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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. Accurate stemming of Dutch for text classification

    NARCIS (Netherlands)

    Gaustad, T; Bouma, G; Theune, M; Nijholt, A; Hondorp, H

    2002-01-01

    This paper investigates the use of stemming for classification of Dutch (email) texts. We introduce a stemmer, which combines dictionary lookup (implemented efficiently as a finite state automaton) with a rule-based backup strategy and,how, that it outperforms the Dutch Porter stemmer in terms of ac

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

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

    Directory of Open Access Journals (Sweden)

    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 .

  11. 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

  12. 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...

  13. A robust and accurate formulation of molecular and colloidal electrostatics

    Science.gov (United States)

    Sun, Qiang; Klaseboer, Evert; Chan, Derek Y. C.

    2016-08-01

    This paper presents a re-formulation of the boundary integral method for the Debye-Hückel model of molecular and colloidal electrostatics that removes the mathematical singularities that have to date been accepted as an intrinsic part of the conventional boundary integral equation method. The essence of the present boundary regularized integral equation formulation consists of subtracting a known solution from the conventional boundary integral method in such a way as to cancel out the singularities associated with the Green's function. This approach better reflects the non-singular physical behavior of the systems on boundaries with the benefits of the following: (i) the surface integrals can be evaluated accurately using quadrature without any need to devise special numerical integration procedures, (ii) being able to use quadratic or spline function surface elements to represent the surface more accurately and the variation of the functions within each element is represented to a consistent level of precision by appropriate interpolation functions, (iii) being able to calculate electric fields, even at boundaries, accurately and directly from the potential without having to solve hypersingular integral equations and this imparts high precision in calculating the Maxwell stress tensor and consequently, intermolecular or colloidal forces, (iv) a reliable way to handle geometric configurations in which different parts of the boundary can be very close together without being affected by numerical instabilities, therefore potentials, fields, and forces between surfaces can be found accurately at surface separations down to near contact, and (v) having the simplicity of a formulation that does not require complex algorithms to handle singularities will result in significant savings in coding effort and in the reduction of opportunities for coding errors. These advantages are illustrated using examples drawn from molecular and colloidal electrostatics.

  14. Quantum-Accurate Molecular Dynamics Potential for Tungsten

    Energy Technology Data Exchange (ETDEWEB)

    Wood, Mitchell; Thompson, Aidan P.

    2017-03-01

    The purpose of this short contribution is to report on the development of a Spectral Neighbor Analysis Potential (SNAP) for tungsten. We have focused on the characterization of elastic and defect properties of the pure material in order to support molecular dynamics simulations of plasma-facing materials in fusion reactors. A parallel genetic algorithm approach was used to efficiently search for fitting parameters optimized against a large number of objective functions. In addition, we have shown that this many-body tungsten potential can be used in conjunction with a simple helium pair potential1 to produce accurate defect formation energies for the W-He binary system.

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

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    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.

  16. 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.

  17. 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.

  18. Machine learning of accurate energy-conserving molecular force fields

    Science.gov (United States)

    Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel E.; Poltavsky, Igor; Schütt, Kristof T.; Müller, Klaus-Robert

    2017-01-01

    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-sized molecules with an accuracy of 0.3 kcal mol−1 for energies and 1 kcal mol−1 Å̊−1 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, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods. PMID:28508076

  19. 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/.

  20. 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.

  1. Accurate Classification of Protein Subcellular Localization from High-Throughput Microscopy Images Using Deep Learning

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    Tanel Pärnamaa

    2017-05-01

    Full Text Available High-throughput microscopy of many single cells generates high-dimensional data that are far from straightforward to analyze. One important problem is automatically detecting the cellular compartment where a fluorescently-tagged protein resides, a task relatively simple for an experienced human, but difficult to automate on a computer. Here, we train an 11-layer neural network on data from mapping thousands of yeast proteins, achieving per cell localization classification accuracy of 91%, and per protein accuracy of 99% on held-out images. We confirm that low-level network features correspond to basic image characteristics, while deeper layers separate localization classes. Using this network as a feature calculator, we train standard classifiers that assign proteins to previously unseen compartments after observing only a small number of training examples. Our results are the most accurate subcellular localization classifications to date, and demonstrate the usefulness of deep learning for high-throughput microscopy.

  2. 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.

  3. Accurate Kirkwood-Buff Integrals from Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Wedberg, Nils Hejle Rasmus Ingemar; O'Connell, John P.; Peters, Günther H.J.

    2010-01-01

    A method is proposed for obtaining thermodynamic properties via Kirkwood–Buff (KB) integrals from molecular simulations. In order to ensure that the KB integration converges, the pair distribution function is extrapolated to large distances using the extension method of Verlet, which enforces...

  4. On the accurate molecular dynamics analysis of biological molecules

    Science.gov (United States)

    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.

  5. 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....

  6. Accurate model selection of relaxed molecular clocks in bayesian phylogenetics.

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    Baele, Guy; Li, Wai Lok Sibon; Drummond, Alexei J; Suchard, Marc A; Lemey, Philippe

    2013-02-01

    Recent implementations of path sampling (PS) and stepping-stone sampling (SS) have been shown to outperform the harmonic mean estimator (HME) and a posterior simulation-based analog of Akaike's information criterion through Markov chain Monte Carlo (AICM), in bayesian model selection of demographic and molecular clock models. Almost simultaneously, a bayesian model averaging approach was developed that avoids conditioning on a single model but averages over a set of relaxed clock models. This approach returns estimates of the posterior probability of each clock model through which one can estimate the Bayes factor in favor of the maximum a posteriori (MAP) clock model; however, this Bayes factor estimate may suffer when the posterior probability of the MAP model approaches 1. Here, we compare these two recent developments with the HME, stabilized/smoothed HME (sHME), and AICM, using both synthetic and empirical data. Our comparison shows reassuringly that MAP identification and its Bayes factor provide similar performance to PS and SS and that these approaches considerably outperform HME, sHME, and AICM in selecting the correct underlying clock model. We also illustrate the importance of using proper priors on a large set of empirical data sets.

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

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    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.

  8. 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.

  9. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  11. 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 ...

  12. Current Trends in the Molecular Classification of Renal Neoplasms

    Directory of Open Access Journals (Sweden)

    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.

  13. Molecular Pathological Classification of Neurodegenerative Diseases: Turning towards Precision Medicine.

    Science.gov (United States)

    Kovacs, Gabor G

    2016-02-02

    Neurodegenerative diseases (NDDs) are characterized by selective dysfunction and loss of neurons associated with pathologically altered proteins that deposit in the human brain but also in peripheral organs. These proteins and their biochemical modifications can be potentially targeted for therapy or used as biomarkers. Despite a plethora of modifications demonstrated for different neurodegeneration-related proteins, such as amyloid-β, prion protein, tau, α-synuclein, TAR DNA-binding protein 43 (TDP-43), or fused in sarcoma protein (FUS), molecular classification of NDDs relies on detailed morphological evaluation of protein deposits, their distribution in the brain, and their correlation to clinical symptoms together with specific genetic alterations. A further facet of the neuropathology-based classification is the fact that many protein deposits show a hierarchical involvement of brain regions. This has been shown for Alzheimer and Parkinson disease and some forms of tauopathies and TDP-43 proteinopathies. The present paper aims to summarize current molecular classification of NDDs, focusing on the most relevant biochemical and morphological aspects. Since the combination of proteinopathies is frequent, definition of novel clusters of patients with NDDs needs to be considered in the era of precision medicine. Optimally, neuropathological categorizing of NDDs should be translated into in vivo detectable biomarkers to support better prediction of prognosis and stratification of patients for therapy trials.

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

    Science.gov (United States)

    2015-09-28

    Perdisci, D. Dagon, W. Lee, and N. Feamster, “Building a dynamic reputation system for dns ,” in USENIX Security , 2010. [24] M. Antonakakis, R. Perdisci...W. Lee, N. V. II, and D. Dagon, “Detecting malware domains at the upper dns hierarchy,” in USENIX Security , 2011. [25] R. Perdisci, A. Lanzi, and W...ABSTRACT 16. SECURITY CLASSIFICATION OF: Labeling malware samples with their appropriate malware family helps understand and track malware evolution and

  15. Accurate HEp-2 cell classification based on sparse bag of words coding.

    Science.gov (United States)

    Ensafi, Shahab; Lu, Shijian; Kassim, Ashraf A; Tan, Chew Lim

    2017-04-01

    Autoimmune diseases (AD) are the abnormal response of the immune system of the body to healthy tissues. ADs have generally been on the increase. Efficient computer aided diagnosis of ADs through classification of the human epithelial type 2 (HEp-2) cells become beneficial. These methods make lower diagnosis costs, faster response and better diagnosis repeatability. In this paper, we present an automated HEp-2 cell image classification technique that exploits the sparse coding of the visual features together with the Bag of Words model (SBoW). In particular, SURF (Speeded Up Robust Features) and SIFT (Scale-invariant feature transform) features are specially integrated to work in a complementary fashion. This method helps greatly improve the cell classification accuracy. Additionally, a hierarchical max-pooling method is proposed to aggregate the local sparse codes in different layers to provide final feature vector. Furthermore, various parameters of the dictionary learning including the dictionary size, the learning iteration number, and the pooling strategy is also investigated. Experiments conducted on publicly available datasets show that the proposed technique clearly outperforms state-of-the-art techniques in cell and specimen levels. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. 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

  17. 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

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

    Science.gov (United States)

    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.

  19. 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

  20. 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...... accurate in comparison to established benchmark models and present an application that illustrates the financial impact of more accurate forecasts obtained using our methodology....

  1. 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.

  2. 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.

  3. 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...

  4. Accurate classification of brain gliomas by discriminate dictionary learning based on projective dictionary pair learning of proton magnetic resonance spectra.

    Science.gov (United States)

    Adebileje, Sikiru Afolabi; Ghasemi, Keyvan; Aiyelabegan, Hammed Tanimowo; Saligheh Rad, Hamidreza

    2017-04-01

    Proton magnetic resonance spectroscopy is a powerful noninvasive technique that complements the structural images of cMRI, which aids biomedical and clinical researches, by identifying and visualizing the compositions of various metabolites within the tissues of interest. However, accurate classification of proton magnetic resonance spectroscopy is still a challenging issue in clinics due to low signal-to-noise ratio, overlapping peaks of metabolites, and the presence of background macromolecules. This paper evaluates the performance of a discriminate dictionary learning classifiers based on projective dictionary pair learning method for brain gliomas proton magnetic resonance spectroscopy spectra classification task, and the result were compared with the sub-dictionary learning methods. The proton magnetic resonance spectroscopy data contain a total of 150 spectra (74 healthy, 23 grade II, 23 grade III, and 30 grade IV) from two databases. The datasets from both databases were first coupled together, followed by column normalization. The Kennard-Stone algorithm was used to split the datasets into its training and test sets. Performance comparison based on the overall accuracy, sensitivity, specificity, and precision was conducted. Based on the overall accuracy of our classification scheme, the dictionary pair learning method was found to outperform the sub-dictionary learning methods 97.78% compared with 68.89%, respectively. Copyright © 2016 John Wiley & Sons, Ltd.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space

    Science.gov (United States)

    2015-01-01

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies. PMID:26113956

  12. Bilateral weighted radiographs are required for accurate classification of acromioclavicular separation: an observational study of 59 cases.

    Science.gov (United States)

    Ibrahim, E F; Forrest, N P; Forester, A

    2015-10-01

    Misinterpretation of the Rockwood classification system for acromioclavicular joint (ACJ) separations has resulted in a trend towards using unilateral radiographs for grading. Further, the use of weighted views to 'unmask' a grade III injury has fallen out of favour. Recent evidence suggests that many radiographic grade III injuries represent only a partial injury to the stabilising ligaments. This study aimed to determine (1) whether accurate classification is possible on unilateral radiographs and (2) the efficacy of weighted bilateral radiographs in unmasking higher-grade injuries. Complete bilateral non-weighted and weighted sets of radiographs for patients presenting with an acromioclavicular separation over a 10-year period were analysed retrospectively, and they were graded I-VI according to Rockwood's criteria. Comparison was made between grading based on (1) a single antero-posterior (AP) view of the injured side, (2) bilateral non-weighted views and (3) bilateral weighted views. Radiographic measurements for cases that changed grade after weighted views were statistically compared to see if this could have been predicted beforehand. Fifty-nine sets of radiographs on 59 patients (48 male, mean age of 33 years) were included. Compared with unilateral radiographs, non-weighted bilateral comparison films resulted in a grade change for 44 patients (74.5%). Twenty-eight of 56 patients initially graded as I, II or III were upgraded to grade V and two of three initial grade V patients were downgraded to grade III. The addition of a weighted view further upgraded 10 patients to grade V. No grade II injury was changed to grade III and no injury of any severity was downgraded by a weighted view. Grade III injuries upgraded on weighted views had a significantly greater baseline median percentage coracoclavicular distance increase than those that were not upgraded (80.7% vs. 55.4%, p=0.015). However, no cut-off point for this value could be identified to predict an

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. Accurate phosphoregulation of kinetochore–microtubule affinity requires unconstrained molecular interactions

    Science.gov (United States)

    Zaytsev, Anatoly V.; Sundin, Lynsie J.R.; DeLuca, Keith F.

    2014-01-01

    Accurate chromosome segregation relies on dynamic interactions between microtubules (MTs) and the NDC80 complex, a major kinetochore MT-binding component. Phosphorylation at multiple residues of its Hec1 subunit may tune kinetochore–MT binding affinity for diverse mitotic functions, but molecular details of such phosphoregulation remain elusive. Using quantitative analyses of mitotic progression in mammalian cells, we show that Hec1 phosphorylation provides graded control of kinetochore–MT affinity. In contrast, modeling the kinetochore interface with repetitive MT binding sites predicts a switchlike response. To reconcile these findings, we hypothesize that interactions between NDC80 complexes and MTs are not constrained, i.e., the NDC80 complexes can alternate their binding between adjacent kinetochore MTs. Experiments using cells with phosphomimetic Hec1 mutants corroborate predictions of such a model but not of the repetitive sites model. We propose that accurate regulation of kinetochore–MT affinity is driven by incremental phosphorylation of an NDC80 molecular “lawn,” in which the NDC80–MT bonds reorganize dynamically in response to the number and stability of MT attachments. PMID:24982430

  18. Seroprofiling at the Candida albicans protein species level unveils an accurate molecular discriminator for candidemia.

    Science.gov (United States)

    Pitarch, Aida; Nombela, César; Gil, Concha

    2016-02-16

    Serum antibodies to specific Candida proteins have been reported as potential diagnostic biomarkers for candidemia. However, their diagnostic usefulness at the protein species level has hardly been examined. Using serological proteome analysis, we explored the IgG-antibody responses to Candida albicans protein species in candidemia and control patients. We found that 87 discrete protein species derived from 34 unique proteins were IgG-targets, although only 43 of them were differentially recognized by candidemia and control sera. An increase in the speciation of the immunome, connectivity and modularity of antigenic species co-recognition networks, and heterogeneity of antigenic species recognition patterns was associated with candidemia. IgG antibodies to certain discrete protein species were better predictors of candidemia than those to their corresponding proteins. A molecular discriminator delineated from the combined fingerprints of IgG antibodies to two distinct species of phosphoglycerate kinase and enolase accurately classified candidemia and control patients. These results provide new insight into the anti-Candida IgG-antibody response development in candidemia, and demonstrate that an immunoproteomic signature at the molecular level may be useful for its diagnosis. Our study further highlights the importance of defining pathogen-specific antigens at the chemical and molecular level for their potential application as immunodiagnostic reagents or even vaccine candidates.

  19. 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.

  20. 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).

  1. 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.

  2. 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

  3. 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...

  4. 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.

  5. Accurate conformation-dependent molecular electrostatic potentials for high-throughput in silico drug discovery.

    Science.gov (United States)

    Puranen, J Santeri; Vainio, Mikko J; Johnson, Mark S

    2010-06-01

    The atom-centered partial charges-approximation is commonly used in current molecular modeling tools as a computationally inexpensive alternative to quantum mechanics for modeling electrostatics. Even today, the use of partial charges remains useful despite significant advances in improving the efficiency of ab initio methods. Here, we report on new parameters for the EEM and SFKEEM electronegativity equalization-based methods for rapidly determining partial charges that will accurately model the electrostatic potential of flexible molecules. The developed parameters cover most pharmaceutically relevant chemistries, and charges obtained using these parameters reproduce the B3LYP/cc-pVTZ reference electrostatic potential of a set of FDA-approved drug molecules at best to an average accuracy of 13 +/- 4 kJ mol(-1); thus, equipped with these parameters electronegativity equalization-based methods rival the current best non-quantum mechanical methods, such as AM1-BCC, in accuracy, yet incur a lower computational cost. Software implementations of EEM and SFKEEM, including the developed parameters, are included in the conformer-generation tool BALLOON, available free of charge at http://web.abo.fi/fak/mnf/bkf/research/johnson/software.php. Copyright 2009 Wiley Periodicals, Inc.

  6. 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

  7. A simple method to combine multiple molecular biomarkers for dichotomous diagnostic classification

    Directory of Open Access Journals (Sweden)

    Amin Manik A

    2006-10-01

    Full Text Available Abstract Background In spite of the recognized diagnostic potential of biomarkers, the quest for squelching noise and wringing in information from a given set of biomarkers continues. Here, we suggest a statistical algorithm that – assuming each molecular biomarker to be a diagnostic test – enriches the diagnostic performance of an optimized set of independent biomarkers employing established statistical techniques. We validated the proposed algorithm using several simulation datasets in addition to four publicly available real datasets that compared i subjects having cancer with those without; ii subjects with two different cancers; iii subjects with two different types of one cancer; and iv subjects with same cancer resulting in differential time to metastasis. Results Our algorithm comprises of three steps: estimating the area under the receiver operating characteristic curve for each biomarker, identifying a subset of biomarkers using linear regression and combining the chosen biomarkers using linear discriminant function analysis. Combining these established statistical methods that are available in most statistical packages, we observed that the diagnostic accuracy of our approach was 100%, 99.94%, 96.67% and 93.92% for the real datasets used in the study. These estimates were comparable to or better than the ones previously reported using alternative methods. In a synthetic dataset, we also observed that all the biomarkers chosen by our algorithm were indeed truly differentially expressed. Conclusion The proposed algorithm can be used for accurate diagnosis in the setting of dichotomous classification of disease states.

  8. 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

  9. Determinants of molecular marker based classification of rice (Oryza ...

    African Journals Online (AJOL)

    mr devi singh

    2015-01-07

    Jan 7, 2015 ... development of molecular fingerprints of diverse varieties of Basmati and non Basmati rice adapted to irrigated and .... nm and 280 nm, using UV Bio-Rad spectrophotometer. ...... A rapid technique for scent determination.

  10. [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.

  11. 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…

  12. Use of DNA methylation for cancer detection and molecular classification.

    Science.gov (United States)

    Zhu, Jingde; Yao, Xuebiao

    2007-03-31

    Conjugation of the methyl group at the fifth carbon of cytosines within the palindromic dinucleotide 5'-CpG-3' sequence (DNA methylation) is the best studied epigenetic mechanism, which acts together with other epigenetic entities: histone modification, chromatin remodeling and microRNAs to shape the chromatin structure of DNA according to its functional state. The cancer genome is frequently characterized by hypermethylation of specific genes concurrently with an overall decrease in the level of 5-methyl cytosine, the pathological implication of which to the cancerous state has been well established. While the latest genome-wide technologies have been applied to classify and interpret the epigenetic layer of gene regulation in the physiological and disease states, the epigenetic testing has also been seriously explored in clinical practice for early detection, refining tumor staging and predicting disease recurrence. This critique reviews the latest research findings on the use of DNA methylation in cancer diagnosis, prognosis and staging/classification.

  13. Molecular systematics of higher primates: genealogical relations and classification.

    Science.gov (United States)

    Miyamoto, M M; Koop, B F; Slightom, J L; Goodman, M; Tennant, M R

    1988-01-01

    We obtained 5' and 3' flanking sequences (5.4 kilobase pairs) from the psi eta-globin gene region of the rhesus macaque (Macaca mulatta) and combined them with available nucleotide data. The completed sequence, representing 10.8 kilobase pairs of contiguous noncoding DNA, was compared to the same orthologous regions available for human (Homo sapiens, as represented by five different alleles), common chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla), and orangutan (Pongo pygmaeus). The nucleotide sequence for Macaca mulatta provided the outgroup perspective needed to evaluate better the relationships of humans and great apes. Pairwise comparisons and parsimony analysis of these orthologues clearly demonstrated (i) that humans and great apes share a high degree of genetic similarity and (ii) that humans, chimpanzees, and gorillas form a natural monophyletic group. These conclusions strongly favor a genealogical classification for higher primates consisting of a single family (Hominidae) with two subfamilies (Homininae for Homo, Pan, and Gorilla and Ponginae for Pongo). PMID:3174657

  14. Molecular phylogeny of the Bothriocephalidea (Cestoda): molecular data challenge morphological classification.

    Science.gov (United States)

    Brabec, Jan; Waeschenbach, Andrea; Scholz, Tomáš; Littlewood, D Timothy J; Kuchta, Roman

    2015-10-01

    In this study, the relationships of the cestode order Bothriocephalidea, parasites of marine and freshwater bony fish, were assessed using multi-gene molecular phylogenetic analyses. The dataset included 59 species, covering approximately 70% of currently recognised genera, a sample of bothriocephalidean biodiversity gathered through an intense 15year effort. The order as currently circumscribed, while monophyletic, includes three non-monophyletic and one monophyletic families. Bothriocephalidae is monophyletic and forms the most derived lineage of the order, comprised of a single freshwater and several marine clades. Biogeographic patterns within the freshwater clade are indicative of past radiations having occurred in Africa and North America. The earliest diverging lineages of the order comprise a paraphyletic Triaenophoridae. The Echinophallidae, consisting nearly exclusively of parasites of pelagic fish, was also resolved as paraphyletic with respect to the Bothriocephalidae. Philobythoides sp., the only representative included from the Philobythiidae, a unique family of parasites of bathypelagic fish, was sister to the genus Eubothrium, the latter constituting one of the lineages of the paraphyletic Triaenophoridae. Due to the weak statistical support for most of the basal nodes of the Triaenophoridae and Echinophallidae, as well as the lack of obvious morphological synapomorphies shared by taxa belonging to the statistically well-supported lineages, the current family-level classification, although mostly non-monophyletic, is provisionally retained, with the exception of the family Philobythiidae, which is recognised as a synonym of the Triaenophoridae. In addition, Schyzocotyle is resurrected to accommodate the invasive Asian fish tapeworm, Schyzocotyle acheilognathi (Yamaguti, 1934) n. comb. (syn. Bothriocephalus acheilognathi Yamaguti, 1934), which is of veterinary importance, and Schyzocotyle nayarensis (Malhotra, 1983) n. comb. (syn. Ptychobothrium

  15. Classification

    DEFF Research Database (Denmark)

    Hjørland, Birger

    2017-01-01

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

  16. 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.

  17. 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.

  18. 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.

  19. Accurate white matter lesion segmentation by k nearest neighbor classification with tissue type priors (kNN-TTPs).

    Science.gov (United States)

    Steenwijk, Martijn D; Pouwels, Petra J W; Daams, Marita; van Dalen, Jan Willem; Caan, Matthan W A; Richard, Edo; Barkhof, Frederik; Vrenken, Hugo

    2013-01-01

    The segmentation and volumetric quantification of white matter (WM) lesions play an important role in monitoring and studying neurological diseases such as multiple sclerosis (MS) or cerebrovascular disease. This is often interactively done using 2D magnetic resonance images. Recent developments in acquisition techniques allow for 3D imaging with much thinner sections, but the large number of images per subject makes manual lesion outlining infeasible. This warrants the need for a reliable automated approach. Here we aimed to improve k nearest neighbor (kNN) classification of WM lesions by optimizing intensity normalization and using spatial tissue type priors (TTPs). The kNN-TTP method used kNN classification with 3.0 T 3DFLAIR and 3DT1 intensities as well as MNI-normalized spatial coordinates as features. Additionally, TTPs were computed by nonlinear registration of data from healthy controls. Intensity features were normalized using variance scaling, robust range normalization or histogram matching. The algorithm was then trained and evaluated using a leave-one-out experiment among 20 patients with MS against a reference segmentation that was created completely manually. The performance of each normalization method was evaluated both with and without TTPs in the feature set. Volumetric agreement was evaluated using intra-class coefficient (ICC), and voxelwise spatial agreement was evaluated using Dice similarity index (SI). Finally, the robustness of the method across different scanners and patient populations was evaluated using an independent sample of elderly subjects with hypertension. The intensity normalization method had a large influence on the segmentation performance, with average SI values ranging from 0.66 to 0.72 when no TTPs were used. Independent of the normalization method, the inclusion of TTPs as features increased performance particularly by reducing the lesion detection error. Best performance was achieved using variance scaled intensity

  20. Magnetic resonance imaging is comparable to computed tomography for determination of glenoid version but does not accurately distinguish between Walch B2 and C classifications.

    Science.gov (United States)

    Lowe, Jeremiah T; Testa, Edward J; Li, Xinning; Miller, Suzanne; DeAngelis, Joseph P; Jawa, Andrew

    2017-04-01

    Computed tomography (CT) scan is the standard for the preoperative assessment of glenoid version and morphology before total shoulder arthroplasty. However, the capacity of magnetic resonance imaging (MRI) to visualize bone morphology has improved with advancing technology. The purpose of this study was to compare the accuracy of MRI to CT for assessment of glenoid version and Walch classification. Three fellowship-trained shoulder surgeons assessed glenoid version and Walch classification of 30 patients with primary shoulder osteoarthritis who received both CT and MRI scans before total shoulder arthroplasty. Version measurements, Walch classification, and observer agreement were compared. Mean glenoid version was -15.5° and -18.6° by CT and MRI, respectively (P = .17). Interobserver reliability coefficients were good for both imaging modalities (CT, 0.73; MRI, 0.62). Intraobserver coefficients were good to excellent for CT (range, 0.76-0.87) and good for MRI (range, 0.75-0.79). For Walch classification, interobserver reliability for both modalities was merely fair, whereas intraobserver reliability was moderate to good. Although identification of type A1, A2, and B1 was nearly identical between CT and MRI, there was observer disagreement on type B2 (P = .001) and C glenoids (P = .03). Specifically, MRI underidentified type B2 and overidentified type C compared with CT. MRI is largely comparable to CT scan for evaluation of the glenoid, with similar measurements of version and identification of less extreme Walch glenoids. However, MRI is less accurate at distinguishing between type B2 and C glenoids. Copyright © 2017 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

  1. 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...

  2. 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.

  3. MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data.

    Science.gov (United States)

    Fosso, B; Santamaria, M; D'Antonio, M; Lovero, D; Corrado, G; Vizza, E; Passaro, N; Garbuglia, A R; Capobianchi, M R; Crescenzi, M; Valiente, G; Pesole, G

    2017-06-01

    Shotgun metagenomics by high-throughput sequencing may allow deep and accurate characterization of host-associated total microbiomes, including bacteria, viruses, protists and fungi. However, the analysis of such sequencing data is still extremely challenging in terms of both overall accuracy and computational efficiency, and current methodologies show substantial variability in misclassification rate and resolution at lower taxonomic ranks or are limited to specific life domains (e.g. only bacteria). We present here MetaShot, a workflow for assessing the total microbiome composition from host-associated shotgun sequence data, and show its overall optimal accuracy performance by analyzing both simulated and real datasets. https://github.com/bfosso/MetaShot. graziano.pesole@uniba.it. Supplementary data are available at Bioinformatics online.

  4. 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.

  5. 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.

  6. 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

  7. [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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. Accurate schemes for calculation of thermodynamic properties of liquid mixtures from molecular dynamics simulations

    Science.gov (United States)

    Caro, Miguel A.; Laurila, Tomi; Lopez-Acevedo, Olga

    2016-12-01

    We explore different schemes for improved accuracy of entropy calculations in aqueous liquid mixtures from molecular dynamics (MD) simulations. We build upon the two-phase thermodynamic (2PT) model of Lin et al. [J. Chem. Phys. 119, 11792 (2003)] and explore new ways to obtain the partition between the gas-like and solid-like parts of the density of states, as well as the effect of the chosen ideal "combinatorial" entropy of mixing, both of which have a large impact on the results. We also propose a first-order correction to the issue of kinetic energy transfer between degrees of freedom (DoF). This problem arises when the effective temperatures of translational, rotational, and vibrational DoF are not equal, either due to poor equilibration or reduced system size/time sampling, which are typical problems for ab initio MD. The new scheme enables improved convergence of the results with respect to configurational sampling, by up to one order of magnitude, for short MD runs. To ensure a meaningful assessment, we perform MD simulations of liquid mixtures of water with several other molecules of varying sizes: methanol, acetonitrile, N, N-dimethylformamide, and n-butanol. Our analysis shows that results in excellent agreement with experiment can be obtained with little computational effort for some systems. However, the ability of the 2PT method to succeed in these calculations is strongly influenced by the choice of force field, the fluidicity (hard-sphere) formalism employed to obtain the solid/gas partition, and the assumed combinatorial entropy of mixing. We tested two popular force fields, GAFF and OPLS with SPC/E water. For the mixtures studied, the GAFF force field seems to perform as a slightly better "all-around" force field when compared to OPLS+SPC/E.

  20. 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...

  1. 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.

  2. 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

  3. 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

  4. Microarray gene expression analysis of fixed archival tissue permits molecular classification and identification of potential therapeutic targets in diffuse large B-cell lymphoma.

    Science.gov (United States)

    Linton, Kim; Howarth, Christopher; Wappett, Mark; Newton, Gillian; Lachel, Cynthia; Iqbal, Javeed; Pepper, Stuart; Byers, Richard; Chan, Wing John; Radford, John

    2012-01-01

    Refractory/relapsed diffuse large B-cell lymphoma (DLBCL) has a poor prognosis. Novel drugs targeting the constitutively activated NF-κB pathway characteristic of ABC-DLBCL are promising, but evaluation depends on accurate activated B cell-like (ABC)/germinal center B cell-like (GCB) molecular classification. This is traditionally performed on gene microarray expression profiles of fresh biopsies, which are not routinely collected, or by immunohistochemistry on formalin-fixed, paraffin-embedded (FFPE) tissue, which lacks reproducibility and classification accuracy. We explored the possibility of using routine archival FFPE tissue for gene microarray applications. We examined Affymetrix HG U133 Plus 2.0 gene expression profiles from paired archival FFPE and fresh-frozen tissues of 40 ABC/GCB-classified DLBCL cases to compare classification accuracy and test the potential for this approach to aid the discovery of therapeutic targets and disease classifiers in DLBCL. Unsupervised hierarchical clustering of unselected present probe sets distinguished ABC/GCB in FFPE with remarkable accuracy, and a Bayesian classifier correctly assigned 32 of 36 cases with >90% probability. Enrichment for NF-κB genes was appropriately seen in ABC-DLBCL FFPE tissues. The top discriminatory genes expressed in FFPE separated cases with high statistical significance and contained novel biology with potential therapeutic insights, warranting further investigation. These results support a growing understanding that archival FFPE tissues can be used in microarray experiments aimed at molecular classification, prognostic biomarker discovery, and molecular exploration of rare diseases. Copyright © 2012 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  5. Leveraging external knowledge on molecular interactions in classification methods for risk prediction of patients.

    Science.gov (United States)

    Porzelius, Christine; Johannes, Marc; Binder, Harald; Beissbarth, Tim

    2011-03-01

    Classification of patients based on molecular markers, for example into different risk groups, is a modern field in medical research. The aim of this classification is often a better diagnosis or individualized therapy. The search for molecular markers often utilizes extremely high-dimensional data sets (e.g. gene-expression microarrays). However, in situations where the number of measured markers (genes) is intrinsically higher than the number of available patients, standard methods from statistical learning fail to deal correctly with this so-called "curse of dimensionality". Also feature or dimension reduction techniques based on statistical models promise only limited success. Several recent methods explore ideas of how to quantify and incorporate biological prior knowledge of molecular interactions and known cellular processes into the feature selection process. This article aims to give an overview of such current methods as well as the databases, where this external knowledge can be obtained from. For illustration, two recent methods are compared in detail, a feature selection approach for support vector machines as well as a boosting approach for regression models. As a practical example, data on patients with acute lymphoblastic leukemia are considered, where the binary endpoint "relapse within first year" should be predicted. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. 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.

  7. 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.

  8. 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.

  9. 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.).

  10. 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.

  11. 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.

  12. Theory of bi-molecular association dynamics in 2D for accurate model and experimental parameterization of binding rates.

    Science.gov (United States)

    Yogurtcu, Osman N; Johnson, Margaret E

    2015-08-28

    The dynamics of association between diffusing and reacting molecular species are routinely quantified using simple rate-equation kinetics that assume both well-mixed concentrations of species and a single rate constant for parameterizing the binding rate. In two-dimensions (2D), however, even when systems are well-mixed, the assumption of a single characteristic rate constant for describing association is not generally accurate, due to the properties of diffusional searching in dimensions d ≤ 2. Establishing rigorous bounds for discriminating between 2D reactive systems that will be accurately described by rate equations with a single rate constant, and those that will not, is critical for both modeling and experimentally parameterizing binding reactions restricted to surfaces such as cellular membranes. We show here that in regimes of intrinsic reaction rate (ka) and diffusion (D) parameters ka/D > 0.05, a single rate constant cannot be fit to the dynamics of concentrations of associating species independently of the initial conditions. Instead, a more sophisticated multi-parametric description than rate-equations is necessary to robustly characterize bimolecular reactions from experiment. Our quantitative bounds derive from our new analysis of 2D rate-behavior predicted from Smoluchowski theory. Using a recently developed single particle reaction-diffusion algorithm we extend here to 2D, we are able to test and validate the predictions of Smoluchowski theory and several other theories of reversible reaction dynamics in 2D for the first time. Finally, our results also mean that simulations of reactive systems in 2D using rate equations must be undertaken with caution when reactions have ka/D > 0.05, regardless of the simulation volume. We introduce here a simple formula for an adaptive concentration dependent rate constant for these chemical kinetics simulations which improves on existing formulas to better capture non-equilibrium reaction dynamics from dilute

  13. 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.

  14. 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.

  15. Institutional prevalence of malignancy of indeterminate thyroid cytology is necessary but insufficient to accurately interpret molecular marker tests.

    Science.gov (United States)

    Valderrabano, Pablo; Leon, Marino E; Centeno, Barbara A; Otto, Kristen J; Khazai, Laila; McCaffrey, Judith C; Russell, Jeffery S; McIver, Bryan

    2016-05-01

    Several molecular marker tests are available to refine the diagnosis of thyroid nodules. Knowing the true prevalence of malignancy (PoM) within each cytological category is considered necessary to select the most appropriate test and to interpret results accurately. We describe our institutional PoM among cytological categories and report our experience with molecular markers. Single-center retrospective study. We calculated the institutional PoM for each category of the Bethesda system (Bethesda) on all thyroid nodules with cytological evaluation from October 2008 to May 2014. We estimated the predictive values for Afirma, miRInform, and ThyroSeq v2, based on published sensitivity and specificity. Finally, we assessed our own experience with miRInform. The PoMs for Bethesda III and IV categories were 21 and 28%, respectively. ThyroSeq v2 achieves the highest theoretical negative and positive predictive values (NPV and PPV) in Bethesda III (98 and 75%) and Bethesda IV categories (96 and 83%). At our institution, miRInform detected a mutation in 16% of 109 indeterminate nodules tested, all in Bethesda IV specimens. Histology was available in 56 (51%) nodules. The observed sensitivity and specificity in Bethesda IV specimens were 63 and 86%, yielding an NPV and a PPV of 75 and 77%, respectively. For our current Bethesda III and IV PoM, the actual performance of miRInform was worse than expected. Theoretically ThyroSeq v2 should have the best performance, but it could be affected in the same way as miRInform, given the similarities between the tests. Assessing the institutional performance of each test is necessary along with PoM individualization. © 2016 European Society of Endocrinology.

  16. 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.

  17. 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.

  18. 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.

  19. 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

    2017-04-01

    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.

  20. Integrating molecular markers into the World Health Organization classification of CNS tumors: a survey of the neuro-oncology community.

    Science.gov (United States)

    Aldape, Kenneth; Nejad, Romina; Louis, David N; Zadeh, Gelareh

    2017-03-01

    Molecular markers provide important biological and clinical information related to the classification of brain tumors, and the integration of relevant molecular parameters into brain tumor classification systems has been a widely discussed topic in neuro-oncology over the past decade. With recent advances in the development of clinically relevant molecular signatures and the 2016 World Health Organization (WHO) update, the views of the neuro-oncology community on such changes would be informative for implementing this process. A survey with 8 questions regarding molecular markers in tumor classification was sent to an email list of Society for Neuro-Oncology members and attendees of prior meetings (n=5065). There were 403 respondents. Analysis was performed using whole group response, based on self-reported subspecialty. The survey results show overall strong support for incorporating molecular knowledge into the classification and clinical management of brain tumors. Across all 7 subspecialty groups, ≥70% of respondents agreed to this integration. Interestingly, some variability is seen among subspecialties, notably with lowest support from neuropathologists, which may reflect their roles in implementing such diagnostic technologies. Based on a survey provided to the neuro-oncology community, we report strong support for the integration of molecular markers into the WHO classification of brain tumors, as well as for using an integrated "layered" diagnostic format. While membership from each specialty showed support, there was variation by specialty in enthusiasm regarding proposed changes. The initial results of this survey influenced the deliberations underlying the 2016 WHO classification of tumors of the central nervous system.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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。

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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. Copyright © 2016. Published by Elsevier Inc.

  4. 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.

  5. A preliminary phylogeny of the 'didymocarpoid Gesneriaceae' based on three molecular data sets: Incongruence with available tribal classifications.

    Science.gov (United States)

    Möller, Michael; Pfosser, Martin; Jang, Chang-Gee; Mayer, Veronika; Clark, Alexandra; Hollingsworth, Michelle L; Barfuss, Michael H J; Wang, Yin-Zheng; Kiehn, Michael; Weber, Anton

    2009-05-01

    The 'didymocarpoid Gesneriaceae' (traditional subfam. Cyrtandroideae excluding Epithemateae) are the largest group of Old World Gesneriaceae, comprising 85 genera and 1800 species. We attempt to resolve their hitherto poorly understood generic relationships using three molecular markers on 145 species, of which 128 belong to didymocarpoid Gesneriaceae. Our analyses demonstrate that consistent topological relationships can be retrieved from data sets with missing data using subsamples and different combinations of gene sequences. We show that all available classifications in Old World Gesneriaceae are artificial and do not reflect natural relationships. At the base of the didymocarpoids are grades of clades comprising isolated genera and small groups from Asia and Europe. These are followed by a clade comprising the African and Madagascan genera. The remaining clades represent the advanced Asiatic and Malesian genera. They include a major group with mostly twisted capsules. The much larger group of remaining genera comprises exclusively genera with straight capsules and the huge genus Cyrtandra with indehiscent fruits. Several genera such as Briggsia, Henckelia, and Chirita are not monophyletic; Chirita is even distributed throughout five clades. This degree of incongruence between molecular phylogenies, traditional classifications, and generic delimitations indicates the problems with classifications based on, sometimes a single, morphological characters.

  6. Quantitative MRI radiomics in the prediction of molecular classifications of breast cancer subtypes in the TCGA/TCIA data set.

    Science.gov (United States)

    Li, Hui; Zhu, Yitan; Burnside, Elizabeth S; Huang, Erich; Drukker, Karen; Hoadley, Katherine A; Fan, Cheng; Conzen, Suzanne D; Zuley, Margarita; Net, Jose M; Sutton, Elizabeth; Whitman, Gary J; Morris, Elizabeth; Perou, Charles M; Ji, Yuan; Giger, Maryellen L

    2016-01-01

    Using quantitative radiomics, we demonstrate that computer-extracted magnetic resonance (MR) image-based tumor phenotypes can be predictive of the molecular classification of invasive breast cancers. Radiomics analysis was performed on 91 MRIs of biopsy-proven invasive breast cancers from National Cancer Institute's multi-institutional TCGA/TCIA. Immunohistochemistry molecular classification was performed including estrogen receptor, progesterone receptor, human epidermal growth factor receptor 2, and for 84 cases, the molecular subtype (normal-like, luminal A, luminal B, HER2-enriched, and basal-like). Computerized quantitative image analysis included: three-dimensional lesion segmentation, phenotype extraction, and leave-one-case-out cross validation involving stepwise feature selection and linear discriminant analysis. The performance of the classifier model for molecular subtyping was evaluated using receiver operating characteristic analysis. The computer-extracted tumor phenotypes were able to distinguish between molecular prognostic indicators; area under the ROC curve values of 0.89, 0.69, 0.65, and 0.67 in the tasks of distinguishing between ER+ versus ER-, PR+ versus PR-, HER2+ versus HER2-, and triple-negative versus others, respectively. Statistically significant associations between tumor phenotypes and receptor status were observed. More aggressive cancers are likely to be larger in size with more heterogeneity in their contrast enhancement. Even after controlling for tumor size, a statistically significant trend was observed within each size group (P = 0.04 for lesions ≤ 2 cm; P = 0.02 for lesions >2 to ≤5 cm) as with the entire data set (P-value = 0.006) for the relationship between enhancement texture (entropy) and molecular subtypes (normal-like, luminal A, luminal B, HER2-enriched, basal-like). In conclusion, computer-extracted image phenotypes show promise for high-throughput discrimination of breast cancer subtypes and may yield a

  7. Combining multiple hypothesis testing and affinity propagation clustering leads to accurate, robust and sample size independent classification on gene expression data

    Directory of Open Access Journals (Sweden)

    Sakellariou Argiris

    2012-10-01

    Full Text Available Abstract Background A feature selection method in microarray gene expression data should be independent of platform, disease and dataset size. Our hypothesis is that among the statistically significant ranked genes in a gene list, there should be clusters of genes that share similar biological functions related to the investigated disease. Thus, instead of keeping N top ranked genes, it would be more appropriate to define and keep a number of gene cluster exemplars. Results We propose a hybrid FS method (mAP-KL, which combines multiple hypothesis testing and affinity propagation (AP-clustering algorithm along with the Krzanowski & Lai cluster quality index, to select a small yet informative subset of genes. We applied mAP-KL on real microarray data, as well as on simulated data, and compared its performance against 13 other feature selection approaches. Across a variety of diseases and number of samples, mAP-KL presents competitive classification results, particularly in neuromuscular diseases, where its overall AUC score was 0.91. Furthermore, mAP-KL generates concise yet biologically relevant and informative N-gene expression signatures, which can serve as a valuable tool for diagnostic and prognostic purposes, as well as a source of potential disease biomarkers in a broad range of diseases. Conclusions mAP-KL is a data-driven and classifier-independent hybrid feature selection method, which applies to any disease classification problem based on microarray data, regardless of the available samples. Combining multiple hypothesis testing and AP leads to subsets of genes, which classify unknown samples from both, small and large patient cohorts with high accuracy.

  8. 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.

  9. 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.

  10. 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.

  11. Accurate age classification of 6 and 12 month-old infants based on resting-state functional connectivity magnetic resonance imaging data.

    Science.gov (United States)

    Pruett, John R; Kandala, Sridhar; Hoertel, Sarah; Snyder, Abraham Z; Elison, Jed T; Nishino, Tomoyuki; Feczko, Eric; Dosenbach, Nico U F; Nardos, Binyam; Power, Jonathan D; Adeyemo, Babatunde; Botteron, Kelly N; McKinstry, Robert C; Evans, Alan C; Hazlett, Heather C; Dager, Stephen R; Paterson, Sarah; Schultz, Robert T; Collins, D Louis; Fonov, Vladimir S; Styner, Martin; Gerig, Guido; Das, Samir; Kostopoulos, Penelope; Constantino, John N; Estes, Annette M; Petersen, Steven E; Schlaggar, Bradley L; Piven, Joseph

    2015-04-01

    Human large-scale functional brain networks are hypothesized to undergo significant changes over development. Little is known about these functional architectural changes, particularly during the second half of the first year of life. We used multivariate pattern classification of resting-state functional connectivity magnetic resonance imaging (fcMRI) data obtained in an on-going, multi-site, longitudinal study of brain and behavioral development to explore whether fcMRI data contained information sufficient to classify infant age. Analyses carefully account for the effects of fcMRI motion artifact. Support vector machines (SVMs) classified 6 versus 12 month-old infants (128 datasets) above chance based on fcMRI data alone. Results demonstrate significant changes in measures of brain functional organization that coincide with a special period of dramatic change in infant motor, cognitive, and social development. Explorations of the most different correlations used for SVM lead to two different interpretations about functional connections that support 6 versus 12-month age categorization. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  12. Accurate age classification of 6 and 12 month-old infants based on resting-state functional connectivity magnetic resonance imaging data

    Directory of Open Access Journals (Sweden)

    John R. Pruett, Jr.

    2015-04-01

    Full Text Available Human large-scale functional brain networks are hypothesized to undergo significant changes over development. Little is known about these functional architectural changes, particularly during the second half of the first year of life. We used multivariate pattern classification of resting-state functional connectivity magnetic resonance imaging (fcMRI data obtained in an on-going, multi-site, longitudinal study of brain and behavioral development to explore whether fcMRI data contained information sufficient to classify infant age. Analyses carefully account for the effects of fcMRI motion artifact. Support vector machines (SVMs classified 6 versus 12 month-old infants (128 datasets above chance based on fcMRI data alone. Results demonstrate significant changes in measures of brain functional organization that coincide with a special period of dramatic change in infant motor, cognitive, and social development. Explorations of the most different correlations used for SVM lead to two different interpretations about functional connections that support 6 versus 12-month age categorization.

  13. 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.

  14. 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.

    Science.gov (United States)

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

    2015-01-07

    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 initio approaches can be applied only to small numbers of atoms, while large numbers of atoms are required for having configurations that are representative of a liquid. Here we show that a high-accuracy value for the electronic band gap of water can be obtained by combining beyond-DFT methods and statistical time-averaging. Liquid water is simulated at 300 K using a plane-wave density functional theory molecular dynamics (PW-DFT-MD) simulation and a van der Waals density functional (optB88-vdW). After applying a self-consistent GW correction the band gap of liquid water at 300 K is calculated as 7.3 eV, in good agreement with recent experimental observations in the literature (6.9 eV). For simulations of phase transformations and chemical reactions in water or aqueous solutions whereby an accurate description of the electronic structure is required, we suggest to use these advanced GW corrections in combination with the statistical analysis of quantum mechanical MD simulations.

  15. 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.

  16. 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.

  17. Simple Sequence Repeat Polymorphisms (SSRPs for Evaluation of Molecular Diversity and Germplasm Classification of Minor Crops

    Directory of Open Access Journals (Sweden)

    Nam-Soo Kim

    2009-11-01

    Full Text Available Evaluation of the genetic diversity among populations is an essential prerequisite for the preservation of endangered species. Thousands of new accessions are introduced into germplasm institutes each year, thereby necessitating assessment of their molecular diversity before elimination of the redundant genotypes. Of the protocols that facilitate the assessment of molecular diversity, SSRPs (simple sequence repeat polymorphisms or microsatellite variation is the preferred system since it detects a large number of DNA polymorphisms with relatively simple technical complexity. The paucity of information on DNA sequences has limited their widespread utilization in the assessment of genetic diversity of minor or neglected crop species. However, recent advancements in DNA sequencing and PCR technologies in conjunction with sophisticated computer software have facilitated the development of SSRP markers in minor crops. This review examines the development and molecular nature of SSR markers, and their utilization in many aspects of plant genetics and ecology.

  18. Molecular phylogeny of Amphora sensu lato (Bacillariophyta): an investigation into the monophyly and classification of the amphoroid diatoms.

    Science.gov (United States)

    Stepanek, Joshua G; Kociolek, J Patrick

    2014-03-01

    Amphora sensu lato encompasses a large group of raphid diatoms, diverse in both form and ecology. The defining feature of this group has been an extreme asymmetry of the valve mantle and girdle bands, bringing both faces of the cell onto a single plane. Although this 'amphoroid' structure has long been the diagnostic feature and thus considered 'conservative' for the group, many have argued that the diversity of forms presently assigned to Amphora likely does not represent a monophyletic group. With the exception of several taxonomic transfers and the recent elevation of Halamphora to the level of genus, much of Amphora classification has remained unchanged for over 100 years. This study presents a phylogenetic analysis of Amphora s.l. based on a concatenated molecular alignment including the nuclear marker SSU rDNA and the chloroplast markers rbcL and psbC. These results are discussed within the framework of the current classification system of Amphora and Halamphora and lay the groundwork for a taxonomic revision of the group based on monophyly. The results of this analysis demonstrate that the genus Amphora is polyphyletic and that lineages assigned to the genus are distributed widely across the raphid diatom tree of life. The feature of amphoroid symmetry appears to have evolved independently several times. We discuss the nature of conservative characters in the raphid diatoms and their usefulness as a guide to phylogenetic relationships.

  19. 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.

  20. 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

  1. 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.

  2. Molecular phylogeny of the subfamily Stevardiinae Gill, 1858 (Characiformes: Characidae): classification and the evolution of reproductive traits.

    Science.gov (United States)

    Thomaz, Andréa T; Arcila, Dahiana; Ortí, Guillermo; Malabarba, Luiz R

    2015-07-21

    The subfamily Stevardiinae is a diverse and widely distributed clade of freshwater fishes from South and Central America, commonly known as "tetras" (Characidae). The group was named "clade A" when first proposed as a monophyletic unit of Characidae and later designated as a subfamily. Stevardiinae includes 48 genera and around 310 valid species with many species presenting inseminating reproductive strategy. No global hypothesis of relationships is available for this group and currently many genera are listed as incertae sedis or are suspected to be non-monophyletic. We present a molecular phylogeny with the largest number of stevardiine species analyzed so far, including 355 samples representing 153 putative species distributed in 32 genera, to test the group's monophyly and internal relationships. The phylogeny was inferred using DNA sequence data from seven gene fragments (mtDNA: 12S, 16S and COI; nuclear: RAG1, RAG2, MYH6 and PTR). The results support the Stevardiinae as a monophyletic group and a detailed hypothesis of the internal relationships for this subfamily. A revised classification based on the molecular phylogeny is proposed that includes seven tribes and also defines monophyletic genera, including a resurrected genus Eretmobrycon, and new definitions for Diapoma, Hemibrycon, Bryconamericus sensu stricto, and Knodus sensu stricto, placing some small genera as junior synonyms. Inseminating species are distributed in several clades suggesting that reproductive strategy is evolutionarily labile in this group of fishes.

  3. 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

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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...

  10. 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).

  11. Choice of adjuvant drug therapy on the basis of the molecular classification of breast cancer

    Directory of Open Access Journals (Sweden)

    N. S. Besova

    2012-01-01

    Full Text Available Molecular genetic analysis identified some biological subtypes of breast cancer (BC: luminal A, luminal B, HER2 positive, and basal-like (including triple negative. The surrogate clinical and morphological criteria including the immunohistochemical determination of estrogen and progesterone receptors, the hyperexpression and/or amplification of HER2, Ki-67, or tumor grade (G are used to identify the biological subtypes of BC in clinical practice. The biological subtypes are distinguished by their biological course and susceptibility to various systemic treatments, which requires different therapeutic tactics. The paper presents tactics of adjuvant therapy for BC in relation to its biological subtype according to the recommendations of the 12th St. Gallen International Breast Cancer Conference (2011 and considers the place of taxans.

  12. 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

  13. 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.

  14. 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+.

  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. 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.

  17. Phylogeny, classification and evolution of ladybird beetles (Coleoptera: Coccinellidae) based on simultaneous analysis of molecular and morphological data.

    Science.gov (United States)

    Seago, Ainsley E; Giorgi, Jose Adriano; Li, Jiahui; Slipiński, Adam

    2011-07-01

    Ladybird beetles (family Coccinellidae) are a species-rich, ecologically diverse group of substantial agricultural significance, yet have been consistently problematic to classify, with evolutionary relationships poorly understood. In order to identify major clades within Coccinellidae, evaluate the current classification system, and identify likely drivers of diversification in this polyphagous group, we conducted the first simultaneous Bayesian analysis of morphological and multi-locus molecular data for any beetle family. Addition of morphological data significantly improved phylogenetic resolution and support for early diverging lineages, thereby better resolving evolutionary relationships than either data type alone. On the basis of these results, we formally recognize the subfamilies Microweisinae and Coccinellinae sensuŚlipiński (2007). No significant support was found for the subfamilies Coccidulinae, Scymninae, Sticholotidinae, or Ortaliinae. Our phylogenetic results suggest that the evolutionary success of Coccinellidae is in large part attributable to the exploitation of ant-tended sternorrhynchan insects as a food source, enabled by the key innovation of unusual defense mechanisms in larvae. Copyright © 2011 Elsevier Inc. All rights reserved.

  18. 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.

  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. A novel asymmetric-loop molecular beacon-based two-phase hybridization assay for accurate and high-throughput detection of multiple drug resistance-conferring point mutations in Mycobacterium tuberculosis.

    Science.gov (United States)

    Chen, Qinghai; Wu, Nan; Xie, Meng; Zhang, Bo; Chen, Ming; Li, Jianjun; Zhuo, Lisha; Kuang, Hong; Fu, Weiling

    2012-04-01

    The accurate and high-throughput detection of drug resistance-related multiple point mutations remains a challenge. Although the combination of molecular beacons with bio-immobilization technology, such as microarray, is promising, its application is difficult due to the ineffective immobilization of molecular beacons on the chip surface. Here, we propose a novel asymmetric-loop molecular beacon in which the loop consists of 2 parts. One is complementary to a target, while the other is complementary to an oligonucleotide probe immobilized on the chip surface. With this novel probe, a two-phase hybridization assay can be used for simultaneously detecting multiple point mutations. This assay will have advantages, such as easy probe availability, multiplex detection, low background, and high-efficiency hybridization, and may provide a new avenue for the immobilization of molecular beacons and high-throughput detection of point mutations.

  1. 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.

  2. 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

  3. 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...

  4. On the accurate calculation of the dielectric constant from molecular dynamics simulations: The case of SPC/E and SWM4-DP water

    Science.gov (United States)

    Gereben, Orsolya; Pusztai, László

    2011-04-01

    The effect of the applied trajectory length on the convergence of the static dielectric constant was examined for the SPC/E water model with different system sizes. Very long simulation times of 6-8 ns were employed in order to track the convergence of this property. Temperature dependence and isotope effects were also investigated. A simulation for the polarizable SWM4-DP model was also carried out to compare the effect of different potential models. It is clearly shown that trajectories shorter than about 6 ns are not sufficient for a sufficiently accurate determination of the dielectric constant of these water models.

  5. 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.

  6. 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.

    Science.gov (United States)

    Hwang, Pei-Ing; Wu, Huan-Bin; Wang, Chin-Di; Lin, Bai-Ling; Chen, Cheng-Tao; Yuan, Shinsheng; Wu, Guani; Li, Ker-Chau

    2011-09-01

    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. 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. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. MLVA based classification of Mycobacterium tuberculosis complex lineages for a robust phylogeographic snapshot of its worldwide molecular diversity.

    Directory of Open Access Journals (Sweden)

    Véronique Hill

    Full Text Available Multiple-locus variable-number tandem repeat analysis (MLVA is useful to establish transmission routes and sources of infections for various microorganisms including Mycobacterium tuberculosis complex (MTC. The recently released SITVITWEB database contains 12-loci Mycobacterial Interspersed Repetitive Units--Variable Number of Tandem DNA Repeats (MIRU-VNTR profiles and spoligotype patterns for thousands of MTC strains; it uses MIRU International Types (MIT and Spoligotype International Types (SIT to designate clustered patterns worldwide. Considering existing doubts on the ability of spoligotyping alone to reveal exact phylogenetic relationships between MTC strains, we developed a MLVA based classification for MTC genotypic lineages. We studied 6 different subsets of MTC isolates encompassing 7793 strains worldwide. Minimum spanning trees (MST were constructed to identify major lineages, and the most common representative located as a central node was taken as the prototype defining different phylogenetic groups. A total of 7 major lineages with their respective prototypes were identified: Indo-Oceanic/MIT57, East Asian and African Indian/MIT17, Euro American/MIT116, West African-I/MIT934, West African-II/MIT664, M. bovis/MIT49, M.canettii/MIT60. Further MST subdivision identified an additional 34 sublineage MIT prototypes. The phylogenetic relationships among the 37 newly defined MIRU-VNTR lineages were inferred using a classification algorithm based on a bayesian approach. This information was used to construct an updated phylogenetic and phylogeographic snapshot of worldwide MTC diversity studied both at the regional, sub-regional, and country level according to the United Nations specifications. We also looked for IS6110 insertional events that are known to modify the results of the spoligotyping in specific circumstances, and showed that a fair portion of convergence leading to the currently observed bias in phylogenetic classification of

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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. 

  9. Accurate Classification of Germinal Center B-Cell-Like/Activated B-Cell-Like Diffuse Large B-Cell Lymphoma Using a Simple and Rapid Reverse Transcriptase-Multiplex Ligation-Dependent Probe Amplification Assay: A CALYM Study.

    Science.gov (United States)

    Mareschal, Sylvain; Ruminy, Philippe; Bagacean, Cristina; Marchand, Vinciane; Cornic, Marie; Jais, Jean-Philippe; Figeac, Martin; Picquenot, Jean-Michel; Molina, Thierry Jo; Fest, Thierry; Salles, Gilles; Haioun, Corinne; Leroy, Karen; Tilly, Hervé; Jardin, Fabrice

    2015-04-09

    Diffuse large B-cell lymphoma, the most common non-Hodgkin lymphoma, is subdivided into germinal center B-cell-like and activated B-cell-like subtypes. Unfortunately, these lymphomas are difficult to differentiate in routine diagnosis, impeding the development of treatments. Patients with these lymphomas can benefit from specific therapies. We therefore developed a simple and rapid classifier based on a reverse transcriptase multiplex ligation-dependent probe amplification assay and 14 gene signatures. Compared with the Affymetrix U133+2 gold standard, all 46 samples (95% CI, 92%-100%) of a validation cohort classified by both techniques were attributed to the expected subtype. Similarly, 93% of the 55 samples (95% CI, 82%-98%) of a second independent series characterized with a mid-throughput gene expression profiling method were classified correctly. Unclassifiable sample proportions reached 13.2% and 13.8% in these cohorts, comparable with the frequency originally reported. The developed assay was also sensitive enough to obtain reliable results from formalin-fixed, paraffin-embedded samples and flexible enough to include prognostic factors such as MYC/BCL2 co-expression. Finally, in a series of 135 patients, both overall (P = 0.01) and progression-free (P = 0.004) survival differences between the two subtypes were confirmed. Because the multiplex ligation-dependent probe amplification method is already in use and requires only common instruments and reagents, it could easily be applied to clinical trial patient stratification to help in treatment decisions. Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  10. 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.

  11. 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.

  12. Angle′s Molar Classification Revisited

    Directory of Open Access Journals (Sweden)

    Devanshi Yadav

    2014-01-01

    Results: Of the 500 pretreatment study casts assessed 52.4% were definitive Class I, 23.6% were Class II, 2.6% were Class III and the ambiguous cases were 21%. These could be easily classified with our method of classification. Conclusion: This improvised classification technique will help orthodontists in making classification of malocclusion accurate and simple.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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...

  18. 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.

  19. 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。

  20. 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.

  1. Accelerating metagenomic read classification on CUDA-enabled GPUs

    National Research Council Canada - National Science Library

    Kobus, Robin; Hundt, Christian; Müller, André; Schmidt, Bertil

    2017-01-01

    ... metagenomic read classification are urgently needed. Results We present cuCLARK, a read-level classifier for CUDA-enabled GPUs, based on the fast and accurate classification of metagenomic sequences using reduced k-mers (CLARK) method...

  2. 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.

  3. Multiclass cancer classification based on gene expression comparison

    Science.gov (United States)

    Yang, Sitan; Naiman, Daniel Q.

    2016-01-01

    As the complexity and heterogeneity of cancer is being increasingly appreciated through genomic analyses, microarray-based cancer classification comprising multiple discriminatory molecular markers is an emerging trend. Such multiclass classification problems pose new methodological and computational challenges for developing novel and effective statistical approaches. In this paper, we introduce a new approach for classifying multiple disease states associated with cancer based on gene expression profiles. Our method focuses on detecting small sets of genes in which the relative comparison of their expression values leads to class discrimination. For an m-class problem, the classification rule typically depends on a small number of m-gene sets, which provide transparent decision boundaries and allow for potential biological interpretations. We first test our approach on seven common gene expression datasets and compare it with popular classification methods including support vector machines and random forests. We then consider an extremely large cohort of leukemia cancer to further assess its effectiveness. In both experiments, our method yields comparable or even better results to benchmark classifiers. In addition, we demonstrate that our approach can integrate pathway analysis of gene expression to provide accurate and biological meaningful classification. PMID:24918456

  4. 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

  5. BIOACCESSIBILITY TESTS ACCURATELY ESTIMATE ...

    Science.gov (United States)

    Hazards of soil-borne Pb to wild birds may be more accurately quantified if the bioavailability of that Pb is known. To better understand the bioavailability of Pb to birds, we measured blood Pb concentrations in Japanese quail (Coturnix japonica) fed diets containing Pb-contaminated soils. Relative bioavailabilities were expressed by comparison with blood Pb concentrations in quail fed a Pb acetate reference diet. Diets containing soil from five Pb-contaminated Superfund sites had relative bioavailabilities from 33%-63%, with a mean of about 50%. Treatment of two of the soils with P significantly reduced the bioavailability of Pb. The bioaccessibility of the Pb in the test soils was then measured in six in vitro tests and regressed on bioavailability. They were: the “Relative Bioavailability Leaching Procedure” (RBALP) at pH 1.5, the same test conducted at pH 2.5, the “Ohio State University In vitro Gastrointestinal” method (OSU IVG), the “Urban Soil Bioaccessible Lead Test”, the modified “Physiologically Based Extraction Test” and the “Waterfowl Physiologically Based Extraction Test.” All regressions had positive slopes. Based on criteria of slope and coefficient of determination, the RBALP pH 2.5 and OSU IVG tests performed very well. Speciation by X-ray absorption spectroscopy demonstrated that, on average, most of the Pb in the sampled soils was sorbed to minerals (30%), bound to organic matter 24%, or present as Pb sulfate 18%. Ad

  6. 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.

  7. 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.

  8. Groundwater recharge: Accurately representing evapotranspiration

    CSIR Research Space (South Africa)

    Bugan, Richard DH

    2011-09-01

    Full Text Available Groundwater recharge is the basis for accurate estimation of groundwater resources, for determining the modes of water allocation and groundwater resource susceptibility to climate change. Accurate estimations of groundwater recharge with models...

  9. 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...

  10. 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...

  11. 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...

  12. 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.

  13. 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)...

  14. 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

  15. Xenolog classification.

    Science.gov (United States)

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

    2017-03-01

    Orthology analysis is a fundamental tool in comparative genomics. Sophisticated methods have been developed to distinguish between orthologs and paralogs and to classify paralogs into subtypes depending on the duplication mechanism and timing, relative to speciation. However, no comparable framework exists for xenologs: gene pairs whose history, since their divergence, includes a horizontal transfer. Further, the diversity of gene pairs that meet this broad definition calls for classification of xenologs with similar properties into subtypes. We present a xenolog classification that uses phylogenetic reconciliation to assign each pair of genes to a class based on the event responsible for their divergence and the historical association between genes and species. Our classes distinguish between genes related through transfer alone and genes related through duplication and transfer. Further, they separate closely-related genes in distantly-related species from distantly-related genes in closely-related species. We present formal rules that assign gene pairs to specific xenolog classes, given a reconciled gene tree with an arbitrary number of duplications and transfers. These xenology classification rules have been implemented in software and tested on a collection of ∼13 000 prokaryotic gene families. In addition, we present a case study demonstrating the connection between xenolog classification and gene function prediction. The xenolog classification rules have been implemented in N otung 2.9, a freely available phylogenetic reconciliation software package. http://www.cs.cmu.edu/~durand/Notung . Gene trees are available at http://dx.doi.org/10.7488/ds/1503 . durand@cmu.edu. Supplementary data are available at Bioinformatics online.

  16. 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...

  17. 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

  18. 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.

  19. [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...

  20. 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.

  1. 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.

  2. NNLOPS accurate associated HW production

    CERN Document Server

    Astill, William; Re, Emanuele; Zanderighi, Giulia

    2016-01-01

    We present a next-to-next-to-leading order accurate description of associated HW production consistently matched to a parton shower. The method is based on reweighting events obtained with the HW plus one jet NLO accurate calculation implemented in POWHEG, extended with the MiNLO procedure, to reproduce NNLO accurate Born distributions. Since the Born kinematics is more complex than the cases treated before, we use a parametrization of the Collins-Soper angles to reduce the number of variables required for the reweighting. We present phenomenological results at 13 TeV, with cuts suggested by the Higgs Cross Section Working Group.

  3. 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.

  4. On the nature of global classification

    Science.gov (United States)

    Wheelis, M. L.; Kandler, O.; Woese, C. R.

    1992-01-01

    Molecular sequencing technology has brought biology into the era of global (universal) classification. Methodologically and philosophically, global classification differs significantly from traditional, local classification. The need for uniformity requires that higher level taxa be defined on the molecular level in terms of universally homologous functions. A global classification should reflect both principal dimensions of the evolutionary process: genealogical relationship and quality and extent of divergence within a group. The ultimate purpose of a global classification is not simply information storage and retrieval; such a system should also function as an heuristic representation of the evolutionary paradigm that exerts a directing influence on the course of biology. The global system envisioned allows paraphyletic taxa. To retain maximal phylogenetic information in these cases, minor notational amendments in existing taxonomic conventions should be adopted.

  5. 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.

  6. 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.

  7. 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....

  8. Classification in Australia.

    Science.gov (United States)

    McKinlay, John

    Despite some inroads by the Library of Congress Classification and short-lived experimentation with Universal Decimal Classification and Bliss Classification, Dewey Decimal Classification, with its ability in recent editions to be hospitable to local needs, remains the most widely used classification system in Australia. Although supplemented at…

  9. 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

  10. 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....

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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...

  17. 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

  18. 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...

  19. 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.

  20. 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.

  1. 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

  2. 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.

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

    Science.gov (United States)

    Van der Auwera, Sandra; Bulla, Ingo; Ziller, Mario; Pohlmann, Anne; Harder, Timm; Stanke, Mario

    2014-01-01

    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.

  4. 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.

  5. 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.

  6. 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.

  7. 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。

  8. 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...

  9. $H_{2}^{+}$ 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 $1\\sigma_u$.

  10. Improved Sparse Multi-Class SVM and Its Application for Gene Selection in Cancer Classification.

    Science.gov (United States)

    Huang, Lingkang; Zhang, Hao Helen; Zeng, Zhao-Bang; Bushel, Pierre R

    2013-01-01

    Microarray techniques provide promising tools for cancer diagnosis using gene expression profiles. However, molecular diagnosis based on high-throughput platforms presents great challenges due to the overwhelming number of variables versus the small sample size and the complex nature of multi-type tumors. Support vector machines (SVMs) have shown superior performance in cancer classification due to their ability to handle high dimensional low sample size data. The multi-class SVM algorithm of Crammer and Singer provides a natural framework for multi-class learning. Despite its effective performance, the procedure utilizes all variables without selection. In this paper, we propose to improve the procedure by imposing shrinkage penalties in learning to enforce solution sparsity. The original multi-class SVM of Crammer and Singer is effective for multi-class classification but does not conduct variable selection. We improved the method by introducing soft-thresholding type penalties to incorporate variable selection into multi-class classification for high dimensional data. The new methods were applied to simulated data and two cancer gene expression data sets. The results demonstrate that the new methods can select a small number of genes for building accurate multi-class classification rules. Furthermore, the important genes selected by the methods overlap significantly, suggesting general agreement among different variable selection schemes. High accuracy and sparsity make the new methods attractive for cancer diagnostics with gene expression data and defining targets of therapeutic intervention. The source MATLAB code are available from http://math.arizona.edu/~hzhang/software.html.

  11. 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

  12. Aphasia Classification Using Neural Networks

    DEFF Research Database (Denmark)

    Axer, H.; Jantzen, Jan; Berks, G.

    2000-01-01

    of the Aachen Aphasia Test (AAT). First a coarse classification was achieved by using an assessment of spontaneous speech of the patient. This classifier produced correct results in 87% of the test cases. For a second test, data analysis tools were used to select four features out of the 30 available test...... features to yield a more accurate diagnosis. This second classifier produced correct results in 92% of the test cases. This test requires four AAT scores as input for the multilayer perceptron. In practice, the second test requires hours of work on behalf of the clinician, whereas the first test can...

  13. 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.

  14. Cluster Based Text Classification Model

    DEFF Research Database (Denmark)

    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 th...... datasets. Our model also outperforms A Decision Cluster Classification (ADCC) and the Decision Cluster Forest Classification (DCFC) models on the Reuters-21578 dataset....

  15. Automated Decision Tree Classification of Corneal Shape

    Science.gov (United States)

    Twa, Michael D.; Parthasarathy, Srinivasan; Roberts, Cynthia; Mahmoud, Ashraf M.; Raasch, Thomas W.; Bullimore, Mark A.

    2011-01-01

    Purpose The volume and complexity of data produced during videokeratography examinations present a challenge of interpretation. As a consequence, results are often analyzed qualitatively by subjective pattern recognition or reduced to comparisons of summary indices. We describe the application of decision tree induction, an automated machine learning classification method, to discriminate between normal and keratoconic corneal shapes in an objective and quantitative way. We then compared this method with other known classification methods. Methods The corneal surface was modeled with a seventh-order Zernike polynomial for 132 normal eyes of 92 subjects and 112 eyes of 71 subjects diagnosed with keratoconus. A decision tree classifier was induced using the C4.5 algorithm, and its classification performance was compared with the modified Rabinowitz–McDonnell index, Schwiegerling’s Z3 index (Z3), Keratoconus Prediction Index (KPI), KISA%, and Cone Location and Magnitude Index using recommended classification thresholds for each method. We also evaluated the area under the receiver operator characteristic (ROC) curve for each classification method. Results Our decision tree classifier performed equal to or better than the other classifiers tested: accuracy was 92% and the area under the ROC curve was 0.97. Our decision tree classifier reduced the information needed to distinguish between normal and keratoconus eyes using four of 36 Zernike polynomial coefficients. The four surface features selected as classification attributes by the decision tree method were inferior elevation, greater sagittal depth, oblique toricity, and trefoil. Conclusions Automated decision tree classification of corneal shape through Zernike polynomials is an accurate quantitative method of classification that is interpretable and can be generated from any instrument platform capable of raw elevation data output. This method of pattern classification is extendable to other classification

  16. 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...

  17. 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...

  18. 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...

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  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. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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...

  13. Gallstone Classification in Western Countries.

    Science.gov (United States)

    Cariati, Andrea

    2015-12-01

    In order to compare gallstone disease data from India and Asian countries with Western countries, it is fundamental to follow a common gallstone classification. Gallstone disease has afflicted humans since the time of Egyptian kings, and gallstones have been found during autopsies on mummies. Gallstone prevalence in adult population ranges from 10 to 15 %. Gallstones in Western countries are distinguished into the following classes: cholesterol gallstones that contain more than 50 % of cholesterol (nearly 75 % of gallstones) and pigment gallstones that contain less than 30 % of cholesterol by weight, which can be subdivided into black pigment gallstones and brown pigment gallstones. It has been shown that ultrastructural analysis with scanning electron microscopy is useful in the classification and study of pigment gallstones. Moreover, x-ray diffractometry analysis and infrared spectroscopy of gallstones are of fundamental importance for an accurate stone analysis. An accurate study of gallstones is useful to understand gallstone pathogenesis. In fact, bacteria are not important in cholesterol gallstone nucleation and growth, but they are important in brown pigment gallstone formation. On the contrary, calcium bilirubinate is fundamental in black pigment gallstone formation and probably also plays an important role in cholesterol gallstone nucleation and growth.

  14. Classification of refrigerants; Classification des fluides frigorigenes

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2001-07-01

    This document was made from the US standard ANSI/ASHRAE 34 published in 2001 and entitled 'designation and safety classification of refrigerants'. This classification allows to clearly organize in an international way the overall refrigerants used in the world thanks to a codification of the refrigerants in correspondence with their chemical composition. This note explains this codification: prefix, suffixes (hydrocarbons and derived fluids, azeotropic and non-azeotropic mixtures, various organic compounds, non-organic compounds), safety classification (toxicity, flammability, case of mixtures). (J.S.)

  15. 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.

  16. 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

  17. A higher-level phylogenetic classification of the Fungi

    NARCIS (Netherlands)

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

    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. 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

  19. 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

  20. 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.

  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. 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.

  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. 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...

  5. 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...

  6. 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.

  7. 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...

  8. 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.

  9. 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....

  10. 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.

  11. 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.

  12. 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...

  13. 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...

  14. 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

  15. 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

  16. 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...

  17. The development of the TNM classification of gastric cancer.

    Science.gov (United States)

    Wittekind, Christian

    2015-08-01

    The first tumor, node, metastasis (TNM) classification for stomach tumors was published in the second edition of the TNM classification of malignant tumors in 1974 and was followed by additional editions up to the seventh edition published in 2010. In the Buffalo Meeting 2008 a harmonization between the Eastern (Japanese) and Western stomach tumor classification was achieved with only minor remaing differences. The present TNM classification of stomach tumors has been criticized but it can be considered generally accepted worldwide. For generating data based on this new TNM classification it is important to correctly use TNM and pTNM. The decions on therapy and the estimation of prognosis are based on TNM. New molecular factor studies will be correlated and based on the results of the TNM classification. © 2015 Japanese Society of Pathology and Wiley Publishing Asia Pty Ltd.

  18. 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…

  19. 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

  20. 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…

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. Improved Surgical Site Infection (SSI) rate through accurately assessed surgical wounds.

    Science.gov (United States)

    John, Honeymol; Nimeri, Abdelrahman; Ellahham, Samer

    2015-01-01

    Sheikh Khalifa Medical City's (SKMC) Surgery Institute was identified as a high outlier in Surgical Site Infections (SSI) based on the American College of Surgeons National Surgical Quality Improvement Program (ACS NSQIP) - Semi-Annual Report (SAR) in January 2012. The aim of this project was to improve SSI rates through accurate wound classification. We identified SSI rate reduction as a performance improvement and safety priority at SKMC, a tertiary referral center. We used the American College of Surgeons National Surgical Quality Improvement Program (ACS NSQIP) best practice guidelines as a guide. ACS NSQIP is a clinical registry that provides risk-adjusted clinical outcome reports every six months. The rates of SSI are reported in an observed/expected ratio. The expected ratio is calculated based on the risk factors of the patients which include wound classification. We established a multidisciplinary SSI taskforce. The members of the SSI taskforce included the ACS NSQIP team members, quality, surgeons, nurses, infection control, IT, pharmacy, microbiology, and it was chaired by a colorectal surgeon. The taskforce focused on five areas: pre-op showering and hair removal, skin antisepsis, prophylactic antibiotics, peri-operative maintenance of glycaemia, and normothermia. We planned audits to evaluate our wound classification and our SSI rates based on the SAR. Our expected SSI rates in general surgery and the whole department were 2.52% and 1.70% respectively, while our observed SSI rates were 4.68% and 3.57% respectively, giving us a high outlier status with an odd's ratio of 1.72 and 2.03. Wound classifications were identified as an area of concern. For example, wound classifications were preoperatively selected based on the default wound classification of the booked procedure in the Electronic Medical Record (EMR) which led to under classifying wounds in many occasions. A total of 998 cases were reviewed, our rate of incorrect wound classification

  8. 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.

  9. 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

  10. New classification criteria for gout: a framework for progress

    Science.gov (United States)

    Dalbeth, Nicola; Fransen, Jaap; Jansen, Tim L.; Neogi, Tuhina; Schumacher, H. Ralph; Taylor, William J.

    2013-01-01

    The definitive classification or diagnosis of gout normally relies upon the identification of MSU crystals in SF or from tophi. Where microscopic examination of SF is not available or is impractical, the best approach may differ depending upon the context. For many types of research, clinical classification criteria are necessary. The increasing prevalence of gout, advances in therapeutics and the development of international research collaborations to understand the impact, mechanisms and optimal treatment of this condition emphasize the need for accurate and uniform classification criteria for gout. Five clinical classification criteria for gout currently exist. However, none of the currently available criteria has been adequately validated. An international project is currently under way to develop new validated gout classification criteria. These criteria will be an essential step forward to advance the research agenda in the modern era of gout management. PMID:23611919

  11. 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.

  12. 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.

  13. 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.

  14. Morphological classification of plant cell deaths

    DEFF Research Database (Denmark)

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

    2011-01-01

    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 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......, 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...

  15. 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.

  16. 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.

  17. [Classification of human sleep stages based on EEG processing using hidden Markov models].

    Science.gov (United States)

    Doroshenkov, L G; Konyshev, V A; Selishchev, S V

    2007-01-01

    The goal of this work was to describe an automated system for classification of human sleep stages. Classification of sleep stages is an important problem of diagnosis and treatment of human sleep disorders. The developed classification method is based on calculation of characteristics of the main sleep rhythms. It uses hidden Markov models. The method is highly accurate and provides reliable identification of the main stages of sleep. The results of automatic classification are in good agreement with the results of sleep stage identification performed by an expert somnologist using Rechtschaffen and Kales rules. This substantiates the applicability of the developed classification system to clinical diagnosis.

  18. 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...

  19. 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....

  20. 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.

  1. [Classification of cardiomyopathy].

    Science.gov (United States)

    Asakura, Masanori; Kitakaze, Masafumi

    2014-01-01

    Cardiomyopathy is a group of cardiovascular diseases with poor prognosis. Some patients with dilated cardiomyopathy need heart transplantations due to severe heart failure. Some patients with hypertrophic cardiomyopathy die unexpectedly due to malignant ventricular arrhythmias. Various phenotypes of cardiomyopathies are due to the heterogeneous group of diseases. The classification of cardiomyopathies is important and indispensable in the clinical situation. However, their classification has not been established, because the causes of cardiomyopathies have not been fully elucidated. We usually use definition and classification offered by WHO/ISFC task force in 1995. Recently, several new definitions and classifications of the cardiomyopathies have been published by American Heart Association, European Society of Cardiology and Japanese Circulation Society.

  2. Carbohydrate terminology and classification

    National Research Council Canada - National Science Library

    Cummings, J H; Stephen, A M

    2007-01-01

    ...) and polysaccharides (DP> or =10). Within this classification, a number of terms are used such as mono- and disaccharides, polyols, oligosaccharides, starch, modified starch, non-starch polysaccharides, total carbohydrate, sugars, etc...

  3. 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.

  4. 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.

  5. 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.

  6. Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis.

    Science.gov (United States)

    Riesenfeld, Samantha J; Pollard, Katherine S

    2013-06-22

    Sequence-based phylogenetic trees are a well-established tool for characterizing diversity of both macroorganisms and microorganisms. Phylogenetic methods have recently been applied to shotgun metagenomic data from microbial communities, particularly with the aim of classifying reads. But the accuracy of gene-family phylogenies that characterize evolutionary relationships among short, non-overlapping sequencing reads has not been thoroughly evaluated. To quantify errors in metagenomic read trees, we developed MetaPASSAGE, a software pipeline to generate in silico bacterial communities, simulate a sample of shotgun reads from a gene family represented in the community, orient or translate reads, and produce a profile-based alignment of the reads from which a gene-family phylogenetic tree can be built. We applied MetaPASSAGE to a variety of RNA and protein-coding gene families, built trees using a range of different phylogenetic methods, and compared the resulting trees using topological and branch-length error metrics. We identified read length as one of the major sources of error. Because phylogenetic methods use a reference database of full-length sequences from the gene family to guide construction of alignments and trees, we found that error can also be substantially reduced through increasing the size and diversity of the reference database. Finally, UniFrac analysis, which compares metagenomic samples based on a summary statistic computed over all branches in a read tree, is very robust to the level of error we observe. Bacterial community diversity can be quantified using phylogenetic approaches applied to shotgun metagenomic data. As sequencing reads get longer and more genomes across the bacterial tree of life are sequenced, the accuracy of this approach will continue to improve, opening the door to more applications.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. Recent Advances in Conotoxin Classification by Using Machine Learning Methods

    Directory of Open Access Journals (Sweden)

    Fu-Ying Dao

    2017-06-01

    Full Text Available Conotoxins are disulfide-rich small peptides, which are invaluable peptides that target ion channel and neuronal receptors. Conotoxins have been demonstrated as potent pharmaceuticals in the treatment of a series of diseases, such as Alzheimer’s disease, Parkinson’s disease, and epilepsy. In addition, conotoxins are also ideal molecular templates for the development of new drug lead compounds and play important roles in neurobiological research as well. Thus, the accurate identification of conotoxin types will provide key clues for the biological research and clinical medicine. Generally, conotoxin types are confirmed when their sequence, structure, and function are experimentally validated. However, it is time-consuming and costly to acquire the structure and function information by using biochemical experiments. Therefore, it is important to develop computational tools for efficiently and effectively recognizing conotoxin types based on sequence information. In this work, we reviewed the current progress in computational identification of conotoxins in the following aspects: (i construction of benchmark dataset; (ii strategies for extracting sequence features; (iii feature selection techniques; (iv machine learning methods for classifying conotoxins; (v the results obtained by these methods and the published tools; and (vi future perspectives on conotoxin classification. The paper provides the basis for in-depth study of conotoxins and drug therapy research.

  12. 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

  13. 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.

  14. Interobserver agreement of the old and the newly proposed ILAE epilepsy classification in children

    NARCIS (Netherlands)

    van Campen, Jolien S.; Jansen, Floor E.; Brouwer, Oebele F.; Nicolai, Joost; Braun, Kees P. J.

    Purpose Accurate classification of epileptic seizures, epilepsies, and epilepsy syndromes is mandatory in both clinical practice and epilepsy research. In 2010, the International League Against Epilepsy (ILAE) proposed a new classification scheme. The aim of this study is to determine whether

  15. 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

  16. 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.

  17. Accelerating metagenomic read classification on CUDA-enabled GPUs.

    Science.gov (United States)

    Kobus, Robin; Hundt, Christian; Müller, André; Schmidt, Bertil

    2017-01-03

    Metagenomic sequencing studies are becoming increasingly popular with prominent examples including the sequencing of human microbiomes and diverse environments. A fundamental computational problem in this context is read classification; i.e. the assignment of each read to a taxonomic label. Due to the large number of reads produced by modern high-throughput sequencing technologies and the rapidly increasing number of available reference genomes software tools for fast and accurate metagenomic read classification are urgently needed. We present cuCLARK, a read-level classifier for CUDA-enabled GPUs, based on the fast and accurate classification of metagenomic sequences using reduced k-mers (CLARK) method. Using the processing power of a single Titan X GPU, cuCLARK can reach classification speeds of up to 50 million reads per minute. Corresponding speedups for species- (genus-)level classification range between 3.2 and 6.6 (3.7 and 6.4) compared to multi-threaded CLARK executed on a 16-core Xeon CPU workstation. cuCLARK can perform metagenomic read classification at superior speeds on CUDA-enabled GPUs. It is free software licensed under GPL and can be downloaded at https://github.com/funatiq/cuclark free of charge.

  18. 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/.

  19. 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...

  20. 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...

  1. Human sapovirus classification based on complete capsid nucleotide sequences.

    Science.gov (United States)

    Oka, Tomoichiro; Mori, Kohji; Iritani, Nobuhiro; Harada, Seiya; Ueki, You; Iizuka, Setsuko; Mise, Keiji; Murakami, Kosuke; Wakita, Takaji; Katayama, Kazuhiko

    2012-02-01

    The genetically diverse sapoviruses (SaVs) are a significant cause of acute human gastroenteritis. Human SaV surveillance is becoming more critical, and a better understanding of the diversity and distribution of the viral genotypes is needed. In this study, we analyzed 106 complete human SaV capsid nucleotide sequences to provide a better understanding of their diversity. Based on those results, we propose a novel standardized classification scheme that meets the requirements of the International Calicivirus Scientific Committee. We believe the classification scheme and strains described here will be of value for the molecular characterization and classification of newly detected SaV genotypes and for comparing data worldwide.

  2. 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

  3. 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.

  4. 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.

  5. 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).

  6. An analysis of network traffic classification for botnet detection

    DEFF Research Database (Denmark)

    Stevanovic, Matija; Pedersen, Jens Myrup

    2015-01-01

    Botnets represent one of the most serious threats to the Internet security today. This paper explores how can network traffic classification be used for accurate and efficient identification of botnet network activity at local and enterprise networks. The paper examines the effectiveness of detec......Botnets represent one of the most serious threats to the Internet security today. This paper explores how can network traffic classification be used for accurate and efficient identification of botnet network activity at local and enterprise networks. The paper examines the effectiveness...... of detecting botnet network traffic using three methods that target protocols widely considered as the main carriers of botnet Command and Control (C&C) and attack traffic, i.e. TCP, UDP and DNS. We propose three traffic classification methods based on capable Random Forests classifier. The proposed methods...

  7. 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...

  8. 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-...

  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......, a good metric is required to measure distance or similarity between feature points so that the classification becomes feasible. Furthermore, in order to build a successful classifier, one needs to deeply understand how classifiers work. This thesis focuses on these three aspects of classification...... 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. 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...

  11. 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...

  12. 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.

  13. 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...

  14. 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...

  15. 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.

  16. 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.

  17. 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...

  18. Acoustic classification of dwellings

    DEFF Research Database (Denmark)

    Berardi, Umberto; Rasmussen, Birgit

    2014-01-01

    insulation performance, national schemes for sound classification of dwellings have been developed in several European countries. These schemes define acoustic classes according to different levels of sound insulation. Due to the lack of coordination among countries, a significant diversity in terms...... of descriptors, number of classes, and class intervals occurred between national schemes. However, a proposal “acoustic classification scheme for dwellings” has been developed recently in the European COST Action TU0901 with 32 member countries. This proposal has been accepted as an ISO work item. This paper...

  19. 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...

  20. 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 ...

  1. 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....

  2. 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.

  3. Constructing criticality by classification

    DEFF Research Database (Denmark)

    Machacek, Erika

    2017-01-01

    This paper explores the role of expertise, the nature of criticality, and their relationship to securitisation as mineral raw materials are classified. It works with the construction of risk along the liberal logic of security to explore how "key materials" are turned into "critical materials......, legitimizing a criticality discourse.Specifically, the paper introduces a typology delineating the inferences made by the experts from their produced recommendations in the classification of rare earth element criticality. The paper argues that the classification is a specific process of constructing risk...

  4. 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.

  5. [Hard and soft classification method of multi-spectral remote sensing image based on adaptive thresholds].

    Science.gov (United States)

    Hu, Tan-Gao; Xu, Jun-Feng; Zhang, Deng-Rong; Wang, Jie; Zhang, Yu-Zhou

    2013-04-01

    Hard and soft classification techniques are the conventional methods of image classification for satellite data, but they have their own advantages and drawbacks. In order to obtain accurate classification results, we took advantages of both traditional hard classification methods (HCM) and soft classification models (SCM), and developed a new method called the hard and soft classification model (HSCM) based on adaptive threshold calculation. The authors tested the new method in land cover mapping applications. According to the results of confusion matrix, the overall accuracy of HCM, SCM, and HSCM is 71.06%, 67.86%, and 71.10%, respectively. And the kappa coefficient is 60.03%, 56.12%, and 60.07%, respectively. Therefore, the HSCM is better than HCM and SCM. Experimental results proved that the new method can obviously improve the land cover and land use classification accuracy.

  6. 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.

  7. 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.

  8. 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...

  9. 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....

  10. 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.

  11. Classification using diffraction patterns for single-particle analysis

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Hongli; Zhang, Kaiming [Department of Biophysics, the Health Science Centre, Peking University, Beijing 100191 (China); Meng, Xing, E-mail: xmeng101@gmail.com [Wadsworth Centre, New York State Department of Health, Albany, New York 12201 (United States)

    2016-05-15

    An alternative method has been assessed; diffraction patterns derived from the single particle data set were used to perform the first round of classification in creating the initial averages for proteins data with symmetrical morphology. The test protein set was a collection of Caenorhabditis elegans small heat shock protein 17 obtained by Cryo EM, which has a tetrahedral (12-fold) symmetry. It is demonstrated that the initial classification on diffraction patterns is workable as well as the real-space classification that is based on the phase contrast. The test results show that the information from diffraction patterns has the enough details to make the initial model faithful. The potential advantage using the alternative method is twofold, the ability to handle the sets with poor signal/noise or/and that break the symmetry properties. - Highlights: • New classification method. • Create the accurate initial model. • Better in handling noisy data.

  12. 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.

  13. 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.

  14. [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.

  15. 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

  16. 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.

  17. 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

  18. 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.

  19. [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.

  20. 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…

  1. 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.

  2. 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....

  3. An automated cirrus classification

    Science.gov (United States)

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

    2017-04-01

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

  4. 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

  5. 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

  6. Principles for ecological classification

    Science.gov (United States)

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

    1999-01-01

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

  7. 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…

  8. 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.)

  9. 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

  10. Munitions Classification Library

    Science.gov (United States)

    2016-04-04

    the MM and TEMTADS 2x2 systems , with dynamic data handling for these systems on the horizon. Using UX-Analyze, a data processor can apply physics ... classification libraries. DRAFT 4 2.0 TECHNOLOGY Three different sensor systems were used during the initial phase of the data collection: a modified...

  11. 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.

  12. 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

  13. Fast and accurate methods for phylogenomic analyses

    Directory of Open Access Journals (Sweden)

    Warnow Tandy

    2011-10-01

    Full Text Available Abstract Background Species phylogenies are not estimated directly, but rather through phylogenetic analyses of different gene datasets. However, true gene trees can differ from the true species tree (and hence from one another due to biological processes such as horizontal gene transfer, incomplete lineage sorting, and gene duplication and loss, so that no single gene tree is a reliable estimate of the species tree. Several methods have been developed to estimate species trees from estimated gene trees, differing according to the specific algorithmic technique used and the biological model used to explain differences between species and gene trees. Relatively little is known about the relative performance of these methods. Results We report on a study evaluating several different methods for estimating species trees from sequence datasets, simulating sequence evolution under a complex model including indels (insertions and deletions, substitutions, and incomplete lineage sorting. The most important finding of our study is that some fast and simple methods are nearly as accurate as the most accurate methods, which employ sophisticated statistical methods and are computationally quite intensive. We also observe that methods that explicitly consider errors in the estimated gene trees produce more accurate trees than methods that assume the estimated gene trees are correct. Conclusions Our study shows that highly accurate estimations of species trees are achievable, even when gene trees differ from each other and from the species tree, and that these estimations can be obtained using fairly simple and computationally tractable methods.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Accurate estimation of indoor travel times

    DEFF Research Database (Denmark)

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

    2014-01-01

    The ability to accurately estimate indoor travel times is crucial for enabling improvements within application areas such as indoor navigation, logistics for mobile workers, and facility management. In this paper, we study the challenges inherent in indoor travel time estimation, and we propose...... 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. InTraTime...... allows to specify temporal and other query parameters, such as time-of-day, day-of-week or the identity of the traveling individual. As input the method is designed to take generic position traces and is thus interoperable with a variety of indoor positioning systems. The method's advantages include...

  3. 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.

  4. 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.

  5. 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...

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. Accurate integration of forced and damped oscillators

    OpenAIRE

    García Alonso, Fernando Luis; Cortés Molina, Mónica; Villacampa, Yolanda; Reyes Perales, José Antonio

    2016-01-01

    The new methods accurately integrate forced and damped oscillators. A family of analytical functions is introduced known as T-functions which are dependent on three parameters. The solution is expressed as a series of T-functions calculating their coefficients by means of recurrences which involve the perturbation function. In the T-functions series method the perturbation parameter is the factor in the local truncation error. Furthermore, this method is zero-stable and convergent. An applica...

  11. Accurate finite element modeling of acoustic waves

    Science.gov (United States)

    Idesman, A.; Pham, D.

    2014-07-01

    In the paper we suggest an accurate finite element approach for the modeling of acoustic waves under a suddenly applied load. We consider the standard linear elements and the linear elements with reduced dispersion for the space discretization as well as the explicit central-difference method for time integration. The analytical study of the numerical dispersion shows that the most accurate results can be obtained with the time increments close to the stability limit. However, even in this case and the use of the linear elements with reduced dispersion, mesh refinement leads to divergent numerical results for acoustic waves under a suddenly applied load. This is explained by large spurious high-frequency oscillations. For the quantification and the suppression of spurious oscillations, we have modified and applied a two-stage time-integration technique that includes the stage of basic computations and the filtering stage. This technique allows accurate convergent results at mesh refinement as well as significantly reduces the numerical anisotropy of solutions. We should mention that the approach suggested is very general and can be equally applied to any loading as well as for any space-discretization technique and any explicit or implicit time-integration method.

  12. Generative supervised classification using Dirichlet process priors.

    Science.gov (United States)

    Davy, Manuel; Tourneret, Jean-Yves

    2010-10-01

    Choosing the appropriate parameter prior distributions associated to a given bayesian model is a challenging problem. Conjugate priors can be selected for simplicity motivations. However, conjugate priors can be too restrictive to accurately model the available prior information. This paper studies a new generative supervised classifier which assumes that the parameter prior distributions conditioned on each class are mixtures of Dirichlet processes. The motivations for using mixtures of Dirichlet processes is their known ability to model accurately a large class of probability distributions. A Monte Carlo method allowing one to sample according to the resulting class-conditional posterior distributions is then studied. The parameters appearing in the class-conditional densities can then be estimated using these generated samples (following bayesian learning). The proposed supervised classifier is applied to the classification of altimetric waveforms backscattered from different surfaces (oceans, ices, forests, and deserts). This classification is a first step before developing tools allowing for the extraction of useful geophysical information from altimetric waveforms backscattered from nonoceanic surfaces.

  13. 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.

  14. Nominated Texture Based Cervical Cancer Classification

    Directory of Open Access Journals (Sweden)

    Edwin Jayasingh Mariarputham

    2015-01-01

    Full Text Available Accurate classification of Pap smear images becomes the challenging task in medical image processing. This can be improved in two ways. One way is by selecting suitable well defined specific features and the other is by selecting the best classifier. This paper presents a nominated texture based cervical cancer (NTCC classification system which classifies the Pap smear images into any one of the seven classes. This can be achieved by extracting well defined texture features and selecting best classifier. Seven sets of texture features (24 features are extracted which include relative size of nucleus and cytoplasm, dynamic range and first four moments of intensities of nucleus and cytoplasm, relative displacement of nucleus within the cytoplasm, gray level cooccurrence matrix, local binary pattern histogram, tamura features, and edge orientation histogram. Few types of support vector machine (SVM and neural network (NN classifiers are used for the classification. The performance of the NTCC algorithm is tested and compared to other algorithms on public image database of Herlev University Hospital, Denmark, with 917 Pap smear images. The output of SVM is found to be best for the most of the classes and better results for the remaining classes.

  15. 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.

  16. Deep learning for brain tumor classification

    Science.gov (United States)

    Paul, Justin S.; Plassard, Andrew J.; Landman, Bennett A.; Fabbri, Daniel

    2017-03-01

    Recent research has shown that deep learning methods have performed well on supervised machine learning, image classification tasks. The purpose of this study is to apply deep learning methods to classify brain images with different tumor types: meningioma, glioma, and pituitary. A dataset was publicly released containing 3,064 T1-weighted contrast enhanced MRI (CE-MRI) brain images from 233 patients with either meningioma, glioma, or pituitary tumors split across axial, coronal, or sagittal planes. This research focuses on the 989 axial images from 191 patients in order to avoid confusing the neural networks with three different planes containing the same diagnosis. Two types of neural networks were used in classification: fully connected and convolutional neural networks. Within these two categories, further tests were computed via the augmentation of the original 512×512 axial images. Training neural networks over the axial data has proven to be accurate in its classifications with an average five-fold cross validation of 91.43% on the best trained neural network. This result demonstrates that a more general method (i.e. deep learning) can outperform specialized methods that require image dilation and ring-forming subregions on tumors.

  17. 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...

  18. BIRADS classification in mammography.

    Science.gov (United States)

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

    2007-02-01

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

  19. [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.

  20. 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...

  1. 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.

  2. Sound classification of dwellings

    DEFF Research Database (Denmark)

    Rasmussen, Birgit

    2012-01-01

    dwellings, facade sound insulation and installation noise. The schemes have been developed, implemented and revised gradually since the early 1990s. However, due to lack of coordination between countries, there are significant discrepancies, and new standards and revisions continue to increase the diversity....... 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...

  3. Improved supervised classification of accelerometry data to distinguish behaviors of soaring birds

    Science.gov (United States)

    Sur, Maitreyi; Suffredini, Tony; Wessells, Stephen M.; Bloom, Peter H; Lanzone, Michael; Blackshire, Sheldon; Sridhar, Srisarguru; Katzner, Todd

    2017-01-01

    Soaring birds can balance the energetic costs of movement by switching between flapping, soaring and gliding flight. Accelerometers can allow quantification of flight behavior and thus a context to interpret these energetic costs. However, models to interpret accelerometry data are still being developed, rarely trained with supervised datasets, and difficult to apply. We collected accelerometry data at 140Hz from a trained golden eagle (Aquila chrysaetos) whose flight we recorded with video that we used to characterize behavior. We applied two forms of supervised classifications, random forest (RF) models and K-nearest neighbor (KNN) models. The KNN model was substantially easier to implement than the RF approach but both were highly accurate in classifying basic behaviors such as flapping (85.5% and 83.6% accurate, respectively), soaring (92.8% and 87.6%) and sitting (84.1% and 88.9%) with overall accuracies of 86.6% and 92.3% respectively. More detailed classification schemes, with specific behaviors such as banking and straight flights were well classified only by the KNN model (91.24% accurate; RF = 61.64% accurate). The RF model maintained its accuracy of classifying basic behavior classification accuracy of basic behaviors at sampling frequencies as low as 10Hz, the KNN at sampling frequencies as low as 20Hz. Classification of accelerometer data collected from free ranging birds demonstrated a strong dependence of predicted behavior on the type of classification model used. Our analyses demonstrate the consequence of different approaches to classification of accelerometry data, the potential to optimize classification algorithms with validated flight behaviors to improve classification accuracy, ideal sampling frequencies for different classification algorithms, and a number of ways to improve commonly used analytical techniques and best practices for classification of accelerometry data.

  4. 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 ...

  5. 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

  6. 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.

  7. Robust Vertex Classification

    OpenAIRE

    Chen, Li; Shen, Cencheng; Vogelstein, Joshua; Priebe, Carey

    2013-01-01

    For random graphs distributed according to stochastic blockmodels, a special case of latent position graphs, adjacency spectral embedding followed by appropriate vertex classification is asymptotically Bayes optimal; but this approach requires knowledge of and critically depends on the model dimension. In this paper, we propose a sparse representation vertex classifier which does not require information about the model dimension. This classifier represents a test vertex as a sparse combinatio...

  8. 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.

  9. Towards secondary fingerprint classification

    CSIR Research Space (South Africa)

    Msiza, IS

    2011-07-01

    Full Text Available . INTRODUCTION The classification of samples in an automated recognition system is primarily important because of the need to virtually divide the template database into smaller, manageable parti- tions. This virtual division is done before executing a... database search procedure, and it is done in order to avoid having to search the entire template database and, for this reason, minimize the database search time and improve the overall performance of an automated recognition system. Sample...

  10. 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)

  11. 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 supply of oxygen in the myocardium. However, no specific criteria for type 2 myocardial infarction have been established....

  12. Decimal Classification Editions

    Directory of Open Access Journals (Sweden)

    Zenovia Niculescu

    2009-01-01

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

  13. 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...... 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...

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. Molecular epidemiology of Blastocystis

    Directory of Open Access Journals (Sweden)

    Fadime Eroğlu

    2015-12-01

    Full Text Available Blastocystis pathogenicity and classification was newly illuminated with molecular genetic studies and recently the parasite was found in the focus of many researchers. Several molecular methods such as; polymerase chain reaction (PCR, PCR-restriction fragment length polymorphism, random amplified polymorphic DNA, real-time polymerase chain reaction and DNA sequencing analyses can be used in genotyping of Blastocystis. Blastocystis parasites may cause diarrhea, abdominal pain, bloating, gas, irritability, anorexia, cramps, vomiting, dehydration, insomnia, nausea, loss of appetite, weight loss, fatigue symptoms and also could be asymptomatic cases. In this review, it was aimed to summarize the associations between Blastocystis subtypes and pathogenicity.

  19. 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.

  20. 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. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. 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...

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Algorithms for Hyperspectral Signature Classification in Non-resolved Object Characterization Using Tabular Nearest Neighbor Encoding

    Science.gov (United States)

    Schmalz, M.; Key, G.

    Accurate spectral signature classification is key to the nonimaging detection and recognition of spaceborne objects. In classical hyperspectral recognition applications, signature classification accuracy depends on accurate spectral endmember determination [1]. However, in selected target recognition (ATR) applications, it is possible to circumvent the endmember detection problem by employing a Bayesian classifier. Previous approaches to Bayesian classification of spectral signatures have been rule- based, or predicated on a priori parameterized information obtained from offline training, as in the case of neural networks [1,2]. Unfortunately, class separation and classifier refinement results in these methods tends to be suboptimal, and the number of signatures that can be accurately classified often depends linearly on the number of inputs. This can lead to potentially significant classification errors in the presence of noise or densely interleaved signatures. In this paper, we present an emerging technology for nonimaging spectral signature classfication based on a highly accurate but computationally efficient search engine called Tabular Nearest Neighbor Encoding (TNE) [3]. Based on prior results, TNE can optimize its classifier performance to track input nonergodicities, as well as yield measures of confidence or caution for evaluation of classification results. Unlike neural networks, TNE does not have a hidden intermediate data structure (e.g., the neural net weight matrix). Instead, TNE generates and exploits a user-accessible data structure called the agreement map (AM), which can be manipulated by Boolean logic operations to effect accurate classifier refinement algorithms. This allows the TNE programmer or user to determine parameters for classification accuracy, and to mathematically analyze the signatures for which TNE did not obtain classification matches. This dual approach to analysis (i.e., correct vs. incorrect classification) has been shown to

  13. Noise-Tolerant Hyperspectral Signature Classification in Unresolved Object Detection with Adaptive Tabular Nearest Neighbor Encoding

    Science.gov (United States)

    Schmalz, M.; Key, G.

    Accurate spectral signature classification is a crucial step in the nonimaging detection and recognition of spaceborne objects. In classical hyperspectral recognition applications, especially where linear mixing models are employed, signature classification accuracy depends on accurate spectral endmember discrimination. In selected target recognition (ATR) applications, previous non-adaptive techniques for signature classification have yielded class separation and classifier refinement results that tend to be suboptimal. In practice, the number of signatures accurately classified often depends linearly on the number of inputs. This can lead to potentially severe classification errors in the presence of noise or densely interleaved signatures. In this paper, we present an enhancement of an emerging technology for nonimaging spectral signature classification based on a highly accurate, efficient search engine called Tabular Nearest Neighbor Encoding (TNE). Adaptive TNE can optimize its classifier performance to track input nonergodicities and yield measures of confidence or caution for evaluation of classification results. Unlike neural networks, TNE does not have a hidden intermediate data structure (e.g., a neural net weight matrix). Instead, TNE generates and exploits a user-accessible data structure called the agreement map (AM), which can be manipulated by Boolean logic operations to effect accurate classifier refinement through programmable algorithms. The open architecture and programmability of TNE's pattern-space (AM) processing allows a TNE developer to determine the qualitative and quantitative reasons for classification accuracy, as well as characterize in detail the signatures for which TNE does not obtain classification matches, and why such mis-matches occur. In this study AM-based classification has been modified to partially compensate for input statistical changes, in response to performance metrics such as probability of correct classification (Pd

  14. 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.

  15. 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.

  16. Accurate Stellar Parameters for Exoplanet Host Stars

    Science.gov (United States)

    Brewer, John Michael; Fischer, Debra; Basu, Sarbani; Valenti, Jeff A.

    2015-01-01

    A large impedement to our understanding of planet formation is obtaining a clear picture of planet radii and densities. Although determining precise ratios between planet and stellar host are relatively easy, determining accurate stellar parameters is still a difficult and costly undertaking. High resolution spectral analysis has traditionally yielded precise values for some stellar parameters but stars in common between catalogs from different authors or analyzed using different techniques often show offsets far in excess of their uncertainties. Most analyses now use some external constraint, when available, to break observed degeneracies between surface gravity, effective temperature, and metallicity which can otherwise lead to correlated errors in results. However, these external constraints are impossible to obtain for all stars and can require more costly observations than the initial high resolution spectra. We demonstrate that these discrepencies can be mitigated by use of a larger line list that has carefully tuned atomic line data. We use an iterative modeling technique that does not require external constraints. We compare the surface gravity obtained with our spectral synthesis modeling to asteroseismically determined values for 42 Kepler stars. Our analysis agrees well with only a 0.048 dex offset and an rms scatter of 0.05 dex. Such accurate stellar gravities can reduce the primary source of uncertainty in radii by almost an order of magnitude over unconstrained spectral analysis.

  17. 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.

  18. 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.

  19. Accurate basis set truncation for wavefunction embedding

    Science.gov (United States)

    Barnes, Taylor A.; Goodpaster, Jason D.; Manby, Frederick R.; Miller, Thomas F.

    2013-07-01

    Density functional theory (DFT) provides a formally exact framework for performing embedded subsystem electronic structure calculations, including DFT-in-DFT and wavefunction theory-in-DFT descriptions. In the interest of efficiency, it is desirable to truncate the atomic orbital basis set in which the subsystem calculation is performed, thus avoiding high-order scaling with respect to the size of the MO virtual space. In this study, we extend a recently introduced projection-based embedding method [F. R. Manby, M. Stella, J. D. Goodpaster, and T. F. Miller III, J. Chem. Theory Comput. 8, 2564 (2012)], 10.1021/ct300544e to allow for the systematic and accurate truncation of the embedded subsystem basis set. The approach is applied to both covalently and non-covalently bound test cases, including water clusters and polypeptide chains, and it is demonstrated that errors associated with basis set truncation are controllable to well within chemical accuracy. Furthermore, we show that this approach allows for switching between accurate projection-based embedding and DFT embedding with approximate kinetic energy (KE) functionals; in this sense, the approach provides a means of systematically improving upon the use of approximate KE functionals in DFT embedding.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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 ...

  5. 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 ...

  6. 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

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

    Directory of Open Access Journals (Sweden)

    Anunchai Assawamakin

    2013-01-01

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

  8. [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.

  9. Latent classification models

    DEFF Research Database (Denmark)

    Langseth, Helge; Nielsen, Thomas Dyhre

    2005-01-01

    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...... of the \\NB classifier. In theproposed model the continuous attributes are described by amixture of multivariate Gaussians, where the conditionaldependencies among the attributes are encoded using latentvariables. We present algorithms for learning both the parametersand the structure of a latent...

  10. 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...

  11. 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.

  12. 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.

  13. Method: automatic segmentation of mitochondria utilizing patch classification, contour pair classification, and automatically seeded level sets.

    Science.gov (United States)

    Giuly, Richard J; Martone, Maryann E; Ellisman, Mark H

    2012-02-09

    While progress has been made to develop automatic segmentation techniques for mitochondria, there remains a need for more accurate and robust techniques to delineate mitochondria in serial blockface scanning electron microscopic data. Previously developed texture based methods are limited for solving this problem because texture alone is often not sufficient to identify mitochondria. This paper presents a new three-step method, the Cytoseg process, for automated segmentation of mitochondria contained in 3D electron microscopic volumes generated through serial block face scanning electron microscopic imaging. The method consists of three steps. The first is a random forest patch classification step operating directly on 2D image patches. The second step consists of contour-pair classification. At the final step, we introduce a method to automatically seed a level set operation with output from previous steps. We report accuracy of the Cytoseg process on three types of tissue and compare it to a previous method based on Radon-Like Features. At step 1, we show that the patch classifier identifies mitochondria texture but creates many false positive pixels. At step 2, our contour processing step produces contours and then filters them with a second classification step, helping to improve overall accuracy. We show that our final level set operation, which is automatically seeded with output from previous steps, helps to smooth the results. Overall, our results show that use of contour pair classification and level set operations improve segmentation accuracy beyond patch classification alone. We show that the Cytoseg process performs well compared to another modern technique based on Radon-Like Features. We demonstrated that texture based methods for mitochondria segmentation can be enhanced with multiple steps that form an image processing pipeline. While we used a random-forest based patch classifier to recognize texture, it would be possible to replace this with

  14. Method: automatic segmentation of mitochondria utilizing patch classification, contour pair classification, and automatically seeded level sets

    Directory of Open Access Journals (Sweden)

    Giuly Richard J

    2012-02-01

    Full Text Available Abstract Background While progress has been made to develop automatic segmentation techniques for mitochondria, there remains a need for more accurate and robust techniques to delineate mitochondria in serial blockface scanning electron microscopic data. Previously developed texture based methods are limited for solving this problem because texture alone is often not sufficient to identify mitochondria. This paper presents a new three-step method, the Cytoseg process, for automated segmentation of mitochondria contained in 3D electron microscopic volumes generated through serial block face scanning electron microscopic imaging. The method consists of three steps. The first is a random forest patch classification step operating directly on 2D image patches. The second step consists of contour-pair classification. At the final step, we introduce a method to automatically seed a level set operation with output from previous steps. Results We report accuracy of the Cytoseg process on three types of tissue and compare it to a previous method based on Radon-Like Features. At step 1, we show that the patch classifier identifies mitochondria texture but creates many false positive pixels. At step 2, our contour processing step produces contours and then filters them with a second classification step, helping to improve overall accuracy. We show that our final level set operation, which is automatically seeded with output from previous steps, helps to smooth the results. Overall, our results show that use of contour pair classification and level set operations improve segmentation accuracy beyond patch classification alone. We show that the Cytoseg process performs well compared to another modern technique based on Radon-Like Features. Conclusions We demonstrated that texture based methods for mitochondria segmentation can be enhanced with multiple steps that form an image processing pipeline. While we used a random-forest based patch classifier to

  15. Forested land cover classification on the Cumberland Plateau, Jackson County, Alabama: a comparison of Landsat ETM+ and SPOT5 images

    Science.gov (United States)

    Yong Wang; Shanta Parajuli; Callie Schweitzer; Glendon Smalley; Dawn Lemke; Wubishet Tadesse; Xiongwen Chen

    2010-01-01

    Forest cover classifications focus on the overall growth form (physiognomy) of the community, dominant vegetation, and species composition of the existing forest. Accurately classifying the forest cover type is important for forest inventory and silviculture. We compared classification accuracy based on Landsat Enhanced Thematic Mapper Plus (Landsat ETM+) and Satellite...

  16. 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...

  17. 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.

  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. 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...

  20. 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%...