulk water

    Science.gov (United States)

    Fukuda, Ikuo; Kamiya, Narutoshi; Yonezawa, Yasushige; Nakamura, Haruki

    2012-08-01

    The zero-dipole summation method was extended to general molecular systems, and then applied to molecular dynamics simulations of an isotropic water system. In our previous paper [I. Fukuda, Y. Yonezawa, and H. Nakamura, J. Chem. Phys. 134, 164107 (2011), 10.1063/1.3582791], for evaluating the electrostatic energy of a classical particle system, we proposed the zero-dipole summation method, which conceptually prevents the nonzero-charge and nonzero-dipole states artificially generated by a simple cutoff truncation. Here, we consider the application of this scheme to molecular systems, as well as some fundamental aspects of general cutoff truncation protocols. Introducing an idea to harmonize the bonding interactions and the electrostatic interactions in the scheme, we develop a specific algorithm. As in the previous study, the resulting energy formula is represented by a simple pairwise function sum, enabling facile applications to high-performance computation. The accuracy of the electrostatic energies calculated by the zero-dipole summation method with the atom-based cutoff was numerically investigated, by comparison with those generated by the Ewald method. We obtained an electrostatic energy error of less than 0.01% at a cutoff length longer than 13 Å for a TIP3P isotropic water system, and the errors were quite small, as compared to those obtained by conventional truncation methods. The static property and the stability in an MD simulation were also satisfactory. In addition, the dielectric constants and the distance-dependent Kirkwood factors were measured, and their coincidences with those calculated by the particle mesh Ewald method were confirmed, although such coincidences are not easily attained by truncation methods. We found that the zero damping-factor gave the best results in a practical cutoff distance region. In fact, in contrast to the zero-charge scheme, the damping effect was insensitive in the zero-charge and zero-dipole scheme, in the

  8. Clinical application of a microfluidic chip for immunocapture and quantification of circulating exosomes to assist breast cancer diagnosis and molecular classification

    Science.gov (United States)

    Fang, Shimeng; Tian, Hongzhu; Li, Xiancheng; Jin, Dong; Li, Xiaojie; Kong, Jing; Yang, Chun; Yang, Xuesong; Lu, Yao; Luo, Yong; Lin, Bingcheng; Niu, Weidong

    2017-01-01

    Increasing attention has been attracted by exosomes in blood-based diagnosis because cancer cells release more exosomes in serum than normal cells and these exosomes overexpress a certain number of cancer-related biomarkers. However, capture and biomarker analysis of exosomes for clinical application are technically challenging. In this study, we developed a microfluidic chip for immunocapture and quantification of circulating exosomes from small sample volume and applied this device in clinical study. Circulating EpCAM-positive exosomes were measured in 6 cases breast cancer patients and 3 healthy controls to assist diagnosis. A significant increase in the EpCAM-positive exosome level in these patients was detected, compared to healthy controls. Furthermore, we quantified circulating HER2-positive exosomes in 19 cases of breast cancer patients for molecular classification. We demonstrated that the exosomal HER2 expression levels were almost consistent with that in tumor tissues assessed by immunohistochemical staining. The microfluidic chip might provide a new platform to assist breast cancer diagnosis and molecular classification. PMID:28369094

  9. Trimodal color-fluorescence-polarization endoscopy aided by a tumor selective molecular probe accurately detects flat lesions in colitis-associated cancer

    Science.gov (United States)

    Charanya, Tauseef; York, Timothy; Bloch, Sharon; Sudlow, Gail; Liang, Kexian; Garcia, Missael; Akers, Walter J.; Rubin, Deborah; Gruev, Viktor; Achilefu, Samuel

    2014-12-01

    Colitis-associated cancer (CAC) arises from premalignant flat lesions of the colon, which are difficult to detect with current endoscopic screening approaches. We have developed a complementary fluorescence and polarization reporting strategy that combines the unique biochemical and physical properties of dysplasia and cancer for real-time detection of these lesions. Using azoxymethane-dextran sodium sulfate (AOM-DSS) treated mice, which recapitulates human CAC and dysplasia, we show that an octapeptide labeled with a near-infrared (NIR) fluorescent dye selectively identified all precancerous and cancerous lesions. A new thermoresponsive sol-gel formulation allowed topical application of the molecular probe during endoscopy. This method yielded high contrast-to-noise ratios (CNR) between adenomatous tumors (20.6±1.65) and flat lesions (12.1±1.03) and surrounding uninvolved colon tissue versus CNR of inflamed tissues (1.62±0.41). Incorporation of nanowire-filtered polarization imaging into NIR fluorescence endoscopy shows a high depolarization contrast in both adenomatous tumors and flat lesions in CAC, reflecting compromised structural integrity of these tissues. Together, the real-time polarization imaging provides real-time validation of suspicious colon tissue highlighted by molecular fluorescence endoscopy.

  10. Elastic collisions between Si and D atoms at low temperatures and accurate analytic potential energy function and molecular constants of the SiD(X2∏) radical

    Institute of Scientific and Technical Information of China (English)

    Shi De-Heng; Zhang Jin-Ping; Sun Jin-Feng; Zhu Zun-Lue

    2009-01-01

    Interaction potential of the SiD(X2∏) radical is constructed by using the CCSD(T) theory in combination with the largest correlation-consistent quintuple basis set augmented with the diffuse functions in the valence range. Using the interaction potential, the spectroscopic parameters are accurately determined. The present D0, De, Re, ωe, αe and Be values are of 3.0956 eV, 3.1863 eV, 0.15223 nm, 1472.894 cm-1, 0.07799 cm-1 and 3.8717 cm-1, respectively,which are in excellent agreement with the measurements. A total of 26 vibrational states is predicted when J = 0 by solving the radial Schr(o)dinger equation of nuclear motion. The complete vibrational levels, classical turning points,initial rotation and centrifugal distortion constants when J = 0 are reported for the first time, which are in good accord with the available experiments. The total and various partial-wave cross sections are calculated for the elastic collisions between Si and D atoms in their ground states at 1.0×10-11-1.0×10-3 a.u. when the two atoms approach each other along the SiD(X2∏) potential energy curve. Four shape resonances are found in the total elastic cross sections, and their resonant energies are of 1.73×10-5, 4.0×10-5, 6.45×10-5 and 5.5×10-4 a.u., respectively. Each shape resonance in the total elastic cross sections is carefully investigated. The results show that the shape of the total elastic cross sections is mainly dominated by the s partial wave at very low temperatures. Because of the weakness of the shape resonances coming from the higher partial waves, most of them are passed into oblivion by the strong s partial-wave elastic cross sections.

  11. Taxonomy of Plant Genetic Resources – Use of Morphological, Molecular and Phytochemical Data in Order to Verify Existing Classifications

    Directory of Open Access Journals (Sweden)

    Ulrike Lohwasser

    2010-12-01

    Full Text Available Taxonomy of plant genetic resources is an important input in characterising and evaluating cultivated plants and it is essential for identification and documentation of the diversity of genebank collections. In former times taxonomical determination was based only on morphological characters. Nowadays, new molecular and chemical methods and techniques are available for providing additional information. As examples of the interaction of morphological, molecular and phytochemical data, investigations of a parsley (Petroselinum crispum [Mill.] Nyman, Apiaceae and an opium poppy (Papaver somniferum L., Papaveraceae collection of the German genebank are demonstrated. 220 parsley and 300 opium poppy accessions were cultivated and described morphologically. In addition, the molecular distance and the phylogenetic relationship of the accessions were performed with molecular marker analysis. Essential oil compound and content for parsley and the content of the five main alkaloids (morphine, codeine, thebaine, noscapine, papaverine for opium poppy were measured with GC (gas chromatography and HPLC (high pressure liquid chromatography, respectively. For parsley the results of the three methods support the existing taxonomy partly, a separation of root and leaf parsley was confirmed. However, the taxonomy of opium poppy should be revised because molecular and chemical data do not verify the morphological results. But nevertheless taxonomy of cultivated plants is an important tool to describe the variability of plant genetic resources.

  12. 分子生物学技术在带绦虫分类中的应用%Application of molecular biological techniques for classification of Taenia

    Institute of Scientific and Technical Information of China (English)

    杨立军; 周本江

    2010-01-01

    传统的带绦虫分类是根据成虫和囊尾蚴的形态特征,有一定的局限性,尤其是对形态相近的虫种鉴别困难.近年来发展的分子生物学技术从基因水平检测带绦虫种间或种内个体间的遗传差异,若将两者有机结合,虫种鉴别将更加全面和客观.该文综述了PCR-限制性片段长度多态性技术(polymerase chain reaction-restriction fragment length polymorphism,PCR-RFLP)、随机扩增多态性DNA(randomly amplified polymorphic DNA,RAPD)、DNA序列分析等分子生物学技术在带绦虫分类研究中的应用.%The traditional classification of Taenia based on morphological features of adult and cysticer-cosis has some limitations with difficulty to identify morphologically similar species. The development of molecu-lar biology techniques in recent years can detect interspecific or intraspecific genetic differences of Taenia at the gene level. If these two methods are integrated, insect species identification will become more comprehensive and objective. This paper reviewed the application of molecular biological technology, such as PCR-RFLP,RAPD and analysis of DNA sequence in classification and identification of Taenia.

  13. A systematic and functional classification of Streptococcus pyogenes that serves as a new tool for molecular typing and vaccine development.

    Science.gov (United States)

    Sanderson-Smith, Martina; De Oliveira, David M P; Guglielmini, Julien; McMillan, David J; Vu, Therese; Holien, Jessica K; Henningham, Anna; Steer, Andrew C; Bessen, Debra E; Dale, James B; Curtis, Nigel; Beall, Bernard W; Walker, Mark J; Parker, Michael W; Carapetis, Jonathan R; Van Melderen, Laurence; Sriprakash, Kadaba S; Smeesters, Pierre R

    2014-10-15

    Streptococcus pyogenes ranks among the main causes of mortality from bacterial infections worldwide. Currently there is no vaccine to prevent diseases such as rheumatic heart disease and invasive streptococcal infection. The streptococcal M protein that is used as the substrate for epidemiological typing is both a virulence factor and a vaccine antigen. Over 220 variants of this protein have been described, making comparisons between proteins difficult, and hindering M protein-based vaccine development. A functional classification based on 48 emm-clusters containing closely related M proteins that share binding and structural properties is proposed. The need for a paradigm shift from type-specific immunity against S. pyogenes to emm-cluster based immunity for this bacterium should be further investigated. Implementation of this emm-cluster-based system as a standard typing scheme for S. pyogenes will facilitate the design of future studies of M protein function, streptococcal virulence, epidemiological surveillance, and vaccine development.

  14. Classifications within Molecular Subtypes Enables Identification of BRCA1/BRCA2 Mutation Carriers by RNA Tumor Profiling

    DEFF Research Database (Denmark)

    Larsen, Martin Jakob; Kruse, Torben A; Tan, Qihua;

    2013-01-01

    Pathogenic germline mutations in BRCA1 or BRCA2 are detected in less than one third of families with a strong history of breast cancer. It is therefore expected that mutations still remain undetected by currently used screening methods. In addition, a growing number of BRCA1/2 sequence variants...... of unclear pathogen significance are found in the families, constituting an increasing clinical challenge. New methods are therefore needed to improve the detection rate and aid the interpretation of the clinically uncertain variants. In this study we analyzed a series of 33 BRCA1, 22 BRCA2, and 128 sporadic...... tumors by RNA profiling to investigate the classification potential of RNA profiles to predict BRCA1/2 mutation status. We found that breast tumors from BRCA1 and BRCA2 mutation carriers display characteristic RNA expression patterns, allowing them to be distinguished from sporadic tumors. The majority...

  15. Efficient and accurate fragmentation methods.

    Science.gov (United States)

    Pruitt, Spencer R; Bertoni, Colleen; Brorsen, Kurt R; Gordon, Mark S

    2014-09-16

    Conspectus Three novel fragmentation methods that are available in the electronic structure program GAMESS (general atomic and molecular electronic structure system) are discussed in this Account. The fragment molecular orbital (FMO) method can be combined with any electronic structure method to perform accurate calculations on large molecular species with no reliance on capping atoms or empirical parameters. The FMO method is highly scalable and can take advantage of massively parallel computer systems. For example, the method has been shown to scale nearly linearly on up to 131 000 processor cores for calculations on large water clusters. There have been many applications of the FMO method to large molecular clusters, to biomolecules (e.g., proteins), and to materials that are used as heterogeneous catalysts. The effective fragment potential (EFP) method is a model potential approach that is fully derived from first principles and has no empirically fitted parameters. Consequently, an EFP can be generated for any molecule by a simple preparatory GAMESS calculation. The EFP method provides accurate descriptions of all types of intermolecular interactions, including Coulombic interactions, polarization/induction, exchange repulsion, dispersion, and charge transfer. The EFP method has been applied successfully to the study of liquid water, π-stacking in substituted benzenes and in DNA base pairs, solvent effects on positive and negative ions, electronic spectra and dynamics, non-adiabatic phenomena in electronic excited states, and nonlinear excited state properties. The effective fragment molecular orbital (EFMO) method is a merger of the FMO and EFP methods, in which interfragment interactions are described by the EFP potential, rather than the less accurate electrostatic potential. The use of EFP in this manner facilitates the use of a smaller value for the distance cut-off (Rcut). Rcut determines the distance at which EFP interactions replace fully quantum

  16. Communication: Rate coefficients of the H + CH{sub 4} → H{sub 2} + CH{sub 3} reaction from ring polymer molecular dynamics on a highly accurate potential energy surface

    Energy Technology Data Exchange (ETDEWEB)

    Meng, Qingyong, E-mail: mengqingyong@dicp.ac.cn; Chen, Jun, E-mail: chenjun@dicp.ac.cn; Zhang, Dong H., E-mail: zhangdh@dicp.ac.cn [State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, 116023 Dalian (China)

    2015-09-14

    The ring polymer molecular dynamics (RPMD) calculations are performed to calculate rate constants for the title reaction on the recently constructed potential energy surface based on permutation invariant polynomial (PIP) neural-network (NN) fitting [J. Li et al., J. Chem. Phys. 142, 204302 (2015)]. By inspecting convergence, 16 beads are used in computing free-energy barriers at 300 K ≤ T ≤ 1000 K, while different numbers of beads are used for transmission coefficients. The present RPMD rates are in excellent agreement with quantum rates computed on the same potential energy surface, as well as with the experimental measurements, demonstrating further that the RPMD is capable of producing accurate rates for polyatomic chemical reactions even at rather low temperatures.

  17. Comprehensive phylogenetic reconstructions of African swine fever virus: proposal for a new classification and molecular dating of the virus.

    Directory of Open Access Journals (Sweden)

    Vincent Michaud

    Full Text Available African swine fever (ASF is a highly lethal disease of domestic pigs caused by the only known DNA arbovirus. It was first described in Kenya in 1921 and since then many isolates have been collected worldwide. However, although several phylogenetic studies have been carried out to understand the relationships between the isolates, no molecular dating analyses have been achieved so far. In this paper, comprehensive phylogenetic reconstructions were made using newly generated, publicly available sequences of hundreds of ASFV isolates from the past 70 years. Analyses focused on B646L, CP204L, and E183L genes from 356, 251, and 123 isolates, respectively. Phylogenetic analyses were achieved using maximum likelihood and Bayesian coalescence methods. A new lineage-based nomenclature is proposed to designate 35 different clusters. In addition, dating of ASFV origin was carried out from the molecular data sets. To avoid bias, diversity due to positive selection or recombination events was neutralized. The molecular clock analyses revealed that ASFV strains currently circulating have evolved over 300 years, with a time to the most recent common ancestor (TMRCA in the early 18(th century.

  18. Integration of Chinese medicine with Western medicine could lead to future medicine: molecular module medicine.

    Science.gov (United States)

    Zhang, Chi; Zhang, Ge; Chen, Ke-ji; Lu, Ai-ping

    2016-04-01

    The development of an effective classification method for human health conditions is essential for precise diagnosis and delivery of tailored therapy to individuals. Contemporary classification of disease systems has properties that limit its information content and usability. Chinese medicine pattern classification has been incorporated with disease classification, and this integrated classification method became more precise because of the increased understanding of the molecular mechanisms. However, we are still facing the complexity of diseases and patterns in the classification of health conditions. With continuing advances in omics methodologies and instrumentation, we are proposing a new classification approach: molecular module classification, which is applying molecular modules to classifying human health status. The initiative would be precisely defining the health status, providing accurate diagnoses, optimizing the therapeutics and improving new drug discovery strategy. Therefore, there would be no current disease diagnosis, no disease pattern classification, and in the future, a new medicine based on this classification, molecular module medicine, could redefine health statuses and reshape the clinical practice.

  19. Accurate Methods for Large Molecular Systems (Preprint)

    Science.gov (United States)

    2009-01-06

    Phys. 2006, 125, 104011. (c) ROCBS- QB3 : Wood, G. P. F. ; Random, L. ; Petersson, G. A. ; Barnes, E. C.; Frisch, M. J.; Montgomery, J. A. J. Chem... QB3 : Montgomery, J. A.; Frisch, M. J.; Ochterski, J. W.; Petersson, G. A. J. Chem. Phys. 1999, 110, 2822. (f) SAC: Gordon, M.; Truhlar, D. G. J. Am

  20. Accurate Methods for Large Molecular Systems (Postprint)

    Science.gov (United States)

    2009-01-06

    DeYonker, N. J.; Grimes, T.; Yockel, S.; Dinescu, A.; Mintz, B.; Cundari, T. R.; Wilson, A. K. J. Chem. Phys. 2006, 125, 104011. (c) ROCBS- QB3 : Wood...A.; Frisch, M. J.; Ochterski, J. W.; Petersson, G. A. J. Chem. Phys. 2000, 112, 6532. (e) CBS- QB3 : Montgomery, J. A.; Frisch, M. J.; Ochterski, J. W

  1. Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: Sequential sampling and optimization on the potential of mean force surface

    Science.gov (United States)

    Hu, Hao; Lu, Zhenyu; Parks, Jerry M.; Burger, Steven K.; Yang, Weitao

    2008-01-01

    To accurately determine the reaction path and its energetics for enzymatic and solution-phase reactions, we present a sequential sampling and optimization approach that greatly enhances the efficiency of the ab initio quantum mechanics/molecular mechanics minimum free-energy path (QM/MM-MFEP) method. In the QM/MM-MFEP method, the thermodynamics of a complex reaction system is described by the potential of mean force (PMF) surface of the quantum mechanical (QM) subsystem with a small number of degrees of freedom, somewhat like describing a reaction process in the gas phase. The main computational cost of the QM/MM-MFEP method comes from the statistical sampling of conformations of the molecular mechanical (MM) subsystem required for the calculation of the QM PMF and its gradient. In our new sequential sampling and optimization approach, we aim to reduce the amount of MM sampling while still retaining the accuracy of the results by first carrying out MM phase-space sampling and then optimizing the QM subsystem in the fixed-size ensemble of MM conformations. The resulting QM optimized structures are then used to obtain more accurate sampling of the MM subsystem. This process of sequential MM sampling and QM optimization is iterated until convergence. The use of a fixed-size, finite MM conformational ensemble enables the precise evaluation of the QM potential of mean force and its gradient within the ensemble, thus circumventing the challenges associated with statistical averaging and significantly speeding up the convergence of the optimization process. To further improve the accuracy of the QM/MM-MFEP method, the reaction path potential method developed by Lu and Yang [Z. Lu and W. Yang, J. Chem. Phys. 121, 89 (2004)] is employed to describe the QM/MM electrostatic interactions in an approximate yet accurate way with a computational cost that is comparable to classical MM simulations. The new method was successfully applied to two example reaction processes, the

  2. Design and evaluation of a molecular fingerprint involving the transformation of property descriptor values into a binary classification scheme.

    Science.gov (United States)

    Xue, Ling; Godden, Jeffrey W; Stahura, Florence L; Bajorath, Jürgen

    2003-01-01

    A new fingerprint design concept is introduced that transforms molecular property descriptors into two-state descriptors and thus permits binary encoding. This transformation is based on the calculation of statistical medians of descriptor distributions in large compound collections and alleviates the need for value range encoding of these descriptors. For binary encoded property descriptors, bit positions that are set off capture as much information as bit positions that are set on, different from conventional fingerprint representations. Accordingly, a variant of the Tanimoto coefficient has been defined for comparison of these fingerprints. Following our design idea, a prototypic fingerprint termed MP-MFP was implemented by combining 61 binary encoded property descriptors with 110 structural fragment-type descriptors. The performance of this fingerprint was evaluated in systematic similarity search calculations in a database containing 549 molecules belonging to 38 different activity classes and 5000 background molecules. In these calculations, MP-MFP correctly recognized approximately 34% of all similarity relationships, with only 0.04% false positives, and performed better than previous designs and MACCS keys. The results suggest that combinations of simplified two-state property descriptors have predictive value in the analysis of molecular similarity.

  3. A molecular phylogeny for yponomeutoidea (insecta, Lepidoptera, ditrysia and its implications for classification, biogeography and the evolution of host plant use.

    Directory of Open Access Journals (Sweden)

    Jae-Cheon Sohn

    suggesting parallel phylogenesis. Our analyses suggest that previous characterizations of yponomeutoids as predominantly Holarctic were based on insufficient sampling. CONCLUSIONS/SIGNIFICANCE: We provide the first robust molecular phylogeny for Yponomeutoidea, together with a revised classification and new insights into their life history evolution and biogeography.

  4. Update on diabetes classification.

    Science.gov (United States)

    Thomas, Celeste C; Philipson, Louis H

    2015-01-01

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

  5. Classification of Omalisidae based on molecular data and morphology, with description of Paradrilinae subfam. nov. (Coleoptera: Elateroidea).

    Science.gov (United States)

    Kundrata, Robin; Baena, Manuel; Bocak, Ladislav

    2015-02-04

    Omalisidae, a species-poor family of elateroid beetles, are distributed mostly in the Mediterranean region. The morphology of females is modified due to neotenic development and the males share some traits with other neotenic lineages in Elateroidea, namely Drilini (Elateridae: Agrypninae) and Lyropaeinae (Lycidae). A molecular phylogeny was inferred from six omalisid species representing four genera and the previously published dataset of Elateroidea. The DNA based phylogeny suggests that small-bodied males, reduced pronotal carinae and missing elytral costae evolved independently in multiple elateroid lineages. The limits of Omalisidae are redefined and seven genera, i.e., Omalisus Geoffroy, 1762, Phaeopterus Costa, 1857, Thilmanus Gemminger, 1869, Euanoma Reitter, 1889, Pseudeuanoma Pic, 1901, Paradrilus Kiesenwetter, 1865 and Cimbrion Kazantsev, 2010, are currently placed in the family. Thilmaninae Kazantsev, 2005 and Paradrilus Kiesenwetter, 1865 are transferred from Drilini (Elateridae: Agrypninae) to Omalisidae and the Paradrilinae subfam. nov. is proposed. Paradrilus differs from other Omalisidae in prolonged cranium, wide robust prosternum with two apical processes and absent sharp edge of the pronotum. The morphology of Paradrilus is described in detail, illustrated and all taxa currently classified in Omalisidae are listed. 

  6. A network-based classification model for deriving novel drug-disease associations and assessing their molecular actions.

    Science.gov (United States)

    Oh, Min; Ahn, Jaegyoon; Yoon, Youngmi

    2014-01-01

    The growing number and variety of genetic network datasets increases the feasibility of understanding how drugs and diseases are associated at the molecular level. Properly selected features of the network representations of existing drug-disease associations can be used to infer novel indications of existing drugs. To find new drug-disease associations, we generated an integrative genetic network using combinations of interactions, including protein-protein interactions and gene regulatory network datasets. Within this network, network adjacencies of drug-drug and disease-disease were quantified using a scored path between target sets of them. Furthermore, the common topological module of drugs or diseases was extracted, and thereby the distance between topological drug-module and disease (or disease-module and drug) was quantified. These quantified scores were used as features for the prediction of novel drug-disease associations. Our classifiers using Random Forest, Multilayer Perceptron and C4.5 showed a high specificity and sensitivity (AUC score of 0.855, 0.828 and 0.797 respectively) in predicting novel drug indications, and displayed a better performance than other methods with limited drug and disease properties. Our predictions and current clinical trials overlap significantly across the different phases of drug development. We also identified and visualized the topological modules of predicted drug indications for certain types of cancers, and for Alzheimer's disease. Within the network, those modules show potential pathways that illustrate the mechanisms of new drug indications, including propranolol as a potential anticancer agent and telmisartan as treatment for Alzheimer's disease.

  7. A network-based classification model for deriving novel drug-disease associations and assessing their molecular actions.

    Directory of Open Access Journals (Sweden)

    Min Oh

    Full Text Available The growing number and variety of genetic network datasets increases the feasibility of understanding how drugs and diseases are associated at the molecular level. Properly selected features of the network representations of existing drug-disease associations can be used to infer novel indications of existing drugs. To find new drug-disease associations, we generated an integrative genetic network using combinations of interactions, including protein-protein interactions and gene regulatory network datasets. Within this network, network adjacencies of drug-drug and disease-disease were quantified using a scored path between target sets of them. Furthermore, the common topological module of drugs or diseases was extracted, and thereby the distance between topological drug-module and disease (or disease-module and drug was quantified. These quantified scores were used as features for the prediction of novel drug-disease associations. Our classifiers using Random Forest, Multilayer Perceptron and C4.5 showed a high specificity and sensitivity (AUC score of 0.855, 0.828 and 0.797 respectively in predicting novel drug indications, and displayed a better performance than other methods with limited drug and disease properties. Our predictions and current clinical trials overlap significantly across the different phases of drug development. We also identified and visualized the topological modules of predicted drug indications for certain types of cancers, and for Alzheimer's disease. Within the network, those modules show potential pathways that illustrate the mechanisms of new drug indications, including propranolol as a potential anticancer agent and telmisartan as treatment for Alzheimer's disease.

  8. Evaluation of the use of partition coefficients and molecular surface properties as predictors of drug absorption: a provisional biopharmaceutical classification of the list of national essential medi

    Directory of Open Access Journals (Sweden)

    NU Rahman

    2011-05-01

    Full Text Available Background and the purpose of the study: Partition coefficients (log D and log P and molecular surface area (PSA are potential predictors of the intestinal permeability of drugs. The aim of this investigation was to evaluate and compare these intestinal permeability indicators.   Methods: Aqueous solubility data were obtained from literature or calculated using ACD/Labs and ALOGPS. Permeability data were predicted based on log P, log D at pH 6.0 (log D6.0, and PSA.  Results: Metoprolol's log P, log D6.0 and a PSA of <65 Å correctly predicted 55.9%, 50.8% and 54.2% of permeability classes, respectively. Labetalol's log P, log D6.0, and PSA correctly predicted 54.2%, 64.4% and 61% of permeability classes, respectively. Log D6.0 correlated well (81% with Caco-2 permeability (Papp. Of the list of national essential medicines, 135 orally administered drugs were classified into biopharmaceutical classification system (BCS. Of these, 57 (42.2%, 28 (20.7%, 44 (32.6%, and 6 (4.4% were class I, II, III and IV respectively. Conclusion: Log D6.0 showed better prediction capability than log P. Metoprolol as permeability internal standard was more conservative than labetalol.

  9. Síndromes mielodisplásicas: aspectos moleculares, laboratoriais e a classificação OMS 2008 Myelodysplasic symdrome: molecular and laboratorial aspects and the 2008 WHO classification

    Directory of Open Access Journals (Sweden)

    Ana Carolina R. Moraes

    2009-01-01

    defined etiology, or as secondary to chemotherapy or radiotherapy for other neoplasias. The evolution of diagnostic tests has improved comprehension of the process involved in the genesis and evolution of MDSs, making the development of earlier and more specific tests for diagnosis and follow ups possible. In 2008, the World Health Organization (WHO redefined the criteria for the classification of MDSs, dividing them into seven subgroups. This classification included new immunophenotypic, genetic, cytomorphologic and molecular features, which are essential for the diagnosis of MDSs and for a better comprehension of the disease. Despite technological advances, some details, such as the molecular basis of the transformation of MDS to AML, are still not completely understood, which makes further studies in this field necessary. Hence, the objective of this review is to make a compilation of recent molecular and laboratory aspects of MDS.

  10. Application of Data Mining in Protein Sequence Classification

    Directory of Open Access Journals (Sweden)

    Suprativ Saha

    2012-11-01

    Full Text Available Protein sequence classification involves feature selection for accurate classification. Popular protein sequence classification techniques involve extraction of specific features from the sequences. Researchers apply some well-known classification techniques like neural networks, Genetic algorithm, Fuzzy ARTMAP,Rough Set Classifier etc for accurate classification. This paper presents a review is with three different classification models such as neural network model, fuzzy ARTMAP model and Rough set classifier model.This is followed by a new technique for classifying protein sequences. The proposed model is typicallyimplemented with an own designed tool and tries to reduce the computational overheads encountered by earlier approaches and increase the accuracy of classification.

  11. Speaking Fluently And Accurately

    Institute of Scientific and Technical Information of China (English)

    JosephDeVeto

    2004-01-01

    Even after many years of study,students make frequent mistakes in English. In addition, many students still need a long time to think of what they want to say. For some reason, in spite of all the studying, students are still not quite fluent.When I teach, I use one technique that helps students not only speak more accurately, but also more fluently. That technique is dictations.

  12. Semiparametric Gaussian copula classification

    OpenAIRE

    Zhao, Yue; Wegkamp, Marten

    2014-01-01

    This paper studies the binary classification of two distributions with the same Gaussian copula in high dimensions. Under this semiparametric Gaussian copula setting, we derive an accurate semiparametric estimator of the log density ratio, which leads to our empirical decision rule and a bound on its associated excess risk. Our estimation procedure takes advantage of the potential sparsity as well as the low noise condition in the problem, which allows us to achieve faster convergence rate of...

  13. Contextual classification of multispectral image data: Approximate algorithm

    Science.gov (United States)

    Tilton, J. C. (Principal Investigator)

    1980-01-01

    An approximation to a classification algorithm incorporating spatial context information in a general, statistical manner is presented which is computationally less intensive. Classifications that are nearly as accurate are produced.

  14. Taxonomic update on proposed nomenclature and classification changes for bacteria of medical importance, 2016.

    Science.gov (United States)

    Janda, J Michael

    2017-02-13

    A key aspect of medical, public health, and diagnostic microbiology laboratories is the accurate identification and rapid reporting and communication to medical staff regarding patients with infectious agents of clinical importance. Microbial taxonomy in the age of molecular diagnostics and phylogenetics creates changes in taxonomy at a logarithmic rate further complicating this process. This update focuses on the description of new species and classification changes proposed in 2016.

  15. Research progress on the molecular classification of tumors by quantum dot-based nanotechnology%基于量子点标记探针技术的肿瘤分子分型研究进展

    Institute of Scientific and Technical Information of China (English)

    方敏; 彭春伟; 陈创; 庞代文; 李雁

    2014-01-01

    Malignant tumors are highly heterogeneous in terms of molecular phenotypes such that personalized therapy will be-come the standard for tumor therapy. Molecular classifications of cancer based on differences in biological behavior are important for selecting treatment strategies and prognostication. The unique optical and chemical properties of quantum dots have been widely used in biomedical applications such as tumor diagnosis, monitoring, pathogenesis, treatment, molecular pathology, and heterogeneity based on biological markers. In this study, we discuss the application of quantum dot-based nanotechnology and the molecular classification of cancer in personalized oncology.%恶性肿瘤在分子水平上具有高度异质性,是个体化治疗的依据。发展同时显示肿瘤原位多分子指标的技术对研究肿瘤生物学行为至关重要。量子点标记探针技术因其具有独特的光学和化学特性,在肿瘤诊断、监测、治疗、发病机制、分子分型及异质性研究中均有广阔应用前景。本文总结该技术在肿瘤分子分型方面的应用进展。

  16. Research progress on integrated molecular pathological classification of diffuse lower-grade gliomas%弥漫性较低级别胶质瘤的整合性分子病理分型研究进展

    Institute of Scientific and Technical Information of China (English)

    李朝晖; 郭志钢(综述); 李庆伟(审校)

    2016-01-01

    弥漫性较低级别胶质瘤包含WHOⅡ级和Ⅲ级的星形细胞瘤、少突胶质细胞瘤和少突星形细胞瘤,其临床表现具有高度可变性,目前的组织病理学无法准确地预测其预后。近年来,胶质瘤分子病理取得了重大进展,已经发现一系列与胶质瘤临床特征和预后密切相关的分子标志物如异柠檬酸脱氢酶(isocitrate dehydrogenase,IDH)突变、染色体1p/19q共缺失、ATRX基因突变、TERT启动子突变、MGMT启动子甲基化等。在此基础上,结合这些分子标志物对弥漫性较低级别胶质瘤进行整合性分子病理分型的研究相继开展,且这些研究的结果一致表明,整合性分子病理分型能够更好地预测弥漫性较低级别胶质瘤的预后和指导治疗。本研究对弥漫性较低级别胶质瘤的整合性分子病理分型研究进展进行综述。%Diffuse lower-grade glioma is a diversified group of infiltrative brain tumors comprising WHO grades II and III astrocytomas, oligodendrogliomas, and mixed oligoastrocytomas. These tumors exhibit a wide range of clinical heterogeneity;thus, histopathological classification does not adequately predict clinical outcomes. In recent years, a number of molecular markers closely related to the clini-cal features and prognosis of gliomas have been discovered. These molecular markers include isocitrate dehydrogenase (IDH) muta-tion, chromosome 1p/19q codeletion, ATRX mutation, TERT promoter mutation, and MGMT promoter methylation. Furthermore, nu-merous studies focusing on the integrated molecular classification of diffuse lower-grade gliomas combined with these molecular markers have been conducted. Results indicate that integrated molecular pathological classification can improve the diagnostic and prognostic accuracy and facilitate therapeutic formulation. This paper reviews the research progress on integrated molecular classifica-tion of diffuse lower-grade gliomas.

  17. Molecular phylogeny of advanced snakes (Serpentes, Caenophidia with an emphasis on South American Xenodontines: a revised classification and descriptions of new taxa

    Directory of Open Access Journals (Sweden)

    Hussam Zaher

    2009-01-01

    Full Text Available We present a molecular phylogenetic analysis of caenophidian (advanced snakes using sequences from two mitochondrial genes (12S and 16S rRNA and one nuclear (c-mos gene (1681 total base pairs, and with 131 terminal taxa sampled from throughout all major caenophidian lineages but focussing on Neotropical xenodontines. Direct optimization parsimony analysis resulted in a well-resolved phylogenetic tree, which corroborates some clades identified in previous analyses and suggests new hypotheses for the composition and relationships of others. The major salient points of our analysis are: (1 placement of Acrochordus, Xenodermatids, and Pareatids as successive outgroups to all remaining caenophidians (including viperids, elapids, atractaspidids, and all other "colubrid" groups; (2 within the latter group, viperids and homalopsids are sucessive sister clades to all remaining snakes; (3 the following monophyletic clades within crown group caenophidians: Afro-Asian psammophiids (including Mimophis from Madagascar, Elapidae (including hydrophiines but excluding Homoroselaps, Pseudoxyrhophiinae, Colubrinae, Natricinae, Dipsadinae, and Xenodontinae. Homoroselaps is associated with atractaspidids. Our analysis suggests some taxonomic changes within xenodontines, including new taxonomy for Alsophis elegans, Liophis amarali, and further taxonomic changes within Xenodontini and the West Indian radiation of xenodontines. Based on our molecular analysis, we present a revised classification for caenophidians and provide morphological diagnoses for many of the included clades; we also highlight groups where much more work is needed. We name as new two higher taxonomic clades within Caenophidia, one new subfamily within Dipsadidae, and, within Xenodontinae five new tribes, six new genera and two resurrected genera. We synonymize Xenoxybelis and Pseudablabes with Philodryas; Erythrolamprus with Liophis; and Lystrophis and Waglerophis with Xenodon.Este trabalho

  18. HYBRID INTERNET TRAFFIC CLASSIFICATION TECHNIQUE1

    Institute of Scientific and Technical Information of China (English)

    Li Jun; Zhang Shunyi; Lu Yanqing; Yan Junrong

    2009-01-01

    Accurate and real-time classification of network traffic is significant to network operation and management such as QoS differentiation, traffic shaping and security surveillance. However, with many newly emerged P2P applications using dynamic port numbers, masquerading techniques, and payload encryption to avoid detection, traditional classification approaches turn to be ineffective. In this paper, we present a layered hybrid system to classify current Internet traffic, motivated by variety of network activities and their requirements of traffic classification. The proposed method could achieve fast and accurate traffic classification with low overheads and robustness to accommodate both known and unknown/encrypted applications. Furthermore, it is feasible to be used in the context of real-time traffic classification. Our experimental results show the distinct advantages of the proposed classification system, compared with the one-step Machine Learning (ML) approach.

  19. Classification of seizures and epilepsy.

    Science.gov (United States)

    Riviello, James J

    2003-07-01

    The management of seizures and epilepsy begins with forming a differential diagnosis, making the diagnosis, and then classifying seizure type and epileptic syndrome. Classification guides treatment, including ancillary testing, management, prognosis, and if needed, selection of the appropriate antiepileptic drug (AED). Many AEDs are available, and certain seizure types or epilepsy syndromes respond to specific AEDs. The identification of the genetics, molecular basis, and pathophysiologic mechanisms of epilepsy has resulted from classification of specific epileptic syndromes. The classification system used by the International League Against Epilepsy is periodically revised. The proposed revision changes the classification emphasis from the anatomic origin of seizures (focal vs generalized) to seizure semiology (ie, the signs or clinical manifestations). Modified systems have been developed for specific circumstances (eg, neonatal seizures, infantile seizures, status epilepticus, and epilepsy surgery). This article reviews seizure and epilepsy classification, emphasizing new data.

  20. Tissue Classification

    DEFF Research Database (Denmark)

    Van Leemput, Koen; Puonti, Oula

    2015-01-01

    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...

  1. Text Classification using Artificial Intelligence

    CERN Document Server

    Kamruzzaman, S M

    2010-01-01

    Text classification is the process of classifying documents into predefined categories based on their content. It is the automated assignment of natural language texts to predefined categories. Text classification is the primary requirement of text retrieval systems, which retrieve texts in response to a user query, and text understanding systems, which transform text in some way such as producing summaries, answering questions or extracting data. Existing supervised learning algorithms for classifying text need sufficient documents to learn accurately. This paper presents a new algorithm for text classification using artificial intelligence technique that requires fewer documents for training. Instead of using words, word relation i.e. association rules from these words is used to derive feature set from pre-classified text documents. The concept of na\\"ive Bayes classifier is then used on derived features and finally only a single concept of genetic algorithm has been added for final classification. A syste...

  2. Text Classification using Data Mining

    CERN Document Server

    Kamruzzaman, S M; Hasan, Ahmed Ryadh

    2010-01-01

    Text classification is the process of classifying documents into predefined categories based on their content. It is the automated assignment of natural language texts to predefined categories. Text classification is the primary requirement of text retrieval systems, which retrieve texts in response to a user query, and text understanding systems, which transform text in some way such as producing summaries, answering questions or extracting data. Existing supervised learning algorithms to automatically classify text need sufficient documents to learn accurately. This paper presents a new algorithm for text classification using data mining that requires fewer documents for training. Instead of using words, word relation i.e. association rules from these words is used to derive feature set from pre-classified text documents. The concept of Naive Bayes classifier is then used on derived features and finally only a single concept of Genetic Algorithm has been added for final classification. A system based on the...

  3. Transporter Classification Database (TCDB)

    Data.gov (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)...

  4. Insights into the classification of small GTPases

    Directory of Open Access Journals (Sweden)

    Dominik Heider

    2010-05-01

    Full Text Available Dominik Heider1, Sascha Hauke3, Martin Pyka4, Daniel Kessler21Department of Bioinformatics, Center for Medical Biotechnology, 2Institute of Cell Biology (Cancer Research, University of Duisburg-Essen, Essen, Germany; 3Institute of Computer Science, University of Münster, Münster, Germany; 4Interdisciplinary Center for Clinical Research, University Hospital of Münster, Münster, GermanyAbstract: In this study we used a Random Forest-based approach for an assignment of small guanosine triphosphate proteins (GTPases to specific subgroups. Small GTPases represent an important functional group of proteins that serve as molecular switches in a wide range of fundamental cellular processes, including intracellular transport, movement and signaling events. These proteins have further gained a special emphasis in cancer research, because within the last decades a huge variety of small GTPases from different subgroups could be related to the development of all types of tumors. Using a random forest approach, we were able to identify the most important amino acid positions for the classification process within the small GTPases superfamily and its subgroups. These positions are in line with the results of earlier studies and have been shown to be the essential elements for the different functionalities of the GTPase families. Furthermore, we provide an accurate and reliable software tool (GTPasePred to identify potential novel GTPases and demonstrate its application to genome sequences.Keywords: cancer, machine learning, classification, Random Forests, proteins

  5. Molecular Classification of indica-japonica Rice According to Wide-compatibility Gene S5 Sequence with Endonuclease CEL Ⅰ%利用CELⅠ酶鉴定水稻广亲和基因S5位点的籼粳属性

    Institute of Scientific and Technical Information of China (English)

    倪深; 肖文斐; 陈红旗; 王跃星; 朱旭东

    2012-01-01

    广亲和基因S5的克隆为水稻品种亲和特性的鉴定提供了分子学依据.利用PCR技术对水稻S5位点中籼、粳序列间存在差异的区段进行扩增,并结合芹菜核酸内切酶CEL Ⅰ对其进行酶切鉴定,从而区分S5不同的基因型.研究结果表明该方法能准确鉴定不同水稻品种中S5位点的籼粳特性,并能发现新的差异序列.%Cloning of the major locus S5. a wide-compatibility gene has laid a molecular basis for identification of the wide-compatibility varieties(WCV). According to the difference in S5 locus sequence among indica, japonica and WCV. PCR was conducted and celery endonuclease CEL I, which cleaves DNA with high specificity at sites of base-substitution mismatch, was used to digest PCR products so as to distinguish various S5 DNA fragments. The results showed that the method is accurate in indica-japonica classification. At the same time, 8 new genotype on the SS locus was found.

  6. Classification and Analysis of Computer Network Traffic

    DEFF Research Database (Denmark)

    Bujlow, Tomasz

    2014-01-01

    various classification modes (decision trees, rulesets, boosting, softening thresholds) regarding the classification accuracy and the time required to create the classifier. We showed how to use our VBS tool to obtain per-flow, per-application, and per-content statistics of traffic in computer networks...... classification (as by using transport layer port numbers, Deep Packet Inspection (DPI), statistical classification) and assessed their usefulness in particular areas. We found that the classification techniques based on port numbers are not accurate anymore as most applications use dynamic port numbers, while...... DPI is relatively slow, requires a lot of processing power, and causes a lot of privacy concerns. Statistical classifiers based on Machine Learning Algorithms (MLAs) were shown to be fast and accurate. At the same time, they do not consume a lot of resources and do not cause privacy concerns. However...

  7. Neuromuscular disease classification system

    Science.gov (United States)

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

    2013-06-01

    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.

  8. Molecular classification of anaplastic oligodendroglioma using next-generation sequencing: A report of the prospective randomized EORTC Brain Tumor Group 26951 phase III trial

    NARCIS (Netherlands)

    H.J. Dubbink (Erik Jan); P.N. Atmodimedjo; J.M. Kros (Johan); P.J. French (Pim); M. Sanson (Marc); A. Idbaih (Ahmed); P. Wesseling (Pieter); R. Enting (Roelien); W.G.M. Spliet (Wim); C.C. Tijssen (Cees); W.N.M. Dinjens (Winand); T.S. Gorlia (Thierry); M.J. van den Bent (Martin)

    2016-01-01

    textabstractBackground Histopathological diagnosis of diffuse gliomas is subject to interobserver variation and correlates modestly with major prognostic and predictive molecular abnormalities. We investigated a series of patients with locally diagnosed anaplastic oligodendroglial tumors included in

  9. [Eosinophilia--pathogenesis, classification and therapy

    DEFF Research Database (Denmark)

    Andersen, C.L.; Vestergaard, H.; Norgaard, P.;

    2009-01-01

    only by specific tests. The diagnostic and therapeutic approach, including a new classification for eosinophilia, is reviewed, and the importance of molecular biological technique is highlighted. Unexplained eosinophilia should be managed in collaboration with a haematology department Udgivelsesdato...

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

    LENUS (Irish Health Repository)

    Irvine, Alan D

    2012-02-01

    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.

  11. Molecular Tools for Rapid and Accurate Detection of Black Truffle (Tuber melanosporum Vitt. in Inoculated Nursery Plants and Commercial Plantations in Chile Uso de Marcadores Moleculares para la Detección Rápida y Precisa de Trufa Negra (Tuber melanosporum Vitt. en Plantas de Vivero y Plantaciones Comerciales de Chile

    Directory of Open Access Journals (Sweden)

    Cecilia Cordero

    2011-09-01

    Full Text Available Truffle (Tuber melanosporum Vitt. culture is an agroforestry sector in Chile of increasing interest due to the high prices that truffles fetch in the national market and the recent evidence that its commercial production is possible in Chilean climatic and soil conditions. In this study, the efficiency of three methods of DNA extraction from a mix of 5 g of soil and roots from both nursery and field plants of Quercus ilex L. mycorrhized with T. melanosporum were evaluated, and a simple and reproducible protocol was established. Detection of T. melanosporum was performed by the technique of cleaved amplified polymorphic sequence (CAPS from amplicons generated with the primers ADL1 (5´-GTAACGATAAAGGCCATCTATAGG-3´ and ADL3 (5´-CGTTTTTCCTGAACTCTTCATCAC-3`, where a restriction fragment of 160 bp specific for T. melanosporum was generated, which allows the discrimination of this species from the rest of the species belonging to the Tuber sp. genus. Direct detection of T. melanosporum in one step was also obtained by polymerase chain reaction (PCR from total DNA isolated from mycorrhized roots and with the primers ITSML (5´-TGGCCATGTGTCAGATTTAGTA-3´ and ITSLNG (5´-TGATATGCTTAAGTTCAGCGGG-3´, generating a single amplicon of 440 bp. The molecular detection of T. melanosporum by the methods presented here will allow the rapid and accurate detection of mycorrhization of trees, both under nursery and field conditions. This technology will also provide more security to farmers by controlling the quality of the mycorrhized trees they will plant and also by following the mycorrhization status of established orchards.

  12. Accurate determination of optical bandgap and lattice parameters of Zn{sub 1-x}Mg{sub x}O epitaxial films (0{<=}x{<=}0.3) grown by plasma-assisted molecular beam epitaxy on a-plane sapphire

    Energy Technology Data Exchange (ETDEWEB)

    Laumer, Bernhard [Walter Schottky Institut and Physics Department, Technische Universitaet Muenchen, Am Coulombwall 4, 85748 Garching (Germany); I. Physikalisches Institut, Justus-Liebig-Universitaet Giessen, Heinrich-Buff-Ring 16, 35392 Giessen (Germany); Schuster, Fabian; Stutzmann, Martin [Walter Schottky Institut and Physics Department, Technische Universitaet Muenchen, Am Coulombwall 4, 85748 Garching (Germany); Bergmaier, Andreas; Dollinger, Guenther [Universitaet der Bundeswehr Muenchen, Fakultaet fuer Luft- und Raumfahrttechnik, Werner-Heisenberg-Weg 39, 85577 Neubiberg (Germany); Eickhoff, Martin [I. Physikalisches Institut, Justus-Liebig-Universitaet Giessen, Heinrich-Buff-Ring 16, 35392 Giessen (Germany)

    2013-06-21

    Zn{sub 1-x}Mg{sub x}O epitaxial films with Mg concentrations 0{<=}x{<=}0.3 were grown by plasma-assisted molecular beam epitaxy on a-plane sapphire substrates. Precise determination of the Mg concentration x was performed by elastic recoil detection analysis. The bandgap energy was extracted from absorption measurements with high accuracy taking electron-hole interaction and exciton-phonon complexes into account. From these results a linear relationship between bandgap energy and Mg concentration is established for x{<=}0.3. Due to alloy disorder, the increase of the photoluminescence emission energy with Mg concentration is less pronounced. An analysis of the lattice parameters reveals that the epitaxial films grow biaxially strained on a-plane sapphire.

  13. Automatic web services classification based on rough set theory

    Institute of Scientific and Technical Information of China (English)

    陈立; 张英; 宋自林; 苗壮

    2013-01-01

    With development of web services technology, the number of existing services in the internet is growing day by day. In order to achieve automatic and accurate services classification which can be beneficial for service related tasks, a rough set theory based method for services classification was proposed. First, the services descriptions were preprocessed and represented as vectors. Elicited by the discernibility matrices based attribute reduction in rough set theory and taking into account the characteristic of decision table of services classification, a method based on continuous discernibility matrices was proposed for dimensionality reduction. And finally, services classification was processed automatically. Through the experiment, the proposed method for services classification achieves approving classification result in all five testing categories. The experiment result shows that the proposed method is accurate and could be used in practical web services classification.

  14. Proteomic classification of breast cancer.

    LENUS (Irish Health Repository)

    Kamel, Dalia

    2012-11-01

    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.

  15. Classification in context

    DEFF Research Database (Denmark)

    Mai, Jens Erik

    2004-01-01

    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....

  16. Efficient segmentation by sparse pixel classification

    DEFF Research Database (Denmark)

    Dam, Erik B; Loog, Marco

    2008-01-01

    Segmentation methods based on pixel classification are powerful but often slow. We introduce two general algorithms, based on sparse classification, for optimizing the computation while still obtaining accurate segmentations. The computational costs of the algorithms are derived......, and they are demonstrated on real 3-D magnetic resonance imaging and 2-D radiograph data. We show that each algorithm is optimal for specific tasks, and that both algorithms allow a speedup of one or more orders of magnitude on typical segmentation tasks....

  17. Predicting the Metabolic Sites by Flavin-Containing Monooxygenase on Drug Molecules Using SVM Classification on Computed Quantum Mechanics and Circular Fingerprints Molecular Descriptors

    Science.gov (United States)

    Fu, Chien-wei; Lin, Thy-Hou

    2017-01-01

    As an important enzyme in Phase I drug metabolism, the flavin-containing monooxygenase (FMO) also metabolizes some xenobiotics with soft nucleophiles. The site of metabolism (SOM) on a molecule is the site where the metabolic reaction is exerted by an enzyme. Accurate prediction of SOMs on drug molecules will assist the search for drug leads during the optimization process. Here, some quantum mechanics features such as the condensed Fukui function and attributes from circular fingerprints (called Molprint2D) are computed and classified using the support vector machine (SVM) for predicting some potential SOMs on a series of drugs that can be metabolized by FMO enzymes. The condensed Fukui function fA− representing the nucleophilicity of central atom A and the attributes from circular fingerprints accounting the influence of neighbors on the central atom. The total number of FMO substrates and non-substrates collected in the study is 85 and they are equally divided into the training and test sets with each carrying roughly the same number of potential SOMs. However, only N-oxidation and S-oxidation features were considered in the prediction since the available C-oxidation data was scarce. In the training process, the LibSVM package of WEKA package and the option of 10-fold cross validation are employed. The prediction performance on the test set evaluated by accuracy, Matthews correlation coefficient and area under ROC curve computed are 0.829, 0.659, and 0.877 respectively. This work reveals that the SVM model built can accurately predict the potential SOMs for drug molecules that are metabolizable by the FMO enzymes. PMID:28072829

  18. Accurate structural correlations from maximum likelihood superpositions.

    Directory of Open Access Journals (Sweden)

    Douglas L Theobald

    2008-02-01

    Full Text Available The cores of globular proteins are densely packed, resulting in complicated networks of structural interactions. These interactions in turn give rise to dynamic structural correlations over a wide range of time scales. Accurate analysis of these complex correlations is crucial for understanding biomolecular mechanisms and for relating structure to function. Here we report a highly accurate technique for inferring the major modes of structural correlation in macromolecules using likelihood-based statistical analysis of sets of structures. This method is generally applicable to any ensemble of related molecules, including families of nuclear magnetic resonance (NMR models, different crystal forms of a protein, and structural alignments of homologous proteins, as well as molecular dynamics trajectories. Dominant modes of structural correlation are determined using principal components analysis (PCA of the maximum likelihood estimate of the correlation matrix. The correlations we identify are inherently independent of the statistical uncertainty and dynamic heterogeneity associated with the structural coordinates. We additionally present an easily interpretable method ("PCA plots" for displaying these positional correlations by color-coding them onto a macromolecular structure. Maximum likelihood PCA of structural superpositions, and the structural PCA plots that illustrate the results, will facilitate the accurate determination of dynamic structural correlations analyzed in diverse fields of structural biology.

  19. Hyperspectral image classification using functional data analysis.

    Science.gov (United States)

    Li, Hong; Xiao, Guangrun; Xia, Tian; Tang, Y Y; Li, Luoqing

    2014-09-01

    The large number of spectral bands acquired by hyperspectral imaging sensors allows us to better distinguish many subtle objects and materials. Unlike other classical hyperspectral image classification methods in the multivariate analysis framework, in this paper, a novel method using functional data analysis (FDA) for accurate classification of hyperspectral images has been proposed. The central idea of FDA is to treat multivariate data as continuous functions. From this perspective, the spectral curve of each pixel in the hyperspectral images is naturally viewed as a function. This can be beneficial for making full use of the abundant spectral information. The relevance between adjacent pixel elements in the hyperspectral images can also be utilized reasonably. Functional principal component analysis is applied to solve the classification problem of these functions. Experimental results on three hyperspectral images show that the proposed method can achieve higher classification accuracies in comparison to some state-of-the-art hyperspectral image classification methods.

  20. The Application of Classification and Regression Trees for the Triage of Women for Referral to Colposcopy and the Estimation of Risk for Cervical Intraepithelial Neoplasia: A Study Based on 1625 Cases with Incomplete Data from Molecular Tests

    Directory of Open Access Journals (Sweden)

    Abraham Pouliakis

    2015-01-01

    Full Text Available Objective. Nowadays numerous ancillary techniques detecting HPV DNA and mRNA compete with cytology; however no perfect test exists; in this study we evaluated classification and regression trees (CARTs for the production of triage rules and estimate the risk for cervical intraepithelial neoplasia (CIN in cases with ASCUS+ in cytology. Study Design. We used 1625 cases. In contrast to other approaches we used missing data to increase the data volume, obtain more accurate results, and simulate real conditions in the everyday practice of gynecologic clinics and laboratories. The proposed CART was based on the cytological result, HPV DNA typing, HPV mRNA detection based on NASBA and flow cytometry, p16 immunocytochemical expression, and finally age and parous status. Results. Algorithms useful for the triage of women were produced; gynecologists could apply these in conjunction with available examination results and conclude to an estimation of the risk for a woman to harbor CIN expressed as a probability. Conclusions. The most important test was the cytological examination; however the CART handled cases with inadequate cytological outcome and increased the diagnostic accuracy by exploiting the results of ancillary techniques even if there were inadequate missing data. The CART performance was better than any other single test involved in this study.

  1. Classification and molecular diagnostic procedure for Chacort-Marie-Tooth disease%腓骨肌萎缩症的分型与分子诊断流程

    Institute of Scientific and Technical Information of China (English)

    张如旭; 唐北沙

    2012-01-01

    Charcot-Marie-Tooth disease (CMT) is the most common form of hereditary neuropathy with significant clinical and genetic heterogeneity.So far 28 genes have been cloned.The main clinical manifestations of CMT include progressive distal muscle wasting and weakness,impaired distal sensation,and diminishing or loss of tendon reflex.Patients may be classified into demyelinating type (CMT1) and axonal type (CMT2) according to electrophysiological and pathological characteristics.Establishment of a standard diagnostic procedure based on clinical,electrophysiological and pathological findings will enable accurate diagnosis in most CMT patients and provide guidance for gene consulting and prognosis.%腓骨肌萎缩症(Charcot-Marie-Tooth disease,CMT)是一组最常见的具有高度临床和遗传异质性的周围神经单基因遗传病,目前已有28个疾病基因被克隆.主要临床症状包括进行性对称性肢体远端肌无力和肌萎缩,感觉障碍和腱反射减退或消失.根据电生理和病理特点,CMT可分为脱髓鞘型和轴突型.通过临床表现、电生理病理特点进行临床和遗传学分型,选择可能的疾病基因进行突变分析等一系列具有逻辑性的诊断流程,可明确分子诊断,为疾病预后和遗传咨询提供指导性意见.

  2. Spectral Classification Beyond M

    CERN Document Server

    Leggett, S K; Burgasser, A J; Jones, H R A; Marley, M S; Tsuji, T

    2004-01-01

    Significant populations of field L and T dwarfs are now known, and we anticipate the discovery of even cooler dwarfs by Spitzer and ground-based infrared surveys. However, as the number of known L and T dwarfs increases so does the range in their observational properties, and difficulties have arisen in interpreting the observations. Although modellers have made significant advances, the complexity of the very low temperature, high pressure, photospheres means that problems remain such as the treatment of grain condensation as well as incomplete and non-equilibrium molecular chemistry. Also, there are several parameters which control the observed spectral energy distribution - effective temperature, grain sedimentation efficiency, metallicity and gravity - and their effects are not well understood. In this paper, based on a splinter session, we discuss classification schemes for L and T dwarfs, their dependency on wavelength, and the effects of the parameters T_eff, f_sed, [m/H] and log g on optical and infra...

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

    Directory of Open Access Journals (Sweden)

    Verscheure M.

    2002-01-01

    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.

  4. Molecular phylogenetics of Alchemilla, Aphanes and Lachemilla (Rosaceae) inferred from plastid and nuclear intron and spacer DNA sequences, with comments on generic classification.

    Science.gov (United States)

    Gehrke, B; Bräuchler, C; Romoleroux, K; Lundberg, M; Heubl, G; Eriksson, T

    2008-06-01

    Alchemilla (the lady's mantles) is a well known but inconspicuous group in the Rosaceae, notable for its ornamental leaves and pharmaceutical properties. The systematics of Alchemilla has remained poorly understood, most likely due to confusion resulting from apomixis, polyploidisation and hybridisation, which are frequently observed in the group, and which have led to the description of a large number of (micro-) species. A molecular phylogeny of the genus, including all sections of Alchemilla and Lachemilla as well as five representatives of Aphanes, based on the analysis of the chloroplast trnL-trnF and the nuclear ITS regions is presented here. Gene phylogenies reconstructed from the nuclear and chloroplast sequence data were largely congruent. Limited conflict between the data partitions was observed with respect to a small number of taxa. This is likely to be the result of hybridisation/introgression or incomplete lineage sorting. Four distinct clades were resolved, corresponding to major geographical division and life forms: Eurasian Alchemilla, annual Aphanes, South American Lachemilla and African Alchemilla. We argue for a wider circumscription of the genus Alchemilla, including Lachemilla and Aphanes, based on the morphology and the phylogenetic relationships between the different clades.

  5. Classification of the web

    DEFF Research Database (Denmark)

    Mai, Jens Erik

    2004-01-01

    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...

  6. Cluster Based Text Classification Model

    DEFF Research Database (Denmark)

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

    2011-01-01

    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...

  7. Classification issues related to neuropathic trigeminal pain.

    Science.gov (United States)

    Zakrzewska, Joanna M

    2004-01-01

    The goal of a classification system of medical conditions is to facilitate accurate communication, to ensure that each condition is described uniformly and universally and that all data banks for the storage and retrieval of research and clinical data related to the conditions are consistent. Classification entails deciding which kinds of diagnostic entities should be recognized and how to order them in a meaningful way. Currently there are 3 major pain classification systems of relevance to orofacial pain: The International Association for the Study of Pain classification system, the International Headache Society classification system, and the Research Diagnostic Criteria for Temporomandibular Disorders (RDC/TMD). All use different methodologies, and only the RDC/TMD take into account social and psychologic factors in the classification of conditions. Classification systems need to be reliable, valid, comprehensive, generalizable, and flexible, and they need to be tested using consensus views of experts as well as the available literature. There is an urgent need for a robust classification system for neuropathic trigeminal pain.

  8. 肺癌细胞病理学样本组织学分类及分子病理学检测%Histological classification and molecular pathology of lung cancer cytopathology sample

    Institute of Scientific and Technical Information of China (English)

    徐海苗; 程晔; 孙文勇

    2013-01-01

    Objective To study histological classification and molecular detection solutions of cytopathology samples in lung cancer.Methods 120 cases of lung cancer cytopathology samples have made qualitative diagnosis in conventional smear,and have made the histological classification in part,and then carried out 8 immunohistochemical staining of thyroid transcription factor 1 (TIF-1),p63,E-calcium mucins (E-CAD),creatine kinase 5/6 (CK5/6),epithelial membrane antigen (EMA),synaptic element (Syn),neural cell adhesion molecule 56 (CD56),chromogranin A (CgA) and Calretinin (CR) combined with cell block section,classification again and comparative study both;Part cases of adenocarcinoma have made epidermal growth factor receptor (EGFR) mutation detection.Results Overall parting rate of conventional smear lung cancer histologic and parting rate of non-small cell carcinoma were significantly lower than that in parting rate basis on cell block combined with immunohistochemical stains (39.2% vs.88.3% ;29.7% vs.85.1%,x2 =60.359,72.098,P <0.01),EGFR mutation detection 94.7% (36/38) success.Conclusion Lung cancer cell biology sample should be conducted conventional smear,cell blocksection and combined with immunohistochemical staining,and then make histologic classification;Cell blockprovides a effective platform for cytopathology samples detection.%目的 探讨肺癌在细胞病理学样本组织学分类及分子学检测解决方案.方法 120例肺癌细胞学样本在常规涂片做出定性诊断并部分予以组织学分类后,结合细胞蜡块切片进行甲状腺转录因子-1(TTF-1)、p63、E-钙黏蛋白(E-cad)、细胞角蛋白(CK5/6)、上皮膜抗原(EMA)、突触素(Syn)、神经细胞黏附分子(CD56)、嗜铬素A(CgA)、视网膜钙蛋白(CR)等8项的免疫组织化学染色后再分类并对两者进行比较;部分腺癌病例进行表皮生长因子受体(EGFR)突变检测.结果 常规涂片肺癌组织学总体分型率及非小细胞癌的分

  9. ClassyFlu: classification of influenza A viruses with Discriminatively trained profile-HMMs.

    Directory of Open Access Journals (Sweden)

    Sandra Van der Auwera

    Full Text Available Accurate and rapid characterization of influenza A virus (IAV hemagglutinin (HA and neuraminidase (NA sequences with respect to subtype and clade is at the basis of extended diagnostic services and implicit to molecular epidemiologic studies. ClassyFlu is a new tool and web service for the classification of IAV sequences of the HA and NA gene into subtypes and phylogenetic clades using discriminatively trained profile hidden Markov models (HMMs, one for each subtype or clade. ClassyFlu merely requires as input unaligned, full-length or partial HA or NA DNA sequences. It enables rapid and highly accurate assignment of HA sequences to subtypes H1-H17 but particularly focusses on the finer grained assignment of sequences of highly pathogenic avian influenza viruses of subtype H5N1 according to the cladistics proposed by the H5N1 Evolution Working Group. NA sequences are classified into subtypes N1-N10. ClassyFlu was compared to semiautomatic classification approaches using BLAST and phylogenetics and additionally for H5 sequences to the new "Highly Pathogenic H5N1 Clade Classification Tool" (IRD-CT proposed by the Influenza Research Database. Our results show that both web tools (ClassyFlu and IRD-CT, although based on different methods, are nearly equivalent in performance and both are more accurate and faster than semiautomatic classification. A retraining of ClassyFlu to altered cladistics as well as an extension of ClassyFlu to other IAV genome segments or fragments thereof is undemanding. This is exemplified by unambiguous assignment to a distinct cluster within subtype H7 of sequences of H7N9 viruses which emerged in China early in 2013 and caused more than 130 human infections. http://bioinf.uni-greifswald.de/ClassyFlu is a free web service. For local execution, the ClassyFlu source code in PERL is freely available.

  10. Establishment and application of medication error classification standards in nursing care based on the International Classification of Patient Safety

    Directory of Open Access Journals (Sweden)

    Xiao-Ping Zhu

    2014-09-01

    Conclusion: Application of this classification system will help nursing administrators to accurately detect system- and process-related defects leading to medication errors, and enable the factors to be targeted to improve the level of patient safety management.

  11. On the importance of having accurate data for astrophysical modelling

    Science.gov (United States)

    Lique, Francois

    2016-06-01

    The Herschel telescope and the ALMA and NOEMA interferometers have opened new windows of observation for wavelengths ranging from far infrared to sub-millimeter with spatial and spectral resolutions previously unmatched. To make the most of these observations, an accurate knowledge of the physical and chemical processes occurring in the interstellar and circumstellar media is essential.In this presentation, I will discuss what are the current needs of astrophysics in terms of molecular data and I will show that accurate molecular data are crucial for the proper determination of the physical conditions in molecular clouds.First, I will focus on collisional excitation studies that are needed for molecular lines modelling beyond the Local Thermodynamic Equilibrium (LTE) approach. In particular, I will show how new collisional data for the HCN and HNC isomers, two tracers of star forming conditions, have allowed solving the problem of their respective abundance in cold molecular clouds. I will also present the last collisional data that have been computed in order to analyse new highly resolved observations provided by the ALMA interferometer.Then, I will present the calculation of accurate rate constants for the F+H2 → HF+H and Cl+H2 ↔ HCl+H reactions, which have allowed a more accurate determination of the physical conditions in diffuse molecular clouds. I will also present the recent work on the ortho-para-H2 conversion due to hydrogen exchange that allow more accurate determination of the ortho-to-para-H2 ratio in the universe and that imply a significant revision of the cooling mechanism in astrophysical media.

  12. Molecular Classification and Individual Treatment of Type 2 Diabetes Mellitus%2型糖尿病分子分型和个体化诊疗技术

    Institute of Scientific and Technical Information of China (English)

    韩学尧; 张思敏; 胡承; 梁华; 邢丹

    2016-01-01

    In this year, this group has been working hard on establishing and improving the study cohorts including random samples, samples with pre-diabetes, samples with diabetes and coronary heart disease (CHD), pre-diabetes samples with different interventions, samples with treatments of different anti-diabetic drugs. Several cross sectional studies and prospective studies are conducting, a lot of clinical information and biological samples were colected, and some biomarkers were screened for predicting type 2 diabetes and its large vessel complication. By exome sequencing, we identified an insulin mutation, which is being confirmed to cause diabetes through molecular biological laboratory methods. By case control study, we confirmed the association of PAX4-rs10229583 with type 2 diabetes in Chinese Han. By proteomics study, we screened three special protein associated with NOS1AP-rs12742393, which was proven to relate to the risk for type 2 diabetes in Chinese Han. Some genetic markers of KCNQ1 were found to have an effect on QTc of EKG. In pre-diabetes cohort, we found a few of SNPs might associate with weight changes or insulin sensitivity folowing interventions of life style and pioglitazone. In type 2 diabetes cohort with treatment of metformin, we screened some DNA variations maybe contributing to the different responses to metfromin in lowering blood glucose and weight loss.In type 2 diabetes with CHD, nonalcoholic fat liver, higher blood glucose, radialis bone mass and mild increased urinary albumin excretion might increase the risk of CHD.In addition, Mir-22 also were identified to associate with obesity, fat liver and insulin resistance. Al the finding need to be confirmed in independent studies,and some might become the real biaomarker for predicting the development of diabetes and CHD, responses to anti-diabetic drugs,molecular typing of type 2 diabetes, and regimens of individualized treatment of diabetes.%本年度课题组继续完善建设各种研究队

  13. Accurate determination of antenna directivity

    DEFF Research Database (Denmark)

    Dich, Mikael

    1997-01-01

    The derivation of a formula for accurate estimation of the total radiated power from a transmitting antenna for which the radiated power density is known in a finite number of points on the far-field sphere is presented. The main application of the formula is determination of directivity from power......-pattern measurements. The derivation is based on the theory of spherical wave expansion of electromagnetic fields, which also establishes a simple criterion for the required number of samples of the power density. An array antenna consisting of Hertzian dipoles is used to test the accuracy and rate of convergence...

  14. 重庆市缙云山部分蕨类植物的SRAP分子标记与分类%Classification of Partial Mountain of Chongqing Molecular Marker Pteridophytes in Jinyun City Based on SRAP

    Institute of Scientific and Technical Information of China (English)

    党辉; 沈洁; 罗安才; 柳建平

    2011-01-01

    [Objective] The aim was to classify pteridophytes by using SRAP molecular marker.[Method] 27 species of pteridophytes collected from Jinyun Mountain in Chongqing were classified based on SRAP molecular marker.The tender leaves of the 27 species of city pteridophytes were use for extracting genonic DNA of pteridophytes by using improved CPAB method,and then the quality of total DNA was tested by using gel-lectro phoresis method and obsorbance method.[Result] The results of clustering analysis showed that there was close genetic relationship between Selaginellaceae and Gleicheniaceae,Equisaceae and Dryopteridaceae,Blechnaceae and Dryopteridaceae,Lindsaeaceae and Dryopteridaceae,Aspleniaceae and Athyriaceae.Close genetic relationship between Cyrtomium fortunei and Dryopteridaceae differed from traditional taxonomy that classified Cyrtomium fortunei in Dryopteridaceae,indicating that classification of pteridophytes by SRAP molecular marker technology had some differences from traditional taxonomy.[Conclusion] The results can be referred to rebuild phylogenetic relationships of pteridophytes.%[目的]利用SRAP分子标记的方法对蕨类植物进行种属分类。[方法]以采集于重庆市缙云山的27种蕨类植物为研究对象,以其嫩叶为材料用改良后的CTAB法提取蕨类植物的基因组DNA,用凝胶电泳和吸光值法对总DNA的质量进行检测,用SRAP分子标记技术对这27种蕨类植物进行了分类研究。[结果]27种蕨类植物的SRAP标记聚类分析图谱表明,卷柏科与里白科、木贼科与鳞毛蕨科、乌毛蕨科与鳞毛蕨科、铁角蕨科与蹄盖蕨科、鳞始蕨科与鳞毛蕨科的亲缘关系比较接近;试验结果与传统分类学中贯众属属于鳞毛蕨科有冲突。[结论]用SRAP分子标记的方法得到的结果与传统分类结果存在一定的差异,但这种差异很小,试验结果可以为重建蕨类植物的系统演化关系提供参考。

  15. A time-calibrated molecular phylogeny of the precious corals: reconciling discrepancies in the taxonomic classification and insights into their evolutionary history

    Directory of Open Access Journals (Sweden)

    Ardila Néstor E

    2012-12-01

    delineated 11 morphospecies that were congruent with the general mixed Yule-coalescent (GMYC model. A multilocus species-tree approach also identified the same two well-supported clades, being Clade I-B more recent in the species tree (18.0-15.9 mya than in the gene tree (35.2-15.9 mya. In contrast, the diversification times for Clade II were more ancient in the species tree (136.4-41.7 mya than in the gene tree (66.3-16.9 mya. Conclusions Our results provide no support for the taxonomic status of the two currently recognized genera in the family Coralliidae. Given that Paracorallium species were all nested within Corallium, we recognize the coralliid genus Corallium, which includes the type species of the family, and thus consider Paracorallium a junior synonym of Corallium. We propose the use of the genus Hemicorallium Gray for clade I-B (species with long rod sclerites, cylindrical autozooids and smooth axis. Species delimitation in clade I-B remains unclear and the molecular resolution for Coralliidae species is inconsistent in the two main clades. Some species have wide distributions, recent diversification times and low mtDNA divergence whereas other species exhibit narrower allopatric distributions, older diversification times and greater levels of mtDNA resolution.

  16. $H_{2}^{+}$ ion in strong magnetic field an accurate calculation

    CERN Document Server

    López, J C; Turbiner, A V

    1997-01-01

    Using a unique trial function we perform an accurate calculation of the ground state $1\\sigma_g$ of the hydrogenic molecular ion $H^+_2$ in a constant uniform magnetic field ranging $0-10^{13}$ G. We show that this trial function also makes it possible to study the negative parity ground state $1\\sigma_u$.

  17. Texture Classification based on Gabor Wavelet

    Directory of Open Access Journals (Sweden)

    Amandeep Kaur

    2012-07-01

    Full Text Available This paper presents the comparison of Texture classification algorithms based on Gabor Wavelets. The focus of this paper is on feature extraction scheme for texture classification. The texture feature for an image can be classified using texture descriptors. In this paper we have used Homogeneous texture descriptor that uses Gabor Wavelets concept. For texture classification, we have used online texture database that is Brodatz’s database and three advanced well known classifiers: Support Vector Machine, K-nearest neighbor method and decision tree induction method. The results shows that classification using Support vector machines gives better results as compare to the other classifiers. It can accurately discriminate between a testing image data and training data.

  18. Voxel classification methodology for rapid Monte Carlo simulation of light propagation in complex media

    Institute of Scientific and Technical Information of China (English)

    Nunu Ren; Heng Zhao; Shouping Zhu; Xiaochao Qu; Hongliang Liu; Zhenhua Hu; Jimin Liang; Jie Tian

    2011-01-01

    @@ Monte Carlo (MC) method is a statistical method for simulating photon propagation in media in the optical molecular imaging field.However, obtaining an accurate result using the method is quite time-consuming,especially because the boundary of the media is complex.A voxel classification method is proposed to reduce the computation cost.All the voxels generated by dividing the media are classified into three types (outside, boundary, and inside) according to the position of the voxel.The classified information is used to determine the relative position of the photon and the intersection between photon path and media boundary in the MC method.The influencing factor8 and effectiveness of the proposed method are analyzed and validated by simulation experiments.%Monte Carlo (MC) method is a statistical method for simulating photon propagation in media in the optical molecular imaging field. However, obtaining an accurate result using the method is quite time-consuming,especially because the boundary of the media is complex. A voxel classification method is proposed to reduce the computation cost. All the voxels generated by dividing the media are classified into three types (outside, boundary, and inside) according to the position of the voxel. The classified information is used to determine the relative position of the photon and the intersection between photon path and media boundary in the MC method. The influencing factors and effectiveness of the proposed method are analyzed and validated by simulation experiments.

  19. Influence of pansharpening techniques in obtaining accurate vegetation thematic maps

    Science.gov (United States)

    Ibarrola-Ulzurrun, Edurne; Gonzalo-Martin, Consuelo; Marcello-Ruiz, Javier

    2016-10-01

    In last decades, there have been a decline in natural resources, becoming important to develop reliable methodologies for their management. The appearance of very high resolution sensors has offered a practical and cost-effective means for a good environmental management. In this context, improvements are needed for obtaining higher quality of the information available in order to get reliable classified images. Thus, pansharpening enhances the spatial resolution of the multispectral band by incorporating information from the panchromatic image. The main goal in the study is to implement pixel and object-based classification techniques applied to the fused imagery using different pansharpening algorithms and the evaluation of thematic maps generated that serve to obtain accurate information for the conservation of natural resources. A vulnerable heterogenic ecosystem from Canary Islands (Spain) was chosen, Teide National Park, and Worldview-2 high resolution imagery was employed. The classes considered of interest were set by the National Park conservation managers. 7 pansharpening techniques (GS, FIHS, HCS, MTF based, Wavelet `à trous' and Weighted Wavelet `à trous' through Fractal Dimension Maps) were chosen in order to improve the data quality with the goal to analyze the vegetation classes. Next, different classification algorithms were applied at pixel-based and object-based approach, moreover, an accuracy assessment of the different thematic maps obtained were performed. The highest classification accuracy was obtained applying Support Vector Machine classifier at object-based approach in the Weighted Wavelet `à trous' through Fractal Dimension Maps fused image. Finally, highlight the difficulty of the classification in Teide ecosystem due to the heterogeneity and the small size of the species. Thus, it is important to obtain accurate thematic maps for further studies in the management and conservation of natural resources.

  20. Accurate Modeling of Advanced Reflectarrays

    DEFF Research Database (Denmark)

    Zhou, Min

    Analysis and optimization methods for the design of advanced printed re ectarrays have been investigated, and the study is focused on developing an accurate and efficient simulation tool. For the analysis, a good compromise between accuracy and efficiency can be obtained using the spectral domain...... to the POT. The GDOT can optimize for the size as well as the orientation and position of arbitrarily shaped array elements. Both co- and cross-polar radiation can be optimized for multiple frequencies, dual polarization, and several feed illuminations. Several contoured beam reflectarrays have been designed...... using the GDOT to demonstrate its capabilities. To verify the accuracy of the GDOT, two offset contoured beam reflectarrays that radiate a high-gain beam on a European coverage have been designed and manufactured, and subsequently measured at the DTU-ESA Spherical Near-Field Antenna Test Facility...

  1. The Accurate Particle Tracer Code

    CERN Document Server

    Wang, Yulei; Qin, Hong; Yu, Zhi

    2016-01-01

    The Accurate Particle Tracer (APT) code is designed for large-scale particle simulations on dynamical systems. Based on a large variety of advanced geometric algorithms, APT possesses long-term numerical accuracy and stability, which are critical for solving multi-scale and non-linear problems. Under the well-designed integrated and modularized framework, APT serves as a universal platform for researchers from different fields, such as plasma physics, accelerator physics, space science, fusion energy research, computational mathematics, software engineering, and high-performance computation. The APT code consists of seven main modules, including the I/O module, the initialization module, the particle pusher module, the parallelization module, the field configuration module, the external force-field module, and the extendible module. The I/O module, supported by Lua and Hdf5 projects, provides a user-friendly interface for both numerical simulation and data analysis. A series of new geometric numerical methods...

  2. Accurate ab initio spin densities

    CERN Document Server

    Boguslawski, Katharina; Legeza, Örs; Reiher, Markus

    2012-01-01

    We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys. 2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CA...

  3. MOLECULAR STRUCTURE RELATED TO GENETIC CODE DEGENERACY AND TWO DIMENSION CLASSIFICATION OF AMINO ACIDS%氨基酸的分子结构与遗传密码简并及二维集合分类

    Institute of Scientific and Technical Information of China (English)

    陈志华; 陈惟昌; 邱红霞; 王自强

    2001-01-01

    According to the degree of degeneracy of genetic codes,64 geneticcodons can be subdivided into two groups,the high degenerate group (3,4,6 triplets degeneracy)and the low degenerate group (single and 2 triplets degeneracy).There are 9 amino acids which belong to the high degenerate group (G,A,S,P,V,T,L,I,R)and 11 amino acids to the low degenerate group (C,N,D,Q,K,E,M,H,F,Y,W).Amino acids of the high degenerate group have relatively simple molecular structure,rather small molecular weights and comparatively concentrated distribution of isoelectric points.While in the low degenerate group,molecular structure is more complex,with relatively large molecular weights,and the distribution of their isoelectric points is more dispersed.Based on the two dimension distribution of molecular weights (M)and isoelectric points (P)of amino acids,a set of classification graph (Venn's diagram)of amino acids can be obtained.The MP classification graph can demonstrate many chemical properties of amino acids,such as:size of molecular weights,degree of degeneracy,polar or non-polar,charged or non-charged,hydrophobic or hydrophilic,and the functional groups of the residues.It is suggested that the amino acids of high degenerate group are mostly small and simple,and constitute the transmembranic structure or the structural domains of protein molecules.So,amino acids of high degenerate group might appear in the early evolution stage.On the other hand,the amino acids of low degenerate group are rather large and complex,and ultimately correlate to the functional domains of protein molecules,then,the amino acids of low degenerate group might appear more lately during evolution.%根据氨基酸遗传密码子的简并程度,可将64个遗传密码子分为高简并度类(3,4,6度简并组)和低简并度类(1,2度简并组)两大类[1]。高简并度类有9个氨基酸,其分子量比较小,等电点的分布比较集中。低简并度类有11个氨基酸,其分子结构

  4. Accurate thickness measurement of graphene.

    Science.gov (United States)

    Shearer, Cameron J; Slattery, Ashley D; Stapleton, Andrew J; Shapter, Joseph G; Gibson, Christopher T

    2016-03-29

    Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.

  5. Accurate thickness measurement of graphene

    Science.gov (United States)

    Shearer, Cameron J.; Slattery, Ashley D.; Stapleton, Andrew J.; Shapter, Joseph G.; Gibson, Christopher T.

    2016-03-01

    Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.

  6. Typology, classification and systematization of innovative projects and initiatives in the company

    OpenAIRE

    Baklanova Julia O.

    2012-01-01

    The author presents a comparison of definitions of typology, classification and systematization, and treats them as an example of innovative projects and initiatives of the company. The basis of typology and classification laid methodical Benko K., Mc Farlan. In order to obtain a more accurate result it is necessary to integrate the task typology, classification and systematization.

  7. Typology, classification and systematization of innovative projects and initiatives in the company

    Directory of Open Access Journals (Sweden)

    Baklanova Julia O.

    2012-04-01

    Full Text Available The author presents a comparison of definitions of typology, classification and systematization, and treats them as an example of innovative projects and initiatives of the company. The basis of typology and classification laid methodical Benko K., Mc Farlan. In order to obtain a more accurate result it is necessary to integrate the task typology, classification and systematization.

  8. Inter-rater reliability of the EPUAP pressure ulcer classification system using photographs.

    NARCIS (Netherlands)

    Defloor, T.; Schoonhoven, L.

    2004-01-01

    BACKGROUND: Many classification systems for grading pressure ulcers are discussed in the literature. Correct identification and classification of a pressure ulcer is important for accurate reporting of the magnitude of the problem, and for timely prevention. The reliability of pressure ulcer classif

  9. FREE RADICALS, REACTIVE OXYGEN SPECIES, OXIDATIVE STRESSES AND THEIR CLASSIFICATIONS.

    Science.gov (United States)

    Lushchak, V I

    2015-01-01

    The phrases "free radicals" and "reactive oxygen species" (ROS) are frequently used interchangeably although this is not always correct. This article gives a brief description of two mentioned oxygen forms. During the first two-three decades after ROS discovery in biological systems (1950-1970 years) they were considered only as damaging agents, but later their involvement in organism protection and regulation of the expression of certain genes was found. The physiological state of increased steady-state ROS level along with certain physiological effects has been called oxidative stress. This paper describes ROS homeostasis and provides several classifications of oxidative stresses. The latter are based on time-course and intensity principles. Therefore distinguishing between acute and chronic stresses on the basis of the dynamics, and the basal oxidative stress, low intensity oxidative stress, strong oxidative stress, and finally a very strong oxidative stress based on the intensity of the action of the inductor of the stress are described. Potential areas of research include the development of this field with complex classification of oxidative stresses, an accurate identification of cellular targets of ROS action, determination of intracellular spatial and temporal distribution of ROS and their effects, deciphering the molecular mechanisms responsible for cell response to ROS attacks, and their participation in the normal cellular functions, i.e. cellular homeostasis and its regulation.

  10. Classification of cultivated plants.

    NARCIS (Netherlands)

    Brandenburg, W.A.

    1986-01-01

    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

  11. Aircraft Operations Classification System

    Science.gov (United States)

    Harlow, Charles; Zhu, Weihong

    2001-01-01

    Accurate data is important in the aviation planning process. In this project we consider systems for measuring aircraft activity at airports. This would include determining the type of aircraft such as jet, helicopter, single engine, and multiengine propeller. Some of the issues involved in deploying technologies for monitoring aircraft operations are cost, reliability, and accuracy. In addition, the system must be field portable and acceptable at airports. A comparison of technologies was conducted and it was decided that an aircraft monitoring system should be based upon acoustic technology. A multimedia relational database was established for the study. The information contained in the database consists of airport information, runway information, acoustic records, photographic records, a description of the event (takeoff, landing), aircraft type, and environmental information. We extracted features from the time signal and the frequency content of the signal. A multi-layer feed-forward neural network was chosen as the classifier. Training and testing results were obtained. We were able to obtain classification results of over 90 percent for training and testing for takeoff events.

  12. Classification of Pteridophytes in Jinyun Mountain of Chongqing Based on SRAP Molecular Marker%重庆市缙云山部分蕨类植物的SRAP分子标记与分类

    Institute of Scientific and Technical Information of China (English)

    党辉; 沈洁; 罗安才; 柳建平

    2011-01-01

    [Objective] The aim was to classify pteridophytes by using SRAP molecular marker. [ Method] 27 species of pteridophytes collected from Jinyun Mountain in Chongqing were classified based on SRAP polymorphism. [ Result] The results of clustering analysis showed that there was close genetic relationship between Selaginellaceae and Gleicheniaceae, Equisaceae and Dryopteridaceae, Blechnaceae and Dryopteridaceae, Lindsaeaceae and Dryopteridaceae, Aspleniaceae and Athyriaceae. Close genetic relationship between Cyrtomium fortunei and Dryopteridaceae differed from traditional taxonomy that classified Cyrtomium fortunei in Dryopteridaceae, indicating that classification of pteridophytes by SRAP molecular marker technology had some differences from traditional taxonomy. [ Conclusion]The results can be referred to rebuild phylogenetic relationships of pteridophytes.%[目的]利用SRAP分子标记的方法对蕨类植物进行种属分类.[方法]以采集于重庆市缙云山的27种蕨类植物为研究对象,以其嫩叶为材料,用改良后的CTAB法提取蕨类植物的基因组DNA,用凝胶电泳和吸光值法对总DNA的质量进行检测,用SRAP分子标记技术对这27种蕨类植物进行了分类研究.[结果]27种蕨类植物的SRAP标记聚类分析图谱表明,卷柏科与里白科、木贼科与鳞毛蕨科、乌毛蕨科与鳞毛蕨科、铁角蕨科与蹄盖蕨科、鳞始蕨科与鳞毛蕨科的亲缘关系比较接近;试验结果与传统分类学中贯众属属于鳞毛蕨科有冲突.[结论]用SRAP分子标记的方法得到的结果与传统分类结果存在一定的差异,但这种差异很小,试验结果可以为重建蕨类植物的系统演化关系提供参考.

  13. Cirrhosis Classification Based on Texture Classification of Random Features

    Directory of Open Access Journals (Sweden)

    Hui Liu

    2014-01-01

    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.

  14. Cirrhosis classification based on texture classification of random features.

    Science.gov (United States)

    Liu, Hui; Shao, Ying; Guo, Dongmei; Zheng, Yuanjie; Zhao, Zuowei; Qiu, Tianshuang

    2014-01-01

    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.

  15. Random forest classification of etiologies for an orphan disease.

    Science.gov (United States)

    Speiser, Jaime Lynn; Durkalski, Valerie L; Lee, William M

    2015-02-28

    Classification of objects into pre-defined groups based on known information is a fundamental problem in the field of statistics. Although approaches for solving this problem exist, finding an accurate classification method can be challenging in an orphan disease setting, where data are minimal and often not normally distributed. The purpose of this paper is to illustrate the application of the random forest (RF) classification procedure in a real clinical setting and discuss typical questions that arise in the general classification framework as well as offer interpretations of RF results. This paper includes methods for assessing predictive performance, importance of predictor variables, and observation-specific information.

  16. A More Accurate Fourier Transform

    CERN Document Server

    Courtney, Elya

    2015-01-01

    Fourier transform methods are used to analyze functions and data sets to provide frequencies, amplitudes, and phases of underlying oscillatory components. Fast Fourier transform (FFT) methods offer speed advantages over evaluation of explicit integrals (EI) that define Fourier transforms. This paper compares frequency, amplitude, and phase accuracy of the two methods for well resolved peaks over a wide array of data sets including cosine series with and without random noise and a variety of physical data sets, including atmospheric $\\mathrm{CO_2}$ concentrations, tides, temperatures, sound waveforms, and atomic spectra. The FFT uses MIT's FFTW3 library. The EI method uses the rectangle method to compute the areas under the curve via complex math. Results support the hypothesis that EI methods are more accurate than FFT methods. Errors range from 5 to 10 times higher when determining peak frequency by FFT, 1.4 to 60 times higher for peak amplitude, and 6 to 10 times higher for phase under a peak. The ability t...

  17. A higher-level phylogenetic classification of the Fungi

    NARCIS (Netherlands)

    Hibbett, D.S.; Binder, M.; Bischoff, J.F.; Blackwell, M.; Cannon, P.F.; Eriksson, O.E.; Huhndorf, S.; James, T.; Kirk, P.M.; Lücking, R.; Thorsten Lumbsch, H.; Lutzoni, F.; Brandon Matheny, P.; McLaughlin, D.J.; Powell, M.J.; Redhead, S.; Schoch, C.L.; Spatafora, J.W.; Stalpers, J.A.; Vilgalys, R.; Aime, M.C.; Aptroot, A.; Bauer, R.; Begerow, D.; Benny, G.L.; Castlebury, L.A.; Crous, P.W.; Dai, Y.C.; Gams, W.; Geiser, D.M.; Griffith, G.W.; Gueidan, C.; Hawksworth, D.L.; Hestmark, G.; Hosaka, K.; Humber, R.A.; Hyde, K.D.; Ironside, J.E.; Koljalg, U.; Kurtzman, C.P.; Larsson, K.H.; Lichtwardt, R.; Longcore, J.; Miadlikowska, J.; Miller, A.; Moncalvo, J.M.; Mozley-Standridge, S.; Oberwinkler, F.; Parmasto, E.; Reeb, V.; Rogers, J.D.; Roux, Le C.; Ryvarden, L.; Sampaio, J.P.; Schüssler, A.; Sugiyama, J.; Thorn, R.G.; Tibell, L.; Untereiner, W.A.; Walker, C.; Wang, Z.; Weir, A.; Weiss, M.; White, M.M.; Winka, K.; Yao, Y.J.; Zhang, N.

    2007-01-01

    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 o

  18. Classification, disease, and diagnosis.

    Science.gov (United States)

    Jutel, Annemarie

    2011-01-01

    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. Automatic classification of blank substrate defects

    Science.gov (United States)

    Boettiger, Tom; Buck, Peter; Paninjath, Sankaranarayanan; Pereira, Mark; Ronald, Rob; Rost, Dan; Samir, Bhamidipati

    2014-10-01

    Mask preparation stages are crucial in mask manufacturing, since this mask is to later act as a template for considerable number of dies on wafer. Defects on the initial blank substrate, and subsequent cleaned and coated substrates, can have a profound impact on the usability of the finished mask. This emphasizes the need for early and accurate identification of blank substrate defects and the risk they pose to the patterned reticle. While Automatic Defect Classification (ADC) is a well-developed technology for inspection and analysis of defects on patterned wafers and masks in the semiconductors industry, ADC for mask blanks is still in the early stages of adoption and development. Calibre ADC is a powerful analysis tool for fast, accurate, consistent and automatic classification of defects on mask blanks. Accurate, automated classification of mask blanks leads to better usability of blanks by enabling defect avoidance technologies during mask writing. Detailed information on blank defects can help to select appropriate job-decks to be written on the mask by defect avoidance tools [1][4][5]. Smart algorithms separate critical defects from the potentially large number of non-critical defects or false defects detected at various stages during mask blank preparation. Mechanisms used by Calibre ADC to identify and characterize defects include defect location and size, signal polarity (dark, bright) in both transmitted and reflected review images, distinguishing defect signals from background noise in defect images. The Calibre ADC engine then uses a decision tree to translate this information into a defect classification code. Using this automated process improves classification accuracy, repeatability and speed, while avoiding the subjectivity of human judgment compared to the alternative of manual defect classification by trained personnel [2]. This paper focuses on the results from the evaluation of Automatic Defect Classification (ADC) product at MP Mask

  20. The Heidelberg classification of renal cell tumours

    NARCIS (Netherlands)

    Kovacs, G; Akhtar, M; Beckwith, BJ; Bugert, P; Cooper, CS; Delahunt, B; Eble, JN; Fleming, S; Ljungberg, B; Medeiros, LJ; Moch, H; Reuter, VE; Ritz, E; Roos, G; Schmidt, D; Srigley, [No Value; Storkel, S; VandenBerg, E; Zbar, B

    1997-01-01

    This paper presents the conclusions of a workshop entitled 'Impact of Molecular Genetics on the Classification of Renal Cell Tumours', which was held in Heidelberg in October 1996, The focus on 'renal cell tumours' excludes any discussion of Wilms' tumour and its variants, or of tumours metastatic t

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

    Directory of Open Access Journals (Sweden)

    Hongxia Cai

    2014-01-01

    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.

  2. Accurate free energy calculation along optimized paths.

    Science.gov (United States)

    Chen, Changjun; Xiao, Yi

    2010-05-01

    The path-based methods of free energy calculation, such as thermodynamic integration and free energy perturbation, are simple in theory, but difficult in practice because in most cases smooth paths do not exist, especially for large molecules. In this article, we present a novel method to build the transition path of a peptide. We use harmonic potentials to restrain its nonhydrogen atom dihedrals in the initial state and set the equilibrium angles of the potentials as those in the final state. Through a series of steps of geometrical optimization, we can construct a smooth and short path from the initial state to the final state. This path can be used to calculate free energy difference. To validate this method, we apply it to a small 10-ALA peptide and find that the calculated free energy changes in helix-helix and helix-hairpin transitions are both self-convergent and cross-convergent. We also calculate the free energy differences between different stable states of beta-hairpin trpzip2, and the results show that this method is more efficient than the conventional molecular dynamics method in accurate free energy calculation.

  3. Security classification of information

    Energy Technology Data Exchange (ETDEWEB)

    Quist, A.S.

    1989-09-01

    Certain governmental information must be classified for national security reasons. However, the national security benefits from classifying information are usually accompanied by significant costs -- those due to a citizenry not fully informed on governmental activities, the extra costs of operating classified programs and procuring classified materials (e.g., weapons), the losses to our nation when advances made in classified programs cannot be utilized in unclassified programs. The goal of a classification system should be to clearly identify that information which must be protected for national security reasons and to ensure that information not needing such protection is not classified. This document was prepared to help attain that goal. This document is the first of a planned four-volume work that comprehensively discusses the security classification of information. Volume 1 broadly describes the need for classification, the basis for classification, and the history of classification in the United States from colonial times until World War 2. Classification of information since World War 2, under Executive Orders and the Atomic Energy Acts of 1946 and 1954, is discussed in more detail, with particular emphasis on the classification of atomic energy information. Adverse impacts of classification are also described. Subsequent volumes will discuss classification principles, classification management, and the control of certain unclassified scientific and technical information. 340 refs., 6 tabs.

  4. Security classification of information

    Energy Technology Data Exchange (ETDEWEB)

    Quist, A.S.

    1993-04-01

    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.

  5. 38 CFR 4.46 - Accurate measurement.

    Science.gov (United States)

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  6. Ontologies vs. Classification Systems

    DEFF Research Database (Denmark)

    Madsen, Bodil Nistrup; Erdman Thomsen, Hanne

    2009-01-01

    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 d...... classification systems and meta data taxonomies, should be based on ontologies.......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...

  7. AGN Zoo and Classifications of Active Galaxies

    Science.gov (United States)

    Mickaelian, Areg M.

    2015-07-01

    We review the variety of Active Galactic Nuclei (AGN) classes (so-called "AGN zoo") and classification schemes of galaxies by activity types based on their optical emission-line spectrum, as well as other parameters and other than optical wavelength ranges. A historical overview of discoveries of various types of active galaxies is given, including Seyfert galaxies, radio galaxies, QSOs, BL Lacertae objects, Starbursts, LINERs, etc. Various kinds of AGN diagnostics are discussed. All known AGN types and subtypes are presented and described to have a homogeneous classification scheme based on the optical emission-line spectra and in many cases, also other parameters. Problems connected with accurate classifications and open questions related to AGN and their classes are discussed and summarized.

  8. Text Classification Using Sentential Frequent Itemsets

    Institute of Scientific and Technical Information of China (English)

    Shi-Zhu Liu; He-Ping Hu

    2007-01-01

    Text classification techniques mostly rely on single term analysis of the document data set, while more concepts,especially the specific ones, are usually conveyed by set of terms. To achieve more accurate text classifier, more informative feature including frequent co-occurring words in the same sentence and their weights are particularly important in such scenarios. In this paper, we propose a novel approach using sentential frequent itemset, a concept comes from association rule mining, for text classification, which views a sentence rather than a document as a transaction, and uses a variable precision rough set based method to evaluate each sentential frequent itemset's contribution to the classification. Experiments over the Reuters and newsgroup corpus are carried out, which validate the practicability of the proposed system.

  9. Information gathering for CLP classification

    OpenAIRE

    Ida Marcello; Felice Giordano; Francesca Marina Costamagna

    2011-01-01

    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 requireme...

  10. Classification of Spreadsheet Errors

    OpenAIRE

    Rajalingham, Kamalasen; Chadwick, David R.; Knight, Brian

    2008-01-01

    This paper describes a framework for a systematic classification of spreadsheet errors. This classification or taxonomy of errors is aimed at facilitating analysis and comprehension of the different types of spreadsheet errors. The taxonomy is an outcome of an investigation of the widespread problem of spreadsheet errors and an analysis of specific types of these errors. This paper contains a description of the various elements and categories of the classification and is supported by appropri...

  11. Adenocarcinoma of Mullerian origin: review of pathogenesis, molecular biology, and emerging treatment paradigms.

    Science.gov (United States)

    Cobb, Lauren Patterson; Gaillard, Stephanie; Wang, Yihong; Shih, Ie-Ming; Secord, Angeles Alvarez

    2015-01-01

    Traditionally, epithelial ovarian, tubal, and peritoneal cancers have been viewed as separate entities with disparate origins, pathogenesis, clinical features, and outcomes. Additionally, previous classification systems for ovarian cancer have proposed two primary histologic groups that encompass the standard histologic subtypes. Recent data suggest that these groupings no longer accurately reflect our knowledge surrounding these cancers. In this review, we propose that epithelial ovarian, tubal, and peritoneal carcinomas represent a spectrum of disease that originates in the Mullerian compartment. We will discuss the incidence, classification, origin, molecular determinants, and pathologic analysis of these cancers that support the conclusion they should be collectively referred to as adenocarcinomas of Mullerian origin. As our understanding of the molecular and pathologic profiling of adenocarcinomas of Mullerian origin advances, we anticipate treatment paradigms will shift towards genomic driven therapeutic interventions.

  12. Study for Updated Gout Classification Criteria

    DEFF Research Database (Denmark)

    Taylor, William J; Fransen, Jaap; Jansen, Tim L

    2015-01-01

    OBJECTIVE: To determine which clinical, laboratory, and imaging features most accurately distinguished gout from non-gout. METHODS: We performed a cross-sectional study of consecutive rheumatology clinic patients with ≥1 swollen joint or subcutaneous tophus. Gout was defined by synovial fluid or ...... (MTP1) joint ever involved (multivariate OR 2.30), location of currently tender joints in other foot/ankle (multivariate OR 2.28) or MTP1 joint (multivariate OR 2.82), serum urate level >6 mg/dl (0.36 mmoles/liter; multivariate OR 3.35), ultrasound double contour sign (multivariate OR 7...... been identified for further evaluation for new gout classification criteria. Ultrasound findings and degree of uricemia add discriminating value, and will significantly contribute to more accurate classification criteria....

  13. Automatic lexical classification: bridging research and practice.

    Science.gov (United States)

    Korhonen, Anna

    2010-08-13

    Natural language processing (NLP)--the automatic analysis, understanding and generation of human language by computers--is vitally dependent on accurate knowledge about words. Because words change their behaviour between text types, domains and sub-languages, a fully accurate static lexical resource (e.g. a dictionary, word classification) is unattainable. Researchers are now developing techniques that could be used to automatically acquire or update lexical resources from textual data. If successful, the automatic approach could considerably enhance the accuracy and portability of language technologies, such as machine translation, text mining and summarization. This paper reviews the recent and on-going research in automatic lexical acquisition. Focusing on lexical classification, it discusses the many challenges that still need to be met before the approach can benefit NLP on a large scale.

  14. Concepts of Classification and Taxonomy. Phylogenetic Classification

    CERN Document Server

    Fraix-Burnet, Didier

    2016-01-01

    Phylogenetic approaches to classification have been heavily developed in biology by bioinformaticians. But these techniques have applications in other fields, in particular in linguistics. Their main characteristics is to search for relationships between the objects or species in study, instead of grouping them by similarity. They are thus rather well suited for any kind of evolutionary objects. For nearly fifteen years, astrocladistics has explored the use of Maximum Parsimony (or cladistics) for astronomical objects like galaxies or globular clusters. In this lesson we will learn how it works. 1 Why phylogenetic tools in astrophysics? 1.1 History of classification The need for classifying living organisms is very ancient, and the first classification system can be dated back to the Greeks. The goal was very practical since it was intended to distinguish between eatable and toxic aliments, or kind and dangerous animals. Simple resemblance was used and has been used for centuries. Basically, until the XVIIIth...

  15. Independent Comparison of Popular DPI Tools for Traffic Classification

    DEFF Research Database (Denmark)

    Bujlow, Tomasz; Carela-Español, Valentín; Barlet-Ros, Pere

    2015-01-01

    Deep Packet Inspection (DPI) is the state-of-the-art technology for traffic classification. According to the conventional wisdom, DPI is the most accurate classification technique. Consequently, most popular products, either commercial or open-source, rely on some sort of DPI for traffic classifi......Deep Packet Inspection (DPI) is the state-of-the-art technology for traffic classification. According to the conventional wisdom, DPI is the most accurate classification technique. Consequently, most popular products, either commercial or open-source, rely on some sort of DPI for traffic......, application and web service). We carefully built a labeled dataset with more than 750K flows, which contains traffic from popular applications. We used the Volunteer-Based System (VBS), developed at Aalborg University, to guarantee the correct labeling of the dataset. We released this dataset, including full...

  16. Genome wide molecular analysis of minimally differentiated acute myeloid leukemia

    NARCIS (Netherlands)

    Silva, Fernando P. G.; Almeida, Ines; Morolli, Bruno; Brouwer-Mandema, Geeske; Wessels, Hans; Vossen, Rolf; Vrieling, Harry; Marijt, Erik W. A.; Valk, Peter J. M.; Kluin-Nelemans, Hanneke C.; Sperr, Wolfgang R.; Ludwig, Wolf-Dieter; Giphart-Gassler, Micheline

    2009-01-01

    Background Minimally differentiated acute myeloid leukemia is heterogeneous in karyotype and is defined by immature morphological and molecular characteristics. This originally French-American-British classification is still used in the new World Health Organization classification when other criteri

  17. A jackknife-like method for classification and uncertainty assessment of multi-category tumor samples using gene expression information

    Directory of Open Access Journals (Sweden)

    Bertrand Keith

    2010-04-01

    Full Text Available Abstract Background The use of gene expression profiling for the classification of human cancer tumors has been widely investigated. Previous studies were successful in distinguishing several tumor types in binary problems. As there are over a hundred types of cancers, and potentially even more subtypes, it is essential to develop multi-category methodologies for molecular classification for any meaningful practical application. Results A jackknife-based supervised learning method called paired-samples test algorithm (PST, coupled with a binary classification model based on linear regression, was proposed and applied to two well known and challenging datasets consisting of 14 (GCM dataset and 9 (NC160 dataset tumor types. The results showed that the proposed method improved the prediction accuracy of the test samples for the GCM dataset, especially when t-statistic was used in the primary feature selection. For the NCI60 dataset, the application of PST improved prediction accuracy when the numbers of used genes were relatively small (100 or 200. These improvements made the binary classification method more robust to the gene selection mechanism and the size of genes to be used. The overall prediction accuracies were competitive in comparison to the most accurate results obtained by several previous studies on the same datasets and with other methods. Furthermore, the relative confidence R(T provided a unique insight into the sources of the uncertainty shown in the statistical classification and the potential variants within the same tumor type. Conclusion We proposed a novel bagging method for the classification and uncertainty assessment of multi-category tumor samples using gene expression information. The strengths were demonstrated in the application to two bench datasets.

  18. Multiple sparse representations classification

    NARCIS (Netherlands)

    E. Plenge (Esben); S.K. Klein (Stefan); W.J. Niessen (Wiro); E. Meijering (Erik)

    2015-01-01

    textabstractSparse 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 t

  19. Library Classification 2020

    Science.gov (United States)

    Harris, Christopher

    2013-01-01

    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…

  20. Trends and concepts in fern classification

    Science.gov (United States)

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

    2014-01-01

    Background and Aims Throughout the history of fern classification, familial and generic concepts have been highly labile. Many classifications and evolutionary schemes have been proposed during the last two centuries, reflecting different interpretations of the available evidence. Knowledge of fern structure and life histories has increased through time, providing more evidence on which to base ideas of possible relationships, and classification has changed accordingly. This paper reviews previous classifications of ferns and presents ideas on how to achieve a more stable consensus. Scope An historical overview is provided from the first to the most recent fern classifications, from which conclusions are drawn on past changes and future trends. The problematic concept of family in ferns is discussed, with a particular focus on how this has changed over time. The history of molecular studies and the most recent findings are also presented. Key Results Fern classification generally shows a trend from highly artificial, based on an interpretation of a few extrinsic characters, via natural classifications derived from a multitude of intrinsic characters, towards more evolutionary circumscriptions of groups that do not in general align well with the distribution of these previously used characters. It also shows a progression from a few broad family concepts to systems that recognized many more narrowly and highly controversially circumscribed families; currently, the number of families recognized is stabilizing somewhere between these extremes. Placement of many genera was uncertain until the arrival of molecular phylogenetics, which has rapidly been improving our understanding of fern relationships. As a collective category, the so-called ‘fern allies’ (e.g. Lycopodiales, Psilotaceae, Equisetaceae) were unsurprisingly found to be polyphyletic, and the term should be abandoned. Lycopodiaceae, Selaginellaceae and Isoëtaceae form a clade (the lycopods) that is

  1. Enhancing Accuracy of Plant Leaf Classification Techniques

    Directory of Open Access Journals (Sweden)

    C. S. Sumathi

    2014-03-01

    Full Text Available Plants have become an important source of energy, and are a fundamental piece in the puzzle to solve the problem of global warming. Living beings also depend on plants for their food, hence it is of great importance to know about the plants growing around us and to preserve them. Automatic plant leaf classification is widely researched. This paper investigates the efficiency of learning algorithms of MLP for plant leaf classification. Incremental back propagation, Levenberg–Marquardt and batch propagation learning algorithms are investigated. Plant leaf images are examined using three different Multi-Layer Perceptron (MLP modelling techniques. Back propagation done in batch manner increases the accuracy of plant leaf classification. Results reveal that batch training is faster and more accurate than MLP with incremental training and Levenberg– Marquardt based learning for plant leaf classification. Various levels of semi-batch training used on 9 species of 15 sample each, a total of 135 instances show a roughly linear increase in classification accuracy.

  2. Classifier in Age classification

    Directory of Open Access Journals (Sweden)

    B. Santhi

    2012-12-01

    Full Text Available Face is the important feature of the human beings. We can derive various properties of a human by analyzing the face. The objective of the study is to design a classifier for age using facial images. Age classification is essential in many applications like crime detection, employment and face detection. The proposed algorithm contains four phases: preprocessing, feature extraction, feature selection and classification. The classification employs two class labels namely child and Old. This study addresses the limitations in the existing classifiers, as it uses the Grey Level Co-occurrence Matrix (GLCM for feature extraction and Support Vector Machine (SVM for classification. This improves the accuracy of the classification as it outperforms the existing methods.

  3. Photometric Supernova Classification with Machine Learning

    Science.gov (United States)

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

    2016-08-01

    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.

  4. Multisensor Target Detection And Classification

    Science.gov (United States)

    Ruck, Dennis W.; Rogers, Steven K.; Mills, James P.; Kabrisky, Matthew

    1988-08-01

    In this paper a new approach to the detection and classification of tactical targets using a multifunction laser radar sensor is developed. Targets of interest are tanks, jeeps, trucks, and other vehicles. Doppler images are segmented by developing a new technique which compensates for spurious doppler returns. Relative range images are segmented using an approach based on range gradients. The resultant shapes in the segmented images are then classified using Zernike moment invariants as shape descriptors. Two classification decision rules are implemented: a classical statistical nearest-neighbor approach and a multilayer perceptron architecture. The doppler segmentation algorithm was applied to a set of 180 real sensor images. An accurate segmentation was obtained for 89 percent of the images. The new doppler segmentation proved to be a robust method, and the moment invariants were effective in discriminating the tactical targets. Tanks were classified correctly 86 percent of the time. The most important result of this research is the demonstration of the use of a new information processing architecture for image processing applications.

  5. A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification

    Directory of Open Access Journals (Sweden)

    Wang Lily

    2008-07-01

    Full Text Available Abstract Background Cancer diagnosis and clinical outcome prediction are among the most important emerging applications of gene expression microarray technology with several molecular signatures on their way toward clinical deployment. Use of the most accurate classification algorithms available for microarray gene expression data is a critical ingredient in order to develop the best possible molecular signatures for patient care. As suggested by a large body of literature to date, support vector machines can be considered "best of class" algorithms for classification of such data. Recent work, however, suggests that random forest classifiers may outperform support vector machines in this domain. Results In the present paper we identify methodological biases of prior work comparing random forests and support vector machines and conduct a new rigorous evaluation of the two algorithms that corrects these limitations. Our experiments use 22 diagnostic and prognostic datasets and show that support vector machines outperform random forests, often by a large margin. Our data also underlines the importance of sound research design in benchmarking and comparison of bioinformatics algorithms. Conclusion We found that both on average and in the majority of microarray datasets, random forests are outperformed by support vector machines both in the settings when no gene selection is performed and when several popular gene selection methods are used.

  6. Kappa Coefficients for Circular Classifications

    NARCIS (Netherlands)

    Warrens, Matthijs J.; Pratiwi, Bunga C.

    2016-01-01

    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 coefficie

  7. A New Classification Method to Overcome Over-Branching

    Institute of Scientific and Technical Information of China (English)

    ZHOU Aoying(周傲英); QIAN Weining(钱卫宁); QIAN Hailei(钱海蕾); JIN Wen(金文)

    2002-01-01

    Classification is an important technique in data mining. The decision trees built by most of the existing classification algorithms commonly feature over-branching, which will lead to poor efficiency in the subsequent classification period. In this paper, we present a new value-oriented classification method, which aims at building accurately proper-sized decision trees while reducing over-branching as much as possible, based on the concepts of frequentpattern-node and exceptive-child-node. The experiments show that while using relevant analysis as pre-processing, our classification method, without loss of accuracy, can eliminate the over-branching greatly in decision trees more effectively and efficiently than other algorithms do.

  8. Intraregional classification of wine via ICP-MS elemental fingerprinting.

    Science.gov (United States)

    Coetzee, P P; van Jaarsveld, F P; Vanhaecke, F

    2014-12-01

    The feasibility of elemental fingerprinting in the classification of wines according to their provenance vineyard soil was investigated in the relatively small geographical area of a single wine district. Results for the Stellenbosch wine district (Western Cape Wine Region, South Africa), comprising an area of less than 1,000 km(2), suggest that classification of wines from different estates (120 wines from 23 estates) is indeed possible using accurate elemental data and multivariate statistical analysis based on a combination of principal component analysis, cluster analysis, and discriminant analysis. This is the first study to demonstrate the successful classification of wines at estate level in a single wine district in South Africa. The elements B, Ba, Cs, Cu, Mg, Rb, Sr, Tl and Zn were identified as suitable indicators. White and red wines were grouped in separate data sets to allow successful classification of wines. Correlation between wine classification and soil type distributions in the area was observed.

  9. Behavior Based Social Dimensions Extraction for Multi-Label Classification.

    Science.gov (United States)

    Li, Le; Xu, Junyi; Xiao, Weidong; Ge, Bin

    2016-01-01

    Classification based on social dimensions is commonly used to handle the multi-label classification task in heterogeneous networks. However, traditional methods, which mostly rely on the community detection algorithms to extract the latent social dimensions, produce unsatisfactory performance when community detection algorithms fail. In this paper, we propose a novel behavior based social dimensions extraction method to improve the classification performance in multi-label heterogeneous networks. In our method, nodes' behavior features, instead of community memberships, are used to extract social dimensions. By introducing Latent Dirichlet Allocation (LDA) to model the network generation process, nodes' connection behaviors with different communities can be extracted accurately, which are applied as latent social dimensions for classification. Experiments on various public datasets reveal that the proposed method can obtain satisfactory classification results in comparison to other state-of-the-art methods on smaller social dimensions.

  10. Cancer classification based on gene expression using neural networks.

    Science.gov (United States)

    Hu, H P; Niu, Z J; Bai, Y P; Tan, X H

    2015-12-21

    Based on gene expression, we have classified 53 colon cancer patients with UICC II into two groups: relapse and no relapse. Samples were taken from each patient, and gene information was extracted. Of the 53 samples examined, 500 genes were considered proper through analyses by S-Kohonen, BP, and SVM neural networks. Classification accuracy obtained by S-Kohonen neural network reaches 91%, which was more accurate than classification by BP and SVM neural networks. The results show that S-Kohonen neural network is more plausible for classification and has a certain feasibility and validity as compared with BP and SVM neural networks.

  11. Morphological classification of plant cell deaths

    DEFF Research Database (Denmark)

    van Doorn, W.G.; Beers, E.P.; Dangl, J.L.;

    2011-01-01

    the classification of PCD in plants. Here we suggest a classification based on morphological criteria. According to this classification, the use of the term 'apoptosis' is not justified in plants, but at least two classes of PCD can be distinguished: vacuolar cell death and necrosis. During vacuolar cell death......Programmed cell death (PCD) is an integral part of plant development and of responses to abiotic stress or pathogens. Although the morphology of plant PCD is, in some cases, well characterised and molecular mechanisms controlling plant PCD are beginning to emerge, there is still confusion about......, the cell contents are removed by a combination of autophagy-like process and release of hydrolases from collapsed lytic vacuoles. Necrosis is characterised by early rupture of the plasma membrane, shrinkage of the protoplast and absence of vacuolar cell death features. Vacuolar cell death is common during...

  12. Molecular classification of cervical squamous cell carcinoma using cDNA microarrays%利用cDNA微阵列进行宫颈鳞癌的分子筛查

    Institute of Scientific and Technical Information of China (English)

    吴素慧; 解军; 李颖; 张静; 郭素堂; 何显峰; 牛勃; 王泽华

    2006-01-01

    metastases, all 677 genes were identified with differential expression, 494 of which showed increased expression(72.97% ), 183 decreased expression (27.03%), and ESTs were 61(9.01% ), including genes of metabolism,development, signal transduction and differentiation. Thereinto, 14 6-fold differential genes were up-regulated except that nel (chicken)-like 2 was down-regulated. The results of RT-PCR and immunohistochemistry were in agreement with the microarray data.Conclusion The results demonstrate that gene expression profiling can be used as a predictor of lymph node metastasis and prognosis of cervical carcinoma. The prediction of cervical malignancy based on the lack of Cx43 and superabundance of ETV5 and integrin alpha 2 might serve as specific diagnostic biomarkers for ICC. These expression may be suitable for molecular classification of disease stages and prediction of treatment response in cervical carcinoma.

  13. 78 FR 54970 - Cotton Futures Classification: Optional Classification Procedure

    Science.gov (United States)

    2013-09-09

    ... process in March 2012 (77 FR 5379). When verified by a futures classification, Smith-Doxey data serves as... Classification: Optional Classification Procedure AGENCY: Agricultural Marketing Service, USDA. ACTION: Proposed... for the addition of an optional cotton futures classification procedure--identified and known...

  14. Learning Apache Mahout classification

    CERN Document Server

    Gupta, Ashish

    2015-01-01

    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. Pitch Based Sound Classification

    DEFF Research Database (Denmark)

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

    2006-01-01

    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......, and that even though classification gets marginally better, not much is achieved by increasing the window size beyond 1 s....

  16. Completion of the classification

    CERN Document Server

    Strade, Helmut

    2012-01-01

    This is the last of three volumes about ""Simple Lie Algebras over Fields of Positive Characteristic""by Helmut Strade, presenting the state of the art of the structure and classification of Lie algebras over fields of positive characteristic. In this monograph the proof of the Classification Theorem presented in the first volumeis concluded.Itcollects all the important results on the topic whichcan be found only in scatteredscientific literaturso far.

  17. Twitter content classification

    OpenAIRE

    2010-01-01

    This paper delivers a new Twitter content classification framework based sixteen existing Twitter studies and a grounded theory analysis of a personal Twitter history. It expands the existing understanding of Twitter as a multifunction tool for personal, profession, commercial and phatic communications with a split level classification scheme that offers broad categorization and specific sub categories for deeper insight into the real world application of the service.

  18. Expected Classification Accuracy

    Directory of Open Access Journals (Sweden)

    Lawrence M. Rudner

    2005-08-01

    Full Text Available Every time we make a classification based on a test score, we should expect some number..of misclassifications. Some examinees whose true ability is within a score range will have..observed scores outside of that range. A procedure for providing a classification table of..true and expected scores is developed for polytomously scored items under item response..theory and applied to state assessment data. A simplified procedure for estimating the..table entries is also presented.

  19. Accurate Medium-Term Wind Power Forecasting in a Censored Classification Framework

    DEFF Research Database (Denmark)

    Dahl, Christian M.; Croonenbroeck, Carsten

    2014-01-01

    We provide a wind power forecasting methodology that exploits many of the actual data's statistical features, in particular both-sided censoring. While other tools ignore many of the important “stylized facts” or provide forecasts for short-term horizons only, our approach focuses on medium......-term forecasts, which are especially necessary for practitioners in the forward electricity markets of many power trading places; for example, NASDAQ OMX Commodities (formerly Nord Pool OMX Commodities) in northern Europe. We show that our model produces turbine-specific forecasts that are significantly more...

  20. Separation of Benign and Malicious Network Events for Accurate Malware Family Classification

    Science.gov (United States)

    2015-09-28

    unseen malicious behavior, while addressing code obfuscation, but they cost more time and resources to run the given malware sample in the sandbox...they come at a high cost [10] Observed Traffic Web S/W Updates Malware Blend  All  Sources   Fig. 1. Observed Traffic from a Host due to the...First, CHATTER relies on fine-grained events, since attributes extracted from one packet are treated as different events, e.g., inbound , DNS, and

  1. Accurate studies on dissociation energies of diatomic molecules

    Institute of Scientific and Technical Information of China (English)

    SUN; WeiGuo; FAN; QunChao

    2007-01-01

    The molecular dissociation energies of some electronic states of hydride and N2 molecules were studied using a parameter-free analytical formula suggested in this study and the algebraic method (AM) proposed recently. The results show that the accurate AM dissociation energies DeAM agree excellently with experimental dissociation energies Deexpt, and that the dissociation energy of an electronic state such as the 23△g state of 7Li2 whose experimental value is not available can be predicted using the new formula.

  2. Laboratory Building for Accurate Determination of Plutonium

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    <正>The accurate determination of plutonium is one of the most important assay techniques of nuclear fuel, also the key of the chemical measurement transfer and the base of the nuclear material balance. An

  3. Understanding the Code: keeping accurate records.

    Science.gov (United States)

    Griffith, Richard

    2015-10-01

    In his continuing series looking at the legal and professional implications of the Nursing and Midwifery Council's revised Code of Conduct, Richard Griffith discusses the elements of accurate record keeping under Standard 10 of the Code. This article considers the importance of accurate record keeping for the safety of patients and protection of district nurses. The legal implications of records are explained along with how district nurses should write records to ensure these legal requirements are met.

  4. A Novel Vehicle Classification Using Embedded Strain Gauge Sensors

    Directory of Open Access Journals (Sweden)

    Qi Wang

    2008-11-01

    Full Text Available Abstract: This paper presents a new vehicle classification and develops a traffic monitoring detector to provide reliable vehicle classification to aid traffic management systems. The basic principle of this approach is based on measuring the dynamic strain caused by vehicles across pavement to obtain the corresponding vehicle parameters – wheelbase and number of axles – to then accurately classify the vehicle. A system prototype with five embedded strain sensors was developed to validate the accuracy and effectiveness of the classification method. According to the special arrangement of the sensors and the different time a vehicle arrived at the sensors one can estimate the vehicle’s speed accurately, corresponding to the estimated vehicle wheelbase and number of axles. Because of measurement errors and vehicle characteristics, there is a lot of overlap between vehicle wheelbase patterns. Therefore, directly setting up a fixed threshold for vehicle classification often leads to low-accuracy results. Using the machine learning pattern recognition method to deal with this problem is believed as one of the most effective tools. In this study, support vector machines (SVMs were used to integrate the classification features extracted from the strain sensors to automatically classify vehicles into five types, ranging from small vehicles to combination trucks, along the lines of the Federal Highway Administration vehicle classification guide. Test bench and field experiments will be introduced in this paper. Two support vector machines classification algorithms (one-against-all, one-against-one are used to classify single sensor data and multiple sensor combination data. Comparison of the two classification method results shows that the classification accuracy is very close using single data or multiple data. Our results indicate that using multiclass SVM-based fusion multiple sensor data significantly improves

  5. Molecular cytogenetics.

    Science.gov (United States)

    Carpenter, N J

    2001-09-01

    In the past decade, clinical cytogenetics has undergone remarkable advancement as molecular biology techniques have been applied to conventional chromosome analysis. The limitations of conventional banding analysis in the accurate diagnosis and interpretation of certain chromosome abnormalities have largely been overcome by these new technologies, which include fluorescence in situ hybridization (FISH), comparative genomic hybridization (CGH), and multicolor FISH (M-FISH, SKY, and Rx-FISH). Clinical applications include diagnosis of microdeletion and microduplication syndromes, detection of subtelomeric rearrangements in idiopathic mental retardation, identification of marker and derivative chromosomes, prenatal diagnosis of trisomy syndromes, and gene rearrangements and gene amplification in tumors. Molecular cytogenetic methods have expanded the possibilities for precise genetic diagnoses, which are extremely important for clinical management of patients and appropriate counseling of their families.

  6. Concepts of Classification and Taxonomy Phylogenetic Classification

    Science.gov (United States)

    Fraix-Burnet, D.

    2016-05-01

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

  7. Segmentation Assisted Food Classification for Dietary Assessment.

    Science.gov (United States)

    Zhu, Fengqing; Bosch, Marc; Schap, Tusarebecca; Khanna, Nitin; Ebert, David S; Boushey, Carol J; Delp, Edward J

    2011-01-24

    Accurate methods and tools to assess food and nutrient intake are essential for the association between diet and health. Preliminary studies have indicated that the use of a mobile device with a built-in camera to obtain images of the food consumed may provide a less burdensome and more accurate method for dietary assessment. We are developing methods to identify food items using a single image acquired from the mobile device. Our goal is to automatically determine the regions in an image where a particular food is located (segmentation) and correctly identify the food type based on its features (classification or food labeling). Images of foods are segmented using Normalized Cuts based on intensity and color. Color and texture features are extracted from each segmented food region. Classification decisions for each segmented region are made using support vector machine methods. The segmentation of each food region is refined based on feedback from the output of classifier to provide more accurate estimation of the quantity of food consumed.

  8. Prediction and classification of respiratory motion

    CERN Document Server

    Lee, Suk Jin

    2014-01-01

    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...

  9. GPCRTree: online hierarchical classification of GPCR function

    Directory of Open Access Journals (Sweden)

    Timmis Jon

    2008-08-01

    Full Text Available Abstract Background G protein-coupled receptors (GPCRs play important physiological roles transducing extracellular signals into intracellular responses. Approximately 50% of all marketed drugs target a GPCR. There remains considerable interest in effectively predicting the function of a GPCR from its primary sequence. Findings Using techniques drawn from data mining and proteochemometrics, an alignment-free approach to GPCR classification has been devised. It uses a simple representation of a protein's physical properties. GPCRTree, a publicly-available internet server, implements an algorithm that classifies GPCRs at the class, sub-family and sub-subfamily level. Conclusion A selective top-down classifier was developed which assigns sequences within a GPCR hierarchy. Compared to other publicly available GPCR prediction servers, GPCRTree is considerably more accurate at every level of classification. The server has been available online since March 2008 at URL: http://igrid-ext.cryst.bbk.ac.uk/gpcrtree/.

  10. Search techniques in intelligent classification systems

    CERN Document Server

    Savchenko, Andrey V

    2016-01-01

    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...

  11. Application of fuzzy classification in modern primary dental care

    Directory of Open Access Journals (Sweden)

    Yauheni Veryha

    2005-03-01

    Full Text Available This paper describes a framework for implementing fuzzy classifications in primary dental care services. Dental practices aim to provide the highest quality services for their patients. To achieve this, it is important that dentists are able to obtain patients' opinions about their experiences in the dental practice and are able to accurately evaluate this. We propose the use of fuzzy classification to combine various assessment criteria into one general measure to assess patients' satisfaction with primary dental care services. The proposed framework can be used in conventional dental practice information systems and easily integrated with those already used. The benefits of using the proposed fuzzy classification approach include more flexible and accurate analysis of patients' feedback, combining verbal and numeric data. To confirm our theory, a prototype was developed based on the Microsoft TM SQL Server database management system for two criteria used in dental practices, namely making an appointment with a dentist and waiting time for dental care services.

  12. Platelet-rich plasma: the PAW classification system.

    Science.gov (United States)

    DeLong, Jeffrey M; Russell, Ryan P; Mazzocca, Augustus D

    2012-07-01

    Platelet-rich plasma (PRP) has been the subject of hundreds of publications in recent years. Reports of its effects in tissue, both positive and negative, have generated great interest in the orthopaedic community. Protocols for PRP preparation vary widely between authors and are often not well documented in the literature, making results difficult to compare or replicate. A classification system is needed to more accurately compare protocols and results and effectively group studies together for meta-analysis. Although some classification systems have been proposed, no single system takes into account the multitude of variables that determine the efficacy of PRP. In this article we propose a simple method for organizing and comparing results in the literature. The PAW classification system is based on 3 components: (1) the absolute number of Platelets, (2) the manner in which platelet Activation occurs, and (3) the presence or absence of White cells. By analyzing these 3 variables, we are able to accurately compare publications.

  13. Convolutional Neural Networks for patient-specific ECG classification.

    Science.gov (United States)

    Kiranyaz, Serkan; Ince, Turker; Hamila, Ridha; Gabbouj, Moncef

    2015-01-01

    We propose a fast and accurate patient-specific electrocardiogram (ECG) classification and monitoring system using an adaptive implementation of 1D Convolutional Neural Networks (CNNs) that can fuse feature extraction and classification into a unified learner. In this way, a dedicated CNN will be trained for each patient by using relatively small common and patient-specific training data and thus it can also be used to classify long ECG records such as Holter registers in a fast and accurate manner. Alternatively, such a solution can conveniently be used for real-time ECG monitoring and early alert system on a light-weight wearable device. The experimental results demonstrate that the proposed system achieves a superior classification performance for the detection of ventricular ectopic beats (VEB) and supraventricular ectopic beats (SVEB).

  14. Dilated Chi-Square : a novel interestingness measure to build accurate and compact decion list

    OpenAIRE

    Lan, Yu; Janssens, Davy; Chen, Guoqing; Wets, Geert

    2005-01-01

    Associative classification has aroused significant attention in recent years. This paper proposed a novel interestingness measure, named dilated chi-square, to statistically reveal the interdependence between the antecedents and the consequent of classificaton rules. Using dilated chi-square, instead of confidence, as the primary ranking criterion for rules under the framework of popular CBA algorithm, the adapted algorithm presented in this paper can empirically generate more accurate and mu...

  15. Acoustic classification of dwellings

    DEFF Research Database (Denmark)

    Berardi, Umberto; Rasmussen, Birgit

    2014-01-01

    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 soun...... exchanging experiences about constructions fulfilling different classes, reducing trade barriers, and finally increasing the sound insulation of dwellings.......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...

  16. Classification of hand eczema

    DEFF Research Database (Denmark)

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

    2015-01-01

    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...... HE, protein contact dermatitis/contact urticaria, hyperkeratotic endogenous eczema and vesicular endogenous eczema, respectively. An additional diagnosis was given if symptoms indicated that factors additional to the main diagnosis were of importance for the disease. RESULTS: Four hundred and twenty......%) 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...

  17. Cellular image classification

    CERN Document Server

    Xu, Xiang; Lin, Feng

    2017-01-01

    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...

  18. Sound classification of dwellings

    DEFF Research Database (Denmark)

    Rasmussen, Birgit

    2012-01-01

    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....... Descriptors, range of quality levels, number of quality classes, class intervals, denotations and descriptions vary across Europe. The diversity is an obstacle for exchange of experience about constructions fulfilling different classes, implying also trade barriers. Thus, a harmonized classification scheme...... 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...

  19. Classification problem in CBIR

    Directory of Open Access Journals (Sweden)

    Tatiana Jaworska

    2013-04-01

    Full Text Available At present a great deal of research is being done in different aspects of Content-Based Im-age Retrieval (CBIR. Image classification is one of the most important tasks in image re-trieval that must be dealt with. The primary issue we have addressed is: how can the fuzzy set theory be used to handle crisp image data. We propose fuzzy rule-based classification of image objects. To achieve this goal we have built fuzzy rule-based classifiers for crisp data. In this paper we present the results of fuzzy rule-based classification in our CBIR. Further-more, these results are used to construct a search engine taking into account data mining.

  20. Supernova Photometric Classification Challenge

    CERN Document Server

    Kessler, Richard; Jha, Saurabh; Kuhlmann, Stephen

    2010-01-01

    We have publicly released a blinded mix of simulated SNe, with types (Ia, Ib, Ic, II) selected in proportion to their expected rate. The simulation is realized in the griz filters of the Dark Energy Survey (DES) with realistic observing conditions (sky noise, point spread function and atmospheric transparency) based on years of recorded conditions at the DES site. Simulations of non-Ia type SNe are based on spectroscopically confirmed light curves that include unpublished non-Ia samples donated from the Carnegie Supernova Project (CSP), the Supernova Legacy Survey (SNLS), and the Sloan Digital Sky Survey-II (SDSS-II). We challenge scientists to run their classification algorithms and report a type for each SN. A spectroscopically confirmed subset is provided for training. The goals of this challenge are to (1) learn the relative strengths and weaknesses of the different classification algorithms, (2) use the results to improve classification algorithms, and (3) understand what spectroscopically confirmed sub-...

  1. Information gathering for CLP classification.

    Science.gov (United States)

    Marcello, Ida; Giordano, Felice; Costamagna, Francesca Marina

    2011-01-01

    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.

  2. The paradox of atheoretical classification

    DEFF Research Database (Denmark)

    Hjørland, Birger

    2016-01-01

    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...... support for the view that a natural classification should be based on a theory (and, of course, that the most fruitful theory provides the most fruitful classification). Nevertheless, atheoretical (or “descriptive”) classifications are often produced. Paradoxically, atheoretical classifications may...... 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...

  3. Information gathering for CLP classification

    Directory of Open Access Journals (Sweden)

    Ida Marcello

    2011-01-01

    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.

  4. Molecular Cloning of Adenosinediphosphoribosyl Transferase.

    Science.gov (United States)

    1987-09-08

    ACCESSION NO.D,. 03261102F 2312 A~5 11. TITLE (include Securqt Classification) 0 Molecular Cloning of Adenosinediphosphoribosyl Transferase 12. PERSONAL...I’:- AFOSR.Tlt. 8 7 - 0 9 8,2 0IL * pi AFOSR- 85 -0377 PROGRESS REPORT Molecular Cloning of Adenosinediphosphoribosyl Transferase 5." Period of...Pharmacology and the Cardiovascular Research Institute September 8, 1987 .’, 5.’- "’S ". -f, AFOSR - 85 -0377 PROGRESS REPORT Molecular Cloning of

  5. Minimum Error Entropy Classification

    CERN Document Server

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

    2013-01-01

    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. Latent classification models

    DEFF Research Database (Denmark)

    Langseth, Helge; Nielsen, Thomas Dyhre

    2005-01-01

    One of the simplest, and yet most consistently well-performing setof classifiers is the \\NB models. These models rely on twoassumptions: $(i)$ All the attributes used to describe an instanceare conditionally independent given the class of that instance,and $(ii)$ all attributes follow a specific...... 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....

  7. Bosniak Classification system

    DEFF Research Database (Denmark)

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

    2014-01-01

    . Purpose: To investigate the inter- and intra-observer agreement among experienced uroradiologists when categorizing complex renal cysts according to the Bosniak classification. Material and Methods: The original categories of 100 cystic renal masses were chosen as “Gold Standard” (GS), established...... to the calculated weighted κ all readers performed “very good” for both inter-observer and intra-observer variation. Most variation was seen in cysts catagorized as Bosniak II, IIF, and III. These results show that radiologists who evaluate complex renal cysts routinely may apply the Bosniak classification...

  8. Classification problem in CBIR

    OpenAIRE

    Tatiana Jaworska

    2013-01-01

    At present a great deal of research is being done in different aspects of Content-Based Im-age Retrieval (CBIR). Image classification is one of the most important tasks in image re-trieval that must be dealt with. The primary issue we have addressed is: how can the fuzzy set theory be used to handle crisp image data. We propose fuzzy rule-based classification of image objects. To achieve this goal we have built fuzzy rule-based classifiers for crisp data. In this paper we present the results ...

  9. Classification of iconic images

    OpenAIRE

    Zrianina, Mariia; Kopf, Stephan

    2016-01-01

    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...

  10. Assessing Measures of Order Flow Toxicity via Perfect Trade Classification

    DEFF Research Database (Denmark)

    Andersen, Torben G.; Bondarenko, Oleg

    . The VPIN metric involves decomposing volume into active buys and sells. We use the best-bid-offer (BBO) files from the CME Group to construct (near) perfect trade classification measures for the E-mini S&P 500 futures contract. We investigate the accuracy of the ELO Bulk Volume Classification (BVC) scheme...... and find it inferior to a standard tick rule based on individual transactions. Moreover, when VPIN is constructed from accurate classification, it behaves in a diametrically opposite way to BVC-VPIN. We also find the latter to have forecast power for short-term volatility solely because it generates...... systematic classification errors that are correlated with trading volume and return volatility. When controlling for trading intensity and volatility, the BVC-VPIN measure has no incremental predictive power for future volatility. We conclude that VPIN is not suitable for measuring order flow imbalances....

  11. A Syntactic Classification based Web Page Ranking Algorithm

    CERN Document Server

    Mukhopadhyay, Debajyoti; Kim, Young-Chon

    2011-01-01

    The existing search engines sometimes give unsatisfactory search result for lack of any categorization of search result. If there is some means to know the preference of user about the search result and rank pages according to that preference, the result will be more useful and accurate to the user. In the present paper a web page ranking algorithm is being proposed based on syntactic classification of web pages. Syntactic Classification does not bother about the meaning of the content of a web page. The proposed approach mainly consists of three steps: select some properties of web pages based on user's demand, measure them, and give different weightage to each property during ranking for different types of pages. The existence of syntactic classification is supported by running fuzzy c-means algorithm and neural network classification on a set of web pages. The change in ranking for difference in type of pages but for same query string is also being demonstrated.

  12. Land Cover Classification Using ALOS Imagery For Penang, Malaysia

    Science.gov (United States)

    Sim, C. K.; Abdullah, K.; MatJafri, M. Z.; Lim, H. S.

    2014-02-01

    This paper presents the potential of integrating optical and radar remote sensing data to improve automatic land cover mapping. The analysis involved standard image processing, and consists of spectral signature extraction and application of a statistical decision rule to identify land cover categories. A maximum likelihood classifier is utilized to determine different land cover categories. Ground reference data from sites throughout the study area are collected for training and validation. The land cover information was extracted from the digital data using PCI Geomatica 10.3.2 software package. The variations in classification accuracy due to a number of radar imaging processing techniques are studied. The relationship between the processing window and the land classification is also investigated. The classification accuracies from the optical and radar feature combinations are studied. Our research finds that fusion of radar and optical significantly improved classification accuracies. This study indicates that the land cover/use can be mapped accurately by using this approach.

  13. Automatic classification of time-variable X-ray sources

    CERN Document Server

    Lo, Kitty K; Murphy, Tara; Gaensler, B M

    2014-01-01

    To maximize the discovery potential of future synoptic surveys, especially in the field of transient science, it will be necessary to use automatic classification to identify some of the astronomical sources. The data mining technique of supervised classification is suitable for this problem. Here, we present a supervised learning method to automatically classify variable X-ray sources in the second \\textit{XMM-Newton} serendipitous source catalog (2XMMi-DR2). Random Forest is our classifier of choice since it is one of the most accurate learning algorithms available. Our training set consists of 873 variable sources and their features are derived from time series, spectra, and other multi-wavelength contextual information. The 10-fold cross validation accuracy of the training data is ${\\sim}$97% on a seven-class data set. We applied the trained classification model to 411 unknown variable 2XMM sources to produce a probabilistically classified catalog. Using the classification margin and the Random Forest der...

  14. Ensemble polarimetric SAR image classification based on contextual sparse representation

    Science.gov (United States)

    Zhang, Lamei; Wang, Xiao; Zou, Bin; Qiao, Zhijun

    2016-05-01

    Polarimetric SAR image interpretation has become one of the most interesting topics, in which the construction of the reasonable and effective technique of image classification is of key importance. Sparse representation represents the data using the most succinct sparse atoms of the over-complete dictionary and the advantages of sparse representation also have been confirmed in the field of PolSAR classification. However, it is not perfect, like the ordinary classifier, at different aspects. So ensemble learning is introduced to improve the issue, which makes a plurality of different learners training and obtained the integrated results by combining the individual learner to get more accurate and ideal learning results. Therefore, this paper presents a polarimetric SAR image classification method based on the ensemble learning of sparse representation to achieve the optimal classification.

  15. Flying insect detection and classification with inexpensive sensors.

    Science.gov (United States)

    Chen, Yanping; Why, Adena; Batista, Gustavo; Mafra-Neto, Agenor; Keogh, Eamonn

    2014-10-15

    An inexpensive, noninvasive system that could accurately classify flying insects would have important implications for entomological research, and allow for the development of many useful applications in vector and pest control for both medical and agricultural entomology. Given this, the last sixty years have seen many research efforts devoted to this task. To date, however, none of this research has had a lasting impact. In this work, we show that pseudo-acoustic optical sensors can produce superior data; that additional features, both intrinsic and extrinsic to the insect's flight behavior, can be exploited to improve insect classification; that a Bayesian classification approach allows to efficiently learn classification models that are very robust to over-fitting, and a general classification framework allows to easily incorporate arbitrary number of features. We demonstrate the findings with large-scale experiments that dwarf all previous works combined, as measured by the number of insects and the number of species considered.

  16. [Classification of diabetes: an increasing heterogeneity].

    Science.gov (United States)

    Corcillo, Antonella; Corcillo Vionnet, Antonella; Jornayvaz, François R

    2015-06-03

    Diabetes mellitus is usually subdivided into type 1 and type 2. Despite precise criteria, distinction between these two types of diabetes can be difficult because of cases with superposition of the two classes. Adults aged 20 to 40 are particularly at risk of presenting an intermediary type of diabetes and thus are subject to misclassification. The distinction between these subtypes is relevant because of the therapeutic decision and the outcome which relies on insulin supply and therefore the evolution to insulin dependence. Thus, it seems important to review a new and more accurate classification of diabetes to offer a more appropriated care to patients.

  17. Spectral classification using convolutional neural networks

    CERN Document Server

    Hála, Pavel

    2014-01-01

    There is a great need for accurate and autonomous spectral classification methods in astrophysics. This thesis is about training a convolutional neural network (ConvNet) to recognize an object class (quasar, star or galaxy) from one-dimension spectra only. Author developed several scripts and C programs for datasets preparation, preprocessing and postprocessing of the data. EBLearn library (developed by Pierre Sermanet and Yann LeCun) was used to create ConvNets. Application on dataset of more than 60000 spectra yielded success rate of nearly 95%. This thesis conclusively proved great potential of convolutional neural networks and deep learning methods in astrophysics.

  18. Accurate tracking control in LOM application

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    The fabrication of accurate prototype from CAD model directly in short time depends on the accurate tracking control and reference trajectory planning in (Laminated Object Manufacture) LOM application. An improvement on contour accuracy is acquired by the introduction of a tracking controller and a trajectory generation policy. A model of the X-Y positioning system of LOM machine is developed as the design basis of tracking controller. The ZPETC (Zero Phase Error Tracking Controller) is used to eliminate single axis following error, thus reduce the contour error. The simulation is developed on a Maltab model based on a retrofitted LOM machine and the satisfied result is acquired.

  19. Classification of neocortical interneurons using affinity propagation

    Science.gov (United States)

    Santana, Roberto; McGarry, Laura M.; Bielza, Concha; Larrañaga, Pedro; Yuste, Rafael

    2013-01-01

    In spite of over a century of research on cortical circuits, it is still unknown how many classes of cortical neurons exist. In fact, neuronal classification is a difficult problem because it is unclear how to designate a neuronal cell class and what are the best characteristics to define them. Recently, unsupervised classifications using cluster analysis based on morphological, physiological, or molecular characteristics, have provided quantitative and unbiased identification of distinct neuronal subtypes, when applied to selected datasets. However, better and more robust classification methods are needed for increasingly complex and larger datasets. Here, we explored the use of affinity propagation, a recently developed unsupervised classification algorithm imported from machine learning, which gives a representative example or exemplar for each cluster. As a case study, we applied affinity propagation to a test dataset of 337 interneurons belonging to four subtypes, previously identified based on morphological and physiological characteristics. We found that affinity propagation correctly classified most of the neurons in a blind, non-supervised manner. Affinity propagation outperformed Ward's method, a current standard clustering approach, in classifying the neurons into 4 subtypes. Affinity propagation could therefore be used in future studies to validly classify neurons, as a first step to help reverse engineer neural circuits. PMID:24348339

  20. Classification of neocortical interneurons using affinity propagation.

    Science.gov (United States)

    Santana, Roberto; McGarry, Laura M; Bielza, Concha; Larrañaga, Pedro; Yuste, Rafael

    2013-01-01

    In spite of over a century of research on cortical circuits, it is still unknown how many classes of cortical neurons exist. In fact, neuronal classification is a difficult problem because it is unclear how to designate a neuronal cell class and what are the best characteristics to define them. Recently, unsupervised classifications using cluster analysis based on morphological, physiological, or molecular characteristics, have provided quantitative and unbiased identification of distinct neuronal subtypes, when applied to selected datasets. However, better and more robust classification methods are needed for increasingly complex and larger datasets. Here, we explored the use of affinity propagation, a recently developed unsupervised classification algorithm imported from machine learning, which gives a representative example or exemplar for each cluster. As a case study, we applied affinity propagation to a test dataset of 337 interneurons belonging to four subtypes, previously identified based on morphological and physiological characteristics. We found that affinity propagation correctly classified most of the neurons in a blind, non-supervised manner. Affinity propagation outperformed Ward's method, a current standard clustering approach, in classifying the neurons into 4 subtypes. Affinity propagation could therefore be used in future studies to validly classify neurons, as a first step to help reverse engineer neural circuits.

  1. Classification of neocortical interneurons using affinity propagation

    Directory of Open Access Journals (Sweden)

    Roberto eSantana

    2013-12-01

    Full Text Available In spite of over a century of research on cortical circuits, it is still unknown how many classes of cortical neurons exist. Neuronal classification has been a difficult problem because it is unclear what a neuronal cell class actually is and what are the best characteristics are to define them. Recently, unsupervised classifications using cluster analysis based on morphological, physiological or molecular characteristics, when applied to selected datasets, have provided quantitative and unbiased identification of distinct neuronal subtypes. However, better and more robust classification methods are needed for increasingly complex and larger datasets. We explored the use of affinity propagation, a recently developed unsupervised classification algorithm imported from machine learning, which gives a representative example or exemplar for each cluster. As a case study, we applied affinity propagation to a test dataset of 337 interneurons belonging to four subtypes, previously identified based on morphological and physiological characteristics. We found that affinity propagation correctly classified most of the neurons in a blind, non-supervised manner. In fact, using a combined anatomical/physiological dataset, our algorithm differentiated parvalbumin from somatostatin interneurons in 49 out of 50 cases. Affinity propagation could therefore be used in future studies to validly classify neurons, as a first step to help reverse engineer neural circuits.

  2. Validation and Classification of Web Services using Equalization Validation Classification

    Directory of Open Access Journals (Sweden)

    ALAMELU MUTHUKRISHNAN

    2012-12-01

    Full Text Available In the business process world, web services present a managed and middleware to connect huge number of services. Web service transaction is a mechanism to compose services with their desired quality parameters. If enormous transactions occur, the provider could not acquire the accurate data at the correct time. So it is necessary to reduce the overburden of web service t ransactions. In order to reduce the excess of transactions form customers to providers, this paper propose a new method called Equalization Validation Classification. This method introduces a new weight - reducing algorithm called Efficient Trim Down algorit hm to reduce the overburden of the incoming client requests. When this proposed algorithm is compared with Decision tree algorithms of (J48, Random Tree, Random Forest, AD Tree it produces a better accuracy and Validation than the existing algorithms. The proposed trimming method was analyzed with the Decision tree algorithms and the results implementation shows that the ETD algorithm provides better performance in terms of improved accuracy with Effective Validation. Therefore, the proposed method provide s a good gateway to reduce the overburden of the client requests in web services. Moreover analyzing the requests arrived from a vast number of clients and preventing the illegitimate requests save the service provider time

  3. Classification of waste packages

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, H.P.; Sauer, M.; Rojahn, T. [Versuchsatomkraftwerk GmbH, Kahl am Main (Germany)

    2001-07-01

    A barrel gamma scanning unit has been in use at the VAK for the classification of radioactive waste materials since 1998. The unit provides the facility operator with the data required for classification of waste barrels. Once these data have been entered into the AVK data processing system, the radiological status of raw waste as well as pre-treated and processed waste can be tracked from the point of origin to the point at which the waste is delivered to a final storage. Since the barrel gamma scanning unit was commissioned in 1998, approximately 900 barrels have been measured and the relevant data required for classification collected and analyzed. Based on the positive results of experience in the use of the mobile barrel gamma scanning unit, the VAK now offers the classification of barrels as a service to external users. Depending upon waste quantity accumulation, this measurement unit offers facility operators a reliable and time-saving and cost-effective means of identifying and documenting the radioactivity inventory of barrels scheduled for final storage. (orig.)

  4. Improving Student Question Classification

    Science.gov (United States)

    Heiner, Cecily; Zachary, Joseph L.

    2009-01-01

    Students in introductory programming classes often articulate their questions and information needs incompletely. Consequently, the automatic classification of student questions to provide automated tutorial responses is a challenging problem. This paper analyzes 411 questions from an introductory Java programming course by reducing the natural…

  5. Event Classification using Concepts

    NARCIS (Netherlands)

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

    2013-01-01

    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 mod

  6. Nearest convex hull classification

    NARCIS (Netherlands)

    G.I. Nalbantov (Georgi); P.J.F. Groenen (Patrick); J.C. Bioch (Cor)

    2006-01-01

    textabstractConsider the classification task of assigning a test object to one of two or more possible groups, or classes. An intuitive way to proceed is to assign the object to that class, to which the distance is minimal. As a distance measure to a class, we propose here to use the distance to the

  7. Classification of myocardial infarction

    DEFF Research Database (Denmark)

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

    2013-01-01

    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 and...

  8. Recurrent neural collective classification.

    Science.gov (United States)

    Monner, Derek D; Reggia, James A

    2013-12-01

    With the recent surge in availability of data sets containing not only individual attributes but also relationships, classification techniques that take advantage of predictive relationship information have gained in popularity. The most popular existing collective classification techniques have a number of limitations-some of them generate arbitrary and potentially lossy summaries of the relationship data, whereas others ignore directionality and strength of relationships. Popular existing techniques make use of only direct neighbor relationships when classifying a given entity, ignoring potentially useful information contained in expanded neighborhoods of radius greater than one. We present a new technique that we call recurrent neural collective classification (RNCC), which avoids arbitrary summarization, uses information about relationship directionality and strength, and through recursive encoding, learns to leverage larger relational neighborhoods around each entity. Experiments with synthetic data sets show that RNCC can make effective use of relationship data for both direct and expanded neighborhoods. Further experiments demonstrate that our technique outperforms previously published results of several collective classification methods on a number of real-world data sets.

  9. Sandwich classification theorem

    Directory of Open Access Journals (Sweden)

    Alexey Stepanov

    2015-09-01

    Full Text Available The present note arises from the author's talk at the conference ``Ischia Group Theory 2014''. For subgroups FleN of a group G denote by Lat(F,N the set of all subgroups of N , containing F . Let D be a subgroup of G . In this note we study the lattice LL=Lat(D,G and the lattice LL ′ of subgroups of G , normalized by D . We say that LL satisfies sandwich classification theorem if LL splits into a disjoint union of sandwiches Lat(F,N G (F over all subgroups F such that the normal closure of D in F coincides with F . Here N G (F denotes the normalizer of F in G . A similar notion of sandwich classification is introduced for the lattice LL ′ . If D is perfect, i.,e. coincides with its commutator subgroup, then it turns out that sandwich classification theorem for LL and LL ′ are equivalent. We also show how to find basic subroup F of sandwiches for LL ′ and review sandwich classification theorems in algebraic groups over rings.

  10. Dynamic Latent Classification Model

    DEFF Research Database (Denmark)

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

    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....

  11. Classifications in popular music

    NARCIS (Netherlands)

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

    2015-01-01

    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 questio

  12. Shark Teeth Classification

    Science.gov (United States)

    Brown, Tom; Creel, Sally; Lee, Velda

    2009-01-01

    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…

  13. Accurate Switched-Voltage voltage averaging circuit

    OpenAIRE

    金光, 一幸; 松本, 寛樹

    2006-01-01

    Abstract ###This paper proposes an accurate Switched-Voltage (SV) voltage averaging circuit. It is presented ###to compensated for NMOS missmatch error at MOS differential type voltage averaging circuit. ###The proposed circuit consists of a voltage averaging and a SV sample/hold (S/H) circuit. It can ###operate using nonoverlapping three phase clocks. Performance of this circuit is verified by PSpice ###simulations.

  14. Accurate overlaying for mobile augmented reality

    NARCIS (Netherlands)

    Pasman, W; van der Schaaf, A; Lagendijk, RL; Jansen, F.W.

    1999-01-01

    Mobile augmented reality requires accurate alignment of virtual information with objects visible in the real world. We describe a system for mobile communications to be developed to meet these strict alignment criteria using a combination of computer vision. inertial tracking and low-latency renderi

  15. Efficient Fingercode Classification

    Science.gov (United States)

    Sun, Hong-Wei; Law, Kwok-Yan; Gollmann, Dieter; Chung, Siu-Leung; Li, Jian-Bin; Sun, Jia-Guang

    In this paper, we present an efficient fingerprint classification algorithm which is an essential component in many critical security application systems e. g. systems in the e-government and e-finance domains. Fingerprint identification is one of the most important security requirements in homeland security systems such as personnel screening and anti-money laundering. The problem of fingerprint identification involves searching (matching) the fingerprint of a person against each of the fingerprints of all registered persons. To enhance performance and reliability, a common approach is to reduce the search space by firstly classifying the fingerprints and then performing the search in the respective class. Jain et al. proposed a fingerprint classification algorithm based on a two-stage classifier, which uses a K-nearest neighbor classifier in its first stage. The fingerprint classification algorithm is based on the fingercode representation which is an encoding of fingerprints that has been demonstrated to be an effective fingerprint biometric scheme because of its ability to capture both local and global details in a fingerprint image. We enhance this approach by improving the efficiency of the K-nearest neighbor classifier for fingercode-based fingerprint classification. Our research firstly investigates the various fast search algorithms in vector quantization (VQ) and the potential application in fingerprint classification, and then proposes two efficient algorithms based on the pyramid-based search algorithms in VQ. Experimental results on DB1 of FVC 2004 demonstrate that our algorithms can outperform the full search algorithm and the original pyramid-based search algorithms in terms of computational efficiency without sacrificing accuracy.

  16. [Biology molecular of glioblastomas].

    Science.gov (United States)

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

    2007-10-01

    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.

  17. Changing Histopathological Diagnostics by Genome-Based Tumor Classification

    Directory of Open Access Journals (Sweden)

    Michael Kloth

    2014-05-01

    Full Text Available Traditionally, tumors are classified by histopathological criteria, i.e., based on their specific morphological appearances. Consequently, current therapeutic decisions in oncology are strongly influenced by histology rather than underlying molecular or genomic aberrations. The increase of information on molecular changes however, enabled by the Human Genome Project and the International Cancer Genome Consortium as well as the manifold advances in molecular biology and high-throughput sequencing techniques, inaugurated the integration of genomic information into disease classification. Furthermore, in some cases it became evident that former classifications needed major revision and adaption. Such adaptations are often required by understanding the pathogenesis of a disease from a specific molecular alteration, using this molecular driver for targeted and highly effective therapies. Altogether, reclassifications should lead to higher information content of the underlying diagnoses, reflecting their molecular pathogenesis and resulting in optimized and individual therapeutic decisions. The objective of this article is to summarize some particularly important examples of genome-based classification approaches and associated therapeutic concepts. In addition to reviewing disease specific markers, we focus on potentially therapeutic or predictive markers and the relevance of molecular diagnostics in disease monitoring.

  18. Free classification of American English dialects by native and non-native listeners.

    Science.gov (United States)

    Clopper, Cynthia G; Bradlow, Ann R

    2009-10-01

    Most second language acquisition research focuses on linguistic structures, and less research has examined the acquisition of sociolinguistic patterns. The current study explored the perceptual classification of regional dialects of American English by native and non-native listeners using a free classification task. Results revealed similar classification strategies for the native and non-native listeners. However, the native listeners were more accurate overall than the non-native listeners. In addition, the non-native listeners were less able to make use of constellations of cues to accurately classify the talkers by dialect. However, the non-native listeners were able to attend to cues that were either phonologically or sociolinguistically relevant in their native language. These results suggest that non-native listeners can use information in the speech signal to classify talkers by regional dialect, but that their lack of signal-independent cultural knowledge about variation in the second language leads to less accurate classification performance.

  19. A Multi-Classification Method of Improved SVM-based Information Fusion for Traffic Parameters Forecasting

    Directory of Open Access Journals (Sweden)

    Hongzhuan Zhao

    2016-04-01

    Full Text Available With the enrichment of perception methods, modern transportation system has many physical objects whose states are influenced by many information factors so that it is a typical Cyber-Physical System (CPS. Thus, the traffic information is generally multi-sourced, heterogeneous and hierarchical. Existing research results show that the multisourced traffic information through accurate classification in the process of information fusion can achieve better parameters forecasting performance. For solving the problem of traffic information accurate classification, via analysing the characteristics of the multi-sourced traffic information and using redefined binary tree to overcome the shortcomings of the original Support Vector Machine (SVM classification in information fusion, a multi-classification method using improved SVM in information fusion for traffic parameters forecasting is proposed. The experiment was conducted to examine the performance of the proposed scheme, and the results reveal that the method can get more accurate and practical outcomes.

  20. Automated, high accuracy classification of Parkinsonian disorders: a pattern recognition approach.

    Directory of Open Access Journals (Sweden)

    Andre F Marquand

    Full Text Available Progressive supranuclear palsy (PSP, multiple system atrophy (MSA and idiopathic Parkinson's disease (IPD can be clinically indistinguishable, especially in the early stages, despite distinct patterns of molecular pathology. Structural neuroimaging holds promise for providing objective biomarkers for discriminating these diseases at the single subject level but all studies to date have reported incomplete separation of disease groups. In this study, we employed multi-class pattern recognition to assess the value of anatomical patterns derived from a widely available structural neuroimaging sequence for automated classification of these disorders. To achieve this, 17 patients with PSP, 14 with IPD and 19 with MSA were scanned using structural MRI along with 19 healthy controls (HCs. An advanced probabilistic pattern recognition approach was employed to evaluate the diagnostic value of several pre-defined anatomical patterns for discriminating the disorders, including: (i a subcortical motor network; (ii each of its component regions and (iii the whole brain. All disease groups could be discriminated simultaneously with high accuracy using the subcortical motor network. The region providing the most accurate predictions overall was the midbrain/brainstem, which discriminated all disease groups from one another and from HCs. The subcortical network also produced more accurate predictions than the whole brain and all of its constituent regions. PSP was accurately predicted from the midbrain/brainstem, cerebellum and all basal ganglia compartments; MSA from the midbrain/brainstem and cerebellum and IPD from the midbrain/brainstem only. This study demonstrates that automated analysis of structural MRI can accurately predict diagnosis in individual patients with Parkinsonian disorders, and identifies distinct patterns of regional atrophy particularly useful for this process.

  1. Accurate colorimetric feedback for RGB LED clusters

    Science.gov (United States)

    Man, Kwong; Ashdown, Ian

    2006-08-01

    We present an empirical model of LED emission spectra that is applicable to both InGaN and AlInGaP high-flux LEDs, and which accurately predicts their relative spectral power distributions over a wide range of LED junction temperatures. We further demonstrate with laboratory measurements that changes in LED spectral power distribution with temperature can be accurately predicted with first- or second-order equations. This provides the basis for a real-time colorimetric feedback system for RGB LED clusters that can maintain the chromaticity of white light at constant intensity to within +/-0.003 Δuv over a range of 45 degrees Celsius, and to within 0.01 Δuv when dimmed over an intensity range of 10:1.

  2. Accurate guitar tuning by cochlear implant musicians.

    Directory of Open Access Journals (Sweden)

    Thomas Lu

    Full Text Available Modern cochlear implant (CI users understand speech but find difficulty in music appreciation due to poor pitch perception. Still, some deaf musicians continue to perform with their CI. Here we show unexpected results that CI musicians can reliably tune a guitar by CI alone and, under controlled conditions, match simultaneously presented tones to <0.5 Hz. One subject had normal contralateral hearing and produced more accurate tuning with CI than his normal ear. To understand these counterintuitive findings, we presented tones sequentially and found that tuning error was larger at ∼ 30 Hz for both subjects. A third subject, a non-musician CI user with normal contralateral hearing, showed similar trends in performance between CI and normal hearing ears but with less precision. This difference, along with electric analysis, showed that accurate tuning was achieved by listening to beats rather than discriminating pitch, effectively turning a spectral task into a temporal discrimination task.

  3. Efficient Accurate Context-Sensitive Anomaly Detection

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    For program behavior-based anomaly detection, the only way to ensure accurate monitoring is to construct an efficient and precise program behavior model. A new program behavior-based anomaly detection model,called combined pushdown automaton (CPDA) model was proposed, which is based on static binary executable analysis. The CPDA model incorporates the optimized call stack walk and code instrumentation technique to gain complete context information. Thereby the proposed method can detect more attacks, while retaining good performance.

  4. On accurate determination of contact angle

    Science.gov (United States)

    Concus, P.; Finn, R.

    1992-01-01

    Methods are proposed that exploit a microgravity environment to obtain highly accurate measurement of contact angle. These methods, which are based on our earlier mathematical results, do not require detailed measurement of a liquid free-surface, as they incorporate discontinuous or nearly-discontinuous behavior of the liquid bulk in certain container geometries. Physical testing is planned in the forthcoming IML-2 space flight and in related preparatory ground-based experiments.

  5. Accurate Control of Josephson Phase Qubits

    Science.gov (United States)

    2016-04-14

    61 ~1986!. 23 K. Kraus, States, Effects, and Operations: Fundamental Notions of Quantum Theory, Lecture Notes in Physics , Vol. 190 ~Springer-Verlag... PHYSICAL REVIEW B 68, 224518 ~2003!Accurate control of Josephson phase qubits Matthias Steffen,1,2,* John M. Martinis,3 and Isaac L. Chuang1 1Center...for Bits and Atoms and Department of Physics , MIT, Cambridge, Massachusetts 02139, USA 2Solid State and Photonics Laboratory, Stanford University

  6. Accurate guitar tuning by cochlear implant musicians.

    Science.gov (United States)

    Lu, Thomas; Huang, Juan; Zeng, Fan-Gang

    2014-01-01

    Modern cochlear implant (CI) users understand speech but find difficulty in music appreciation due to poor pitch perception. Still, some deaf musicians continue to perform with their CI. Here we show unexpected results that CI musicians can reliably tune a guitar by CI alone and, under controlled conditions, match simultaneously presented tones to electric analysis, showed that accurate tuning was achieved by listening to beats rather than discriminating pitch, effectively turning a spectral task into a temporal discrimination task.

  7. Synthesizing Accurate Floating-Point Formulas

    OpenAIRE

    Ioualalen, Arnault; Martel, Matthieu

    2013-01-01

    International audience; Many critical embedded systems perform floating-point computations yet their accuracy is difficult to assert and strongly depends on how formulas are written in programs. In this article, we focus on the synthesis of accurate formulas mathematically equal to the original formulas occurring in source codes. In general, an expression may be rewritten in many ways. To avoid any combinatorial explosion, we use an intermediate representation, called APEG, enabling us to rep...

  8. Fast Image Texture Classification Using Decision Trees

    Science.gov (United States)

    Thompson, David R.

    2011-01-01

    Texture analysis would permit improved autonomous, onboard science data interpretation for adaptive navigation, sampling, and downlink decisions. These analyses would assist with terrain analysis and instrument placement in both macroscopic and microscopic image data products. Unfortunately, most state-of-the-art texture analysis demands computationally expensive convolutions of filters involving many floating-point operations. This makes them infeasible for radiation- hardened computers and spaceflight hardware. A new method approximates traditional texture classification of each image pixel with a fast decision-tree classifier. The classifier uses image features derived from simple filtering operations involving integer arithmetic. The texture analysis method is therefore amenable to implementation on FPGA (field-programmable gate array) hardware. Image features based on the "integral image" transform produce descriptive and efficient texture descriptors. Training the decision tree on a set of training data yields a classification scheme that produces reasonable approximations of optimal "texton" analysis at a fraction of the computational cost. A decision-tree learning algorithm employing the traditional k-means criterion of inter-cluster variance is used to learn tree structure from training data. The result is an efficient and accurate summary of surface morphology in images. This work is an evolutionary advance that unites several previous algorithms (k-means clustering, integral images, decision trees) and applies them to a new problem domain (morphology analysis for autonomous science during remote exploration). Advantages include order-of-magnitude improvements in runtime, feasibility for FPGA hardware, and significant improvements in texture classification accuracy.

  9. BIOPHARMACEUTICAL CLASSIFICATION SYSTEM AND BIOWAVER: AN OVERVIEW

    Directory of Open Access Journals (Sweden)

    Puranik Prashant K

    2011-05-01

    Full Text Available The biopharmaceutical classification system (BCS has been developed to provide a scientific approach for classifying drug compounds based on solubility as related to dose and intestinal permeability in combination with the dissolution properties of the oral immediate release dosage form. BCS is to provide a regulatory tool for replacing certain bioequivalence (BE studies by accurate in vitro dissolution tests. This review gives three dimensionless numbers which are used in BCS are absorption number, dissolution number, dose number.Biowaver is an important tool for formulation development. Bioavailability (BA and BE play a central role in pharmaceutical product development, and BE studies are presently being conducted for New Drug Applications (NDAs of new compounds, in supplementary NDAs for new medical indications and product line extensions, in Abbreviated New Drug Applications (ANDAs of generic products, and in applications for scale-up and post-approval changes. The principles of the BCS classification system can be applied to NDA and ANDA approvals as well as to scale-up and post approval changes in drug manufacturing. BCS classification can therefore save pharmaceutical companies a significant amount in development time and reduce costs. The aim of the present review is to present the status of BCS and discuss its future application in pharmaceutical product development.

  10. Object Based and Pixel Based Classification Using Rapideye Satellite Imager of ETI-OSA, Lagos, Nigeria

    Directory of Open Access Journals (Sweden)

    Esther Oluwafunmilayo Makinde

    2016-12-01

    Full Text Available Several studies have been carried out to find an appropriate method to classify the remote sensing data. Traditional classification approaches are all pixel-based, and do not utilize the spatial information within an object which is an important source of information to image classification. Thus, this study compared the pixel based and object based classification algorithms using RapidEye satellite image of Eti-Osa LGA, Lagos. In the object-oriented approach, the image was segmented to homogenous area by suitable parameters such as scale parameter, compactness, shape etc. Classification based on segments was done by a nearest neighbour classifier. In the pixel-based classification, the spectral angle mapper was used to classify the images. The user accuracy for each class using object based classification were 98.31% for waterbody, 92.31% for vegetation, 86.67% for bare soil and 90.57% for Built up while the user accuracy for the pixel based classification were 98.28% for waterbody, 84.06% for Vegetation 86.36% and 79.41% for Built up. These classification techniques were subjected to accuracy assessment and the overall accuracy of the Object based classification was 94.47%, while that of Pixel based classification yielded 86.64%. The result of classification and accuracy assessment show that the object-based approach gave more accurate and satisfying results

  11. Hand eczema classification

    DEFF Research Database (Denmark)

    Diepgen, T L; Andersen, Klaus Ejner; Brandao, F M;

    2008-01-01

    Summary Background Hand eczema is a long-lasting disease with a high prevalence in the background population. The disease has severe, negative effects on quality of life and sometimes on social status. Epidemiological studies have identified risk factors for onset and prognosis, but treatment...... of the disease is rarely evidence based, and a classification system for different subdiagnoses of hand eczema is not agreed upon. Randomized controlled trials investigating the treatment of hand eczema are called for. For this, as well as for clinical purposes, a generally accepted classification system...... for hand eczema is needed. Objectives The present study attempts to characterize subdiagnoses of hand eczema with respect to basic demographics, medical history and morphology. Methods Clinical data from 416 patients with hand eczema from 10 European patch test clinics were assessed. Results...

  12. Multilingual documentation and classification.

    Science.gov (United States)

    Donnelly, Kevin

    2008-01-01

    Health care providers around the world have used classification systems for decades as a basis for documentation, communications, statistical reporting, reimbursement and research. In more recent years machine-readable medical terminologies have taken on greater importance with the adoption of electronic health records and the need for greater granularity of data in clinical systems. Use of a clinical terminology harmonised with classifications, implemented within a clinical information system, will enable the delivery of many patient health benefits including electronic clinical decision support, disease screening and enhanced patient safety. In order to be usable these systems must be translated into the language of use, without losing meaning. It is evident that today one system cannot meet all requirements which call for collaboration and harmonisation in order to achieve true interoperability on a multilingual basis.

  13. [New classification of vasculitis].

    Science.gov (United States)

    Anić, Branimir

    2014-01-01

    Vasculitis syndrome comprises a heterogenic group of inflammatory rheumatic diseases whose common feature is inflammation in the blood vessel wall. Establishing the diagnosis of vasculitis is one of the greatest challenges in medicine. Clinical presentation of vasculitis depends on the extent of an organ system affection, as well as on the total number of affected organs. A great range of clinical presentations of vasculitis and the low incidence of the disease impede systematic clinical investigation of vasculitis. The needs of clinical routine and the need for conducting systemic clinical investigations require a clear distinction of individual clinical entities. Different classifications of vasculitis syndrome have been proposed: according to etiology, pathogenesis, histological finding in the affected vessels, affection of individual organs and organ systems. This paper presents and comments news and recent classifications and nomenclature of vasculitic entities proposed at the second conference in Chapel Hill.

  14. Bosniak classification system

    DEFF Research Database (Denmark)

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

    2016-01-01

    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...... one category lower. Pathologic correlation in six lesions revealed four malignant and two benign lesions. CONCLUSION: CEUS and MR both up- and downgraded renal cysts compared to CT, and until these non-radiation modalities have been refined and adjusted, CT should remain the gold standard...

  15. 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: alarena@etsii.upm.es

    2008-03-15

    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)

  16. Evolvement of Classification Society

    Institute of Scientific and Technical Information of China (English)

    Xu Hua

    2011-01-01

    As an independent industry, the emergence of the classification society was perhaps the demand of beneficial interests between shipowners, cargo owners and insurers at the earliest time. Today, as an indispensable link of the international maritime industry, class role has changed fundamentally. Start off from the demand of the insurersSeaborne trade, transport and insurance industries began to emerge successively in the 17th century. The massive risk and benefit brought by seaborne transport provided a difficult problem to insurers.

  17. Classification and regression trees

    CERN Document Server

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

    1984-01-01

    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.

  18. Sequence Classification: 389042 [

    Lifescience Database Archive (English)

    Full Text Available Non-TMB TMH TMB TMB TMB Non-TMB >gi|31793553|ref|NP_856046.1| LOW MOLECULAR WEIGHT ANTI...GEN CFP2 (LOW MOLECULAR WEIGHT PROTEIN ANTIGEN 2) (CFP-2) || http://www.ncbi.nlm.nih.gov/protein/31793553 ...

  19. Nonlinear Time Series Model for Shape Classification Using Neural Networks

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A complex nonlinear exponential autoregressive (CNEAR) model for invariant feature extraction is developed for recognizing arbitrary shapes on a plane. A neural network is used to calculate the CNEAR coefficients. The coefficients, which constitute the feature set, are proven to be invariant to boundary transformations such as translation, rotation, scale and choice of starting point in tracing the boundary. The feature set is then used as the input to a complex multilayer perceptron (C-MLP) network for learning and classification. Experimental results show that complicated shapes can be accurately recognized even with the low-order model and that the classification method has good fault tolerance when noise is present.

  20. Classification of Meteorological Drought

    Institute of Scientific and Technical Information of China (English)

    Zhang Qiang; Zou Xukai; Xiao Fengjin; Lu Houquan; Liu Haibo; Zhu Changhan; An Shunqing

    2011-01-01

    Background The national standard of the Classification of Meteorological Drought (GB/T 20481-2006) was developed by the National Climate Center in cooperation with Chinese Academy of Meteorological Sciences,National Meteorological Centre and Department of Forecasting and Disaster Mitigation under the China Meteorological Administration (CMA),and was formally released and implemented in November 2006.In 2008,this Standard won the second prize of the China Standard Innovation and Contribution Awards issued by SAC.Developed through independent innovation,it is the first national standard published to monitor meteorological drought disaster and the first standard in China and around the world specifying the classification of drought.Since its release in 2006,the national standard of Classification of Meteorological Drought has been used by CMA as the operational index to monitor and drought assess,and gradually used by provincial meteorological sureaus,and applied to the drought early warning release standard in the Methods of Release and Propagation of Meteorological Disaster Early Warning Signal.

  1. Short Text Classification: A Survey

    Directory of Open Access Journals (Sweden)

    Ge Song

    2014-05-01

    Full Text Available With the recent explosive growth of e-commerce and online communication, a new genre of text, short text, has been extensively applied in many areas. So many researches focus on short text mining. It is a challenge to classify the short text owing to its natural characters, such as sparseness, large-scale, immediacy, non-standardization. It is difficult for traditional methods to deal with short text classification mainly because too limited words in short text cannot represent the feature space and the relationship between words and documents. Several researches and reviews on text classification are shown in recent times. However, only a few of researches focus on short text classification. This paper discusses the characters of short text and the difficulty of short text classification. Then we introduce the existing popular works on short text classifiers and models, including short text classification using sematic analysis, semi-supervised short text classification, ensemble short text classification, and real-time classification. The evaluations of short text classification are analyzed in our paper. Finally we summarize the existing classification technology and prospect for development trend of short text classification

  2. Maximum mutual information regularized classification

    KAUST Repository

    Wang, Jim Jing-Yan

    2014-09-07

    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.

  3. Mechanisms of disease: mechanism-based classification of neuropathic pain - a critical analysis

    DEFF Research Database (Denmark)

    Finnerup, Nanna Brix; Jensen, Troels Staehelin

    2006-01-01

    Classification of neuropathic pain according to etiology or localization has clear limitations. The discovery of specific molecular and cellular events following experimental nerve injury has raised the possibility of classifying neuropathic pain on the basis of the underlying neurobiological...

  4. Utility of molecular tests in cytopathology

    Directory of Open Access Journals (Sweden)

    Arthur David Somoza

    2014-01-01

    Full Text Available With the popularity of interventional radiology, diagnostic material obtained can be limited requiring critical decisions on making the best use of it. Molecular testing using nanogram amounts of tissue can add useful diagnostic information by improving sensitivity and/or specificity of the diagnosis. This review examines the use of molecular tests in cervical cytology, "indeterminate" thyroid cytology specimens, pancreatic cyst fluid, urinary tract and pulmonary adenocarcinoma cytologic material. Molecular human papillomavirus (HPV testing combined with cervical cytology increases sensitivity of detection of high grade lesions. In cytologically negative cases, the HPV negative predictive value endorses longer screening intervals. With the high prevalence of benign thyroid nodules, cytology plays a vital role in screening. However, 10-40% of the specimens obtained are cytologically indeterminate. Molecular analysis of these specimens can predict the malignant risk in these cases. Increased detection of pancreatic cysts has necessitated accurate pre-operative diagnosis delineating non-mucinous from mucinous cysts, which have a potential for progression to adenocarcinoma. Multimodal diagnosis of pancreatic cysts and molecular analysis help to clarify neoplastic risk; and in cases of limited fluid, may be the only available diagnostic information. Urothelial carcinoma (UC of the bladder, a common cancer with frequent recurrences, requires lifelong surveillance. The UroVysion ™ test kit can increase the sensitivity of detection of UC especially in cases of residual/recurrent carcinoma after therapy. Subsets of lung adenocarcinomas are now commonly targeted by therapies based on molecular mutation results of epidermal growth factor receptor, KRAS or echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase re-arrangements. The move toward standardization of reporting of cytology specimens commencing with cervical smears and more

  5. Polarimetric Synthetic Aperture Radar Image Classification by a Hybrid Method

    Institute of Scientific and Technical Information of China (English)

    Kamran Ullah Khan; YANG Jian

    2007-01-01

    Different methods proposed so far for accurate classification of land cover types in polarimetric synthetic aperture radar (SAR) image are data specific and no general method is available. A novel hybrid framework for this classification was developed in this work. A set of effective features derived from the coherence matrix of polarimetric SARdata was proposed.Constituents of the feature set are wavelet,texture,and nonlinear features.The proposed feature set has a strong discrimination power. A neural network was used as the classification engine in a unique way. By exploiting the speed of the conjugate gradient method and the convergence rate of the Levenberg-Marquardt method (near the optimal point), an overall speed up of the classification procedure was achieved. Principal component analysis(PCA)was used to shrink the dimension of the feature vector without sacrificing much of the classification accuracy. The proposed approach is compared with the maximum likelihood estimator (MLE)based on the complex Wishart distribution and the results show the superiority of the proposed method,with the average classification accuracy by the proposed method(95.4%)higher than that of the MLE(93.77%). Use of PCA to reduce the dimensionality of the feature vector helps reduce the memory requirements and computational cost, thereby enhancing the speed of the process.

  6. Exploiting multi-context analysis in semantic image classification

    Institute of Scientific and Technical Information of China (English)

    TIAN Yong-hong; HUANG Tie-jun; GAO Wen

    2005-01-01

    As the popularity of digital images is rapidly increasing on the Internet, research on technologies for semantic image classification has become an important research topic. However, the well-known content-based image classification methods do not overcome the so-called semantic gap problem in which low-level visual features cannot represent the high-level semantic content of images. Image classification using visual and textual information often performs poorly since the extracted textual features are often too limited to accurately represent the images. In this paper, we propose a semantic image classification approach using multi-context analysis. For a given image, we model the relevant textual information as its multi-modal context, and regard the related images connected by hyperlinks as its link context. Two kinds of context analysis models, i.e., cross-modal correlation analysis and link-based correlation model, are used to capture the correlation among different modals of features and the topical dependency among images induced by the link structure. We propose a new collective classification model called relational support vector classifier (RSVC) based on the well-known Support Vector Machines (SVMs) and the link-based correlation model. Experiments showed that the proposed approach significantly improved classification accuracy over that of SVM classifiers using visual and/or textual features.

  7. Fuzzy Aspect Based Opinion Classification System for Mining Tourist Reviews

    Directory of Open Access Journals (Sweden)

    Muhammad Afzaal

    2016-01-01

    Full Text Available Due to the large amount of opinions available on the websites, tourists are often overwhelmed with information and find it extremely difficult to use the available information to make a decision about the tourist places to visit. A number of opinion mining methods have been proposed in the past to identify and classify an opinion into positive or negative. Recently, aspect based opinion mining has been introduced which targets the various aspects present in the opinion text. A number of existing aspect based opinion classification methods are available in the literature but very limited research work has targeted the automatic aspect identification and extraction of implicit, infrequent, and coreferential aspects. Aspect based classification suffers from the presence of irrelevant sentences in a typical user review. Such sentences make the data noisy and degrade the classification accuracy of the machine learning algorithms. This paper presents a fuzzy aspect based opinion classification system which efficiently extracts aspects from user opinions and perform near to accurate classification. We conducted experiments on real world datasets to evaluate the effectiveness of our proposed system. Experimental results prove that the proposed system not only is effective in aspect extraction but also improves the classification accuracy.

  8. Prostate cancer heterogeneity: Discovering novel molecular targets for therapy.

    Science.gov (United States)

    Ciccarese, Chiara; Massari, Francesco; Iacovelli, Roberto; Fiorentino, Michelangelo; Montironi, Rodolfo; Di Nunno, Vincenzo; Giunchi, Francesca; Brunelli, Matteo; Tortora, Giampaolo

    2017-03-01

    Prostate cancer (PCa) shows a broad spectrum of biological and clinical behavior, which represents the epiphenomenon of an extreme genetic heterogeneity. Recent genomic profiling studies have deeply improved the knowledge of the genomic landscape of localized and metastatic PCa. The AR and PI3K/Akt/mTOR signaling pathways are the two most frequently altered, representing therefore interestingly targets for therapy. Moreover, somatic or germline aberrations of DNA repair genes (DRGs) have been observed at high frequency, supporting the potential role of platinum derivatives and PARP inhibitors as effective therapeutic strategies. In the future, the identification of driver mutations present at a specific stage of the disease, the classification PCa based on specific molecular alterations, and the selection of the most appropriate therapy based on biomarkers predictors of response represent the foundations for an increasingly more accurate personalized medicine.

  9. Accurate measurement of unsteady state fluid temperature

    Science.gov (United States)

    Jaremkiewicz, Magdalena

    2017-03-01

    In this paper, two accurate methods for determining the transient fluid temperature were presented. Measurements were conducted for boiling water since its temperature is known. At the beginning the thermometers are at the ambient temperature and next they are immediately immersed into saturated water. The measurements were carried out with two thermometers of different construction but with the same housing outer diameter equal to 15 mm. One of them is a K-type industrial thermometer widely available commercially. The temperature indicated by the thermometer was corrected considering the thermometers as the first or second order inertia devices. The new design of a thermometer was proposed and also used to measure the temperature of boiling water. Its characteristic feature is a cylinder-shaped housing with the sheath thermocouple located in its center. The temperature of the fluid was determined based on measurements taken in the axis of the solid cylindrical element (housing) using the inverse space marching method. Measurements of the transient temperature of the air flowing through the wind tunnel using the same thermometers were also carried out. The proposed measurement technique provides more accurate results compared with measurements using industrial thermometers in conjunction with simple temperature correction using the inertial thermometer model of the first or second order. By comparing the results, it was demonstrated that the new thermometer allows obtaining the fluid temperature much faster and with higher accuracy in comparison to the industrial thermometer. Accurate measurements of the fast changing fluid temperature are possible due to the low inertia thermometer and fast space marching method applied for solving the inverse heat conduction problem.

  10. Contribution of genosystematics to current concepts of phylogeny and classification of bryophytes.

    Science.gov (United States)

    Troitsky, A V; Ignatov, M S; Bobrova, V K; Milyutina, I A

    2007-12-01

    This paper is a survey of the current state of molecular studies on bryophyte phylogeny. Molecular data have greatly contributed to developing a phylogeny and classification of bryophytes. The previous traditional systems of classification based on morphological data are being significantly revised. New data of the authors are presented on phylogeny of Hypnales pleurocarpous mosses inferred from nucleotide sequence data of the nuclear DNA internal transcribed spacers ITS1-2 and the trnL-F region of the chloroplast genome.

  11. Niche Genetic Algorithm with Accurate Optimization Performance

    Institute of Scientific and Technical Information of China (English)

    LIU Jian-hua; YAN De-kun

    2005-01-01

    Based on crowding mechanism, a novel niche genetic algorithm was proposed which can record evolutionary direction dynamically during evolution. After evolution, the solutions's precision can be greatly improved by means of the local searching along the recorded direction. Simulation shows that this algorithm can not only keep population diversity but also find accurate solutions. Although using this method has to take more time compared with the standard GA, it is really worth applying to some cases that have to meet a demand for high solution precision.

  12. Accurate estimation of indoor travel times

    DEFF Research Database (Denmark)

    Prentow, Thor Siiger; Blunck, Henrik; Stisen, Allan

    2014-01-01

    the InTraTime method for accurately estimating indoor travel times via mining of historical and real-time indoor position traces. The method learns during operation both travel routes, travel times and their respective likelihood---both for routes traveled as well as for sub-routes thereof. In...... are collected within the building complex. Results indicate that InTraTime is superior with respect to metrics such as deployment cost, maintenance cost and estimation accuracy, yielding an average deviation from actual travel times of 11.7 %. This accuracy was achieved despite using a minimal-effort setup...

  13. Accurate diagnosis is essential for amebiasis

    Institute of Scientific and Technical Information of China (English)

    2004-01-01

    @@ Amebiasis is one of the three most common causes of death from parasitic disease, and Entamoeba histolytica is the most widely distributed parasites in the world. Particularly, Entamoeba histolytica infection in the developing countries is a significant health problem in amebiasis-endemic areas with a significant impact on infant mortality[1]. In recent years a world wide increase in the number of patients with amebiasis has refocused attention on this important infection. On the other hand, improving the quality of parasitological methods and widespread use of accurate tecniques have improved our knowledge about the disease.

  14. The first accurate description of an aurora

    Science.gov (United States)

    Schröder, Wilfried

    2006-12-01

    As technology has advanced, the scientific study of auroral phenomena has increased by leaps and bounds. A look back at the earliest descriptions of aurorae offers an interesting look into how medieval scholars viewed the subjects that we study.Although there are earlier fragmentary references in the literature, the first accurate description of the aurora borealis appears to be that published by the German Catholic scholar Konrad von Megenberg (1309-1374) in his book Das Buch der Natur (The Book of Nature). The book was written between 1349 and 1350.

  15. New law requires 'medically accurate' lesson plans.

    Science.gov (United States)

    1999-09-17

    The California Legislature has passed a bill requiring all textbooks and materials used to teach about AIDS be medically accurate and objective. Statements made within the curriculum must be supported by research conducted in compliance with scientific methods, and published in peer-reviewed journals. Some of the current lesson plans were found to contain scientifically unsupported and biased information. In addition, the bill requires material to be "free of racial, ethnic, or gender biases." The legislation is supported by a wide range of interests, but opposed by the California Right to Life Education Fund, because they believe it discredits abstinence-only material.

  16. Universality: Accurate Checks in Dyson's Hierarchical Model

    Science.gov (United States)

    Godina, J. J.; Meurice, Y.; Oktay, M. B.

    2003-06-01

    In this talk we present high-accuracy calculations of the susceptibility near βc for Dyson's hierarchical model in D = 3. Using linear fitting, we estimate the leading (γ) and subleading (Δ) exponents. Independent estimates are obtained by calculating the first two eigenvalues of the linearized renormalization group transformation. We found γ = 1.29914073 ± 10 -8 and, Δ = 0.4259469 ± 10-7 independently of the choice of local integration measure (Ising or Landau-Ginzburg). After a suitable rescaling, the approximate fixed points for a large class of local measure coincide accurately with a fixed point constructed by Koch and Wittwer.

  17. Decision Fusion Based on Hyperspectral and Multispectral Satellite Imagery for Accurate Forest Species Mapping

    Directory of Open Access Journals (Sweden)

    Dimitris G. Stavrakoudis

    2014-07-01

    Full Text Available This study investigates the effectiveness of combining multispectral very high resolution (VHR and hyperspectral satellite imagery through a decision fusion approach, for accurate forest species mapping. Initially, two fuzzy classifications are conducted, one for each satellite image, using a fuzzy output support vector machine (SVM. The classification result from the hyperspectral image is then resampled to the multispectral’s spatial resolution and the two sources are combined using a simple yet efficient fusion operator. Thus, the complementary information provided from the two sources is effectively exploited, without having to resort to computationally demanding and time-consuming typical data fusion or vector stacking approaches. The effectiveness of the proposed methodology is validated in a complex Mediterranean forest landscape, comprising spectrally similar and spatially intermingled species. The decision fusion scheme resulted in an accuracy increase of 8% compared to the classification using only the multispectral imagery, whereas the increase was even higher compared to the classification using only the hyperspectral satellite image. Perhaps most importantly, its accuracy was significantly higher than alternative multisource fusion approaches, although the latter are characterized by much higher computation, storage, and time requirements.

  18. Classification of LiDAR Data with Point Based Classification Methods

    Science.gov (United States)

    Yastikli, N.; Cetin, Z.

    2016-06-01

    LiDAR is one of the most effective systems for 3 dimensional (3D) data collection in wide areas. Nowadays, airborne LiDAR data is used frequently in various applications such as object extraction, 3D modelling, change detection and revision of maps with increasing point density and accuracy. The classification of the LiDAR points is the first step of LiDAR data processing chain and should be handled in proper way since the 3D city modelling, building extraction, DEM generation, etc. applications directly use the classified point clouds. The different classification methods can be seen in recent researches and most of researches work with the gridded LiDAR point cloud. In grid based data processing of the LiDAR data, the characteristic point loss in the LiDAR point cloud especially vegetation and buildings or losing height accuracy during the interpolation stage are inevitable. In this case, the possible solution is the use of the raw point cloud data for classification to avoid data and accuracy loss in gridding process. In this study, the point based classification possibilities of the LiDAR point cloud is investigated to obtain more accurate classes. The automatic point based approaches, which are based on hierarchical rules, have been proposed to achieve ground, building and vegetation classes using the raw LiDAR point cloud data. In proposed approaches, every single LiDAR point is analyzed according to their features such as height, multi-return, etc. then automatically assigned to the class which they belong to. The use of un-gridded point cloud in proposed point based classification process helped the determination of more realistic rule sets. The detailed parameter analyses have been performed to obtain the most appropriate parameters in the rule sets to achieve accurate classes. The hierarchical rule sets were created for proposed Approach 1 (using selected spatial-based and echo-based features) and Approach 2 (using only selected spatial-based features

  19. Accurate, noninvasive detection of Helicobacter pylori DNA from stool samples: potential usefulness for monitoring treatment.

    Science.gov (United States)

    Shuber, Anthony P; Ascaño, Jennifer J; Boynton, Kevin A; Mitchell, Anastasia; Frierson, Henry F; El-Rifai, Wa'el; Powell, Steven M

    2002-01-01

    A novel DNA assay demonstrating sensitive and accurate detection of Helicobacter pylori from stool samples is reported. Moreover, in three individuals tested for therapeutic response, the assay showed the disappearance of H. pylori DNA during treatment. Thus, this noninvasive molecular biology-based assay has the potential to be a powerful diagnostic tool given its ability to specifically identify H. pylori DNA.

  20. Accurate, Noninvasive Detection of Helicobacter pylori DNA from Stool Samples: Potential Usefulness for Monitoring Treatment

    OpenAIRE

    Shuber, Anthony P; Ascaño, Jennifer J.; Boynton, Kevin A.; Mitchell, Anastasia; Frierson, Henry F.; El-Rifai, Wa’el; Powell, Steven M

    2002-01-01

    A novel DNA assay demonstrating sensitive and accurate detection of Helicobacter pylori from stool samples is reported. Moreover, in three individuals tested for therapeutic response, the assay showed the disappearance of H. pylori DNA during treatment. Thus, this noninvasive molecular biology-based assay has the potential to be a powerful diagnostic tool given its ability to specifically identify H. pylori DNA.

  1. How Accurately can we Calculate Thermal Systems?

    Energy Technology Data Exchange (ETDEWEB)

    Cullen, D; Blomquist, R N; Dean, C; Heinrichs, D; Kalugin, M A; Lee, M; Lee, Y; MacFarlan, R; Nagaya, Y; Trkov, A

    2004-04-20

    I would like to determine how accurately a variety of neutron transport code packages (code and cross section libraries) can calculate simple integral parameters, such as K{sub eff}, for systems that are sensitive to thermal neutron scattering. Since we will only consider theoretical systems, we cannot really determine absolute accuracy compared to any real system. Therefore rather than accuracy, it would be more precise to say that I would like to determine the spread in answers that we obtain from a variety of code packages. This spread should serve as an excellent indicator of how accurately we can really model and calculate such systems today. Hopefully, eventually this will lead to improvements in both our codes and the thermal scattering models that they use in the future. In order to accomplish this I propose a number of extremely simple systems that involve thermal neutron scattering that can be easily modeled and calculated by a variety of neutron transport codes. These are theoretical systems designed to emphasize the effects of thermal scattering, since that is what we are interested in studying. I have attempted to keep these systems very simple, and yet at the same time they include most, if not all, of the important thermal scattering effects encountered in a large, water-moderated, uranium fueled thermal system, i.e., our typical thermal reactors.

  2. Accurate pattern registration for integrated circuit tomography

    Energy Technology Data Exchange (ETDEWEB)

    Levine, Zachary H.; Grantham, Steven; Neogi, Suneeta; Frigo, Sean P.; McNulty, Ian; Retsch, Cornelia C.; Wang, Yuxin; Lucatorto, Thomas B.

    2001-07-15

    As part of an effort to develop high resolution microtomography for engineered structures, a two-level copper integrated circuit interconnect was imaged using 1.83 keV x rays at 14 angles employing a full-field Fresnel zone plate microscope. A major requirement for high resolution microtomography is the accurate registration of the reference axes in each of the many views needed for a reconstruction. A reconstruction with 100 nm resolution would require registration accuracy of 30 nm or better. This work demonstrates that even images that have strong interference fringes can be used to obtain accurate fiducials through the use of Radon transforms. We show that we are able to locate the coordinates of the rectilinear circuit patterns to 28 nm. The procedure is validated by agreement between an x-ray parallax measurement of 1.41{+-}0.17 {mu}m and a measurement of 1.58{+-}0.08 {mu}m from a scanning electron microscope image of a cross section.

  3. Accurate determination of characteristic relative permeability curves

    Science.gov (United States)

    Krause, Michael H.; Benson, Sally M.

    2015-09-01

    A recently developed technique to accurately characterize sub-core scale heterogeneity is applied to investigate the factors responsible for flowrate-dependent effective relative permeability curves measured on core samples in the laboratory. The dependency of laboratory measured relative permeability on flowrate has long been both supported and challenged by a number of investigators. Studies have shown that this apparent flowrate dependency is a result of both sub-core scale heterogeneity and outlet boundary effects. However this has only been demonstrated numerically for highly simplified models of porous media. In this paper, flowrate dependency of effective relative permeability is demonstrated using two rock cores, a Berea Sandstone and a heterogeneous sandstone from the Otway Basin Pilot Project in Australia. Numerical simulations of steady-state coreflooding experiments are conducted at a number of injection rates using a single set of input characteristic relative permeability curves. Effective relative permeability is then calculated from the simulation data using standard interpretation methods for calculating relative permeability from steady-state tests. Results show that simplified approaches may be used to determine flowrate-independent characteristic relative permeability provided flow rate is sufficiently high, and the core heterogeneity is relatively low. It is also shown that characteristic relative permeability can be determined at any typical flowrate, and even for geologically complex models, when using accurate three-dimensional models.

  4. Accurate pose estimation for forensic identification

    Science.gov (United States)

    Merckx, Gert; Hermans, Jeroen; Vandermeulen, Dirk

    2010-04-01

    In forensic authentication, one aims to identify the perpetrator among a series of suspects or distractors. A fundamental problem in any recognition system that aims for identification of subjects in a natural scene is the lack of constrains on viewing and imaging conditions. In forensic applications, identification proves even more challenging, since most surveillance footage is of abysmal quality. In this context, robust methods for pose estimation are paramount. In this paper we will therefore present a new pose estimation strategy for very low quality footage. Our approach uses 3D-2D registration of a textured 3D face model with the surveillance image to obtain accurate far field pose alignment. Starting from an inaccurate initial estimate, the technique uses novel similarity measures based on the monogenic signal to guide a pose optimization process. We will illustrate the descriptive strength of the introduced similarity measures by using them directly as a recognition metric. Through validation, using both real and synthetic surveillance footage, our pose estimation method is shown to be accurate, and robust to lighting changes and image degradation.

  5. Accurate taxonomic assignment of short pyrosequencing reads.

    Science.gov (United States)

    Clemente, José C; Jansson, Jesper; Valiente, Gabriel

    2010-01-01

    Ambiguities in the taxonomy dependent assignment of pyrosequencing reads are usually resolved by mapping each read to the lowest common ancestor in a reference taxonomy of all those sequences that match the read. This conservative approach has the drawback of mapping a read to a possibly large clade that may also contain many sequences not matching the read. A more accurate taxonomic assignment of short reads can be made by mapping each read to the node in the reference taxonomy that provides the best precision and recall. We show that given a suffix array for the sequences in the reference taxonomy, a short read can be mapped to the node of the reference taxonomy with the best combined value of precision and recall in time linear in the size of the taxonomy subtree rooted at the lowest common ancestor of the matching sequences. An accurate taxonomic assignment of short reads can thus be made with about the same efficiency as when mapping each read to the lowest common ancestor of all matching sequences in a reference taxonomy. We demonstrate the effectiveness of our approach on several metagenomic datasets of marine and gut microbiota.

  6. Sequence Classification: 893607 [

    Lifescience Database Archive (English)

    Full Text Available ial component of the MIND kinetochore complex (Mtw1p Including Nnf1p-Nsl1p-Dsn1p) which joins kinetochore subunits contact...ing DNA to those contacting microtubules; required for accurate chromosome segregation; Nsl1p || http://www.ncbi.nlm.nih.gov/protein/6325023 ...

  7. Sequence Classification: 894861 [

    Lifescience Database Archive (English)

    Full Text Available ial component of the MIND kinetochore complex (Mtw1p Including Nnf1p-Nsl1p-Dsn1p) which joins kinetochore subunits contact...ing DNA to those contacting microtubules; required for accurate chromosome segregation; Nnf1p || http://www.ncbi.nlm.nih.gov/protein/6322572 ...

  8. Identification of Microorganisms by High Resolution Tandem Mass Spectrometry with Accurate Statistical Significance

    Science.gov (United States)

    Alves, Gelio; Wang, Guanghui; Ogurtsov, Aleksey Y.; Drake, Steven K.; Gucek, Marjan; Suffredini, Anthony F.; Sacks, David B.; Yu, Yi-Kuo

    2016-02-01

    Correct and rapid identification of microorganisms is the key to the success of many important applications in health and safety, including, but not limited to, infection treatment, food safety, and biodefense. With the advance of mass spectrometry (MS) technology, the speed of identification can be greatly improved. However, the increasing number of microbes sequenced is challenging correct microbial identification because of the large number of choices present. To properly disentangle candidate microbes, one needs to go beyond apparent morphology or simple `fingerprinting'; to correctly prioritize the candidate microbes, one needs to have accurate statistical significance in microbial identification. We meet these challenges by using peptidome profiles of microbes to better separate them and by designing an analysis method that yields accurate statistical significance. Here, we present an analysis pipeline that uses tandem MS (MS/MS) spectra for microbial identification or classification. We have demonstrated, using MS/MS data of 81 samples, each composed of a single known microorganism, that the proposed pipeline can correctly identify microorganisms at least at the genus and species levels. We have also shown that the proposed pipeline computes accurate statistical significances, i.e., E-values for identified peptides and unified E-values for identified microorganisms. The proposed analysis pipeline has been implemented in MiCId, a freely available software for Microorganism Classification and Identification. MiCId is available for download at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html.

  9. 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...

  10. SPORT FOOD ADDITIVE CLASSIFICATION

    Directory of Open Access Journals (Sweden)

    I. P. Prokopenko

    2015-01-01

    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.

  11. [Classification of headache disorders].

    Science.gov (United States)

    Heinze, A; Heinze-Kuhn, K; Göbel, H

    2007-06-01

    In 2003 the International Headache Society (IHS) published the second edition of the International Classification of Headache Disorders. Diagnostic criteria for no less than 206 separate headache diagnoses are presented in the parts (I) primary headaches, (II) secondary headaches and (III) cranial neuralgia, central and primary facial pain. The headaches are classified according to the etiology in case of the secondary headaches and according to the phenomenology in case of the primary headaches. It is the task of the headache specialist to identify the correct headache diagnose with the smallest effort possible. Both, the differentiation between secondary and primary headaches and the differentiation between the various primary headaches are of equal importance.

  12. Classification of smooth Fano polytopes

    DEFF Research Database (Denmark)

    Øbro, Mikkel

    Fano polytopes up to isomorphism. A smooth Fano -polytope can have at most vertices. In case of vertices an explicit classification is known. The thesis contains the classification in case of vertices. Classifications of smooth Fano -polytopes for fixed exist only for . In the thesis an algorithm...... for the classification of smooth Fano -polytopes for any given is presented. The algorithm has been implemented and used to obtain the complete classification for .......A simplicial lattice polytope containing the origin in the interior is called a smooth Fano polytope, if the vertices of every facet is a basis of the lattice. The study of smooth Fano polytopes is motivated by their connection to toric varieties. The thesis concerns the classification of smooth...

  13. Link prediction boosted psychiatry disorder classification for functional connectivity network

    Science.gov (United States)

    Li, Weiwei; Mei, Xue; Wang, Hao; Zhou, Yu; Huang, Jiashuang

    2017-02-01

    Functional connectivity network (FCN) is an effective tool in psychiatry disorders classification, and represents cross-correlation of the regional blood oxygenation level dependent signal. However, FCN is often incomplete for suffering from missing and spurious edges. To accurate classify psychiatry disorders and health control with the incomplete FCN, we first `repair' the FCN with link prediction, and then exact the clustering coefficients as features to build a weak classifier for every FCN. Finally, we apply a boosting algorithm to combine these weak classifiers for improving classification accuracy. Our method tested by three datasets of psychiatry disorder, including Alzheimer's Disease, Schizophrenia and Attention Deficit Hyperactivity Disorder. The experimental results show our method not only significantly improves the classification accuracy, but also efficiently reconstructs the incomplete FCN.

  14. Hierarchical Maximum Margin Learning for Multi-Class Classification

    CERN Document Server

    Yang, Jian-Bo

    2012-01-01

    Due to myriads of classes, designing accurate and efficient classifiers becomes very challenging for multi-class classification. Recent research has shown that class structure learning can greatly facilitate multi-class learning. In this paper, we propose a novel method to learn the class structure for multi-class classification problems. The class structure is assumed to be a binary hierarchical tree. To learn such a tree, we propose a maximum separating margin method to determine the child nodes of any internal node. The proposed method ensures that two classgroups represented by any two sibling nodes are most separable. In the experiments, we evaluate the accuracy and efficiency of the proposed method over other multi-class classification methods on real world large-scale problems. The results show that the proposed method outperforms benchmark methods in terms of accuracy for most datasets and performs comparably with other class structure learning methods in terms of efficiency for all datasets.

  15. AdaBoost for Improved Voice-Band Signal Classification

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A good voice-band signal classification can not only enable the safe application of speech coding techniques,the implementation of a Digital Signal Interpolation (DSI)system, but also facilitate network administration and planning by providing accurate voice-band traffic analysis.A new method is proposed to detect and classify the presence of various voice-band signals on the General Switched Telephone Network ( GSTN ). The method uses a combination of simple base classifiers through the AdaBoost algorithm. The conventional classification features for voiceband data classification are combined and optimized by the AdaBoost algorithm and spectral subtraction method.Experiments show the simpleness, effectiveness, efficiency and flexibility of the method.

  16. Classification of Pulse Waveforms Using Edit Distance with Real Penalty

    Directory of Open Access Journals (Sweden)

    Zhang Dongyu

    2010-01-01

    Full Text Available Abstract Advances in sensor and signal processing techniques have provided effective tools for quantitative research in traditional Chinese pulse diagnosis (TCPD. Because of the inevitable intraclass variation of pulse patterns, the automatic classification of pulse waveforms has remained a difficult problem. In this paper, by referring to the edit distance with real penalty (ERP and the recent progress in -nearest neighbors (KNN classifiers, we propose two novel ERP-based KNN classifiers. Taking advantage of the metric property of ERP, we first develop an ERP-induced inner product and a Gaussian ERP kernel, then embed them into difference-weighted KNN classifiers, and finally develop two novel classifiers for pulse waveform classification. The experimental results show that the proposed classifiers are effective for accurate classification of pulse waveform.

  17. Combinatorial Approach of Associative Classification

    OpenAIRE

    P. R. Pal; R.C. Jain

    2010-01-01

    Association rule mining and classification are two important techniques of data mining in knowledge discovery process. Integration of these two has produced class association rule mining or associative classification techniques, which in many cases have shown better classification accuracy than conventional classifiers. Motivated by this study we have explored and applied the combinatorial mathematics in class association rule mining in this paper. Our algorithm is based on producing co...

  18. The future of general classification

    DEFF Research Database (Denmark)

    Mai, Jens Erik

    2013-01-01

    Discusses problems related to accessing multiple collections using a single retrieval language. Surveys the concepts of interoperability and switching language. Finds that mapping between more indexing languages always will be an approximation. Surveys the issues related to general classification...... and contrasts that to special classifications. Argues for the use of general classifications to provide access to collections nationally and internationally. © 2003 by The Haworth Press, Inc. All rights reserved....

  19. A Classification Leveraged Object Detector

    OpenAIRE

    Sun, Miao; Han, Tony X.; He, Zhihai

    2016-01-01

    Currently, the state-of-the-art image classification algorithms outperform the best available object detector by a big margin in terms of average precision. We, therefore, propose a simple yet principled approach that allows us to leverage object detection through image classification on supporting regions specified by a preliminary object detector. Using a simple bag-of- words model based image classification algorithm, we leveraged the performance of the deformable model objector from 35.9%...

  20. A new classification of glaucomas

    Directory of Open Access Journals (Sweden)

    Bordeianu CD

    2014-09-01

    Full Text Available Constantin-Dan Bordeianu Private Practice, Ploiesti, Prahova, Romania Purpose: To suggest a new glaucoma classification that is pathogenic, etiologic, and clinical.Methods: After discussing the logical pathway used in criteria selection, the paper presents the new classification and compares it with the classification currently in use, that is, the one issued by the European Glaucoma Society in 2008.Results: The paper proves that the new classification is clear (being based on a coherent and consistently followed set of criteria, is comprehensive (framing all forms of glaucoma, and helps in understanding the sickness understanding (in that it uses a logical framing system. The great advantage is that it facilitates therapeutic decision making in that it offers direct therapeutic suggestions and avoids errors leading to disasters. Moreover, the scheme remains open to any new development.Conclusion: The suggested classification is a pathogenic, etiologic, and clinical classification that fulfills the conditions of an ideal classification. The suggested classification is the first classification in which the main criterion is consistently used for the first 5 to 7 crossings until its differentiation capabilities are exhausted. Then, secondary criteria (etiologic and clinical pick up the relay until each form finds its logical place in the scheme. In order to avoid unclear aspects, the genetic criterion is no longer used, being replaced by age, one of the clinical criteria. The suggested classification brings only benefits to all categories of ophthalmologists: the beginners will have a tool to better understand the sickness and to ease their decision making, whereas the experienced doctors will have their practice simplified. For all doctors, errors leading to therapeutic disasters will be less likely to happen. Finally, researchers will have the object of their work gathered in the group of glaucoma with unknown or uncertain pathogenesis, whereas

  1. Toward Accurate and Quantitative Comparative Metagenomics

    Science.gov (United States)

    Nayfach, Stephen; Pollard, Katherine S.

    2016-01-01

    Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341

  2. Apparatus for accurately measuring high temperatures

    Science.gov (United States)

    Smith, D.D.

    The present invention is a thermometer used for measuring furnace temperatures in the range of about 1800/sup 0/ to 2700/sup 0/C. The thermometer comprises a broadband multicolor thermal radiation sensor positioned to be in optical alignment with the end of a blackbody sight tube extending into the furnace. A valve-shutter arrangement is positioned between the radiation sensor and the sight tube and a chamber for containing a charge of high pressure gas is positioned between the valve-shutter arrangement and the radiation sensor. A momentary opening of the valve shutter arrangement allows a pulse of the high gas to purge the sight tube of air-borne thermal radiation contaminants which permits the radiation sensor to accurately measure the thermal radiation emanating from the end of the sight tube.

  3. Accurate renormalization group analyses in neutrino sector

    Energy Technology Data Exchange (ETDEWEB)

    Haba, Naoyuki [Graduate School of Science and Engineering, Shimane University, Matsue 690-8504 (Japan); Kaneta, Kunio [Kavli IPMU (WPI), The University of Tokyo, Kashiwa, Chiba 277-8568 (Japan); Takahashi, Ryo [Graduate School of Science and Engineering, Shimane University, Matsue 690-8504 (Japan); Yamaguchi, Yuya [Department of Physics, Faculty of Science, Hokkaido University, Sapporo 060-0810 (Japan)

    2014-08-15

    We investigate accurate renormalization group analyses in neutrino sector between ν-oscillation and seesaw energy scales. We consider decoupling effects of top quark and Higgs boson on the renormalization group equations of light neutrino mass matrix. Since the decoupling effects are given in the standard model scale and independent of high energy physics, our method can basically apply to any models beyond the standard model. We find that the decoupling effects of Higgs boson are negligible, while those of top quark are not. Particularly, the decoupling effects of top quark affect neutrino mass eigenvalues, which are important for analyzing predictions such as mass squared differences and neutrinoless double beta decay in an underlying theory existing at high energy scale.

  4. CLASSIFICATION OF CRIMINAL GROUPS

    Directory of Open Access Journals (Sweden)

    Natalia Romanova

    2013-06-01

    Full Text Available 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 criminal group, method of testing the members of the criminal group and method of observation. As a result of the conducted research, we have created a new classification of criminal groups. The first type is a lawful group in its form and criminal according to its content (i.e., its target is criminal enrichment. The second type is a criminal organization which is run by so-called "white-collars" that "remain in the shadow". The third type is traditional criminal groups.  The fourth type is the criminal group, which openly demonstrates its criminal activity.

  5. Supply chain planning classification

    Science.gov (United States)

    Hvolby, Hans-Henrik; Trienekens, Jacques; Bonde, Hans

    2001-10-01

    Industry experience a need to shift in focus from internal production planning towards planning in the supply network. In this respect customer oriented thinking becomes almost a common good amongst companies in the supply network. An increase in the use of information technology is needed to enable companies to better tune their production planning with customers and suppliers. Information technology opportunities and supply chain planning systems facilitate companies to monitor and control their supplier network. In spite if these developments, most links in today's supply chains make individual plans, because the real demand information is not available throughout the chain. The current systems and processes of the supply chains are not designed to meet the requirements now placed upon them. For long term relationships with suppliers and customers, an integrated decision-making process is needed in order to obtain a satisfactory result for all parties. Especially when customized production and short lead-time is in focus. An effective value chain makes inventory available and visible among the value chain members, minimizes response time and optimizes total inventory value held throughout the chain. In this paper a supply chain planning classification grid is presented based current manufacturing classifications and supply chain planning initiatives.

  6. PSC: protein surface classification.

    Science.gov (United States)

    Tseng, Yan Yuan; Li, Wen-Hsiung

    2012-07-01

    We recently proposed to classify proteins by their functional surfaces. Using the structural attributes of functional surfaces, we inferred the pairwise relationships of proteins and constructed an expandable database of protein surface classification (PSC). As the functional surface(s) of a protein is the local region where the protein performs its function, our classification may reflect the functional relationships among proteins. Currently, PSC contains a library of 1974 surface types that include 25,857 functional surfaces identified from 24,170 bound structures. The search tool in PSC empowers users to explore related surfaces that share similar local structures and core functions. Each functional surface is characterized by structural attributes, which are geometric, physicochemical or evolutionary features. The attributes have been normalized as descriptors and integrated to produce a profile for each functional surface in PSC. In addition, binding ligands are recorded for comparisons among homologs. PSC allows users to exploit related binding surfaces to reveal the changes in functionally important residues on homologs that have led to functional divergence during evolution. The substitutions at the key residues of a spatial pattern may determine the functional evolution of a protein. In PSC (http://pocket.uchicago.edu/psc/), a pool of changes in residues on similar functional surfaces is provided.

  7. Holistic facial expression classification

    Science.gov (United States)

    Ghent, John; McDonald, J.

    2005-06-01

    This paper details a procedure for classifying facial expressions. This is a growing and relatively new type of problem within computer vision. One of the fundamental problems when classifying facial expressions in previous approaches is the lack of a consistent method of measuring expression. This paper solves this problem by the computation of the Facial Expression Shape Model (FESM). This statistical model of facial expression is based on an anatomical analysis of facial expression called the Facial Action Coding System (FACS). We use the term Action Unit (AU) to describe a movement of one or more muscles of the face and all expressions can be described using the AU's described by FACS. The shape model is calculated by marking the face with 122 landmark points. We use Principal Component Analysis (PCA) to analyse how the landmark points move with respect to each other and to lower the dimensionality of the problem. Using the FESM in conjunction with Support Vector Machines (SVM) we classify facial expressions. SVMs are a powerful machine learning technique based on optimisation theory. This project is largely concerned with statistical models, machine learning techniques and psychological tools used in the classification of facial expression. This holistic approach to expression classification provides a means for a level of interaction with a computer that is a significant step forward in human-computer interaction.

  8. Accurate Weather Forecasting for Radio Astronomy

    Science.gov (United States)

    Maddalena, Ronald J.

    2010-01-01

    The NRAO Green Bank Telescope routinely observes at wavelengths from 3 mm to 1 m. As with all mm-wave telescopes, observing conditions depend upon the variable atmospheric water content. The site provides over 100 days/yr when opacities are low enough for good observing at 3 mm, but winds on the open-air structure reduce the time suitable for 3-mm observing where pointing is critical. Thus, to maximum productivity the observing wavelength needs to match weather conditions. For 6 years the telescope has used a dynamic scheduling system (recently upgraded; www.gb.nrao.edu/DSS) that requires accurate multi-day forecasts for winds and opacities. Since opacity forecasts are not provided by the National Weather Services (NWS), I have developed an automated system that takes available forecasts, derives forecasted opacities, and deploys the results on the web in user-friendly graphical overviews (www.gb.nrao.edu/ rmaddale/Weather). The system relies on the "North American Mesoscale" models, which are updated by the NWS every 6 hrs, have a 12 km horizontal resolution, 1 hr temporal resolution, run to 84 hrs, and have 60 vertical layers that extend to 20 km. Each forecast consists of a time series of ground conditions, cloud coverage, etc, and, most importantly, temperature, pressure, humidity as a function of height. I use the Liebe's MWP model (Radio Science, 20, 1069, 1985) to determine the absorption in each layer for each hour for 30 observing wavelengths. Radiative transfer provides, for each hour and wavelength, the total opacity and the radio brightness of the atmosphere, which contributes substantially at some wavelengths to Tsys and the observational noise. Comparisons of measured and forecasted Tsys at 22.2 and 44 GHz imply that the forecasted opacities are good to about 0.01 Nepers, which is sufficient for forecasting and accurate calibration. Reliability is high out to 2 days and degrades slowly for longer-range forecasts.

  9. Homotopy Classification of Multiaxial Actions

    CERN Document Server

    Cappell, Sylvain; Yan, Min

    2011-01-01

    A U(n)-manifold is multiaxial if the isotropy groups are always conjugate to unitary subgroups. The classification and the concordance of such manifolds have been studied by Davis, Hsiang and Morgan under much more strict conditions. We show that in general, without much extra condition, the homotopy classification of multiaxial manifolds can be split into a direct sum of the classification of pairs of adjacent strata, which can be computed by the classical surgery theory. Moreover, we also compute the homotopy classification for the case of the standard representation sphere. We also present the result for the similar multiaxial Sp(n)-manifolds.

  10. IMAGE RECONSTRUCTION AND OBJECT CLASSIFICATION IN CT IMAGING SYSTEM

    Institute of Scientific and Technical Information of China (English)

    张晓明; 蒋大真; 等

    1995-01-01

    By obtaining a feasible filter function,reconstructed images can be got with linear interpolation and filtered backoprojection techniques.Considering the gray and spatial correlation neighbour informations of each pixel,a new supervised classification method is put forward for the reconstructed images,and an experiment with noise image is done,the result shows that the method is feasible and accurate compared with ideal phantoms.

  11. Reconstruction-classification method for quantitative photoacoustic tomography

    CERN Document Server

    Malone, Emma; Cox, Ben T; Arridge, Simon R

    2015-01-01

    We propose a combined reconstruction-classification method for simultaneously recovering absorption and scattering in turbid media from images of absorbed optical energy. This method exploits knowledge that optical parameters are determined by a limited number of classes to iteratively improve their estimate. Numerical experiments show that the proposed approach allows for accurate recovery of absorption and scattering in 2 and 3 dimensions, and delivers superior image quality with respect to traditional reconstruction-only approaches.

  12. Approaching system equilibrium with accurate or not accurate feedback information in a two-route system

    Science.gov (United States)

    Zhao, Xiao-mei; Xie, Dong-fan; Li, Qi

    2015-02-01

    With the development of intelligent transport system, advanced information feedback strategies have been developed to reduce traffic congestion and enhance the capacity. However, previous strategies provide accurate information to travelers and our simulation results show that accurate information brings negative effects, especially in delay case. Because travelers prefer to the best condition route with accurate information, and delayed information cannot reflect current traffic condition but past. Then travelers make wrong routing decisions, causing the decrease of the capacity and the increase of oscillations and the system deviating from the equilibrium. To avoid the negative effect, bounded rationality is taken into account by introducing a boundedly rational threshold BR. When difference between two routes is less than the BR, routes have equal probability to be chosen. The bounded rationality is helpful to improve the efficiency in terms of capacity, oscillation and the gap deviating from the system equilibrium.

  13. The European Clinical, Molecular, and Pathological (ECMP Criteria and the 2007/2008 Revisions of the World Health Organization for the Diagnosis, Classification, and Staging of Prefibrotic Myeloproliferative Neoplasms Carrying the JAK2V617F Mutation

    Directory of Open Access Journals (Sweden)

    Jan Jacques Michiels

    2014-09-01

    Full Text Available OBJECTIVE: The prefibrotic stages of JAK2V617F essential thrombocythemia (ET and JAK2V617F polycythemia vera (PV can easily be diagnosed clinically without use of bone marrow biopsy histology. We assessed the 2008 WHO and European Clinical, Molecular, and Pathological (ECMP criteria for the diagnosis of myeloproliferative neoplasms (MPNs. METHODS: Studied patients included 6 JAK2V617F-mutated ET and 4 PV patients during long-term follow-up in view of critical analysis of the literature. The bone marrow biopsy histology diagnosis without use of clinical data was PV in 7 (of which 3 were cases of ET with features of early prodromal PV and classical PV in 4. RESULTS: The ECMP criteria distinguish 3 sequential phenotypes (1, 2, or 3 of JAK2V617F-mutated ET: normocellular ET-1; ET-2, with clinical and bone marrow features of PV (prodromal PV, and ET-3, with hypercellular dysmorphic megakaryocytic and granulocytic myeloproliferation (ET.MGM. The 3 patients with ET-2 or prodromal PV developed slow-onset PV after a follow-up of about 10 years. Bone marrow biopsy histology differentiates MPNs of various molecular etiologies from all variants of primary or secondary erythrocytoses and thrombocytoses with sensitivity and specificity of near 100%. CONCLUSION: Normocellular ET (WHO-ET, prodromal PV, and classical PV show overlapping bone marrow biopsy histology features with similar pleomorphic clustered megakaryocytes in the prefibrotic stages of JAK2V617F mutated MPN. Erythrocytes are below 6x1012/L in normocellular ET and prodromal PV, and are consistently above 6x1012/L in classical PV and at the time of transition from prodromal PV into classical PV. Red cell count at a cut-off level of 6x1012/L separates ET from PV and obviates the need for red cell mass measurement when bone marrow histology and JAK2V617F mutation screening are included in the diagnostic work-up of MPNs.

  14. Accurate simulation of optical properties in dyes.

    Science.gov (United States)

    Jacquemin, Denis; Perpète, Eric A; Ciofini, Ilaria; Adamo, Carlo

    2009-02-17

    Since Antiquity, humans have produced and commercialized dyes. To this day, extraction of natural dyes often requires lengthy and costly procedures. In the 19th century, global markets and new industrial products drove a significant effort to synthesize artificial dyes, characterized by low production costs, huge quantities, and new optical properties (colors). Dyes that encompass classes of molecules absorbing in the UV-visible part of the electromagnetic spectrum now have a wider range of applications, including coloring (textiles, food, paintings), energy production (photovoltaic cells, OLEDs), or pharmaceuticals (diagnostics, drugs). Parallel to the growth in dye applications, researchers have increased their efforts to design and synthesize new dyes to customize absorption and emission properties. In particular, dyes containing one or more metallic centers allow for the construction of fairly sophisticated systems capable of selectively reacting to light of a given wavelength and behaving as molecular devices (photochemical molecular devices, PMDs).Theoretical tools able to predict and interpret the excited-state properties of organic and inorganic dyes allow for an efficient screening of photochemical centers. In this Account, we report recent developments defining a quantitative ab initio protocol (based on time-dependent density functional theory) for modeling dye spectral properties. In particular, we discuss the importance of several parameters, such as the methods used for electronic structure calculations, solvent effects, and statistical treatments. In addition, we illustrate the performance of such simulation tools through case studies. We also comment on current weak points of these methods and ways to improve them.

  15. [A accurate identification method for Chinese materia medica--systematic identification of Chinese materia medica].

    Science.gov (United States)

    Wang, Xue-Yong; Liao, Cai-Li; Liu, Si-Qi; Liu, Chun-Sheng; Shao, Ai-Juan; Huang, Lu-Qi

    2013-05-01

    This paper put forward a more accurate identification method for identification of Chinese materia medica (CMM), the systematic identification of Chinese materia medica (SICMM) , which might solve difficulties in CMM identification used the ordinary traditional ways. Concepts, mechanisms and methods of SICMM were systematically introduced and possibility was proved by experiments. The establishment of SICMM will solve problems in identification of Chinese materia medica not only in phenotypic characters like the mnorphous, microstructure, chemical constituents, but also further discovery evolution and classification of species, subspecies and population in medical plants. The establishment of SICMM will improve the development of identification of CMM and create a more extensive study space.

  16. Detection of Acanthamoeba on the ocular surface in a Spanish population using the Schirmer strip test: pathogenic potential, molecular classification and evaluation of the sensitivity to chlorhexidine and voriconazole of the isolated Acanthamoeba strains.

    Science.gov (United States)

    Rocha-Cabrera, Pedro; Reyes-Batlle, María; Martín-Navarro, Carmen María; Dorta-Gorrín, Alexis; López-Arencibia, Atteneri; Sifaoui, Ines; Martínez-Carretero, Enrique; Piñero, José E; Martín-Barrera, Fernando; Valladares, Basilio; Lorenzo-Morales, Jacob

    2015-08-01

    Pathogenic strains of Acanthamoeba are causative agents of a sight-threatening infection of the cornea known as Acanthamoeba keratitis, which is often associated with the misuse of contact lenses. However, there is still a question remaining to be answered, which is whether these micro-organisms are present on the ocular surface of healthy individuals. Therefore, the aim of this study was to determine the presence of Acanthamoeba on the ocular surface in healthy patients and also in those with other ocular surface infections. Sterile Schirmer test strips were used to collect samples from a group of patients who attended an ophthalmology consultation at the Hospital del Norte, Icod de los Vinos, Tenerife, Canary Islands. Most of the patients (46 individuals, 79.31  %) presented ocular surface pathologies such as blepharitis or conjunctivitis; the rest did not present any pathology. None of the patients included in the study wore contact lenses. The collected samples were cultured in 2  % non-nutrient agar plates and positive plates were then cultured in axenic conditions for further analyses. Molecular analysis classified all isolated strains as belonging to Acanthamoeba genotype tbl4, and osmotolerance and thermotolerance assays revealed that all strains were potentially pathogenic. Furthermore, all strains were assayed for sensitivity against voriconazole and chlorhexidine. Assays showed that both drugs were active against the tested strains. In conclusion, the Schirmer strip test is proposed as an effective tool for the detection of Acanthamoeba on the ocular surface.

  17. Automatically high accurate and efficient photomask defects management solution for advanced lithography manufacture

    Science.gov (United States)

    Zhu, Jun; Chen, Lijun; Ma, Lantao; Li, Dejian; Jiang, Wei; Pan, Lihong; Shen, Huiting; Jia, Hongmin; Hsiang, Chingyun; Cheng, Guojie; Ling, Li; Chen, Shijie; Wang, Jun; Liao, Wenkui; Zhang, Gary

    2014-04-01

    Defect review is a time consuming job. Human error makes result inconsistent. The defects located on don't care area would not hurt the yield and no need to review them such as defects on dark area. However, critical area defects can impact yield dramatically and need more attention to review them such as defects on clear area. With decrease in integrated circuit dimensions, mask defects are always thousands detected during inspection even more. Traditional manual or simple classification approaches are unable to meet efficient and accuracy requirement. This paper focuses on automatic defect management and classification solution using image output of Lasertec inspection equipment and Anchor pattern centric image process technology. The number of mask defect found during an inspection is always in the range of thousands or even more. This system can handle large number defects with quick and accurate defect classification result. Our experiment includes Die to Die and Single Die modes. The classification accuracy can reach 87.4% and 93.3%. No critical or printable defects are missing in our test cases. The missing classification defects are 0.25% and 0.24% in Die to Die mode and Single Die mode. This kind of missing rate is encouraging and acceptable to apply on production line. The result can be output and reloaded back to inspection machine to have further review. This step helps users to validate some unsure defects with clear and magnification images when captured images can't provide enough information to make judgment. This system effectively reduces expensive inline defect review time. As a fully inline automated defect management solution, the system could be compatible with current inspection approach and integrated with optical simulation even scoring function and guide wafer level defect inspection.

  18. Lubricant characterization by molecular simulation

    Energy Technology Data Exchange (ETDEWEB)

    Moore, J.D.; Cui, S.T.; Cummings, P.T.; Cochran, H.D. [Univ. of Tennessee, Knoxville, TN (United States). Dept. of Chemical Engineering]|[Oak Ridge National Lab., TN (United States). Chemical Technology Div.

    1997-12-01

    The authors have reported the calculation of the kinematic viscosity index of squalane from nonequilibrium molecular dynamics simulations. This represents the first accurate quantitative prediction of this measure of lubricant performance by molecular simulation. Using the same general alkane potential model, this computational approach offers the possibility of predicting the performance of potential lubricants prior to synthesis. Consequently, molecular simulation is poised to become an important tool for future lubricant development.

  19. 15 CFR 2008.9 - Classification guides.

    Science.gov (United States)

    2010-01-01

    ... 15 Commerce and Foreign Trade 3 2010-01-01 2010-01-01 false Classification guides. 2008.9 Section... REPRESENTATIVE Derivative Classification § 2008.9 Classification guides. Classification guides shall be issued by... direct derivative classification, shall identify the information to be protected in specific and...

  20. 32 CFR 2400.15 - Classification guides.

    Science.gov (United States)

    2010-07-01

    ... 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...

  1. 14 CFR 1203.412 - Classification guides.

    Science.gov (United States)

    2010-01-01

    ... 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...

  2. 7 CFR 27.34 - Classification procedure.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Classification procedure. 27.34 Section 27.34... REGULATIONS COTTON CLASSIFICATION UNDER COTTON FUTURES LEGISLATION Regulations Classification and Micronaire Determinations § 27.34 Classification procedure. Classification shall proceed as rapidly as possible, but...

  3. 22 CFR 9.6 - Derivative classification.

    Science.gov (United States)

    2010-04-01

    ... CFR 2001.22. (c) Department of State Classification Guide. The Department of State Classification... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Derivative classification. 9.6 Section 9.6... classification. (a) Definition. Derivative classification is the incorporating, paraphrasing, restating...

  4. Genotype phenotype classification of hepatocellular adenoma

    Institute of Scientific and Technical Information of China (English)

    Paulette Bioulac-Sage; Jean Frédéric Blanc; Sandra Rebouissou; Charles Balabaud; Jessica Zucman-Rossi

    2007-01-01

    Studies that compare tumor genotype with phenotype have provided the basis of a new histological/molecular classification of hepatocellular adenomas. Based on two molecular criteria (presence of a TCF1/HNF1α or β-catenin mutation), and an additional histological criterion (presence or absence of an inflammatory infiltrate), subgroups of hepatocellular adenoma can be defined and distinguished from focal nodular hyperplasia. Analysis of 96 hepatocellular adenomas performed by a French collaborative network showed that they can be divided into four broad subgroups: the first one is defined by the presence of mutations in TCF1 gene inactivating the hepatocyte nuclear factor 1 (HNF1α); the second by the presence of β-catenin activating mutations; the category without mutations of HNF1α or β-catenin is further divided into 2 subgroups depending on the presence or absence of inflammation. Therefore, the approach to the diagnosis of problematic benign hepatocytic nodules may be entering a new era directed by new molecular information. It is hoped that immunohistological tools will improve significantly diagnosis of liver biopsy in our ability to distinguish hepatocellular adenoma from focal nodular hyperplasia (FNH), and to delineate clinically meaningful entities within each group to define the best clinical management. The optimal care of patients with a liver nodule will benefit from the recent knowledge coming from molecular biology and the combined expertise of hepatologists, pathologists, radiologists, and surgeons.

  5. Transient Detection and Classification

    CERN Document Server

    Becker, Andrew C

    2008-01-01

    I provide an incomplete inventory of the astronomical variability that will be found by next-generation time-domain astronomical surveys. These phenomena span the distance range from near-Earth satellites to the farthest Gamma Ray Bursts. The surveys that detect these transients will issue alerts to the greater astronomical community; this decision process must be extremely robust to avoid a slew of ``false'' alerts, and to maintain the community's trust in the surveys. I review the functionality required of both the surveys and the telescope networks that will be following them up, and the role of VOEvents in this process. Finally, I offer some ideas about object and event classification, which will be explored more thoroughly by other articles in these proceedings.

  6. Nonlinear estimation and classification

    CERN Document Server

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

    2003-01-01

    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

  7. Estuary Classification Revisited

    CERN Document Server

    Guha, Anirban

    2012-01-01

    The governing equations of a tidally averaged, width averaged, rectangular estuary has been investigated. It's theoretically shown that the dynamics of an estuary is entirely controlled by three parameters: (i) the Estuarine Froude number, (ii) the Tidal Froude number and (iii) the Estuarine Aspect ratio. The momentum, salinity and integral salt balance equations can be completely expressed in terms of these control variables. The estuary classification problem has also been reinvestigated. It's found that these three control variables can completely specify the estuary type. Comparison with real estuary data shows very good match. Additionally, we show that the well accepted leading order estuarine integral salt balance equation is inconsitent with the leading order salinity equation in an order of magnitude sense.

  8. Automatic classification of protein structures using physicochemical parameters.

    Science.gov (United States)

    Mohan, Abhilash; Rao, M Divya; Sunderrajan, Shruthi; Pennathur, Gautam

    2014-09-01

    Protein classification is the first step to functional annotation; SCOP and Pfam databases are currently the most relevant protein classification schemes. However, the disproportion in the number of three dimensional (3D) protein structures generated versus their classification into relevant superfamilies/families emphasizes the need for automated classification schemes. Predicting function of novel proteins based on sequence information alone has proven to be a major challenge. The present study focuses on the use of physicochemical parameters in conjunction with machine learning algorithms (Naive Bayes, Decision Trees, Random Forest and Support Vector Machines) to classify proteins into their respective SCOP superfamily/Pfam family, using sequence derived information. Spectrophores™, a 1D descriptor of the 3D molecular field surrounding a structure was used as a benchmark to compare the performance of the physicochemical parameters. The machine learning algorithms were modified to select features based on information gain for each SCOP superfamily/Pfam family. The effect of combining physicochemical parameters and spectrophores on classification accuracy (CA) was studied. Machine learning algorithms trained with the physicochemical parameters consistently classified SCOP superfamilies and Pfam families with a classification accuracy above 90%, while spectrophores performed with a CA of around 85%. Feature selection improved classification accuracy for both physicochemical parameters and spectrophores based machine learning algorithms. Combining both attributes resulted in a marginal loss of performance. Physicochemical parameters were able to classify proteins from both schemes with classification accuracy ranging from 90-96%. These results suggest the usefulness of this method in classifying proteins from amino acid sequences.

  9. Invasive breast cancer molecular classification and the choice of adjuvant chemotherapy regimens%浸润性乳腺癌分子分型与辅助化疗方案选择

    Institute of Scientific and Technical Information of China (English)

    陈嘉健; 柳光宇

    2011-01-01

    随着基因表达谱与基因芯片技术的开展,乳腺癌在分子水平上表现出的高度异质性也逐渐受到关注.不同分子分型的乳腺癌,其流行病学危险因素、疾病自然进展过程以及对全身或局部治疗的反应性都不尽相同;对于乳腺癌的准确分型能够较为精确地反映肿瘤的生物学行为,对于判断预后、制定更具个体化的治疗策略具有深刻的意义.2011年的St.Gallen共识已针对不同的乳腺癌分子分型给出了原则性的治疗建议,标志着乳腺癌的治疗已逐步进入了在规范化多学科综合治疗模式的基础上,倡导个体化治疗的时代.%With the adoption and development of gene expression technique, the heterogeneity at the molecular level of the breast cancer has attracted attention gradually. The different breast cancer subtypes have different epidemiological risk factors, different natural histories and different responses to systemic and local therapies. To identify the exact subtype of the breast cancer has profound significance on making individualized therapies. The consensus of St. Gallen BreastCancer Conference 2011 has provided different treatment suggestions according to different subtypes, which indicates that the management of breast cancer has entered the age of advocating individualized treatment on the basis of the standardization multi-disciplinary treatment gradually.

  10. ATRX mRNA expression combined with IDH1/2 mutational status and Ki-67 expression refines the molecular classification of astrocytic tumors: evidence from the whole transcriptome sequencing of 169 samples samples.

    Science.gov (United States)

    Cai, Jinquan; Yang, Pei; Zhang, Chuanbao; Zhang, Wei; Liu, Yanwei; Bao, Zhaoshi; Liu, Xing; Du, Wenzhong; Wang, Hongjun; Jiang, Tao; Jiang, Chuanlu

    2014-05-15

    Astrocytic tumors are the most common primary brain tumors in adults. ATRX mutations have been identified in gliomas and are correlated with its loss of expression, which causes alternative lengthening of telomeres (ALT) leading to genomic instability. In this study, we aimed to explore the role of ATRX mRNA expression alteration in the progression and subclassification of astrocytic tumors and examine its impact on clinical outcome. We investigated ATRX mRNA expression and its association with IDH1 and IDH2 mutations in 169 adult astrocytic tumors using whole transcriptome sequencing. In our cohort, low ATRX mRNA expression was detected in 68% of astrocytomas, 50% of anaplastic astrocytomas and 41.6% of glioblastomas. Low ATRX expression closely overlapped with mutations in IDH1/2 (PATRX expression and longer overall survival was identified in our cohort (PATRX combined with IDH1/2 and Ki-67 was used to re-classify patients with astrocytic tumors: group A1 containing IDH1/2 mutations and low ATRX expression predicted a better prognostic outcome, whereas group A3 carrying wild-type IDH1/2 and high Ki-67 expression had the shortest overall survival; IDH-mutant tumors with low ATRX expression and IDH-wild-type tumors with high Ki-67 expression were grouped into group A2. In summary, our results showed that ATRX in cooperation with IDH1/2 and Ki-67 defines three subgroups of astrocytic tumors regardless of the conventional WHO grades consensus. The molecular stratification in astrocytic tumors may aid in treatment strategy selection, therapeutic trial design, and clinical prognosis evaluation.

  11. Toward Accurate Adsorption Energetics on Clay Surfaces

    CERN Document Server

    Zen, Andrea; Cox, Stephen J; Hu, Xiao L; Sorella, Sandro; Alfè, Dario; Michaelides, Angelos

    2016-01-01

    Clay minerals are ubiquitous in nature, and the manner in which they interact with their surroundings has important industrial and environmental implications. Consequently, a molecular-level understanding of the adsorption of molecules on clay surfaces is crucial. In this regard computer simulations play an important role, yet the accuracy of widely used empirical force fields (FF) and density functional theory (DFT) exchange-correlation functionals is often unclear in adsorption systems dominated by weak interactions. Herein we present results from quantum Monte Carlo (QMC) for water and methanol adsorption on the prototypical clay kaolinite. To the best of our knowledge, this is the first time QMC has been used to investigate adsorption at a complex, natural surface such as a clay. As well as being valuable in their own right, the QMC benchmarks obtained provide reference data against which the performance of cheaper DFT methods can be tested. Indeed using various DFT exchange-correlation functionals yields...

  12. Classification of Noncommutative Domain Algebras

    CERN Document Server

    Arias, Alvaro

    2012-01-01

    Noncommutative domain algebras are noncommutative analogues of the algebras of holomorphic functions on domains of $\\C^n$ defined by holomorphic polynomials, and they generalize the noncommutative Hardy algebras. We present here a complete classification of these algebras based upon techniques inspired by multivariate complex analysis, and more specifically the classification of domains in hermitian spaces up to biholomorphic equivalence.

  13. Classification of subtrochanteric femoral fractures.

    Science.gov (United States)

    Loizou, C L; McNamara, I; Ahmed, K; Pryor, G A; Parker, M J

    2010-07-01

    A review of the literature identified 15 different classification methods for subtrochanteric femoral fractures. Only eight of those classifications defined the area of bone, which constituted a subtrochanteric fracture. The actual length of femur defined as the subtrochanteric zone varied from 3 cm up to the level of the femoral isthmus. There was no agreement between the different classifications regarding the proximal and distal border or for those fractures, which traverse anatomical boundaries. In the various classifications, fractures were subdivided into 2-15 subgroups. The majority of the identified studies were unable to find the classifications useful in either determining treatment or predicting the outcome after treatment. We subdivided subtrochanteric fractures into three types based on the degree of fracture comminution. We examined the inter- and intra-observer agreement of our recommended classification. One orthopaedic consultant, one specialist hip fracture surgeon, two trainee registrar orthopaedic surgeons and one specialty trainee in orthopaedics, on two different occasions, 8 weeks apart, independently classified the radiographs of 20 patients with a subtrochanteric fracture. The mean kappa value for inter- and intra-observer variation was 0.71 and 0.79, respectively, with both showing substantial agreement and, therefore, this simpler classification is recommended. Based on the review of previous classification methods, we also recommend that the subtrochanteric zone be defined as the one in which the fracture line crossing the femur is predominantly within the area of bone extending 5 cm below the lower border of the lesser trochanter.

  14. Classification Accuracy Is Not Enough

    DEFF Research Database (Denmark)

    Sturm, Bob L.

    2013-01-01

    A recent review of the research literature evaluating music genre recognition (MGR) systems over the past two decades shows that most works (81\\%) measure the capacity of a system to recognize genre by its classification accuracy. We show here, by implementing and testing three categorically diff...... classification accuracy obscures the aim of MGR: to select labels indistinguishable from those a person would choose....

  15. Seismic texture classification. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Vinther, R.

    1997-12-31

    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)

  16. Fast and accurate exhaled breath ammonia measurement.

    Science.gov (United States)

    Solga, Steven F; Mudalel, Matthew L; Spacek, Lisa A; Risby, Terence H

    2014-06-11

    This exhaled breath ammonia method uses a fast and highly sensitive spectroscopic method known as quartz enhanced photoacoustic spectroscopy (QEPAS) that uses a quantum cascade based laser. The monitor is coupled to a sampler that measures mouth pressure and carbon dioxide. The system is temperature controlled and specifically designed to address the reactivity of this compound. The sampler provides immediate feedback to the subject and the technician on the quality of the breath effort. Together with the quick response time of the monitor, this system is capable of accurately measuring exhaled breath ammonia representative of deep lung systemic levels. Because the system is easy to use and produces real time results, it has enabled experiments to identify factors that influence measurements. For example, mouth rinse and oral pH reproducibly and significantly affect results and therefore must be controlled. Temperature and mode of breathing are other examples. As our understanding of these factors evolves, error is reduced, and clinical studies become more meaningful. This system is very reliable and individual measurements are inexpensive. The sampler is relatively inexpensive and quite portable, but the monitor is neither. This limits options for some clinical studies and provides rational for future innovations.

  17. Noninvasive hemoglobin monitoring: how accurate is enough?

    Science.gov (United States)

    Rice, Mark J; Gravenstein, Nikolaus; Morey, Timothy E

    2013-10-01

    Evaluating the accuracy of medical devices has traditionally been a blend of statistical analyses, at times without contextualizing the clinical application. There have been a number of recent publications on the accuracy of a continuous noninvasive hemoglobin measurement device, the Masimo Radical-7 Pulse Co-oximeter, focusing on the traditional statistical metrics of bias and precision. In this review, which contains material presented at the Innovations and Applications of Monitoring Perfusion, Oxygenation, and Ventilation (IAMPOV) Symposium at Yale University in 2012, we critically investigated these metrics as applied to the new technology, exploring what is required of a noninvasive hemoglobin monitor and whether the conventional statistics adequately answer our questions about clinical accuracy. We discuss the glucose error grid, well known in the glucose monitoring literature, and describe an analogous version for hemoglobin monitoring. This hemoglobin error grid can be used to evaluate the required clinical accuracy (±g/dL) of a hemoglobin measurement device to provide more conclusive evidence on whether to transfuse an individual patient. The important decision to transfuse a patient usually requires both an accurate hemoglobin measurement and a physiologic reason to elect transfusion. It is our opinion that the published accuracy data of the Masimo Radical-7 is not good enough to make the transfusion decision.

  18. Accurate fission data for nuclear safety

    CERN Document Server

    Solders, A; Jokinen, A; Kolhinen, V S; Lantz, M; Mattera, A; Penttila, H; Pomp, S; Rakopoulos, V; Rinta-Antila, S

    2013-01-01

    The Accurate fission data for nuclear safety (AlFONS) project aims at high precision measurements of fission yields, using the renewed IGISOL mass separator facility in combination with a new high current light ion cyclotron at the University of Jyvaskyla. The 30 MeV proton beam will be used to create fast and thermal neutron spectra for the study of neutron induced fission yields. Thanks to a series of mass separating elements, culminating with the JYFLTRAP Penning trap, it is possible to achieve a mass resolving power in the order of a few hundred thousands. In this paper we present the experimental setup and the design of a neutron converter target for IGISOL. The goal is to have a flexible design. For studies of exotic nuclei far from stability a high neutron flux (10^12 neutrons/s) at energies 1 - 30 MeV is desired while for reactor applications neutron spectra that resembles those of thermal and fast nuclear reactors are preferred. It is also desirable to be able to produce (semi-)monoenergetic neutrons...

  19. Towards Accurate Modeling of Moving Contact Lines

    CERN Document Server

    Holmgren, Hanna

    2015-01-01

    A main challenge in numerical simulations of moving contact line problems is that the adherence, or no-slip boundary condition leads to a non-integrable stress singularity at the contact line. In this report we perform the first steps in developing the macroscopic part of an accurate multiscale model for a moving contact line problem in two space dimensions. We assume that a micro model has been used to determine a relation between the contact angle and the contact line velocity. An intermediate region is introduced where an analytical expression for the velocity exists. This expression is used to implement boundary conditions for the moving contact line at a macroscopic scale, along a fictitious boundary located a small distance away from the physical boundary. Model problems where the shape of the interface is constant thought the simulation are introduced. For these problems, experiments show that the errors in the resulting contact line velocities converge with the grid size $h$ at a rate of convergence $...

  20. Does a pneumotach accurately characterize voice function?

    Science.gov (United States)

    Walters, Gage; Krane, Michael

    2016-11-01

    A study is presented which addresses how a pneumotach might adversely affect clinical measurements of voice function. A pneumotach is a device, typically a mask, worn over the mouth, in order to measure time-varying glottal volume flow. By measuring the time-varying difference in pressure across a known aerodynamic resistance element in the mask, the glottal volume flow waveform is estimated. Because it adds aerodynamic resistance to the vocal system, there is some concern that using a pneumotach may not accurately portray the behavior of the voice. To test this hypothesis, experiments were performed in a simplified airway model with the principal dimensions of an adult human upper airway. A compliant constriction, fabricated from silicone rubber, modeled the vocal folds. Variations of transglottal pressure, time-averaged volume flow, model vocal fold vibration amplitude, and radiated sound with subglottal pressure were performed, with and without the pneumotach in place, and differences noted. Acknowledge support of NIH Grant 2R01DC005642-10A1.

  1. Accurate lineshape spectroscopy and the Boltzmann constant.

    Science.gov (United States)

    Truong, G-W; Anstie, J D; May, E F; Stace, T M; Luiten, A N

    2015-10-14

    Spectroscopy has an illustrious history delivering serendipitous discoveries and providing a stringent testbed for new physical predictions, including applications from trace materials detection, to understanding the atmospheres of stars and planets, and even constraining cosmological models. Reaching fundamental-noise limits permits optimal extraction of spectroscopic information from an absorption measurement. Here, we demonstrate a quantum-limited spectrometer that delivers high-precision measurements of the absorption lineshape. These measurements yield a very accurate measurement of the excited-state (6P1/2) hyperfine splitting in Cs, and reveals a breakdown in the well-known Voigt spectral profile. We develop a theoretical model that accounts for this breakdown, explaining the observations to within the shot-noise limit. Our model enables us to infer the thermal velocity dispersion of the Cs vapour with an uncertainty of 35 p.p.m. within an hour. This allows us to determine a value for Boltzmann's constant with a precision of 6 p.p.m., and an uncertainty of 71 p.p.m.

  2. Accurate upper body rehabilitation system using kinect.

    Science.gov (United States)

    Sinha, Sanjana; Bhowmick, Brojeshwar; Chakravarty, Kingshuk; Sinha, Aniruddha; Das, Abhijit

    2016-08-01

    The growing importance of Kinect as a tool for clinical assessment and rehabilitation is due to its portability, low cost and markerless system for human motion capture. However, the accuracy of Kinect in measuring three-dimensional body joint center locations often fails to meet clinical standards of accuracy when compared to marker-based motion capture systems such as Vicon. The length of the body segment connecting any two joints, measured as the distance between three-dimensional Kinect skeleton joint coordinates, has been observed to vary with time. The orientation of the line connecting adjoining Kinect skeletal coordinates has also been seen to differ from the actual orientation of the physical body segment. Hence we have proposed an optimization method that utilizes Kinect Depth and RGB information to search for the joint center location that satisfies constraints on body segment length and as well as orientation. An experimental study have been carried out on ten healthy participants performing upper body range of motion exercises. The results report 72% reduction in body segment length variance and 2° improvement in Range of Motion (ROM) angle hence enabling to more accurate measurements for upper limb exercises.

  3. Accurate thermoplasmonic simulation of metallic nanoparticles

    Science.gov (United States)

    Yu, Da-Miao; Liu, Yan-Nan; Tian, Fa-Lin; Pan, Xiao-Min; Sheng, Xin-Qing

    2017-01-01

    Thermoplasmonics leads to enhanced heat generation due to the localized surface plasmon resonances. The measurement of heat generation is fundamentally a complicated task, which necessitates the development of theoretical simulation techniques. In this paper, an efficient and accurate numerical scheme is proposed for applications with complex metallic nanostructures. Light absorption and temperature increase are, respectively, obtained by solving the volume integral equation (VIE) and the steady-state heat diffusion equation through the method of moments (MoM). Previously, methods based on surface integral equations (SIEs) were utilized to obtain light absorption. However, computing light absorption from the equivalent current is as expensive as O(NsNv), where Ns and Nv, respectively, denote the number of surface and volumetric unknowns. Our approach reduces the cost to O(Nv) by using VIE. The accuracy, efficiency and capability of the proposed scheme are validated by multiple simulations. The simulations show that our proposed method is more efficient than the approach based on SIEs under comparable accuracy, especially for the case where many incidents are of interest. The simulations also indicate that the temperature profile can be tuned by several factors, such as the geometry configuration of array, beam direction, and light wavelength.

  4. Fast and Provably Accurate Bilateral Filtering.

    Science.gov (United States)

    Chaudhury, Kunal N; Dabhade, Swapnil D

    2016-06-01

    The bilateral filter is a non-linear filter that uses a range filter along with a spatial filter to perform edge-preserving smoothing of images. A direct computation of the bilateral filter requires O(S) operations per pixel, where S is the size of the support of the spatial filter. In this paper, we present a fast and provably accurate algorithm for approximating the bilateral filter when the range kernel is Gaussian. In particular, for box and Gaussian spatial filters, the proposed algorithm can cut down the complexity to O(1) per pixel for any arbitrary S . The algorithm has a simple implementation involving N+1 spatial filterings, where N is the approximation order. We give a detailed analysis of the filtering accuracy that can be achieved by the proposed approximation in relation to the target bilateral filter. This allows us to estimate the order N required to obtain a given accuracy. We also present comprehensive numerical results to demonstrate that the proposed algorithm is competitive with the state-of-the-art methods in terms of speed and accuracy.

  5. Sequence Classification: 386956 [

    Lifescience Database Archive (English)

    Full Text Available TMB Non-TMH TMB TMB Non-TMB Non-TMB >gi|31791467|ref|NP_853960.1| LOW MOLECULAR WEIGHT PROTEIN ANTI...GEN 7 CFP7 (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4) || http://www.ncbi.nlm.nih.gov/protein/31791467 ...

  6. Sequence Classification: 396671 [

    Lifescience Database Archive (English)

    Full Text Available TMB Non-TMH TMB TMB Non-TMB Non-TMB >gi|15607429|ref|NP_214802.1| LOW MOLECULAR WEIGHT PROTEIN ANTI...GEN 7 ESXH (10 kDa ANTIGEN) (CFP-7) (PROTEIN TB10.4) || http://www.ncbi.nlm.nih.gov/protein/15607429 ...

  7. Applications of feature selection. [development of classification algorithms for LANDSAT data

    Science.gov (United States)

    Guseman, L. F., Jr.

    1976-01-01

    The use of satellite-acquired (LANDSAT) multispectral scanner (MSS) data to conduct an inventory of some crop of economic interest such as wheat over a large geographical area is considered in relation to the development of accurate and efficient algorithms for data classification. The dimension of the measurement space and the computational load for a classification algorithm is increased by the use of multitemporal measurements. Feature selection/combination techniques used to reduce the dimensionality of the problem are described.

  8. Automatic Mining of Numerical Classification Rules with Parliamentary Optimization Algorithm

    Directory of Open Access Journals (Sweden)

    KIZILOLUK, S.

    2015-11-01

    Full Text Available In recent years, classification rules mining has been one of the most important data mining tasks. In this study, one of the newest social-based metaheuristic methods, Parliamentary Optimization Algorithm (POA, is firstly used for automatically mining of comprehensible and accurate classification rules within datasets which have numerical attributes. Four different numerical datasets have been selected from UCI data warehouse and classification rules of high quality have been obtained. Furthermore, the results obtained from designed POA have been compared with the results obtained from four different popular classification rules mining algorithms used in WEKA. Although POA is very new and no applications in complex data mining problems have been performed, the results seem promising. The used objective function is very flexible and many different objectives can easily be added to. The intervals of the numerical attributes in the rules have been automatically found without any a priori process, as done in other classification rules mining algorithms, which causes the modification of datasets.

  9. Agent Collaborative Target Localization and Classification in Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Sheng Wang

    2007-07-01

    Full Text Available Wireless sensor networks (WSNs are autonomous networks that have beenfrequently deployed to collaboratively perform target localization and classification tasks.Their autonomous and collaborative features resemble the characteristics of agents. Suchsimilarities inspire the development of heterogeneous agent architecture for WSN in thispaper. The proposed agent architecture views WSN as multi-agent systems and mobileagents are employed to reduce in-network communication. According to the architecture,an energy based acoustic localization algorithm is proposed. In localization, estimate oftarget location is obtained by steepest descent search. The search algorithm adapts tomeasurement environments by dynamically adjusting its termination condition. With theagent architecture, target classification is accomplished by distributed support vectormachine (SVM. Mobile agents are employed for feature extraction and distributed SVMlearning to reduce communication load. Desirable learning performance is guaranteed bycombining support vectors and convex hull vectors. Fusion algorithms are designed tomerge SVM classification decisions made from various modalities. Real world experimentswith MICAz sensor nodes are conducted for vehicle localization and classification.Experimental results show the proposed agent architecture remarkably facilitates WSNdesigns and algorithm implementation. The localization and classification algorithms alsoprove to be accurate and energy efficient.

  10. A Soft Intelligent Risk Evaluation Model for Credit Scoring Classification

    Directory of Open Access Journals (Sweden)

    Mehdi Khashei

    2015-09-01

    Full Text Available Risk management is one of the most important branches of business and finance. Classification models are the most popular and widely used analytical group of data mining approaches that can greatly help financial decision makers and managers to tackle credit risk problems. However, the literature clearly indicates that, despite proposing numerous classification models, credit scoring is often a difficult task. On the other hand, there is no universal credit-scoring model in the literature that can be accurately and explanatorily used in all circumstances. Therefore, the research for improving the efficiency of credit-scoring models has never stopped. In this paper, a hybrid soft intelligent classification model is proposed for credit-scoring problems. In the proposed model, the unique advantages of the soft computing techniques are used in order to modify the performance of the traditional artificial neural networks in credit scoring. Empirical results of Australian credit card data classifications indicate that the proposed hybrid model outperforms its components, and also other classification models presented for credit scoring. Therefore, the proposed model can be considered as an appropriate alternative tool for binary decision making in business and finance, especially in high uncertainty conditions.

  11. Classification and Segmentation of Satellite Orthoimagery Using Convolutional Neural Networks

    Directory of Open Access Journals (Sweden)

    Martin Längkvist

    2016-04-01

    Full Text Available The availability of high-resolution remote sensing (HRRS data has opened up the possibility for new interesting applications, such as per-pixel classification of individual objects in greater detail. This paper shows how a convolutional neural network (CNN can be applied to multispectral orthoimagery and a digital surface model (DSM of a small city for a full, fast and accurate per-pixel classification. The predicted low-level pixel classes are then used to improve the high-level segmentation. Various design choices of the CNN architecture are evaluated and analyzed. The investigated land area is fully manually labeled into five categories (vegetation, ground, roads, buildings and water, and the classification accuracy is compared to other per-pixel classification works on other land areas that have a similar choice of categories. The results of the full classification and segmentation on selected segments of the map show that CNNs are a viable tool for solving both the segmentation and object recognition task for remote sensing data.

  12. USING GOOGLE’S KEYWORD RELATION IN MULTIDOMAIN DOCUMENT CLASSIFICATION

    Directory of Open Access Journals (Sweden)

    Ping-I Chen

    2013-07-01

    Full Text Available People can collect all kinds of knowledge from search engines to improve the quality of decision making, and use document classification systems to manage the knowledge repository. Document classification systems always need to construct a keyword vector, which always contains thousands of words, to represent the knowledge domain. Thus, the computation complexity of the classification algorithm is very high. Also, users need to download all the documents before extracting the keywords and classifying the documents. In our previous work, we described a new algorithm called “Word AdHoc Network” (WANET and used it to extract the most important sequences of keywords for each document. In this paper, we adapt the WANET system to make it more precise. We will also use a new similarity measurement algorithm, called “Google Purity,” to calculate the similarity between the extracted keyword sequences to classify similar documents together. By using this system, we can easily classify the information in different knowledge domains at the same time, and all the executions are without any pre-established keyword repository. Our experiments show that the classification results are very accurate and useful. This new system can improve the efficiency of document classification and make it more usable in Web-based information management.

  13. Automatic classification of time-variable X-ray sources

    Energy Technology Data Exchange (ETDEWEB)

    Lo, Kitty K.; Farrell, Sean; Murphy, Tara; Gaensler, B. M. [Sydney Institute for Astronomy, School of Physics, The University of Sydney, Sydney, NSW 2006 (Australia)

    2014-05-01

    To maximize the discovery potential of future synoptic surveys, especially in the field of transient science, it will be necessary to use automatic classification to identify some of the astronomical sources. The data mining technique of supervised classification is suitable for this problem. Here, we present a supervised learning method to automatically classify variable X-ray sources in the Second XMM-Newton Serendipitous Source Catalog (2XMMi-DR2). Random Forest is our classifier of choice since it is one of the most accurate learning algorithms available. Our training set consists of 873 variable sources and their features are derived from time series, spectra, and other multi-wavelength contextual information. The 10 fold cross validation accuracy of the training data is ∼97% on a 7 class data set. We applied the trained classification model to 411 unknown variable 2XMM sources to produce a probabilistically classified catalog. Using the classification margin and the Random Forest derived outlier measure, we identified 12 anomalous sources, of which 2XMM J180658.7–500250 appears to be the most unusual source in the sample. Its X-ray spectra is suggestive of a ultraluminous X-ray source but its variability makes it highly unusual. Machine-learned classification and anomaly detection will facilitate scientific discoveries in the era of all-sky surveys.

  14. Artificial Neural Network Approach in Radar Target Classification

    Directory of Open Access Journals (Sweden)

    N. K. Ibrahim

    2009-01-01

    Full Text Available Problem statement: This study unveils the potential and utilization of Neural Network (NN in radar applications for target classification. The radar system under test is a special of it kinds and known as Forward Scattering Radar (FSR. In this study the target is a ground vehicle which is represented by typical public road transport. The features from raw radar signal were extracted manually prior to classification process using Neural Network (NN. Features given to the proposed network model are identified through radar theoretical analysis. Multi-Layer Perceptron (MLP back-propagation neural network trained with three back-propagation algorithm was implemented and analyzed. In NN classifier, the unknown target is sent to the network trained by the known targets to attain the accurate output. Approach: Two types of classifications were analyzed. The first one is to classify the exact type of vehicle, four vehicle types were selected. The second objective is to grouped vehicle into their categories. The proposed NN architecture is compared to the K Nearest Neighbor classifier and the performance is evaluated. Results: Based on the results, the proposed NN provides a higher percentage of successful classification than the KNN classifier. Conclusion/Recommendation: The result presented here show that NN can be effectively employed in radar classification applications.

  15. [Classification of viruses by computer].

    Science.gov (United States)

    Ageeva, O N; Andzhaparidze, O G; Kibardin, V M; Nazarova, G M; Pleteneva, E A

    1982-01-01

    The study used the information mass containing information on 83 viruses characterized by 41 markers. The suitability of one of the variants of cluster analysis for virus classification was demonstrated. It was established that certain stages of automatic allotment of viruses into groups by the degree of similarity of their properties end the formation of groups which consist of viruses sufficiently close to each other by their properties and are sufficiently isolated. Comparison of these groups with the classification proposed by the ICVT established their correspondence to individual families. Analysis of the obtained classification system permits sufficiently grounded conclusions to be drawn with regard to the classification position of certain viruses, the classification of which has not yet been completed by the ICVT.

  16. Information Classification on University Websites

    DEFF Research Database (Denmark)

    Nawaz, Ather; Clemmensen, Torkil; Hertzum, Morten

    2011-01-01

    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 taskperformance differences. The main implications of the study are that (a) the edit distance appears a useful measure in cross-country HCI research and practice...

  17. Information Classification on University Websites

    DEFF Research Database (Denmark)

    Nawaz, Ather; Clemmensen, Torkil; Hertzum, Morten

    2011-01-01

    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 indicated group differences in user classification and related task performances differences. The main implications of the study were that (a) the edit distance appears a useful measure in cross-country HCI research and practice...

  18. Information Classification on University Websites

    DEFF Research Database (Denmark)

    Nawaz, Ather; Clemmensen, Torkil; Hertzum, Morten

    2011-01-01

    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...

  19. Single-trial EEG RSVP classification using convolutional neural networks

    Science.gov (United States)

    Shamwell, Jared; Lee, Hyungtae; Kwon, Heesung; Marathe, Amar R.; Lawhern, Vernon; Nothwang, William

    2016-05-01

    Traditionally, Brain-Computer Interfaces (BCI) have been explored as a means to return function to paralyzed or otherwise debilitated individuals. An emerging use for BCIs is in human-autonomy sensor fusion where physiological data from healthy subjects is combined with machine-generated information to enhance the capabilities of artificial systems. While human-autonomy fusion of physiological data and computer vision have been shown to improve classification during visual search tasks, to date these approaches have relied on separately trained classification models for each modality. We aim to improve human-autonomy classification performance by developing a single framework that builds codependent models of human electroencephalograph (EEG) and image data to generate fused target estimates. As a first step, we developed a novel convolutional neural network (CNN) architecture and applied it to EEG recordings of subjects classifying target and non-target image presentations during a rapid serial visual presentation (RSVP) image triage task. The low signal-to-noise ratio (SNR) of EEG inherently limits the accuracy of single-trial classification and when combined with the high dimensionality of EEG recordings, extremely large training sets are needed to prevent overfitting and achieve accurate classification from raw EEG data. This paper explores a new deep CNN architecture for generalized multi-class, single-trial EEG classification across subjects. We compare classification performance from the generalized CNN architecture trained across all subjects to the individualized XDAWN, HDCA, and CSP neural classifiers which are trained and tested on single subjects. Preliminary results show that our CNN meets and slightly exceeds the performance of the other classifiers despite being trained across subjects.

  20. Using support vector classification for SAR of fentanyl derivatives

    Institute of Scientific and Technical Information of China (English)

    Ning DONG; Wen-cong LU; Nian-yi CHEN; You-cheng ZHU; Kai-xian CHEN

    2005-01-01

    Aim: To discriminate between fentanyl derivatives with high and low activities.Methods: The support vector classification (SVC) method, a novel approach,was employed to investigate structure-activity relationship (SAR) of fentanyl derivatives based on the molecular descriptors, which were quantum parameters including △E [energy difference between highest occupied molecular orbital energy (HOMO) and lowest empty molecular orbital energy (LUMO)], MR(molecular refractivity) and Mr (molecular weight). Results: By using leave-oneout cross-validation test, the accuracies of prediction for activities of fentanyl derivatives in SVC, principal component analysis (PCA), artificial neural network (ANN) and K-nearest neighbor (KNN) models were 93%, 86%, 57%, and 71%, respectively. The results indicated that the performance of the SVC model was better than those of PCA, ANN, and KNN models for this data. Conclusion:SVC can be used to investigate SAR of fentanyl derivatives and could be a promising tool in the field of SAR research.

  1. 75 FR 10529 - Mail Classification Change

    Science.gov (United States)

    2010-03-08

    ... Mail Classification Change AGENCY: Postal Regulatory Commission. ACTION: Notice. SUMMARY: The... Classification Schedule. The change affects a change in terminology. This notice addresses procedural steps....90 et seq. concerning a change in classification which reflects a change in terminology from...

  2. 75 FR 70754 - Postal Classification Changes

    Science.gov (United States)

    2010-11-18

    ... Postal Classification Changes AGENCY: Postal Regulatory Commission. ACTION: Notice. SUMMARY: The Commission is noticing a recently-filed Postal Service request announcing a classification change affecting... Notice with the Commission announcing a classification change ] established by the Governors.\\1\\...

  3. Land cover classification using random forest with genetic algorithm-based parameter optimization

    Science.gov (United States)

    Ming, Dongping; Zhou, Tianning; Wang, Min; Tan, Tian

    2016-07-01

    Land cover classification based on remote sensing imagery is an important means to monitor, evaluate, and manage land resources. However, it requires robust classification methods that allow accurate mapping of complex land cover categories. Random forest (RF) is a powerful machine-learning classifier that can be used in land remote sensing. However, two important parameters of RF classification, namely, the number of trees and the number of variables tried at each split, affect classification accuracy. Thus, optimal parameter selection is an inevitable problem in RF-based image classification. This study uses the genetic algorithm (GA) to optimize the two parameters of RF to produce optimal land cover classification accuracy. HJ-1B CCD2 image data are used to classify six different land cover categories in Changping, Beijing, China. Experimental results show that GA-RF can avoid arbitrariness in the selection of parameters. The experiments also compare land cover classification results by using GA-RF method, traditional RF method (with default parameters), and support vector machine method. When the GA-RF method is used, classification accuracies, respectively, improved by 1.02% and 6.64%. The comparison results show that GA-RF is a feasible solution for land cover classification without compromising accuracy or incurring excessive time.

  4. Towards Accurate Application Characterization for Exascale (APEX)

    Energy Technology Data Exchange (ETDEWEB)

    Hammond, Simon David [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)

    2015-09-01

    Sandia National Laboratories has been engaged in hardware and software codesign activities for a number of years, indeed, it might be argued that prototyping of clusters as far back as the CPLANT machines and many large capability resources including ASCI Red and RedStorm were examples of codesigned solutions. As the research supporting our codesign activities has moved closer to investigating on-node runtime behavior a nature hunger has grown for detailed analysis of both hardware and algorithm performance from the perspective of low-level operations. The Application Characterization for Exascale (APEX) LDRD was a project concieved of addressing some of these concerns. Primarily the research was to intended to focus on generating accurate and reproducible low-level performance metrics using tools that could scale to production-class code bases. Along side this research was an advocacy and analysis role associated with evaluating tools for production use, working with leading industry vendors to develop and refine solutions required by our code teams and to directly engage with production code developers to form a context for the application analysis and a bridge to the research community within Sandia. On each of these accounts significant progress has been made, particularly, as this report will cover, in the low-level analysis of operations for important classes of algorithms. This report summarizes the development of a collection of tools under the APEX research program and leaves to other SAND and L2 milestone reports the description of codesign progress with Sandia’s production users/developers.

  5. Optimizing cell arrays for accurate functional genomics

    Directory of Open Access Journals (Sweden)

    Fengler Sven

    2012-07-01

    Full Text Available Abstract Background Cellular responses emerge from a complex network of dynamic biochemical reactions. In order to investigate them is necessary to develop methods that allow perturbing a high number of gene products in a flexible and fast way. Cell arrays (CA enable such experiments on microscope slides via reverse transfection of cellular colonies growing on spotted genetic material. In contrast to multi-well plates, CA are susceptible to contamination among neighboring spots hindering accurate quantification in cell-based screening projects. Here we have developed a quality control protocol for quantifying and minimizing contamination in CA. Results We imaged checkered CA that express two distinct fluorescent proteins and segmented images into single cells to quantify the transfection efficiency and interspot contamination. Compared with standard procedures, we measured a 3-fold reduction of contaminants when arrays containing HeLa cells were washed shortly after cell seeding. We proved that nucleic acid uptake during cell seeding rather than migration among neighboring spots was the major source of contamination. Arrays of MCF7 cells developed without the washing step showed 7-fold lower percentage of contaminant cells, demonstrating that contamination is dependent on specific cell properties. Conclusions Previously published methodological works have focused on achieving high transfection rate in densely packed CA. Here, we focused in an equally important parameter: The interspot contamination. The presented quality control is essential for estimating the rate of contamination, a major source of false positives and negatives in current microscopy based functional genomics screenings. We have demonstrated that a washing step after seeding enhances CA quality for HeLA but is not necessary for MCF7. The described method provides a way to find optimal seeding protocols for cell lines intended to be used for the first time in CA.

  6. Accurate paleointensities - the multi-method approach

    Science.gov (United States)

    de Groot, Lennart

    2016-04-01

    The accuracy of models describing rapid changes in the geomagnetic field over the past millennia critically depends on the availability of reliable paleointensity estimates. Over the past decade methods to derive paleointensities from lavas (the only recorder of the geomagnetic field that is available all over the globe and through geologic times) have seen significant improvements and various alternative techniques were proposed. The 'classical' Thellier-style approach was optimized and selection criteria were defined in the 'Standard Paleointensity Definitions' (Paterson et al, 2014). The Multispecimen approach was validated and the importance of additional tests and criteria to assess Multispecimen results must be emphasized. Recently, a non-heating, relative paleointensity technique was proposed -the pseudo-Thellier protocol- which shows great potential in both accuracy and efficiency, but currently lacks a solid theoretical underpinning. Here I present work using all three of the aforementioned paleointensity methods on suites of young lavas taken from the volcanic islands of Hawaii, La Palma, Gran Canaria, Tenerife, and Terceira. Many of the sampled cooling units are <100 years old, the actual field strength at the time of cooling is therefore reasonably well known. Rather intuitively, flows that produce coherent results from two or more different paleointensity methods yield the most accurate estimates of the paleofield. Furthermore, the results for some flows pass the selection criteria for one method, but fail in other techniques. Scrutinizing and combing all acceptable results yielded reliable paleointensity estimates for 60-70% of all sampled cooling units - an exceptionally high success rate. This 'multi-method paleointensity approach' therefore has high potential to provide the much-needed paleointensities to improve geomagnetic field models for the Holocene.

  7. How flatbed scanners upset accurate film dosimetry.

    Science.gov (United States)

    van Battum, L J; Huizenga, H; Verdaasdonk, R M; Heukelom, S

    2016-01-21

    Film is an excellent dosimeter for verification of dose distributions due to its high spatial resolution. Irradiated film can be digitized with low-cost, transmission, flatbed scanners. However, a disadvantage is their lateral scan effect (LSE): a scanner readout change over its lateral scan axis. Although anisotropic light scattering was presented as the origin of the LSE, this paper presents an alternative cause. Hereto, LSE for two flatbed scanners (Epson 1680 Expression Pro and Epson 10000XL), and Gafchromic film (EBT, EBT2, EBT3) was investigated, focused on three effects: cross talk, optical path length and polarization. Cross talk was examined using triangular sheets of various optical densities. The optical path length effect was studied using absorptive and reflective neutral density filters with well-defined optical characteristics (OD range 0.2-2.0). Linear polarizer sheets were used to investigate light polarization on the CCD signal in absence and presence of (un)irradiated Gafchromic film. Film dose values ranged between 0.2 to 9 Gy, i.e. an optical density range between 0.25 to 1.1. Measurements were performed in the scanner's transmission mode, with red-green-blue channels. LSE was found to depend on scanner construction and film type. Its magnitude depends on dose: for 9 Gy increasing up to 14% at maximum lateral position. Cross talk was only significant in high contrast regions, up to 2% for very small fields. The optical path length effect introduced by film on the scanner causes 3% for pixels in the extreme lateral position. Light polarization due to film and the scanner's optical mirror system is the main contributor, different in magnitude for the red, green and blue channel. We concluded that any Gafchromic EBT type film scanned with a flatbed scanner will face these optical effects. Accurate dosimetry requires correction of LSE, therefore, determination of the LSE per color channel and dose delivered to the film.

  8. Automatic Classification of Marine Mammals with Speaker Classification Methods.

    Science.gov (United States)

    Kreimeyer, Roman; Ludwig, Stefan

    2016-01-01

    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.

  9. A Statistical Approach of Texton Based Texture Classification Using LPboosting Classifier

    Directory of Open Access Journals (Sweden)

    C. Vivek

    2014-05-01

    Full Text Available The aim of the study in this research deals with the accurate texture classification and the image texture analysis has a voluminous errand prospective in real world applications. In this study, the texton co-occurrence matrix applied to the Broadatz database images that derive the template texton grid images and it undergoes to the discrete shearlet transform to decompose the image. The entropy lineage parameters of redundant and interpolate at a certain point which congregating adjacent regions based on geometric properties then the classification is apprehended by comparing the similarity between the estimated distributions of all detail sub bands through the strong LP boosting classification with various weak classifier configurations. We show that the resulted texture features while incurring the maximum of the discriminative information. Our hybrid classification method significantly outperforms the existing texture descriptors and stipulates classification accuracy in the state-of-the-art real world imaging applications.

  10. On Machine-Learned Classification of Variable Stars with Sparse and Noisy Time-Series Data

    CERN Document Server

    Richards, Joseph W; Butler, Nathaniel R; Bloom, Joshua S; Brewer, John M; Crellin-Quick, Arien; Higgins, Justin; Kennedy, Rachel; Rischard, Maxime

    2011-01-01

    With the coming data deluge from synoptic surveys, there is a growing need for frameworks that can quickly and automatically produce calibrated classification probabilities for newly-observed variables based on a small number of time-series measurements. In this paper, we introduce a methodology for variable-star classification, drawing from modern machine-learning techniques. We describe how to homogenize the information gleaned from light curves by selection and computation of real-numbered metrics ("feature"), detail methods to robustly estimate periodic light-curve features, introduce tree-ensemble methods for accurate variable star classification, and show how to rigorously evaluate the classification results using cross validation. On a 25-class data set of 1542 well-studied variable stars, we achieve a 22.8% overall classification error using the random forest classifier; this represents a 24% improvement over the best previous classifier on these data. This methodology is effective for identifying sam...

  11. International Society Of Neuropathology--Haarlem consensus guidelines for nervous system tumor classification and grading.

    Science.gov (United States)

    Louis, David N; Perry, Arie; Burger, Peter; Ellison, David W; Reifenberger, Guido; von Deimling, Andreas; Aldape, Kenneth; Brat, Daniel; Collins, V Peter; Eberhart, Charles; Figarella-Branger, Dominique; Fuller, Gregory N; Giangaspero, Felice; Giannini, Caterina; Hawkins, Cynthia; Kleihues, Paul; Korshunov, Andrey; Kros, Johan M; Beatriz Lopes, M; Ng, Ho-Keung; Ohgaki, Hiroko; Paulus, Werner; Pietsch, Torsten; Rosenblum, Marc; Rushing, Elisabeth; Soylemezoglu, Figen; Wiestler, Otmar; Wesseling, Pieter

    2014-09-01

    Major discoveries in the biology of nervous system tumors have raised the question of how non-histological data such as molecular information can be incorporated into the next World Health Organization (WHO) classification of central nervous system tumors. To address this question, a meeting of neuropathologists with expertise in molecular diagnosis was held in Haarlem, the Netherlands, under the sponsorship of the International Society of Neuropathology (ISN). Prior to the meeting, participants solicited input from clinical colleagues in diverse neuro-oncological specialties. The present "white paper" catalogs the recommendations of the meeting, at which a consensus was reached that incorporation of molecular information into the next WHO classification should follow a set of provided "ISN-Haarlem" guidelines. Salient recommendations include that (i) diagnostic entities should be defined as narrowly as possible to optimize interobserver reproducibility, clinicopathological predictions and therapeutic planning; (ii) diagnoses should be "layered" with histologic classification, WHO grade and molecular information listed below an "integrated diagnosis"; (iii) determinations should be made for each tumor entity as to whether molecular information is required, suggested or not needed for its definition; (iv) some pediatric entities should be separated from their adult counterparts; (v) input for guiding decisions regarding tumor classification should be solicited from experts in complementary disciplines of neuro-oncology; and (iv) entity-specific molecular testing and reporting formats should be followed in diagnostic reports. It is hoped that these guidelines will facilitate the forthcoming update of the fourth edition of the WHO classification of central nervous system tumors.

  12. Molecular physics

    CERN Document Server

    Williams, Dudley

    2013-01-01

    Methods of Experimental Physics, Volume 3: Molecular Physics focuses on molecular theory, spectroscopy, resonance, molecular beams, and electric and thermodynamic properties. The manuscript first considers the origins of molecular theory, molecular physics, and molecular spectroscopy, as well as microwave spectroscopy, electronic spectra, and Raman effect. The text then ponders on diffraction methods of molecular structure determination and resonance studies. Topics include techniques of electron, neutron, and x-ray diffraction and nuclear magnetic, nuclear quadropole, and electron spin reson

  13. Molecular Dynamics in the Vacuum Ultraviolet

    Science.gov (United States)

    1989-01-30

    CLASSIFICATION OF THIS PAGE COMPLETED PROJECT SUMMARY TITLE: Molecular dynamics in the Vacuum Ultraviolet PRINCIPAL INVESTIGATOR: Paul L. Houston...DTIC TAB 0 Unannounced 0 By Distr ibution I Availability Codes Avail and I or Dist Special I Molecular Dynamics In the Vacuum Ultraviolet Final Technical...Further development of tunable vacuum ultraviolet sources has opened wide areas of molecular dynamics for study. Completed Research Photodissociation of

  14. Phylogeny and classification of the trapdoor spider genus Myrmekiaphila: an integrative approach to evaluating taxonomic hypotheses.

    Directory of Open Access Journals (Sweden)

    Ashley L Bailey

    Full Text Available BACKGROUND: Revised by Bond and Platnick in 2007, the trapdoor spider genus Myrmekiaphila comprises 11 species. Species delimitation and placement within one of three species groups was based on modifications of the male copulatory device. Because a phylogeny of the group was not available these species groups might not represent monophyletic lineages; species definitions likewise were untested hypotheses. The purpose of this study is to reconstruct the phylogeny of Myrmekiaphila species using molecular data to formally test the delimitation of species and species-groups. We seek to refine a set of established systematic hypotheses by integrating across molecular and morphological data sets. METHODS AND FINDINGS: Phylogenetic analyses comprising Bayesian searches were conducted for a mtDNA matrix composed of contiguous 12S rRNA, tRNA-val, and 16S rRNA genes and a nuclear DNA matrix comprising the glutamyl and prolyl tRNA synthetase gene each consisting of 1348 and 481 bp, respectively. Separate analyses of the mitochondrial and nuclear genome data and a concatenated data set yield M. torreya and M. millerae paraphyletic with respect to M. coreyi and M. howelli and polyphyletic fluviatilis and foliata species groups. CONCLUSIONS: Despite the perception that molecular data present a solution to a crisis in taxonomy, studies like this demonstrate the efficacy of an approach that considers data from multiple sources. A DNA barcoding approach during the species discovery process would fail to recognize at least two species (M. coreyi and M. howelli whereas a combined approach more accurately assesses species diversity and illuminates speciation pattern and process. Concomitantly these data also demonstrate that morphological characters likewise fail in their ability to recover monophyletic species groups and result in an unnatural classification. Optimizations of these characters demonstrate a pattern of "Dollo evolution" wherein a complex character

  15. Accurate Structure Parameters for Tunneling Ionization Rates of Gas-Phase Linear Molecules

    Science.gov (United States)

    Zhao, Song-Feng; Li, Jian-Ke; Wang, Guo-Li; Li, Peng-Cheng; Zhou, Xiao-Xin

    2017-03-01

    In the molecular Ammosov–Delone–Krainov (MO-ADK) model of Tong et al. [Phys. Rev. A 66 (2002) 033402], the ionization rate depends on the structure parameters of the molecular orbital from which the electron is removed. We determine systematically and tabulate accurate structure parameters of the highest occupied molecular orbital (HOMO) for 123 gas-phase linear molecules by solving time-independent Schrödinger equation with B-spline functions and molecular potentials which are constructed numerically using the modified Leeuwen–Baerends (LBα) model. Supported by National Natural Science Foundation of China under Grant Nos. 11664035, 11674268, 11465016, 11364038, 11364039, the Specialized Research Fund for the Doctoral Program of Higher Education of China under Grant No. 20116203120001 and the Basic Scientific Research Foundation for Institution of Higher Learning of Gansu Province

  16. Molecular classification and morphological traits of two species of Meretrix ( Mollusca, Bivalvia)%浙江和广西两种文蛤的分子鉴定及形态特征分析

    Institute of Scientific and Technical Information of China (English)

    董迎辉; 姚定余; 林志华; 姚韩韩; 陆荣茂

    2011-01-01

    以文蛤如东群体(RD)和北海群体(BH)为对照群,利用线粒体CO Ⅰ基因序列分析技术对苍南文蛤(CN)和北海白壳文蛤(BW)进行了分子鉴定.结果表明,苍南文蛤和斧文蛤的碱基组成非常相似,通过文蛤属贝类基因序列同源性比对和分子系统聚类分析发现,苍南文蛤CN1、CN2与斧文蛤的同源性分别达到100.0%、99.2%,在依据遗传距离构建的系统进化树上,2个苍南文蛤也与斧文蛤单独聚为一支,据此将苍南文蛤确定为斧文蛤,此结果将斧文蛤的分布区域向北扩展到了浙江南部沿海,修正了现有文献中记载的仅在我国南海诸省分布的说法;而自壳文蛤与其它6种文蛤的基因序列同源性都不高(79.6%~85.3%),在系统进化树上单独分出一支,明显是独立于这些文蛤之外的新种.斧文蛤、白壳文蛤与文蛤群体COⅠ基因的遗传多样性分析显示,文蛤BH群体的变异位点数、单倍型数和核苷酸多样性指数均最大,斧文蛤其次,而白壳文蛤10条基因序列完全相同,未发生任何核苷酸位点变异,说明其遗传多样性很低.应用方差分析和Tukey多重比较,分析了斧文蛤、白壳文蛤与文蛤群体的形态差异,发现斧文蛤的壳长明显大于壳高,且SMW/TW、IW/TW 2个参数与文蛤、白壳文蛤群体差异显著(P<0.05);而白壳文蛤的壳宽指数大、壳型相对膨胀,SW/SL和SW/SH值均最大,与文蛤和斧文蛤群体差异显著(P<0.05).本研究结果可为文蛤属贝类种间鉴别、种质资源保护及系统进化研究提供基础资料.%Although many species of the genus Meretrix are commercially-important cultured bivalves,the taxonomy of Meretrix is still in argument over several discrepancies among scientists in the world. Compared with the groups of Meretrix meretrix (RD & BH) ,two groups of Meretrix clam( CN & BW), collected from Cangnan and Beihai, were phylogenetically analyzed and molecularly classified

  17. Classification of Building Object Types

    DEFF Research Database (Denmark)

    Jørgensen, Kaj Asbjørn

    2011-01-01

    Development of the existing classification systems has been very difficult and time consuming tasks, where many considerations have been taken and many compromises have been made. The results reveal that, although the theoretical foundation was clarified, many deviations and shortcuts have been...... made. This is certainly the case in the Danish development. Based on the theories about these abstraction mechanisms, the basic principles for classification systems are presented and the observed misconceptions are analyses and explained. Furthermore, it is argued that the purpose of classification...

  18. Music classification with MPEG-7

    Science.gov (United States)

    Crysandt, Holger; Wellhausen, Jens

    2003-01-01

    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.

  19. Classification of Rainbows

    Science.gov (United States)

    Adams, Peter; Ricard, Jean; Barckicke, Jean

    2016-04-01

    Rainbows are the most beautiful and most spectacular optical atmospheric phenomenon. Humphreys (1964) pointedly noted that "the "explanations" generally given of the rainbow [ in textbooks] may well be said to explain beautifully that which does not occur, and to leave unexplained which does" . . . "The records of close observations of rainbows soon show that not even the colors are always the same". Textbooks stress that the main factor affecting the aspect of the rainbow is the radius of the water droplets. In his well-known textbook entitled "the nature of light & colour in the open air", Minnaert (1954) gives the chief features of the rainbow depending on the diameter of the drops producing it. For this study, we have gathered hundreds of pictures of primary bows. We sort out the pictures into classes. The classes are defined in a such way that rainbows belonging to the same class look similar. Our results are surprising and do not confirm Minnaert's classification. In practice, the size of the water droplets is only a minor factor controlling the overall aspect of the rainbow. The main factor appears to be the height of the sun above the horizon. At sunset, the width of the red band increases, while the width of the other bands of colours decreases. The orange, the violet, the blue and the green bands disappear completely in this order. At the end, the primary bow is mainly red and slightly yellow. Picture = taken from the CNRM in Toulouse after a summer storm (Jean Ricard)

  20. Radar clutter classification

    Science.gov (United States)

    Stehwien, Wolfgang

    1989-11-01

    The problem of classifying radar clutter as found on air traffic control radar systems is studied. An algorithm based on Bayes decision theory and the parametric maximum a posteriori probability classifier is developed to perform this classification automatically. This classifier employs a quadratic discriminant function and is optimum for feature vectors that are distributed according to the multivariate normal density. Separable clutter classes are most likely to arise from the analysis of the Doppler spectrum. Specifically, a feature set based on the complex reflection coefficients of the lattice prediction error filter is proposed. The classifier is tested using data recorded from L-band air traffic control radars. The Doppler spectra of these data are examined; the properties of the feature set computed using these data are studied in terms of both the marginal and multivariate statistics. Several strategies involving different numbers of features, class assignments, and data set pretesting according to Doppler frequency and signal to noise ratio were evaluated before settling on a workable algorithm. Final results are presented in terms of experimental misclassification rates and simulated and classified plane position indicator displays.

  1. Satellite image classification methods and Landsat 5TM bands

    CERN Document Server

    Tamouk, Jamshid; Farmanbar, Mina

    2013-01-01

    This paper attempts to find the most accurate classification method among parallelepiped, minimum distance and chain methods. Moreover, this study also challenges to find the suitable combination of bands, which can lead to better results in case combinations of bands occur. After comparing these three methods, the chain method over perform the other methods with 79% overall accuracy. Hence, it is more accurate than minimum distance with 67% and parallelepiped with 65%. On the other hand, based on bands features, and also by combining several researchers' findings, a table was created which includes the main objects on the land and the suitable combination of the bands for accurately detecting of landcover objects. During this process, it was observed that band 4 (out of 7 bands of Landsat 5TM) is the band, which can be used for increasing the accuracy of the combined bands in detecting objects on the land.

  2. Classification of Fuel Types Using Envisat Data

    Science.gov (United States)

    Wozniak, Edyta; Nasilowska, Sylwia

    2010-12-01

    Forest fires have an important impact on landscape structure and ecosystems biodiversity. Moreover, wild land fires have strong influence on forest planning and management. Furthermore, forest fires affect not only woodworking industry but also arable fields and inhabitants life too. A precise knowledge of the spatial distribution of fuels is necessary to predict, analyse and model fire behaviour. Modelling of fire spread is difficult and complicated because it depends on many factors. First of all, it depends on undergrowth and brushwood moisture and thickness, and tree species. There are many fuel types classification developed for regional environmental condition. The main drawback of implemented systems is utility for particular region of interest. That causes a need of permanent, consequent and more accurate researches in specific habitat not only in continental scale. In this paper a new system is proposed. It organizes fuels into three major groups (coniferous, deciduous wood and open) and four subcategories which describes a fuel structure (trees lower then 4m, trees higher than 4 m: without bushes; with low bushes lower them 2m; with high bushes higher then 2m). This classification is adapted into Polish lowlands environmental condition. The classification was carried out on the base of 120 training plots, which were determinate during a field experiment in north-eastern Poland. The plots discriminate homogeneous parts of forest which correspond to fuel classes. In the study we used the ENVISAT Alternating Polarization (HH/HV) image. The most popular classifiers were tried out and the maximum likelihood method resulted the most efficient. To map fuel types many methods are employed. The use of remote sensing systems gives the possibility of low- costs and time-consuming fuels mapping and updating. The employ of SAR systems permits mapping independently of weather condition. The microwave data has the potential to estimate fuel loads and map fuel types. The

  3. Integrated Classification of Prostate Cancer Reveals a Novel Luminal Subtype with Poor Outcome.

    Science.gov (United States)

    You, Sungyong; Knudsen, Beatrice S; Erho, Nicholas; Alshalalfa, Mohammed; Takhar, Mandeep; Al-Deen Ashab, Hussam; Davicioni, Elai; Karnes, R Jeffrey; Klein, Eric A; Den, Robert B; Ross, Ashley E; Schaeffer, Edward M; Garraway, Isla P; Kim, Jayoung; Freeman, Michael R

    2016-09-01

    Prostate cancer is a biologically heterogeneous disease with variable molecular alterations underlying cancer initiation and progression. Despite recent advances in understanding prostate cancer heterogeneity, better methods for classification of prostate cancer are still needed to improve prognostic accuracy and therapeutic outcomes. In this study, we computationally assembled a large virtual cohort (n = 1,321) of human prostate cancer transcriptome profiles from 38 distinct cohorts and, using pathway activation signatures of known relevance to prostate cancer, developed a novel classification system consisting of three distinct subtypes (named PCS1-3). We validated this subtyping scheme in 10 independent patient cohorts and 19 laboratory models of prostate cancer, including cell lines and genetically engineered mouse models. Analysis of subtype-specific gene expression patterns in independent datasets derived from luminal and basal cell models provides evidence that PCS1 and PCS2 tumors reflect luminal subtypes, while PCS3 represents a basal subtype. We show that PCS1 tumors progress more rapidly to metastatic disease in comparison with PCS2 or PCS3, including PSC1 tumors of low Gleason grade. To apply this finding clinically, we developed a 37-gene panel that accurately assigns individual tumors to one of the three PCS subtypes. This panel was also applied to circulating tumor cells (CTC) and provided evidence that PCS1 CTCs may reflect enzalutamide resistance. In summary, PCS subtyping may improve accuracy in predicting the likelihood of clinical progression and permit treatment stratification at early and late disease stages. Cancer Res; 76(17); 4948-58. ©2016 AACR.

  4. Hazard classification or risk assessment

    DEFF Research Database (Denmark)

    Hass, Ulla

    2013-01-01

    The EU classification of substances for e.g. reproductive toxicants is hazard based and does not to address the risk suchsubstances may pose through normal, or extreme, use. Such hazard classification complies with the consumer's right to know. It is also an incentive to careful use and storage...... and to substitute with less toxic compounds. Actually, if exposure is constant across product class, producersmay make substitution decisions based on hazard. Hazard classification is also useful during major accidents where there is no time for risk assessment and the exposure is likely to be substantial enough...... be a poor substitute for a proper risk assessment as low potency substances can constitute a risk if the exposure is high enough and vice versa. Examples illustrating the strength and limitations of hazard classification, risk assessment and toxicological potency will be presented with focus on reproductive...

  5. [Definition and classification of epilepsy].

    Science.gov (United States)

    Jibiki, Itsuki

    2014-05-01

    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.

  6. Biogeography based Satellite Image Classification

    CERN Document Server

    Panchal, V K; Kaur, Navdeep; Kundra, Harish

    2009-01-01

    Biogeography is the study of the geographical distribution of biological organisms. The mindset of the engineer is that we can learn from nature. Biogeography Based Optimization is a burgeoning nature inspired technique to find the optimal solution of the problem. Satellite image classification is an important task because it is the only way we can know about the land cover map of inaccessible areas. Though satellite images have been classified in past by using various techniques, the researchers are always finding alternative strategies for satellite image classification so that they may be prepared to select the most appropriate technique for the feature extraction task in hand. This paper is focused on classification of the satellite image of a particular land cover using the theory of Biogeography based Optimization. The original BBO algorithm does not have the inbuilt property of clustering which is required during image classification. Hence modifications have been proposed to the original algorithm and...

  7. The classification on short message

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    This paper discusses the importance of the classification of short message, and details some key technologies related. Through implementing a fundamental prototype, some basic models and technical references are provided.

  8. Formaldehyde in Absorption: Tracing Molecular Gas in Early-Type Galaxies

    Science.gov (United States)

    Dollhopf, Niklaus M.; Donovan Meyer, Jennifer

    2016-01-01

    Early-Type Galaxies (ETGs) have been long-classified as the red, ellipsoidal branch of the classic Hubble tuning fork diagram of galactic structure. In part with this classification, ETGs are thought to be molecular and atomic gas-poor with little to no recent star formation. However, recent efforts have questioned this ingrained classification. Most notably, the ATLAS3D survey of 260 ETGs within ~40 Mpc found 22% contain CO, a common tracer for molecular gas. The presence of cold molecular gas also implies the possibility for current star formation within these galaxies. Simulations do not accurately predict the recent observations and further studies are necessary to understand the mechanisms of ETGs.CO traces molecular gas starting at densities of ~102 cm-3, which makes it a good tracer of bulk molecular gas, but does little to constrain the possible locations of star formation within the cores of dense molecular gas clouds. Formaldehyde (H2CO) traces molecular gas on the order of ~104 cm-3, providing a further constraint on the location of star-forming gas, while being simple enough to possibly be abundant in gas-poor ETGs. In cold molecular clouds at or above ~104 cm-3 densities, the structure of formaldehyde enables a phenomenon in which rotational transitions have excitation temperatures driven below the temperature of the cosmic microwave background (CMB), ~2.7 K. Because the CMB radiates isotropically, formaldehyde can be observed in absorption, independent of distance, as a tracer of moderately-dense molecular clouds and star formation.This novel observation technique of formaldehyde was incorporated for observations of twelve CO-detected ETGs from the ATLAS3D sample, including NGC 4710 and PGC 8815, to investigate the presence of cold molecular gas, and possible star formation, in ETGs. We present images from the Very Large Array, used in its C-array configuration, of the J = 11,0 - 11,1 transition of formaldehyde towards these sources. We report our

  9. Personality: Description, Classification and Evaluation

    OpenAIRE

    Ibrahim Taymur; M. Hakan TURKCAPAR

    2012-01-01

    Many descriptions and classifications of personality have been made to understand and acknowledge human being through out the history. During the developmental process of psychiatry, almost every school defined and assessed personality regarding to their own perspective. As DSM (Diagnostical and Statistical Manual of Mental Disorders) and ICD (International Classification of Diseases) being available to common usage, scientists conducted studies to set a common terminology for personality. Ca...

  10. Map Classification In Image Data

    Science.gov (United States)

    2015-09-25

    trained on 1,000 classes, and provides an immense learning capacity. The BOW method uses a visual vocabulary , con- structed by clustering higher-level...this thesis , BOW, was originally developed for text classification problems. By counting the occurrence of words in a document, the resulting vocabulary ...NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS MAP CLASSIFICATION IN IMAGE DATA by Frank Fiebiger September 2015 Thesis Advisor: Mathias N

  11. Product Work Classification and Coding

    Science.gov (United States)

    1986-06-01

    detail is much more useful in planning steel welding processes. In this regard remember that mild steel , HSLA steel , and high-yield steel (e.g. HY80 ...manufacturing facility. In Figure 2.3-2, a classification and coding system for steel parts is shown. This classification and coding system sorts steel parts...system would provide a shop which produced steel parts with a means of organizing parts. Rather than attempting to manage all of its parts as a single

  12. Classification and clinical assessment

    Directory of Open Access Journals (Sweden)

    F. Cantini

    2012-06-01

    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.

  13. Piroxicam derivatives THz classification

    Science.gov (United States)

    Sterczewski, Lukasz A.; Grzelczak, Michal P.; Nowak, Kacper; Szlachetko, Bogusław; Plinska, Stanislawa; Szczesniak-Siega, Berenika; Malinka, Wieslaw; Plinski, Edward F.

    2016-02-01

    In this paper we report a new approach to linking the terahertz spectral shapes of drug candidates having a similar molecular structure to their chemical and physical parameters. We examined 27 newly-synthesized derivatives of a well-known nonsteroidal anti-inflammatory drug Piroxicam used for treatment of inflammatory arthritis and chemoprevention of colon cancer. The testing was carried out by means of terahertz pulsed spectroscopy (TPS). Using chemometric techniques we evaluated their spectral similarity in the terahertz range and attempted to link the position on the principal component analysis (PCA) score map to the similarity of molecular descriptors. A simplified spectral model preserved 75% and 85.1% of the variance in 2 and 3 dimensions respectively, compared to the input 1137. We have found that in 85% of the investigated samples a similarity of the physical and chemical parameters corresponds to a similarity in the terahertz spectra. The effects of data preprocessing on the generated maps are also discussed. The technique presented can support the choice of the most promising drug candidates for clinical trials in pharmacological research.

  14. The Mechanistic Approach to Psychiatric Classification

    Directory of Open Access Journals (Sweden)

    Elisabetta Sirgiovanni

    2009-01-01

    Full Text Available A Kuhnian reformulation of the recent debate in psychiatric nosography suggested that the current psychiatric classification system (the DSM is in crisis and that a sort of paradigm shift is awaited (Aragona, 2009. Among possible revolutionary alternatives, the proposed fi ve-axes etiopathogenetic taxonomy (Charney et al., 2002 emphasizes the primacy of the genotype over the phenomenological level as the relevant basis for psychiatric nosography. Such a position is along the lines of the micro-reductionist perspective of E. Kandel (1998, 1999, which sees mental disorders reducible to explanations at a fundamental epistemic level of genes and neurotransmitters. This form of micro-reductionism has been criticized as a form of genetic-molecular fundamentalism (e.g. Murphy, 2006 and a multi-level approach, in the form of the burgeoning Cognitive Neuropsychiatry, was proposed. This article focuses on multi-level mechanistic explanations, coming from Cognitive Science, as a possible alternative etiopathogenetic basis for psychiatric classification. The idea of a mechanistic approach to psychiatric taxonomy is here defended on the basis of a better conception of levels and causality. Nevertheless some critical remarks of Mechanism as a psychiatric general view are also offered.

  15. Environmental endocrine disruptors: A proposed classification scheme

    Energy Technology Data Exchange (ETDEWEB)

    Fur, P.L. de; Roberts, J. [Environmental Defense Fund, Washington, DC (United States)

    1995-12-31

    A number of chemicals known to act on animal systems through the endocrine system have been termed environmental endocrine disruptors. This group includes some of the PCBs and TCDDs, as well as lead, mercury and a large number of pesticides. The common feature is that the chemicals interact with endogenous endocrine systems at the cellular and/or molecular level to alter normal processes that are controlled or regulated by hormones. Although the existence of artificial or environmental estrogens (e.g. chlordecone and DES) has been known for some time, recent data indicate that this phenomenon is widespread. Indeed, anti-androgens have been held responsible for reproductive dysfunction in alligator populations in Florida. But the significance of endocrine disruption was recognized by pesticide manufacturers when insect growth regulators were developed to interfere with hormonal control of growth. Controlling, regulating or managing these chemicals depends in no small part on the ability to identify, screen or otherwise know that a chemical is an endocrine disrupter. Two possible classifications schemes are: using the effects caused in an animal, or animals as an exposure indicator; and using a known screen for the point of contact with the animal. The former would require extensive knowledge of cause and effect relationships in dozens of animal groups; the latter would require a screening tool comparable to an estrogen binding assay. The authors present a possible classification based on chemicals known to disrupt estrogenic, androgenic and ecdysone regulated hormonal systems.

  16. Advances in Glomeromycota taxonomy and classification.

    Science.gov (United States)

    Oehl, Fritz; Sieverding, Ewald; Palenzuela, Javier; Ineichen, Kurt; Alves da Silva, Gladstone

    2011-12-01

    Concomitant morphological and molecular analyses have led to major breakthroughs in the taxonomic organization of the phylum Glomeromycota. Fungi in this phylum are known to form arbuscular mycorrhiza, and so far three classes, five orders, 14 families and 29 genera have been described. Sensulato, spore formation in 10 of the arbuscular mycorrhiza-forming genera is exclusively glomoid, one is gigasporoid, seven are scutellosporoid, four are entrophosporoid, two are acaulosporoid, and one is pacisporoid. Spore bimorphism is found in three genera, and one genus is associated with cyanobacteria. Here we present the current classification developed in several recent publications and provide a summary to facilitate the identification of taxa from genus to class level.

  17. Multisite functional connectivity MRI classification of autism: ABIDE results

    Directory of Open Access Journals (Sweden)

    Jared A Nielsen

    2013-09-01

    Full Text Available Background: Systematic differences in functional connectivity MRI metrics have been consistently observed in autism, with predominantly decreased cortico-cortical connectivity. Previous attempts at single subject classification in high-functioning autism using whole brain point-to-point functional connectivity have yielded about 80% accurate classification of autism vs. control subjects across a wide age range. We attempted to replicate the method and results using the Autism Brain Imaging Data Exchange including resting state fMRI data obtained from 964 subjects and 16 separate international sites.Methods: For each of 964 subjects, we obtained pairwise functional connectivity measurements from a lattice of 7266 regions of interest covering the gray matter (26.4 million "connections" after preprocessing that included motion and slice timing correction, coregistration to an anatomic image, normalization to standard space, and voxelwise removal by regression of motion parameters, soft tissue, CSF, and white matter signals. Connections were grouped into multiple bins, and a leave-one-out classifier was evaluated on connections comprising each set of bins. Age, age-squared, gender, handedness, and site were included as covariates for the classifier.Results: Classification accuracy significantly outperformed chance but was much lower for multisite prediction than for previous single site results. As high as 60% accuracy was obtained for whole brain classification, with the best accuracy from connections involving regions of the default mode network, parahippocampal and fusiform gyri, insula, Wernicke Area, and intraparietal sulcus. The classifier score was related to symptom severity, social function, daily living skills, and verbal IQ. Classification accuracy was significantly higher for sites with longer BOLD imaging times.Conclusions: Multisite functional connectivity classification of autism outperformed chance using a simple leave

  18. CREST--classification resources for environmental sequence tags.

    Directory of Open Access Journals (Sweden)

    Anders Lanzén

    Full Text Available Sequencing of taxonomic or phylogenetic markers is becoming a fast and efficient method for studying environmental microbial communities. This has resulted in a steadily growing collection of marker sequences, most notably of the small-subunit (SSU ribosomal RNA gene, and an increased understanding of microbial phylogeny, diversity and community composition patterns. However, to utilize these large datasets together with new sequencing technologies, a reliable and flexible system for taxonomic classification is critical. We developed CREST (Classification Resources for Environmental Sequence Tags, a set of resources and tools for generating and utilizing custom taxonomies and reference datasets for classification of environmental sequences. CREST uses an alignment-based classification method with the lowest common ancestor algorithm. It also uses explicit rank similarity criteria to reduce false positives and identify novel taxa. We implemented this method in a web server, a command line tool and the graphical user interfaced program MEGAN. Further, we provide the SSU rRNA reference database and taxonomy SilvaMod, derived from the publicly available SILVA SSURef, for classification of sequences from bacteria, archaea and eukaryotes. Using cross-validation and environmental datasets, we compared the performance of CREST and SilvaMod to the RDP Classifier. We also utilized Greengenes as a reference database, both with CREST and the RDP Classifier. These analyses indicate that CREST performs better than alignment-free methods with higher recall rate (sensitivity as well as precision, and with the ability to accurately identify most sequences from novel taxa. Classification using SilvaMod performed better than with Greengenes, particularly when applied to environmental sequences. CREST is freely available under a GNU General Public License (v3 from http://apps.cbu.uib.no/crest and http://lcaclassifier.googlecode.com.

  19. 28 CFR 345.20 - Position classification.

    Science.gov (United States)

    2010-07-01

    ... 28 Judicial Administration 2 2010-07-01 2010-07-01 false Position classification. 345.20 Section... INDUSTRIES (FPI) INMATE WORK PROGRAMS Position Classification § 345.20 Position classification. (a) Inmate... the objectives and principles of pay classification as a part of the routine orientation of new...

  20. 32 CFR 2400.6 - Classification levels.

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 6 2010-07-01 2010-07-01 false Classification levels. 2400.6 Section 2400.6... Original Classification § 2400.6 Classification levels. (a) National security information (hereinafter... three authorized classification levels, such as “Secret Sensitive” or “Agency Confidential.” The...