WorldWideScience

Sample records for gc motifs embedded

  1. An Optimized Method of Metabolite Extraction from Formalin-Fixed Paraffin-Embedded Tissue for GC/MS Analysis.

    Science.gov (United States)

    Wojakowska, Anna; Marczak, Łukasz; Jelonek, Karol; Polanski, Krzysztof; Widlak, Piotr; Pietrowska, Monika

    2015-01-01

    Formalin-fixed paraffin-embedded (FFPE) tissue specimens constitute a highly valuable source of clinical material for retrospective molecular studies. However, metabolomic assessment of such archival material remains still in its infancy. Hence, there is an urgent need for efficient methods enabling extraction and profiling of metabolites present in FFPE tissue specimens. Here we demonstrate the methodology for isolation of primary metabolites from archival tissues; either fresh-frozen, formalin-fixed or formalin-fixed and paraffin-embedded specimens of mouse kidney were analysed and compared in this work. We used gas chromatography followed by mass spectrometry (GC/MS approach) to identify about 80 metabolites (including amino acids, saccharides, carboxylic acids, fatty acids) present in such archive material. Importantly, about 75% of identified compounds were detected in all three types of specimens. Moreover, we observed that fixation with formalin itself (and their duration) did not affect markedly the presence of particular metabolites in tissue-extracted material, yet fixation for 24h could be recommended as a practical standard. Paraffin embedding influenced efficiency of extraction, which resulted in reduced quantities of several compounds. Nevertheless, we proved applicability of FFPE specimens for non-targeted GS/MS-based profiling of tissue metabolome, which is of great importance for feasibility of metabolomics studies using retrospective clinical material.

  2. Embedding

    DEFF Research Database (Denmark)

    Høyrup, Jens

    2016-01-01

    “Embedding” as a technical concept comes from linguistics, more precisely from grammar. The present paper investigates whether it can be applied fruitfully to certain questions that have been investigated by historians (and sometimes philosophers) of mathematics: 1. The construction of numeral sy...... spatial and linguistic embedding and concludes that the spatio-linguistic notion of embedding can be meaningfully applied to the former two discussions, whereas the apparent embedding of older within new theories is rather an ideological mirage....

  3. Embedding

    DEFF Research Database (Denmark)

    Høyrup, Jens

    2015-01-01

    to become the starting point not only for theoretical algebra, but for the whole transformation of mathematics from his time onward: the possibility of embedding, that is, of making a symbol or an element of a calculation stand not only for a single number, determined or undetermined, but for a whole...

  4. Hitchcock's Motifs

    NARCIS (Netherlands)

    Walker, Michael

    2005-01-01

    Among the abundant Alfred Hitchcock literature, Hitchcock's Motifs has found a fresh angle. Starting from recurring objects, settings, character-types and events, Michael Walker tracks some forty motifs, themes and clusters across the whole of Hitchcock's oeuvre, including not only all his 52 extant

  5. Embedded Leverage

    DEFF Research Database (Denmark)

    Frazzini, Andrea; Heje Pedersen, Lasse

    Many financial instruments are designed with embedded leverage such as options and leveraged exchange traded funds (ETFs). Embedded leverage alleviates investors’ leverage constraints and, therefore, we hypothesize that embedded leverage lowers required returns. Consistent with this hypothesis, we...... find that asset classes with embedded leverage offer low risk-adjusted returns and, in the cross-section, higher embedded leverage is associated with lower returns. A portfolio which is long low-embedded-leverage securities and short high-embedded-leverage securities earns large abnormal returns......, with t-statistics of 8.6 for equity options, 6.3 for index options, and 2.5 for ETFs. We provide extensive robustness tests and discuss the broader implications of embedded leverage for financial economics....

  6. The Motif Tracking Algorithm

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The search for patterns or motifs in data represents a problem area of key interest to finance and economic researchers. In this paper, we introduce the motif tracking algorithm (MTA), a novel immune inspired (IS) pattern identification tool that is able to identify unknown motifs of a non specified length which repeat within time series data. The power of the algorithm comes from the fact that it uses a small number of parameters with minimal assumptions regarding the data being examined or the underlying motifs. Our interest lies in applying the algorithm to financial time series data to identify unknown patterns that exist. The algorithm is tested using three separate data sets. Particular suitability to financial data is shown by applying it to oil price data. In all cases, the algorithm identifies the presence of a motif population in a fast and efficient manner due to the utilization of an intuitive symbolic representation.The resulting population of motifs is shown to have considerable potential value for other applications such as forecasting and algorithm seeding.

  7. The Motif Tracking Algorithm

    CERN Document Server

    Wilson, William; Aickelin, Uwe; 10.1007/s11633.008.0032.0

    2010-01-01

    The search for patterns or motifs in data represents a problem area of key interest to finance and economic researchers. In this paper we introduce the Motif Tracking Algorithm, a novel immune inspired pattern identification tool that is able to identify unknown motifs of a non specified length which repeat within time series data. The power of the algorithm comes from the fact that it uses a small number of parameters with minimal assumptions regarding the data being examined or the underlying motifs. Our interest lies in applying the algorithm to financial time series data to identify unknown patterns that exist. The algorithm is tested using three separate data sets. Particular suitability to financial data is shown by applying it to oil price data. In all cases the algorithm identifies the presence of a motif population in a fast and efficient manner due to the utilisation of an intuitive symbolic representation. The resulting population of motifs is shown to have considerable potential value for other ap...

  8. Visibility graph motifs

    CERN Document Server

    Iacovacci, Jacopo

    2015-01-01

    Visibility algorithms transform time series into graphs and encode dynamical information in their topology, paving the way for graph-theoretical time series analysis as well as building a bridge between nonlinear dynamics and network science. In this work we introduce and study the concept of visibility graph motifs, smaller substructures that appear with characteristic frequencies. We develop a theory to compute in an exact way the motif profiles associated to general classes of deterministic and stochastic dynamics. We find that this simple property is indeed a highly informative and computationally efficient feature capable to distinguish among different dynamics and robust against noise contamination. We finally confirm that it can be used in practice to perform unsupervised learning, by extracting motif profiles from experimental heart-rate series and being able, accordingly, to disentangle meditative from other relaxation states. Applications of this general theory include the automatic classification a...

  9. 1-t-motifs

    CERN Document Server

    Taelman, Lenny

    2009-01-01

    We show that the module of rational points on an abelian t-module E is canonically isomorphic with the module Ext^1(M_E, K[t]) of extensions of the trivial t-motif K[t] by the t-motif M_E associated with E. This generalizes prior results of Anderson and Thakur and of Papanikolas and Ramachandran. In case E is uniformizable then we show that this extension module is canonically isomorphic with the corresponding extension module of Pink-Hodge structures. This situation is formally very similar to Deligne's theory of 1-motifs and we have tried to build up the theory in a way that makes this analogy as clear as possible.

  10. MHC motif viewer

    DEFF Research Database (Denmark)

    Rapin, Nicolas Philippe Jean-Pierre; Hoof, Ilka; Lund, Ole

    2008-01-01

    . Algorithms that predict which peptides MHC molecules bind have recently been developed and cover many different alleles, but the utility of these algorithms is hampered by the lack of tools for browsing and comparing the specificity of these molecules. We have, therefore, developed a web server, MHC motif...... viewer, that allows the display of the likely binding motif for all human class I proteins of the loci HLA A, B, C, and E and for MHC class I molecules from chimpanzee (Pan troglodytes), rhesus monkey (Macaca mulatta), and mouse (Mus musculus). Furthermore, it covers all HLA-DR protein sequences...

  11. [Personal motif in art].

    Science.gov (United States)

    Gerevich, József

    2015-01-01

    One of the basic questions of the art psychology is whether a personal motif is to be found behind works of art and if so, how openly or indirectly it appears in the work itself. Analysis of examples and documents from the fine arts and literature allow us to conclude that the personal motif that can be identified by the viewer through symbols, at times easily at others with more difficulty, gives an emotional plus to the artistic product. The personal motif may be found in traumatic experiences, in communication to the model or with other emotionally important persons (mourning, disappointment, revenge, hatred, rivalry, revolt etc.), in self-searching, or self-analysis. The emotions are expressed in artistic activity either directly or indirectly. The intention nourished by the artist's identity (Kunstwollen) may stand in the way of spontaneous self-expression, channelling it into hidden paths. Under the influence of certain circumstances, the artist may arouse in the viewer, consciously or unconsciously, an illusionary, misleading image of himself. An examination of the personal motif is one of the important research areas of art therapy.

  12. Gc protein (vitamin D-binding protein): Gc genotyping and GcMAF precursor activity.

    Science.gov (United States)

    Nagasawa, Hideko; Uto, Yoshihiro; Sasaki, Hideyuki; Okamura, Natsuko; Murakami, Aya; Kubo, Shinichi; Kirk, Kenneth L; Hori, Hitoshi

    2005-01-01

    The Gc protein (human group-specific component (Gc), a vitamin D-binding protein or Gc globulin), has important physiological functions that include involvement in vitamin D transport and storage, scavenging of extracellular G-actin, enhancement of the chemotactic activity of C5a for neutrophils in inflammation and macrophage activation (mediated by a GalNAc-modified Gc protein (GcMAF)). In this review, the structure and function of the Gc protein is focused on especially with regard to Gc genotyping and GcMAF precursor activity. A discussion of the research strategy "GcMAF as a target for drug discovery" is included, based on our own research.

  13. Carleson embeddings

    Directory of Open Access Journals (Sweden)

    Helmut J. Heiming

    1996-01-01

    Full Text Available In this paper we discuss several operator ideal properties for so called Carleson embeddings of tent spaces into specific L q(μ-spaces, where μ is a Carleson measure on the complex unit disc. Characterizing absolutely q-summing, absolutely continuous and q-integral Carleson embeddings in terms of the underlying measure is our main topic. The presented results extend and integrate results especially known for composition operators on Hardy spaces as well as embedding theorems for function spaces of similar kind.

  14. Cromatografia gasosa bidimensional abrangente (GC × GC Comprehensive two-dimensional gas chromatography (GC × GC

    Directory of Open Access Journals (Sweden)

    Marcio Pozzobon Pedroso

    2009-01-01

    Full Text Available This paper presents the fundamental principles, instrumentation and selected applications of comprehensive two-dimensional gas chromatography (GC × GC. In this technique, introduced in 1991, two capillary columns are coupled and proper modulating interfaces continuously collect the eluate from the first column, transferring it to the second column. The result is a geometric increment in the chromatographic resolution, ensuring separation of extremely complex mixtures in time periods shorter or comparable to those of analysis using conventional gas chromatography and with better detectabilities and sensitivities.

  15. Efficient motif finding algorithms for large-alphabet inputs

    Directory of Open Access Journals (Sweden)

    Pavlovic Vladimir

    2010-10-01

    Full Text Available Abstract Background We consider the problem of identifying motifs, recurring or conserved patterns, in the biological sequence data sets. To solve this task, we present a new deterministic algorithm for finding patterns that are embedded as exact or inexact instances in all or most of the input strings. Results The proposed algorithm (1 improves search efficiency compared to existing algorithms, and (2 scales well with the size of alphabet. On a synthetic planted DNA motif finding problem our algorithm is over 10× more efficient than MITRA, PMSPrune, and RISOTTO for long motifs. Improvements are orders of magnitude higher in the same setting with large alphabets. On benchmark TF-binding site problems (FNP, CRP, LexA we observed reduction in running time of over 12×, with high detection accuracy. The algorithm was also successful in rapidly identifying protein motifs in Lipocalin, Zinc metallopeptidase, and supersecondary structure motifs for Cadherin and Immunoglobin families. Conclusions Our algorithm reduces computational complexity of the current motif finding algorithms and demonstrate strong running time improvements over existing exact algorithms, especially in important and difficult cases of large-alphabet sequences.

  16. On Equivariant Embedding of Hilbert C^* modules

    OpenAIRE

    Goswami, Debashish

    2007-01-01

    We prove that an arbitrary (not necessarily countably generated) Hilbert $G$-$\\cla$ module on a G-C^* algebra $\\cla$ admits an equivariant embedding into a trivial $G-\\cla$ module, provided G is a compact Lie group and its action on $\\cla$ is ergodic.

  17. On Equivariant Embedding of Hilbert $C^*$ modules

    CERN Document Server

    Goswami, Debashish

    2007-01-01

    We prove that an arbitrary (not necessarily countably generated) Hilbert $G$-$\\cla$ module on a $G-C^*$ algebra $\\cla$ admits an equivariant embedding into a trivial $G-\\cla$ module, provided $G$ is a compact Lie group and its action on $\\cla$ is ergodic.

  18. Hunting Motifs in Situla Art

    Directory of Open Access Journals (Sweden)

    Andrej Preložnik

    2013-07-01

    Full Text Available Situla art developed as an echo of the toreutic style which had spread from the Near East through the Phoenicians, Greeks and Etruscans as far as the Veneti, Raeti, Histri, and their eastern neighbours in the region of Dolenjska (Lower Carniola. An Early Iron Age phenomenon (c. 600—300 BC, it rep- resents the major and most arresting form of the contemporary visual arts in an area stretching from the foot of the Apennines in the south to the Drava and Sava rivers in the east. Indeed, individual pieces have found their way across the Alpine passes and all the way north to the Danube. In the world and art of the situlae, a prominent role is accorded to ani- mals. They are displayed in numerous representations of human activities on artefacts crafted in the classic situla style – that is, between the late 6th  and early 5th centuries BC – as passive participants (e.g. in pageants or in harness or as an active element of the situla narrative. The most typical example of the latter is the hunting scene. Today we know at least four objects decorat- ed exclusively with hunting themes, and a number of situlae and other larger vessels where hunting scenes are embedded in composite narratives. All this suggests a popularity unparallelled by any other genre. Clearly recognisable are various hunting techniques and weapons, each associated with a particu- lar type of game (Fig. 1. The chase of a stag with javelin, horse and hound is depicted on the long- familiar and repeatedly published fibula of Zagorje (Fig. 2. It displays a hound mauling the stag’s back and a hunter on horseback pursuing a hind, her neck already pierced by the javelin. To judge by the (so far unnoticed shaft end un- der the stag’s muzzle, the hunter would have been brandishing a second jave- lin as well, like the warrior of the Vače fibula or the rider of the Nesactium situla, presumably himself a hunter. Many parallels to his motif are known from Greece, Etruria, and

  19. An RNA motif that binds ATP

    Science.gov (United States)

    Sassanfar, M.; Szostak, J. W.

    1993-01-01

    RNAs that contain specific high-affinity binding sites for small molecule ligands immobilized on a solid support are present at a frequency of roughly one in 10(10)-10(11) in pools of random sequence RNA molecules. Here we describe a new in vitro selection procedure designed to ensure the isolation of RNAs that bind the ligand of interest in solution as well as on a solid support. We have used this method to isolate a remarkably small RNA motif that binds ATP, a substrate in numerous biological reactions and the universal biological high-energy intermediate. The selected ATP-binding RNAs contain a consensus sequence, embedded in a common secondary structure. The binding properties of ATP analogues and modified RNAs show that the binding interaction is characterized by a large number of close contacts between the ATP and RNA, and by a change in the conformation of the RNA.

  20. Embedded Hardware

    CERN Document Server

    Ganssle, Jack G; Eady, Fred; Edwards, Lewin; Katz, David J; Gentile, Rick

    2007-01-01

    The Newnes Know It All Series takes the best of what our authors have written to create hard-working desk references that will be an engineer's first port of call for key information, design techniques and rules of thumb. Guaranteed not to gather dust on a shelf!. Circuit design using microcontrollers is both a science and an art. This book covers it all. It details all of the essential theory and facts to help an engineer design a robust embedded system. Processors, memory, and the hot topic of interconnects (I/O) are completely covered. Our authors bring a wealth of experience and ideas; thi

  1. Distinct cagA EPIYA motifs are associated with ethnic diversity in Malaysia and Singapore.

    Science.gov (United States)

    Schmidt, Heather-Marie A; Goh, Khean-Lee; Fock, Kwong Ming; Hilmi, Ida; Dhamodaran, Subbiah; Forman, David; Mitchell, Hazel

    2009-08-01

    In vitro studies have shown that the biologic activity of CagA is influenced by the number and class of EPIYA motifs present in its variable region as these motifs correspond to the CagA phosphorylation sites. It has been hypothesized that strains possessing specific combinations of these motifs may be responsible for gastric cancer development. This study investigated the prevalence of cagA and the EPIYA motifs with regard to number, class, and patterns in strains from the three major ethnic groups within the Malaysian and Singaporean populations in relation to disease development. Helicobacter pylori isolates from 49 Chinese, 43 Indian, and 14 Malay patients with functional dyspepsia (FD) and 21 gastric cancer (GC) cases were analyzed using polymerase chain reaction for the presence of cagA and the number, type, and pattern of EPIYA motifs. Additionally, the EPIYA motifs of 47 isolates were sequenced. All 126 isolates possessed cagA, with the majority encoding EPIYA-A (97.6%) and all encoding EPIYA-B. However, while the cagA of 93.0% of Indian FD isolates encoded EPIYA-C as the third motif, 91.8% of Chinese FD isolates and 81.7% of Chinese GC isolates encoded EPIYA-D (p Malaysia and Singapore, these genotypes appear unassociated with the development of GC in the ethnic Chinese population. The phenomenon of distinct strains circulating within different ethnic groups, in combination with host and certain environmental factors, may help to explain the rates of GC development in Malaysia.

  2. Network motifs in music sequences

    CERN Document Server

    Zanette, Damian H

    2010-01-01

    In this note, I summarize ongoing research on motif distribution in networks built up out of symbolic sequences of Western musical origin. Their motif significance profiles exhibit remarkable consistency over different styles and periods, and define a class that cannot be identified with any of the four "superfamilies" to which most real networks seem to belong. Networks from music sequences possess an unusual abundance of bidirectional connections, due to the inherent reversibility of short musical note patterns. This property contributes to motif significance from both local and large-scale features of musical structure.

  3. Motif Yggdrasil: sampling sequence motifs from a tree mixture model.

    Science.gov (United States)

    Andersson, Samuel A; Lagergren, Jens

    2007-06-01

    In phylogenetic foot-printing, putative regulatory elements are found in upstream regions of orthologous genes by searching for common motifs. Motifs in different upstream sequences are subject to mutations along the edges of the corresponding phylogenetic tree, consequently taking advantage of the tree in the motif search is an appealing idea. We describe the Motif Yggdrasil sampler; the first Gibbs sampler based on a general tree that uses unaligned sequences. Previous tree-based Gibbs samplers have assumed a star-shaped tree or partially aligned upstream regions. We give a probabilistic model (MY model) describing upstream sequences with regulatory elements and build a Gibbs sampler with respect to this model. The model allows toggling, i.e., the restriction of a position to a subset of nucleotides, but does not require aligned sequences nor edge lengths, which may be difficult to come by. We apply the collapsing technique to eliminate the need to sample nuisance parameters, and give a derivation of the predictive update formula. We show that the MY model improves the modeling of difficult motif instances and that the use of the tree achieves a substantial increase in nucleotide level correlation coefficient both for synthetic data and 37 bacterial lexA genes. We investigate the sensitivity to errors in the tree and show that using random trees MY sampler still has a performance similar to the original version.

  4. Methods for sequencing GC-rich and CCT repeat DNA templates

    Science.gov (United States)

    Robinson, Donna L.

    2007-02-20

    The present invention is directed to a PCR-based method of cycle sequencing DNA and other polynucleotide sequences having high CG content and regions of high GC content, and includes for example DNA strands with a high Cytosine and/or Guanosine content and repeated motifs such as CCT repeats.

  5. Network motifs provide signatures that characterize metabolism†

    OpenAIRE

    Shellman, Erin R.; Burant, Charles F.; Schnell, Santiago

    2013-01-01

    Motifs are repeating patterns that determine the local properties of networks. In this work, we characterized all 3-node motifs using enzyme commission numbers of the International Union of Biochemistry and Molecular Biology to show that motif abundance is related to biochemical function. Further, we present a comparative analysis of motif distributions in the metabolic networks of 21 species across six kingdoms of life. We found the distribution of motif abundances to be similar between spec...

  6. Embedded Processor Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Embedded Processor Laboratory provides the means to design, develop, fabricate, and test embedded computers for missile guidance electronics systems in support...

  7. Steady-State Fluorescence and Lifetime Emission Study of pH-Sensitive Probes Based on i-motif Forming Oligonucleotides Single and Double Labeled with Pyrene

    Directory of Open Access Journals (Sweden)

    Anna Dembska

    2015-09-01

    Full Text Available Cytosine-rich nucleic acids undergo pH-stimulated structural transitions leading to formation of an i-motif architecture at an acidic pH. Thus, i-motifs are good foundation for designing simple pH-sensitive fluorescent probes. We report here steady-state and time-resolved fluorescence studies of pyrene-labeled probes based on RET sequence: C4GC4GC4GC4TA (RET21, AC4GC4GC4GC4TA (RET21A and C4GC4GC4GC4T (RET20. Comparative studies with single- and double-labeled i-motif probes were carried out. For each probe, we have measured fluorescence spectra and decays for emission wavelength of 390 nm over a wide range of pH (from 4.0 to 8.0. Effect of the oligonucleotide sequence and the number of pyrene labels on the spectral characteristics of probes were discussed.

  8. Reference: TCA1MOTIF [PLACE

    Lifescience Database Archive (English)

    Full Text Available TCA1MOTIF Goldsbrough AP, Albrecht H, Stratford R Salicylic acid-inducible binding ...of a tobacco nuclear protein to a 10 bp sequence which is highly conserved amongst stress-inducible genes. Plant J 3:563-571 (1993) PubMed: 8220463; ...

  9. Motif signatures of transcribed enhancers

    KAUST Repository

    Kleftogiannis, Dimitrios

    2017-09-14

    In mammalian cells, transcribed enhancers (TrEn) play important roles in the initiation of gene expression and maintenance of gene expression levels in spatiotemporal manner. One of the most challenging questions in biology today is how the genomic characteristics of enhancers relate to enhancer activities. This is particularly critical, as several recent studies have linked enhancer sequence motifs to specific functional roles. To date, only a limited number of enhancer sequence characteristics have been investigated, leaving space for exploring the enhancers genomic code in a more systematic way. To address this problem, we developed a novel computational method, TELS, aimed at identifying predictive cell type/tissue specific motif signatures. We used TELS to compile a comprehensive catalog of motif signatures for all known TrEn identified by the FANTOM5 consortium across 112 human primary cells and tissues. Our results confirm that distinct cell type/tissue specific motif signatures characterize TrEn. These signatures allow discriminating successfully a) TrEn from random controls, proxy of non-enhancer activity, and b) cell type/tissue specific TrEn from enhancers expressed and transcribed in different cell types/tissues. TELS codes and datasets are publicly available at http://www.cbrc.kaust.edu.sa/TELS.

  10. Conceptualizing Embedded Configuration

    DEFF Research Database (Denmark)

    Oddsson, Gudmundur Valur; Hvam, Lars; Lysgaard, Ole

    2006-01-01

    and services. The general idea can be named embedded configuration. In this article we intend to conceptualize embedded configuration, what it is and is not. The difference between embedded configuration, sales configuration and embedded software is explained. We will look at what is needed to make embedded...... configuration systems. That will include requirements to product modelling techniques. An example with consumer electronics will illuminate the elements of embedded configuration in settings that most can relate to. The question of where embedded configuration would be relevant is discussed, and the current...

  11. Extrinsic Curvature Embedding Diagrams

    CERN Document Server

    Lu, J L

    2003-01-01

    Embedding diagrams have been used extensively to visualize the properties of curved space in Relativity. We introduce a new kind of embedding diagram based on the {\\it extrinsic} curvature (instead of the intrinsic curvature). Such an extrinsic curvature embedding diagram, when used together with the usual kind of intrinsic curvature embedding diagram, carries the information of how a surface is {\\it embedded} in the higher dimensional curved space. Simple examples are given to illustrate the idea.

  12. Parametric bootstrapping for biological sequence motifs.

    Science.gov (United States)

    O'Neill, Patrick K; Erill, Ivan

    2016-10-06

    Biological sequence motifs drive the specific interactions of proteins and nucleic acids. Accordingly, the effective computational discovery and analysis of such motifs is a central theme in bioinformatics. Many practical questions about the properties of motifs can be recast as random sampling problems. In this light, the task is to determine for a given motif whether a certain feature of interest is statistically unusual among relevantly similar alternatives. Despite the generality of this framework, its use has been frustrated by the difficulties of defining an appropriate reference class of motifs for comparison and of sampling from it effectively. We define two distributions over the space of all motifs of given dimension. The first is the maximum entropy distribution subject to mean information content, and the second is the truncated uniform distribution over all motifs having information content within a given interval. We derive exact sampling algorithms for each. As a proof of concept, we employ these sampling methods to analyze a broad collection of prokaryotic and eukaryotic transcription factor binding site motifs. In addition to positional information content, we consider the informational Gini coefficient of the motif, a measure of the degree to which information is evenly distributed throughout a motif's positions. We find that both prokaryotic and eukaryotic motifs tend to exhibit higher informational Gini coefficients (IGC) than would be expected by chance under either reference distribution. As a second application, we apply maximum entropy sampling to the motif p-value problem and use it to give elementary derivations of two new estimators. Despite the historical centrality of biological sequence motif analysis, this study constitutes to our knowledge the first use of principled null hypotheses for sequence motifs given information content. Through their use, we are able to characterize for the first time differerences in global motif statistics

  13. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    Energy Technology Data Exchange (ETDEWEB)

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

  14. Main: TCA1MOTIF [PLACE

    Lifescience Database Archive (English)

    Full Text Available TCA1MOTIF S000159 17-May-1998 (last modified) kehi TCA-1 (tobacco nuclear protein 1...) binding site; Related to salicylic acid-inducible expression of many genes; Found in barley beta-1,3-gluca...nase and over 30 different plant genes which are known to be induced by one or more forms of stress; A similar sequence (TCA... et al., 1997); SA; salicylic acid; stress; TCA-1; barley (Hordeum vulgare); tobacco (Nicotiana tabacum); TCATCTTCTT ...

  15. Comprehensive discovery of DNA motifs in 349 human cells and tissues reveals new features of motifs.

    Science.gov (United States)

    Zheng, Yiyu; Li, Xiaoman; Hu, Haiyan

    2015-01-01

    Comprehensive motif discovery under experimental conditions is critical for the global understanding of gene regulation. To generate a nearly complete list of human DNA motifs under given conditions, we employed a novel approach to de novo discover significant co-occurring DNA motifs in 349 human DNase I hypersensitive site datasets. We predicted 845 to 1325 motifs in each dataset, for a total of 2684 non-redundant motifs. These 2684 motifs contained 54.02 to 75.95% of the known motifs in seven large collections including TRANSFAC. In each dataset, we also discovered 43 663 to 2 013 288 motif modules, groups of motifs with their binding sites co-occurring in a significant number of short DNA regions. Compared with known interacting transcription factors in eight resources, the predicted motif modules on average included 84.23% of known interacting motifs. We further showed new features of the predicted motifs, such as motifs enriched in proximal regions rarely overlapped with motifs enriched in distal regions, motifs enriched in 5' distal regions were often enriched in 3' distal regions, etc. Finally, we observed that the 2684 predicted motifs classified the cell or tissue types of the datasets with an accuracy of 81.29%. The resources generated in this study are available at http://server.cs.ucf.edu/predrem/.

  16. An Expedient Regio- and Diastereoselective Synthesis of Hybrid Frameworks with Embedded Spiro[9,10]dihydroanthracene [9,3′]-pyrrolidine and Spiro[oxindole-3,2′-pyrrolidine] Motifs via an Ionic Liquid-Mediated Multicomponent Reaction

    Directory of Open Access Journals (Sweden)

    Natarajan Arumugam

    2015-09-01

    Full Text Available A series of hitherto unreported anthracene-embedded dispirooxindoles has been synthesized via a one-pot three-component 1,3-dipolar cycloaddition reaction of an azomethine ylide, generated in situ from the reaction of isatin and sarcosine to 10-benzylideneanthracen-9(10H-one as a dipolarophile in 1-butyl-3-methylimidazolium bromide([bmim]Br, an ionic liquid. This reaction proceeded regio- and diastereoselectively, in good to excellent yields.

  17. Water and side-chain embedded π-turns.

    Science.gov (United States)

    Dasgupta, Bhaskar; Dey, Sucharita; Chakrabarti, Pinak

    2014-05-01

    Elucidating protein function from its structure is central to the understanding of cellular mechanisms. This involves deciphering the dependence of local structural motifs on sequence. These structural motifs may be stabilized by direct or water-mediated hydrogen bonding among the constituent residues. π-Turns, defined by interactions between (i) and (i + 5) positions, are large enough to contain a central space that can embed a water molecule (or a protein moiety) to form a stable structure. This work is an analysis of such embedded π-turns using a nonredundant dataset of protein structures. A total of 2965 embedded π-turns have been identified, as also 281 embedded Schellman motif, a type of π-turn which occurs at the C-termini of α-helices. Embedded π-turns and Schellman motifs have been classified on the basis of the protein atoms of the terminal turn residues that are linked by the embedded moiety, conformation, residue composition, and compared with the turns that have terminal residues connected by direct hydrogen bonds. Geometrically, the turns have been fitted to a circle and the position of the linker relative to its center analyzed. The hydroxyl group of Ser and Thr, located at (i + 3) position, is the most prominent linker for the side-chain mediated π-turns. Consideration of residue conservation among homologous sequences indicates the terminal and the linker positions to be the most conserved. The embedded π-turn as a binding site (for the linker) is discussed in the context of "nest," a concave depression that is formed in protein structures with adjacent residues having enantiomeric main-chain conformations.

  18. seeMotif: exploring and visualizing sequence motifs in 3D structures

    OpenAIRE

    2009-01-01

    Sequence motifs are important in the study of molecular biology. Motif discovery tools efficiently deliver many function related signatures of proteins and largely facilitate sequence annotation. As increasing numbers of motifs are detected experimentally or predicted computationally, characterizing the functional roles of motifs and identifying the potential synergetic relationships between them are important next steps. A good way to investigate novel motifs is to utilize the abundant 3D st...

  19. Detecting correlations among functional-sequence motifs

    Science.gov (United States)

    Pirino, Davide; Rigosa, Jacopo; Ledda, Alice; Ferretti, Luca

    2012-06-01

    Sequence motifs are words of nucleotides in DNA with biological functions, e.g., gene regulation. Identification of such words proceeds through rejection of Markov models on the expected motif frequency along the genome. Additional biological information can be extracted from the correlation structure among patterns of motif occurrences. In this paper a log-linear multivariate intensity Poisson model is estimated via expectation maximization on a set of motifs along the genome of E. coli K12. The proposed approach allows for excitatory as well as inhibitory interactions among motifs and between motifs and other genomic features like gene occurrences. Our findings confirm previous stylized facts about such types of interactions and shed new light on genome-maintenance functions of some particular motifs. We expect these methods to be applicable to a wider set of genomic features.

  20. Statistical tests to compare motif count exceptionalities

    Directory of Open Access Journals (Sweden)

    Vandewalle Vincent

    2007-03-01

    Full Text Available Abstract Background Finding over- or under-represented motifs in biological sequences is now a common task in genomics. Thanks to p-value calculation for motif counts, exceptional motifs are identified and represent candidate functional motifs. The present work addresses the related question of comparing the exceptionality of one motif in two different sequences. Just comparing the motif count p-values in each sequence is indeed not sufficient to decide if this motif is significantly more exceptional in one sequence compared to the other one. A statistical test is required. Results We develop and analyze two statistical tests, an exact binomial one and an asymptotic likelihood ratio test, to decide whether the exceptionality of a given motif is equivalent or significantly different in two sequences of interest. For that purpose, motif occurrences are modeled by Poisson processes, with a special care for overlapping motifs. Both tests can take the sequence compositions into account. As an illustration, we compare the octamer exceptionalities in the Escherichia coli K-12 backbone versus variable strain-specific loops. Conclusion The exact binomial test is particularly adapted for small counts. For large counts, we advise to use the likelihood ratio test which is asymptotic but strongly correlated with the exact binomial test and very simple to use.

  1. rMotifGen: random motif generator for DNA and protein sequences

    Directory of Open Access Journals (Sweden)

    Hardin C Timothy

    2007-08-01

    Full Text Available Abstract Background Detection of short, subtle conserved motif regions within a set of related DNA or amino acid sequences can lead to discoveries about important regulatory domains such as transcription factor and DNA binding sites as well as conserved protein domains. In order to help assess motif detection algorithms on motifs with varying properties and levels of conservation, we have developed a computational tool, rMotifGen, with the sole purpose of generating a number of random DNA or protein sequences containing short sequence motifs. Each motif consensus can be user-defined, randomly generated, or created from a position-specific scoring matrix (PSSM. Insertions and mutations within these motifs are created according to user-defined parameters and substitution matrices. The resulting sequences can be helpful in mutational simulations and in testing the limits of motif detection algorithms. Results Two implementations of rMotifGen have been created, one providing a graphical user interface (GUI for random motif construction, and the other serving as a command line interface. The second implementation has the added advantages of platform independence and being able to be called in a batch mode. rMotifGen was used to construct sample sets of sequences containing DNA motifs and amino acid motifs that were then tested against the Gibbs sampler and MEME packages. Conclusion rMotifGen provides an efficient and convenient method for creating random DNA or amino acid sequences with a variable number of motifs, where the instance of each motif can be incorporated using a position-specific scoring matrix (PSSM or by creating an instance mutated from its corresponding consensus using an evolutionary model based on substitution matrices. rMotifGen is freely available at: http://bioinformatics.louisville.edu/brg/rMotifGen/.

  2. Discovering novel sequence motifs with MEME.

    Science.gov (United States)

    Bailey, Timothy L

    2002-11-01

    This unit illustrates how to use MEME to discover motifs in a group of related nucleotide or peptide sequences. A MEME motif is a sequence pattern that occurs repeatedly in one or more sequences in the input group. MEME can be used to discover novel patterns because it bases its discoveries only on the input sequences, not on any prior knowledge (such as databases of known motifs). The input to MEME is a set of unaligned sequences of the same type (peptide or nucleotide). For each motif it discovers, MEME reports the occurrences (sites), consensus sequence, and the level of conservation (information content) at each position in the pattern. MEME also produces block diagrams showing where all of the discovered motifs occur in the training set sequences. MEME's hypertext (HTML) output also contains buttons that allow for the convenient use of the motifs in other searches.

  3. Derivatization of carbohydrates for GC and GC-MS analyses.

    Science.gov (United States)

    Ruiz-Matute, A I; Hernández-Hernández, O; Rodríguez-Sánchez, S; Sanz, M L; Martínez-Castro, I

    2011-05-15

    GC and GC-MS are excellent techniques for the analysis of carbohydrates; nevertheless the preparation of adequate derivatives is necessary. The different functional groups that can be found and the diversity of samples require specific methods. This review aims to collect the most important methodologies currently used, either published as new procedures or as new applications, for the analysis of carbohydrates. A high diversity of compounds with diverse functionalities has been selected: neutral carbohydrates (saccharides and polyalcohols), sugar acids, amino and iminosugars, polysaccharides, glycosides, glycoconjugates, anhydrosugars, difructose anhydrides and products resulting of Maillard reaction (osuloses, Amadori compounds). Chiral analysis has also been considered, describing the use of diastereomers and derivatives to be eluted on chiral stationary phases.

  4. Computational design of model scaffold for anion recognition based on the 'C(α) NN' motif.

    Science.gov (United States)

    Sheet, Tridip; Ghosh, Suvankar; Pal, Debnath; Banerjee, Raja

    2017-01-01

    The 'novel phosphate binding 'C(α) NN' motif', consisting of three consecutive amino acid residues, usually occurs in the protein loop regions preceding a helix. Recent computational and complementary biophysical experiments on a series of chimeric peptides containing the naturally occurring 'C(α) NN' motif at the N-terminus of a designed helix establishes that the motif segment recognizes the anion (sulfate and phosphate ions) through local interaction along with extension of the helical conformation which is thermodynamically favored even in a context-free, nonproteinaceous isolated system. However, the strength of the interaction depends on the amino acid sequence/conformation of the motif. Such a locally-mediated recognition of anions validates its intrinsic affinity towards anions and confirms that the affinity for recognition of anions is embedded within the 'local sequence' of the motif. Based on the knowledge gathered on the sequence/structural aspects of the naturally occurring 'C(α) NN' segment, which provides the guideline for rationally engineering model scaffolds, we have modeled a series of templates and investigated their interactions with anions using computational approach. Two of these designed scaffolds show more efficient anion recognition than those of the naturally occurring 'C(α) NN' motif which have been studied. This may provide an avenue in designing better anion receptors suitable for various biochemical applications.

  5. Quantitative analysis of Boehm's GC

    Institute of Scientific and Technical Information of China (English)

    GUAN Xue-tao; ZHANG Yuan-rui; GOU Xiao-gang; CHENG Xu

    2003-01-01

    The term garbage collection describes the automated process of finding previously allocated memorythatis no longer in use in order to make the memory available to satisfy subsequent allocation requests. Wehave reviewed existing papers and implementations of GC, and especially analyzed Boehm' s C codes, which isa real-time mark-sweep GC running under Linux and ANSI C standard. In this paper, we will quantitatively an-alyze the performance of different configurations of Boehm' s collector subjected to different workloads. Reportedmeasurements demonstrate that a refined garbage collector is a viable alternative to traditional explicit memorymanagement techniques, even for low-level languages. It is more a trade-off for certain system than an all-or-nothing proposition.

  6. Embedded systems handbook

    CERN Document Server

    Zurawski, Richard

    2005-01-01

    Embedded systems are nearly ubiquitous, and books on individual topics or components of embedded systems are equally abundant. Unfortunately, for those designers who thirst for knowledge of the big picture of embedded systems there is not a drop to drink. Until now. The Embedded Systems Handbook is an oasis of information, offering a mix of basic and advanced topics, new solutions and technologies arising from the most recent research efforts, and emerging trends to help you stay current in this ever-changing field.With preeminent contributors from leading industrial and academic institutions

  7. Pro Linux Embedded Systems

    CERN Document Server

    Sally, Gene

    2010-01-01

    Today, Linux is included with nearly every embedded platform. Embedded developers can take a more modern route and spend more time tuning Linux and taking advantage of open source code to build more robust, feature-rich applications. While Gene Sally does not neglect porting Linux to new hardware, modern embedded hardware is more sophisticated than ever: most systems include the capabilities found on desktop systems. This book is written from the perspective of a user employing technologies and techniques typically reserved for desktop systems. * Modern guide for developing embedded Linux syst

  8. Embedding beyond electrostatics

    DEFF Research Database (Denmark)

    Nåbo, Lina J.; Olsen, Jógvan Magnus Haugaard; Holmgaard List, Nanna;

    2016-01-01

    We study excited states of cholesterol in solution and show that, in this specific case, solute wave-function confinement is the main effect of the solvent. This is rationalized on the basis of the polarizable density embedding scheme, which in addition to polarizable embedding includes non-electrostatic...... repulsion that effectively confines the solute wave function to its cavity. We illustrate how the inclusion of non-electrostatic repulsion results in a successful identification of the intense π → π∗ transition, which was not possible using an embedding method that only includes electrostatics....... This underlines the importance of non-electrostatic repulsion in quantum-mechanical embedding-based methods....

  9. MSDmotif: exploring protein sites and motifs

    Directory of Open Access Journals (Sweden)

    Henrick Kim

    2008-07-01

    Full Text Available Abstract Background Protein structures have conserved features – motifs, which have a sufficient influence on the protein function. These motifs can be found in sequence as well as in 3D space. Understanding of these fragments is essential for 3D structure prediction, modelling and drug-design. The Protein Data Bank (PDB is the source of this information however present search tools have limited 3D options to integrate protein sequence with its 3D structure. Results We describe here a web application for querying the PDB for ligands, binding sites, small 3D structural and sequence motifs and the underlying database. Novel algorithms for chemical fragments, 3D motifs, ϕ/ψ sequences, super-secondary structure motifs and for small 3D structural motif associations searches are incorporated. The interface provides functionality for visualization, search criteria creation, sequence and 3D multiple alignment options. MSDmotif is an integrated system where a results page is also a search form. A set of motif statistics is available for analysis. This set includes molecule and motif binding statistics, distribution of motif sequences, occurrence of an amino-acid within a motif, correlation of amino-acids side-chain charges within a motif and Ramachandran plots for each residue. The binding statistics are presented in association with properties that include a ligand fragment library. Access is also provided through the distributed Annotation System (DAS protocol. An additional entry point facilitates XML requests with XML responses. Conclusion MSDmotif is unique by combining chemical, sequence and 3D data in a single search engine with a range of search and visualisation options. It provides multiple views of data found in the PDB archive for exploring protein structures.

  10. Assessment of composite motif discovery methods

    Directory of Open Access Journals (Sweden)

    Johansen Jostein

    2008-02-01

    Full Text Available Abstract Background Computational discovery of regulatory elements is an important area of bioinformatics research and more than a hundred motif discovery methods have been published. Traditionally, most of these methods have addressed the problem of single motif discovery – discovering binding motifs for individual transcription factors. In higher organisms, however, transcription factors usually act in combination with nearby bound factors to induce specific regulatory behaviours. Hence, recent focus has shifted from single motifs to the discovery of sets of motifs bound by multiple cooperating transcription factors, so called composite motifs or cis-regulatory modules. Given the large number and diversity of methods available, independent assessment of methods becomes important. Although there have been several benchmark studies of single motif discovery, no similar studies have previously been conducted concerning composite motif discovery. Results We have developed a benchmarking framework for composite motif discovery and used it to evaluate the performance of eight published module discovery tools. Benchmark datasets were constructed based on real genomic sequences containing experimentally verified regulatory modules, and the module discovery programs were asked to predict both the locations of these modules and to specify the single motifs involved. To aid the programs in their search, we provided position weight matrices corresponding to the binding motifs of the transcription factors involved. In addition, selections of decoy matrices were mixed with the genuine matrices on one dataset to test the response of programs to varying levels of noise. Conclusion Although some of the methods tested tended to score somewhat better than others overall, there were still large variations between individual datasets and no single method performed consistently better than the rest in all situations. The variation in performance on individual

  11. Embedded systems handbook networked embedded systems

    CERN Document Server

    Zurawski, Richard

    2009-01-01

    Considered a standard industry resource, the Embedded Systems Handbook provided researchers and technicians with the authoritative information needed to launch a wealth of diverse applications, including those in automotive electronics, industrial automated systems, and building automation and control. Now a new resource is required to report on current developments and provide a technical reference for those looking to move the field forward yet again. Divided into two volumes to accommodate this growth, the Embedded Systems Handbook, Second Edition presents a comprehensive view on this area

  12. The data embedding method

    Energy Technology Data Exchange (ETDEWEB)

    Sandford, M.T. II; Bradley, J.N.; Handel, T.G.

    1996-06-01

    Data embedding is a new steganographic method for combining digital information sets. This paper describes the data embedding method and gives examples of its application using software written in the C-programming language. Sandford and Handel produced a computer program (BMPEMBED, Ver. 1.51 written for IBM PC/AT or compatible, MS/DOS Ver. 3.3 or later) that implements data embedding in an application for digital imagery. Information is embedded into, and extracted from, Truecolor or color-pallet images in Microsoft{reg_sign} bitmap (.BMP) format. Hiding data in the noise component of a host, by means of an algorithm that modifies or replaces the noise bits, is termed {open_quote}steganography.{close_quote} Data embedding differs markedly from conventional steganography, because it uses the noise component of the host to insert information with few or no modifications to the host data values or their statistical properties. Consequently, the entropy of the host data is affected little by using data embedding to add information. The data embedding method applies to host data compressed with transform, or {open_quote}lossy{close_quote} compression algorithms, as for example ones based on discrete cosine transform and wavelet functions. Analysis of the host noise generates a key required for embedding and extracting the auxiliary data from the combined data. The key is stored easily in the combined data. Images without the key cannot be processed to extract the embedded information. To provide security for the embedded data, one can remove the key from the combined data and manage it separately. The image key can be encrypted and stored in the combined data or transmitted separately as a ciphertext much smaller in size than the embedded data. The key size is typically ten to one-hundred bytes, and it is in data an analysis algorithm.

  13. Data embedding method

    Science.gov (United States)

    Sandford, Maxwell T., II; Bradley, Jonathan N.; Handel, Theodore G.

    1996-01-01

    Data embedding is a new steganographic method for combining digital information sets. This paper describes the data embedding method and gives examples of its application using software written in the C-programming language. Sandford and Handel produced a computer program (BMPEMBED, Ver. 1.51 written for IBM PC/AT or compatible, MS/DOS Ver. 3.3 or later) that implements data embedding in an application for digital imagery. Information is embedded into, and extracted from, Truecolor or color-pallet images in MicrosoftTM bitmap (BMP) format. Hiding data in the noise component of a host, by means of an algorithm that modifies or replaces the noise bits, is termed `steganography.' Data embedding differs markedly from conventional steganography, because it uses the noise component of the host to insert information with few or no modifications to the host data values or their statistical properties. Consequently, the entropy of the host data is affected little by using data embedding to add information. The data embedding method applies to host data compressed with transform, or `lossy' compression algorithms, as for example ones based on discrete cosine transform and wavelet functions. Analysis of the host noise generates a key required for embedding and extracting the auxiliary data from the combined data. The key is stored easily in the combined data. Images without the key cannot be processed to extract the embedded information. To provide security for the embedded data, one can remove the key from the combined data and manage it separately. The image key can be encrypted and stored in the combined data or transmitted separately as a ciphertext much smaller in size than the embedded data. The key size is typically ten to one-hundred bytes, and it is derived from the original host data by an analysis algorithm.

  14. Fitness for synchronization of network motifs

    DEFF Research Database (Denmark)

    Vega, Y.M.; Vázquez-Prada, M.; Pacheco, A.F.

    2004-01-01

    We study the synchronization of Kuramoto's oscillators in small parts of networks known as motifs. We first report on the system dynamics for the case of a scale-free network and show the existence of a non-trivial critical point. We compute the probability that network motifs synchronize, and fi...

  15. Helix-packing motifs in membrane proteins.

    Science.gov (United States)

    Walters, R F S; DeGrado, W F

    2006-09-12

    The fold of a helical membrane protein is largely determined by interactions between membrane-imbedded helices. To elucidate recurring helix-helix interaction motifs, we dissected the crystallographic structures of membrane proteins into a library of interacting helical pairs. The pairs were clustered according to their three-dimensional similarity (rmsd universe of common transmembrane helix-pairing motifs is relatively simple. The largest cluster, which comprises 29% of the library members, consists of an antiparallel motif with left-handed packing angles, and it is frequently stabilized by packing of small side chains occurring every seven residues in the sequence. Right-handed parallel and antiparallel structures show a similar tendency to segregate small residues to the helix-helix interface but spaced at four-residue intervals. Position-specific sequence propensities were derived for the most populated motifs. These structural and sequential motifs should be quite useful for the design and structural prediction of membrane proteins.

  16. Embedded engineering education

    CERN Document Server

    Kaštelan, Ivan; Temerinac, Miodrag; Barak, Moshe; Sruk, Vlado

    2016-01-01

    This book focuses on the outcome of the European research project “FP7-ICT-2011-8 / 317882: Embedded Engineering Learning Platform” E2LP. Additionally, some experiences and researches outside this project have been included. This book provides information about the achieved results of the E2LP project as well as some broader views about the embedded engineering education. It captures project results and applications, methodologies, and evaluations. It leads to the history of computer architectures, brings a touch of the future in education tools and provides a valuable resource for anyone interested in embedded engineering education concepts, experiences and material. The book contents 12 original contributions and will open a broader discussion about the necessary knowledge and appropriate learning methods for the new profile of embedded engineers. As a result, the proposed Embedded Computer Engineering Learning Platform will help to educate a sufficient number of future engineers in Europe, capable of d...

  17. [Psychopathological study of lie motif in schizophrenia].

    Science.gov (United States)

    Otsuka, Koichiro; Kato, Satoshi

    2006-01-01

    The theme of a statement is called "lie motif" by the authors when schizophrenic patients say "I have lied to anybody". We tried to analyse of the psychopathological characteristics and anthropological meanings of the lie motifs in schizophrenia, which has not been thematically examined until now, based on 4 cases, and contrasting with the lie motif (Lügenmotiv) in depression taken up by A. Kraus (1989). We classified the lie motifs in schizophrenia into the following two types: a) the past directive lie motif: the patients speak about their real lie regarding it as a 'petty fault' in their distant past with self-guilty feeling, b) the present directive lie motif: the patients say repeatedly 'I have lied' (about their present speech and behavior), retreating from their previous commitments. The observed false confessions of innocent fault by the patients seem to belong to the present directed lie motif. In comparison with the lie motif in depression, it is characteristic for the lie motif in schizophrenia that the patients feel themselves to already have been caught out by others before they confess the lie. The lie motif in schizophrenia seems to come into being through the attribution process of taking the others' blame on ones' own shoulders, which has been pointed out to be common in the guilt experience in schizophrenia. The others' blame on this occasion is due to "the others' gaze" in the experience of the initial self-centralization (i.e. non delusional self-referential experience) in the early stage of schizophrenia (S. Kato 1999). The others' gaze is supposed to bring about the feeling of amorphous self-revelation which could also be regarded as the guilt feeling without content, to the patients. When the guilt feeling is bound with a past concrete fault, the patients tell the past directive lie motif. On the other hand, when the patients cannot find a past fixed content, and feel their present actions as uncertain and experience them as lies, the

  18. Purification of equine Gc-globulin

    DEFF Research Database (Denmark)

    Houen, Gunnar; Pihl, Tina Holberg; Andersen, Pia Haubro

    Objectives With the aim of producing antibodies for an equine Group specific component (Gc)-globulin assay, the protein was purified from normal equine plasma. Methods Equine Gc-globulin was purified from healthy horse plasma using ion exchange chromatography (Q-Sepharose, CM......-Sepharose) and preparative PAGE. Results Equine Gc-globulin has successfully been purified from healthy horse plasma and rabbits and mice are being immunized to produce specific antibodies. Conclusions Purification of equine Gc-globulin and the production of specific antibodies will make it possible to develop an assay...... to be a sensitive marker of acute tissue injury and fatal outcome in humans. Patients with a low plasma concentration of Gc-globulin due to severe tissue injury might potentially benefit from infusions with purified Gc-globulin [1]. With an equine Gc-globulin assay, future studies will investigate the concentration...

  19. A “GC-rich” method for mammalian gene expression:A dominant role of non-coding DNA GC content in the regulation of mammalian gene expression

    Institute of Scientific and Technical Information of China (English)

    Gilbert; Rishton; Matthew; (Mizhou); HUI

    2010-01-01

    High mammalian gene expression was obtained for more than twenty different proteins in different cell types by just a few laboratory scale stable gene transfections for each protein.The stable expression vectors were constructed by inserting a naturally-occurring 1.006 kb or a synthetic 0.733 kb DNA fragment(including intron) of extremely GC-rich at the 5’ or/and 3’ flanking regions of these protein genes or their gene promoters.This experiment is the first experimental evidence showing that a non-coding extremely GC-rich DNA fragment is a super "chromatin opening element" and plays an important role in mammalian gene expression.This experiment has further indicated that chromatin-based regulation of mammalian gene expression is at least partially embedded in DNA primary structure,namely DNA GC-content.

  20. VARUN: discovering extensible motifs under saturation constraints.

    Science.gov (United States)

    Apostolico, Alberto; Comin, Matteo; Parida, Laxmi

    2010-01-01

    The discovery of motifs in biosequences is frequently torn between the rigidity of the model on one hand and the abundance of candidates on the other hand. In particular, motifs that include wild cards or "don't cares" escalate exponentially with their number, and this gets only worse if a don't care is allowed to stretch up to some prescribed maximum length. In this paper, a notion of extensible motif in a sequence is introduced and studied, which tightly combines the structure of the motif pattern, as described by its syntactic specification, with the statistical measure of its occurrence count. It is shown that a combination of appropriate saturation conditions and the monotonicity of probabilistic scores over regions of constant frequency afford us significant parsimony in the generation and testing of candidate overrepresented motifs. A suite of software programs called Varun is described, implementing the discovery of extensible motifs of the type considered. The merits of the method are then documented by results obtained in a variety of experiments primarily targeting protein sequence families. Of equal importance seems the fact that the sets of all surprising motifs returned in each experiment are extracted faster and come in much more manageable sizes than would be obtained in the absence of saturation constraints.

  1. Detecting Motifs in System Call Sequences

    CERN Document Server

    Wilson, William O; Aickelin, Uwe

    2010-01-01

    The search for patterns or motifs in data represents an area of key interest to many researchers. In this paper we present the Motif Tracking Algorithm, a novel immune inspired pattern identification tool that is able to identify unknown motifs which repeat within time series data. The power of the algorithm is derived from its use of a small number of parameters with minimal assumptions. The algorithm searches from a completely neutral perspective that is independent of the data being analysed, and the underlying motifs. In this paper the motif tracking algorithm is applied to the search for patterns within sequences of low level system calls between the Linux kernel and the operating system's user space. The MTA is able to compress data found in large system call data sets to a limited number of motifs which summarise that data. The motifs provide a resource from which a profile of executed processes can be built. The potential for these profiles and new implications for security research are highlighted. A...

  2. MOMA GC-MS coupling

    Science.gov (United States)

    Buch, A.; Pinnick, V. T.; Grand, N.; Szopa, C.; Danell, R.; Lustrement, B.; Freissinet, C.; van Amerom, F. H.; Raulin, F.; Glavin, D. P.; Stalport, F.; Coll, P. J.; Arevalo, R. D.; Brinckerhoff, W. B.; Goesmann, F.; Mahaffy, P. R.

    2013-12-01

    The joint ESA-Roscosmos Exo-Mars-2018 rover mission seeks the signs of past or present life on Mars. The Mars Organic Molecule Analyzer (MOMA) aboard the ExoMars rover will be a key analytical tool in providing chemical (molecular) information from the solid samples, with particular focus on the characterization of organic content. Central to MOMA instrumentation is a gas chromatograph-mass spectrometer (GC-MS) which provides the unique ability to characterize a broad range of compounds allowing chemical analyses of volatile and non-volatile species. The Gas chromatograph and the oven have been built at LATMOS/LISA (France) and at MPS (Germany) respectively whereas the mass spectrometer has been built at the NASA Goddard Space Flight Center (USA). Both instruments have been tested separately first and have been coupled in order to test the efficiency of the future MOMA GC-MS instrument. The main objective of the second step has been to test the quantitative response of both instruments while they are coupled and to characterize the combined instrument detection limit for several compounds. A final experiment has been done in order to test the feasibility of the separation and detection of a mixture contained in a soil sample introduced in the MOMA oven.

  3. On Distributed Embedded Systems

    Directory of Open Access Journals (Sweden)

    Arvindra Sehmi

    2013-01-01

    Full Text Available Thinking of distributed embedded systems (DES—let alone the more general area of embedded computing—as a unified topic is difficult. Nevertheless, it is a vastly important topic and potentially represents a revolution in information technology (IT. DES is driven by the increasing capabilities and ever-declining costs of computing and communications devices, resulting in networked systems of embedded computers whose functional components are nearly invisible to end users. Systems have the potential to alter radically the way in which people interact with their environment by linking a range of devices and sensors that will allow information to be collected, shared, and processed in unprecedented ways.

  4. seeMotif: exploring and visualizing sequence motifs in 3D structures

    Science.gov (United States)

    Chang, Darby Tien-Hao; Chien, Ting-Ying; Chen, Chien-Yu

    2009-01-01

    Sequence motifs are important in the study of molecular biology. Motif discovery tools efficiently deliver many function related signatures of proteins and largely facilitate sequence annotation. As increasing numbers of motifs are detected experimentally or predicted computationally, characterizing the functional roles of motifs and identifying the potential synergetic relationships between them are important next steps. A good way to investigate novel motifs is to utilize the abundant 3D structures that have also been accumulated at an astounding rate in recent years. This article reports the development of the web service seeMotif, which provides users with an interactive interface for visualizing sequence motifs on protein structures from the Protein Data Bank (PDB). Researchers can quickly see the locations and conformation of multiple motifs among a number of related structures simultaneously. Considering the fact that PDB sequences are usually shorter than those in sequence databases and/or may have missing residues, seeMotif has two complementary approaches for selecting structures and mapping motifs to protein chains in structures. As more and more structures belonging to previously uncharacterized protein families become available, combining sequence and structure information gives good opportunities to facilitate understanding of protein functions in large-scale genome projects. Available at: http://seemotif.csie.ntu.edu.tw,http://seemotif.ee.ncku.edu.tw or http://seemotif.csbb.ntu.edu.tw. PMID:19477961

  5. seeMotif: exploring and visualizing sequence motifs in 3D structures.

    Science.gov (United States)

    Chang, Darby Tien-Hao; Chien, Ting-Ying; Chen, Chien-Yu

    2009-07-01

    Sequence motifs are important in the study of molecular biology. Motif discovery tools efficiently deliver many function related signatures of proteins and largely facilitate sequence annotation. As increasing numbers of motifs are detected experimentally or predicted computationally, characterizing the functional roles of motifs and identifying the potential synergetic relationships between them are important next steps. A good way to investigate novel motifs is to utilize the abundant 3D structures that have also been accumulated at an astounding rate in recent years. This article reports the development of the web service seeMotif, which provides users with an interactive interface for visualizing sequence motifs on protein structures from the Protein Data Bank (PDB). Researchers can quickly see the locations and conformation of multiple motifs among a number of related structures simultaneously. Considering the fact that PDB sequences are usually shorter than those in sequence databases and/or may have missing residues, seeMotif has two complementary approaches for selecting structures and mapping motifs to protein chains in structures. As more and more structures belonging to previously uncharacterized protein families become available, combining sequence and structure information gives good opportunities to facilitate understanding of protein functions in large-scale genome projects. Available at: http://seemotif.csie.ntu.edu.tw,http://seemotif.ee.ncku.edu.tw or http://seemotif.csbb.ntu.edu.tw.

  6. Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas.

    Science.gov (United States)

    Petrov, Anton I; Zirbel, Craig L; Leontis, Neocles B

    2013-10-01

    The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-Watson-Crick base pairs. Structurally similar loops define RNA 3D motifs that are conserved in homologous RNA molecules, but can also occur at nonhomologous sites in diverse RNAs, and which often vary in sequence. To further our understanding of RNA motif structure and sequence variability and to provide a useful resource for structure modeling and prediction, we present a new method for automated classification of internal and hairpin loop RNA 3D motifs and a new online database called the RNA 3D Motif Atlas. To classify the motif instances, a representative set of internal and hairpin loops is automatically extracted from a nonredundant list of RNA-containing PDB files. Their structures are compared geometrically, all-against-all, using the FR3D program suite. The loops are clustered into motif groups, taking into account geometric similarity and structural annotations and making allowance for a variable number of bulged bases. The automated procedure that we have implemented identifies all hairpin and internal loop motifs previously described in the literature. All motif instances and motif groups are assigned unique and stable identifiers and are made available in the RNA 3D Motif Atlas (http://rna.bgsu.edu/motifs), which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access.

  7. Embedded Fragments Registry (EFR)

    Data.gov (United States)

    Department of Veterans Affairs — In 2009, the Department of Defense estimated that approximately 40,000 service members who served in OEF/OIF may have embedded fragment wounds as the result of small...

  8. Electronics for embedded systems

    CERN Document Server

    Bindal, Ahmet

    2017-01-01

    This book provides semester-length coverage of electronics for embedded systems, covering most common analog and digital circuit-related issues encountered while designing embedded system hardware. It is written for students and young professionals who have basic circuit theory background and want to learn more about passive circuits, diode and bipolar transistor circuits, the state-of-the-art CMOS logic family and its interface with older logic families such as TTL, sensors and sensor physics, operational amplifier circuits to condition sensor signals, data converters and various circuits used in electro-mechanical device control in embedded systems. The book also provides numerous hardware design examples by integrating the topics learned in earlier chapters. The last chapter extensively reviews the combinational and sequential logic design principles to be able to design the digital part of embedded system hardware.

  9. Smart Multicore Embedded Systems

    DEFF Research Database (Denmark)

    This book provides a single-source reference to the state-of-the-art of high-level programming models and compilation tool-chains for embedded system platforms. The authors address challenges faced by programmers developing software to implement parallel applications in embedded systems, where very...... specificities of various embedded systems from different industries. Parallel programming tool-chains are described that take as input parameters both the application and the platform model, then determine relevant transformations and mapping decisions on the concrete platform, minimizing user intervention...... and hiding the difficulties related to the correct and efficient use of memory hierarchy and low level code generation. Describes tools and programming models for multicore embedded systems Emphasizes throughout performance per watt scalability Discusses realistic limits of software parallelization Enables...

  10. Embedded Data Representations.

    Science.gov (United States)

    Willett, Wesley; Jansen, Yvonne; Dragicevic, Pierre

    2017-01-01

    We introduce embedded data representations, the use of visual and physical representations of data that are deeply integrated with the physical spaces, objects, and entities to which the data refers. Technologies like lightweight wireless displays, mixed reality hardware, and autonomous vehicles are making it increasingly easier to display data in-context. While researchers and artists have already begun to create embedded data representations, the benefits, trade-offs, and even the language necessary to describe and compare these approaches remain unexplored. In this paper, we formalize the notion of physical data referents - the real-world entities and spaces to which data corresponds - and examine the relationship between referents and the visual and physical representations of their data. We differentiate situated representations, which display data in proximity to data referents, and embedded representations, which display data so that it spatially coincides with data referents. Drawing on examples from visualization, ubiquitous computing, and art, we explore the role of spatial indirection, scale, and interaction for embedded representations. We also examine the tradeoffs between non-situated, situated, and embedded data displays, including both visualizations and physicalizations. Based on our observations, we identify a variety of design challenges for embedded data representation, and suggest opportunities for future research and applications.

  11. Chaotic motifs in gene regulatory networks.

    Science.gov (United States)

    Zhang, Zhaoyang; Ye, Weiming; Qian, Yu; Zheng, Zhigang; Huang, Xuhui; Hu, Gang

    2012-01-01

    Chaos should occur often in gene regulatory networks (GRNs) which have been widely described by nonlinear coupled ordinary differential equations, if their dimensions are no less than 3. It is therefore puzzling that chaos has never been reported in GRNs in nature and is also extremely rare in models of GRNs. On the other hand, the topic of motifs has attracted great attention in studying biological networks, and network motifs are suggested to be elementary building blocks that carry out some key functions in the network. In this paper, chaotic motifs (subnetworks with chaos) in GRNs are systematically investigated. The conclusion is that: (i) chaos can only appear through competitions between different oscillatory modes with rivaling intensities. Conditions required for chaotic GRNs are found to be very strict, which make chaotic GRNs extremely rare. (ii) Chaotic motifs are explored as the simplest few-node structures capable of producing chaos, and serve as the intrinsic source of chaos of random few-node GRNs. Several optimal motifs causing chaos with atypically high probability are figured out. (iii) Moreover, we discovered that a number of special oscillators can never produce chaos. These structures bring some advantages on rhythmic functions and may help us understand the robustness of diverse biological rhythms. (iv) The methods of dominant phase-advanced driving (DPAD) and DPAD time fraction are proposed to quantitatively identify chaotic motifs and to explain the origin of chaotic behaviors in GRNs.

  12. Split Left GC-Lpp Semigroups

    Institute of Scientific and Technical Information of China (English)

    Zhen Zhen LI; Xiao Jiang GUO; Zhi Qing FU

    2012-01-01

    A left GC-lpp semigroup S is called split if the natural homomorphism γb of S onto S/γ induced by γ is split.It is proved that a left GC-lpp semigroup is split if and only if it has a left adequate transversal.In particular,a construction theorem for split left GC-lpp semigroups is established.

  13. Purification of equine Gc-globulin

    DEFF Research Database (Denmark)

    Houen, Gunnar; Pihl, Tina Holberg; Andersen, Pia Haubro;

    Objectives With the aim of producing antibodies for an equine Group specific component (Gc)-globulin assay, the protein was purified from normal equine plasma. Methods Equine Gc-globulin was purified from healthy horse plasma using ion exchange chromatography (Q-Sepharose, CM-Sepharose) and prepa......Objectives With the aim of producing antibodies for an equine Group specific component (Gc)-globulin assay, the protein was purified from normal equine plasma. Methods Equine Gc-globulin was purified from healthy horse plasma using ion exchange chromatography (Q-Sepharose, CM......-Sepharose) and preparative PAGE. Results Equine Gc-globulin has successfully been purified from healthy horse plasma and rabbits and mice are being immunized to produce specific antibodies. Conclusions Purification of equine Gc-globulin and the production of specific antibodies will make it possible to develop an assay...... for measuring Gc-globulin in horses. Studies in rodents and humans have shown that Gc-globulin is a multifunctional acute phase plasma protein, which removes actin from the blood by binding it and facilitating its clearance from the circulation by the liver. As such, Gc-globulin prevents hyper coagulation...

  14. Embedded Systems Design: Optimization Challenges

    DEFF Research Database (Denmark)

    Pop, Paul

    2005-01-01

    Summary form only given. Embedded systems are everywhere: from alarm clocks to PDAs, from mobile phones to cars, almost all the devices we use are controlled by embedded systems. Over 99% of the microprocessors produced today are used in embedded systems, and recently the number of embedded systems...

  15. EMBEDDING FLOWS AND SMOOTH CONJUGACY

    Institute of Scientific and Technical Information of China (English)

    ZHANGMEIRONG; LIWEIGU

    1997-01-01

    The authors use the functional equation for embedding vector fields to study smooth embedding flows of one-dimensional diffeomorphisms. The existence and uniqueness for smooth embedding flows and vector fields are proved. As an application of embedding flows, some classification results about local and giobal diffeomorphisms under smooth conjugacy are given.

  16. WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches.

    Science.gov (United States)

    Romer, Katherine A; Kayombya, Guy-Richard; Fraenkel, Ernest

    2007-07-01

    WebMOTIFS provides a web interface that facilitates the discovery and analysis of DNA-sequence motifs. Several studies have shown that the accuracy of motif discovery can be significantly improved by using multiple de novo motif discovery programs and using randomized control calculations to identify the most significant motifs or by using Bayesian approaches. WebMOTIFS makes it easy to apply these strategies. Using a single submission form, users can run several motif discovery programs and score, cluster and visualize the results. In addition, the Bayesian motif discovery program THEME can be used to determine the class of transcription factors that is most likely to regulate a set of sequences. Input can be provided as a list of gene or probe identifiers. Used with the default settings, WebMOTIFS accurately identifies biologically relevant motifs from diverse data in several species. WebMOTIFS is freely available at http://fraenkel.mit.edu/webmotifs.

  17. Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets.

    Science.gov (United States)

    Chiu, Yi-Yuan; Lin, Chun-Yu; Lin, Chih-Ta; Hsu, Kai-Cheng; Chang, Li-Zen; Yang, Jinn-Moon

    2012-01-01

    To discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). In general, the polypharmacological proteins often share similar local binding environments and motifs. As the exponential growth of the number of protein structures, to find the similar structural binding motifs (pharma-motifs) is an emergency task for drug discovery (e.g. side effects and new uses for old drugs) and protein functions. We have developed a Space-Related Pharmamotifs (called SRPmotif) method to recognize the binding motifs by searching against protein structure database. SRPmotif is able to recognize conserved binding environments containing spatially discontinuous pharma-motifs which are often short conserved peptides with specific physico-chemical properties for protein functions. Among 356 pharma-motifs, 56.5% interacting residues are highly conserved. Experimental results indicate that 81.1% and 92.7% polypharmacological targets of each protein-ligand complex are annotated with same biological process (BP) and molecular function (MF) terms, respectively, based on Gene Ontology (GO). Our experimental results show that the identified pharma-motifs often consist of key residues in functional (active) sites and play the key roles for protein functions. The SRPmotif is available at http://gemdock.life.nctu.edu.tw/SRP/. SRPmotif is able to identify similar pharma-interfaces and pharma-motifs sharing similar binding environments for polypharmacological targets by rapidly searching against the protein structure database. Pharma-motifs describe the conservations of binding environments for drug discovery and protein functions. Additionally, these pharma-motifs provide the clues for discovering new sequence-based motifs to predict protein functions from protein sequence databases. We believe that SRPmotif is useful for elucidating protein functions and drug discovery.

  18. Specific regulatory motifs predict glucocorticoid responsiveness of hippocampal gene expression.

    Science.gov (United States)

    Datson, N A; Polman, J A E; de Jonge, R T; van Boheemen, P T M; van Maanen, E M T; Welten, J; McEwen, B S; Meiland, H C; Meijer, O C

    2011-10-01

    The glucocorticoid receptor (GR) is an ubiquitously expressed ligand-activated transcription factor that mediates effects of cortisol in relation to adaptation to stress. In the brain, GR affects the hippocampus to modulate memory processes through direct binding to glucocorticoid response elements (GREs) in the DNA. However, its effects are to a high degree cell specific, and its target genes in different cell types as well as the mechanisms conferring this specificity are largely unknown. To gain insight in hippocampal GR signaling, we characterized to which GRE GR binds in the rat hippocampus. Using a position-specific scoring matrix, we identified evolutionary-conserved putative GREs from a microarray based set of hippocampal target genes. Using chromatin immunoprecipitation, we were able to confirm GR binding to 15 out of a selection of 32 predicted sites (47%). The majority of these 15 GREs are previously undescribed and thus represent novel GREs that bind GR and therefore may be functional in the rat hippocampus. GRE nucleotide composition was not predictive for binding of GR to a GRE. A search for conserved flanking sequences that may predict GR-GRE interaction resulted in the identification of GC-box associated motifs, such as Myc-associated zinc finger protein 1, within 2 kb of GREs with GR binding in the hippocampus. This enrichment was not present around nonbinding GRE sequences nor around proven GR-binding sites from a mesenchymal stem-like cell dataset that we analyzed. GC-binding transcription factors therefore may be unique partners for DNA-bound GR and may in part explain cell-specific transcriptional regulation by glucocorticoids in the context of the hippocampus.

  19. Smart multicore embedded systems

    CERN Document Server

    Bertels, Koen; Karlsson, Sven; Pacull, François

    2014-01-01

    This book provides a single-source reference to the state-of-the-art of high-level programming models and compilation tool-chains for embedded system platforms. The authors address challenges faced by programmers developing software to implement parallel applications in embedded systems, where very often they are forced to rewrite sequential programs into parallel software, taking into account all the low level features and peculiarities of the underlying platforms. Readers will benefit from these authors’ approach, which takes into account both the application requirements and the platform specificities of various embedded systems from different industries. Parallel programming tool-chains are described that take as input parameters both the application and the platform model, then determine relevant transformations and mapping decisions on the concrete platform, minimizing user intervention and hiding the difficulties related to the correct and efficient use of memory hierarchy and low level code generati...

  20. Embedded data representations

    DEFF Research Database (Denmark)

    Willett, Wesley; Jansen, Yvonne; Dragicevic, Pierre

    2017-01-01

    We introduce embedded data representations, the use of visual and physical representations of data that are deeply integrated with the physical spaces, objects, and entities to which the data refers. Technologies like lightweight wireless displays, mixed reality hardware, and autonomous vehicles...... are making it increasingly easier to display data in-context. While researchers and artists have already begun to create embedded data representations, the benefits, trade-offs, and even the language necessary to describe and compare these approaches remain unexplored. In this paper, we formalize the notion...... of physical data referents – the real-world entities and spaces to which data corresponds – and examine the relationship between referents and the visual and physical representations of their data. We differentiate situated representations, which display data in proximity to data referents, and embedded...

  1. Structural motifs are closed into cycles in proteins.

    Science.gov (United States)

    Efimov, Alexander V

    2010-08-27

    Beta-hairpins, triple-strand beta-sheets and betaalphabeta-units represent simple structural motifs closed into cycles by systems of hydrogen bonds. Secondary closing of these simple motifs into large cycles by means of different superhelices, split beta-hairpins or SS-bridges results in the formation of more complex structural motifs having unique overall folds and unique handedness such as abcd-units, phi-motifs, five- and seven-segment alpha/beta-motifs. Apparently, the complex structural motifs are more cooperative and stable and this may be one of the main reasons of high frequencies of occurrence of the motifs in proteins.

  2. Functional characterization of variations on regulatory motifs.

    Directory of Open Access Journals (Sweden)

    Michal Lapidot

    2008-03-01

    Full Text Available Transcription factors (TFs regulate gene expression through specific interactions with short promoter elements. The same regulatory protein may recognize a variety of related sequences. Moreover, once they are detected it is hard to predict whether highly similar sequence motifs will be recognized by the same TF and regulate similar gene expression patterns, or serve as binding sites for distinct regulatory factors. We developed computational measures to assess the functional implications of variations on regulatory motifs and to compare the functions of related sites. We have developed computational means for estimating the functional outcome of substituting a single position within a binding site and applied them to a collection of putative regulatory motifs. We predict the effects of nucleotide variations within motifs on gene expression patterns. In cases where such predictions could be compared to suitable published experimental evidence, we found very good agreement. We further accumulated statistics from multiple substitutions across various binding sites in an attempt to deduce general properties that characterize nucleotide substitutions that are more likely to alter expression. We found that substitutions involving Adenine are more likely to retain the expression pattern and that substitutions involving Guanine are more likely to alter expression compared to the rest of the substitutions. Our results should facilitate the prediction of the expression outcomes of binding site variations. One typical important implication is expected to be the ability to predict the phenotypic effect of variation in regulatory motifs in promoters.

  3. Sublinear Time Motif Discovery from Multiple Sequences

    Directory of Open Access Journals (Sweden)

    Yunhui Fu

    2013-10-01

    Full Text Available In this paper, a natural probabilistic model for motif discovery has been used to experimentally test the quality of motif discovery programs. In this model, there are k background sequences, and each character in a background sequence is a random character from an alphabet, Σ. A motif G = g1g2 ... gm is a string of m characters. In each background sequence is implanted a probabilistically-generated approximate copy of G. For a probabilistically-generated approximate copy b1b2 ... bm of G, every character, bi, is probabilistically generated, such that the probability for bi ≠ gi is at most α. We develop two new randomized algorithms and one new deterministic algorithm. They make advancements in the following aspects: (1 The algorithms are much faster than those before. Our algorithms can even run in sublinear time. (2 They can handle any motif pattern. (3 The restriction for the alphabet size is a lower bound of four. This gives them potential applications in practical problems, since gene sequences have an alphabet size of four. (4 All algorithms have rigorous proofs about their performances. The methods developed in this paper have been used in the software implementation. We observed some encouraging results that show improved performance for motif detection compared with other software.

  4. Polarizable Density Embedding

    DEFF Research Database (Denmark)

    Olsen, Jógvan Magnus Haugaard; Steinmann, Casper; Ruud, Kenneth

    2015-01-01

    We present a new QM/QM/MM-based model for calculating molecular properties and excited states of solute-solvent systems. We denote this new approach the polarizable density embedding (PDE) model and it represents an extension of our previously developed polarizable embedding (PE) strategy. The PDE...... model is a focused computational approach in which a core region of the system studied is represented by a quantum-chemical method, whereas the environment is divided into two other regions: an inner and an outer region. Molecules belonging to the inner region are described by their exact densities...

  5. Protein chemical characterization of Gc globulin (vitamin D-binding protein) isoforms; Gc-1f, Gc-1s and Gc-2

    DEFF Research Database (Denmark)

    Christiansen, Maja; Jørgensen, Charlotte S; Laursen, Inga;

    2007-01-01

    exchange chromatography. The separated isoforms and several commercial preparations of individual isoforms were characterized by mass spectrometry. This revealed that the major isoforms were non-glycosylated. Compared to the Gc-1f isoform the other dominating isoforms represented an Asp/Glu substitution......Gc globulin, also called vitamin D-binding protein, is a plasma protein involved in the extracellular actin-scavenger system, vitamin D transport and possibly also other biological activities. Low levels of Gc globulin have been found to correlate with multiple organ failure and non......-survival of patients with fulminant hepatic failure and trauma. Here, we characterize the dominant isoforms of plasma-derived Gc globulin from Cohn fraction IV paste with respect to amino acid sequence and posttranslational modifications. Gc globulin was purified in large scale and the isoforms separated by ion...

  6. Purification of equine Gc-globulin

    DEFF Research Database (Denmark)

    Houen, Gunnar; Pihl, Tina Holberg; Andersen, Pia Haubro;

    Objectives With the aim of producing antibodies for an equine Group specific component (Gc)-globulin assay, the protein was purified from normal equine plasma. Methods Equine Gc-globulin was purified from healthy horse plasma using ion exchange chromatography (Q-Sepharose, CM...... for measuring Gc-globulin in horses. Studies in rodents and humans have shown that Gc-globulin is a multifunctional acute phase plasma protein, which removes actin from the blood by binding it and facilitating its clearance from the circulation by the liver. As such, Gc-globulin prevents hyper coagulation......-globulin infusions. Reference List    1.   Vasconcellos CA and Lind SE. Coordinated inhibition of actin-induced platelet aggregation by plasma gelsolin and vitamin D-binding protein. Blood 1993;82:3648-3657....

  7. Unsupervised statistical discovery of spaced motifs in prokaryotic genomes.

    Science.gov (United States)

    Tong, Hao; Schliekelman, Paul; Mrázek, Jan

    2017-01-05

    DNA sequences contain repetitive motifs which have various functions in the physiology of the organism. A number of methods have been developed for discovery of such sequence motifs with a primary focus on detection of regulatory motifs and particularly transcription factor binding sites. Most motif-finding methods apply probabilistic models to detect motifs characterized by unusually high number of copies of the motif in the analyzed sequences. We present a novel method for detection of pairs of motifs separated by spacers of variable nucleotide sequence but conserved length. Unlike existing methods for motif discovery, the motifs themselves are not required to occur at unusually high frequency but only to exhibit a significant preference to occur at a specific distance from each other. In the present implementation of the method, motifs are represented by pentamers and all pairs of pentamers are evaluated for statistically significant preference for a specific distance. An important step of the algorithm eliminates motif pairs where the spacers separating the two motifs exhibit a high degree of sequence similarity; such motif pairs likely arise from duplications of the whole segment including the motifs and the spacer rather than due to selective constraints indicative of a functional importance of the motif pair. The method was used to scan 569 complete prokaryotic genomes for novel sequence motifs. Some motifs detected were previously known but other motifs found in the search appear to be novel. Selected motif pairs were subjected to further investigation and in some cases their possible biological functions were proposed. We present a new motif-finding technique that is applicable to scanning complete genomes for sequence motifs. The results from analysis of 569 genomes suggest that the method detects previously known motifs that are expected to be found as well as new motifs that are unlikely to be discovered by traditional motif-finding methods. We conclude

  8. Sequential motif profile of natural visibility graphs

    CERN Document Server

    Iacovacci, Jacopo

    2016-01-01

    The concept of sequential visibility graph motifs -subgraphs appearing with characteristic frequencies in the visibility graphs associated to time series- has been advanced recently along with a theoretical framework to compute analytically the motif profiles associated to Horizontal Visibility Graphs (HVGs). Here we develop a theory to compute the profile of sequential visibility graph motifs in the context of Natural Visibility Graphs (VGs). This theory gives exact results for deterministic aperiodic processes with a smooth invariant density or stochastic processes that fulfil the Markov property and have a continuous marginal distribution. The framework also allows for a linear time numerical estimation in the case of empirical time series. A comparison between the HVG and the VG case (including evaluation of their robustness for short series polluted with measurement noise) is also presented.

  9. GC-rich sequence elements recruit PRC2 in mammalian ES cells.

    Directory of Open Access Journals (Sweden)

    Eric M Mendenhall

    2010-12-01

    Full Text Available Polycomb proteins are epigenetic regulators that localize to developmental loci in the early embryo where they mediate lineage-specific gene repression. In Drosophila, these repressors are recruited to sequence elements by DNA binding proteins associated with Polycomb repressive complex 2 (PRC2. However, the sequences that recruit PRC2 in mammalian cells have remained obscure. To address this, we integrated a series of engineered bacterial artificial chromosomes into embryonic stem (ES cells and examined their chromatin. We found that a 44 kb region corresponding to the Zfpm2 locus initiates de novo recruitment of PRC2. We then pinpointed a CpG island within this locus as both necessary and sufficient for PRC2 recruitment. Based on this causal demonstration and prior genomic analyses, we hypothesized that large GC-rich elements depleted of activating transcription factor motifs mediate PRC2 recruitment in mammals. We validated this model in two ways. First, we showed that a constitutively active CpG island is able to recruit PRC2 after excision of a cluster of activating motifs. Second, we showed that two 1 kb sequence intervals from the Escherichia coli genome with GC-contents comparable to a mammalian CpG island are both capable of recruiting PRC2 when integrated into the ES cell genome. Our findings demonstrate a causal role for GC-rich sequences in PRC2 recruitment and implicate a specific subset of CpG islands depleted of activating motifs as instrumental for the initial localization of this key regulator in mammalian genomes.

  10. Embedded foveation image coding.

    Science.gov (United States)

    Wang, Z; Bovik, A C

    2001-01-01

    The human visual system (HVS) is highly space-variant in sampling, coding, processing, and understanding. The spatial resolution of the HVS is highest around the point of fixation (foveation point) and decreases rapidly with increasing eccentricity. By taking advantage of this fact, it is possible to remove considerable high-frequency information redundancy from the peripheral regions and still reconstruct a perceptually good quality image. Great success has been obtained previously by a class of embedded wavelet image coding algorithms, such as the embedded zerotree wavelet (EZW) and the set partitioning in hierarchical trees (SPIHT) algorithms. Embedded wavelet coding not only provides very good compression performance, but also has the property that the bitstream can be truncated at any point and still be decoded to recreate a reasonably good quality image. In this paper, we propose an embedded foveation image coding (EFIC) algorithm, which orders the encoded bitstream to optimize foveated visual quality at arbitrary bit-rates. A foveation-based image quality metric, namely, foveated wavelet image quality index (FWQI), plays an important role in the EFIC system. We also developed a modified SPIHT algorithm to improve the coding efficiency. Experiments show that EFIC integrates foveation filtering with foveated image coding and demonstrates very good coding performance and scalability in terms of foveated image quality measurement.

  11. Embedded computer vision

    CERN Document Server

    Kisacanin, Branislav

    2008-01-01

    Brings together experiences from researchers in the field of embedded computer vision, from both academic and industrial research centers, and covers a broad range of challenges and trade-offs brought about by this paradigm shift. This title offers emphasis on tackling important problems for society, safety, security, health, and mobility.

  12. Embedded-monolith armor

    Science.gov (United States)

    McElfresh, Michael W.; Groves, Scott E; Moffet, Mitchell L.; Martin, Louis P.

    2016-07-19

    A lightweight armor system utilizing a face section having a multiplicity of monoliths embedded in a matrix supported on low density foam. The face section is supported with a strong stiff backing plate. The backing plate is mounted on a spall plate.

  13. MEME SUITE: tools for motif discovery and searching.

    Science.gov (United States)

    Bailey, Timothy L; Boden, Mikael; Buske, Fabian A; Frith, Martin; Grant, Charles E; Clementi, Luca; Ren, Jingyuan; Li, Wilfred W; Noble, William S

    2009-07-01

    The MEME Suite web server provides a unified portal for online discovery and analysis of sequence motifs representing features such as DNA binding sites and protein interaction domains. The popular MEME motif discovery algorithm is now complemented by the GLAM2 algorithm which allows discovery of motifs containing gaps. Three sequence scanning algorithms--MAST, FIMO and GLAM2SCAN--allow scanning numerous DNA and protein sequence databases for motifs discovered by MEME and GLAM2. Transcription factor motifs (including those discovered using MEME) can be compared with motifs in many popular motif databases using the motif database scanning algorithm TOMTOM. Transcription factor motifs can be further analyzed for putative function by association with Gene Ontology (GO) terms using the motif-GO term association tool GOMO. MEME output now contains sequence LOGOS for each discovered motif, as well as buttons to allow motifs to be conveniently submitted to the sequence and motif database scanning algorithms (MAST, FIMO and TOMTOM), or to GOMO, for further analysis. GLAM2 output similarly contains buttons for further analysis using GLAM2SCAN and for rerunning GLAM2 with different parameters. All of the motif-based tools are now implemented as web services via Opal. Source code, binaries and a web server are freely available for noncommercial use at http://meme.nbcr.net.

  14. Highly scalable Ab initio genomic motif identification

    KAUST Repository

    Marchand, Benoit

    2011-01-01

    We present results of scaling an ab initio motif family identification system, Dragon Motif Finder (DMF), to 65,536 processor cores of IBM Blue Gene/P. DMF seeks groups of mutually similar polynucleotide patterns within a set of genomic sequences and builds various motif families from them. Such information is of relevance to many problems in life sciences. Prior attempts to scale such ab initio motif-finding algorithms achieved limited success. We solve the scalability issues using a combination of mixed-mode MPI-OpenMP parallel programming, master-slave work assignment, multi-level workload distribution, multi-level MPI collectives, and serial optimizations. While the scalability of our algorithm was excellent (94% parallel efficiency on 65,536 cores relative to 256 cores on a modest-size problem), the final speedup with respect to the original serial code exceeded 250,000 when serial optimizations are included. This enabled us to carry out many large-scale ab initio motiffinding simulations in a few hours while the original serial code would have needed decades of execution time. Copyright 2011 ACM.

  15. Bioactive motifs of agouti signal protein.

    Science.gov (United States)

    Virador, V M; Santis, C; Furumura, M; Kalbacher, H; Hearing, V J

    2000-08-25

    The switch between the synthesis of eu- and pheomelanins is modulated by the interaction of two paracrine signaling molecules, alpha-melanocyte stimulating hormone (MSH) and agouti signal protein (ASP), which interact with melanocytes via the MSH receptor (MC1R). Comparison of the primary sequence of ASP with the known MSH pharmacophore provides no suggestion about the putative bioactive domain(s) of ASP. To identify such bioactive motif(s), we synthesized 15-mer peptides that spanned the primary sequence of ASP and determined their effects on the melanogenic activities of murine melanocytes. Northern and Western blotting were used, together with chemical analysis of melanins and enzymatic assays, to identify three distinct bioactive regions of ASP that down-regulate eumelanogenesis. The decrease in eumelanin production was mediated by down-regulation of mRNA levels for tyrosinase and other melanogenic enzymes, as occurs in vivo, and these effects were comparable to those elicited by intact recombinant ASP. Shorter peptides in those motifs were synthesized and their effects on melanogenesis were further investigated. The amino acid arginine, which is present in the MSH peptide pharmacophore (HFRW), is also in the most active domain of ASP (KVARP). Our data suggest that lysines and an arginine (in motifs such as KxxxxKxxR or KxxRxxxxK) are important for the bioactivity of ASP. Identification of the specific ASP epitope that interacts with the MC1R has potential pharmacological applications in treating dysfunctions of skin pigmentation.

  16. Identifying motifs in folktales using topic models

    NARCIS (Netherlands)

    Karsdorp, F.; Bosch, A.P.J. van den

    2013-01-01

    With the undertake of various folktale digitalization initiatives, the need for computational aids to explore these collections is increasing. In this paper we compare Labeled LDA (L-LDA) to a simple retrieval model on the task of identifying motifs in folktales. We show that both methods are well a

  17. Immunotherapy for Prostate Cancer with Gc Protein-Derived Macrophage-Activating Factor, GcMAF.

    Science.gov (United States)

    Yamamoto, Nobuto; Suyama, Hirofumi; Yamamoto, Nobuyuki

    2008-07-01

    Serum Gc protein (known as vitamin D(3)-binding protein) is the precursor for the principal macrophage-activating factor (MAF). The MAF precursor activity of serum Gc protein of prostate cancer patients was lost or reduced because Gc protein was deglycosylated by serum alpha-N-acetylgalactosaminidase (Nagalase) secreted from cancerous cells. Therefore, macrophages of prostate cancer patients having deglycosylated Gc protein cannot be activated, leading to immunosuppression. Stepwise treatment of purified Gc protein with immobilized beta-galactosidase and sialidase generated the most potent MAF (termed GcMAF) ever discovered, which produces no adverse effect in humans. Macrophages activated by GcMAF develop a considerable variation of receptors that recognize the abnormality in malignant cell surface and are highly tumoricidal. Sixteen nonanemic prostate cancer patients received weekly administration of 100 ng of GcMAF. As the MAF precursor activity increased, their serum Nagalase activity decreased. Because serum Nagalase activity is proportional to tumor burden, the entire time course analysis for GcMAF therapy was monitored by measuring the serum Nagalase activity. After 14 to 25 weekly administrations of GcMAF (100 ng/week), all 16 patients had very low serum Nagalase levels equivalent to those of healthy control values, indicating that these patients are tumor-free. No recurrence occurred for 7 years.

  18. DNA motif elucidation using belief propagation.

    Science.gov (United States)

    Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei

    2013-09-01

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k=8∼10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors' websites: e.g. http://www.cs.toronto.edu/∼wkc/kmerHMM.

  19. Parallel motif extraction from very long sequences

    KAUST Repository

    Sahli, Majed

    2013-01-01

    Motifs are frequent patterns used to identify biological functionality in genomic sequences, periodicity in time series, or user trends in web logs. In contrast to a lot of existing work that focuses on collections of many short sequences, modern applications require mining of motifs in one very long sequence (i.e., in the order of several gigabytes). For this case, there exist statistical approaches that are fast but inaccurate; or combinatorial methods that are sound and complete. Unfortunately, existing combinatorial methods are serial and very slow. Consequently, they are limited to very short sequences (i.e., a few megabytes), small alphabets (typically 4 symbols for DNA sequences), and restricted types of motifs. This paper presents ACME, a combinatorial method for extracting motifs from a single very long sequence. ACME arranges the search space in contiguous blocks that take advantage of the cache hierarchy in modern architectures, and achieves almost an order of magnitude performance gain in serial execution. It also decomposes the search space in a smart way that allows scalability to thousands of processors with more than 90% speedup. ACME is the only method that: (i) scales to gigabyte-long sequences; (ii) handles large alphabets; (iii) supports interesting types of motifs with minimal additional cost; and (iv) is optimized for a variety of architectures such as multi-core systems, clusters in the cloud, and supercomputers. ACME reduces the extraction time for an exact-length query from 4 hours to 7 minutes on a typical workstation; handles 3 orders of magnitude longer sequences; and scales up to 16, 384 cores on a supercomputer. Copyright is held by the owner/author(s).

  20. DNA motif elucidation using belief propagation

    KAUST Repository

    Wong, Ka-Chun

    2013-06-29

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k = 8 ?10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors\\' websites: e.g. http://www.cs.toronto.edu/?wkc/kmerHMM. 2013 The Author(s).

  1. Emerging Trends in Embedded Processors

    Directory of Open Access Journals (Sweden)

    Gurvinder Singh

    2014-05-01

    Full Text Available An Embedded Processors is simply a µProcessors that has been “Embedded” into a device. Embedded systems are important part of human life. For illustration, one cannot visualize life without mobile phones for personal communication. Embedded systems are used in many places like healthcare, automotive, daily life, and in different offices and industries.Embedded Processors develop new research area in the field of hardware designing.

  2. Embedment of Employee?

    DEFF Research Database (Denmark)

    Buhl, Henrik

    1998-01-01

    The purpose of the paper is to discuss the influence of different approaches and work life conditions on the conception of embedment of employee participation. The discussion is based on three connected approaches: a theoretical research, a research into participation in working life and an empir......The purpose of the paper is to discuss the influence of different approaches and work life conditions on the conception of embedment of employee participation. The discussion is based on three connected approaches: a theoretical research, a research into participation in working life...... and an empirical case study. My starting point will be a case study of a Danish ABB company which will form the framework of my discussion and reflect my present experience. This analysis will emphasize the possibilities of making employee participation a permanent part of the company at all levels....

  3. Embeddings of Iteration Trees

    OpenAIRE

    Mitchell, William

    1992-01-01

    This paper, dating from May 1991, contains preliminary (and unpublishable) notes on investigations about iteration trees. They will be of interest only to the specialist. In the first two sections I define notions of support and embeddings for tree iterations, proving for example that every tree iteration is a direct limit of finite tree iterations. This is a generalization to models with extenders of basic ideas of iterated ultrapowers using only ultrapowers. In the final section (which is m...

  4. The GC-heterogeneity of teleost fishes

    Directory of Open Access Journals (Sweden)

    Gautier Christian

    2008-12-01

    Full Text Available Abstract Background One of the most striking features of mammalian and birds chromosomes is the variation in the guanine-cytosine (GC content that occurs over scales of hundreds of kilobases to megabases; this is known as the "isochore" structure. Among other vertebrates the presence of isochores depends upon the taxon; isochore are clearly present in Crocodiles and turtles but fish genome seems very homogeneous on GC content. This has suggested a unique isochore origin after the divergence between Sarcopterygii and Actinopterygii, but before that between Sauropsida and mammals. However during more than 30 years of analysis, isochore characteristics have been studied and many important biological properties have been associated with the isochore structure of human genomes. For instance, the genes are more compact and their density is highest in GC rich isochores. Results This paper shows in teleost fish genomes the existence of "GC segmentation" sharing some of the characteristics of isochores although teleost fish genomes presenting a particular homogeneity in CG content. The entire genomes of T nigroviridis and D rerio are now available, and this has made it possible to check whether a mosaic structure associated with isochore properties can be found in these fishes. In this study, hidden Markov models were trained on fish genes (T nigroviridis and D rerio which were classified by using the isochore class of their human orthologous. A clear segmentation of these genomes was detected. Conclusion The GC content is an excellent indicator of isochores in heterogeneous genomes as mammals. The segmentation we obtained were well correlated with GC content and other properties associated to GC content such as gene density, the number of exons per gene and the length of introns. Therefore, the GC content is the main property that allows the detection of isochore but more biological properties have to be taken into account. This method allows detecting

  5. Security Embedding Codes

    CERN Document Server

    Ly, Hung D; Blankenship, Yufei

    2011-01-01

    This paper considers the problem of simultaneously communicating two messages, a high-security message and a low-security message, to a legitimate receiver, referred to as the security embedding problem. An information-theoretic formulation of the problem is presented. A coding scheme that combines rate splitting, superposition coding, nested binning and channel prefixing is considered and is shown to achieve the secrecy capacity region of the channel in several scenarios. Specifying these results to both scalar and independent parallel Gaussian channels (under an average individual per-subchannel power constraint), it is shown that the high-security message can be embedded into the low-security message at full rate (as if the low-security message does not exist) without incurring any loss on the overall rate of communication (as if both messages are low-security messages). Extensions to the wiretap channel II setting of Ozarow and Wyner are also considered, where it is shown that "perfect" security embedding...

  6. Modulation techniques and applications in comprehensive two-dimensional gas chromatography (GC x GC)

    Energy Technology Data Exchange (ETDEWEB)

    Pursch, Matthias [Dow Deutschland GmbH and Co. OHG, Analytical Sciences, 77836 Rheinmuenster (Germany); Sun, Kefu; Winniford, Bill; Weber, Andy [Dow Chemical Company, Analytical Sciences, Freeport, TX 77541 (United States); Cortes, Hernan; McCabe, Terry [Dow Chemical Company, Analytical Sciences, Midland MI 48667 (United States); Luong, Jim [Dow Canada, Analytical Sciences, Fort Saskatchewan (Canada)

    2002-07-01

    More than a decade after Phillips' first published work this article reviews recent developments in comprehensive two-dimensional gas chromatography (GC x GC). Special attention is devoted to the further development and diversity of modulation devices. These include heated sweepers, cryofocused modulators, and a variety of diaphragm valve-switching strategies. It is demonstrated that all modulation approaches can be very well suited to GC x GC, depending on the particular application. Diaphragm-valve modulation is very powerful for volatile organic compounds. Slotted heater and cryofocused modulation are preferred for samples that contain non-volatile components. Applications ranging from petroleum to environmental and biological samples are illustrated. Extension of the technique to GC x GC-mass spectrometry (MS) is also discussed and trends for future research activity are pointed out. (orig.)

  7. A discriminative approach for unsupervised clustering of DNA sequence motifs.

    Directory of Open Access Journals (Sweden)

    Philip Stegmaier

    Full Text Available Algorithmic comparison of DNA sequence motifs is a problem in bioinformatics that has received increased attention during the last years. Its main applications concern characterization of potentially novel motifs and clustering of a motif collection in order to remove redundancy. Despite growing interest in motif clustering, the question which motif clusters to aim at has so far not been systematically addressed. Here we analyzed motif similarities in a comprehensive set of vertebrate transcription factor classes. For this we developed enhanced similarity scores by inclusion of the information coverage (IC criterion, which evaluates the fraction of information an alignment covers in aligned motifs. A network-based method enabled us to identify motif clusters with high correspondence to DNA-binding domain phylogenies and prior experimental findings. Based on this analysis we derived a set of motif families representing distinct binding specificities. These motif families were used to train a classifier which was further integrated into a novel algorithm for unsupervised motif clustering. Application of the new algorithm demonstrated its superiority to previously published methods and its ability to reproduce entrained motif families. As a result, our work proposes a probabilistic approach to decide whether two motifs represent common or distinct binding specificities.

  8. A Caenorhabditis motif compendium for studying transcriptional gene regulation

    Science.gov (United States)

    Dieterich, Christoph; Sommer, Ralf J

    2008-01-01

    Background Controlling gene expression is fundamental to biological complexity. The nematode Caenorhabditis elegans is an important model for studying principles of gene regulation in multi-cellular organisms. A comprehensive parts list of putative regulatory motifs was yet missing for this model system. In this study, we compile a set of putative regulatory motifs by combining evidence from conservation and expression data. Description We present an unbiased comparative approach to a regulatory motif compendium for Caenorhabditis species. This involves the assembly of a new nematode genome, whole genome alignments and assessment of conserved k-mers counts. Candidate motifs are selected from a set of 9,500 randomly picked genes by three different motif discovery strategies. Motif candidates have to pass a conservation enrichment filter. Motif degeneracy and length are optimized. Retained motif descriptions are evaluated by expression data using a non-parametric test, which assesses expression changes due to the presence/absence of individual motifs. Finally, we also provide condition-specific motif ensembles by conditional tree analysis. Conclusion The nematode genomes align surprisingly well despite high neutral substitution rates. Our pipeline delivers motif sets by three alternative strategies. Each set contains less than 400 motifs, which are significantly conserved and correlated with 214 out of 270 tested gene expression conditions. This motif compendium is an entry point to comprehensive studies on nematode gene regulation. The website: http://corg.eb.tuebingen.mpg.de/CMC has extensive query capabilities, supplements this article and supports the experimental list. PMID:18215260

  9. DNA regulatory motif selection based on support vector machine ...

    African Journals Online (AJOL)

    DNA regulatory motif selection based on support vector machine (SVM) and its application in microarray ... African Journal of Biotechnology ... experiments to explore the underlying relationships between motif types and gene functions.

  10. Using SCOPE to identify potential regulatory motifs in coregulated genes.

    Science.gov (United States)

    Martyanov, Viktor; Gross, Robert H

    2011-05-31

    SCOPE is an ensemble motif finder that uses three component algorithms in parallel to identify potential regulatory motifs by over-representation and motif position preference. Each component algorithm is optimized to find a different kind of motif. By taking the best of these three approaches, SCOPE performs better than any single algorithm, even in the presence of noisy data. In this article, we utilize a web version of SCOPE to examine genes that are involved in telomere maintenance. SCOPE has been incorporated into at least two other motif finding programs and has been used in other studies. The three algorithms that comprise SCOPE are BEAM, which finds non-degenerate motifs (ACCGGT), PRISM, which finds degenerate motifs (ASCGWT), and SPACER, which finds longer bipartite motifs (ACCnnnnnnnnGGT). These three algorithms have been optimized to find their corresponding type of motif. Together, they allow SCOPE to perform extremely well. Once a gene set has been analyzed and candidate motifs identified, SCOPE can look for other genes that contain the motif which, when added to the original set, will improve the motif score. This can occur through over-representation or motif position preference. Working with partial gene sets that have biologically verified transcription factor binding sites, SCOPE was able to identify most of the rest of the genes also regulated by the given transcription factor. Output from SCOPE shows candidate motifs, their significance, and other information both as a table and as a graphical motif map. FAQs and video tutorials are available at the SCOPE web site which also includes a "Sample Search" button that allows the user to perform a trial run. Scope has a very friendly user interface that enables novice users to access the algorithm's full power without having to become an expert in the bioinformatics of motif finding. As input, SCOPE can take a list of genes, or FASTA sequences. These can be entered in browser text fields, or read from

  11. Embedded software verification and debugging

    CERN Document Server

    Winterholer, Markus

    2017-01-01

    This book provides comprehensive coverage of verification and debugging techniques for embedded software, which is frequently used in safety critical applications (e.g., automotive), where failures are unacceptable. Since the verification of complex systems needs to encompass the verification of both hardware and embedded software modules, this book focuses on verification and debugging approaches for embedded software with hardware dependencies. Coverage includes the entire flow of design, verification and debugging of embedded software and all key approaches to debugging, dynamic, static, and hybrid verification. This book discusses the current, industrial embedded software verification flow, as well as emerging trends with focus on formal and hybrid verification and debugging approaches. Includes in a single source the entire flow of design, verification and debugging of embedded software; Addresses the main techniques that are currently being used in the industry for assuring the quality of embedded softw...

  12. Bases of motifs for generating repeated patterns with wild cards

    OpenAIRE

    Pisanti, Nadia; Crochemore, Maxime; Grossi, Roberto; Sagot, Marie-France

    2005-01-01

    Motif inference represents one of the most important areas of research in computational biology, and one of its oldest ones. Despite this, the problem remains very much open in the sense that no existing definition is fully satisfying, either in formal terms, or in relation to the biological questions that involve finding such motifs. Two main types of motifs have been considered in the literature: matrices (of letter frequency per position in the motif) and patterns. There is no conclusive e...

  13. Anticipated synchronization in neuronal network motifs

    Science.gov (United States)

    Matias, F. S.; Gollo, L. L.; Carelli, P. V.; Copelli, M.; Mirasso, C. R.

    2013-01-01

    Two identical dynamical systems coupled unidirectionally (in a so called master-slave configuration) exhibit anticipated synchronization (AS) if the one which receives the coupling (the slave) also receives a negative delayed self-feedback. In oscillatory neuronal systems AS is characterized by a phase-locking with negative time delay τ between the spikes of the master and of the slave (slave fires before the master), while in the usual delayed synchronization (DS) regime τ is positive (slave fires after the master). A 3-neuron motif in which the slave self-feedback is replaced by a feedback loop mediated by an interneuron can exhibits both AS and DS regimes. Here we show that AS is robust in the presence of noise in a 3 Hodgkin-Huxley type neuronal motif. We also show that AS is stable for large values of τ in a chain of connected slaves-interneurons.

  14. Chiral Alkyl Halides: Underexplored Motifs in Medicine

    Directory of Open Access Journals (Sweden)

    Bálint Gál

    2016-11-01

    Full Text Available While alkyl halides are valuable intermediates in synthetic organic chemistry, their use as bioactive motifs in drug discovery and medicinal chemistry is rare in comparison. This is likely attributable to the common misconception that these compounds are merely non-specific alkylators in biological systems. A number of chlorinated compounds in the pharmaceutical and food industries, as well as a growing number of halogenated marine natural products showing unique bioactivity, illustrate the role that chiral alkyl halides can play in drug discovery. Through a series of case studies, we demonstrate in this review that these motifs can indeed be stable under physiological conditions, and that halogenation can enhance bioactivity through both steric and electronic effects. Our hope is that, by placing such compounds in the minds of the chemical community, they may gain more traction in drug discovery and inspire more synthetic chemists to develop methods for selective halogenation.

  15. Trading networks, abnormal motifs and stock manipulation

    OpenAIRE

    2012-01-01

    We study trade-based manipulation of stock prices from the perspective of complex trading networks constructed by using detailed information of trades. A stock trading network consists of nodes and directed links, where every trader is a node and a link is formed from one trader to the other if the former sells shares to the latter. Specifically, three abnormal network motifs are investigated, which are found to be formed by a few traders, implying potential intention of price manipulation. W...

  16. MENGUNGKAP SEJARAH DAN MOTIF BATIK SEMARANGAN

    Directory of Open Access Journals (Sweden)

    Dewi Yuliati

    2011-10-01

    Full Text Available Batik Semarang was born in line with the needs of the people of Hyderabad of the material with a new motif or style tailored to the taste, intention, and creativity of the craftsmen. Batik is a combination of several countries influence developing in Indonesian culture. Based on its shape, Batik designs can be divided into two major groups, namely geometric and non-Geometric. The development of Semarangan batik was due to the fact that certain motif of batik can only be worn by certain people, not for all group of people. Batik semarangan craftments are found in coastal regions. It displays the design composing of ornaments plucked from marine environment. Indonesian Batik develops not only to display a blending of court Batik designs with the coastal Batik technique, but also to incorporate other ornaments which come from many various ethnic groups in Indonesia.   Key words: batik, history, ornaments, marine environment, designs   Batik Semarang lahirkan sejalan dengan kebutuhan dari orang-orang dari Hyderabad akan bahan dengan motif atau gaya baru yang berdasarkan pada rasa, niat, dan kreatifitas dari pembuatnya. Batik merupakan perpaduan dari pengaruh beberapa negara yang berkembang dalam budaya Indonesia. Ditinjau dari desainnya, desain batik dapat dibagi menjadi dua kelompok utama, yakni geometrik dan nongeometrik. Pengembangan yang dilakukan terhadap batik semarangan disebabkan adanya beberapa motif batik yang hanya digunakan oleh kalangan tertentu, dan tidak boleh untuk kalangan umum. Pengrajin batik Semarangan berkembang di kawasan pesisir. Ia menampilkan desain yang terdiri atas berbagai ornamen yang menunjukkan ciri khas kemaritiman. Batik ini dikembangakan tidak hanya menampilkan desain batik khas pesisiran, tetapi juga memasukkan berbagai ornament dari beragam kelompok etnis di Indonesia.   Kata kunci: batik, sejarah, ragam hias, lingkungan pesisir, desain  

  17. Social Network Analysis Based on Network Motifs

    OpenAIRE

    2014-01-01

    Based on the community structure characteristics, theory, and methods of frequent subgraph mining, network motifs findings are firstly introduced into social network analysis; the tendentiousness evaluation function and the importance evaluation function are proposed for effectiveness assessment. Compared with the traditional way based on nodes centrality degree, the new approach can be used to analyze the properties of social network more fully and judge the roles of the nodes effectively. I...

  18. MINER: software for phylogenetic motif identification

    OpenAIRE

    La, David; Livesay, Dennis R.

    2005-01-01

    MINER is web-based software for phylogenetic motif (PM) identification. PMs are sequence regions (fragments) that conserve the overall familial phylogeny. PMs have been shown to correspond to a wide variety of catalytic regions, substrate-binding sites and protein interfaces, making them ideal functional site predictions. The MINER output provides an intuitive interface for interactive PM sequence analysis and structural visualization. The web implementation of MINER is freely available at . ...

  19. Specificity of the chromodomain Y chromosome family of chromodomains for lysine-methylated ARK(S/T) motifs.

    Science.gov (United States)

    Fischle, Wolfgang; Franz, Henriette; Jacobs, Steven A; Allis, C David; Khorasanizadeh, Sepideh

    2008-07-11

    Previous studies have shown two homologous chromodomain modules in the HP1 and Polycomb proteins exhibit discriminatory binding to related methyllysine residues (embedded in ARKS motifs) of the histone H3 tail. Methylated ARK(S/T) motifs have recently been identified in other chromatin factors (e.g. linker histone H1.4 and lysine methyltransferase G9a). These are thought to function as peripheral docking sites for the HP1 chromodomain. In vertebrates, HP1-like chromodomains are also present in the chromodomain Y chromosome (CDY) family of proteins adjacent to a putative catalytic motif. The human genome encodes three CDY family proteins, CDY, CDYL, and CDYL2. These have putative functions ranging from establishment of histone H4 acetylation during spermiogenesis to regulation of transcription co-repressor complexes. To delineate the biochemical functions of the CDY family chromodomains, we analyzed their specificity of methyllysine recognition. We detected substantial differences among these factors. The CDY chromodomain exhibits discriminatory binding to lysine-methylated ARK(S/T) motifs, whereas the CDYL2 chromodomain binds with comparable strength to multiple ARK(S/T) motifs. Interestingly, subtle amino acid changes in the CDYL chromodomain prohibit such binding interactions in vitro and in vivo. However, point mutations can rescue binding. In support of the in vitro binding properties of the chromodomains, the full-length CDY family proteins exhibit substantial variability in chromatin localization. Our studies underscore the significance of subtle sequence differences in a conserved signaling module for diverse epigenetic regulatory pathways.

  20. Unsteady Flame Embedding

    KAUST Repository

    El-Asrag, Hossam A.

    2011-01-01

    Direct simulation of all the length and time scales relevant to practical combustion processes is computationally prohibitive. When combustion processes are driven by reaction and transport phenomena occurring at the unresolved scales of a numerical simulation, one must introduce a dynamic subgrid model that accounts for the multiscale nature of the problem using information available on a resolvable grid. Here, we discuss a model that captures unsteady flow-flame interactions- including extinction, re-ignition, and history effects-via embedded simulations at the subgrid level. The model efficiently accounts for subgrid flame structure and incorporates detailed chemistry and transport, allowing more accurate prediction of the stretch effect and the heat release. In this chapter we first review the work done in the past thirty years to develop the flame embedding concept. Next we present a formulation for the same concept that is compatible with Large Eddy Simulation in the flamelet regimes. The unsteady flame embedding approach (UFE) treats the flame as an ensemble of locally one-dimensional flames, similar to the flamelet approach. However, a set of elemental one-dimensional flames is used to describe the turbulent flame structure directly at the subgrid level. The calculations employ a one-dimensional unsteady flame model that incorporates unsteady strain rate, curvature, and mixture boundary conditions imposed by the resolved scales. The model is used for closure of the subgrid terms in the context of large eddy simulation. Direct numerical simulation (DNS) data from a flame-vortex interaction problem is used for comparison. © Springer Science+Business Media B.V. 2011.

  1. Dynamic motifs in socio-economic networks

    Science.gov (United States)

    Zhang, Xin; Shao, Shuai; Stanley, H. Eugene; Havlin, Shlomo

    2014-12-01

    Socio-economic networks are of central importance in economic life. We develop a method of identifying and studying motifs in socio-economic networks by focusing on “dynamic motifs,” i.e., evolutionary connection patterns that, because of “node acquaintances” in the network, occur much more frequently than random patterns. We examine two evolving bi-partite networks: i) the world-wide commercial ship chartering market and ii) the ship build-to-order market. We find similar dynamic motifs in both bipartite networks, even though they describe different economic activities. We also find that “influence” and “persistence” are strong factors in the interaction behavior of organizations. When two companies are doing business with the same customer, it is highly probable that another customer who currently only has business relationship with one of these two companies, will become customer of the second in the future. This is the effect of influence. Persistence means that companies with close business ties to customers tend to maintain their relationships over a long period of time.

  2. Multilayer motif analysis of brain networks

    CERN Document Server

    Battiston, Federico; Chavez, Mario; Latora, Vito

    2016-01-01

    In the last decade network science has shed new light on the anatomical connectivity and on correlations in the activity of different areas of the human brain. The study of brain networks has made possible in fact to detect the central areas of a neural system, and to identify its building blocks by looking at overabundant small subgraphs, known as motifs. However, network analysis of the brain has so far mainly focused on structural and functional networks as separate entities. The recently developed mathematical framework of multi-layer networks allows to perform a multiplex analysis of the human brain where the structural and functional layers are considered at the same time. In this work we describe how to classify subgraphs in multiplex networks, and we extend motif analysis to networks with many layers. We then extract multi-layer motifs in brain networks of healthy subjects by considering networks with two layers, respectively obtained from diffusion and functional magnetic resonance imaging. Results i...

  3. Spatially Embedded Inequality

    DEFF Research Database (Denmark)

    Holck, Lotte

    2016-01-01

    /methodology/approach: – The (re)production of inequality is explored by linking research on organizational space with HRM diversity management. Data from an ethnographic study undertaken in a Danish municipal center illustrates how a substructure of inequality is spatially upheld alongside a formal diversity policy. Archer...... the more subtle, spatially embedded forms of inequality. Originality/value: – Theoretical and empirical connections between research on organizational space and HRM diversity management have thus far not been systematically studied. This combination might advance knowledge on the persistence of micro...

  4. Quantization of submanifold embeddings

    Energy Technology Data Exchange (ETDEWEB)

    Bahns, Dorothea; Zahn, Jochen [Courant Research Centre ' ' Higher Order Structures' ' , Universitaet Goettingen (Germany); Rejzner, Katarzyna [II. Institut fuer Theoretische Physik, Universitaet Hamburg (Germany)

    2013-07-01

    We describe a perturbative quantization of the embedding of d-dimensional submanifolds into n-dimensional Minkowski space, based on suitable generalizations of the Nambu-Goto action. We use tools from perturbative algebraic quantum field theory, quantum field theory on curved spacetimes, and the Batalin-Vilkovisky formalism. The resulting theory is perturbatively non-renormalizable, but well-defined as an effective theory, i.e., there are no anomalies, for any dimension d,n. In particular there is no critical dimension for the case of string theory (d=2).

  5. Shutters with embedded microprocessors

    Science.gov (United States)

    Stephenson, S.

    2015-06-01

    Shutters are used to periodically provide a non-uniformity correction (NUC) calibration surface to micro bolometers. Many bolometer applications, such as TWS and DVE, require compact, power efficient actuators. Actuators in these applications, such as bistable solenoids and stepper motors, benefit from complex drive schemes. Consumer electronics products have generated compact, low-cost drive components that can be used to embed complex drives into these shutters. Shutter drives using these components maintain compactness and power efficiency while simplifying interfaces at minimal cost. Recently, several commercially available shutter systems have been created that incorporate embedded microprocessors into shutters usable for NUC correction of micro bolometers.

  6. Embedded microcontroller interfacing

    CERN Document Server

    Gupta, Gourab Sen

    2010-01-01

    Mixed-Signal Embedded Microcontrollers are commonly used in integrating analog components needed to control non-digital electronic systems. They are used in automatically controlled devices and products, such as automobile engine control systems, wireless remote controllers, office machines, home appliances, power tools, and toys. Microcontrollers make it economical to digitally control even more devices and processes by reducing the size and cost, compared to a design that uses a separate microprocessor, memory, and input/output devices. In many undergraduate and post-graduate courses, teachi

  7. HeliCis: a DNA motif discovery tool for colocalized motif pairs with periodic spacing

    Directory of Open Access Journals (Sweden)

    Mostad Petter

    2007-10-01

    Full Text Available Abstract Background Correct temporal and spatial gene expression during metazoan development relies on combinatorial interactions between different transcription factors. As a consequence, cis-regulatory elements often colocalize in clusters termed cis-regulatory modules. These may have requirements on organizational features such as spacing, order and helical phasing (periodic spacing between binding sites. Due to the turning of the DNA helix, a small modification of the distance between a pair of sites may sometimes drastically disrupt function, while insertion of a full helical turn of DNA (10–11 bp between cis elements may cause functionality to be restored. Recently, de novo motif discovery methods which incorporate organizational properties such as colocalization and order preferences have been developed, but there are no tools which incorporate periodic spacing into the model. Results We have developed a web based motif discovery tool, HeliCis, which features a flexible model which allows de novo detection of motifs with periodic spacing. Depending on the parameter settings it may also be used for discovering colocalized motifs without periodicity or motifs separated by a fixed gap of known or unknown length. We show on simulated data that it can efficiently capture the synergistic effects of colocalization and periodic spacing to improve detection of weak DNA motifs. It provides a simple to use web interface which interactively visualizes the current settings and thereby makes it easy to understand the parameters and the model structure. Conclusion HeliCis provides simple and efficient de novo discovery of colocalized DNA motif pairs, with or without periodic spacing. Our evaluations show that it can detect weak periodic patterns which are not easily discovered using a sequential approach, i.e. first finding the binding sites and second analyzing the properties of their pairwise distances.

  8. Large-scale discovery of promoter motifs in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Thomas A Down

    2007-01-01

    Full Text Available A key step in understanding gene regulation is to identify the repertoire of transcription factor binding motifs (TFBMs that form the building blocks of promoters and other regulatory elements. Identifying these experimentally is very laborious, and the number of TFBMs discovered remains relatively small, especially when compared with the hundreds of transcription factor genes predicted in metazoan genomes. We have used a recently developed statistical motif discovery approach, NestedMICA, to detect candidate TFBMs from a large set of Drosophila melanogaster promoter regions. Of the 120 motifs inferred in our initial analysis, 25 were statistically significant matches to previously reported motifs, while 87 appeared to be novel. Analysis of sequence conservation and motif positioning suggested that the great majority of these discovered motifs are predictive of functional elements in the genome. Many motifs showed associations with specific patterns of gene expression in the D. melanogaster embryo, and we were able to obtain confident annotation of expression patterns for 25 of our motifs, including eight of the novel motifs. The motifs are available through Tiffin, a new database of DNA sequence motifs. We have discovered many new motifs that are overrepresented in D. melanogaster promoter regions, and offer several independent lines of evidence that these are novel TFBMs. Our motif dictionary provides a solid foundation for further investigation of regulatory elements in Drosophila, and demonstrates techniques that should be applicable in other species. We suggest that further improvements in computational motif discovery should narrow the gap between the set of known motifs and the total number of transcription factors in metazoan genomes.

  9. Hybrid manifold embedding.

    Science.gov (United States)

    Liu, Yang; Liu, Yan; Chan, Keith C C; Hua, Kien A

    2014-12-01

    In this brief, we present a novel supervised manifold learning framework dubbed hybrid manifold embedding (HyME). Unlike most of the existing supervised manifold learning algorithms that give linear explicit mapping functions, the HyME aims to provide a more general nonlinear explicit mapping function by performing a two-layer learning procedure. In the first layer, a new clustering strategy called geodesic clustering is proposed to divide the original data set into several subsets with minimum nonlinearity. In the second layer, a supervised dimensionality reduction scheme called locally conjugate discriminant projection is performed on each subset for maximizing the discriminant information and minimizing the dimension redundancy simultaneously in the reduced low-dimensional space. By integrating these two layers in a unified mapping function, a supervised manifold embedding framework is established to describe both global and local manifold structure as well as to preserve the discriminative ability in the learned subspace. Experiments on various data sets validate the effectiveness of the proposed method.

  10. Gc globulin as a diagnostic and prognostic marker in horses

    DEFF Research Database (Denmark)

    Pihl, Tina Holberg

    can prevent development of shock and thereby increase survival chances. The in vivo toxicity of Gc-globulin infusion is currently being investigated in horses and other species. Gc-globulin has been demonstrated in horse plasma and its structure closely resembles that of human Gc-globulin. Gc...

  11. ET-Motif: Solving the Exact (l, d)-Planted Motif Problem Using Error Tree Structure.

    Science.gov (United States)

    Al-Okaily, Anas; Huang, Chun-Hsi

    2016-07-01

    Motif finding is an important and a challenging problem in many biological applications such as discovering promoters, enhancers, locus control regions, transcription factors, and more. The (l, d)-planted motif search, PMS, is one of several variations of the problem. In this problem, there are n given sequences over alphabets of size [Formula: see text], each of length m, and two given integers l and d. The problem is to find a motif m of length l, where in each sequence there is at least an l-mer at a Hamming distance of [Formula: see text] of m. In this article, we propose ET-Motif, an algorithm that can solve the PMS problem in [Formula: see text] time and [Formula: see text] space. The time bound can be further reduced by a factor of m with [Formula: see text] space. In case the suffix tree that is built for the input sequences is balanced, the problem can be solved in [Formula: see text] time and [Formula: see text] space. Similarly, the time bound can be reduced by a factor of m using [Formula: see text] space. Moreover, the variations of the problem, namely the edit distance PMS and edited PMS (Quorum), can be solved using ET-Motif with simple modifications but upper bands of space and time. For edit distance PMS, the time and space bounds will be increased by [Formula: see text], while for edited PMS the increase will be of [Formula: see text] in the time bound.

  12. Dynamics of network motifs in genetic regulatory networks

    Institute of Scientific and Technical Information of China (English)

    Li Ying; Liu Zeng-Rong; Zhang Jian-Bao

    2007-01-01

    Network motifs hold a very important status in genetic regulatory networks. This paper aims to analyse the dynamical property of the network motifs in genetic regulatory networks. The main result we obtained is that the dynamical property of a single motif is very simple with only an asymptotically stable equilibrium point, but the combination of several motifs can make more complicated dynamical properties emerge such as limit cycles. The above-mentioned result shows that network motif is a stable substructure in genetic regulatory networks while their combinations make the genetic regulatory network more complicated.

  13. No tradeoff between versatility and robustness in gene circuit motifs

    Science.gov (United States)

    Payne, Joshua L.

    2016-05-01

    Circuit motifs are small directed subgraphs that appear in real-world networks significantly more often than in randomized networks. In the Boolean model of gene circuits, most motifs are realized by multiple circuit genotypes. Each of a motif's constituent circuit genotypes may have one or more functions, which are embodied in the expression patterns the circuit forms in response to specific initial conditions. Recent enumeration of a space of nearly 17 million three-gene circuit genotypes revealed that all circuit motifs have more than one function, with the number of functions per motif ranging from 12 to nearly 30,000. This indicates that some motifs are more functionally versatile than others. However, the individual circuit genotypes that constitute each motif are less robust to mutation if they have many functions, hinting that functionally versatile motifs may be less robust to mutation than motifs with few functions. Here, I explore the relationship between versatility and robustness in circuit motifs, demonstrating that functionally versatile motifs are robust to mutation despite the inherent tradeoff between versatility and robustness at the level of an individual circuit genotype.

  14. CLIMP: Clustering Motifs via Maximal Cliques with Parallel Computing Design.

    Science.gov (United States)

    Zhang, Shaoqiang; Chen, Yong

    2016-01-01

    A set of conserved binding sites recognized by a transcription factor is called a motif, which can be found by many applications of comparative genomics for identifying over-represented segments. Moreover, when numerous putative motifs are predicted from a collection of genome-wide data, their similarity data can be represented as a large graph, where these motifs are connected to one another. However, an efficient clustering algorithm is desired for clustering the motifs that belong to the same groups and separating the motifs that belong to different groups, or even deleting an amount of spurious ones. In this work, a new motif clustering algorithm, CLIMP, is proposed by using maximal cliques and sped up by parallelizing its program. When a synthetic motif dataset from the database JASPAR, a set of putative motifs from a phylogenetic foot-printing dataset, and a set of putative motifs from a ChIP dataset are used to compare the performances of CLIMP and two other high-performance algorithms, the results demonstrate that CLIMP mostly outperforms the two algorithms on the three datasets for motif clustering, so that it can be a useful complement of the clustering procedures in some genome-wide motif prediction pipelines. CLIMP is available at http://sqzhang.cn/climp.html.

  15. Volume overload cleanup: An approach for on-line SPE-GC, GPC-GC, and GPC-SPE-GC

    NARCIS (Netherlands)

    Kerkdijk, H.; Mol, H.G.J.; Nagel, B. van der

    2007-01-01

    A new concept for cleanup, based on volume overloading of the cleanup column, has been developed for on-line coupling of gel permeation chromatography (GPC), solid-phase extraction (SPE), or both, to gas chromatography (GC). The principle is outlined and the applicability demonstrated by the determi

  16. CONTEMPORARY USAGE OF TRADITIONAL TURKISH MOTIFS IN PRODUCT DESIGNS

    Directory of Open Access Journals (Sweden)

    Tulay Gumuser

    2012-12-01

    Full Text Available The aim of this study is to identify the traditional Turkish motifs and its relations among present industrial designs. Traditional Turkish motifs played a very important role in 16th century onwards. The arts of the Ottoman Empire were used because of their symbolic meanings and unique styles. When we examine these motifs we encounter; Tiger Stripe, Three Spot (Çintemani, Rumi, Hatayi, Penç, Cloud, Crescent, Star, Crown, Hyacinth, Tulip and Carnation motifs. Nowadays, Turkish designers have begun to use these traditional Turkish motifs in their designs so as to create differences and awareness in the world design. The examples of these industrial designs, using the Turkish motifs, have survived and have Ottoman heritage and historical value. In this study, the Turkish motifs will be examined along with their focus on contemporary Turkish industrial designs used today.

  17. RNA structural motif recognition based on least-squares distance.

    Science.gov (United States)

    Shen, Ying; Wong, Hau-San; Zhang, Shaohong; Zhang, Lin

    2013-09-01

    RNA structural motifs are recurrent structural elements occurring in RNA molecules. RNA structural motif recognition aims to find RNA substructures that are similar to a query motif, and it is important for RNA structure analysis and RNA function prediction. In view of this, we propose a new method known as RNA Structural Motif Recognition based on Least-Squares distance (LS-RSMR) to effectively recognize RNA structural motifs. A test set consisting of five types of RNA structural motifs occurring in Escherichia coli ribosomal RNA is compiled by us. Experiments are conducted for recognizing these five types of motifs. The experimental results fully reveal the superiority of the proposed LS-RSMR compared with four other state-of-the-art methods.

  18. AISMOTIF-An Artificial Immune System for DNA Motif Discovery

    CERN Document Server

    Seeja, K R

    2011-01-01

    Discovery of transcription factor binding sites is a much explored and still exploring area of research in functional genomics. Many computational tools have been developed for finding motifs and each of them has their own advantages as well as disadvantages. Most of these algorithms need prior knowledge about the data to construct background models. However there is not a single technique that can be considered as best for finding regulatory motifs. This paper proposes an artificial immune system based algorithm for finding the transcription factor binding sites or motifs and two new weighted scores for motif evaluation. The algorithm is enumerative, but sufficient pruning of the pattern search space has been incorporated using immune system concepts. The performance of AISMOTIF has been evaluated by comparing it with eight state of art composite motif discovery algorithms and found that AISMOTIF predicts known motifs as well as new motifs from the benchmark dataset without any prior knowledge about the data...

  19. Semi-automated non-target processing in GC × GC-MS metabolomics analysis: Applicability for biomedical studies

    NARCIS (Netherlands)

    Koek, M.M.; Kloet, F.M. van der; Kleemann, R.; Kooistra, T.; Verheij, E.R.; Hankemeier, T.

    2011-01-01

    Due to the complexity of typical metabolomics samples and the many steps required to obtain quantitative data in GC × GC-MS consisting of deconvolution, peak picking, peak merging, and integration, the unbiased non-target quantification of GC × GC-MS data still poses a major challenge in metabolomic

  20. Design Methods for Embedded Security

    Directory of Open Access Journals (Sweden)

    I. Verbauwhede

    2009-11-01

    Full Text Available Embedded devices need both an efficient and a secure implementation of cryptographic algorithms. In this overview paper we show a typical top-down approach for secure and efficient implementation of embedded systems. We outline the security pyramid by illustrating the five primary abstraction levels in an embedded system. Focusing only on two levels - architecture and circuit level - we show how the design can be implemented to be both efficient and secure.

  1. Chaotic motif sampler: detecting motifs from biological sequences by using chaotic neurodynamics

    Science.gov (United States)

    Matsuura, Takafumi; Ikeguchi, Tohru

    Identification of a region in biological sequences, motif extraction problem (MEP) is solved in bioinformatics. However, the MEP is an NP-hard problem. Therefore, it is almost impossible to obtain an optimal solution within a reasonable time frame. To find near optimal solutions for NP-hard combinatorial optimization problems such as traveling salesman problems, quadratic assignment problems, and vehicle routing problems, chaotic search, which is one of the deterministic approaches, has been proposed and exhibits better performance than stochastic approaches. In this paper, we propose a new alignment method that employs chaotic dynamics to solve the MEPs. It is called the Chaotic Motif Sampler. We show that the performance of the Chaotic Motif Sampler is considerably better than that of the conventional methods such as the Gibbs Site Sampler and the Neighborhood Optimization for Multiple Alignment Discovery.

  2. Assessing the Exceptionality of Coloured Motifs in Networks

    Directory of Open Access Journals (Sweden)

    Lacroix Vincent

    2009-01-01

    Full Text Available Various methods have been recently employed to characterise the structure of biological networks. In particular, the concept of network motif and the related one of coloured motif have proven useful to model the notion of a functional/evolutionary building block. However, algorithms that enumerate all the motifs of a network may produce a very large output, and methods to decide which motifs should be selected for downstream analysis are needed. A widely used method is to assess if the motif is exceptional, that is, over- or under-represented with respect to a null hypothesis. Much effort has been put in the last thirty years to derive -values for the frequencies of topological motifs, that is, fixed subgraphs. They rely either on (compound Poisson and Gaussian approximations for the motif count distribution in Erdös-Rényi random graphs or on simulations in other models. We focus on a different definition of graph motifs that corresponds to coloured motifs. A coloured motif is a connected subgraph with fixed vertex colours but unspecified topology. Our work is the first analytical attempt to assess the exceptionality of coloured motifs in networks without any simulation. We first establish analytical formulae for the mean and the variance of the count of a coloured motif in an Erdös-Rényi random graph model. Using simulations under this model, we further show that a Pólya-Aeppli distribution better approximates the distribution of the motif count compared to Gaussian or Poisson distributions. The Pólya-Aeppli distribution, and more generally the compound Poisson distributions, are indeed well designed to model counts of clumping events. Altogether, these results enable to derive a -value for a coloured motif, without spending time on simulations.

  3. Bases of motifs for generating repeated patterns with wild cards.

    Science.gov (United States)

    Pisanti, Nadia; Crochemore, Maxime; Grossi, Roberto; Sagot, Marie-France

    2005-01-01

    Motif inference represents one of the most important areas of research in computational biology, and one of its oldest ones. Despite this, the problem remains very much open in the sense that no existing definition is fully satisfying, either in formal terms, or in relation to the biological questions that involve finding such motifs. Two main types of motifs have been considered in the literature: matrices (of letter frequency per position in the motif) and patterns. There is no conclusive evidence in favor of either, and recent work has attempted to integrate the two types into a single model. In this paper, we address the formal issue in relation to motifs as patterns. This is essential to get at a better understanding of motifs in general. In particular, we consider a promising idea that was recently proposed, which attempted to avoid the combinatorial explosion in the number of motifs by means of a generator set for the motifs. Instead of exhibiting a complete list of motifs satisfying some input constraints, what is produced is a basis of such motifs from which all the other ones can be generated. We study the computational cost of determining such a basis of repeated motifs with wild cards in a sequence. We give new upper and lower bounds on such a cost, introducing a notion of basis that is provably contained in (and, thus, smaller) than previously defined ones. Our basis can be computed in less time and space, and is still able to generate the same set of motifs. We also prove that the number of motifs in all bases defined so far grows exponentially with the quorum, that is, with the minimal number of times a motif must appear in a sequence, something unnoticed in previous work. We show that there is no hope to efficiently compute such bases unless the quorum is fixed.

  4. Advances in embedded computer vision

    CERN Document Server

    Kisacanin, Branislav

    2014-01-01

    This illuminating collection offers a fresh look at the very latest advances in the field of embedded computer vision. Emerging areas covered by this comprehensive text/reference include the embedded realization of 3D vision technologies for a variety of applications, such as stereo cameras on mobile devices. Recent trends towards the development of small unmanned aerial vehicles (UAVs) with embedded image and video processing algorithms are also examined. The authoritative insights range from historical perspectives to future developments, reviewing embedded implementation, tools, technolog

  5. Communicating embedded systems networks applications

    CERN Document Server

    Krief, Francine

    2013-01-01

    Embedded systems become more and more complex and require having some knowledge in various disciplines such as electronics, data processing, telecommunications and networks. Without detailing all the aspects related to the design of embedded systems, this book, which was written by specialists in electronics, data processing and telecommunications and networks, gives an interesting point of view of communication techniques and problems in embedded systems. This choice is easily justified by the fact that embedded systems are today massively communicating and that telecommunications and network

  6. Embedded Systems Design with FPGAs

    CERN Document Server

    Pnevmatikatos, Dionisios; Sklavos, Nicolas

    2013-01-01

    This book presents methodologies for modern applications of embedded systems design, using field programmable gate array (FPGA) devices.  Coverage includes state-of-the-art research from academia and industry on a wide range of topics, including advanced electronic design automation (EDA), novel system architectures, embedded processors, arithmetic, dynamic reconfiguration and applications. Describes a variety of methodologies for modern embedded systems design;  Implements methodologies presented on FPGAs; Covers a wide variety of applications for reconfigurable embedded systems, including Bioinformatics, Communications and networking, Application acceleration, Medical solutions, Experiments for high energy physics, Astronomy, Aerospace, Biologically inspired systems and Computational fluid dynamics (CFD).

  7. Embedded sensor systems

    CERN Document Server

    Agrawal, Dharma Prakash

    2017-01-01

    This inspiring textbook provides an introduction to wireless technologies for sensors, explores potential use of sensors for numerous applications, and utilizes probability theory and mathematical methods as a means of embedding sensors in system design. It discusses the need for synchronization and underlying limitations, inter-relation between given coverage and connectivity to number of sensors needed, and the use of geometrical distance to determine location of the base station for data collection and explore use of anchor nodes for relative position determination of sensors. The book explores energy conservation, communication using TCP, the need for clustering and data aggregation, and residual energy determination and energy harvesting. It covers key topics of sensor communication like mobile base stations and relay nodes, delay-tolerant sensor networks, and remote sensing and possible applications. The book defines routing methods and do performance evaluation for random and regular sensor topology an...

  8. Watermark Embedding and Detection

    CERN Document Server

    Zhong, Jidong

    2006-01-01

    The embedder and the detector (or decoder) are the two most important components of the digital watermarking systems. Thus in this work, we discuss how to design a better embedder and detector (or decoder). I first give a summary of the prospective applications of watermarking technology and major watermarking schemes in the literature. My review on the literature closely centers upon how the side information is exploited at both embedders and detectors. In Chapter 3, I explore the optimum detector or decoder according to a particular probability distribution of the host signals. We found that the performance of both multiplicative and additive spread spectrum schemes depends on the shape parameter of the host signals. For spread spectrum schemes, the performance of the detector or the decoder is reduced by the host interference. Thus I present a new host-interference rejection technique for the multiplicative spread spectrum schemes. Its embedding rule is tailored to the optimum detection or decoding rule. T...

  9. Adaptable Embedded Systems

    CERN Document Server

    Lisbôa, Carlos; Carro, Luigi

    2013-01-01

    As embedded systems become more complex, designers face a number of challenges at different levels: they need to boost performance, while keeping energy consumption as low as possible, they need to reuse existent software code, and at the same time they need to take advantage of the extra logic available in the chip, represented by multiple processors working together.  This book describes several strategies to achieve such different and interrelated goals, by the use of adaptability. Coverage includes reconfigurable systems, dynamic optimization techniques such as binary translation and trace reuse, new memory architectures including homogeneous and heterogeneous multiprocessor systems, communication issues and NOCs, fault tolerance against fabrication defects and soft errors, and finally, how one can combine several of these techniques together to achieve higher levels of performance and adaptability.  The discussion also includes how to employ specialized software to improve this new adaptive system, and...

  10. The MHC motif viewer: a visualization tool for MHC binding motifs

    DEFF Research Database (Denmark)

    Rapin, Nicolas; Hoof, Ilka; Lund, Ole

    2010-01-01

    of peptides, and knowledge of their binding specificities is important for understanding differences in the immune response between individuals. Algorithms predicting which peptides bind a given MHC molecule have recently been developed with high prediction accuracy. The utility of these algorithms...... is hampered by the lack of tools for browsing and comparing specificity of these molecules. We have developed a Web server, MHC Motif Viewer, which allows the display of the binding motif for MHC class I proteins for human, chimpanzee, rhesus monkey, mouse, and swine, as well as HLA-DR protein sequences...

  11. Embedding potentials for excited states of embedded species.

    Science.gov (United States)

    Wesolowski, Tomasz A

    2014-05-14

    Frozen-Density-Embedding Theory (FDET) is a formalism to obtain the upper bound of the ground-state energy of the total system and the corresponding embedded wavefunction by means of Euler-Lagrange equations [T. A. Wesolowski, Phys. Rev. A 77(1), 012504 (2008)]. FDET provides the expression for the embedding potential as a functional of the electron density of the embedded species, electron density of the environment, and the field generated by other charges in the environment. Under certain conditions, FDET leads to the exact ground-state energy and density of the whole system. Following Perdew-Levy theorem on stationary states of the ground-state energy functional, the other-than-ground-state stationary states of the FDET energy functional correspond to excited states. In the present work, we analyze such use of other-than-ground-state embedded wavefunctions obtained in practical calculations, i.e., when the FDET embedding potential is approximated. Three computational approaches based on FDET, that assure self-consistent excitation energy and embedded wavefunction dealing with the issue of orthogonality of embedded wavefunctions for different states in a different manner, are proposed and discussed.

  12. DNA motif elucidation using belief propagation

    OpenAIRE

    Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei

    2013-01-01

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k = 8 ∼10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the ...

  13. MINER: software for phylogenetic motif identification.

    Science.gov (United States)

    La, David; Livesay, Dennis R

    2005-07-01

    MINER is web-based software for phylogenetic motif (PM) identification. PMs are sequence regions (fragments) that conserve the overall familial phylogeny. PMs have been shown to correspond to a wide variety of catalytic regions, substrate-binding sites and protein interfaces, making them ideal functional site predictions. The MINER output provides an intuitive interface for interactive PM sequence analysis and structural visualization. The web implementation of MINER is freely available at http://www.pmap.csupomona.edu/MINER/. Source code is available to the academic community on request.

  14. RMOD: a tool for regulatory motif detection in signaling network.

    Directory of Open Access Journals (Sweden)

    Jinki Kim

    Full Text Available Regulatory motifs are patterns of activation and inhibition that appear repeatedly in various signaling networks and that show specific regulatory properties. However, the network structures of regulatory motifs are highly diverse and complex, rendering their identification difficult. Here, we present a RMOD, a web-based system for the identification of regulatory motifs and their properties in signaling networks. RMOD finds various network structures of regulatory motifs by compressing the signaling network and detecting the compressed forms of regulatory motifs. To apply it into a large-scale signaling network, it adopts a new subgraph search algorithm using a novel data structure called path-tree, which is a tree structure composed of isomorphic graphs of query regulatory motifs. This algorithm was evaluated using various sizes of signaling networks generated from the integration of various human signaling pathways and it showed that the speed and scalability of this algorithm outperforms those of other algorithms. RMOD includes interactive analysis and auxiliary tools that make it possible to manipulate the whole processes from building signaling network and query regulatory motifs to analyzing regulatory motifs with graphical illustration and summarized descriptions. As a result, RMOD provides an integrated view of the regulatory motifs and mechanism underlying their regulatory motif activities within the signaling network. RMOD is freely accessible online at the following URL: http://pks.kaist.ac.kr/rmod.

  15. Protein functional-group 3D motif and its applications

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Representing and recognizing protein active sites sequence motif (1D motif) and structural motif (3D motif) is an important topic for predicting and designing protein function. Prevalent methods for extracting and searching 3D motif always consider residue as the minimal unit, which have limited sensitivity. Here we present a new spatial representation of protein active sites, called "functional-group 3D motif ", based on the fact that the functional groups inside a residue contribute mostly to its function. Relevant algorithm and computer program are developed, which could be widely used in the function prediction and the study of structural-function relationship of proteins. As a test, we defined a functional-group 3D motif of the catalytic triad and oxyanion hole with the structure of porcine trypsin (PDB code: 1mct) as the template. With our motif-searching program, we successfully found similar sub-structures in trypsins, subtilisins and a/b hydrolases, which show distinct folds but share similar catalytic mechanism. Moreover, this motif can be used to elucidate the structural basis of other proteins with variant catalytic triads by comparing it to those proteins. Finally, we scanned this motif against a non-redundant protein structure database to find its matches, and the results demonstrated the potential application of functional group 3D motif in function prediction. Above all, compared with the other 3D-motif representations on residues, the functional group 3D motif achieves better representation of protein active region, which is more sensitive for protein function prediction.

  16. Computer algebra in spacetime embedding

    CERN Document Server

    Roque, Waldir L

    2014-01-01

    In this paper we describe an algorithm to determine the vectors normal to a space-time V4 embedded in a pseudo-Euclidean manifold M4+n. An application of this algorithm is given considering the Schwarzchild space-time geometry embedded in a 6 dimensional pseudo-Euclidean manifold, using the algebraic computing system REDUCE.

  17. Molecular Properties through Polarizable Embedding

    DEFF Research Database (Denmark)

    Olsen, Jógvan Magnus Haugaard; Kongsted, Jacob

    2011-01-01

    We review the theory related to the calculation of electric and magnetic molecular properties through polarizable embedding. In particular, we derive the expressions for the response functions up to the level of cubic response within the density functional theory-based polarizable embedding (PE-D...

  18. Certifiable Java for Embedded Systems

    DEFF Research Database (Denmark)

    Schoeberl, Martin; Dalsgaard, Andreas Engelbredt; Hansen, Rene Rydhof

    2014-01-01

    The Certifiable Java for Embedded Systems (CJ4ES) project aimed to develop a prototype development environment and platform for safety-critical software for embedded applications. There are three core constituents: A profile of the Java programming language that is tailored for safety...

  19. Hybridity in Embedded Computing Systems

    Institute of Scientific and Technical Information of China (English)

    虞慧群; 孙永强

    1996-01-01

    An embedded system is a system that computer is used as a component in a larger device.In this paper,we study hybridity in embedded systems and present an interval based temporal logic to express and reason about hybrid properties of such kind of systems.

  20. Collaborative development of embedded systems

    NARCIS (Netherlands)

    Verhoef, Marcel; Pierce, Kenneth; Gamble, Carl; Broenink, Jan; Fitzgerald, John; Larsen, Peter Gorm; Verhoef, Marcel

    2014-01-01

    This chapter presents motivation for taking a collaborative multi-disciplinary approach to the model-based development of embedded systems. Starting from a consideration of the ubiquity of embedded systems in daily life it identifies challenges faced by industry in developing products in a timely ma

  1. A Foundation for Embedded Languages

    DEFF Research Database (Denmark)

    Rhiger, Morten

    2003-01-01

    Recent work on embedding object languages into Haskell use "phantom types" (i.e., parameterized types whose parameter does not occur on the right-hand side of the type definition) to ensure that the embedded object-language terms are simply typed. But is it a safe assumption that only simply...

  2. A Foundation for Embedded Languages

    DEFF Research Database (Denmark)

    Rhiger, Morten

    2002-01-01

    Recent work on embedding object languages into Haskell use "phantom types" (i.e., parameterized types whose parameter does not occur on the right-hand side of the type definition) to ensure that the embedded object-language terms are simply typed. But is it a safe assumption that only simply...

  3. The network motif architecture of dominance hierarchies.

    Science.gov (United States)

    Shizuka, Daizaburo; McDonald, David B

    2015-04-01

    The widespread existence of dominance hierarchies has been a central puzzle in social evolution, yet we lack a framework for synthesizing the vast empirical data on hierarchy structure in animal groups. We applied network motif analysis to compare the structures of dominance networks from data published over the past 80 years. Overall patterns of dominance relations, including some aspects of non-interactions, were strikingly similar across disparate group types. For example, nearly all groups exhibited high frequencies of transitive triads, whereas cycles were very rare. Moreover, pass-along triads were rare, and double-dominant triads were common in most groups. These patterns did not vary in any systematic way across taxa, study settings (captive or wild) or group size. Two factors significantly affected network motif structure: the proportion of dyads that were observed to interact and the interaction rates of the top-ranked individuals. Thus, study design (i.e. how many interactions were observed) and the behaviour of key individuals in the group could explain much of the variations we see in social hierarchies across animals. Our findings confirm the ubiquity of dominance hierarchies across all animal systems, and demonstrate that network analysis provides new avenues for comparative analyses of social hierarchies.

  4. Promoter Motifs in NCLDVs: An Evolutionary Perspective

    Science.gov (United States)

    Oliveira, Graziele Pereira; Andrade, Ana Cláudia dos Santos Pereira; Rodrigues, Rodrigo Araújo Lima; Arantes, Thalita Souza; Boratto, Paulo Victor Miranda; Silva, Ludmila Karen dos Santos; Dornas, Fábio Pio; Trindade, Giliane de Souza; Drumond, Betânia Paiva; La Scola, Bernard; Kroon, Erna Geessien; Abrahão, Jônatas Santos

    2017-01-01

    For many years, gene expression in the three cellular domains has been studied in an attempt to discover sequences associated with the regulation of the transcription process. Some specific transcriptional features were described in viruses, although few studies have been devoted to understanding the evolutionary aspects related to the spread of promoter motifs through related viral families. The discovery of giant viruses and the proposition of the new viral order Megavirales that comprise a monophyletic group, named nucleo-cytoplasmic large DNA viruses (NCLDV), raised new questions in the field. Some putative promoter sequences have already been described for some NCLDV members, bringing new insights into the evolutionary history of these complex microorganisms. In this review, we summarize the main aspects of the transcription regulation process in the three domains of life, followed by a systematic description of what is currently known about promoter regions in several NCLDVs. We also discuss how the analysis of the promoter sequences could bring new ideas about the giant viruses’ evolution. Finally, considering a possible common ancestor for the NCLDV group, we discussed possible promoters’ evolutionary scenarios and propose the term “MEGA-box” to designate an ancestor promoter motif (‘TATATAAAATTGA’) that could be evolved gradually by nucleotides’ gain and loss and point mutations. PMID:28117683

  5. Promoter Motifs in NCLDVs: An Evolutionary Perspective

    Directory of Open Access Journals (Sweden)

    Graziele Pereira Oliveira

    2017-01-01

    Full Text Available For many years, gene expression in the three cellular domains has been studied in an attempt to discover sequences associated with the regulation of the transcription process. Some specific transcriptional features were described in viruses, although few studies have been devoted to understanding the evolutionary aspects related to the spread of promoter motifs through related viral families. The discovery of giant viruses and the proposition of the new viral order Megavirales that comprise a monophyletic group, named nucleo-cytoplasmic large DNA viruses (NCLDV, raised new questions in the field. Some putative promoter sequences have already been described for some NCLDV members, bringing new insights into the evolutionary history of these complex microorganisms. In this review, we summarize the main aspects of the transcription regulation process in the three domains of life, followed by a systematic description of what is currently known about promoter regions in several NCLDVs. We also discuss how the analysis of the promoter sequences could bring new ideas about the giant viruses’ evolution. Finally, considering a possible common ancestor for the NCLDV group, we discussed possible promoters’ evolutionary scenarios and propose the term “MEGA-box” to designate an ancestor promoter motif (‘TATATAAAATTGA’ that could be evolved gradually by nucleotides’ gain and loss and point mutations.

  6. Asymmetric distances for binary embeddings.

    Science.gov (United States)

    Gordo, Albert; Perronnin, Florent; Gong, Yunchao; Lazebnik, Svetlana

    2014-01-01

    In large-scale query-by-example retrieval, embedding image signatures in a binary space offers two benefits: data compression and search efficiency. While most embedding algorithms binarize both query and database signatures, it has been noted that this is not strictly a requirement. Indeed, asymmetric schemes that binarize the database signatures but not the query still enjoy the same two benefits but may provide superior accuracy. In this work, we propose two general asymmetric distances that are applicable to a wide variety of embedding techniques including locality sensitive hashing (LSH), locality sensitive binary codes (LSBC), spectral hashing (SH), PCA embedding (PCAE), PCAE with random rotations (PCAE-RR), and PCAE with iterative quantization (PCAE-ITQ). We experiment on four public benchmarks containing up to 1M images and show that the proposed asymmetric distances consistently lead to large improvements over the symmetric Hamming distance for all binary embedding techniques.

  7. Maximum Genus of Strong Embeddings

    Institute of Scientific and Technical Information of China (English)

    Er-ling Wei; Yan-pei Liu; Han Ren

    2003-01-01

    The strong embedding conjecture states that any 2-connected graph has a strong embedding on some surface. It implies the circuit double cover conjecture: Any 2-connected graph has a circuit double cover.Conversely, it is not true. But for a 3-regular graph, the two conjectures are equivalent. In this paper, a characterization of graphs having a strong embedding with exactly 3 faces, which is the strong embedding of maximum genus, is given. In addition, some graphs with the property are provided. More generally, an upper bound of the maximum genus of strong embeddings of a graph is presented too. Lastly, it is shown that the interpolation theorem is true to planar Halin graph.

  8. Lattice Embedding of Heronian Simplices

    CERN Document Server

    Lunnon, W Fred

    2012-01-01

    A rational triangle has rational edge-lengths and area; a rational tetrahedron has rational faces and volume; either is Heronian when its edge-lengths are integer, and proper when its content is nonzero. A variant proof is given, via complex number GCD, of the previously known result that any Heronian triangle may be embedded in the Cartesian lattice Z^2; it is then shown that, for a proper triangle, such an embedding is unique modulo lattice isometry; finally the method is extended via quaternion GCD to tetrahedra in Z^3, where uniqueness no longer obtains, and embeddings also exist which are unobtainable by this construction. The requisite complex and quaternionic number theoretic background is summarised beforehand. Subsequent sections engage with subsidiary implementation issues: initial rational embedding, canonical reduction, exhaustive search for embeddings additional to those yielded via GCD; and illustrative numerical examples are provided. A counter-example shows that this approach must fail in high...

  9. An unusual helix turn helix motif in the catalytic core of HIV-1 integrase binds viral DNA and LEDGF.

    Directory of Open Access Journals (Sweden)

    Hayate Merad

    Full Text Available BACKGROUND: Integrase (IN of the type 1 human immunodeficiency virus (HIV-1 catalyzes the integration of viral DNA into host cellular DNA. We identified a bi-helix motif (residues 149-186 in the crystal structure of the catalytic core (CC of the IN-Phe185Lys variant that consists of the alpha(4 and alpha(5 helices connected by a 3 to 5-residue turn. The motif is embedded in a large array of interactions that stabilize the monomer and the dimer. PRINCIPAL FINDINGS: We describe the conformational and binding properties of the corresponding synthetic peptide. This displays features of the protein motif structure thanks to the mutual intramolecular interactions of the alpha(4 and alpha(5 helices that maintain the fold. The main properties are the binding to: 1- the processing-attachment site at the LTR (long terminal repeat ends of virus DNA with a K(d (dissociation constant in the sub-micromolar range; 2- the whole IN enzyme; and 3- the IN binding domain (IBD but not the IBD-Asp366Asn variant of LEDGF (lens epidermal derived growth factor lacking the essential Asp366 residue. In our motif, in contrast to the conventional HTH (helix-turn-helix, it is the N terminal helix (alpha(4 which has the role of DNA recognition helix, while the C terminal helix (alpha(5 would rather contribute to the motif stabilization by interactions with the alpha(4 helix. CONCLUSION: The motif, termed HTHi (i, for inverted emerges as a central piece of the IN structure and function. It could therefore represent an attractive target in the search for inhibitors working at the DNA-IN, IN-IN and IN-LEDGF interfaces.

  10. Outdoor and indoor benzene evaluation by GC-FID and GC-MS/MS

    OpenAIRE

    José A. Sousa; Domingues, Valentina F.; Rosas, Mónica S.; Ribeiro, Susana; Alvim-Ferraz, Maria da Conceição M.

    2011-01-01

    The evaluation of benzene in different environments such as indoor (with and without tobacco smoke), a city area, countryside, gas stations and near exhaust pipes from cars running on different types of fuels was performed. The samples were analyzed using gas chromatography (GC) with flame ionization detection (FID) and tandem mass spectrometric detection (MS/MS) (to confirm the identification of benzene in the air samples). Operating conditions for the GC-MS analysis were optimized ...

  11. Identification and determination of (+)-sesamin in Semen Cuscutae by capillary GC and GC-MS

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    (+)-Sesamin was found in Semen Cuscutae for the first time. A rapid and simple approach for the analysis of (+)-sesamin in different sources of Semen Cuscutae is proposed, which used GC-FID for the determination of (+)-sesamin and GC-MS for its identification. The result suggested that this approach could be used to identify Semen Cuscutae from various sources based on the different content of (+)-sesamin in them.

  12. Parole, Sintagmatik, dan Paradigmatik Motif Batik Mega Mendung

    Directory of Open Access Journals (Sweden)

    Rudi - Nababan

    2012-04-01

    Full Text Available ABSTRACT   Discussing traditional batik is related a lot to the organization system of fine arts element ac- companying it, either the pattern of the motif or the technique of the making. In this case, the motif of Mega Mendung Cirebon certainly has patterns and rules which are traditionally different from the other motifs in other areas. Through  semiotics analysis especially with Saussure and Pierce concept, it can be traced that batik with Cirebon motif, in this case Mega Mendung motif, has parole and langue system, as unique fine arts language in batik, and structure of visual syntagmatic and paradigmatic. In the context of batik motif as fine arts language, it is surely related to sign system as symbol and icon.       Keywords: visual semiotic, Cirebon’s batik.

  13. An Affinity Propagation-Based DNA Motif Discovery Algorithm

    Directory of Open Access Journals (Sweden)

    Chunxiao Sun

    2015-01-01

    Full Text Available The planted (l,d motif search (PMS is one of the fundamental problems in bioinformatics, which plays an important role in locating transcription factor binding sites (TFBSs in DNA sequences. Nowadays, identifying weak motifs and reducing the effect of local optimum are still important but challenging tasks for motif discovery. To solve the tasks, we propose a new algorithm, APMotif, which first applies the Affinity Propagation (AP clustering in DNA sequences to produce informative and good candidate motifs and then employs Expectation Maximization (EM refinement to obtain the optimal motifs from the candidate motifs. Experimental results both on simulated data sets and real biological data sets show that APMotif usually outperforms four other widely used algorithms in terms of high prediction accuracy.

  14. An Affinity Propagation-Based DNA Motif Discovery Algorithm.

    Science.gov (United States)

    Sun, Chunxiao; Huo, Hongwei; Yu, Qiang; Guo, Haitao; Sun, Zhigang

    2015-01-01

    The planted (l, d) motif search (PMS) is one of the fundamental problems in bioinformatics, which plays an important role in locating transcription factor binding sites (TFBSs) in DNA sequences. Nowadays, identifying weak motifs and reducing the effect of local optimum are still important but challenging tasks for motif discovery. To solve the tasks, we propose a new algorithm, APMotif, which first applies the Affinity Propagation (AP) clustering in DNA sequences to produce informative and good candidate motifs and then employs Expectation Maximization (EM) refinement to obtain the optimal motifs from the candidate motifs. Experimental results both on simulated data sets and real biological data sets show that APMotif usually outperforms four other widely used algorithms in terms of high prediction accuracy.

  15. Probabilistic models for semisupervised discriminative motif discovery in DNA sequences.

    Science.gov (United States)

    Kim, Jong Kyoung; Choi, Seungjin

    2011-01-01

    Methods for discriminative motif discovery in DNA sequences identify transcription factor binding sites (TFBSs), searching only for patterns that differentiate two sets (positive and negative sets) of sequences. On one hand, discriminative methods increase the sensitivity and specificity of motif discovery, compared to generative models. On the other hand, generative models can easily exploit unlabeled sequences to better detect functional motifs when labeled training samples are limited. In this paper, we develop a hybrid generative/discriminative model which enables us to make use of unlabeled sequences in the framework of discriminative motif discovery, leading to semisupervised discriminative motif discovery. Numerical experiments on yeast ChIP-chip data for discovering DNA motifs demonstrate that the best performance is obtained between the purely-generative and the purely-discriminative and the semisupervised learning improves the performance when labeled sequences are limited.

  16. Triadic motifs in the dependence networks of virtual societies

    CERN Document Server

    Xie, Wen-Jie; Jiang, Zhi-Qiang; Zhou, Wei-Xing

    2014-01-01

    In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (${\\rm{M}}_9$) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks...

  17. Metric embeddings bilipschitz and coarse embeddings into Banach spaces

    CERN Document Server

    Ostrovskii, Mikhail I

    2013-01-01

    Embeddings of discrete metric spaces into Banach spaces recently became an important tool in computer science and topology. The book will help readers to enter and to work in this very rapidly developing area having many important connections with different parts of mathematics and computer science. The purpose of the book is to present some of the most important techniques and results, mostly on bilipschitz and coarse embeddings. The topics include embeddability of locally finite metric spaces into Banach spaces is finitely determined, constructions of embeddings, distortion in terms of Poinc

  18. Detecting DNA regulatory motifs by incorporating positional trendsin information content

    Energy Technology Data Exchange (ETDEWEB)

    Kechris, Katherina J.; van Zwet, Erik; Bickel, Peter J.; Eisen,Michael B.

    2004-05-04

    On the basis of the observation that conserved positions in transcription factor binding sites are often clustered together, we propose a simple extension to the model-based motif discovery methods. We assign position-specific prior distributions to the frequency parameters of the model, penalizing deviations from a specified conservation profile. Examples with both simulated and real data show that this extension helps discover motifs as the data become noisier or when there is a competing false motif.

  19. STEME: a robust, accurate motif finder for large data sets.

    Directory of Open Access Journals (Sweden)

    John E Reid

    Full Text Available Motif finding is a difficult problem that has been studied for over 20 years. Some older popular motif finders are not suitable for analysis of the large data sets generated by next-generation sequencing. We recently published an efficient approximation (STEME to the EM algorithm that is at the core of many motif finders such as MEME. This approximation allows the EM algorithm to be applied to large data sets. In this work we describe several efficient extensions to STEME that are based on the MEME algorithm. Together with the original STEME EM approximation, these extensions make STEME a fully-fledged motif finder with similar properties to MEME. We discuss the difficulty of objectively comparing motif finders. We show that STEME performs comparably to existing prominent discriminative motif finders, DREME and Trawler, on 13 sets of transcription factor binding data in mouse ES cells. We demonstrate the ability of STEME to find long degenerate motifs which these discriminative motif finders do not find. As part of our method, we extend an earlier method due to Nagarajan et al. for the efficient calculation of motif E-values. STEME's source code is available under an open source license and STEME is available via a web interface.

  20. Motif content comparison between monocot and dicot species

    Directory of Open Access Journals (Sweden)

    Matyas Cserhati

    2015-03-01

    Full Text Available While a number of DNA sequence motifs have been functionally characterized, the full repertoire of motifs in an organism (the motifome is yet to be characterized. The present study wishes to widen the scope of motif content analysis in different monocot and dicot species that include both rice species, Brachypodium, corn, wheat as monocots and Arabidopsis, Lotus japonica, Medicago truncatula, and Populus tremula as dicots. All possible existing motifs were analyzed in different regions of genomes such as were found in different sets of sequences in these species: the whole genome, core proximal and distal promoters, 5′ and 3′ UTRs, and the 1st introns. Due to the increased number of species involved in this study compared to previous works, species relationships were analyzed based on the similarity of common motif content. Certain secondary structure elements were inferred in the genomes of these species as well as new unknown motifs. The distribution of 20 motifs common to the studied species were found to have a significantly larger occurrence within the promoters and 3′ UTRs of genes, both being regulatory regions. Motifs common to the promoter regions of japonica rice, Brachypodium, and corn were also found in a number of orthologous and paralogous genes. Some of our motifs were found to be complementary to miRNA elements in Brachypodium distachyon and japonica rice.

  1. Modeling Network Evolution Using Graph Motifs

    CERN Document Server

    Conway, Drew

    2011-01-01

    Network structures are extremely important to the study of political science. Much of the data in its subfields are naturally represented as networks. This includes trade, diplomatic and conflict relationships. The social structure of several organization is also of interest to many researchers, such as the affiliations of legislators or the relationships among terrorist. A key aspect of studying social networks is understanding the evolutionary dynamics and the mechanism by which these structures grow and change over time. While current methods are well suited to describe static features of networks, they are less capable of specifying models of change and simulating network evolution. In the following paper I present a new method for modeling network growth and evolution. This method relies on graph motifs to generate simulated network data with particular structural characteristic. This technique departs notably from current methods both in form and function. Rather than a closed-form model, or stochastic ...

  2. Complex lasso: new entangled motifs in proteins

    Science.gov (United States)

    Niemyska, Wanda; Dabrowski-Tumanski, Pawel; Kadlof, Michal; Haglund, Ellinor; Sułkowski, Piotr; Sulkowska, Joanna I.

    2016-11-01

    We identify new entangled motifs in proteins that we call complex lassos. Lassos arise in proteins with disulfide bridges (or in proteins with amide linkages), when termini of a protein backbone pierce through an auxiliary surface of minimal area, spanned on a covalent loop. We find that as much as 18% of all proteins with disulfide bridges in a non-redundant subset of PDB form complex lassos, and classify them into six distinct geometric classes, one of which resembles supercoiling known from DNA. Based on biological classification of proteins we find that lassos are much more common in viruses, plants and fungi than in other kingdoms of life. We also discuss how changes in the oxidation/reduction potential may affect the function of proteins with lassos. Lassos and associated surfaces of minimal area provide new, interesting and possessing many potential applications geometric characteristics not only of proteins, but also of other biomolecules.

  3. Rekayasa Pengembangan Desain Motif Batik Khas Melayu

    Directory of Open Access Journals (Sweden)

    Eustasia Sri Murwati

    2016-04-01

    Full Text Available ABSTRAKPengembangan desain batik melalui rancang bangun perekayasaan desain menurut ragam hias Melayu meliputi pengembangan motif dan proses, termasuk pemilihan komposisi warna. Proses yang sering dilakukan yaitu proses celup, penghilangan lilin dan celup warna tumpangan atau proses colet, celup, penghilangan lilin atau celup kemudian penghilangan lilin yang disebut Batik Kelengan. Setiap pulau di Indonesia mempunyai ciri khas budaya dan kesenian yang dikenal dengan corak/ragam hias khas daerah, juga ornamen yang diminati oleh masyarakat dari daerah tersebut atau dari daerah lain. Kondisi demikian mendorong pertumbuhan industri kerajinan yang memanfaatkan unsur–unsur seni. Adapun motif yang diperoleh adalah: Ayam Berlaga, Bungo Matahari, Kuntum Bersanding, Lancang Kuning, Encong Kerinci, Durian Pecah, Bungo Bintang, Bungo Pauh Kecil, Riang-riang, Bungo Nagaro. Pengembangan desain tersebut dipilih 3 produk terbaik yang dinilai oleh 5 penilai yang ahli di bidang desain batik, yaitu motif Durian Pecah, Ayam Berlaga, dan Bungo Matahari. Rancang bangun diversifikasi desain dengan memanfaatkan unsur–unsur seni dan ketrampilan etnis Melayu yaitu pemilihan ragam hias dan motif batik Melayu untuk diterapkan ke bahan sandang dengan komposisi warna yang menarik, sehingga produk memenuhi selera konsumen. Memperbaiki keberagaman batik dengan meningkatkan desain produk antara lain menuangkan ragam hias Melayu ke dalam proses batik yang menggunakan berbagai macam warna sehingga komposisi warna memadai. Diperoleh hasil produk batik dengan ragam hias Melayu yang berkualitas dan komposisi warna yang sesuai dengan karakter ragam hias Melayu. Rancang bangun desain produk untuk mendapatkan formulasi desain serta kelayakan prosesnya dengan penekanan pada teknologi akrab lingkungan dilaksanakan dengan alternatif pendekatan yaitu penciptaan desain bentuk baru.Kata kunci: desain, batik, rancang bangun, ragam hias, MelayuABSTRACTDevelopment of batik design through

  4. Phylogenetic trees and Euclidean embeddings.

    Science.gov (United States)

    Layer, Mark; Rhodes, John A

    2017-01-01

    It was recently observed by de Vienne et al. (Syst Biol 60(6):826-832, 2011) that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on a diffusion model of continuous character evolution along the tree, here we give a direct and elementary explanation for it that provides substantial additional insight. We use this embedding to reinterpret the differences between the NJ and BIONJ tree building algorithms, providing one illustration of how this embedding reflects tree structures in data.

  5. Embedded systems circuits and programming

    CERN Document Server

    Sanchez, Julio

    2012-01-01

    During the development of an engineered product, developers often need to create an embedded system--a prototype--that demonstrates the operation/function of the device and proves its viability. Offering practical tools for the development and prototyping phases, Embedded Systems Circuits and Programming provides a tutorial on microcontroller programming and the basics of embedded design. The book focuses on several development tools and resources: Standard and off-the-shelf components, such as input/output devices, integrated circuits, motors, and programmable microcontrollers The implementat

  6. Analysis of intra-genomic GC content homogeneity within prokaryotes

    DEFF Research Database (Denmark)

    Bohlin, J; Snipen, L; Hardy, S.P.

    2010-01-01

    both aerobic and facultative microbes. Although an association has previously been found between mean genomic GC content and oxygen requirement, our analysis suggests that no such association exits when phylogenetic bias is accounted for. A significant association between GCVAR and mean GC content......Bacterial genomes possess varying GC content (total guanines (Gs) and cytosines (Cs) per total of the four bases within the genome) but within a given genome, GC content can vary locally along the chromosome, with some regions significantly more or less GC rich than on average. We have examined how...... the GC content varies within microbial genomes to assess whether this property can be associated with certain biological functions related to the organism's environment and phylogeny. We utilize a new quantity GCVAR, the intra-genomic GC content variability with respect to the average GC content...

  7. Motif-role-fingerprints: the building-blocks of motifs, clustering-coefficients and transitivities in directed networks.

    Directory of Open Access Journals (Sweden)

    Mark D McDonnell

    Full Text Available Complex networks are frequently characterized by metrics for which particular subgraphs are counted. One statistic from this category, which we refer to as motif-role fingerprints, differs from global subgraph counts in that the number of subgraphs in which each node participates is counted. As with global subgraph counts, it can be important to distinguish between motif-role fingerprints that are 'structural' (induced subgraphs and 'functional' (partial subgraphs. Here we show mathematically that a vector of all functional motif-role fingerprints can readily be obtained from an arbitrary directed adjacency matrix, and then converted to structural motif-role fingerprints by multiplying that vector by a specific invertible conversion matrix. This result demonstrates that a unique structural motif-role fingerprint exists for any given functional motif-role fingerprint. We demonstrate a similar result for the cases of functional and structural motif-fingerprints without node roles, and global subgraph counts that form the basis of standard motif analysis. We also explicitly highlight that motif-role fingerprints are elemental to several popular metrics for quantifying the subgraph structure of directed complex networks, including motif distributions, directed clustering coefficient, and transitivity. The relationships between each of these metrics and motif-role fingerprints also suggest new subtypes of directed clustering coefficients and transitivities. Our results have potential utility in analyzing directed synaptic networks constructed from neuronal connectome data, such as in terms of centrality. Other potential applications include anomaly detection in networks, identification of similar networks and identification of similar nodes within networks. Matlab code for calculating all stated metrics following calculation of functional motif-role fingerprints is provided as S1 Matlab File.

  8. Modern methods of sample preparation for GC analysis

    OpenAIRE

    de Koning; Janssen, H.-G.; Brinkman, U.A.T.

    2009-01-01

    Today, a wide variety of techniques is available for the preparation of (semi-) solid, liquid and gaseous samples, prior to their instrumental analysis by means of capillary gas chromatography (GC) or, increasingly, comprehensive two-dimensional GC (GC × GC). In the past two decades, a large number of ‘modern’ sample-preparation techniques has been introduced, which have partly superseded their ‘classical’ counterparts. These novel techniques include off-line and on-line (sometimes semi- or f...

  9. Identification of novel conserved functional motifs across most Influenza A viral strains

    Directory of Open Access Journals (Sweden)

    El-Azab Iman

    2011-01-01

    Full Text Available Abstract Background Influenza A virus poses a continuous threat to global public health. Design of novel universal drugs and vaccine requires a careful analysis of different strains of Influenza A viral genome from diverse hosts and subtypes. We performed a systematic in silico analysis of Influenza A viral segments of all available Influenza A viral strains and subtypes and grouped them based on host, subtype, and years isolated, and through multiple sequence alignments we extrapolated conserved regions, motifs, and accessible regions for functional mapping and annotation. Results Across all species and strains 87 highly conserved regions (conservation percentage > = 90% and 19 functional motifs (conservation percentage = 100% were found in PB2, PB1, PA, NP, M, and NS segments. The conservation percentage of these segments ranged between 94 - 98% in human strains (the most conserved, 85 - 93% in swine strains (the most variable, and 91 - 94% in avian strains. The most conserved segment was different in each host (PB1 for human strains, NS for avian strains, and M for swine strains. Target accessibility prediction yielded 324 accessible regions, with a single stranded probability > 0.5, of which 78 coincided with conserved regions. Some of the interesting annotations in these regions included sites for protein-protein interactions, the RNA binding groove, and the proton ion channel. Conclusions The influenza virus has evolved to adapt to its host through variations in the GC content and conservation percentage of the conserved regions. Nineteen universal conserved functional motifs were discovered, of which some were accessible regions with interesting biological functions. These regions will serve as a foundation for universal drug targets as well as universal vaccine design.

  10. EXTREME: an online EM algorithm for motif discovery

    Science.gov (United States)

    Quang, Daniel; Xie, Xiaohui

    2014-01-01

    Motivation: Identifying regulatory elements is a fundamental problem in the field of gene transcription. Motif discovery—the task of identifying the sequence preference of transcription factor proteins, which bind to these elements—is an important step in this challenge. MEME is a popular motif discovery algorithm. Unfortunately, MEME’s running time scales poorly with the size of the dataset. Experiments such as ChIP-Seq and DNase-Seq are providing a rich amount of information on the binding preference of transcription factors. MEME cannot discover motifs in data from these experiments in a practical amount of time without a compromising strategy such as discarding a majority of the sequences. Results: We present EXTREME, a motif discovery algorithm designed to find DNA-binding motifs in ChIP-Seq and DNase-Seq data. Unlike MEME, which uses the expectation-maximization algorithm for motif discovery, EXTREME uses the online expectation-maximization algorithm to discover motifs. EXTREME can discover motifs in large datasets in a practical amount of time without discarding any sequences. Using EXTREME on ChIP-Seq and DNase-Seq data, we discover many motifs, including some novel and infrequent motifs that can only be discovered by using the entire dataset. Conservation analysis of one of these novel infrequent motifs confirms that it is evolutionarily conserved and possibly functional. Availability and implementation: All source code is available at the Github repository http://github.com/uci-cbcl/EXTREME. Contact: xhx@ics.uci.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24532725

  11. Encoded expansion: an efficient algorithm to discover identical string motifs.

    Directory of Open Access Journals (Sweden)

    Aqil M Azmi

    Full Text Available A major task in computational biology is the discovery of short recurring string patterns known as motifs. Most of the schemes to discover motifs are either stochastic or combinatorial in nature. Stochastic approaches do not guarantee finding the correct motifs, while the combinatorial schemes tend to have an exponential time complexity with respect to motif length. To alleviate the cost, the combinatorial approach exploits dynamic data structures such as trees or graphs. Recently (Karci (2009 Efficient automatic exact motif discovery algorithms for biological sequences, Expert Systems with Applications 36:7952-7963 devised a deterministic algorithm that finds all the identical copies of string motifs of all sizes [Formula: see text] in theoretical time complexity of [Formula: see text] and a space complexity of [Formula: see text] where [Formula: see text] is the length of the input sequence and [Formula: see text] is the length of the longest possible string motif. In this paper, we present a significant improvement on Karci's original algorithm. The algorithm that we propose reports all identical string motifs of sizes [Formula: see text] that occur at least [Formula: see text] times. Our algorithm starts with string motifs of size 2, and at each iteration it expands the candidate string motifs by one symbol throwing out those that occur less than [Formula: see text] times in the entire input sequence. We use a simple array and data encoding to achieve theoretical worst-case time complexity of [Formula: see text] and a space complexity of [Formula: see text] Encoding of the substrings can speed up the process of comparison between string motifs. Experimental results on random and real biological sequences confirm that our algorithm has indeed a linear time complexity and it is more scalable in terms of sequence length than the existing algorithms.

  12. The limits of de novo DNA motif discovery.

    Directory of Open Access Journals (Sweden)

    David Simcha

    Full Text Available A major challenge in molecular biology is reverse-engineering the cis-regulatory logic that plays a major role in the control of gene expression. This program includes searching through DNA sequences to identify "motifs" that serve as the binding sites for transcription factors or, more generally, are predictive of gene expression across cellular conditions. Several approaches have been proposed for de novo motif discovery-searching sequences without prior knowledge of binding sites or nucleotide patterns. However, unbiased validation is not straightforward. We consider two approaches to unbiased validation of discovered motifs: testing the statistical significance of a motif using a DNA "background" sequence model to represent the null hypothesis and measuring performance in predicting membership in gene clusters. We demonstrate that the background models typically used are "too null," resulting in overly optimistic assessments of significance, and argue that performance in predicting TF binding or expression patterns from DNA motifs should be assessed by held-out data, as in predictive learning. Applying this criterion to common motif discovery methods resulted in universally poor performance, although there is a marked improvement when motifs are statistically significant against real background sequences. Moreover, on synthetic data where "ground truth" is known, discriminative performance of all algorithms is far below the theoretical upper bound, with pronounced "over-fitting" in training. A key conclusion from this work is that the failure of de novo discovery approaches to accurately identify motifs is basically due to statistical intractability resulting from the fixed size of co-regulated gene clusters, and thus such failures do not necessarily provide evidence that unfound motifs are not active biologically. Consequently, the use of prior knowledge to enhance motif discovery is not just advantageous but necessary. An implementation of

  13. Observability of multivariate differential embeddings

    Energy Technology Data Exchange (ETDEWEB)

    Aguirre, Luis Antonio [Laboratorio de Modelagem, Analise e Controle de Sistemas Nao Lineares, Departamento de Engenharia Eletronica, Universidade Federeal de Minas Gerais, Av. Antonio Carlos 6627, 31270-901 Belo Horizonte, MG (Brazil); Letellier, Christophe [Universite de Rouen-CORIA UMR 6614, Av. de l' Universite, BP 12, F-76801 Saint-Etienne du Rouvray Cedex (France)

    2005-07-15

    The present paper extends some results recently developed for the analysis of observability in nonlinear dynamical systems. The aim of the paper is to address the problem of embedding an attractor using more than one observable. A multivariate nonlinear observability matrix is proposed which includes the monovariable nonlinear and linear observability matrices as particular cases. Using the developed framework and a number of worked examples, it is shown that the choice of embedding coordinates is critical. Moreover, in some cases, to reconstruct the dynamics using more than one observable could be worse than to reconstruct using a scalar measurement. Finally, using the developed framework it is shown that increasing the embedding dimension, observability problems diminish and can even be eliminated. This seems to be a physically meaningful interpretation of the Takens embedding theorem.

  14. Embedded Systems Design: Optimization Challenges

    DEFF Research Database (Denmark)

    Pop, Paul

    2005-01-01

    of designing such systems is becoming increasingly important and difficult at the same time. New automated design optimization techniques are needed, which are able to: successfully manage the complexity of embedded systems, meet the constraints imposed by the application domain, shorten the time...... in use has become larger than the number of humans on the planet. The complexity of embedded systems is growing at a very high pace and the constraints in terms of functionality, performance, low energy consumption, reliability, cost and time-to-market are getting tighter. Therefore, the task......-to-market, and reduce development and manufacturing costs. In this paper, the author introduces several embedded systems design problems, and shows how they can be formulated as optimization problems. Solving such challenging design optimization problems are the key to the success of the embedded systems design...

  15. Visualizing spacetimes via embedding diagrams

    CERN Document Server

    Hledik, Stanislav; Cipko, Alois

    2016-01-01

    It is hard to imagine curved spacetimes of General Relativity. A simple but powerful way how to achieve this is visualizing them via embedding diagrams of both ordinary geometry and optical reference geometry. They facilitate to gain an intuitive insight into the gravitational field rendered into a curved spacetime, and to assess the influence of parameters like electric charge and spin of a black hole, magnetic field or cosmological constant. Optical reference geometry and related inertial forces and their relationship to embedding diagrams are particularly useful for investigation of test particles motion. Embedding diagrams of static and spherically symmetric, or stationary and axially symmetric black-hole and naked-singularity spacetimes thus present a useful concept for intuitive understanding of these spacetimes' nature. We concentrate on general way of embedding into 3-dimensional Euclidean space, and give a set of illustrative examples.

  16. A three-dimensional RNA motif in Potato spindle tuber viroid mediates trafficking from palisade mesophyll to spongy mesophyll in Nicotiana benthamiana.

    Science.gov (United States)

    Takeda, Ryuta; Petrov, Anton I; Leontis, Neocles B; Ding, Biao

    2011-01-01

    Cell-to-cell trafficking of RNA is an emerging biological principle that integrates systemic gene regulation, viral infection, antiviral response, and cell-to-cell communication. A key mechanistic question is how an RNA is specifically selected for trafficking from one type of cell into another type. Here, we report the identification of an RNA motif in Potato spindle tuber viroid (PSTVd) required for trafficking from palisade mesophyll to spongy mesophyll in Nicotiana benthamiana leaves. This motif, called loop 6, has the sequence 5'-CGA-3'...5'-GAC-3' flanked on both sides by cis Watson-Crick G/C and G/U wobble base pairs. We present a three-dimensional (3D) structural model of loop 6 that specifies all non-Watson-Crick base pair interactions, derived by isostericity-based sequence comparisons with 3D RNA motifs from the RNA x-ray crystal structure database. The model is supported by available chemical modification patterns, natural sequence conservation/variations in PSTVd isolates and related species, and functional characterization of all possible mutants for each of the loop 6 base pairs. Our findings and approaches have broad implications for studying the 3D RNA structural motifs mediating trafficking of diverse RNA species across specific cellular boundaries and for studying the structure-function relationships of RNA motifs in other biological processes.

  17. Hardware Support for Embedded Java

    DEFF Research Database (Denmark)

    Schoeberl, Martin

    2012-01-01

    The general Java runtime environment is resource hungry and unfriendly for real-time systems. To reduce the resource consumption of Java in embedded systems, direct hardware support of the language is a valuable option. Furthermore, an implementation of the Java virtual machine in hardware enables...... worst-case execution time analysis of Java programs. This chapter gives an overview of current approaches to hardware support for embedded and real-time Java....

  18. A Foundation for Embedded Languages

    DEFF Research Database (Denmark)

    Rhiger, Morten

    2002-01-01

    Recent work on embedding object languages into Haskell use "phantom types" (i.e., parameterized types whose parameter does not occur on the right-hand side of the type definition) to ensure that the embedded object-language terms are simply typed. But is it a safe assumption that only simply...... be answered affirmatively for an idealized Haskell-like language and discuss to which extent Haskell can be used as a meta-language....

  19. A Foundation for Embedded Languages

    DEFF Research Database (Denmark)

    Rhiger, Morten

    2003-01-01

    Recent work on embedding object languages into Haskell use "phantom types" (i.e., parameterized types whose parameter does not occur on the right-hand side of the type definition) to ensure that the embedded object-language terms are simply typed. But is it a safe assumption that only simply...... be answered affirmatively for an idealized Haskell-like language and discuss to which extent Haskell can be used as a meta-language....

  20. Multilingual Word Embeddings using Multigraphs

    OpenAIRE

    Soricut, Radu; Ding, Nan

    2016-01-01

    We present a family of neural-network--inspired models for computing continuous word representations, specifically designed to exploit both monolingual and multilingual text. This framework allows us to perform unsupervised training of embeddings that exhibit higher accuracy on syntactic and semantic compositionality, as well as multilingual semantic similarity, compared to previous models trained in an unsupervised fashion. We also show that such multilingual embeddings, optimized for semant...

  1. Hardware Support for Embedded Java

    DEFF Research Database (Denmark)

    Schoeberl, Martin

    2012-01-01

    The general Java runtime environment is resource hungry and unfriendly for real-time systems. To reduce the resource consumption of Java in embedded systems, direct hardware support of the language is a valuable option. Furthermore, an implementation of the Java virtual machine in hardware enables...... worst-case execution time analysis of Java programs. This chapter gives an overview of current approaches to hardware support for embedded and real-time Java....

  2. Fresnel Lens with Embedded Vortices

    Directory of Open Access Journals (Sweden)

    Sunil Vyas

    2012-01-01

    Full Text Available Vortices of different charges are embedded in a wavefront that has quadratic phase variation, and the intensity distribution near the focal plane is studied. This method may be useful in realizing complicated beam profiles. We have experimentally demonstrated the generation of vortex arrays having integer as well as fractional topological charges that produce different intensity profiles at the focal plane. The phase variation realized on a spatial light modulator (SLM acts as a Fresnel lens with embedded vortices.

  3. Determination of phthalates in polymer materials - comparison of GC/MS and GC/ECD methods

    Directory of Open Access Journals (Sweden)

    Katarzyna Jaworek

    2013-01-01

    Full Text Available The paper presents two methods for determination of phthalates in polymer materials. The methods compared were gas chromatography combined with the mass spectrometry (GC/MS and gas chromatography with electron capture detector (GC/ECD. The GC/ECD technique was chosen for this comparison, because the ECD detector was one of few capable of detecting phthalates. In both cases the same procedure of sample preparation with ultrasonic extraction was applied. Overall recoveries were 76-100 % with relative of standard deviation (R.S.D. values in the range 0.6-19 %. The values of limit of detection (LOD for GC/MS method ranged from 3.46 µg mL- 1 to 10.10 µg mL- 1, depending on the determined phthalate, while in case of the GC/ECD method they were in the range from 2.97 µg mL- 1 to 4.29 µg mL- 1. The methods were applied for determination of: dimethyl phthalate, diethyl phthalate, di-n-butyl phthalate, benzyl butyl phthalate, bis(2-ethylhexyl phthalate, diisononyl phthalate, diisoocyl phthalate in polymer material. The seventeen kinds of samples were analyzed. Most of the materials selected for the analyses were made from polyethylene (PE, polyvinyl chloride (PVC and polystyrene (PS.

  4. Probing structural changes of self assembled i-motif DNA

    KAUST Repository

    Lee, Iljoon

    2015-01-01

    We report an i-motif structural probing system based on Thioflavin T (ThT) as a fluorescent sensor. This probe can discriminate the structural changes of RET and Rb i-motif sequences according to pH change. This journal is

  5. The effect of orthology and coregulation on detecting regulatory motifs.

    Directory of Open Access Journals (Sweden)

    Valerie Storms

    Full Text Available BACKGROUND: Computational de novo discovery of transcription factor binding sites is still a challenging problem. The growing number of sequenced genomes allows integrating orthology evidence with coregulation information when searching for motifs. Moreover, the more advanced motif detection algorithms explicitly model the phylogenetic relatedness between the orthologous input sequences and thus should be well adapted towards using orthologous information. In this study, we evaluated the conditions under which complementing coregulation with orthologous information improves motif detection for the class of probabilistic motif detection algorithms with an explicit evolutionary model. METHODOLOGY: We designed datasets (real and synthetic covering different degrees of coregulation and orthologous information to test how well Phylogibbs and Phylogenetic sampler, as representatives of the motif detection algorithms with evolutionary model performed as compared to MEME, a more classical motif detection algorithm that treats orthologs independently. RESULTS AND CONCLUSIONS: Under certain conditions detecting motifs in the combined coregulation-orthology space is indeed more efficient than using each space separately, but this is not always the case. Moreover, the difference in success rate between the advanced algorithms and MEME is still marginal. The success rate of motif detection depends on the complex interplay between the added information and the specificities of the applied algorithms. Insights in this relation provide information useful to both developers and users. All benchmark datasets are available at http://homes.esat.kuleuven.be/~kmarchal/Supplementary_Storms_Valerie_PlosONE.

  6. Motif Participation by Genes in E. coli Transcriptional Networks

    Directory of Open Access Journals (Sweden)

    Michael eMayo

    2012-09-01

    Full Text Available Motifs are patterns of recurring connections among the genes of genetic networks that occur more frequently than would be expected from randomized networks with the same degree sequence. Although the abundance of certain three-node motifs, such as the feed-forward loop, is positively correlated with a networks’ ability to tolerate moderate disruptions to gene expression, little is known regarding the connectivity of individual genes participating in multiple motifs. Using the transcriptional network of the bacterium Escherichia coli, we investigate this feature by reconstructing the distribution of genes participating in feed-forward loop motifs from its largest connected network component. We contrast these motif participation distributions with those obtained from model networks built using the preferential attachment mechanism employed by many biological and man-made networks. We report that, although some of these model networks support a motif participation distribution that appears qualitatively similar to that obtained from the bacterium Escherichia coli, the probability for a node to support a feed-forward loop motif may instead be strongly influenced by only a few master transcriptional regulators within the network. From these analyses we conclude that such master regulators may be a crucial ingredient to describe coupling among feed-forward loop motifs in transcriptional regulatory networks.

  7. Discovering large network motifs from a complex biological network

    Energy Technology Data Exchange (ETDEWEB)

    Terada, Aika; Sese, Jun, E-mail: terada@sel.is.ocha.ac.j, E-mail: sesejun@is.ocha.ac.j [Department of Computer Science, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610 (Japan)

    2009-12-01

    Graph structures representing relationships between entries have been studied in statistical analysis, and the results of these studies have been applied to biological networks, whose nodes and edges represent proteins and the relationships between them, respectively. Most of the studies have focused on only graph structures such as scale-free properties and cliques, but the relationships between nodes are also important features since most of the proteins perform their functions by connecting to other proteins. In order to determine such relationships, the problem of network motif discovery has been addressed; network motifs are frequently appearing graph structures in a given graph. However, the methods for network motif discovery are highly restrictive for the application to biological network because they can only be used to find small network motifs or they do not consider noise and uncertainty in observations. In this study, we introduce a new index to measure network motifs called AR index and develop a novel algorithm called ARIANA for finding large motifs even when the network has noise. Experiments using a synthetic network verify that our method can find better network motifs than an existing algorithm. By applying ARIANA to a real complex biological network, we find network motifs associated with regulations of start time of cell functions and generation of cell energies and discover that the cell cycle proteins can be categorized into two different groups.

  8. Aztec, Incan and Mayan Motifs...Lead to Distinctive Designs.

    Science.gov (United States)

    Shields, Joanne

    2001-01-01

    Describes an art project for seventh-grade students in which they choose motifs based on Incan, Aztec, and Mayan Indian materials to incorporate into two-dimensional designs. Explains that the activity objective is to create a unified, balanced and pleasing composition using a minimum of three motifs. (CMK)

  9. MotifCombinator: a web-based tool to search for combinations of cis-regulatory motifs

    Directory of Open Access Journals (Sweden)

    Tsunoda Tatsuhiko

    2007-03-01

    Full Text Available Abstract Background A combination of multiple types of transcription factors and cis-regulatory elements is often required for gene expression in eukaryotes, and the combinatorial regulation confers specific gene expression to tissues or environments. To reveal the combinatorial regulation, computational methods are developed that efficiently infer combinations of cis-regulatory motifs that are important for gene expression as measured by DNA microarrays. One promising type of computational method is to utilize regression analysis between expression levels and scores of motifs in input sequences. This type takes full advantage of information on expression levels because it does not require that the expression level of each gene be dichotomized according to whether or not it reaches a certain threshold level. However, there is no web-based tool that employs regression methods to systematically search for motif combinations and that practically handles combinations of more than two or three motifs. Results We here introduced MotifCombinator, an online tool with a user-friendly interface, to systematically search for combinations composed of any number of motifs based on regression methods. The tool utilizes well-known regression methods (the multivariate linear regression, the multivariate adaptive regression spline or MARS, and the multivariate logistic regression method for this purpose, and uses the genetic algorithm to search for combinations composed of any desired number of motifs. The visualization systems in this tool help users to intuitively grasp the process of the combination search, and the backup system allows users to easily stop and restart calculations that are expected to require large computational time. This tool also provides preparatory steps needed for systematic combination search – i.e., selecting single motifs to constitute combinations and cutting out redundant similar motifs based on clustering analysis. Conclusion

  10. Identification of sequence motifs significantly associated with antisense activity

    Directory of Open Access Journals (Sweden)

    Peek Andrew S

    2007-06-01

    Full Text Available Abstract Background Predicting the suppression activity of antisense oligonucleotide sequences is the main goal of the rational design of nucleic acids. To create an effective predictive model, it is important to know what properties of an oligonucleotide sequence associate significantly with antisense activity. Also, for the model to be efficient we must know what properties do not associate significantly and can be omitted from the model. This paper will discuss the results of a randomization procedure to find motifs that associate significantly with either high or low antisense suppression activity, analysis of their properties, as well as the results of support vector machine modelling using these significant motifs as features. Results We discovered 155 motifs that associate significantly with high antisense suppression activity and 202 motifs that associate significantly with low suppression activity. The motifs range in length from 2 to 5 bases, contain several motifs that have been previously discovered as associating highly with antisense activity, and have thermodynamic properties consistent with previous work associating thermodynamic properties of sequences with their antisense activity. Statistical analysis revealed no correlation between a motif's position within an antisense sequence and that sequences antisense activity. Also, many significant motifs existed as subwords of other significant motifs. Support vector regression experiments indicated that the feature set of significant motifs increased correlation compared to all possible motifs as well as several subsets of the significant motifs. Conclusion The thermodynamic properties of the significantly associated motifs support existing data correlating the thermodynamic properties of the antisense oligonucleotide with antisense efficiency, reinforcing our hypothesis that antisense suppression is strongly associated with probe/target thermodynamics, as there are no enzymatic

  11. Dynamic motifs of strategies in prisoner's dilemma games

    Science.gov (United States)

    Kim, Young Jin; Roh, Myungkyoon; Jeong, Seon-Young; Son, Seung-Woo

    2014-12-01

    We investigate the win-lose relations between strategies of iterated prisoner's dilemma games by using a directed network concept to display the replicator dynamics results. In the giant strongly-connected component of the win/lose network, we find win-lose circulations similar to rock-paper-scissors and analyze the fixed point and its stability. Applying the network motif concept, we introduce dynamic motifs, which describe the population dynamics relations among the three strategies. Through exact enumeration, we find 22 dynamic motifs and display their phase portraits. Visualization using directed networks and motif analysis is a useful method to make complex dynamic behavior simple in order to understand it more intuitively. Dynamic motifs can be building blocks for dynamic behavior among strategies when they are applied to other types of games.

  12. Dynamic Motifs of Strategies in Prisoner's Dilemma Games

    CERN Document Server

    Kim, Young Jin; Jeong, Seon-Young; Son, Seung-Woo

    2014-01-01

    We investigate the win-lose relations between strategies of iterated prisoner's dilemma games by using a directed network concept to display the replicator dynamics results. In the giant strongly-connected component of the win/lose network, we find win-lose circulations similar to rock-paper-scissors and analyze the fixed point and its stability. Applying the network motif concept, we introduce dynamic motifs, which describe the population dynamics relations among the three strategies. Through exact enumeration, we find 22 dynamic motifs and display their phase portraits. Visualization using directed networks and motif analysis is a useful method to make complex dynamic behavior simple in order to understand it more intuitively. Dynamic motifs can be building blocks for dynamic behavior among strategies when they are applied to other types of games.

  13. An algorithm for motif-based network design

    CERN Document Server

    Mäki-Marttunen, Tuomo

    2016-01-01

    A determinant property of the structure of a biological network is the distribution of local connectivity patterns, i.e., network motifs. In this work, a method for creating directed, unweighted networks while promoting a certain combination of motifs is presented. This motif-based network algorithm starts with an empty graph and randomly connects the nodes by advancing or discouraging the formation of chosen motifs. The in- or out-degree distribution of the generated networks can be explicitly chosen. The algorithm is shown to perform well in producing networks with high occurrences of the targeted motifs, both ones consisting of 3 nodes as well as ones consisting of 4 nodes. Moreover, the algorithm can also be tuned to bring about global network characteristics found in many natural networks, such as small-worldness and modularity.

  14. Gc globulin as a diagnostic and prognostic marker in horses

    DEFF Research Database (Denmark)

    Pihl, Tina Holberg

    Group specific (Gc) globulin also known as vitamin D-binding protein is part of the extracellular actin-scavenging system that removes actin from the circulation. Actin is an intracellular structural protein, which is released to blood in patients with tissue injury and cell death. Circulating...... can prevent development of shock and thereby increase survival chances. The in vivo toxicity of Gc-globulin infusion is currently being investigated in horses and other species. Gc-globulin has been demonstrated in horse plasma and its structure closely resembles that of human Gc-globulin. Gc...

  15. Choosing between GC FTIR and GC MS spectra for an efficient intelligent identification of illicit amphetamines

    Science.gov (United States)

    Gosav, S.; Dinica, R.; Praisler, M.

    2008-09-01

    In this paper we are presenting a comparative analysis between several expert systems built for the identification of illicit amphetamines based on their GC-FTIR and GC-MS spectra. The systems were built using Artificial Neural Networks (ANNs), and are dedicated to the recognition of amphetamines. Structure-activity relationships are incorporated into the knowledge base, allowing the systems to identify the amphetamines according to their toxicological activity (stimulant or hallucinogenic). The results show that GC-FTIR data are much more relevant for the efficiency of the expert systems, probably due to the fact that these spectra constitute a "fingerprint" of the molecular structures. We are also presenting a spectroscopic analysis in order to evaluate the relevance of each type of input variable (absorption and abundance) on which the recognition of an unknown sample is based.

  16. Automatic annotation of protein motif function with Gene Ontology terms

    Directory of Open Access Journals (Sweden)

    Gopalakrishnan Vanathi

    2004-09-01

    Full Text Available Abstract Background Conserved protein sequence motifs are short stretches of amino acid sequence patterns that potentially encode the function of proteins. Several sequence pattern searching algorithms and programs exist foridentifying candidate protein motifs at the whole genome level. However, amuch needed and importanttask is to determine the functions of the newly identified protein motifs. The Gene Ontology (GO project is an endeavor to annotate the function of genes or protein sequences with terms from a dynamic, controlled vocabulary and these annotations serve well as a knowledge base. Results This paperpresents methods to mine the GO knowledge base and use the association between the GO terms assigned to a sequence and the motifs matched by the same sequence as evidence for predicting the functions of novel protein motifs automatically. The task of assigning GO terms to protein motifsis viewed as both a binary classification and information retrieval problem, where PROSITE motifs are used as samples for mode training and functional prediction. The mutual information of a motif and aGO term association isfound to be a very useful feature. We take advantageof the known motifs to train a logistic regression classifier, which allows us to combine mutual information with other frequency-based features and obtain a probability of correctassociation. The trained logistic regression model has intuitively meaningful and logically plausible parameter values, and performs very well empirically according to our evaluation criteria. Conclusions In this research, different methods for automatic annotation of protein motifs have been investigated. Empirical result demonstrated that the methods have a great potential for detecting and augmenting information about thefunctions of newly discovered candidate protein motifs.

  17. Analysis of intra-genomic GC content homogeneity within prokaryotes

    Directory of Open Access Journals (Sweden)

    Bohlin Jon

    2010-08-01

    Full Text Available Abstract Background Bacterial genomes possess varying GC content (total guanines (Gs and cytosines (Cs per total of the four bases within the genome but within a given genome, GC content can vary locally along the chromosome, with some regions significantly more or less GC rich than on average. We have examined how the GC content varies within microbial genomes to assess whether this property can be associated with certain biological functions related to the organism's environment and phylogeny. We utilize a new quantity GCVAR, the intra-genomic GC content variability with respect to the average GC content of the total genome. A low GCVAR indicates intra-genomic GC homogeneity and high GCVAR heterogeneity. Results The regression analyses indicated that GCVAR was significantly associated with domain (i.e. archaea or bacteria, phylum, and oxygen requirement. GCVAR was significantly higher among anaerobes than both aerobic and facultative microbes. Although an association has previously been found between mean genomic GC content and oxygen requirement, our analysis suggests that no such association exits when phylogenetic bias is accounted for. A significant association between GCVAR and mean GC content was also found but appears to be non-linear and varies greatly among phyla. Conclusions Our findings show that GCVAR is linked with oxygen requirement, while mean genomic GC content is not. We therefore suggest that GCVAR should be used as a complement to mean GC content.

  18. Analysis of Turkish lignite tar by coupled LC/GC, GC/MS, and capillary SFC

    Energy Technology Data Exchange (ETDEWEB)

    Davies, I.L.; Raynor, M.W.; Urwin, D.J.; Bartle, K.D.; Tolay, M.; Ekinci, E.; Schwartz, H.E.

    1988-11-01

    This work describes the analysis of a pyrolysis product of a lignite sample obtained from the Turkish Goynuk reserve. The aliphatic, aromatic and polar compounds present in the tar are separated and identified by various chromatographic techniques: capillary gas chromatography/mass spectrometry (GC/MS), on-line high performance microbore liquid chromatography/capillary gas chromatography (LC/GC) and capillary supercritical fluid chromatography (SFC). The suitability of each technique for this particular application is discussed, and semi-quantitative results are presented for the major components detected. 35 refs., 6 figs., 3 tabs.

  19. Accumulation of GC donor splice signals in mammals

    Directory of Open Access Journals (Sweden)

    Koonin Eugene V

    2008-07-01

    Full Text Available Abstract The GT dinucleotide in the first two intron positions is the most conserved element of the U2 donor splice signals. However, in a small fraction of donor sites, GT is replaced by GC. A substantial enrichment of GC in donor sites of alternatively spliced genes has been observed previously in human, nematode and Arabidopsis, suggesting that GC signals are important for regulation of alternative splicing. We used parsimony analysis to reconstruct evolution of donor splice sites and inferred 298 GT > GC conversion events compared to 40 GC > GT conversion events in primate and rodent genomes. Thus, there was substantive accumulation of GC donor splice sites during the evolution of mammals. Accumulation of GC sites might have been driven by selection for alternative splicing. Reviewers This article was reviewed by Jerzy Jurka and Anton Nekrutenko. For the full reviews, please go to the Reviewers' Reports section.

  20. De Novo Regulatory Motif Discovery Identifies Significant Motifs in Promoters of Five Classes of Plant Dehydrin Genes.

    Science.gov (United States)

    Zolotarov, Yevgen; Strömvik, Martina

    2015-01-01

    Plants accumulate dehydrins in response to osmotic stresses. Dehydrins are divided into five different classes, which are thought to be regulated in different manners. To better understand differences in transcriptional regulation of the five dehydrin classes, de novo motif discovery was performed on 350 dehydrin promoter sequences from a total of 51 plant genomes. Overrepresented motifs were identified in the promoters of five dehydrin classes. The Kn dehydrin promoters contain motifs linked with meristem specific expression, as well as motifs linked with cold/dehydration and abscisic acid response. KS dehydrin promoters contain a motif with a GATA core. SKn and YnSKn dehydrin promoters contain motifs that match elements connected with cold/dehydration, abscisic acid and light response. YnKn dehydrin promoters contain motifs that match abscisic acid and light response elements, but not cold/dehydration response elements. Conserved promoter motifs are present in the dehydrin classes and across different plant lineages, indicating that dehydrin gene regulation is likely also conserved.

  1. Motif-specific sampling of phosphoproteomes.

    Science.gov (United States)

    Ruse, Cristian I; McClatchy, Daniel B; Lu, Bingwen; Cociorva, Daniel; Motoyama, Akira; Park, Sung Kyu; Yates, John R

    2008-05-01

    Phosphoproteomics, the targeted study of a subfraction of the proteome which is modified by phosphorylation, has become an indispensable tool to study cell signaling dynamics. We described a methodology that linked phosphoproteome and proteome analysis based on Ba2+ binding properties of amino acids. This technology selected motif-specific phosphopeptides independent of the system under analysis. MudPIT (Multidimensional Identification Technology) identified 1037 precipitated phosphopeptides from as little as 250 microg of proteins. To extend coverage of the phosphoproteome, we sampled the nuclear extract of HeLa cells with three values of Ba2+ ions molarity. The presence of more than 70% of identified phosphoproteins was further substantiated by their nonmodified peptides. Upon isoproterenol stimulation of HEK cells, we identified an increasing number of phosphoproteins from MAPK cascades and AKAP signaling hubs. We quantified changes in both protein and phosphorylation levels of 197 phosphoproteins including a critical kinase, MAPK1. Integration of differential phosphorylation of MAPK1 with knowledge bases constructed modules that correlated well with its role as node in cross-talk of canonical pathways.

  2. Tripartite motif 32 prevents pathological cardiac hypertrophy.

    Science.gov (United States)

    Chen, Lijuan; Huang, Jia; Ji, Yanxiao; Zhang, Xiaojing; Wang, Pixiao; Deng, Keqiong; Jiang, Xi; Ma, Genshan; Li, Hongliang

    2016-05-01

    TRIM32 (tripartite motif 32) is widely accepted to be an E3 ligase that interacts with and eventually ubiquitylates multiple substrates. TRIM32 mutants have been associated with LGMD-2H (limb girdle muscular dystrophy 2H). However, whether TRIM32 is involved in cardiac hypertrophy induced by biomechanical stresses and neurohumoral mediators remains unclear. We generated mice and isolated NRCMs (neonatal rat cardiomyocytes) that overexpressed or were deficient in TRIM32 to investigate the effect of TRIM32 on AB (aortic banding) or AngII (angiotensin II)-mediated cardiac hypertrophy. Echocardiography and both pathological and molecular analyses were used to determine the extent of cardiac hypertrophy and subsequent fibrosis. Our results showed that overexpression of TRIM32 in the heart significantly alleviated the hypertrophic response induced by pressure overload, whereas TRIM32 deficiency dramatically aggravated pathological cardiac remodelling. Similar results were also found in cultured NRCMs incubated with AngII. Mechanistically, the present study suggests that TRIM32 exerts cardioprotective action by interruption of Akt- but not MAPK (mitogen-dependent protein kinase)-dependent signalling pathways. Additionally, inactivation of Akt by LY294002 offset the exacerbated hypertrophic response induced by AB in TRIM32-deficient mice. In conclusion, the present study indicates that TRIM32 plays a protective role in AB-induced pathological cardiac remodelling by blocking Akt-dependent signalling. Therefore TRIM32 could be a novel therapeutic target for the prevention of cardiac hypertrophy and heart failure. © 2016 The Author(s).

  3. HOXB9 induction of mesenchymal-to-epithelial transition in gastric carcinoma is negatively regulated by its hexapeptide motif

    Science.gov (United States)

    He, Changyu; Zhang, Baogui; Zhang, Jun; Liu, Bingya; Zeng, Naiyan; Zhu, Zhenggang

    2015-01-01

    HOXB9, a transcription factor, plays an important role in development. While HOXB9 has been implicated in tumorigenesis and metastasis, its mechanisms are variable and its role in gastric carcinoma (GC) remains unclear. In the present study, we demonstrated that the expression of HOXB9 decreased in gastric carcinoma and was associated with malignancy and metastasis. Re-expression of HOXB9 in gastric cell lines resulted in the suppression of cell proliferation, migration, and invasion, which was accompanied by the induction of mesenchymal-to-epithelial transition (MET). Comparative sequence analysis and examination of a HOXB9 structural model indicated that three sites might possibly be involved in MET regulation. The in vitro study of HOXB9 mutants showed that these were unable to inhibit MET induction. However, when overexpressing a HOXB9 mutant lacking the hexapeptide motif, a more potent MET induction and tumor suppression was observed compared to that of the wild-type, indicating that the presence of the hexapeptide motif reduced HOXB9 MET induction and tumor suppression activity. Therefore, the results of the present study suggested that HOXB9 is a tumor suppressor in gastric carcinoma, and its activity was controlled by different regulatory mechanisms such as the hexapeptide motif as a “brake” in this case. The results of these regulatory effects could lead to either oncogenic or tumor suppressive roles of HOXB9, depending on the context of the particular type of cancer involved. PMID:26536658

  4. Embedded Linux projects using Yocto project cookbook

    CERN Document Server

    González, Alex

    2015-01-01

    If you are an embedded developer learning about embedded Linux with some experience with the Yocto project, this book is the ideal way to become proficient and broaden your knowledge with examples that are immediately applicable to your embedded developments. Experienced embedded Yocto developers will find new insight into working methodologies and ARM specific development competence.

  5. Recurrent Motifs: The Fiction of Time in José Manuel Caballero Bonald’s Poetry

    Directory of Open Access Journals (Sweden)

    Olga Guadalupe Mella

    2012-02-01

    Full Text Available Time, memory and forgetfulness are recurring motifs in the work of the poets of the generation of the 50’s or generación del medio siglo. This article focuses on José Manuel Caballero Bonald’s personal revision of the concept of time, one of the most universal poetic themes. The poet takes his rhetoric from the Baroque tradition to re-visit ideas of time and provide a reinterpretation that contrasts sharply with that of contemporary poets while laying down a clear thread of intertextuality with the literary culture of the past. For his meditation on time, the poet's legacy results in a unique amalgam of Borges’ motifs and the Baroque worldview. From Quevedo’s intertext, the author’s new Baroque style blends poetic culteranismo and conceptismo with lexical precision to result in a lyrical universe that reconciles opposites, a poetic writing more nourished by knowledge than by experience, and a form of expression strongly embedded in the formal and conceptual systems of the Baroque.

  6. Trusted computing for embedded systems

    CERN Document Server

    Soudris, Dimitrios; Anagnostopoulos, Iraklis

    2015-01-01

    This book describes the state-of-the-art in trusted computing for embedded systems. It shows how a variety of security and trusted computing problems are addressed currently and what solutions are expected to emerge in the coming years. The discussion focuses on attacks aimed at hardware and software for embedded systems, and the authors describe specific solutions to create security features. Case studies are used to present new techniques designed as industrial security solutions. Coverage includes development of tamper resistant hardware and firmware mechanisms for lightweight embedded devices, as well as those serving as security anchors for embedded platforms required by applications such as smart power grids, smart networked and home appliances, environmental and infrastructure sensor networks, etc. ·         Enables readers to address a variety of security threats to embedded hardware and software; ·         Describes design of secure wireless sensor networks, to address secure authen...

  7. MEME: discovering and analyzing DNA and protein sequence motifs.

    Science.gov (United States)

    Bailey, Timothy L; Williams, Nadya; Misleh, Chris; Li, Wilfred W

    2006-07-01

    MEME (Multiple EM for Motif Elicitation) is one of the most widely used tools for searching for novel 'signals' in sets of biological sequences. Applications include the discovery of new transcription factor binding sites and protein domains. MEME works by searching for repeated, ungapped sequence patterns that occur in the DNA or protein sequences provided by the user. Users can perform MEME searches via the web server hosted by the National Biomedical Computation Resource (http://meme.nbcr.net) and several mirror sites. Through the same web server, users can also access the Motif Alignment and Search Tool to search sequence databases for matches to motifs encoded in several popular formats. By clicking on buttons in the MEME output, users can compare the motifs discovered in their input sequences with databases of known motifs, search sequence databases for matches to the motifs and display the motifs in various formats. This article describes the freely accessible web server and its architecture, and discusses ways to use MEME effectively to find new sequence patterns in biological sequences and analyze their significance.

  8. Profile-based short linear protein motif discovery

    Science.gov (United States)

    2012-01-01

    Background Short linear protein motifs are attracting increasing attention as functionally independent sites, typically 3–10 amino acids in length that are enriched in disordered regions of proteins. Multiple methods have recently been proposed to discover over-represented motifs within a set of proteins based on simple regular expressions. Here, we extend these approaches to profile-based methods, which provide a richer motif representation. Results The profile motif discovery method MEME performed relatively poorly for motifs in disordered regions of proteins. However, when we applied evolutionary weighting to account for redundancy amongst homologous proteins, and masked out poorly conserved regions of disordered proteins, the performance of MEME is equivalent to that of regular expression methods. However, the two approaches returned different subsets within both a benchmark dataset, and a more realistic discovery dataset. Conclusions Profile-based motif discovery methods complement regular expression based methods. Whilst profile-based methods are computationally more intensive, they are likely to discover motifs currently overlooked by regular expression methods. PMID:22607209

  9. Profile-based short linear protein motif discovery

    Directory of Open Access Journals (Sweden)

    Haslam Niall J

    2012-05-01

    Full Text Available Abstract Background Short linear protein motifs are attracting increasing attention as functionally independent sites, typically 3–10 amino acids in length that are enriched in disordered regions of proteins. Multiple methods have recently been proposed to discover over-represented motifs within a set of proteins based on simple regular expressions. Here, we extend these approaches to profile-based methods, which provide a richer motif representation. Results The profile motif discovery method MEME performed relatively poorly for motifs in disordered regions of proteins. However, when we applied evolutionary weighting to account for redundancy amongst homologous proteins, and masked out poorly conserved regions of disordered proteins, the performance of MEME is equivalent to that of regular expression methods. However, the two approaches returned different subsets within both a benchmark dataset, and a more realistic discovery dataset. Conclusions Profile-based motif discovery methods complement regular expression based methods. Whilst profile-based methods are computationally more intensive, they are likely to discover motifs currently overlooked by regular expression methods.

  10. Computational analyses of synergism in small molecular network motifs.

    Directory of Open Access Journals (Sweden)

    Yili Zhang

    2014-03-01

    Full Text Available Cellular functions and responses to stimuli are controlled by complex regulatory networks that comprise a large diversity of molecular components and their interactions. However, achieving an intuitive understanding of the dynamical properties and responses to stimuli of these networks is hampered by their large scale and complexity. To address this issue, analyses of regulatory networks often focus on reduced models that depict distinct, reoccurring connectivity patterns referred to as motifs. Previous modeling studies have begun to characterize the dynamics of small motifs, and to describe ways in which variations in parameters affect their responses to stimuli. The present study investigates how variations in pairs of parameters affect responses in a series of ten common network motifs, identifying concurrent variations that act synergistically (or antagonistically to alter the responses of the motifs to stimuli. Synergism (or antagonism was quantified using degrees of nonlinear blending and additive synergism. Simulations identified concurrent variations that maximized synergism, and examined the ways in which it was affected by stimulus protocols and the architecture of a motif. Only a subset of architectures exhibited synergism following paired changes in parameters. The approach was then applied to a model describing interlocked feedback loops governing the synthesis of the CREB1 and CREB2 transcription factors. The effects of motifs on synergism for this biologically realistic model were consistent with those for the abstract models of single motifs. These results have implications for the rational design of combination drug therapies with the potential for synergistic interactions.

  11. Triadic motifs in the dependence networks of virtual societies

    Science.gov (United States)

    Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Zhou, Wei-Xing

    2014-06-01

    In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (M9) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks is only slightly larger than average. Our findings show that avatars' social status plays an important role in the formation of triadic motifs.

  12. Strategi Mengenali Motif Khas Kain Tenun Cual Bangka Dengan AHP

    Directory of Open Access Journals (Sweden)

    Hilyah Magdalena

    2016-12-01

    Full Text Available Woven fabric cual Bangka currently used as one of the identity of community pride in Bangka Belitung Islands. The specificity of this fart cual fabric interesting to study because of the motives that have similarities with songket palembang. Woven fabric cual Bangka and Palembang songket cloth looks similar because the same cloth-making techniques - both using techniques sungkit. The purpose of this research is how to recognize a particular motif woven fabric cual fart. This research using Analytical Hierarchy Process ( AHP to classify some specific motifs that exist in woven fabric cual fart. Experts in the field of woven fabric cual is to inform you that the woven fabric cual farts have tabled motif, motifs or patterns, motifs fabric edge, motif gold thread, fabric base material, as well as the specific color. The research involved four experts that the results of the questionnaires is processed by software Expert Choice 2000. The results showed that the main peculiarity of the woven fabric cual fart is in a pattern or motif with a percentage of 31.5, and is the chosen alternative product is songket with a percentage of 25.4.

  13. Electrochemical impedance studies of methanol oxidation on GC/Ni and GC/NiCu electrode

    Energy Technology Data Exchange (ETDEWEB)

    Danaee, I.; Jafarian, M.; Forouzandeh, F.; Mahjani, M.G. [Department of Chemistry, K.N. Toosi University of Technology, PO Box 15875-4416, Tehran (Iran); Gobal, F. [Department of Chemistry, Sharif University of Technology, PO Box 11365-9516, Tehran (Iran)

    2009-01-15

    The electro-oxidation of methanol on nickel and nickel-copper alloy modified glassy carbon electrodes (GC/Ni and GC/NiCu) in a 1 M NaOH solution at different concentrations of methanol was studied by the method of ac-impedance spectroscopy. Two semicircles in the first quadrant of a Nyquist diagram were observed for electro-oxidation of methanol on GC/Ni corresponding to charge transfer resistance and adsorption of intermediates. Electro-oxidation of methanol on GC/NiCu shows negative resistance in impedance plots as signified by semi-circles terminating in the second quadrant. The impedance behavior shows different patterns at different applied anodic potential. The influence of the electrode potential on impedance pattern is studied and a mathematical model was put forward to quantitatively account for the impedance behavior of methanol oxidation. At potentials higher than 0.49 V vs. Ag/AgCl, a pseudoinductive behavior is observed but at higher than 0.58 V, impedance patterns terminate in the second quadrant. The conditions required for this behavior are delineated with the use of the impedance model. (author)

  14. Design Methodologies for Secure Embedded Systems

    CERN Document Server

    Biedermann, Alexander

    2011-01-01

    Embedded systems have been almost invisibly pervading our daily lives for several decades. They facilitate smooth operations in avionics, automotive electronics, or telecommunication. New problems arise by the increasing employment, interconnection, and communication of embedded systems in heterogeneous environments: How secure are these embedded systems against attacks or breakdowns? Therefore, how can embedded systems be designed to be more secure? And how can embedded systems autonomically react to threats? Facing these questions, Sorin A. Huss is significantly involved in the exploration o

  15. A speedup technique for (l, d-motif finding algorithms

    Directory of Open Access Journals (Sweden)

    Dinh Hieu

    2011-03-01

    Full Text Available Abstract Background The discovery of patterns in DNA, RNA, and protein sequences has led to the solution of many vital biological problems. For instance, the identification of patterns in nucleic acid sequences has resulted in the determination of open reading frames, identification of promoter elements of genes, identification of intron/exon splicing sites, identification of SH RNAs, location of RNA degradation signals, identification of alternative splicing sites, etc. In protein sequences, patterns have proven to be extremely helpful in domain identification, location of protease cleavage sites, identification of signal peptides, protein interactions, determination of protein degradation elements, identification of protein trafficking elements, etc. Motifs are important patterns that are helpful in finding transcriptional regulatory elements, transcription factor binding sites, functional genomics, drug design, etc. As a result, numerous papers have been written to solve the motif search problem. Results Three versions of the motif search problem have been proposed in the literature: Simple Motif Search (SMS, (l, d-motif search (or Planted Motif Search (PMS, and Edit-distance-based Motif Search (EMS. In this paper we focus on PMS. Two kinds of algorithms can be found in the literature for solving the PMS problem: exact and approximate. An exact algorithm identifies the motifs always and an approximate algorithm may fail to identify some or all of the motifs. The exact version of PMS problem has been shown to be NP-hard. Exact algorithms proposed in the literature for PMS take time that is exponential in some of the underlying parameters. In this paper we propose a generic technique that can be used to speedup PMS algorithms. Conclusions We present a speedup technique that can be used on any PMS algorithm. We have tested our speedup technique on a number of algorithms. These experimental results show that our speedup technique is indeed very

  16. MEME-ChIP: motif analysis of large DNA datasets.

    Science.gov (United States)

    Machanick, Philip; Bailey, Timothy L

    2011-06-15

    Advances in high-throughput sequencing have resulted in rapid growth in large, high-quality datasets including those arising from transcription factor (TF) ChIP-seq experiments. While there are many existing tools for discovering TF binding site motifs in such datasets, most web-based tools cannot directly process such large datasets. The MEME-ChIP web service is designed to analyze ChIP-seq 'peak regions'--short genomic regions surrounding declared ChIP-seq 'peaks'. Given a set of genomic regions, it performs (i) ab initio motif discovery, (ii) motif enrichment analysis, (iii) motif visualization, (iv) binding affinity analysis and (v) motif identification. It runs two complementary motif discovery algorithms on the input data--MEME and DREME--and uses the motifs they discover in subsequent visualization, binding affinity and identification steps. MEME-ChIP also performs motif enrichment analysis using the AME algorithm, which can detect very low levels of enrichment of binding sites for TFs with known DNA-binding motifs. Importantly, unlike with the MEME web service, there is no restriction on the size or number of uploaded sequences, allowing very large ChIP-seq datasets to be analyzed. The analyses performed by MEME-ChIP provide the user with a varied view of the binding and regulatory activity of the ChIP-ed TF, as well as the possible involvement of other DNA-binding TFs. MEME-ChIP is available as part of the MEME Suite at http://meme.nbcr.net.

  17. Embedding Graphs in Lorentzian Spacetime

    CERN Document Server

    Clough, James R

    2016-01-01

    Geometric approaches to network analysis combine simply defined models with great descriptive power. In this work we provide a method for embedding directed acyclic graphs into Minkowski spacetime using Multidimensional scaling (MDS). First we generalise the classical MDS algorithm, defined only for metrics with a Euclidean signature, to manifolds of any metric signature. We then use this general method to develop an algorithm to be used on networks which have causal structure allowing them to be embedded in Lorentzian manifolds. The method is demonstrated by calculating embeddings for both causal sets and citation networks in Minkowski spacetime. We finally suggest a number of applications in citation analysis such as paper recommendation, identifying missing citations and fitting citation models to data using this geometric approach.

  18. Embedded Processor Oriented Compiler Infrastructure

    Directory of Open Access Journals (Sweden)

    DJUKIC, M.

    2014-08-01

    Full Text Available In the recent years, research of special compiler techniques and algorithms for embedded processors broaden the knowledge of how to achieve better compiler performance in irregular processor architectures. However, industrial strength compilers, besides ability to generate efficient code, must also be robust, understandable, maintainable, and extensible. This raises the need for compiler infrastructure that provides means for convenient implementation of embedded processor oriented compiler techniques. Cirrus Logic Coyote 32 DSP is an example that shows how traditional compiler infrastructure is not able to cope with the problem. That is why the new compiler infrastructure was developed for this processor, based on research. in the field of embedded system software tools and experience in development of industrial strength compilers. The new infrastructure is described in this paper. Compiler generated code quality is compared with code generated by the previous compiler for the same processor architecture.

  19. Phase space embedding of electrocardiograms

    CERN Document Server

    Richter, M; Richter, Marcus; Schreiber, Thomas

    1998-01-01

    We study properties of the human electrocardiogram under the working hypothesis that fluctuations beyond the regular structure of single cardiac cycles are unpredictable. On this background we discuss the possibility to use the phase space embedding method for this kind of signal. In particular, the specific nature of the stochastic or high dimensional component allows to use phase space embeddings for certain signal processing tasks. As practical applications, we discuss noise filtering, fetal ECG extraction, and the automatic detection of clinically relevant features. The main purpose of the paper is to connect results of embedding theory which had not been previously applied in practise, and practical applications which had not yet been justified theoretically.

  20. Strong embeddings of minimum genus

    CERN Document Server

    Mohar, Bojan

    2009-01-01

    A "folklore conjecture, probably due to Tutte" (as described in [P.D. Seymour, Sums of circuits, Graph theory and related topics (Proc. Conf., Univ. Waterloo, 1977), pp. 341-355, Academic Press, 1979]) asserts that every bridgeless cubic graph can be embedded on a surface of its own genus in such a way that the face boundaries are cycles of the graph. In this paper we consider closed 2-cell embeddings of graphs and show that certain (cubic) graphs (of any fixed genus) have closed 2-cell embedding only in surfaces whose genus is very large (proportional to the order of these graphs), thus providing plethora of strong counterexamples to the above conjecture. The main result yielding such counterexamples may be of independent interest.

  1. Exploitation of peptide motif sequences and their use in nanobiotechnology.

    Science.gov (United States)

    Shiba, Kiyotaka

    2010-08-01

    Short amino acid sequences extracted from natural proteins or created using in vitro evolution systems are sometimes associated with particular biological functions. These peptides, called peptide motifs, can serve as functional units for the creation of various tools for nanobiotechnology. In particular, peptide motifs that have the ability to specifically recognize the surfaces of solid materials and to mineralize certain inorganic materials have been linking biological science to material science. Here, I review how these peptide motifs have been isolated from natural proteins or created using in vitro evolution systems, and how they have been used in the nanobiotechnology field.

  2. BlockLogo: Visualization of peptide and sequence motif conservation

    DEFF Research Database (Denmark)

    Olsen, Lars Rønn; Kudahl, Ulrich Johan; Simon, Christian

    2013-01-01

    , selection of motif positions, type of sequence, and output format definition. The output has BlockLogo along with the sequence logo, and a table of motif frequencies. We deployed BlockLogo as an online application and have demonstrated its utility through examples that show visualization of T-cell epitopes...... and B-cell epitopes (both continuous and discontinuous). Our additional example shows a visualization and analysis of structural motifs that determine the specificity of peptide binding to HLA-DR molecules. The BlockLogo server also employs selected experimentally validated prediction algorithms...

  3. Identification of protein superfamily from structure- based sequence motif

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The structure-based sequence motif of the distant proteins in evolution, protein tyrosine phosphatases (PTP) Ⅰ and Ⅱ superfamilies, as an example, has been defined by the structural comparison, structure-based sequence alignment and analyses on substitution patterns of residues in common sequence conserved regions. And the phosphatases Ⅰ and Ⅱ can be correctly identified together by the structure-based PTP sequence motif from SWISS-PROT and TrEBML databases. The results show that the correct rates of identification are over 98%. This is the first time to identify PTP Ⅰ and Ⅱ together by this motif.

  4. ROMANIAN FOLKLORE MOTIFS IN FASHION DESIGN

    Directory of Open Access Journals (Sweden)

    MOCENCO Alexandra

    2014-05-01

    Full Text Available The traditional Romanian costume such as the entire popular art (architecture, woodcarvins, pottery etc. was born and lasted in our country since ancient times. Closely related to human existence, the traditional costume reflected over the years as reflected nowadays, the mentality and artistic conception of the people. Today the traditional Romanian costume became an inspiration source to the wholesale fashion production industry designers, both Romanian and international. Although the contemporary designers are working in accordance with a vision, using a wide area of styles, methods and current technology, they usually return to traditional techniques and ethnic folklore motifs, which converts and resize them, integrating them in their contemporary space. Adrian Oianu is a very appreciated Romanian designer who launched two collections inspired by his native’s country traditional costumes: “Suflecata pan’ la brau” (“Turned up ‘til the belt” and “Bucurie” (“Joy”. Dorin Negrau had as inspiration for his “Lost” collection the traditional costume from the Bihor region. Yves Saint Laurent had a collection inspired by the Romanian traditional flax blouses called “La blouse roumaine”. The paper presents the traditional Romanian values throw fashion collections. The research activity will create innovative concepts to support the garment industry in order to develop their own brand and to bring the design activities in Romania at an international level. The research was conducted during the initial stage of a project, financed through national founds, consisting in a documentary study on ethnographic characteristics of the popular costume from different regions of the country.

  5. Targeting functional motifs of a protein family

    Science.gov (United States)

    Bhadola, Pradeep; Deo, Nivedita

    2016-10-01

    The structural organization of a protein family is investigated by devising a method based on the random matrix theory (RMT), which uses the physiochemical properties of the amino acid with multiple sequence alignment. A graphical method to represent protein sequences using physiochemical properties is devised that gives a fast, easy, and informative way of comparing the evolutionary distances between protein sequences. A correlation matrix associated with each property is calculated, where the noise reduction and information filtering is done using RMT involving an ensemble of Wishart matrices. The analysis of the eigenvalue statistics of the correlation matrix for the β -lactamase family shows the universal features as observed in the Gaussian orthogonal ensemble (GOE). The property-based approach captures the short- as well as the long-range correlation (approximately following GOE) between the eigenvalues, whereas the previous approach (treating amino acids as characters) gives the usual short-range correlations, while the long-range correlations are the same as that of an uncorrelated series. The distribution of the eigenvector components for the eigenvalues outside the bulk (RMT bound) deviates significantly from RMT observations and contains important information about the system. The information content of each eigenvector of the correlation matrix is quantified by introducing an entropic estimate, which shows that for the β -lactamase family the smallest eigenvectors (low eigenmodes) are highly localized as well as informative. These small eigenvectors when processed gives clusters involving positions that have well-defined biological and structural importance matching with experiments. The approach is crucial for the recognition of structural motifs as shown in β -lactamase (and other families) and selectively identifies the important positions for targets to deactivate (activate) the enzymatic actions.

  6. Certifiable Java for Embedded Systems

    DEFF Research Database (Denmark)

    Schoeberl, Martin; Dalsgaard, Andreas Engelbredt; Hansen, Rene Rydhof

    2014-01-01

    The Certifiable Java for Embedded Systems (CJ4ES) project aimed to develop a prototype development environment and platform for safety-critical software for embedded applications. There are three core constituents: A profile of the Java programming language that is tailored for safety......-critical applications, a predictable Java processor built with FPGA technology, and an Eclipse based application development environment that binds the profile and the platform together and provides analyses that help to provide evidence that can be used as part of a safety case. This paper summarizes key contributions...

  7. Homogeneous Spaces and Equivariant Embeddings

    CERN Document Server

    Timashev, DA

    2011-01-01

    Homogeneous spaces of linear algebraic groups lie at the crossroads of algebraic geometry, theory of algebraic groups, classical projective and enumerative geometry, harmonic analysis, and representation theory. By standard reasons of algebraic geometry, in order to solve various problems on a homogeneous space it is natural and helpful to compactify it keeping track of the group action, i.e. to consider equivariant completions or, more generally, open embeddings of a given homogeneous space. Such equivariant embeddings are the subject of this book. We focus on classification of equivariant em

  8. Graph Embedding for Pattern Analysis

    CERN Document Server

    Ma, Yunqian

    2013-01-01

    Graph Embedding for Pattern Analysis covers theory methods, computation, and applications widely used in statistics, machine learning, image processing, and computer vision. This book presents the latest advances in graph embedding theories, such as nonlinear manifold graph, linearization method, graph based subspace analysis, L1 graph, hypergraph, undirected graph, and graph in vector spaces. Real-world applications of these theories are spanned broadly in dimensionality reduction, subspace learning, manifold learning, clustering, classification, and feature selection. A selective group of experts contribute to different chapters of this book which provides a comprehensive perspective of this field.

  9. Certifiable Java for Embedded Systems

    DEFF Research Database (Denmark)

    Schoeberl, Martin; Hansen, René Rydhof; Ravn, Anders P.;

    2014-01-01

    The Certifiable Java for Embedded Systems (CJ4ES) project aimed to develop a prototype development environment and platform for safety-critical software for embedded applications. There are three core constituents: A profile of the Java programming language that is tailored for safety......-critical applications, a predictable Java processor built with FPGA technology, and an Eclipse based application development environment that binds the profile and the platform together and provides analyses that help to provide evidence that can be used as part of a safety case. This paper summarizes key contributions...

  10. Habitual Tastes and Embedded Taste

    DEFF Research Database (Denmark)

    Hedegaard, Liselotte

    2016-01-01

    of the national cuisine indicates continuity over time. There seems, hence, to be a gap between the multiplicity of instances of experience and recollection that belongs to the sphere of the individual and a historical memory embedded in the larger context of a society. From a common-sense perspective, this gap...... may be bridged by story-telling or other ways of handing over historically embedded practices, but this leaves a more fundamental question unanswered. Namely, that given that all remembrance has individual recollection as the point of departure, then how does individual recollection of tastes...

  11. Perturbation Theory of Embedded Eigenvalues

    DEFF Research Database (Denmark)

    Engelmann, Matthias

    We study problems connected to perturbation theory of embedded eigenvalues in two different setups. The first part deals with second order perturbation theory of mass shells in massive translation invariant Nelson type models. To this end an expansion of the eigenvalues w.r.t. fiber parameter up...... project gives a general and systematic approach to analytic perturbation theory of embedded eigenvalues. The spectral deformation technique originally developed in the theory of dilation analytic potentials in the context of Schrödinger operators is systematized by the use of Mourre theory. The group...

  12. Evolution of Deeply Embedded Protostars

    DEFF Research Database (Denmark)

    Frimann, Søren

    of this comparison is both to benchmark the simulations by testing if observational results can be reproduced, and to use the simulations to aid in the interpretation of the observations. The research deals with the earliest stages of star formation – the protostellar phase – where the protostars are still embedded...... tolink evidence of accretion bursts together with evidence of circumstellardisks. The study targets 20 embedded protostars in the Perseusmolecular cloud, and reveals plenty of evidence for variable accretionthrough observations of C18O (an optically thin isotopologue of CO).The study also reveals...

  13. Embedded EZ-Source Inverters

    DEFF Research Database (Denmark)

    Chiang Loh, Poh; Gao, Feng; Blaabjerg, Frede

    2010-01-01

    of embedded EZ-source inverters that can produce the same gain as the Z-source inverters but with smoother and smaller current/voltage maintained across the dc input source and within the impedance network. These latter features are attained without using any additional passive filter, which surely...... is a favorable advantage, since an added filter will raise the system cost and, at times, can complicate the dynamic tuning and resonant consideration of the inverters. The same embedded concept can also be used for designing a full range of voltage- and current-type inverters with each of them tested...

  14. Embedded EZ-Source Inverters

    DEFF Research Database (Denmark)

    Blaabjerg, Frede; Loh, Poh Chiang; Gao, F.

    2008-01-01

    -voltage oscillations to the system. Therefore, Z-source inverters are in effect safer and less complex, and can be implemented using only passive elements with no additional active semiconductor needed. Believing in the prospects of Z-source inverters, this paper contributes by introducing a new family of embedded EZ...... since an added filter will raise the system cost, and at times can complicate the dynamic tuning and resonant consideration of the inverters. The same embedded concept can also be used for designing a full range of voltage and current-type inverters with each of them tested experimentally using a number...

  15. New structural and functional contexts of the Dx[DN]xDG linear motif: insights into evolution of calcium-binding proteins.

    Science.gov (United States)

    Rigden, Daniel J; Woodhead, Duncan D; Wong, Prudence W H; Galperin, Michael Y

    2011-01-01

    Binding of calcium ions (Ca²⁺) to proteins can have profound effects on their structure and function. Common roles of calcium binding include structure stabilization and regulation of activity. It is known that diverse families--EF-hands being one of at least twelve--use a Dx[DN]xDG linear motif to bind calcium in near-identical fashion. Here, four novel structural contexts for the motif are described. Existing experimental data for one of them, a thermophilic archaeal subtilisin, demonstrate for the first time a role for Dx[DN]xDG-bound calcium in protein folding. An integrin-like embedding of the motif in the blade of a β-propeller fold--here named the calcium blade--is discovered in structures of bacterial and fungal proteins. Furthermore, sensitive database searches suggest a common origin for the calcium blade in β-propeller structures of different sizes and a pan-kingdom distribution of these proteins. Factors favouring the multiple convergent evolution of the motif appear to include its general Asp-richness, the regular spacing of the Asp residues and the fact that change of Asp into Gly and vice versa can occur though a single nucleotide change. Among the known structural contexts for the Dx[DN]xDG motif, only the calcium blade and the EF-hand are currently found intracellularly in large numbers, perhaps because the higher extracellular concentration of Ca²⁺ allows for easier fixing of newly evolved motifs that have acquired useful functions. The analysis presented here will inform ongoing efforts toward prediction of similar calcium-binding motifs from sequence information alone.

  16. DWPF GC FILTER ASSEMBLY SAMPLING AND ANALYSIS

    Energy Technology Data Exchange (ETDEWEB)

    Bannochie, C.; Imrich, K.

    2009-11-11

    On March 18, 2009 a Defense Waste Processing Facility (DWPF) GC Line Filter Assembly was received at the Savannah River National Laboratory (SRNL). This filter assembly was removed from operation following the completion of Sludge Batch 4 processing in the DWPF. Work on this sample was requested in a Technical Assistance Request. This document reports the pictures, observations, samples collected, and analytical results for the assembly. The assembly arrived at SRNL separated into its three component filters: high efficiency particulate air (HEPA)-1, HEPA-2, and a high efficiency mist evaporator (HEME). Each stage of the assembly's media was sampled and examined visually and by scanning electron microscopy (SEM). Solids built up in the filter housing following the first stage HEME, were dissolved in dilute nitric acid and analyzed by ICP-AES and the undissolved white solids were analyzed by x-ray diffraction (XRD). The vast majority of the material in each of the three stages of the DWPF GC Line Filter Assembly appears to be contaminated with a Hg compound that is {approx}59 wt% Hg on a total solids basis. The Hg species was identified by XRD analysis to contain a mixture of Hg{sub 4}(OH)(NO{sub 3}){sub 3} and Hg{sub 10}(OH){sub 4}(NO{sub 3}){sub 6}. Only in the core sample of the second stage HEPA, did this material appear to be completely covering portions of the filter media, possibly explaining the pressure drops observed by DWPF. The fact that the material migrates through the HEME filter and both HEPA filters, and that it was seen collecting on the outlet side of the HEME filter, would seem to indicate that these filters are not efficient at removing this material. Further SRAT off-gas system modeling should help determine the extent of Hg breakthrough past the Mercury Water Wash Tank (MWWT). The SRAT off-gas system has not been modeled since startup of the facility. Improvements to the efficiency of Hg stripping prior to the ammonia scrubber would seem

  17. An autoinhibited conformation of LGN reveals a distinct interaction mode between GoLoco motifs and TPR motifs.

    Science.gov (United States)

    Pan, Zhu; Zhu, Jinwei; Shang, Yuan; Wei, Zhiyi; Jia, Min; Xia, Caihao; Wen, Wenyu; Wang, Wenning; Zhang, Mingjie

    2013-06-01

    LGN plays essential roles in asymmetric cell divisions via its N-terminal TPR-motif-mediated binding to mInsc and NuMA. This scaffolding activity requires the release of the autoinhibited conformation of LGN by binding of Gα(i) to its C-terminal GoLoco (GL) motifs. The interaction between the GL and TPR motifs of LGN represents a distinct GL/target binding mode with an unknown mechanism. Here, we show that two consecutive GL motifs of LGN form a minimal TPR-motif-binding unit. GL12 and GL34 bind to TPR0-3 and TPR4-7, respectively. The crystal structure of a truncated LGN reveals that GL34 forms a pair of parallel α helices and binds to the concave surface of TPR4-7, thereby preventing LGN from binding to other targets. Importantly, the GLs bind to TPR motifs with a mode distinct from that observed in the GL/Gα(i)·GDP complexes. Our results also indicate that multiple and orphan GL motif proteins likely respond to G proteins with distinct mechanisms.

  18. Predicting Partitioning and Diffusion Properties of Nonpolar Chemicals in Biotic Media and Passive Sampler Phases by GC × GC.

    Science.gov (United States)

    Nabi, Deedar; Arey, J Samuel

    2017-02-14

    The chemical parameters needed to explain and predict bioavailability, biodynamics, and baseline toxicity are not readily available for most nonpolar chemicals detected in the environment. Here, we demonstrate that comprehensive two-dimensional gas chromatography (GC × GC) retention times can be used to predict 26 relevant properties for nonpolar chemicals, specifically: partition coefficients for diverse biotic media and passive sampler phases; aquatic baseline toxicity; and relevant diffusion coefficients. The considered biotic and passive sampler phases include membrane and storage lipids, serum and muscle proteins, carbohydrates, algae, mussels, polydimethylsiloxane, polyethylene, polyoxymethylene, polyacrylate, polyurethane, and semipermeable membrane devices. GC × GC-based chemical property predictions are validated with a compilation of 1038 experimental property data collected from the literature. As an example application, we overlay a map of baseline toxicity to fathead minnows onto the separated analyte signal of a polychlorinated alkanes (chlorinated paraffins) technical mixture that contains 7820 congeners. In a second application, GC × GC-estimated properties are used to parametrize multiphase partitioning models for mammalian tissues and organs. In a third example, we estimate chemical depuration kinetics for mussels. Finally, we illustrate an approach to screen the GC × GC chromatogram for nonpolar chemicals of potentially high concern, defined based on their GC × GC-estimated biopartitioning properties, diffusion properties, and baseline toxicity.

  19. Immunotherapy for Prostate Cancer with Gc Protein-Derived Macrophage-Activating Factor, GcMAF1

    Science.gov (United States)

    Yamamoto, Nobuto; Suyama, Hirofumi; Yamamoto, Nobuyuki

    2008-01-01

    Serum Gc protein (known as vitamin D3-binding protein) is the precursor for the principal macrophage-activating factor (MAF). The MAF precursor activity of serum Gc protein of prostate cancer patients was lost or reduced because Gc protein was deglycosylated by serum α-N-acetylgalactosaminidase (Nagalase) secreted from cancerous cells. Therefore, macrophages of prostate cancer patients having deglycosylated Gc protein cannot be activated, leading to immunosuppression. Stepwise treatment of purified Gc protein with immobilized β-galactosidase and sialidase generated the most potent MAF (termed GcMAF) ever discovered, which produces no adverse effect in humans. Macrophages activated by GcMAF develop a considerable variation of receptors that recognize the abnormality in malignant cell surface and are highly tumoricidal. Sixteen nonanemic prostate cancer patients received weekly administration of 100 ng of GcMAF. As the MAF precursor activity increased, their serum Nagalase activity decreased. Because serum Nagalase activity is proportional to tumor burden, the entire time course analysis for GcMAF therapy was monitored by measuring the serum Nagalase activity. After 14 to 25 weekly administrations of GcMAF (100 ng/week), all 16 patients had very low serum Nagalase levels equivalent to those of healthy control values, indicating that these patients are tumor-free. No recurrence occurred for 7 years. PMID:18633461

  20. Automatic Network Fingerprinting through Single-Node Motifs

    CERN Document Server

    Echtermeyer, Christoph; Rodrigues, Francisco A; Kaiser, Marcus; 10.1371/journal.pone.0015765

    2011-01-01

    Complex networks have been characterised by their specific connectivity patterns (network motifs), but their building blocks can also be identified and described by node-motifs---a combination of local network features. One technique to identify single node-motifs has been presented by Costa et al. (L. D. F. Costa, F. A. Rodrigues, C. C. Hilgetag, and M. Kaiser, Europhys. Lett., 87, 1, 2009). Here, we first suggest improvements to the method including how its parameters can be determined automatically. Such automatic routines make high-throughput studies of many networks feasible. Second, the new routines are validated in different network-series. Third, we provide an example of how the method can be used to analyse network time-series. In conclusion, we provide a robust method for systematically discovering and classifying characteristic nodes of a network. In contrast to classical motif analysis, our approach can identify individual components (here: nodes) that are specific to a network. Such special nodes...

  1. Review article: The mountain motif in the plot of Matthew

    Directory of Open Access Journals (Sweden)

    Gert J. Volschenk

    2010-02-01

    Full Text Available This article reviewed T.L. Donaldson’s book, Jesus on the mountain: A study in Matthean theology, published in 1985 by JSOT Press, Sheffield, and focused on the mountain motif in the structure and plot of the Gospel of Matthew, in addition to the work of Donaldson on the mountain motif as a literary motif and as theological symbol. The mountain is a primary theological setting for Jesus’ ministry and thus is an important setting, serving as one of the literary devices by which Matthew structured and progressed his narrative. The Zion theological and eschatological significance and Second Temple Judaism serve as the historical and theological background for the mountain motif. The last mountain setting (Mt 28:16–20 is the culmination of the three theological themes in the plot of Matthew, namely Christology, ecclesiology and salvation history.

  2. A combinatorial code for splicing silencing: UAGG and GGGG motifs

    National Research Council Canada - National Science Library

    Han, Kyoungha; Yeo, Gene; An, Ping; Burge, Christopher B; Grabowski, Paula J

    2005-01-01

    .... Here we use molecular approaches to identify a ternary combination of exonic UAGG and 5'-splice-site-proximal GGGG motifs that functions cooperatively to silence the brain-region-specific CI cassette exon (exon 19...

  3. Quantitation using GC-TOF-MS: example of bromazepam.

    Science.gov (United States)

    Aebi, B; Sturny-Jungo, R; Bernhard, W; Blanke, R; Hirsch, R

    2002-08-14

    Time-of-flight mass spectrometry (TOF-MS) offers new perspectives for forensic toxicology. Qualitative and quantitative analyses of a mixture of three selected benzodiazepines (diazepam, nordazepam and bromazepam) were used to compare gas chromatography (GC-TOF-MS, quadrupole GC-MS, GC-ECD) and liquid chromatography (HPLC-DAD) data. Method validation parameters like LOD, LOQ, S/N-ratios reflect the capabilities of GC-TOF-MS. Five-point calibrations for bromazepam in human peripheral blood (50, 100, 160, 200, 300 ng/ml) using medazepam as internal standard (1000 ng/ml) were performed. The calibrations using GC-TOF-MS (using the fragments of m/z 236 and 288), GC-ECD (dual system) and HPLC-DAD (at 235 nm) all showed correlation coefficients close or superior to 0.99. Quadrupole GC-MS data was not used in the comparison of extracted samples due to the low sensitivity in the full scan mode. Two analyses of real cases concerning bromazepam are presented. In the first case, the presence or absence of bromazepam could not be established with both HPLC-DAD and GC-ECD due to background signals. The extracted ion chromatograms and spectrum traces after the analysis with the GC-TOF-MS could clearly excluded the presence of bromazepam. The second case illustrates the quantitation of bromazepam, where both HPLC-DAD and GC-ECD were unable to give satisfactory results, again due to interfering background signals. The analyses performed on the GC-TOF-MS-system demonstrated high sensitivity and also high selectivity due to the high quality of mass spectra obtained. The advantages of GC-TOF-MS make it a promising analytical technique for forensic toxicology.

  4. Direct vs 2-stage approaches to structured motif finding

    Directory of Open Access Journals (Sweden)

    Federico Maria

    2012-08-01

    Full Text Available Abstract Background The notion of DNA motif is a mathematical abstraction used to model regions of the DNA (known as Transcription Factor Binding Sites, or TFBSs that are bound by a given Transcription Factor to regulate gene expression or repression. In turn, DNA structured motifs are a mathematical counterpart that models sets of TFBSs that work in concert in the gene regulations processes of higher eukaryotic organisms. Typically, a structured motif is composed of an ordered set of isolated (or simple motifs, separated by a variable, but somewhat constrained number of “irrelevant” base-pairs. Discovering structured motifs in a set of DNA sequences is a computationally hard problem that has been addressed by a number of authors using either a direct approach, or via the preliminary identification and successive combination of simple motifs. Results We describe a computational tool, named SISMA, for the de-novo discovery of structured motifs in a set of DNA sequences. SISMA is an exact, enumerative algorithm, meaning that it finds all the motifs conforming to the specifications. It does so in two stages: first it discovers all the possible component simple motifs, then combines them in a way that respects the given constraints. We developed SISMA mainly with the aim of understanding the potential benefits of such a 2-stage approach w.r.t. direct methods. In fact, no 2-stage software was available for the general problem of structured motif discovery, but only a few tools that solved restricted versions of the problem. We evaluated SISMA against other published tools on a comprehensive benchmark made of both synthetic and real biological datasets. In a significant number of cases, SISMA outperformed the competitors, exhibiting a good performance also in most of the cases in which it was inferior. Conclusions A reflection on the results obtained lead us to conclude that a 2-stage approach can be implemented with many advantages over direct

  5. Morphware - Fremtidens Embedded System Platform

    DEFF Research Database (Denmark)

    Madsen, Jan

    2006-01-01

    FPGA'er bliver i stigende grad brugt som komponenter i embedded systemer. Faldende priser, større kapacitet og en større felksibilitet har gjort FPGA'en til en attraktiv og konkurrencedygtig teknologi der tillader en stadig stigende grad af system integration, hvor traditionel hardware og software...

  6. Software for Embedded Control Systems

    NARCIS (Netherlands)

    Broenink, Jan F.; Hilderink, Gerald H.; Jovanovic, Dusko S.

    2001-01-01

    The research of our team deals with the realization of control schemes on digital computers. As such the emphasis is on embedded control software implementation. Applications are in the field of mechatronic devices, using a mechatronic design approach (the integrated and optimal design of a mechanic

  7. Simulation and Embedded Smart Control

    DEFF Research Database (Denmark)

    Conrad, Finn; Fan, Zhun; Sørensen, Torben

    2006-01-01

    The paper presents results obtained from a Danish mechatronic research program focusing on intelligent motion control, simulation and embedded smart controllers for hydraulic actuators and robots as well as results from the EU projects. A mechatronic test facility with digital controllers...... and algorithms. Furthermore, a developed IT-tool concept for controller and system design utilizing the ISO 10303 STEP Standard is proposed....

  8. Embedding Sensors During Additive Manufacturing

    Energy Technology Data Exchange (ETDEWEB)

    Sbriglia, Lexey Raylene [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-08-10

    This PowerPoint presentation had the following headings: Fused deposition modeling (FDM); Open source 3D printing; Objectives; Vibration analysis; Equipment; Design; Material choices; Failure causes, such as tension, bubbling; Potential solutions; Simulations; Embedding the sensors; LabView programming; Alternate data acquisition; Problem and proposed solution; and, Conclusions

  9. Embedding Laboratory Experience in Lectures

    Science.gov (United States)

    Morgan, James R.; Barroso, Luciana R.; Simpson, Nancy

    2009-01-01

    Demonstrations can be very effective at enhancing student learning and represent a mechanism for embedding laboratory experiences within a classroom setting. A key component to an effective demonstration is active student engagement throughout the entire process, leading to a guided laboratory experience in a lecture setting. Students are involved…

  10. Robust and Adaptive MicroRNA-Mediated Incoherent Feedforward Motifs

    Institute of Scientific and Technical Information of China (English)

    XU Feng-Dan; LIU Zeng-Rong; ZHANG Zhi-Yong; SHEN Jian-Wei

    2009-01-01

    We integrate transcriptional and post-transcriptional regulation into microRNA-mediated incoherent feedforward motifs and analyse their dynamical behaviour and functions. The analysis show that the behaviour of the system is almost uninfluenced by the varying input in certain ranges and by introducing of delay and noise. The results indicate that microRNA-mediated incoherent feedforward motifs greatly enhance the robustness of gene regulation.

  11. The Origin of Motif Families in Food Webs

    OpenAIRE

    Klaise, Janis; Johnson, Samuel

    2016-01-01

    Food webs have been found to exhibit remarkable motif profiles, patterns in the relative prevalences of all possible three-species sub-graphs, and this has been related to ecosystem properties such as stability and robustness. Analysing 46 food webs of various kinds, we find that most food webs fall into one of two distinct motif families. The separation between the families is well predicted by a global measure of hierarchical order in directed networks - trophic coherence. We find that trop...

  12. Three-Dimensional DNA Nanostructures Assembled from DNA Star Motifs.

    Science.gov (United States)

    Tian, Cheng; Zhang, Chuan

    2017-01-01

    Tile-based DNA self-assembly is a promising method in DNA nanotechnology and has produced a wide range of nanostructures by using a small set of unique DNA strands. DNA star motif, as one of DNA tiles, has been employed to assemble varieties of symmetric one-, two-, three-dimensional (1, 2, 3D) DNA nanostructures. Herein, we describe the design principles, assembly methods, and characterization methods of 3D DNA nanostructures assembled from the DNA star motifs.

  13. SSR Cluster and Fertility Loci Analysis of GC13

    Institute of Scientific and Technical Information of China (English)

    NONG Bao-xuan; XIA Xiu-zhong; LIANG Yao-mao; LU Gang; ZHANG Zong-qiong; LI Dan-ting

    2011-01-01

    [Objective] The research aimed to clarify the genetic mechanism of special wide compatibility of GC13.[Method] The clustering analyses of GC13,five indica,five japonica and five wide compatibility varieties were carried out by using 70 SSR primers.[Result] GC13 was clustered into japonica group and had far genetic relationship with indica and wide compatibility variety.Two fertility loci were detected in GC13,in which one closely linked to RM225 on chromosome 6.According to the position on the chromosome,it speculated that this locus was allelic to S5.GC13 carried the allelic gene S5-n at this locus.The other locus closely linked to RM408 on chromosome 8 and was provisionally designated as Sg(t).At this locus,GC13 carried Sg(t)-i allelic gene,which was consistent with IR36.The effect of S5 locus was stronger than that of Sg(t).[Conclusion] The research laid the good foundation for using the wide compatibility line GC13 to breed the hybrid between subspecies.%[Objective] The research aimed to clarify the genetic mechanism of special wide compatibility of GC13.[Method] The clustering analyses of GC13,five indica,five japonica and five wide compatibility varieties were carried out by using 70 SSR primers.[Result

  14. Transcriptional Network growing Models using Motif-based Preferential Attachment

    Directory of Open Access Journals (Sweden)

    Ahmed Farouk Abdelzaher

    2015-10-01

    Full Text Available Understanding relationships between architectural properties of gene-regulatory networks (GRNs has been one of the major goals in systems biology and bioinformatics, as it can provide insights into, e.g., disease dynamics and drug development. Such GRNs are characterized by their scale-free degree distributions and existence of network motifs--i.e., small-node subgraphs that occur more abundantly in GRNs than expected from chance alone. Because these transcriptional modules represent ``building blocks'' of complex networks and exhibit a wide range of functional and dynamical properties, they may contribute to the remarkable robustness and dynamical stability associated with the whole of GRNs. Here we developed network-construction models to better understand this relationship, which produce randomized GRNs by using transcriptional motifs as the fundamental growth unit in contrast to other methods that construct similar networks on a node-by-node basis. Because this model produces networks with a prescribed lower bound on the number of choice transcriptional motifs (e.g., downlinks, feed-forward loops, its fidelity to the motif distributions observed in model organisms represents an improvement over existing methods, which we validated by contrasting their resultant motif and degree distributions against existing network-growth models and data from the model organism of the bacterium Escherichia coli. These models may therefore serve as novel testbeds for further elucidating relationships between the topology of transcriptional motifs and network-wide dynamical properties.

  15. Transcriptional Network Growing Models Using Motif-Based Preferential Attachment.

    Science.gov (United States)

    Abdelzaher, Ahmed F; Al-Musawi, Ahmad F; Ghosh, Preetam; Mayo, Michael L; Perkins, Edward J

    2015-01-01

    Understanding relationships between architectural properties of gene-regulatory networks (GRNs) has been one of the major goals in systems biology and bioinformatics, as it can provide insights into, e.g., disease dynamics and drug development. Such GRNs are characterized by their scale-free degree distributions and existence of network motifs - i.e., small-node subgraphs that occur more abundantly in GRNs than expected from chance alone. Because these transcriptional modules represent "building blocks" of complex networks and exhibit a wide range of functional and dynamical properties, they may contribute to the remarkable robustness and dynamical stability associated with the whole of GRNs. Here, we developed network-construction models to better understand this relationship, which produce randomized GRNs by using transcriptional motifs as the fundamental growth unit in contrast to other methods that construct similar networks on a node-by-node basis. Because this model produces networks with a prescribed lower bound on the number of choice transcriptional motifs (e.g., downlinks, feed-forward loops), its fidelity to the motif distributions observed in model organisms represents an improvement over existing methods, which we validated by contrasting their resultant motif and degree distributions against existing network-growth models and data from the model organism of the bacterium Escherichia coli. These models may therefore serve as novel testbeds for further elucidating relationships between the topology of transcriptional motifs and network-wide dynamical properties.

  16. A novel pro-Arg motif recognized by WW domains.

    Science.gov (United States)

    Bedford, M T; Sarbassova, D; Xu, J; Leder, P; Yaffe, M B

    2000-04-07

    WW domains mediate protein-protein interactions through binding to short proline-rich sequences. Two distinct sequence motifs, PPXY and PPLP, are recognized by different classes of WW domains, and another class binds to phospho-Ser-Pro sequences. We now describe a novel Pro-Arg sequence motif recognized by a different class of WW domains using data from oriented peptide library screening, expression cloning, and in vitro binding experiments. The prototype member of this group is the WW domain of formin-binding protein 30 (FBP30), a p53-regulated molecule whose WW domains bind to Pro-Arg-rich cellular proteins. This new Pro-Arg sequence motif re-classifies the organization of WW domains based on ligand specificity, and the Pro-Arg class now includes the WW domains of FBP21 and FE65. A structural model is presented which rationalizes the distinct motifs selected by the WW domains of YAP, Pin1, and FBP30. The Pro-Arg motif identified for WW domains often overlaps with SH3 domain motifs within protein sequences, suggesting that the same extended proline-rich sequence could form discrete SH3 or WW domain complexes to transduce distinct cellular signals.

  17. The distribution of RNA motifs in natural sequences.

    Science.gov (United States)

    Bourdeau, V; Ferbeyre, G; Pageau, M; Paquin, B; Cedergren, R

    1999-11-15

    Functional analysis of genome sequences has largely ignored RNA genes and their structures. We introduce here the notion of 'ribonomics' to describe the search for the distribution of and eventually the determination of the physiological roles of these RNA structures found in the sequence databases. The utility of this approach is illustrated here by the identification in the GenBank database of RNA motifs having known binding or chemical activity. The frequency of these motifs indicates that most have originated from evolutionary drift and are selectively neutral. On the other hand, their distribution among species and their location within genes suggest that the destiny of these motifs may be more elaborate. For example, the hammerhead motif has a skewed organismal presence, is phylogenetically stable and recent work on a schistosome version confirms its in vivo biological activity. The under-representation of the valine-binding motif and the Rev-binding element in GenBank hints at a detrimental effect on cell growth or viability. Data on the presence and the location of these motifs may provide critical guidance in the design of experiments directed towards the understanding and the manipulation of RNA complexes and activities in vivo.

  18. Chemical Analysis of Essential oil of "Artemisia haussknechtii Boiss" by GC and GC/ MS

    Directory of Open Access Journals (Sweden)

    A. Nassir- Ahraadi . A. Rustaiyan

    1994-08-01

    Full Text Available The composition of the essential oil from the leaves and flowers of "Artemisia haussknechtii Boiss growing wild in the north-west of Iran, was investigated by GC and GC/MS."nThe main components of the volatile oil were 1,8 - cineol (16.5%, camphor (14.1%. artemisia ketone (10.5%, fragranol (9.0%, Yomogi alcohol (7.5% and B- pinene (5.4%. The total contribution of these compounds to the oil amounted to 63.0%."nMonoterpens and sesquiterpenes represent 90.08% and 1.52% of the oil respectively. Of the twenty oxygen-containing monoterpenes which made up a fairly large fraction of the terpenoid composition, the predominant components were 1,8 - cineole and camphor.

  19. Softwares for comprehensive two-dimensional gas chromatography (GC x GC)

    OpenAIRE

    2010-01-01

    Resumo: A Cromatografia Gasosa Bidimensional Abrangente (GCxGC) é uma técnica analítica capaz de separar e detectar centenas de picos, sendo aplicada a diferentes amostras petroquímicas, ambientais e biológicas. Esta técnica se diferencia da Cromatografia Gasosa (GC) pela utilização de duas colunas cromatográficas de composições e dimensões diferentes conectadas em série e de uma interface para a coleta das frações da primeira coluna e para a reinjeção na segunda em períodos regulares, denomi...

  20. Density Matrix Embedding: A Strong-Coupling Quantum Embedding Theory.

    Science.gov (United States)

    Knizia, Gerald; Chan, Garnet Kin-Lic

    2013-03-12

    We extend our density matrix embedding theory (DMET) [Phys. Rev. Lett.2012, 109, 186404] from lattice models to the full chemical Hamiltonian. DMET allows the many-body embedding of arbitrary fragments of a quantum system, even when such fragments are open systems and strongly coupled to their environment (e.g., by covalent bonds). In DMET, empirical approaches to strong coupling, such as link atoms or boundary regions, are replaced by a small, rigorous quantum bath designed to reproduce the entanglement between a fragment and its environment. We describe the theory and demonstrate its feasibility in strongly correlated hydrogen ring and grid models; these are not only beyond the scope of traditional embeddings but even challenge conventional quantum chemistry methods themselves. We find that DMET correctly describes the notoriously difficult symmetric dissociation of a 4 × 3 hydrogen atom grid, even when the treated fragments are as small as single hydrogen atoms. We expect that DMET will open up new ways of treating complex strongly coupled, strongly correlated systems in terms of their individual fragments.

  1. On Embeddings of Tori in Euclidean Spaces

    Institute of Scientific and Technical Information of China (English)

    Matija CENCELJ; Du(s)an REPOV(S)

    2005-01-01

    Using the relation between the set of embeddings of tori into Euclidean spaces modulo ambient isotopies and the homotopy groups of Stiefel manifolds, we prove new results on embeddings of tori into Euclidean spaces.

  2. Assessing the effects of symmetry on motif discovery and modeling.

    Directory of Open Access Journals (Sweden)

    Lala M Motlhabi

    Full Text Available BACKGROUND: Identifying the DNA binding sites for transcription factors is a key task in modeling the gene regulatory network of a cell. Predicting DNA binding sites computationally suffers from high false positives and false negatives due to various contributing factors, including the inaccurate models for transcription factor specificity. One source of inaccuracy in the specificity models is the assumption of asymmetry for symmetric models. METHODOLOGY/PRINCIPAL FINDINGS: Using simulation studies, so that the correct binding site model is known and various parameters of the process can be systematically controlled, we test different motif finding algorithms on both symmetric and asymmetric binding site data. We show that if the true binding site is asymmetric the results are unambiguous and the asymmetric model is clearly superior to the symmetric model. But if the true binding specificity is symmetric commonly used methods can infer, incorrectly, that the motif is asymmetric. The resulting inaccurate motifs lead to lower sensitivity and specificity than would the correct, symmetric models. We also show how the correct model can be obtained by the use of appropriate measures of statistical significance. CONCLUSIONS/SIGNIFICANCE: This study demonstrates that the most commonly used motif-finding approaches usually model symmetric motifs incorrectly, which leads to higher than necessary false prediction errors. It also demonstrates how alternative motif-finding methods can correct the problem, providing more accurate motif models and reducing the errors. Furthermore, it provides criteria for determining whether a symmetric or asymmetric model is the most appropriate for any experimental dataset.

  3. Embedding complementarity in HCI methods

    DEFF Research Database (Denmark)

    Nielsen, Janni; Yssing, Carsten; Levinsen, Karin

    2007-01-01

    Differences in cultural contexts constitute differences in cognition, and research has shown that different cultures may use different cognitive tools for perception and reasoning. The cultural embeddings are significant in relation to HCI, because the cultural context is also embedded...... in the techniques and the tools that we apply. We lack a framework for discussing what and who we are, when we talk about a person as the user of an ICT system that has to be designed, developed and implemented. As a framework, we suggest a theory of complementary positions that insists on solid accounts from all...... observer posi-tions in relation to perspective, standpoint and focus. We need to develop com-plementary theories that embed complexity, and we need to reflect critically upon forty years of dominance by rationalistic, empirical understandings of the user as illustrated in the literature and practice within...

  4. Cis and trans regulatory mechanisms control AP2-mediated B cell receptor endocytosis via select tyrosine-based motifs.

    Directory of Open Access Journals (Sweden)

    Kathleen Busman-Sahay

    Full Text Available Following antigen recognition, B cell receptor (BCR-mediated endocytosis is the first step of antigen processing and presentation to CD4+ T cells, a crucial component of the initiation and control of the humoral immune response. Despite this, the molecular mechanism of BCR internalization is poorly understood. Recently, studies of activated B cell-like diffuse large B cell lymphoma (ABC DLBCL have shown that mutations within the BCR subunit CD79b leads to increased BCR surface expression, suggesting that CD79b may control BCR internalization. Adaptor protein 2 (AP2 is the major mediator of receptor endocytosis via clathrin-coated pits. The BCR contains five putative AP2-binding YxxØ motifs, including four that are present within two immunoreceptor tyrosine-based activation motifs (ITAMs. Using a combination of in vitro and in situ approaches, we establish that the sole mediator of AP2-dependent BCR internalization is the membrane proximal ITAM YxxØ motif in CD79b, which is a major target of mutation in ABC DLBCL. In addition, we establish that BCR internalization can be regulated at a minimum of two different levels: regulation of YxxØ AP2 binding in cis by downstream ITAM-embedded DCSM and QTAT regulatory elements and regulation in trans by the partner cytoplasmic domain of the CD79 heterodimer. Beyond establishing the basic rules governing BCR internalization, these results illustrate an underappreciated role for ITAM residues in controlling clathrin-dependent endocytosis and highlight the complex mechanisms that control the activity of AP2 binding motifs in this receptor system.

  5. Corrosion Monitors for Embedded Evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Robinson, Alex L. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Pfeifer, Kent B. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Casias, Adrian L. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Howell, Stephen W. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Sorensen, Neil R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Missert, Nancy A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-05-01

    We have developed and characterized novel in-situ corrosion sensors to monitor and quantify the corrosive potential and history of localized environments. Embedded corrosion sensors can provide information to aid health assessments of internal electrical components including connectors, microelectronics, wires, and other susceptible parts. When combined with other data (e.g. temperature and humidity), theory, and computational simulation, the reliability of monitored systems can be predicted with higher fidelity.

  6. Characterization of Embedded BPM Collimators

    CERN Document Server

    VALENTINO, Gianluca

    2015-01-01

    During LS1, 16 tertiary collimators (TCTs) and 2 secondary collimators (TCSGs) in IR6 were replaced by new embedded BPM collimators. The BPM functionality allows the possibility to align the collimators more quickly and therefore be able to respond faster to machine configuration changes, as well as a direct monitoring of the beam orbit at the collimators. Following an initial commissioning phase, an MD was carried out to test the new collimators and acquisition electronics with beam in the LHC.

  7. Cybersecurity of embedded computers systems

    OpenAIRE

    Carlioz, Jean

    2016-01-01

    International audience; Several articles have recently raised the issue of computer security of commercial flights by evoking the "connected aircraft, hackers target" or "Wi-Fi on planes, an open door for hackers ? " Or "Can you hack the computer of an Airbus or a Boeing ?". The feared scenario consists in a takeover of operational aircraft software that intentionally cause an accident. Moreover, several computer security experts have lately announced they had detected flaws in embedded syste...

  8. Fundamental cycles and graph embeddings

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    In this paper, we investigate fundamental cycles in a graph G and their relations with graph embeddings. We show that a graph G may be embedded in an orientable surface with genus at least g if and only if for any spanning tree T , there exists a sequence of fundamental cycles C1, C2, . . . , C2g with C2i-1 ∩ C2i≠ф for 1≤ i ≤g. In particular, among β(G) fundamental cycles of any spanning tree T of a graph G, there are exactly 2γM (G) cycles C1, C2, . . . , C2γM (G) such that C2i-1 ∩ C2i≠ф for 1 ≤i≤γM (G), where β(G) and γM (G) are the Betti number and the maximum genus of G, respectively. This implies that it is possible to construct an orientable embedding with large genus of a graph G from an arbitrary spanning tree T (which may have very large number of odd components in G\\E(T )). This is different from the earlier work of Xuong and Liu, where spanning trees with small odd components are needed. In fact, this makes a common generalization of Xuong, Liu and Fu et al. Furthermore, we show that (1) this result is useful for locating the maximum genus of a graph having a specific edge-cut. Some known results for embedded graphs are also concluded; (2) the maximum genus problem may be reduced to the maximum matching problem. Based on this result and the algorithm of Micali-Vazirani, we present a new efficient algorithm to determine the maximum genus of a graph in O((β(G)) 25 ) steps. Our method is straight and quite different from the algorithm of Furst, Gross and McGeoch which depends on a result of Giles where matroid parity method is needed.

  9. Embedded multiprocessors scheduling and synchronization

    CERN Document Server

    Sriram, Sundararajan

    2009-01-01

    Techniques for Optimizing Multiprocessor Implementations of Signal Processing ApplicationsAn indispensable component of the information age, signal processing is embedded in a variety of consumer devices, including cell phones and digital television, as well as in communication infrastructure, such as media servers and cellular base stations. Multiple programmable processors, along with custom hardware running in parallel, are needed to achieve the computation throughput required of such applications. Reviews important research in key areas related to the multiprocessor implementation of multi

  10. Embedding initial data for black hole collisions

    CERN Document Server

    Romano, J D; Romano, Joseph D; Price, Richard H

    1994-01-01

    We discuss isometric embedding diagrams for the visualization of initial data for the problem of the head-on collision of two black holes. The problem of constructing the embedding diagrams is explicitly presented for the best studied initial data, the Misner geometry. We present a partial solution of the embedding diagrams and discuss issues related to completing the solution.

  11. Embedded Services in Chinese Academic Libraries

    Science.gov (United States)

    Si, Li; Xing, Wenming; Zhou, Limei; Liu, Sha

    2012-01-01

    Embedded librarianship service describes the practice of librarians integrating actively into the user's environment, rather than remaining in the library to await requests for service. This paper examines the concept of embedded service in the recent literature, within the past 5 years. It reports on a survey of embedded service in Chinese…

  12. RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach.

    Science.gov (United States)

    Pan, Xiaoyong; Shen, Hong-Bin

    2017-02-28

    %. Besides the overall enhanced prediction performance, the convolutional neural network module embedded in iDeep is also able to automatically capture the interpretable binding motifs for RBPs. Large-scale experiments demonstrate that these mined binding motifs agree well with the experimentally verified results, suggesting iDeep is a promising approach in the real-world applications. The iDeep framework not only can achieve promising performance than the state-of-the-art predictors, but also easily capture interpretable binding motifs. iDeep is available at http://www.csbio.sjtu.edu.cn/bioinf/iDeep.

  13. Discovering motifs in ranked lists of DNA sequences.

    Directory of Open Access Journals (Sweden)

    Eran Eden

    2007-03-01

    Full Text Available Computational methods for discovery of sequence elements that are enriched in a target set compared with a background set are fundamental in molecular biology research. One example is the discovery of transcription factor binding motifs that are inferred from ChIP-chip (chromatin immuno-precipitation on a microarray measurements. Several major challenges in sequence motif discovery still require consideration: (i the need for a principled approach to partitioning the data into target and background sets; (ii the lack of rigorous models and of an exact p-value for measuring motif enrichment; (iii the need for an appropriate framework for accounting for motif multiplicity; (iv the tendency, in many of the existing methods, to report presumably significant motifs even when applied to randomly generated data. In this paper we present a statistical framework for discovering enriched sequence elements in ranked lists that resolves these four issues. We demonstrate the implementation of this framework in a software application, termed DRIM (discovery of rank imbalanced motifs, which identifies sequence motifs in lists of ranked DNA sequences. We applied DRIM to ChIP-chip and CpG methylation data and obtained the following results. (i Identification of 50 novel putative transcription factor (TF binding sites in yeast ChIP-chip data. The biological function of some of them was further investigated to gain new insights on transcription regulation networks in yeast. For example, our discoveries enable the elucidation of the network of the TF ARO80. Another finding concerns a systematic TF binding enhancement to sequences containing CA repeats. (ii Discovery of novel motifs in human cancer CpG methylation data. Remarkably, most of these motifs are similar to DNA sequence elements bound by the Polycomb complex that promotes histone methylation. Our findings thus support a model in which histone methylation and CpG methylation are mechanistically linked

  14. Binding properties of SUMO-interacting motifs (SIMs) in yeast.

    Science.gov (United States)

    Jardin, Christophe; Horn, Anselm H C; Sticht, Heinrich

    2015-03-01

    Small ubiquitin-like modifier (SUMO) conjugation and interaction play an essential role in many cellular processes. A large number of yeast proteins is known to interact non-covalently with SUMO via short SUMO-interacting motifs (SIMs), but the structural details of this interaction are yet poorly characterized. In the present work, sequence analysis of a large dataset of 148 yeast SIMs revealed the existence of a hydrophobic core binding motif and a preference for acidic residues either within or adjacent to the core motif. Thus the sequence properties of yeast SIMs are highly similar to those described for human. Molecular dynamics simulations were performed to investigate the binding preferences for four representative SIM peptides differing in the number and distribution of acidic residues. Furthermore, the relative stability of two previously observed alternative binding orientations (parallel, antiparallel) was assessed. For all SIMs investigated, the antiparallel binding mode remained stable in the simulations and the SIMs were tightly bound via their hydrophobic core residues supplemented by polar interactions of the acidic residues. In contrary, the stability of the parallel binding mode is more dependent on the sequence features of the SIM motif like the number and position of acidic residues or the presence of additional adjacent interaction motifs. This information should be helpful to enhance the prediction of SIMs and their binding properties in different organisms to facilitate the reconstruction of the SUMO interactome.

  15. Fitting a mixture model by expectation maximization to discover motifs in biopolymers

    Energy Technology Data Exchange (ETDEWEB)

    Bailey, T.L.; Elkan, C. [Univ. of California, La Jolla, CA (United States)

    1994-12-31

    The algorithm described in this paper discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences. Multiple motifs are found by fitting a mixture model to the data, probabilistically erasing the occurrences of the motif thus found, and repeating the process to find successive motifs. The algorithm requires only a set of unaligned sequences and a number specifying the width of the motifs as input. It returns a model of each motif and a threshold which together can be used as a Bayes-optimal classifier for searching for occurrences of the motif in other databases. The algorithm estimates how many times each motif occurs in each sequence in the dataset and outputs an alignment of the occurrences of the motif. The algorithm is capable of discovering several different motifs with differing numbers of occurrences in a single dataset.

  16. Molecular analysis of intact preen waxes of Calidris Canutus (Aves: Scolopacidae) by GC/MS and GC/MS/MS

    NARCIS (Netherlands)

    Sinninghe Damsté, J.S.; Dekker, M.H.A.; Piersma, T.

    2000-01-01

    The intact preen wax esters of the red knot Calidris canutus were studied with gas chromatography/mass spectrometry (GC/MS) and GC/MS/MS. In this latter technique, transitions from the molecular ion to fragment ions representing the fatty acid moiety of the wax esters were measured, providing additi

  17. Interleukin-6 (-174G>C promoter polymorphism in patients infected by hepatitis B virus

    Directory of Open Access Journals (Sweden)

    Seref Demirbas

    2012-04-01

    Full Text Available Objective: Hepatitis B virus (HBV infection is one of the most important health problems in the world. Interleukin-6 (IL-6 has been shown to be a major inflammatory cytokine, inducing cell proliferation and expression of acute response genes, such as fibrinogen and C-reactive protein in hepatocytes. IL-6 levels are elevated in patients acutely infected with HBV and have been associated with progression of infection to chronic hepatitis. Methods: In the present study, the role of IL-6 (-174G/C polymorphism was investigated on individuals which are diagnosed as hepatitis B virus carrier (n=19, chronic hepatitis (n=10 and cirrhosis (n=13, and non-infected individuals with HBV (n=8. In order to determine IL-6 polymorphism, the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP method was applied using genomic DNA extracted from paraffin embedded liver needle biopsy specimens. Results: The genotype frequencies in 50 samples were observed as follows: 76% homozygote typical (GG, 22% heterozygote (GC and 2% homozygote atypical (CC. In this study, limited statistical association was observed between IL-6 polymorphism (GG, GC and CC genotype and chronic hepatitis/cirrhosis compared to hepatitis B virus carriers and non-infected individuals with HBV (p=0.045. Conclusion: As observed in only one patient with chronic hepatitis, IL-6 (-174C/C genotype is very rare in this study group. Because of lower frequency of -174C/C phenotype, studies in larger series can give statistically more precise conclusions. [J Exp Integr Med 2012; 2(2.000: 173-177

  18. Isometric embeddings in cosmology and astrophysics

    Indian Academy of Sciences (India)

    Gareth Amery; Jothi Moodley; James Paul Londal

    2011-09-01

    Recent interest in higher-dimensional cosmological models has prompted some signifi-cant work on the mathematical technicalities of how one goes about embedding spacetimes into some higher-dimensional space. We survey results in the literature (existence theorems and simple explicit embeddings); briefly outline our work on global embeddings as well as explicit results for more complex geometries; and provide some examples. These results are contextualized physically, so as to provide a foundation for a detailed commentary on several key issues in the field such as: the meaning of `Ricci equivalent’ embeddings; the uniqueness of local (or global) embeddings; symmetry inheritance properties; and astrophysical constraints.

  19. Outdoor and indoor benzene evaluation by GC-FID and GC-MS/MS.

    Science.gov (United States)

    Sousa, José A; Domingues, Valentina F; Rosas, Mónica S; Ribeiro, Susana O; Alvim-Ferraz, Conceiçao M; Delerue-Matos, Cristina F

    2011-01-01

    The evaluation of benzene in different environments such as indoor (with and without tobacco smoke), a city area, countryside, gas stations and near exhaust pipes from cars running on different types of fuels was performed. The samples were analyzed using gas chromatography (GC) with flame ionization detection (FID) and tandem mass spectrometric detection (MS/MS) (to confirm the identification of benzene in the air samples). Operating conditions for the GC-MS analysis were optimized as well as the sampling and sample preparation. The results obtained in this work indicate that i) the type of fuel directly influences the benzene concentration in the air. Gasoline with additives provided the highest amount of benzene followed by unleaded gasoline and diesel; ii) the benzene concentration in the gas station was always higher than the advisable limit established by law (5 μg m⁻³) and during the unloading of gasoline the achieved concentration was 8371 μg m⁻³; iii) the data from the countryside (Taliscas) and the urban city (Matosinhos) were below 5 μg m⁻³ except 5 days after a fire on a petroleum refinery plant located near the city; iv) it was proven that in coffee shops where smoking is allowed the benzene concentration is higher (6 μg m⁻³) than in coffee shops where this is forbidden (4 μg m⁻³). This method may also be helpful for environmental analytical chemists who use GC-MS/MS for the confirmation or/and quantification of benzene.

  20. Characterization and classification of complex PAH samples using GC-qMS and GC-TOFMS.

    Science.gov (United States)

    Bergknut, Magnus; Frech, Kristina; Andersson, Patrik L; Haglund, Peter; Tysklind, Mats

    2006-12-01

    The aim of this study was to compare the polycyclic aromatic hydrocarbon (PAH) contents in a number of complex samples, including soil samples from industrial sites, anti-skid sand, urban dust and ash samples from municipal solid waste incinerators. The samples were characterized by routine analysis of PAHs (gas chromatography-quadrupole mass spectrometry) and gas chromatography-time of flight mass spectrometry (GC-TOFMS). Classification of the samples by principal component analysis (PCA) according to their composition of PAHs revealed that samples associated with traffic and the municipal incinerator formed homogeneous clusters, while the PAH-contaminated soils clustered in separate groups. Using spectral data to resolve co-eluting chromatographic peaks, 962 peaks could be identified in the GC-TOFMS analysis of a pooled sample and 123-527 peaks in the individual samples. Many of the studied extracts included a unique set of chemicals, indicating that they had a much more diverse contamination profile than their PAH contents suggested. Compared to routine analysis, GC-TOFMS provided more detailed information about each sample and in this study a large number of alkylated PAHs were found to be associated with the corresponding unsubstituted PAHs. The possibility to filter peaks according to different criteria (e.g. to include only peaks that were detected in the analysis of another sample) was explored and used to identify unique as well as common compounds within samples. This procedure could prove to be valuable for obtaining relevant chemical data for use in conjunction with results from various biological test systems.

  1. Node Embedding via Word Embedding for Network Community Discovery

    CERN Document Server

    Ding, Weicong; Ishwar, Prakash

    2016-01-01

    Neural node embeddings have recently emerged as a powerful representation for supervised learning tasks involving graph-structured data. We leverage this recent advance to develop a novel algorithm for unsupervised community discovery in graphs. Through extensive experimental studies on simulated and real-world data, we demonstrate that the proposed approach consistently improves over the current state-of-the-art. Specifically, our approach empirically attains the information-theoretic limits for community recovery under the benchmark Stochastic Block Models for graph generation and exhibits better stability and accuracy over both Spectral Clustering and Acyclic Belief Propagation in the community recovery limits.

  2. MDMA毒品简介及GC/MS分析%Determination of MDMA by GC/MS

    Institute of Scientific and Technical Information of China (English)

    张春水; 郑珲; 徐鹏

    2004-01-01

    对一例MDMA毒品案件进行技术检测,采用气质联用技术(GC/MS)准确分析了MDMA片剂中物质成分,检出了MDMA、胡椒素甲醛及咖啡因等成分,并建立了该类毒品检验的快速分析方法,为打击毒品犯罪提供了技术保障.

  3. How pathogens use linear motifs to perturb host cell networks

    KAUST Repository

    Via, Allegra

    2015-01-01

    Molecular mimicry is one of the powerful stratagems that pathogens employ to colonise their hosts and take advantage of host cell functions to guarantee their replication and dissemination. In particular, several viruses have evolved the ability to interact with host cell components through protein short linear motifs (SLiMs) that mimic host SLiMs, thus facilitating their internalisation and the manipulation of a wide range of cellular networks. Here we present convincing evidence from the literature that motif mimicry also represents an effective, widespread hijacking strategy in prokaryotic and eukaryotic parasites. Further insights into host motif mimicry would be of great help in the elucidation of the molecular mechanisms behind host cell invasion and the development of anti-infective therapeutic strategies.

  4. Motifs in Triadic Random Graphs based on Steiner Triple Systems

    CERN Document Server

    Winkler, Marco

    2013-01-01

    Conventionally, pairwise relationships between nodes are considered to be the fundamental building blocks of complex networks. However, over the last decade the overabundance of certain sub-network patterns, so called motifs, has attracted high attention. It has been hypothesized, these motifs, instead of links, serve as the building blocks of network structures. Although the relation between a network's topology and the general properties of the system, such as its function, its robustness against perturbations, or its efficiency in spreading information is the central theme of network science, there is still a lack of sound generative models needed for testing the functional role of subgraph motifs. Our work aims to overcome this limitation. We employ the framework of exponential random graphs (ERGMs) to define novel models based on triadic substructures. The fact that only a small portion of triads can actually be set independently poses a challenge for the formulation of such models. To overcome this obst...

  5. Network Motifs in Object-Oriented Software Systems

    CERN Document Server

    Ma, Yutao; Liu, Jing

    2008-01-01

    Nowadays, software has become a complex piece of work that may be beyond our control. Understanding how software evolves over time plays an important role in controlling software development processes. Recently, a few researchers found the quantitative evidence of structural duplication in software systems or web applications, which is similar to the evolutionary trend found in biological systems. To investigate the principles or rules of software evolution, we introduce the relevant theories and methods of complex networks into structural evolution and change of software systems. According to the results of our experiment on network motifs, we find that the stability of a motif shows positive correlation with its abundance and a motif with high Z score tends to have stable structure. These findings imply that the evolution of software systems is based on functional cloning as well as structural duplication and tends to be structurally stable. So, the work presented in this paper will be useful for the analys...

  6. A Literary Study on Embedding Therapy

    Directory of Open Access Journals (Sweden)

    Kwang-Ho Lee

    2003-12-01

    Full Text Available Background : This study focuses on a new acupuncture method of embedding method which inserts a substance on the acupuncture points for continuous stimulation. Clinical applications and cautions were examined through literary investigations. Results : Based on the literary consideration of embedding method, the following results were obtained: 1. Embedding method is a combination of traditional and embedding technique to provide longer duration of stimulation on the acupuncture points. 2. To administer the embedding method, one needs to utilize a embedding thread besides acupuncture apparatus. Sheep gut is commonly used in China and the surgical thread is the choice in Korea. 3. Embedding method may vary from the patient to patient, depending on the nature and location of the illness. Piercing, embedding, and tying are some of the possibilities. 4. Embedding method may have different arrangement of threads based on the choice of usage. 5. Embedding method is effective for various chronic illnesses such as aches, functional diseases, and the diseases of internal organs. 6. When using the embedding methods, cautions against infection and side effects due to strong stimulation are mandatory.

  7. Architecture design of a virtualized embedded system

    Directory of Open Access Journals (Sweden)

    A.Sbaa

    2013-01-01

    Full Text Available Nowadays, embedded systems have become a major driver of technological developments particularly in the industrial sector. In an embedded system, the hardware and software components are so intertwined that evolution is often a big issue. Thanks to the contributions of virtualization it is possible to design more flexible and scalable embedded systems. In fact, virtualization adds an abstraction layer between the hardware and the software to make it less intimately dependent. In this paper we propose system architecture based on embedded virtualization that will be modeled by the multi-agent systems. In the first part, we will discuss the state of the art with respect to embedded systems, multi-agent systems and the concept of virtualization. In the second part, we explain theissues related to traditional embedded systems and the constraints associated with their architecture. Subsequently, we propose a virtualization based architecture for embedded systems. In the last part we will showcase this architecture through a prototype.

  8. [Specific motifs in the genomes of the family Chlamydiaceae].

    Science.gov (United States)

    Demkin, V V; Kirillova, N V

    2012-01-01

    Specific motifs in the genomes of the family Chlamydiaceae were discussed. The search for genetic markers ofbacteria identification and typing is an urgent problem. The progress in sequencing technology resulted in compilation of the database of genomic nucleotide sequences of bacteria. This raised the problem of the search and selection of genetic targets for identification and typing in bacterial genes based on comparative analysis of complete genomic sequences. The goal of this work was to implement comparative genetic analysis of different species of the family Chlamydiaceae. This analysis was focused to detection of specific motifs capable of serving as genetic marker of this family. The consensus domains were detected using the Visual Basic for Application software for MS Excel. Complete coincidence of segments 25 nucleotide long was used as the test for consensus domain selection. One complete genomic sequence for each of 8 bacterial species was taken for the experiment. The experimental sample did not contain complete sequence of C. suis, because at the moment of this research this species was absence in the database GenBank. Comparative assay of the sequences of the C. trachomatis and other representatives of the family Chlamydiaceae revealed 41 common motifs for 8 Chlamydiaceae species tested in this work. The maximal number of consensus motifs was observed in genes of ribosomal RNA and t-RNA. In addition to genes of r-RNA and t-RNA consensus motifs were observed in 5 genes and 6 intergene segments. The gene CTL0299, CTLO800, dagA, and hctA consensus motifs detected in this work can be regarded as identification domains of the family Chlamydiaceae.

  9. Genome Analysis of Conserved Dehydrin Motifs in Vascular Plants

    Directory of Open Access Journals (Sweden)

    Ahmad A. Malik

    2017-05-01

    Full Text Available Dehydrins, a large family of abiotic stress proteins, are defined by the presence of a mostly conserved motif known as the K-segment, and may also contain two other conserved motifs known as the Y-segment and S-segment. Using the dehydrin literature, we developed a sequence motif definition of the K-segment, which we used to create a large dataset of dehydrin sequences by searching the Pfam00257 dehydrin dataset and the Phytozome 10 sequences of vascular plants. A comprehensive analysis of these sequences reveals that lysine residues are highly conserved in the K-segment, while the amino acid type is often conserved at other positions. Despite the Y-segment name, the central tyrosine is somewhat conserved, but can be substituted with two other small aromatic amino acids (phenylalanine or histidine. The S-segment contains a series of serine residues, but in some proteins is also preceded by a conserved LHR sequence. In many dehydrins containing all three of these motifs the S-segment is linked to the K-segment by a GXGGRRKK motif (where X can be any amino acid, suggesting a functional linkage between these two motifs. An analysis of the sequences shows that the dehydrin architecture and several biochemical properties (isoelectric point, molecular mass, and hydrophobicity score are dependent on each other, and that some dehydrin architectures are overexpressed during certain abiotic stress, suggesting that they may be optimized for a specific abiotic stress while others are involved in all forms of dehydration stress (drought, cold, and salinity.

  10. Selection against spurious promoter motifs correlates withtranslational efficiency across bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Froula, Jeffrey L.; Francino, M. Pilar

    2007-05-01

    Because binding of RNAP to misplaced sites could compromise the efficiency of transcription, natural selection for the optimization of gene expression should regulate the distribution of DNA motifs capable of RNAP-binding across the genome. Here we analyze the distribution of the -10 promoter motifs that bind the {sigma}{sup 70} subunit of RNAP in 42 bacterial genomes. We show that selection on these motifs operates across the genome, maintaining an over-representation of -10 motifs in regulatory sequences while eliminating them from the nonfunctional and, in most cases, from the protein coding regions. In some genomes, however, -10 sites are over-represented in the coding sequences; these sites could induce pauses effecting regulatory roles throughout the length of a transcriptional unit. For nonfunctional sequences, the extent of motif under-representation varies across genomes in a manner that broadly correlates with the number of tRNA genes, a good indicator of translational speed and growth rate. This suggests that minimizing the time invested in gene transcription is an important selective pressure against spurious binding. However, selection against spurious binding is detectable in the reduced genomes of host-restricted bacteria that grow at slow rates, indicating that components of efficiency other than speed may also be important. Minimizing the number of RNAP molecules per cell required for transcription, and the corresponding energetic expense, may be most relevant in slow growers. These results indicate that genome-level properties affecting the efficiency of transcription and translation can respond in an integrated manner to optimize gene expression. The detection of selection against promoter motifs in nonfunctional regions also implies that no sequence may evolve free of selective constraints, at least in the relatively small and unstructured genomes of bacteria.

  11. Evidence of selection upon genomic GC-content in bacteria.

    Directory of Open Access Journals (Sweden)

    Falk Hildebrand

    2010-09-01

    Full Text Available The genomic GC-content of bacteria varies dramatically, from less than 20% to more than 70%. This variation is generally ascribed to differences in the pattern of mutation between bacteria. Here we test this hypothesis by examining patterns of synonymous polymorphism using datasets from 149 bacterial species. We find a large excess of synonymous GC→AT mutations over AT→GC mutations segregating in all but the most AT-rich bacteria, across a broad range of phylogenetically diverse species. We show that the excess of GC→AT mutations is inconsistent with mutation bias, since it would imply that most GC-rich bacteria are declining in GC-content; such a pattern would be unsustainable. We also show that the patterns are probably not due to translational selection or biased gene conversion, because optimal codons tend to be AT-rich, and the excess of GC→AT SNPs is observed in datasets with no evidence of recombination. We therefore conclude that there is selection to increase synonymous GC-content in many species. Since synonymous GC-content is highly correlated to genomic GC-content, we further conclude that there is selection on genomic base composition in many bacteria.

  12. Some results on more flexible versions of Graph Motif

    CERN Document Server

    Rizzi, Romeo

    2012-01-01

    The problems studied in this paper originate from Graph Motif, a problem introduced in 2006 in the context of biological networks. Informally speaking, it consists in deciding if a multiset of colors occurs in a connected subgraph of a vertex-colored graph. Due to the high rate of noise in the biological data, more flexible definitions of the problem have been outlined. We present in this paper two inapproximability results for two different optimization variants of Graph Motif. We also study another definition of the problem, when the connectivity constraint is replaced by modularity. While the problem stays NP-complete, it allows algorithms in FPT for biologically relevant parameterizations.

  13. BayesMD: flexible biological modeling for motif discovery

    DEFF Research Database (Denmark)

    Tang, Man-Hung Eric; Krogh, Anders; Winther, Ole

    2008-01-01

    We present BayesMD, a Bayesian Motif Discovery model with several new features. Three different types of biological a priori knowledge are built into the framework in a modular fashion. A mixture of Dirichlets is used as prior over nucleotide probabilities in binding sites. It is trained on trans......We present BayesMD, a Bayesian Motif Discovery model with several new features. Three different types of biological a priori knowledge are built into the framework in a modular fashion. A mixture of Dirichlets is used as prior over nucleotide probabilities in binding sites. It is trained...

  14. Correlating CpG islands, motifs, and sequence variants in human chromosome 21

    Directory of Open Access Journals (Sweden)

    Cercone Nick

    2011-07-01

    Full Text Available Abstract Background CpG islands are important regions in DNA. They usually appear at the 5’ end of genes containing GC-rich dinucleotides. When DNA methylation occurs, gene regulation is affected and it sometimes leads to carcinogenesis. We propose a new detection program using a hidden-markov model alongside the Viterbi algorithm. Methods Our solution provides a graphical user interface not seen in many of the other CGI detection programs and we unify the detection and analysis under one program to allow researchers to scan a genetic sequence, detect the significant CGIs, and analyze the sequence once the scan is complete for any noteworthy findings. Results Using human chromosome 21, we show that our algorithm finds a significant number of CGIs. Running an analysis on a dataset of promoters discovered that the characteristics of methylated and unmethylated CGIs are significantly different. Finally, we detected significantly different motifs between methylated and unmethylated CGI promoters using MEME and MAST. Conclusions Developing this new tool for the community using powerful algorithms has shown that combining analysis with CGI detection will improve the continued research within the field of epigenetics.

  15. Analysis of the Campylobacter jejuni genome by SMRT DNA sequencing identifies restriction-modification motifs.

    Directory of Open Access Journals (Sweden)

    Jason L O'Loughlin

    Full Text Available Campylobacter jejuni is a leading bacterial cause of human gastroenteritis. The goal of this study was to analyze the C. jejuni F38011 strain, recovered from an individual with severe enteritis, at a genomic and proteomic level to gain insight into microbial processes. The C. jejuni F38011 genome is comprised of 1,691,939 bp, with a mol.% (G+C content of 30.5%. PacBio sequencing coupled with REBASE analysis was used to predict C. jejuni F38011 genomic sites and enzymes that may be involved in DNA restriction-modification. A total of five putative methylation motifs were identified as well as the C. jejuni enzymes that could be responsible for the modifications. Peptides corresponding to the deduced amino acid sequence of the C. jejuni enzymes were identified using proteomics. This work sets the stage for studies to dissect the precise functions of the C. jejuni putative restriction-modification enzymes. Taken together, the data generated in this study contributes to our knowledge of the genomic content, methylation profile, and encoding capacity of C. jejuni.

  16. Hyphenated GC-FTIR and GC-MS techniques applied in the analysis of bioactive compounds

    Science.gov (United States)

    Gosav, Steluta; Paduraru, Nicoleta; Praisler, Mirela

    2014-08-01

    The drugs of abuse, which affect human nature and cause numerous crimes, have become a serious problem throughout the world. There are hundreds of amphetamine analogues on the black market. They consist of various alterations of the basic amphetamine molecular structure, which are yet not yet included in the lists of forbidden compounds although they retain or slightly modify the hallucinogenic effects of their parent compound. It is their important variety that makes their identification quite a challenge. A number of analytical procedures for the identification of amphetamines and their analogues have recently been reported. We are presenting the profile of the main hallucinogenic amphetamines obtained with the hyphenated techniques that are recommended for the identification of illicit amphetamines, i. e. gas chromatography combined with mass spectrometry (GC-MS) and gas chromatography coupled with Fourier transform infrared spectrometry (GC-FTIR). The infrared spectra of the analyzed hallucinogenic amphetamines present some absorption bands (1490 cm-1, 1440 cm-1, 1245 cm-1, 1050 cm-1 and 940 cm-1) that are very stable as position and shape, while their intensity depends of the side-chain substitution. The specific ionic fragment of the studied hallucinogenic compounds is the 3,4-methylenedioxybenzyl cation (m/e = 135) which has a small relative abundance (lesser than 20%). The complementarity of the above mentioned techniques for the identification of hallucinogenic compounds is discussed.

  17. Evaluation of GC-APCI/MS and GC-FID as a complementary platform.

    Science.gov (United States)

    Pacchiarotta, Tiziana; Nevedomskaya, Ekaterina; Carrasco-Pancorbo, Alegria; Deelder, André M; Mayboroda, Oleg A

    2010-12-01

    With a development of the metabolomics field, complementary cross-platform approaches started to attract attention, as none of the contemporary analytical methods had the capacity to cover the entire space of the human metabolome. In the current manuscript, we have evaluated an online coupling of gas chromatography (GC)-mass spectrometry (MS) and flame ionization detector (FID) as ways of cross-detector analysis. The possible value of this combination was recognized from the very first days of GC-MS history but was never explored in detail. We have compared the basic analytical parameters of both detectors, such as limit of detection (LOD) and limit of quantification, with intra- and interday reproducibility. We show that for the majority of the tested compounds, MS detector demonstrates lower LOD. At the same time, FID appeared to be more robust, showing lower relative standard deviations (RSDs) for intra- and interday reproducibility. We conclude that the gain of this dual detector acquisition appears to be most evident for complex biological samples, where wide dynamic range and predictable response of FID are useful for an initial quantitative overview of sample composition and estimation of molar proportions of different metabolites. MS provides reliable, structural information and superior, at least in the case of atmospheric pressure chemical ionization, sensitivity. Taken together, both detectors represent a flexible tool for explorative studies and if supported by a powerful data-processing algorithm, would appear to be useful in any metabolic profiling study.

  18. Multipole moments for embedding potentials

    DEFF Research Database (Denmark)

    Nørby, Morten Steen; Olsen, Jógvan Magnus Haugaard; Kongsted, Jacob

    2016-01-01

    Polarizable quantum mechanical (QM)/molecular mechanics (MM)-embedding methods are currently among the most promising methods for computationally feasible, yet reliable, production calculations of localized excitations and molecular response properties of large molecular complexes, such as proteins...... extended with site polarizabilities including internal charge transfer terms. We present a new way of dealing with well-known problems in relation to the use of basis sets with diffuse functions in conventional atomic allocation algorithms, avoiding numerical integration schemes. Using this approach, we...

  19. Testing Complex and Embedded Systems

    CERN Document Server

    Pries, Kim H

    2010-01-01

    Many enterprises regard system-level testing as the final piece of the development effort, rather than as a tool that should be integrated throughout the development process. As a consequence, test teams often execute critical test plans just before product launch, resulting in much of the corrective work being performed in a rush and at the last minute. Presenting combinatorial approaches for improving test coverage, Testing Complex and Embedded Systems details techniques to help you streamline testing and identify problems before they occur--including turbocharged testing using Six Sigma and

  20. Professional Windows Embedded Compact 7

    CERN Document Server

    Phung, Samuel; Joubert, Thierry; Hall, Mike

    2011-01-01

    Learn to program an array of customized devices and solutions As a compact, highly efficient, scalable operating system, Windows Embedded Compact 7 (WEC7) is one of the best options for developing a new generation of network-enabled, media-rich, and service-oriented devices. This in-depth resource takes you through the benefits and capabilities of WEC7 so that you can start using this performance development platform today. Divided into several major sections, the book begins with an introduction and then moves on to coverage of OS design, application development, advanced application developm

  1. [GC x GC measurements of atmospheric aromatic compounds near a busy high-speed road in Beijing].

    Science.gov (United States)

    Mao, Ting; Xu, Xiao-bin; Wang, Ying

    2009-10-15

    Comprehensive two-dimensional gas chromatography (GC x GC) is a powerful instrumental tool often used to analyze complex mixtures. An optimized GC x GC method had been applied to the quantitative analysis of aromatic compounds in air samples collected near a busy high-speed road in Beijing during the 2007 National Holidays. In the resulting GC x GC chromatograms, aromatic species were resolved from other compound classes and were grouped in a manner that facilitated identification and integration, showing more information of aromatic compounds compared to traditional one-dimensional GC. Totally more than 30 aromatic species were identified and quantified. The average concentrations of monocyclic aromatic compounds ranged from 0.75 x 10(-9) to 24.64 x 10(-9) C, with toluene having the highest concentration, followed by m, p-xylene and ethylbenzene. The average concentrations of the measured polycyclic aromatic compounds ranged from 0.03 x 10(-9) to 2.28 x 10(-9) C, with naphthalene having the highest concentration, followed by 2-methyl-naphthalene and 4-methyl-1, 1'-biphenyl. The four-ring and higher polycyclic aromatic compounds were not detectable in the gaseous samples. The levels of aromatic compounds were significantly influenced by meteorological parameters. Benzene and toluene were poorly correlated with higher aromatic compounds though the latter compounds were highly correlated among each other, suggesting that both were significantly influenced by sources other than vehicle exhaust and gasoline evaporation.

  2. Audio Steganography with Embedded Text

    Science.gov (United States)

    Teck Jian, Chua; Chai Wen, Chuah; Rahman, Nurul Hidayah Binti Ab.; Hamid, Isredza Rahmi Binti A.

    2017-08-01

    Audio steganography is about hiding the secret message into the audio. It is a technique uses to secure the transmission of secret information or hide their existence. It also may provide confidentiality to secret message if the message is encrypted. To date most of the steganography software such as Mp3Stego and DeepSound use block cipher such as Advanced Encryption Standard or Data Encryption Standard to encrypt the secret message. It is a good practice for security. However, the encrypted message may become too long to embed in audio and cause distortion of cover audio if the secret message is too long. Hence, there is a need to encrypt the message with stream cipher before embedding the message into the audio. This is because stream cipher provides bit by bit encryption meanwhile block cipher provide a fixed length of bits encryption which result a longer output compare to stream cipher. Hence, an audio steganography with embedding text with Rivest Cipher 4 encryption cipher is design, develop and test in this project.

  3. Testing framework for embedded languages

    Science.gov (United States)

    Leskó, Dániel; Tejfel, Máté

    2012-09-01

    Embedding a new programming language into an existing one is a widely used technique, because it fastens the development process and gives a part of a language infrastructure for free (e.g. lexical, syntactical analyzers). In this paper we are presenting a new advantage of this development approach regarding to adding testing support for these new languages. Tool support for testing is a crucial point for a newly designed programming language. It could be done in the hard way by creating a testing tool from scratch, or we could try to reuse existing testing tools by extending them with an interface to our new language. The second approach requires less work, and also it fits very well for the embedded approach. The problem is that the creation of such interfaces is not straightforward at all, because the existing testing tools were mostly not designed to be extendable and to be able to deal with new languages. This paper presents an extendable and modular model of a testing framework, in which the most basic design decision was to keep the - previously mentioned - interface creation simple and straightforward. Other important aspects of our model are the test data generation, the oracle problem and the customizability of the whole testing phase.

  4. Information embedding meets distributed control

    CERN Document Server

    Grover, Pulkit; Sahai, Anant

    2010-01-01

    We consider the problem of information embedding where the encoder modifies a white Gaussian host signal in a power-constrained manner to encode the message, and the decoder recovers both the embedded message and the modified host signal. This extends the recent work of Sumszyk and Steinberg to the continuous-alphabet Gaussian setting. We show that a dirty-paper-coding based strategy achieves the optimal rate for perfect recovery of the modified host and the message. We also provide bounds for the extension wherein the modified host signal is recovered only to within a specified distortion. When specialized to the zero-rate case, our results provide the tightest known lower bounds on the asymptotic costs for the vector version of a famous open problem in distributed control -- the Witsenhausen counterexample. Using this bound, we characterize the asymptotically optimal costs for the vector Witsenhausen problem numerically to within a factor of 1.3 for all problem parameters, improving on the earlier best know...

  5. Drilling azimuth gamma embedded design

    Directory of Open Access Journals (Sweden)

    Zhou Yi Ren

    2016-01-01

    Full Text Available Embedded drilling azimuth gamma design, the use of radioactive measuring principle embedded gamma measurement while drilling a short section analysis. Monte Carlo method, in response to the density of horizontal well logging numerical simulation of 16 orientation, the orientation of horizontal well analysed, calliper, bed boundary location, space, different formation density, formation thickness, and other factors inclined strata dip the impact by simulating 137Cs sources under different formation conditions of the gamma distribution, to determine the orientation of drilling density tool can detect window size and space, draw depth of the logging methods. The data 360° azimuth imaging, image processing method to obtain graph, display density of the formation, dip and strata thickness and other parameters, the logging methods obtain real-time geo-steering. To establish a theoretical basis for the orientation density logging while drilling method implementation and application of numerical simulation in-depth study of the MWD azimuth and density log response factors of horizontal wells.

  6. Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters

    Directory of Open Access Journals (Sweden)

    Farré Domènec

    2007-12-01

    Full Text Available Abstract Background The arrangement of regulatory motifs in gene promoters, or promoter architecture, is the result of mutation and selection processes that have operated over many millions of years. In mammals, tissue-specific transcriptional regulation is related to the presence of specific protein-interacting DNA motifs in gene promoters. However, little is known about the relative location and spacing of these motifs. To fill this gap, we have performed a systematic search for motifs that show significant bias at specific promoter locations in a large collection of housekeeping and tissue-specific genes. Results We observe that promoters driving housekeeping gene expression are enriched in particular motifs with strong positional bias, such as YY1, which are of little relevance in promoters driving tissue-specific expression. We also identify a large number of motifs that show positional bias in genes expressed in a highly tissue-specific manner. They include well-known tissue-specific motifs, such as HNF1 and HNF4 motifs in liver, kidney and small intestine, or RFX motifs in testis, as well as many potentially novel regulatory motifs. Based on this analysis, we provide predictions for 559 tissue-specific motifs in mouse gene promoters. Conclusion The study shows that motif positional bias is an important feature of mammalian proximal promoters and that it affects both general and tissue-specific motifs. Motif positional constraints define very distinct promoter architectures depending on breadth of expression and type of tissue.

  7. Nephila clavipes Flagelliform silk-like GGX motifs contribute to extensibility and spacer motifs contribute to strength in synthetic spider silk fibers.

    Science.gov (United States)

    Adrianos, Sherry L; Teulé, Florence; Hinman, Michael B; Jones, Justin A; Weber, Warner S; Yarger, Jeffery L; Lewis, Randolph V

    2013-06-10

    Flagelliform spider silk is the most extensible silk fiber produced by orb weaver spiders, though not as strong as the dragline silk of the spider. The motifs found in the core of the Nephila clavipes flagelliform Flag protein are GGX, spacer, and GPGGX. Flag does not contain the polyalanine motif known to provide the strength of dragline silk. To investigate the source of flagelliform fiber strength, four recombinant proteins were produced containing variations of the three core motifs of the Nephila clavipes flagelliform Flag protein that produces this type of fiber. The as-spun fibers were processed in 80% aqueous isopropanol using a standardized process for all four fiber types, which produced improved mechanical properties. Mechanical testing of the recombinant proteins determined that the GGX motif contributes extensibility and the spacer motif contributes strength to the recombinant fibers. Recombinant protein fibers containing the spacer motif were stronger than the proteins constructed without the spacer that contained only the GGX motif or the combination of the GGX and GPGGX motifs. The mechanical and structural X-ray diffraction analysis of the recombinant fibers provide data that suggests a functional role of the spacer motif that produces tensile strength, though the spacer motif is not clearly defined structurally. These results indicate that the spacer is likely a primary contributor of strength, with the GGX motif supplying mobility to the protein network of native N. clavipes flagelliform silk fibers.

  8. Micro GC's for Contaminant Monitoring in Spacecraft Air Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Based on the successful separation of 20 compounds using a 1 m coated microcolumn in Phase I, we propose to design a new micro-gas chromatograph (microGC) system to...

  9. Fast GC for Space Applications Based on PIES Technology Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Development of a novel analytical instrument which combines the advantages of fast GC and a detector capable of identifying species is proposed. Experiments in the...

  10. Fast GC for Space Applications Based on PIES Technology Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This SBIR Phase II project is aimed at the development of an analytical instrument which combines the advantages of fast gas chromatography (GC) and a detector that...

  11. Linear motif atlas for phosphorylation-dependent signaling

    DEFF Research Database (Denmark)

    Miller, Martin Lee; Jensen, LJ; Diella, F;

    2008-01-01

    Systematic and quantitative analysis of protein phosphorylation is revealing dynamic regulatory networks underlying cellular responses to environmental cues. However, matching these sites to the kinases that phosphorylate them and the phosphorylation-dependent binding domains that may subsequently...... sequence models of linear motifs. The atlas is available as a community resource (http://netphorest.info)....

  12. How curved membranes recruit amphipathic helices and protein anchoring motifs

    DEFF Research Database (Denmark)

    Hatzakis, Nikos; Bhatia, Vikram Kjøller; Larsen, Jannik;

    2009-01-01

    Lipids and several specialized proteins are thought to be able to sense the curvature of membranes (MC). Here we used quantitative fluorescence microscopy to measure curvature-selective binding of amphipathic motifs on single liposomes 50-700 nm in diameter. Our results revealed that sensing...

  13. RNA recognition motif (RRM)-containing proteins in Bombyx mori

    African Journals Online (AJOL)

    STORAGESEVER

    2009-03-20

    Mar 20, 2009 ... containing proteins in B. mori and may serve as a basis ... and domain structures, and then orthologous proteins were assigned with similar .... DQ648521. CG10466. RNA binding motif protein,. X-linked. 2. (RBMX2). 1RRM. 1 ... Polymerase delta ... tion or initiation, 8 in transcription, and 3 in apoptosis. For.

  14. Mother goddesses with boat motifs on stone sculptures from Goa

    Digital Repository Service at National Institute of Oceanography (India)

    Kerkar, R.; Gaur, A.S.

    in temples made of laterite dressed stone blocks, which might have been a tradition of the post-Kadamba period. At Savarde, a few architectural members lying Fig.4. Fragmented sculpture with boat motif from Guleli in the vicinity suggest that a temple...

  15. Motifs in triadic random graphs based on Steiner triple systems

    Science.gov (United States)

    Winkler, Marco; Reichardt, Jörg

    2013-08-01

    Conventionally, pairwise relationships between nodes are considered to be the fundamental building blocks of complex networks. However, over the last decade, the overabundance of certain subnetwork patterns, i.e., the so-called motifs, has attracted much attention. It has been hypothesized that these motifs, instead of links, serve as the building blocks of network structures. Although the relation between a network's topology and the general properties of the system, such as its function, its robustness against perturbations, or its efficiency in spreading information, is the central theme of network science, there is still a lack of sound generative models needed for testing the functional role of subgraph motifs. Our work aims to overcome this limitation. We employ the framework of exponential random graph models (ERGMs) to define models based on triadic substructures. The fact that only a small portion of triads can actually be set independently poses a challenge for the formulation of such models. To overcome this obstacle, we use Steiner triple systems (STSs). These are partitions of sets of nodes into pair-disjoint triads, which thus can be specified independently. Combining the concepts of ERGMs and STSs, we suggest generative models capable of generating ensembles of networks with nontrivial triadic Z-score profiles. Further, we discover inevitable correlations between the abundance of triad patterns, which occur solely for statistical reasons and need to be taken into account when discussing the functional implications of motif statistics. Moreover, we calculate the degree distributions of our triadic random graphs analytically.

  16. Insights into the motif preference of APOBEC3 enzymes.

    Directory of Open Access Journals (Sweden)

    Diako Ebrahimi

    Full Text Available We used a multivariate data analysis approach to identify motifs associated with HIV hypermutation by different APOBEC3 enzymes. The analysis showed that APOBEC3G targets G mainly within GG, TG, TGG, GGG, TGGG and also GGGT. The G nucleotides flanked by a C at the 3' end (in +1 and +2 positions were indicated as disfavoured targets by APOBEC3G. The G nucleotides within GGGG were found to be targeted at a frequency much less than what is expected. We found that the infrequent G-to-A mutation within GGGG is not limited to the inaccessibility, to APOBEC3, of poly Gs in the central and 3'polypurine tracts (PPTs which remain double stranded during the HIV reverse transcription. GGGG motifs outside the PPTs were also disfavoured. The motifs GGAG and GAGG were also found to be disfavoured targets for APOBEC3. The motif-dependent mutation of G within the HIV genome by members of the APOBEC3 family other than APOBEC3G was limited to GA→AA changes. The results did not show evidence of other types of context dependent G-to-A changes in the HIV genome.

  17. Insights into the motif preference of APOBEC3 enzymes.

    Science.gov (United States)

    Ebrahimi, Diako; Alinejad-Rokny, Hamid; Davenport, Miles P

    2014-01-01

    We used a multivariate data analysis approach to identify motifs associated with HIV hypermutation by different APOBEC3 enzymes. The analysis showed that APOBEC3G targets G mainly within GG, TG, TGG, GGG, TGGG and also GGGT. The G nucleotides flanked by a C at the 3' end (in +1 and +2 positions) were indicated as disfavoured targets by APOBEC3G. The G nucleotides within GGGG were found to be targeted at a frequency much less than what is expected. We found that the infrequent G-to-A mutation within GGGG is not limited to the inaccessibility, to APOBEC3, of poly Gs in the central and 3'polypurine tracts (PPTs) which remain double stranded during the HIV reverse transcription. GGGG motifs outside the PPTs were also disfavoured. The motifs GGAG and GAGG were also found to be disfavoured targets for APOBEC3. The motif-dependent mutation of G within the HIV genome by members of the APOBEC3 family other than APOBEC3G was limited to GA→AA changes. The results did not show evidence of other types of context dependent G-to-A changes in the HIV genome.

  18. Down regulation of RNA binding motif, single-stranded interacting protein 3, along with up regulation of nuclear HIF1A correlates with poor prognosis in patients with gastric cancer

    Science.gov (United States)

    Zhao, Yingjie; Wang, Yuqi; Sun, Ruochuan; Yan, Qiang; Zhang, Shangxin; Lu, Mingdian; Zhang, Zhen; Lu, Daru; Li, Yongxiang

    2017-01-01

    Frequent loss of multiple regions in short arm of chromosome 3 is found in various tumors including gastric cancer (GC). RNA binding motif, single-stranded interacting protein 3 (RBMS3) is a tumor suppressor gene located in this region and mediates cancer angiogenesis. However, the role of RBMS3 in GC remains unclear. To evaluate whether RBMS3, together with HIF1A, another key regulator of angiogenesis, predicts GC prognosis, the levels of RBMS3 and HIF1A were first examined by quantitative PCR (qPCR) and western blot from 27 fresh frozen GC and paired normal gastric tissues and then tested by immunohistochemistry (IHC) from 191 GC and 46 normal controls. Moreover, uni- and multivariate analysis were employed to assess the correlations between their levels and microvessel density (MVD) and clinical prognosis. To further identify RBMS3 function in vitro, cell proliferation assay, clonogenic assay, flow cytometry analysis and endothelial cell tube formation assay were employed. We found that RBMS3 level was decreased, whereas HIF1A was elevated in GC. Furthermore, we demonstrated that RBMS3 was an independent prognostic factor and the levels of RBMS3 and HIF1A were associated with GC angiogenesis and histopathological differentiation: patients with lower RBMS3 level and higher nuclear HIF1A expression had poorer prognosis. Besides, gain- and loss-of-function study revealed RBMS3 regulation on G1/S progression, cell proliferation and the tube formation of human umbilical vein endothelial cells (HUVECs) in vitro. These findings implicated that RBMS3 and nuclear HIF1A could act as prognostic biomarkers and therapeutic targets for GC. PMID:27902480

  19. Variable structure motifs for transcription factor binding sites.

    Science.gov (United States)

    Reid, John E; Evans, Kenneth J; Dyer, Nigel; Wernisch, Lorenz; Ott, Sascha

    2010-01-14

    Classically, models of DNA-transcription factor binding sites (TFBSs) have been based on relatively few known instances and have treated them as sites of fixed length using position weight matrices (PWMs). Various extensions to this model have been proposed, most of which take account of dependencies between the bases in the binding sites. However, some transcription factors are known to exhibit some flexibility and bind to DNA in more than one possible physical configuration. In some cases this variation is known to affect the function of binding sites. With the increasing volume of ChIP-seq data available it is now possible to investigate models that incorporate this flexibility. Previous work on variable length models has been constrained by: a focus on specific zinc finger proteins in yeast using restrictive models; a reliance on hand-crafted models for just one transcription factor at a time; and a lack of evaluation on realistically sized data sets. We re-analysed binding sites from the TRANSFAC database and found motivating examples where our new variable length model provides a better fit. We analysed several ChIP-seq data sets with a novel motif search algorithm and compared the results to one of the best standard PWM finders and a recently developed alternative method for finding motifs of variable structure. All the methods performed comparably in held-out cross validation tests. Known motifs of variable structure were recovered for p53, Stat5a and Stat5b. In addition our method recovered a novel generalised version of an existing PWM for Sp1 that allows for variable length binding. This motif improved classification performance. We have presented a new gapped PWM model for variable length DNA binding sites that is not too restrictive nor over-parameterised. Our comparison with existing tools shows that on average it does not have better predictive accuracy than existing methods. However, it does provide more interpretable models of motifs of variable

  20. Variable structure motifs for transcription factor binding sites

    Directory of Open Access Journals (Sweden)

    Wernisch Lorenz

    2010-01-01

    Full Text Available Abstract Background Classically, models of DNA-transcription factor binding sites (TFBSs have been based on relatively few known instances and have treated them as sites of fixed length using position weight matrices (PWMs. Various extensions to this model have been proposed, most of which take account of dependencies between the bases in the binding sites. However, some transcription factors are known to exhibit some flexibility and bind to DNA in more than one possible physical configuration. In some cases this variation is known to affect the function of binding sites. With the increasing volume of ChIP-seq data available it is now possible to investigate models that incorporate this flexibility. Previous work on variable length models has been constrained by: a focus on specific zinc finger proteins in yeast using restrictive models; a reliance on hand-crafted models for just one transcription factor at a time; and a lack of evaluation on realistically sized data sets. Results We re-analysed binding sites from the TRANSFAC database and found motivating examples where our new variable length model provides a better fit. We analysed several ChIP-seq data sets with a novel motif search algorithm and compared the results to one of the best standard PWM finders and a recently developed alternative method for finding motifs of variable structure. All the methods performed comparably in held-out cross validation tests. Known motifs of variable structure were recovered for p53, Stat5a and Stat5b. In addition our method recovered a novel generalised version of an existing PWM for Sp1 that allows for variable length binding. This motif improved classification performance. Conclusions We have presented a new gapped PWM model for variable length DNA binding sites that is not too restrictive nor over-parameterised. Our comparison with existing tools shows that on average it does not have better predictive accuracy than existing methods. However, it does

  1. The dynamical fingerprint of gas-expulsion: Insights into the assembly of the Milky Ways' old GC system

    CERN Document Server

    Marks, Michael

    2011-01-01

    Since the oldest globular clusters (GCs) are early residuals from the formation of the Milky Way (MW), GCs were exposed to the likely evolving potential of our Galaxy. The expulsion of the residual-gas from the GC's embedded progenitors is sensitive to the conditions in the pre-MW gas cloud. By means of N-body computations it is shown that gas throw-out from initially mass-segregated GCs affect the shape of the low-mass stellar mass function (MF) and that its imprint might still be visible in the present-day MF (PDMF). The strength of the tidal-field at birth influences the degree of gas-expulsion driven low-mass-star depletion and therefore the PDMF probes the MW potential at the time of GC formation. It is argued that among the old GC population in the MW, younger GCs show stronger low-mass-star loss than older GCs. This is shown to be consistent with a contracting and self-gravitating cloud in which fluctuations in the pre-MW potential grow with time. An initially relatively smooth tidal field evolved into...

  2. Conditional mean embeddings as regressors - supplementary

    CERN Document Server

    Grünewälder, Steffen; Baldassarre, Luca; Patterson, Sam; Gretton, Arthur; Pontil, Massimilano

    2012-01-01

    We demonstrate an equivalence between reproducing kernel Hilbert space (RKHS) embeddings of conditional distributions and vector-valued regressors. This connection introduces a natural regularized loss function which the RKHS embeddings minimise, providing an intuitive understanding of the embeddings and a justification for their use. Furthermore, the equivalence allows the application of vector-valued regression methods and results to the problem of learning conditional distributions. Using this link we derive a sparse version of the embedding by considering alternative formulations. Further, by applying convergence results for vector-valued regression to the embedding problem we derive minimax convergence rates which are O(\\log(n)/n) -- compared to current state of the art rates of O(n^{-1/4}) -- and are valid under milder and more intuitive assumptions. These minimax upper rates coincide with lower rates up to a logarithmic factor, showing that the embedding method achieves nearly optimal rates. We study o...

  3. Operating System Performance Analyzer for Embedded Systems

    Directory of Open Access Journals (Sweden)

    Shahzada Khayyam Nisar

    2011-11-01

    Full Text Available RTOS provides a number of services to an embedded system designs such as case management, memory management, and Resource Management to build a program. Choosing the best OS for an embedded system is based on the available OS for system designers and their previous knowledge and experience. This can cause an imbalance between the OS and embedded systems. RTOS performance analysis is critical in the design and integration of embedded software to ensure that limits the application meet at runtime. To select an appropriate operating system for an embedded system for a particular application, the OS services to be analyzed. These OS services are identified by parameters to establish performance metrics. Performance Metrics selected include context switching, Preemption time and interrupt latency. Performance Metrics are analyzed to choose the right OS for an embedded system for a particular application.

  4. Sequence alignment reveals possible MAPK docking motifs on HIV proteins.

    Directory of Open Access Journals (Sweden)

    Perry Evans

    Full Text Available Over the course of HIV infection, virus replication is facilitated by the phosphorylation of HIV proteins by human ERK1 and ERK2 mitogen-activated protein kinases (MAPKs. MAPKs are known to phosphorylate their substrates by first binding with them at a docking site. Docking site interactions could be viable drug targets because the sequences guiding them are more specific than phosphorylation consensus sites. In this study we use multiple bioinformatics tools to discover candidate MAPK docking site motifs on HIV proteins known to be phosphorylated by MAPKs, and we discuss the possibility of targeting docking sites with drugs. Using sequence alignments of HIV proteins of different subtypes, we show that MAPK docking patterns previously described for human proteins appear on the HIV matrix, Tat, and Vif proteins in a strain dependent manner, but are absent from HIV Rev and appear on all HIV Nef strains. We revise the regular expressions of previously annotated MAPK docking patterns in order to provide a subtype independent motif that annotates all HIV proteins. One revision is based on a documented human variant of one of the substrate docking motifs, and the other reduces the number of required basic amino acids in the standard docking motifs from two to one. The proposed patterns are shown to be consistent with in silico docking between ERK1 and the HIV matrix protein. The motif usage on HIV proteins is sufficiently different from human proteins in amino acid sequence similarity to allow for HIV specific targeting using small-molecule drugs.

  5. Application of GC-FID and GC-MS for assessing PAHs in suspended dust.

    Science.gov (United States)

    Weglarz, A; Skrok, R

    2000-07-01

    The social concern about polycyclic aromatic hydrocarbons (PAHs) is due to the awareness that several of them are carcinogens and are present in polluted air. Several epidemiological investigations have tried to assess the influence of air pollution on the incidence in the population (1). Some authors have suggest that 1-10% of the incidence of lung cancer is caused by air pollution (2, 3). Several sources, e.g. traffic, oil heating, wood stoves, industry may contribute PAHs to the air pollution. Therefore continuous air pollution control applying selective and precise analytical procedures is needed. The submitted work presents results of examination of sixteen polycyclic aromatic hydrocarbons [naphthalene, acenaphthylene, acenaphthene, fluorene, phenanthrene, anthracene, fluoranthene, pyrene, chrysene, benzo(a)anthracene, benzo(b)fluoranthene, benzo(k)fluoranthene, benzo(a)pyrene, indeno(1,2,3-cd)pyrene, dibenzo(a, h)anthracene, benzo(ghi)perylene] settled on particles of 10 microns fractions of ashes, emitted from industrial and communication sources. Samples of suspended dust were collected at twelve measuring points, from May to June 1998, in 24-hour cycles, in accordance with US EPA methodology. PAHs were extracted from suspended dust in a Soxhlet apparatus and then exposed to extraction in a liquid-solid system (solid extraction-SPE) to eliminate redundant pollution, which may interfere with compounds by determined analysis. Samples were then analyzed using by capillary gas chromatographs "Varian" model 3400 with FID and MS detectors. Results of analysis make it possible to determine the influence of industry and traffic on atmospheric pollution, to compare results of two analytical methods (GC-FID and GC-MS).

  6. The analysis of linear and monomethylalkanes in exhaled breath samples by GC×GC-FID and GC-MS/MS.

    Science.gov (United States)

    Hengerics Szabó, Alexandra; Podolec, Peter; Ferenczy, Viktória; Kubinec, Róbert; Blaško, Jaroslav; Soják, Ladislav; Górová, Renáta; Addová, Gabriela; Ostrovský, Ivan; Višňovský, Jozef; Bierhanzl, Václav; Čabala, Radomír; Amann, Anton

    2015-01-26

    A new arrangement of the INCAT (inside needle capillary adsorption trap) device with Carbopack X and Carboxen 1000 as sorbent materials was applied for sampling, preconcentration and injection of C6C19n-alkanes and their monomethyl analogs in exhaled breath samples. For the analysis both GC-MS/MS and GC×GC-FID techniques were used. Identification of the analytes was based on standards, measured retention indices and selective SRM transitions of the individual isomers. The GC-MS/MS detection limits were in the range from 2.1 pg for n-tetradecane to 86 pg for 5-methyloctadecane. The GC×GC-FID detection limits ranged from 19 pg for n-dodecane to 110 pg for 3-methyloctane.

  7. Detection of virgin coconut oil adulteration with animal fats using quantitative cholesterol by GC × GC-TOF/MS analysis.

    Science.gov (United States)

    Xu, Baocheng; Li, Peiwu; Ma, Fei; Wang, Xiuping; Matthäus, Bertrand; Chen, Ran; Yang, Qingqing; Zhang, Wen; Zhang, Qi

    2015-07-01

    A new method based on the cholesterol level was developed to detect the presence of animal fats in virgin coconut oil (VCO). In this study, the sterols in VCO and animal fats was separated using conventional one-dimensional gas chromatography (1D GC) and comprehensive two-dimensional gas chromatography (GC×GC). Compared with 1D GC, the GC×GC system could obtain a complete baseline separation of the sterol trimethylsilyl ethers derived from cholesterol and cholestanol, so that the cholesterol content in pure VCO and false VCO adulterated with animal fats could be accurately determined. Cholesterol, a main sterol found in animal fats, represented less than 5mg/kg of VCO. The study demonstrated that the determination of the cholesterol level in VCO could be used for reliable detection of the presence of lard, chicken fat, mutton tallow, beef tallow, or their mixture in VCO at a level as little as 0.25%.

  8. Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2

    DEFF Research Database (Denmark)

    Miller, Martin Lee; Hanke, S.; Hinsby, A. M.

    2008-01-01

    and validated as a binding motif for the SH2 domain-containing inositol phosphatase SHIP2. Our decomposition of the in vivo Tyr(P) proteome furthermore suggests that two-thirds of the Tyr(P) sites mediate interaction, whereas the remaining third govern processes such as enzyme activation and nucleic acid...

  9. Graphical Model Debugger Framework for Embedded Systems

    DEFF Research Database (Denmark)

    Zeng, Kebin; Guo, Yu; Angelov, Christo K.

    2010-01-01

    Model Driven Software Development has offered a faster way to design and implement embedded real-time software by moving the design to a model level, and by transforming models to code. However, the testing of embedded systems has remained at the code level. This paper presents a Graphical Model...... Debugger Framework, providing an auxiliary avenue of analysis of system models at runtime by executing generated code and updating models synchronously, which allows embedded developers to focus on the model level. With the model debugger, embedded developers can graphically test their design model...

  10. Association of Arabidopsis type-II ROPs with the plasma membrane requires a conserved C-terminal sequence motif and a proximal polybasic domain.

    Science.gov (United States)

    Lavy, Meirav; Yalovsky, Shaul

    2006-06-01

    Plant ROPs (or RACs) are soluble Ras-related small GTPases that are attached to cell membranes by virtue of the post-translational lipid modifications of prenylation and S-acylation. ROPs (RACs) are subdivided into two major subgroups called type-I and type-II. Whereas type-I ROPs terminate with a conserved CaaL box and undergo prenylation, type-II ROPs undergo S-acylation on two or three C-terminal cysteines. In the present work we determined the sequence requirement for association of Arabidopsis type-II ROPs with the plasma membrane. We identified a conserved sequence motif, designated the GC-CG box, in which the modified cysteines are flanked by glycines. The GC-CG box cysteines are separated by five to six mostly non-polar residues. Deletion of this sequence or the introduction of mutations that change its nature disrupted the association of ROPs with the membrane. Mutations that changed the GC-CG box glycines to alanines also interfered with membrane association. Deletion of a polybasic domain proximal to the GC-CG box disrupted the plasma membrane association of AtROP10. A green fluorescent protein fusion protein containing the C-terminal 25 residues of AtROP10, including its polybasic domain and GC-CG box, was primarily associated with the plasma membrane but a similar fusion protein lacking the polybasic domain was exclusively localized in the soluble fraction. These data provide evidence for the minimal sequence required for plasma membrane association of type-II ROPs in Arabidopsis and other plant species.

  11. Determination of elaidic and vaccenic acids in foods using GC×GC-FID and GC×GC-TOFMS.

    Science.gov (United States)

    Ha, Jaeho; Seo, Dongwon; Shin, Dongbin

    2011-07-15

    Trans fatty acids (TFAs) are present in meat and dairy products as m ruminant animals and in vegetable fats due to partial hydrogenation. This study aimed to discriminate between natural (N-TFA) and hydrogenated trans fatty (H-TFA) acids by GC×GC-flame ionization detection (GC×GC-FID) and comprehensive GC×GC-time-of-flight mass spectrometry (GC×GC-TOFMS). The separation of two kinds of trans fats, vaccenic acid (18:1 trans-11) and elaidic acid (18:1 trans-9), was performed using GC×GC-FID and GC×GC-TOFMS. A 100 m×0.25 mm I.D.×0.2 μm (film thickness) SP-2560 (bis-cyanopropyl polysiloxane) fused capillary column (first separation dimension, 1D) was coupled to a 1.5 m×0.18 mm I.D.×0.18 μm (film thickness) RTX-5 (5% diphenyl/95% dimethyl polysiloxane) fused capillary column (second separation dimension, 2D). The RSD of the intra-day repeatability by both GC×GC-FID and GC×GC-TOFMS for elaidic and vaccenic acids was ≤9.56% and ≤9.97%, and the RSD of the inter-day repeatability was ≤8.49 and ≤9.06%, respectively. It was found that the V/E value (vaccenic acid to elaidic acid ratio) could be used to distinguish H-TFA from N-TFA and to evaluate the quality of the fatty foods.

  12. Immunotherapy of HIV-infected patients with Gc protein-derived macrophage activating factor (GcMAF).

    Science.gov (United States)

    Yamamoto, Nobuto; Ushijima, Naofumi; Koga, Yoshihiko

    2009-01-01

    Serum Gc protein (known as vitamin D3-binding protein) is the precursor for the principal macrophage activating factor (MAF). The MAF precursor activity of serum Gc protein of HIV-infected patients was lost or reduced because Gc protein is deglycosylated by alpha-N-acetylgalactosaminidase (Nagalase) secreted from HIV-infected cells. Therefore, macrophages of HIV-infected patients having deglycosylated Gc protein cannot be activated, leading to immunosuppression. Since Nagalase is the intrinsic component of the envelope protein gp120, serum Nagalase activity is the sum of enzyme activities carried by both HIV virions and envelope proteins. These Nagalase carriers were already complexed with anti-HIV immunoglobulin G (IgG) but retained Nagalase activity that is required for infectivity. Stepwise treatment of purified Gc protein with immobilized beta-galactosidase and sialidase generated the most potent macrophage activating factor (termed GcMAF), which produces no side effects in humans. Macrophages activated by administration of 100 ng GcMAF develop a large amount of Fc-receptors as well as an enormous variation of receptors that recognize IgG-bound and unbound HIV virions. Since latently HIV-infected cells are unstable and constantly release HIV virions, the activated macrophages rapidly intercept the released HIV virions to prevent reinfection resulting in exhaustion of infected cells. After less than 18 weekly administrations of 100 ng GcMAF for nonanemic patients, they exhibited low serum Nagalase activities equivalent to healthy controls, indicating eradication of HIV-infection, which was also confirmed by no infectious center formation by provirus inducing agent-treated patient PBMCs. No recurrence occurred and their healthy CD + cell counts were maintained for 7 years.

  13. Power optimized programmable embedded controller

    CERN Document Server

    Kamaraju, M; Tilak, A V N; 10.5121/ijcnc.2010.2409

    2010-01-01

    Now a days, power has become a primary consideration in hardware design, and is critical in computer systems especially for portable devices with high performance and more functionality. Clock-gating is the most common technique used for reducing processor's power. In this work clock gating technique is applied to optimize the power of fully programmable Embedded Controller (PEC) employing RISC architecture. The CPU designed supports i) smart instruction set, ii) I/O port, UART iii) on-chip clocking to provide a range of frequencies , iv) RISC as well as controller concepts. The whole design is captured using VHDL and is implemented on FPGA chip using Xilinx .The architecture and clock gating technique together is found to reduce the power consumption by 33.33% of total power consumed by this chip.

  14. The embedded operating system project

    Science.gov (United States)

    Campbell, R. H.

    1985-01-01

    The design and construction of embedded operating systems for real-time advanced aerospace applications was investigated. The applications require reliable operating system support that must accommodate computer networks. Problems that arise in the construction of such operating systems, reconfiguration, consistency and recovery in a distributed system, and the issues of real-time processing are reported. A thesis that provides theoretical foundations for the use of atomic actions to support fault tolerance and data consistency in real-time object-based system is included. The following items are addressed: (1) atomic actions and fault-tolerance issues; (2) operating system structure; (3) program development; (4) a reliable compiler for path Pascal; and (5) mediators, a mechanism for scheduling distributed system processes.

  15. Differential evolutionary conservation of motif modes in the yeast protein interaction network

    Directory of Open Access Journals (Sweden)

    Yu Chang-Yung

    2006-04-01

    Full Text Available Abstract Background The importance of a network motif (a recurring interconnected pattern of special topology which is over-represented in a biological network lies in its position in the hierarchy between the protein molecule and the module in a protein-protein interaction network. Until now, however, the methods available have greatly restricted the scope of research. While they have focused on the analysis in the resolution of a motif topology, they have not been able to distinguish particular motifs of the same topology in a protein-protein interaction network. Results We have been able to assign the molecular function annotations of Gene Ontology to each protein in the protein-protein interactions of Saccharomyces cerevisiae. For various motif topologies, we have developed an algorithm, enabling us to unveil one million "motif modes", each of which features a unique topological combination of molecular functions. To our surprise, the conservation ratio, i.e., the extent of the evolutionary constraints upon the motif modes of the same motif topology, varies significantly, clearly indicative of distinct differences in the evolutionary constraints upon motifs of the same motif topology. Equally important, for all motif modes, we have found a power-law distribution of the motif counts on each motif mode. We postulate that motif modes may very well represent the evolutionary-conserved topological units of a protein interaction network. Conclusion For the first time, the motifs of a protein interaction network have been investigated beyond the scope of motif topology. The motif modes determined in this study have not only enabled us to differentiate among different evolutionary constraints on motifs of the same topology but have also opened up new avenues through which protein interaction networks can be analyzed.

  16. Overexpression a novel zebra fish spermatogenesis-associated gene 17 (SPATA17) induces apoptosis in GC-1 cells.

    Science.gov (United States)

    Nie, Dongsong; Liu, Y; Xiang, Y

    2011-08-01

    The spermatogenesis-associated 17 gene (SPATA17, previously named MSRG-11) was reported to be a candidate spermatocyte apoptosis-related gene which may play a critical role in human spermatogenesis, especially in meiosis. Analysis of SPATA17 expression and regulation in zebra fish may provide insight into the understanding of the complicated process of gonadogenesis and its potential function in spermatocyte cell apoptosis. In this study, we cloned and characterized the SPATA17 gene from zebra fish which consists of nine exons separated by eight introns. The consensus open reading frame (1258 bp) encodes a polypeptide of 357 amino acids which shares 44% identity with the human SPATA17 gene. Bioinformatic analysis reveals that SPATA17 protein contains three short calmodulin-binding motifs (IQ motif) and is considered to play a critical role in interactions with CaM proteins. Multi-tissue RT-PCR and Northern blot results demonstrated that the zebra fish SPATA17 gene was expressed strongly in testis and a slight amount of expression in ovary. Flow cytometry analysis and genomic DNA ladders result showed that the expression of SPATA17 protein in the GC-1 cell line could accelerate cell apoptosis. Analysis of the SPATA17 sequence and its spatial expression pattern indicate that this gene is highly conserved and may play an important role in the process of zebra fish gonadogenesis.

  17. Aroma active components in aqueous kiwi fruit essence and kiwi fruit puree by GC-MS and multidimensional GC/GC-O.

    Science.gov (United States)

    Jordán, María J; Margaría, Carlos A; Shaw, Philip E; Goodner, Kevin L

    2002-09-11

    Gas chromatography-mass spectrometry (GC-MS) and multidimensional gas chromatography olfactometry (GC/GC-O) were utilized to study the aroma profile and the aroma active components of commercial kiwi essence and the initial fresh fruit puree. Totals of 29 and 33 components were identified and quantified in the essence and the puree, respectively. Ten components were quantified for the first time as constituents of the kiwi fruit including 3-penten-2-ol, 3-hydroxy-2-butanone, 3-methyl-2-butenal, 2-hexanol, nonanal, 3-methyl-1-butanol, 2-methyl-1-butanol, 3-methyl-2-butanone, 3-methyl 3-buten-2-one, and octane. Analysis of these samples by multidimensional gas chromatography-olfactometry (GC-O) allowed for the identification of >80% of the aroma active components present at level traces in this fruit. A total of 35 components appear to contribute to the aroma of kiwi fresh puree and its aqueous essence. Components described for the first time as constituents of the aroma profile in this fruit were 2-ethylfuran, 3-methyl-1-butanol, 2-cyclohexen-1-one, (E,E)-2,6-nonadienal, diethyl succinate, and hexyl hexanoate.

  18. The glycosylation and characterization of the candidate Gc macrophage activating factor

    DEFF Research Database (Denmark)

    Ravnsborg, Tina; Olsen, Dorthe T; Thysen, Anna Hammerich;

    2010-01-01

    The vitamin D binding protein, Gc globulin, has in recent years received some attention for its role as precursor for the extremely potent macrophage activating factor (GcMAF). An O-linked trisaccharide has been allocated to the threonine residue at position 420 in two of the three most common...... isoforms of Gc globulin (Gc1s and Gc1f). A substitution for a lysine residue at position 420 in Gc2 prevents this isoform from being glycosylated at that position. It has been suggested that Gc globulin subjected sequentially to sialidase and galactosidase treatment generates GcMAF in the form of Gc...... globulin with only a single GalNAc attached to T420. In this study we confirm the location of a linear trisaccharide on T420. Furthermore, we provide the first structural evidence of the generation of the proposed GcMAF by use of glycosidase treatment and mass spectrometry. Additionally the generated GcMAF...

  19. A Bioinformatics Approach for Detecting Repetitive Nested Motifs using Pattern Matching

    Science.gov (United States)

    Romero, José R.; Carballido, Jessica A.; Garbus, Ingrid; Echenique, Viviana C.; Ponzoni, Ignacio

    2016-01-01

    The identification of nested motifs in genomic sequences is a complex computational problem. The detection of these patterns is important to allow the discovery of transposable element (TE) insertions, incomplete reverse transcripts, deletions, and/or mutations. In this study, a de novo strategy for detecting patterns that represent nested motifs was designed based on exhaustive searches for pairs of motifs and combinatorial pattern analysis. These patterns can be grouped into three categories, motifs within other motifs, motifs flanked by other motifs, and motifs of large size. The methodology used in this study, applied to genomic sequences from the plant species Aegilops tauschii and Oryza sativa, revealed that it is possible to identify putative nested TEs by detecting these three types of patterns. The results were validated through BLAST alignments, which revealed the efficacy and usefulness of the new method, which is called Mamushka. PMID:27812277

  20. Improvements of embedded zerotree wavelet (EZW) coding

    Science.gov (United States)

    Li, Jin; Cheng, Po-Yuen; Kuo, C.-C. Jay

    1995-04-01

    In this research, we investigate several improvements of embedded zerotree wavelet (EZW) coding. Several topics addressed include: the choice of wavelet transforms and boundary conditions, the use of arithmetic coder and arithmetic context and the design of encoding order for effective embedding. The superior performance of our improvements is demonstrated with extensive experimental results.

  1. Solid methane toward deeply embedded protostars

    NARCIS (Netherlands)

    Boogert, ACA; Schutte, WA; Tielens, AGGM; Whittet, DCB; Helmich, FP; Ehrenfreund, P; Wesselius, PR; deGraauw, T; Prusti, T

    1996-01-01

    We report on the detection of an absorption feature near 7.67 mu m toward the deeply embedded protostellar objects W 33A and NGC 7538 : IRS9. Comparison with laboratory spectra shows that this feature can be identified as the v(4) ('deformation') mode of solid state CH4 embedded in polar molecules

  2. Multithreading for Embedded Reconfigurable Multicore Systems

    NARCIS (Netherlands)

    Zaykov, P.G.

    2014-01-01

    In this dissertation, we address the problem of performance efficient multithreading execution on heterogeneous multicore embedded systems. By heterogeneous multicore embedded systems we refer to those, which have real-time requirements and consist of processor tiles with General Purpose Processor

  3. Verification and Performance Analysis for Embedded Systems

    DEFF Research Database (Denmark)

    Larsen, Kim Guldstrand

    2009-01-01

    This talk provides a thorough tutorial of the UPPAAL tool suite for, modeling, simulation, verification, optimal scheduling, synthesis, testing and performance analysis of embedded and real-time systems.......This talk provides a thorough tutorial of the UPPAAL tool suite for, modeling, simulation, verification, optimal scheduling, synthesis, testing and performance analysis of embedded and real-time systems....

  4. Teaching Embedded System Concepts for Technological Literacy

    Science.gov (United States)

    Winzker, M.; Schwandt, A.

    2011-01-01

    A basic understanding of technology is recognized as important knowledge even for students not connected with engineering and computer science. This paper shows that embedded system concepts can be taught in a technological literacy course. An embedded system teaching block that has been used in an electronics module for non-engineers is…

  5. Embedded Systems Design with 8051 Microcontrollers

    DEFF Research Database (Denmark)

    Karakahayov, Zdravko; Winther, Ole; Christensen, Knud Smed

    Textbook on embedded microcontrollers. Example microcontroller family: Intel 8051 with special emphasis on Philips 80C552. Structure, design examples and programming in C and assembler. Hardware - software codesign. EProm emulator.......Textbook on embedded microcontrollers. Example microcontroller family: Intel 8051 with special emphasis on Philips 80C552. Structure, design examples and programming in C and assembler. Hardware - software codesign. EProm emulator....

  6. Virtually Embedded: Library Instruction within Second Life

    Science.gov (United States)

    Davis, Marian G.; Smith, Carol E.

    2009-01-01

    Embedded librarianship in distance learning courses taught within virtual environments such as Second Life is an emerging, leading-edge practice. This paper describes the experiences of librarians embedded in undergraduate English composition courses taught entirely in Second Life and presents the results of an empirical research study to assess…

  7. MEME-LaB: motif analysis in clusters.

    Science.gov (United States)

    Brown, Paul; Baxter, Laura; Hickman, Richard; Beynon, Jim; Moore, Jonathan D; Ott, Sascha

    2013-07-01

    Genome-wide expression analysis can result in large numbers of clusters of co-expressed genes. Although there are tools for ab initio discovery of transcription factor-binding sites, most do not provide a quick and easy way to study large numbers of clusters. To address this, we introduce a web tool called MEME-LaB. The tool wraps MEME (an ab initio motif finder), providing an interface for users to input multiple gene clusters, retrieve promoter sequences, run motif finding and then easily browse and condense the results, facilitating better interpretation of the results from large-scale datasets. MEME-LaB is freely accessible at: http://wsbc.warwick.ac.uk/wsbcToolsWebpage/. Supplementary data are available at Bioinformatics online.

  8. Genetic analysis of beta1 integrin "activation motifs" in mice

    DEFF Research Database (Denmark)

    Czuchra, Aleksandra; Meyer, Hannelore; Legate, Kyle R

    2006-01-01

    tails, leading to tail separation and integrin activation. We analyzed mice in which we mutated the tyrosines of the beta1 tail and the membrane-proximal aspartic acid required for the salt bridge. Tyrosine-to-alanine substitutions abolished beta1 integrin functions and led to a beta1 integrin......-null phenotype in vivo. Surprisingly, neither the substitution of the tyrosines with phenylalanine nor the aspartic acid with alanine resulted in an obvious defect. These data suggest that the NPXY motifs of the beta1 integrin tail are essential for beta1 integrin function, whereas tyrosine phosphorylation......Akey feature of integrins is their ability to regulate the affinity for ligands, a process termed integrin activation. The final step in integrin activation is talin binding to the NPXY motif of the integrin beta cytoplasmic domains. Talin binding disrupts the salt bridge between the alpha/beta...

  9. A new motif for inhibitors of geranylgeranyl diphosphate synthase.

    Science.gov (United States)

    Foust, Benjamin J; Allen, Cheryl; Holstein, Sarah A; Wiemer, David F

    2016-08-15

    The enzyme geranylgeranyl diphosphate synthase (GGDPS) is believed to receive the substrate farnesyl diphosphate through one lipophilic channel and release the product geranylgeranyl diphosphate through another. Bisphosphonates with two isoprenoid chains positioned on the α-carbon have proven to be effective inhibitors of this enzyme. Now a new motif has been prepared with one isoprenoid chain on the α-carbon, a second included as a phosphonate ester, and the potential for a third at the α-carbon. The pivaloyloxymethyl prodrugs of several compounds based on this motif have been prepared and the resulting compounds have been tested for their ability to disrupt protein geranylgeranylation and induce cytotoxicity in myeloma cells. The initial biological studies reveal activity consistent with GGDPS inhibition, and demonstrate a structure-function relationship which is dependent on the nature of the alkyl group at the α-carbon.

  10. Free Embedding Potentials in General Relativity

    CERN Document Server

    Bustamante, M D; Brachet, M E; Bustamante, Miguel D.; Debbasch, Fabrice; Brachet, Marc-Etienne

    2005-01-01

    The embedding approach to General Relativity (GR), in which the 4-dimensional space-time is embedded in a N-dimensional ($N\\geq 10$) flat host space with hyperbolic signature, is reconsidered. All objections raised by previous authors against this approach are answered. The equations for the embedding potentials are shown to be completely equivalent to the standard GR Einstein equations for the metric, provided that two conditions are met. The first condition is that the embedding fulfills a property closely related to Nash's freeness and the second that physically consistent boundary conditions are considered in the Einstein-Hilbert action. Explicit examples of embeddings whose deformations DO describe gravitational waves around their respective backgrounds are given for both (4-D) cases of flat space-time and Schwarzschild black hole. Beside the Einstein-Hilbert action, a new action principle is considered that is also equivalent to standard GR at both levels of equations of motion and perturbations (waves)...

  11. Graphical Model Debugger Framework for Embedded Systems

    DEFF Research Database (Denmark)

    Zeng, Kebin

    2010-01-01

    Debugger Framework, providing an auxiliary avenue of analysis of system models at runtime by executing generated code and updating models synchronously, which allows embedded developers to focus on the model level. With the model debugger, embedded developers can graphically test their design model......Model Driven Software Development has offered a faster way to design and implement embedded real-time software by moving the design to a model level, and by transforming models to code. However, the testing of embedded systems has remained at the code level. This paper presents a Graphical Model...... and check the running status of the system, which offers a debugging capability on a higher level of abstraction. The framework intends to contribute a tool to the Eclipse society, especially suitable for model-driven development of embedded systems....

  12. A Cooperative Approach for the Extraction of Protein Motifs

    Institute of Scientific and Technical Information of China (English)

    Chao CHEN; Yuan Xin TIAN; Xiao Yong ZOU; Pei Xiang CAI; Jin Yuan MO

    2006-01-01

    By integrating the concept of cooperative approach, an extension of the fast annealing coevolutionary algorithm is presented in this paper. It outperformed the original algorithm in the domain of function optimization, especially in terms of convergence rate. It was also applied to a real optimization problem, protein motif extraction. And a satisfactory result has been obtained with the accuracy of prediction achieving 67.0%, which is in agreement with the result in the PROSITE database.

  13. Neoanalysis, Orality, and Intertextuality: An Examination of Homeric Motif Transference

    Directory of Open Access Journals (Sweden)

    Jonathan Burgess

    2006-03-01

    Full Text Available In Homeric studies scholars have speculated on the influence of (non-surviving preHomeric material on the Iliad. This article expands this line of argument from an oralist perspective, with reference to modern intertextual theory. It concludes that preHomeric and nonHomeric motifs from oral traditions were transferred into the epic poem, creating an intertextually allusive poetics that would have been recognizable to an early Greek audience informed of mythological traditions.

  14. Motif Analysis in the Amazon Product Co-Purchasing Network

    OpenAIRE

    Srivastava, Abhishek

    2010-01-01

    Online stores like Amazon and Ebay are growing by the day. Fewer people go to departmental stores as opposed to the convenience of purchasing from stores online. These stores may employ a number of techniques to advertise and recommend the appropriate product to the appropriate buyer profile. This article evaluates various 3-node and 4-node motifs occurring in such networks. Community structures are evaluated too.These results may provide interesting insights into user behavior and a better u...

  15. Exon silencing by UAGG motifs in response to neuronal excitation.

    Directory of Open Access Journals (Sweden)

    Ping An

    2007-02-01

    Full Text Available Alternative pre-mRNA splicing plays fundamental roles in neurons by generating functional diversity in proteins associated with the communication and connectivity of the synapse. The CI cassette of the NMDA R1 receptor is one of a variety of exons that show an increase in exon skipping in response to cell excitation, but the molecular nature of this splicing responsiveness is not yet understood. Here we investigate the molecular basis for the induced changes in splicing of the CI cassette exon in primary rat cortical cultures in response to KCl-induced depolarization using an expression assay with a tight neuron-specific readout. In this system, exon silencing in response to neuronal excitation was mediated by multiple UAGG-type silencing motifs, and transfer of the motifs to a constitutive exon conferred a similar responsiveness by gain of function. Biochemical analysis of protein binding to UAGG motifs in extracts prepared from treated and mock-treated cortical cultures showed an increase in nuclear hnRNP A1-RNA binding activity in parallel with excitation. Evidence for the role of the NMDA receptor and calcium signaling in the induced splicing response was shown by the use of specific antagonists, as well as cell-permeable inhibitors of signaling pathways. Finally, a wider role for exon-skipping responsiveness is shown to involve additional exons with UAGG-related silencing motifs, and transcripts involved in synaptic functions. These results suggest that, at the post-transcriptional level, excitable exons such as the CI cassette may be involved in strategies by which neurons mount adaptive responses to hyperstimulation.

  16. Characterizing regulatory path motifs in integrated networks using perturbational data

    OpenAIRE

    Joshi, Anagha Madhusudan; Van Parys, Thomas; de Peer, Yves Van; Michoel, Tom

    2010-01-01

    We introduce Pathicular http://bioinformatics.psb.ugent.be/software/details/Pathicular, a Cytoscape plugin for studying the cellular response to perturbations of transcription factors by integrating perturbational expression data with transcriptional, protein-protein and phosphorylation networks. Pathicular searches for 'regulatory path motifs', short paths in the integrated physical networks which occur significantly more often than expected between transcription factors and their targets in...

  17. A combinatorial code for splicing silencing: UAGG and GGGG motifs.

    Directory of Open Access Journals (Sweden)

    Kyoungha Han

    2005-05-01

    Full Text Available Alternative pre-mRNA splicing is widely used to regulate gene expression by tuning the levels of tissue-specific mRNA isoforms. Few regulatory mechanisms are understood at the level of combinatorial control despite numerous sequences, distinct from splice sites, that have been shown to play roles in splicing enhancement or silencing. Here we use molecular approaches to identify a ternary combination of exonic UAGG and 5'-splice-site-proximal GGGG motifs that functions cooperatively to silence the brain-region-specific CI cassette exon (exon 19 of the glutamate NMDA R1 receptor (GRIN1 transcript. Disruption of three components of the motif pattern converted the CI cassette into a constitutive exon, while predominant skipping was conferred when the same components were introduced, de novo, into a heterologous constitutive exon. Predominant exon silencing was directed by the motif pattern in the presence of six competing exonic splicing enhancers, and this effect was retained after systematically repositioning the two exonic UAGGs within the CI cassette. In this system, hnRNP A1 was shown to mediate silencing while hnRNP H antagonized silencing. Genome-wide computational analysis combined with RT-PCR testing showed that a class of skipped human and mouse exons can be identified by searches that preserve the sequence and spatial configuration of the UAGG and GGGG motifs. This analysis suggests that the multi-component silencing code may play an important role in the tissue-specific regulation of the CI cassette exon, and that it may serve more generally as a molecular language to allow for intricate adjustments and the coordination of splicing patterns from different genes.

  18. A combinatorial code for splicing silencing: UAGG and GGGG motifs.

    Science.gov (United States)

    Han, Kyoungha; Yeo, Gene; An, Ping; Burge, Christopher B; Grabowski, Paula J

    2005-05-01

    Alternative pre-mRNA splicing is widely used to regulate gene expression by tuning the levels of tissue-specific mRNA isoforms. Few regulatory mechanisms are understood at the level of combinatorial control despite numerous sequences, distinct from splice sites, that have been shown to play roles in splicing enhancement or silencing. Here we use molecular approaches to identify a ternary combination of exonic UAGG and 5'-splice-site-proximal GGGG motifs that functions cooperatively to silence the brain-region-specific CI cassette exon (exon 19) of the glutamate NMDA R1 receptor (GRIN1) transcript. Disruption of three components of the motif pattern converted the CI cassette into a constitutive exon, while predominant skipping was conferred when the same components were introduced, de novo, into a heterologous constitutive exon. Predominant exon silencing was directed by the motif pattern in the presence of six competing exonic splicing enhancers, and this effect was retained after systematically repositioning the two exonic UAGGs within the CI cassette. In this system, hnRNP A1 was shown to mediate silencing while hnRNP H antagonized silencing. Genome-wide computational analysis combined with RT-PCR testing showed that a class of skipped human and mouse exons can be identified by searches that preserve the sequence and spatial configuration of the UAGG and GGGG motifs. This analysis suggests that the multi-component silencing code may play an important role in the tissue-specific regulation of the CI cassette exon, and that it may serve more generally as a molecular language to allow for intricate adjustments and the coordination of splicing patterns from different genes.

  19. The leitmotif racket in Lolita—marginal notes on Nabokov’s use of motifs

    OpenAIRE

    2013-01-01

    This is a study of Nabokov’s use of leitmotifs in Lolita, a study of how they intertwine and interact, and the problems Nabokov’s stylistic dexterity pose to the reader and critic. It traces prominent occurrences of the toilet and telephone motifs, and their connection with motifs like the slipper and the racket motif.

  20. Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs

    LENUS (Irish Health Repository)

    Casey, Fergal

    2011-08-22

    Abstract Background Gene and protein interactions are commonly represented as networks, with the genes or proteins comprising the nodes and the relationship between them as edges. Motifs, or small local configurations of edges and nodes that arise repeatedly, can be used to simplify the interpretation of networks. Results We examined triplet motifs in a network of quantitative epistatic genetic relationships, and found a non-random distribution of particular motif classes. Individual motif classes were found to be associated with different functional properties, suggestive of an underlying biological significance. These associations were apparent not only for motif classes, but for individual positions within the motifs. As expected, NNN (all negative) motifs were strongly associated with previously reported genetic (i.e. synthetic lethal) interactions, while PPP (all positive) motifs were associated with protein complexes. The two other motif classes (NNP: a positive interaction spanned by two negative interactions, and NPP: a negative spanned by two positives) showed very distinct functional associations, with physical interactions dominating for the former but alternative enrichments, typical of biochemical pathways, dominating for the latter. Conclusion We present a model showing how NNP motifs can be used to recognize supportive relationships between protein complexes, while NPP motifs often identify opposing or regulatory behaviour between a gene and an associated pathway. The ability to use motifs to point toward underlying biological organizational themes is likely to be increasingly important as more extensive epistasis mapping projects in higher organisms begin.

  1. Process-based network decomposition reveals backbone motif structure.

    Science.gov (United States)

    Wang, Guanyu; Du, Chenghang; Chen, Hao; Simha, Rahul; Rong, Yongwu; Xiao, Yi; Zeng, Chen

    2010-06-08

    A central challenge in systems biology today is to understand the network of interactions among biomolecules and, especially, the organizing principles underlying such networks. Recent analysis of known networks has identified small motifs that occur ubiquitously, suggesting that larger networks might be constructed in the manner of electronic circuits by assembling groups of these smaller modules. Using a unique process-based approach to analyzing such networks, we show for two cell-cycle networks that each of these networks contains a giant backbone motif spanning all the network nodes that provides the main functional response. The backbone is in fact the smallest network capable of providing the desired functionality. Furthermore, the remaining edges in the network form smaller motifs whose role is to confer stability properties rather than provide function. The process-based approach used in the above analysis has additional benefits: It is scalable, analytic (resulting in a single analyzable expression that describes the behavior), and computationally efficient (all possible minimal networks for a biological process can be identified and enumerated).

  2. STEME: efficient EM to find motifs in large data sets

    Science.gov (United States)

    Reid, John E.; Wernisch, Lorenz

    2011-01-01

    MEME and many other popular motif finders use the expectation–maximization (EM) algorithm to optimize their parameters. Unfortunately, the running time of EM is linear in the length of the input sequences. This can prohibit its application to data sets of the size commonly generated by high-throughput biological techniques. A suffix tree is a data structure that can efficiently index a set of sequences. We describe an algorithm, Suffix Tree EM for Motif Elicitation (STEME), that approximates EM using suffix trees. To the best of our knowledge, this is the first application of suffix trees to EM. We provide an analysis of the expected running time of the algorithm and demonstrate that STEME runs an order of magnitude more quickly than the implementation of EM used by MEME. We give theoretical bounds for the quality of the approximation and show that, in practice, the approximation has a negligible effect on the outcome. We provide an open source implementation of the algorithm that we hope will be used to speed up existing and future motif search algorithms. PMID:21785132

  3. Insertion of tetracysteine motifs into dopamine transporter extracellular domains.

    Directory of Open Access Journals (Sweden)

    Deanna M Navaroli

    Full Text Available The neuronal dopamine transporter (DAT is a major determinant of extracellular dopamine (DA levels and is the primary target for a variety of addictive and therapeutic psychoactive drugs. DAT is acutely regulated by protein kinase C (PKC activation and amphetamine exposure, both of which modulate DAT surface expression by endocytic trafficking. In order to use live imaging approaches to study DAT endocytosis, methods are needed to exclusively label the DAT surface pool. The use of membrane impermeant, sulfonated biarsenic dyes holds potential as one such approach, and requires introduction of an extracellular tetracysteine motif (tetraCys; CCPGCC to facilitate dye binding. In the current study, we took advantage of intrinsic proline-glycine (Pro-Gly dipeptides encoded in predicted DAT extracellular domains to introduce tetraCys motifs into DAT extracellular loops 2, 3, and 4. [(3H]DA uptake studies, surface biotinylation and fluorescence microscopy in PC12 cells indicate that tetraCys insertion into the DAT second extracellular loop results in a functional transporter that maintains PKC-mediated downregulation. Introduction of tetraCys into extracellular loops 3 and 4 yielded DATs with severely compromised function that failed to mature and traffic to the cell surface. This is the first demonstration of successful introduction of a tetracysteine motif into a DAT extracellular domain, and may hold promise for use of biarsenic dyes in live DAT imaging studies.

  4. Motif structure and cooperation in real-world complex networks

    Science.gov (United States)

    Salehi, Mostafa; Rabiee, Hamid R.; Jalili, Mahdi

    2010-12-01

    Networks of dynamical nodes serve as generic models for real-world systems in many branches of science ranging from mathematics to physics, technology, sociology and biology. Collective behavior of agents interacting over complex networks is important in many applications. The cooperation between selfish individuals is one of the most interesting collective phenomena. In this paper we address the interplay between the motifs’ cooperation properties and their abundance in a number of real-world networks including yeast protein-protein interaction, human brain, protein structure, email communication, dolphins’ social interaction, Zachary karate club and Net-science coauthorship networks. First, the amount of cooperativity for all possible undirected subgraphs with three to six nodes is calculated. To this end, the evolutionary dynamics of the Prisoner’s Dilemma game is considered and the cooperativity of each subgraph is calculated as the percentage of cooperating agents at the end of the simulation time. Then, the three- to six-node motifs are extracted for each network. The significance of the abundance of a motif, represented by a Z-value, is obtained by comparing them with some properly randomized versions of the original network. We found that there is always a group of motifs showing a significant inverse correlation between their cooperativity amount and Z-value, i.e. the more the Z-value the less the amount of cooperativity. This suggests that networks composed of well-structured units do not have good cooperativity properties.

  5. THE MOTIF OF THE PRODIGAL SON IN IVAN TURGENEV'S NOVELS

    Directory of Open Access Journals (Sweden)

    Valentina Ivanovna Gabdullina

    2013-11-01

    Full Text Available The author questions the perception of Ivan Turgenev as a “non- Christian writer” and studies the problem of the prodigal son motif functioning in a series of his novels. In his novels, Turgenev pictured different phases of the archetypal story, originating from the Gospel parable of the prodigal son. In the novel Rudin he depicted the phase of spiritual wanderings of the hero who had lost touch with his native land — Russia. In his next novels (Home of the Gentry, Fathers and Sons and Smoke, after leading his hero in circles and sending him back to his paternal home, Turgenev reconstructs the model of human behavior, represented in the parable, thereby recognizing the immutability of the idea formalized in the Gospel. The motif of the return to Russian land gets its completion in Turgenev's last novel Virgin Soil, in which the author paradoxically connects the Westernist idea with the Gospel imperative. Solomin, the son of a deacon, sent by his wise father out to Europe “to get education”, studies in England, masters the European knowledge and returns back “to his native land” to establish his own business in inland Russia. Thus, a series of Turgenev's novels, in which he portrayed different phases of social life, are interlinked with the motif of the prodigal son, who is represented by novels' main characters.

  6. ROMANIAN TRADITIONAL MOTIF ELEMENT OF MODERNITY IN CLOTHING

    Directory of Open Access Journals (Sweden)

    ŞUTEU Marius Darius

    2017-05-01

    Full Text Available In this paper are presented the phases for improving from an aesthetic point of view a clothing item, the T-shirt for women using software design patterns, computerised graphics and textile different modern technologies including: industrial embroidery, digital printing, sublimation. In the first phase a documentation was prepared in the University of Oradea and traditional motif was selected from a collection comprising a number of Romanian traditional motifs from different parts of the country and were reintepreted and stylized whilst preserving the symbolism and color range specified to the area. For the styling phase was used CorelDraw vector graphics program that allows changing the shape, size and color of the drawings without affecting the identity of the pattern. The embroidery was done using BERNINA Embroidery Software Designer Plus Software. This software allows you to export the model to any domestic or industrial embroidery machine regardless of brand. Finally we observed the resistance of the printed and embroided model to various: elasticity, resistance to abrasion and a sensory analysis on the preservation of color. After testing we noticed the imprint resistance applied to the fabric, resulting in a quality that makes possible to keep the Romanian traditional motif from generation to generation.

  7. MAR characteristic motifs mediate episomal vector in CHO cells.

    Science.gov (United States)

    Lin, Yan; Li, Zhaoxi; Wang, Tianyun; Wang, Xiaoyin; Wang, Li; Dong, Weihua; Jing, Changqin; Yang, Xianjun

    2015-04-01

    An ideal gene therapy vector should enable persistent transgene expression without limitations in safety and reproducibility. Recent researches' insight into the ability of chromosomal matrix attachment regions (MARs) to mediate episomal maintenance of genetic elements allowed the development of a circular episomal vector. Although a MAR-mediated engineered vector has been developed, little is known on which motifs of MAR confer this function during interaction with the host genome. Here, we report an artificially synthesized DNA fragment containing only characteristic motif sequences that served as an alternative to human beta-interferon matrix attachment region sequence. The potential of the vector to mediate gene transfer in CHO cells was investigated. The short synthetic MAR motifs were found to mediate episomal vector at a low copy number for many generations without integration into the host genome. Higher transgene expression was maintained for at least 4 months. In addition, MAR was maintained episomally and conferred sustained EGFP expression even in nonselective CHO cells. All the results demonstrated that MAR characteristic sequence-based vector can function as stable episomes in CHO cells, supporting long-term and effective transgene expression.

  8. Event Networks and the Identification of Crime Pattern Motifs.

    Directory of Open Access Journals (Sweden)

    Toby Davies

    Full Text Available In this paper we demonstrate the use of network analysis to characterise patterns of clustering in spatio-temporal events. Such clustering is of both theoretical and practical importance in the study of crime, and forms the basis for a number of preventative strategies. However, existing analytical methods show only that clustering is present in data, while offering little insight into the nature of the patterns present. Here, we show how the classification of pairs of events as close in space and time can be used to define a network, thereby generalising previous approaches. The application of graph-theoretic techniques to these networks can then offer significantly deeper insight into the structure of the data than previously possible. In particular, we focus on the identification of network motifs, which have clear interpretation in terms of spatio-temporal behaviour. Statistical analysis is complicated by the nature of the underlying data, and we provide a method by which appropriate randomised graphs can be generated. Two datasets are used as case studies: maritime piracy at the global scale, and residential burglary in an urban area. In both cases, the same significant 3-vertex motif is found; this result suggests that incidents tend to occur not just in pairs, but in fact in larger groups within a restricted spatio-temporal domain. In the 4-vertex case, different motifs are found to be significant in each case, suggesting that this technique is capable of discriminating between clustering patterns at a finer granularity than previously possible.

  9. Degenerate polynomial patches of degree 11 for almostGC2 interpolation over triangles

    NARCIS (Netherlands)

    Hogervorst, Bas J.; Damme, van Ruud

    1993-01-01

    We consider the problem of interpolating scattered data in ℝ3 by analmost geometrically smoothGC2 surface, where almostGC2 meansGC2 except in a finite number of points (the vertices), where the surface isGC1. A local method is proposed, based on employing so-called degenerate triangular Bernstein-Bé

  10. Stellar Properties of Embedded Protostars

    CERN Document Server

    White, R J; Doppmann, G W; Covey, Kevin R; Hillenbrand, L A

    2006-01-01

    (Abridged) High dispersion spectrographs on large aperture telescopes have recently allowed observers to study the stellar and accretion properties of deeply embedded young stars, commonly referred to as Class I stars. We summarize these newly determined properties and compare them with observations of more optically revealed Class II (T Tauri) stars. Class I stars have spectral types and stellar luminosities similar to those of Class II stars, suggesting similar masses and ages. Estimates of stellar luminosity and age, however, are especially uncertain given the large extinctions, scattered light emission and continuum excesses typical of Class I stars. Several candidate Class I brown dwarfs are identified. Class I stars appear to rotate more rapidly than T Tauri stars, by roughly a factor of 2. Likewise, Class I disk accretion rates are only a factor of two larger than those of T Tauri stars, less than the mass infall rates predicted by envelope models by 1-2 orders of magnitude. In at least a few cases the...

  11. Environmental trace analysis by means of supersensitive GC-IMS

    Energy Technology Data Exchange (ETDEWEB)

    Leonhardt, J.W. [IUTLimited, Berlin, (Germany)

    1997-10-01

    The effective control of pollutants in ambient air requires their fast in situ identification and concentration determination of chemical compounds in the range of micrograms per m{sup 3}. There are attempts to use conventional analytical techniques as portable GC and GC-MS. These systems are relatively expensive. A new supersensitive ion Mobility Sensor (IMS) was developed and checked by IUT Ltd, which meets the new demands. The use of tritium sources is an advantage in comparison with other IMS being equipped by nickel-63, the application of which is rather critical in respect of the radiation protection. On the other hand an integrated separation column allows to reduce interferences by matrix effects. The technical parameters of the IUT GC- IMS and some of its most important applications are briefly presented 6 refs., 1 tab., 5 figs.

  12. A novel Bayesian DNA motif comparison method for clustering and retrieval.

    Directory of Open Access Journals (Sweden)

    Naomi Habib

    2008-02-01

    Full Text Available Characterizing the DNA-binding specificities of transcription factors is a key problem in computational biology that has been addressed by multiple algorithms. These usually take as input sequences that are putatively bound by the same factor and output one or more DNA motifs. A common practice is to apply several such algorithms simultaneously to improve coverage at the price of redundancy. In interpreting such results, two tasks are crucial: clustering of redundant motifs, and attributing the motifs to transcription factors by retrieval of similar motifs from previously characterized motif libraries. Both tasks inherently involve motif comparison. Here we present a novel method for comparing and merging motifs, based on Bayesian probabilistic principles. This method takes into account both the similarity in positional nucleotide distributions of the two motifs and their dissimilarity to the background distribution. We demonstrate the use of the new comparison method as a basis for motif clustering and retrieval procedures, and compare it to several commonly used alternatives. Our results show that the new method outperforms other available methods in accuracy and sensitivity. We incorporated the resulting motif clustering and retrieval procedures in a large-scale automated pipeline for analyzing DNA motifs. This pipeline integrates the results of various DNA motif discovery algorithms and automatically merges redundant motifs from multiple training sets into a coherent annotated library of motifs. Application of this pipeline to recent genome-wide transcription factor location data in S. cerevisiae successfully identified DNA motifs in a manner that is as good as semi-automated analysis reported in the literature. Moreover, we show how this analysis elucidates the mechanisms of condition-specific preferences of transcription factors.

  13. Determination of Paraffin in Bean Thread Noodles by Employing GC/MS and GC/FID Technology%GC-MS、GC-FID测定粉丝中的石蜡含量

    Institute of Scientific and Technical Information of China (English)

    舒平; 杨卫花; 甘献明

    2010-01-01

    利用GC-MS,GC-FID技术,对粉丝样品中的石蜡检测进行了方法建立及实际样品测试.分析结果表明,该方法对粉丝中百蜡检测的相对标准偏差为2.3%~4.7%,样品的回收率为96%~103%.方法简便、准确、可靠、前处理简单.

  14. GC/MS法测定MDMA毒品成分

    Institute of Scientific and Technical Information of China (English)

    张春水; 刘克林; 何毅; 郑珲; 王朝虹

    2003-01-01

    MDMA是由甲基苯丙胺类毒品衍生而来的一种新型毒品,也属于联合国管制和禁用药品.本文通过对一例MDMA片剂的GC/MS分析,确定了该片剂中的主要毒品成分及辅助成分,建立了一个快速分析检验该类片剂毒品的GC/MS方法.

  15. The Land of the Dead – International Motifs in the Oldest Work of Japanese Literature

    OpenAIRE

    Danijela Vasić

    2010-01-01

    Il existe dans le Kojiki (712), la plus ancienne œuvre littéraire du Japon, une abondance de motifs que l’on peut retrouver dans les cultures de nombreux peuples dans le monde entier. Cet article traite des motifs internationaux tissés dans deux mythes du premier tome, formant une image poétique du Pays des morts, la partie souterraine d’une structure cosmique tripartite. Sont abordés, entre autres, le motif largement connu de Perséphone, le motif orphique ou encore le motif de la fuite du Pa...

  16. Leucine-based receptor sorting motifs are dependent on the spacing relative to the plasma membrane

    DEFF Research Database (Denmark)

    Geisler, C; Dietrich, J; Nielsen, B L;

    1998-01-01

    amino acid, is constitutively active. In this study, we have investigated how the spacing relative to the plasma membrane affects the function of both types of leucine-based motifs. For phosphorylation-dependent leucine-based motifs, a minimal spacing of 7 residues between the plasma membrane...... and the phospho-acceptor was required for phosphorylation and thereby activation of the motifs. For constitutively active leucine-based motifs, a minimal spacing of 6 residues between the plasma membrane and the acidic residue was required for optimal activity of the motifs. In addition, we found that the acidic...

  17. Assessment of the −174G/C (rs1800795 and −572G/C (rs1800796 Interleukin 6 Gene Polymorphisms in Egyptian Patients with Rheumatoid Arthritis

    Directory of Open Access Journals (Sweden)

    Khalda Amr

    2016-10-01

    CONCLUSION: A significant association of IL-6 −174G/C gene polymorphism and RA in Egyptian population was found with significantly higher frequencies of GC and CC genotypes and C allele in RA patients compared to controls. No association was found between IL-6 −572G/C gene polymorphism and RA.

  18. Comparison of Aroma-Active Volatiles in Oolong Tea Infusions Using GC-Olfactometry, GC-FPD, and GC-MS.

    Science.gov (United States)

    Zhu, JianCai; Chen, Feng; Wang, LingYing; Niu, YunWei; Yu, Dan; Shu, Chang; Chen, HeXing; Wang, HongLin; Xiao, ZuoBing

    2015-09-02

    The aroma profile of oolong tea infusions (Dongdingwulong, DDWL; Tieguanyin, TGY; Dahongpao, DHP) were investigated in this study. Gas chromatography-olfactometry (GC-O) with the method of aroma intensity (AI) was employed to investigate the aroma-active compounds in tea infusions. The results presented forty-three, forty-five, and forty-eight aroma-active compounds in the TGY, DHP, and DDWL infusions, including six, seven, and five sulfur compounds, respectively. In addition, the concentration of volatile compounds in the tea infusions was further quantitated by solid phase microextraction-gas chromatography (SPME)-GC-MS and SPME-GC-flame photometric detection (FPD). Totally, seventy-six and thirteen volatile and sulfur compounds were detected in three types of tea infusions, respectively. Quantitative results showed that forty-seven aroma compounds were at concentrations higher than their corresponding odor thresholds. On the basis of the odor activity values (OAVs), 2-methylpropanal (OAV: 230-455), 3-methylbutanal (1-353), 2-methylbutanal (34-68), nerolidol (108-184), (E)-2-heptenal (148-294), hexanal (134-230), octanal (28-131), β-damascenone (29-59), indole (96-138), 6-methyl-5-hepten-2-one (34-67), (R)-(-)-linalool (63-87), and dimethyl sulfide (7-1320) presented relatively higher OAVs than those of other compounds, indicating the importance of these compounds in the overall aroma of tea infusions.

  19. GC/GC-MS analysis, isolation and identification of bioactive essential oil components from the Bhutanese medicinal plant, Pleurospermum amabile.

    Science.gov (United States)

    Wangchuk, Phurpa; Keller, Paul A; Pyne, Stephen G; Taweechotipatr, Malai; Kamchonwongpaisan, Sumalee

    2013-09-01

    We have hydrodistilled the essential oil (EO) from the aerial parts of the Bhutanese medicinal plant, Pleurospermum amabile using a Clevenger apparatus and evaluated this EO by GC/GC-MS and NMR analysis followed by testing for bioactivity. The GC-MS analysis identified 52 compounds with (E)-isomyristicin as a major component (32.2%). Repeated purification yielded four compounds; (E)-isomyristicin (1), (E)-isoapiol (2), methyl eugenol (3) and (E)-isoelemicin (4). Compound 2 and the mother EO showed the best antiplasmodial activity against the Plasmodium falciparum strains, TM4/8.2 (chloroquine and antifolate sensitive) and K1CB1 (multidrug resistant). They exhibited mild antibacterial activity against Bacillus subtilis. None of the test samples showed cytotoxicity.

  20. Aroma compound analysis of Eruca sativa (Brassicaceae) SPME headspace leaf samples using GC, GC-MS, and olfactometry.

    Science.gov (United States)

    Jirovetz, Leopold; Smith, David; Buchbauer, Gerhard

    2002-07-31

    The aroma compounds of rocket salad (Eruca sativa) SPME headspace samples of fresh leaves were analyzed using GC, GC-MS, and olfactometry. More than 50 constituents of the Eruca headspace could be identified to be essential volatiles, responsible for the characteristic intense green; herbal; nutty and almond-like; Brassicaceae-like (direction of cabbage, broccoli, and mustard); and horseradish-like aroma of these salad leaves. As aroma impact compounds, especially isothiocyanates, and derivatives of butane, hexane, octane, and nonane were identified. 4-Methylthiobutyl isothiocyanate (14.2%), cis-3-hexen-1-ol (11.0%), cis-3-hexenyl butanoate (10.8%), 5-methylthiopentyl isothiocyanate (9.3%), cis-3-hexenyl 2-methylbutanoate (5.4%), and 5-methylthiopentanenitrile (5.0%) were found in concentrations higher than 5.0% (calculated as % peak area of GC analysis using a nonpolar column).

  1. MicroRNA Stability in FFPE Tissue Samples: Dependence on GC Content.

    Science.gov (United States)

    Kakimoto, Yu; Tanaka, Masayuki; Kamiguchi, Hiroshi; Ochiai, Eriko; Osawa, Motoki

    2016-01-01

    MicroRNAs (miRNAs) are small non-coding RNAs responsible for fine-tuning of gene expression at post-transcriptional level. The alterations in miRNA expression levels profoundly affect human health and often lead to the development of severe diseases. Currently, high throughput analyses, such as microarray and deep sequencing, are performed in order to identify miRNA biomarkers, using archival patient tissue samples. MiRNAs are more robust than longer RNAs, and resistant to extreme temperatures, pH, and formalin-fixed paraffin-embedding (FFPE) process. Here, we have compared the stability of miRNAs in FFPE cardiac tissues using next-generation sequencing. The mode read length in FFPE samples was 11 nucleotides (nt), while that in the matched frozen samples was 22 nt. Although the read counts were increased 1.7-fold in FFPE samples, compared with those in the frozen samples, the average miRNA mapping rate decreased from 32.0% to 9.4%. These results indicate that, in addition to the fragmentation of longer RNAs, miRNAs are to some extent degraded in FFPE tissues as well. The expression profiles of total miRNAs in two groups were highly correlated (0.88 GC content (p<0.0001). The unequal degradation of each miRNA affected the abundance ranking in the library, and miR-133a was shown to be the most abundant in FFPE cardiac tissues instead of miR-1, which was predominant before fixation. Subsequent quantitative PCR (qPCR) analyses revealed that miRNAs with GC content of less than 40% are more degraded than GC-rich miRNAs (p<0.0001). We showed that deep sequencing data obtained using FFPE samples cannot be directly compared with that of fresh frozen samples. The combination of miRNA deep sequencing and other quantitative analyses, such as qPCR, may improve the utility of archival FFPE tissue samples.

  2. The art of designing embedded systems

    CERN Document Server

    Ganssle, Jack G

    2000-01-01

    Art of Designing Embedded Systems is apart primer and part reference, aimed at practicing embedded engineers, whether working on the code or the hardware design. Embedded systems suffer from a chaotic, ad hoc development process. This books lays out a very simple seven-step plan to get firmware development under control. There are no formal methodologies to master; the ideas are immediately useful. Most designers are unaware that code complexity grows faster than code size. This book shows a number of ways to linearize the complexity/size curve and get products out faster

  3. On Injective Embeddings of Tree Patterns

    CERN Document Server

    Michaliszyn, Jakub; Staworko, Sławek; Wieczorek, Piotr; Wu, Zhilin

    2012-01-01

    We study three different kinds of embeddings of tree patterns: weakly-injective, ancestor-preserving, and lca-preserving. While each of them is often referred to as injective embedding, they form a proper hierarchy and their computational properties vary (from P to NP-complete). We present a thorough study of the complexity of the model checking problem i.e., is there an embedding of a given tree pattern in a given tree, and we investigate the impact of various restrictions imposed on the tree pattern: bound on the degree of a node, bound on the height, and type of allowed labels and edges.

  4. Technology report on Railway Embedded Network solutions

    OpenAIRE

    Wahl, M; BERNOCCHI, M; Just, P.; WEISS, AH; GOIKOETXEA, J; BILLION, J; NEMORIN, J

    2007-01-01

    Deliverable D3D.3.1 Technology report on Railway Embedded Network solutions is a deliverable of Work Package SP3D_WP3 ICOM Specification & Telecom Interfaces of Onboard and Train Train Networks. It takes place within the InteGRail Task 3D_03.1 State of the Art in Embedded Networks. The objectives of this deliverable are: - to consider which embedded communication network technologies are already into ser-vice within the trains; - to analyse Ethernet-based technologies; - to evaluate how Ethe...

  5. Secure smart embedded devices, platforms and applications

    CERN Document Server

    Markantonakis, Konstantinos

    2013-01-01

    New generations of IT users are increasingly abstracted from the underlying devices and platforms that provide and safeguard their services. As a result they may have little awareness that they are critically dependent on the embedded security devices that are becoming pervasive in daily modern life. Secure Smart Embedded Devices, Platforms and Applications provides a broad overview of the many security and practical issues of embedded devices, tokens, and their operation systems, platforms and main applications. It also addresses a diverse range of industry/government initiatives and consider

  6. Embedded Solenoid Transformer for Power Conversion

    DEFF Research Database (Denmark)

    2015-01-01

    A resonant power converter for operation in the radio frequency range, preferably in the VHF, comprises at least one PCB-embedded transformer. The transformer is configured for radio frequency operation and comprises a printed circuit board defining a horizontal plane, the printed circuit board...... and second embedded solenoids are formed in the conductive layers of the printed circuit board, wherein each full turn of an embedded solenoid has a horizontal top portion formed in an upper conductive layer, a horizontal bottom portion formed in a lower conductive layer, and two vertical side portions...

  7. Motif-based analysis of large nucleotide data sets using MEME-ChIP.

    Science.gov (United States)

    Ma, Wenxiu; Noble, William S; Bailey, Timothy L

    2014-01-01

    MEME-ChIP is a web-based tool for analyzing motifs in large DNA or RNA data sets. It can analyze peak regions identified by ChIP-seq, cross-linking sites identified by CLIP-seq and related assays, as well as sets of genomic regions selected using other criteria. MEME-ChIP performs de novo motif discovery, motif enrichment analysis, motif location analysis and motif clustering, providing a comprehensive picture of the DNA or RNA motifs that are enriched in the input sequences. MEME-ChIP performs two complementary types of de novo motif discovery: weight matrix-based discovery for high accuracy; and word-based discovery for high sensitivity. Motif enrichment analysis using DNA or RNA motifs from human, mouse, worm, fly and other model organisms provides even greater sensitivity. MEME-ChIP's interactive HTML output groups and aligns significant motifs to ease interpretation. This protocol takes less than 3 h, and it provides motif discovery approaches that are distinct and complementary to other online methods.

  8. Evolutionarily conserved bias of amino-acid usage refines the definition of PDZ-binding motif.

    Science.gov (United States)

    Chimura, Takahiko; Launey, Thomas; Ito, Masao

    2011-06-08

    The interactions between PDZ (PSD-95, Dlg, ZO-1) domains and PDZ-binding motifs play central roles in signal transductions within cells. Proteins with PDZ domains bind to PDZ-binding motifs almost exclusively when the motifs are located at the carboxyl (C-) terminal ends of their binding partners. However, it remains little explored whether PDZ-binding motifs show any preferential location at the C-terminal ends of proteins, at genome-level. Here, we examined the distribution of the type-I (x-x-S/T-x-I/L/V) or type-II (x-x-V-x-I/V) PDZ-binding motifs in proteins encoded in the genomes of five different species (human, mouse, zebrafish, fruit fly and nematode). We first established that these PDZ-binding motifs are indeed preferentially present at their C-terminal ends. Moreover, we found specific amino acid (AA) bias for the 'x' positions in the motifs at the C-terminal ends. In general, hydrophilic AAs were favored. Our genomics-based findings confirm and largely extend the results of previous interaction-based studies, allowing us to propose refined consensus sequences for all of the examined PDZ-binding motifs. An ontological analysis revealed that the refined motifs are functionally relevant since a large fraction of the proteins bearing the motif appear to be involved in signal transduction. Furthermore, co-precipitation experiments confirmed two new protein interactions predicted by our genomics-based approach. Finally, we show that influenza virus pathogenicity can be correlated with PDZ-binding motif, with high-virulence viral proteins bearing a refined PDZ-binding motif. Our refined definition of PDZ-binding motifs should provide important clues for identifying functional PDZ-binding motifs and proteins involved in signal transduction.

  9. Evolutionarily conserved bias of amino-acid usage refines the definition of PDZ-binding motif

    Directory of Open Access Journals (Sweden)

    Launey Thomas

    2011-06-01

    Full Text Available Abstract Background The interactions between PDZ (PSD-95, Dlg, ZO-1 domains and PDZ-binding motifs play central roles in signal transductions within cells. Proteins with PDZ domains bind to PDZ-binding motifs almost exclusively when the motifs are located at the carboxyl (C- terminal ends of their binding partners. However, it remains little explored whether PDZ-binding motifs show any preferential location at the C-terminal ends of proteins, at genome-level. Results Here, we examined the distribution of the type-I (x-x-S/T-x-I/L/V or type-II (x-x-V-x-I/V PDZ-binding motifs in proteins encoded in the genomes of five different species (human, mouse, zebrafish, fruit fly and nematode. We first established that these PDZ-binding motifs are indeed preferentially present at their C-terminal ends. Moreover, we found specific amino acid (AA bias for the 'x' positions in the motifs at the C-terminal ends. In general, hydrophilic AAs were favored. Our genomics-based findings confirm and largely extend the results of previous interaction-based studies, allowing us to propose refined consensus sequences for all of the examined PDZ-binding motifs. An ontological analysis revealed that the refined motifs are functionally relevant since a large fraction of the proteins bearing the motif appear to be involved in signal transduction. Furthermore, co-precipitation experiments confirmed two new protein interactions predicted by our genomics-based approach. Finally, we show that influenza virus pathogenicity can be correlated with PDZ-binding motif, with high-virulence viral proteins bearing a refined PDZ-binding motif. Conclusions Our refined definition of PDZ-binding motifs should provide important clues for identifying functional PDZ-binding motifs and proteins involved in signal transduction.

  10. Antibiogram and GC analysis of Euphorbia hirta leaf extract

    OpenAIRE

    2007-01-01

    The antibiogram activity of ethanolic and aqueous extract of E.hirta was studied. Ethanol extract of the plant showed the maximal antibacterial activity and G.C Analysis showed the presence of citronellal. The extract showed inhibited the growth of E.coli, S.aureus, P.aeruginosa, Proteus etc.,

  11. On the interpretation of the CHC factor Gc

    NARCIS (Netherlands)

    K.-J. Kan; R.A. Kievit; C. Dolan; H. van der Maas

    2011-01-01

    On the one hand, the factors Gf and Gc in the Cattell-Horn-Carroll (CHC) model of intelligence are hypothesized to represent individual differences in unique psychological or biological capacities. On the other hand, they are interpreted as representing the theoretical variables fluid and crystalliz

  12. DNA nanotechnology based on i-motif structures.

    Science.gov (United States)

    Dong, Yuanchen; Yang, Zhongqiang; Liu, Dongsheng

    2014-06-17

    CONSPECTUS: Most biological processes happen at the nanometer scale, and understanding the energy transformations and material transportation mechanisms within living organisms has proved challenging. To better understand the secrets of life, researchers have investigated artificial molecular motors and devices over the past decade because such systems can mimic certain biological processes. DNA nanotechnology based on i-motif structures is one system that has played an important role in these investigations. In this Account, we summarize recent advances in functional DNA nanotechnology based on i-motif structures. The i-motif is a DNA quadruplex that occurs as four stretches of cytosine repeat sequences form C·CH(+) base pairs, and their stabilization requires slightly acidic conditions. This unique property has produced the first DNA molecular motor driven by pH changes. The motor is reliable, and studies show that it is capable of millisecond running speeds, comparable to the speed of natural protein motors. With careful design, the output of these types of motors was combined to drive micrometer-sized cantilevers bend. Using established DNA nanostructure assembly and functionalization methods, researchers can easily integrate the motor within other DNA assembled structures and functional units, producing DNA molecular devices with new functions such as suprahydrophobic/suprahydrophilic smart surfaces that switch, intelligent nanopores triggered by pH changes, molecular logic gates, and DNA nanosprings. Recently, researchers have produced motors driven by light and electricity, which have allowed DNA motors to be integrated within silicon-based nanodevices. Moreover, some devices based on i-motif structures have proven useful for investigating processes within living cells. The pH-responsiveness of the i-motif structure also provides a way to control the stepwise assembly of DNA nanostructures. In addition, because of the stability of the i-motif, this

  13. Power for Vehicle Embedded MEMS Sensors Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Embedded wireless sensors of the future will enable flight vehicle systems to be "highly aware" of onboard health and performance parameters, as well as the external...

  14. Embedding Moodle into Ubiquitous Computing Environments

    NARCIS (Netherlands)

    Glahn, Christian; Specht, Marcus

    2010-01-01

    Glahn, C., & Specht, M. (2010). Embedding Moodle into Ubiquitous Computing Environments. In M. Montebello, et al. (Eds.), 9th World Conference on Mobile and Contextual Learning (MLearn2010) (pp. 100-107). October, 19-22, 2010, Valletta, Malta.

  15. Conforming finite elements with embedded strong discontinuities

    NARCIS (Netherlands)

    Dias-da-Costa, D.; Alfaiate, J.; Sluys, L.J.; Areias, P.; Fernandes, C.; Julio, E.

    2012-01-01

    The possibility of embedding strong discontinuities into finite elements allowed the simulation of different problems, namely, brickwork masonry fracture, dynamic fracture, failure in finite strain problems and simulation of reinforcement concrete members. However, despite the significant contributi

  16. Power for Vehicle Embedded MEMS Sensors Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Embedded wireless sensors of the future will enable flight vehicle systems to be "highly aware" of onboard health and performance parameters, as well as the...

  17. Female Climacteric Syndrome Treated by Ear Embedding

    Institute of Scientific and Technical Information of China (English)

    王勤

    2003-01-01

    @@ Female climacteric syndrome is a common disease occurring before and after menopause. The author has treated the disease with ear embedding therapy, and achieved satisfactory therapeutic results. The following is a report of the clinical observation.

  18. A randomized model for communicating embedded systems

    NARCIS (Netherlands)

    Bujorianu, M.C.; Bujorianu, L.M.

    2008-01-01

    Nowadays, there is an intense research activity in designing systems that operate in real life, physical environments. This research is spanned by various areas in computer science and engineering: embedded systems, reactive systems, wireless communications, hybrid systems, stochastic processes, etc

  19. Using Buildroot for building Embedded Linux Systems

    OpenAIRE

    Ruiz González, Mariano

    2013-01-01

    This document describes the basic steps to developed and embedded Linux-based system using the BeagleBoard. The document has been specifically written to use a BeagleBoard development system based on the OMAP `processor.

  20. Piecewise flat embeddings for hyperspectral image analysis

    Science.gov (United States)

    Hayes, Tyler L.; Meinhold, Renee T.; Hamilton, John F.; Cahill, Nathan D.

    2017-05-01

    Graph-based dimensionality reduction techniques such as Laplacian Eigenmaps (LE), Local Linear Embedding (LLE), Isometric Feature Mapping (ISOMAP), and Kernel Principal Components Analysis (KPCA) have been used in a variety of hyperspectral image analysis applications for generating smooth data embeddings. Recently, Piecewise Flat Embeddings (PFE) were introduced in the computer vision community as a technique for generating piecewise constant embeddings that make data clustering / image segmentation a straightforward process. In this paper, we show how PFE arises by modifying LE, yielding a constrained ℓ1-minimization problem that can be solved iteratively. Using publicly available data, we carry out experiments to illustrate the implications of applying PFE to pixel-based hyperspectral image clustering and classification.

  1. Time-Scale Invariant Audio Data Embedding

    Directory of Open Access Journals (Sweden)

    Mansour Mohamed F

    2003-01-01

    Full Text Available We propose a novel algorithm for high-quality data embedding in audio. The algorithm is based on changing the relative length of the middle segment between two successive maximum and minimum peaks to embed data. Spline interpolation is used to change the lengths. To ensure smooth monotonic behavior between peaks, a hybrid orthogonal and nonorthogonal wavelet decomposition is used prior to data embedding. The possible data embedding rates are between 20 and 30 bps. However, for practical purposes, we use repetition codes, and the effective embedding data rate is around 5 bps. The algorithm is invariant after time-scale modification, time shift, and time cropping. It gives high-quality output and is robust to mp3 compression.

  2. A randomized model for communicating embedded systems

    NARCIS (Netherlands)

    Bujorianu, M.C.; Bujorianu, L.M.

    2008-01-01

    Nowadays, there is an intense research activity in designing systems that operate in real life, physical environments. This research is spanned by various areas in computer science and engineering: embedded systems, reactive systems, wireless communications, hybrid systems, stochastic processes,

  3. Apparatuses And Systems For Embedded Thermoelectric Generators

    KAUST Repository

    Hussain, Muhammad M.

    2013-08-08

    An apparatus and a system for embedded thermoelectric generators are disclosed. In one embodiment, the apparatus is embedded in an interface where the ambient temperatures on two sides of the interface are different. In one embodiment, the apparatus is fabricated with the interface in integrity as a unitary piece. In one embodiment, the apparatus includes a first thermoelectric material embedded through the interface. The apparatus further includes a second thermoelectric material embedded through the interface. The first thermoelectric material is electrically coupled to the second thermoelectric material. In one embodiment, the apparatus further includes an output structure coupled to the first thermoelectric material and the second thermoelectric material and configured to output a voltage.

  4. Sequence-based classification using discriminatory motif feature selection.

    Directory of Open Access Journals (Sweden)

    Hao Xiong

    Full Text Available Most existing methods for sequence-based classification use exhaustive feature generation, employing, for example, all k-mer patterns. The motivation behind such (enumerative approaches is to minimize the potential for overlooking important features. However, there are shortcomings to this strategy. First, practical constraints limit the scope of exhaustive feature generation to patterns of length ≤ k, such that potentially important, longer (> k predictors are not considered. Second, features so generated exhibit strong dependencies, which can complicate understanding of derived classification rules. Third, and most importantly, numerous irrelevant features are created. These concerns can compromise prediction and interpretation. While remedies have been proposed, they tend to be problem-specific and not broadly applicable. Here, we develop a generally applicable methodology, and an attendant software pipeline, that is predicated on discriminatory motif finding. In addition to the traditional training and validation partitions, our framework entails a third level of data partitioning, a discovery partition. A discriminatory motif finder is used on sequences and associated class labels in the discovery partition to yield a (small set of features. These features are then used as inputs to a classifier in the training partition. Finally, performance assessment occurs on the validation partition. Important attributes of our approach are its modularity (any discriminatory motif finder and any classifier can be deployed and its universality (all data, including sequences that are unaligned and/or of unequal length, can be accommodated. We illustrate our approach on two nucleosome occupancy datasets and a protein solubility dataset, previously analyzed using enumerative feature generation. Our method achieves excellent performance results, with and without optimization of classifier tuning parameters. A Python pipeline implementing the approach is

  5. Analysis of septins across kingdoms reveals orthology and new motifs

    Directory of Open Access Journals (Sweden)

    Malmberg Russell L

    2007-07-01

    Full Text Available Abstract Background Septins are cytoskeletal GTPase proteins first discovered in the fungus Saccharomyces cerevisiae where they organize the septum and link nuclear division with cell division. More recently septins have been found in animals where they are important in processes ranging from actin and microtubule organization to embryonic patterning and where defects in septins have been implicated in human disease. Previous studies suggested that many animal septins fell into independent evolutionary groups, confounding cross-kingdom comparison. Results In the current work, we identified 162 septins from fungi, microsporidia and animals and analyzed their phylogenetic relationships. There was support for five groups of septins with orthology between kingdoms. Group 1 (which includes S. cerevisiae Cdc10p and human Sept9 and Group 2 (which includes S. cerevisiae Cdc3p and human Sept7 contain sequences from fungi and animals. Group 3 (which includes S. cerevisiae Cdc11p and Group 4 (which includes S. cerevisiae Cdc12p contain sequences from fungi and microsporidia. Group 5 (which includes Aspergillus nidulans AspE contains sequences from filamentous fungi. We suggest a modified nomenclature based on these phylogenetic relationships. Comparative sequence alignments revealed septin derivatives of already known G1, G3 and G4 GTPase motifs, four new motifs from two to twelve amino acids long and six conserved single amino acid positions. One of these new motifs is septin-specific and several are group specific. Conclusion Our studies provide an evolutionary history for this important family of proteins and a framework and consistent nomenclature for comparison of septin orthologs across kingdoms.

  6. Identification of imine reductase-specific sequence motifs.

    Science.gov (United States)

    Fademrecht, Silvia; Scheller, Philipp N; Nestl, Bettina M; Hauer, Bernhard; Pleiss, Jürgen

    2016-05-01

    Chiral amines are valuable building blocks for the production of a variety of pharmaceuticals, agrochemicals and other specialty chemicals. Only recently, imine reductases (IREDs) were discovered which catalyze the stereoselective reduction of imines to chiral amines. Although several IREDs were biochemically characterized in the last few years, knowledge of the reaction mechanism and the molecular basis of substrate specificity and stereoselectivity is limited. To gain further insights into the sequence-function relationships, the Imine Reductase Engineering Database (www.IRED.BioCatNet.de) was established and a systematic analysis of 530 putative IREDs was performed. A standard numbering scheme based on R-IRED-Sk was introduced to facilitate the identification and communication of structurally equivalent positions in different proteins. A conservation analysis revealed a highly conserved cofactor binding region and a predominantly hydrophobic substrate binding cleft. Two IRED-specific motifs were identified, the cofactor binding motif GLGxMGx(5 )[ATS]x(4) Gx(4) [VIL]WNR[TS]x(2) [KR] and the active site motif Gx[DE]x[GDA]x[APS]x(3){K}x[ASL]x[LMVIAG]. Our results indicate a preference toward NADPH for all IREDs and explain why, despite their sequence similarity to β-hydroxyacid dehydrogenases (β-HADs), no conversion of β-hydroxyacids has been observed. Superfamily-specific conservations were investigated to explore the molecular basis of their stereopreference. Based on our analysis and previous experimental results on IRED mutants, an exclusive role of standard position 187 for stereoselectivity is excluded. Alternatively, two standard positions 139 and 194 were identified which are superfamily-specifically conserved and differ in R- and S-selective enzymes. © 2016 Wiley Periodicals, Inc.

  7. Embedded Face Detection and Recognition

    Directory of Open Access Journals (Sweden)

    Göksel Günlü

    2012-10-01

    Full Text Available The need to increase security in open or public spaces has in turn given rise to the requirement to monitor these spaces and analyse those images on‐site and on‐time. At this point, the use of smart cameras ‐ of which the popularity has been increasing ‐ is one step ahead. With sensors and Digital Signal Processors (DSPs, smart cameras generate ad hoc results by analysing the numeric images transmitted from the sensor by means of a variety of image‐processing algorithms. Since the images are not transmitted to a distance processing unit but rather are processed inside the camera, it does not necessitate high‐ bandwidth networks or high processor powered systems; it can instantaneously decide on the required access. Nonetheless, on account of restricted memory, processing power and overall power, image processing algorithms need to be developed and optimized for embedded processors. Among these algorithms, one of the most important is for face detection and recognition. A number of face detection and recognition methods have been proposed recently and many of these methods have been tested on general‐purpose processors. In smart cameras ‐ which are real‐life applications of such methods ‐ the widest use is on DSPs. In the present study, the Viola‐Jones face detection method ‐ which was reported to run faster on PCs ‐ was optimized for DSPs; the face recognition method was combined with the developed sub‐region and mask‐based DCT (Discrete Cosine Transform. As the employed DSP is a fixed‐point processor, the processes were performed with integers insofar as it was possible. To enable face recognition, the image was divided into sub‐ regions and from each sub‐region the robust coefficients against disruptive elements ‐ like face expression, illumination, etc. ‐ were selected as the features. The discrimination of the selected features was enhanced via LDA (Linear Discriminant Analysis and then employed for

  8. Embedded Face Detection and Recognition

    Directory of Open Access Journals (Sweden)

    Göksel Günlü

    2012-10-01

    Full Text Available The need to increase security in open or public spaces has in turn given rise to the requirement to monitor these spaces and analyse those images on-site and on-time. At this point, the use of smart cameras – of which the popularity has been increasing – is one step ahead. With sensors and Digital Signal Processors (DSPs, smart cameras generate ad hoc results by analysing the numeric images transmitted from the sensor by means of a variety of image-processing algorithms. Since the images are not transmitted to a distance processing unit but rather are processed inside the camera, it does not necessitate high-bandwidth networks or high processor powered systems; it can instantaneously decide on the required access. Nonetheless, on account of restricted memory, processing power and overall power, image processing algorithms need to be developed and optimized for embedded processors. Among these algorithms, one of the most important is for face detection and recognition. A number of face detection and recognition methods have been proposed recently and many of these methods have been tested on general-purpose processors. In smart cameras – which are real-life applications of such methods – the widest use is on DSPs. In the present study, the Viola-Jones face detection method – which was reported to run faster on PCs – was optimized for DSPs; the face recognition method was combined with the developed sub-region and mask-based DCT (Discrete Cosine Transform. As the employed DSP is a fixed-point processor, the processes were performed with integers insofar as it was possible. To enable face recognition, the image was divided into sub-regions and from each sub-region the robust coefficients against disruptive elements – like face expression, illumination, etc. – were selected as the features. The discrimination of the selected features was enhanced via LDA (Linear Discriminant Analysis and then employed for recognition. Thanks to its

  9. Evolving DNA motifs to predict GeneChip probe performance

    Directory of Open Access Journals (Sweden)

    Harrison AP

    2009-03-01

    Full Text Available Abstract Background Affymetrix High Density Oligonuclotide Arrays (HDONA simultaneously measure expression of thousands of genes using millions of probes. We use correlations between measurements for the same gene across 6685 human tissue samples from NCBI's GEO database to indicated the quality of individual HG-U133A probes. Low correlation indicates a poor probe. Results Regular expressions can be automatically created from a Backus-Naur form (BNF context-free grammar using strongly typed genetic programming. Conclusion The automatically produced motif is better at predicting poor DNA sequences than an existing human generated RE, suggesting runs of Cytosine and Guanine and mixtures should all be avoided.

  10. Indonesian Traditional Toys and the Development of Batik Motifs

    Directory of Open Access Journals (Sweden)

    Bagus Indrayana

    2016-06-01

    Full Text Available There is a wide array of traditional toys in Indonesia. In the past, traditional toys played an important role for skill and creativity development of children. Today, the position of traditional toys in the society is displaced by toys from large-scale manufacturers. Given the critical role of traditional toys for children’s motoric and social development, there is a need to develop media that can be used to promote these traditional products and strengthen their position in the public. We propose to use Batik as a way to effectively disseminate and promote traditional toys to the general public. Apart from this, using traditional toys to create new Batik motifs can have an economic value for the producers of Batik, promote Indonesian products and enrich the Indonesian Batik. This study aims to explore the variety of traditional toys, mainly from Klaten and Magelang, in the Central Java province of Indonesia, and use them as the basis for the development of Batik motif creation. This study used Trilogi Keseimbangan (or Harmony Trilogy aesthetic theory analytical approach that explains the creation of craft consists of the following phases: exploration, design, and materialization. The creation method in this study adopts Tiga Tahap Enam Langkah (Three Phases, Six Steps method offered in the theory. The finding in the field found that the traditional toys material used in Klaten and Magelang, mostly made from waste wood, plywood, and zinc. The manufacturing process is done manually by two or three craftsmen using a simple technology. The traditional toys are designed by the artisans mostly, although there may be designs from the clients. In addition, we also found that the traditional toys have never been used as a Batik motif. The traditional toys Batik motif presented in this work is researcher’s design. For the purposes of this study, we first research the variety of traditional toys available in the market today in Indonesia. We look

  11. Core signalling motif displaying multistability through multi-state enzymes

    DEFF Research Database (Denmark)

    Feng, Song; Saez Cornellana, Meritxell; Wiuf, Carsten Henrik

    2016-01-01

    Bistability, and more generally multistability, is a key system dynamics feature enabling decision-making and memory in cells. Deciphering the molecular determinants of multistability is thus crucial for a better understanding of cellular pathways and their (re)engineering in synthetic biology......-state kinases and the described competition-based motif are part of several natural signalling systems and thereby could enable them to implement complex information processing through multistability. These results indicate that multi-state kinases in signalling systems are readily exploited by natural...

  12. Present status of quinoxaline motifs: excellent pathfinders in therapeutic medicine.

    Science.gov (United States)

    Ajani, Olayinka Oyewale

    2014-10-01

    Quinoxalines belong to a class of excellent heterocyclic scaffolds owing to their wide biological properties and diverse therapeutic applications in medicinal research. They are complementary in shapes and charges to numerous biomolecules they interact with, thereby resulting in increased binding affinity. The pharmacokinetic properties of drugs bearing quinoxaline cores have shown them to be relatively easy to administer either as intramuscular solutions, oral capsules or rectal suppositories. This work deals with recent advances in the synthesis and pharmacological diversities of quinoxaline motifs which might pave ways for novel drugs development.

  13. Nucleic Acid i-Motif Structures in Analytical Chemistry.

    Science.gov (United States)

    Alba, Joan Josep; Sadurní, Anna; Gargallo, Raimundo

    2016-09-02

    Under the appropriate experimental conditions of pH and temperature, cytosine-rich segments in DNA or RNA sequences may produce a characteristic folded structure known as an i-motif. Besides its potential role in vivo, which is still under investigation, this structure has attracted increasing interest in other fields due to its sharp, fast and reversible pH-driven conformational changes. This "on/off" switch at molecular level is being used in nanotechnology and analytical chemistry to develop nanomachines and sensors, respectively. This paper presents a review of the latest applications of this structure in the field of chemical analysis.

  14. Multimode FPGA with Flexible Embedded FPUS

    OpenAIRE

    G.Murugaboopathi; S.Hariharasitaraman; Sankar, G.

    2012-01-01

    The Performance of field-programmable gate arrays used for Floating-point applications are poor due to complexity of floating-point arithmetic. Implementing floating-point units on FPGAs consume a large amount of resources. This makes FPGAs less attractive for use in floating-point intensive applications. There is a need for embedded FPUs in FPGAs. We proposed a flexible multimode embedded FPU for FPGAs that can be configured to perform a wide range of operations. The floatingpoint adder and ...

  15. Embedded adhesive connection for laminated glass plates

    DEFF Research Database (Denmark)

    Hansen, Jens Zangenberg; Poulsen, S.H.; Bagger, A.

    2012-01-01

    The structural behavior of a new connection design, the embedded adhesive connection, used for laminated glass plates is investigated. The connection consists of an aluminum plate encapsulated in-between two adjacent triple layered laminated glass plates. Fastening between glass and aluminum...... usage in a design situation. The embedded connection shows promising potential as a future fastening system for load-carrying laminated glass plates....

  16. Five years of density matrix embedding theory

    CERN Document Server

    Wouters, Sebastian; Chan, Garnet K -L

    2016-01-01

    Density matrix embedding theory (DMET) describes finite fragments in the presence of a surrounding environment. In contrast to most embedding methods, DMET explicitly allows for quantum entanglement between both. In this chapter, we discuss both the ground-state and response theory formulations of DMET, and review several applications. In addition, a proof is given that the local density of states can be obtained by working with a Fock space of bath orbitals.

  17. Accelerated Monte Carlo by Embedded Cluster Dynamics

    Science.gov (United States)

    Brower, R. C.; Gross, N. A.; Moriarty, K. J. M.

    1991-07-01

    We present an overview of the new methods for embedding Ising spins in continuous fields to achieve accelerated cluster Monte Carlo algorithms. The methods of Brower and Tamayo and Wolff are summarized and variations are suggested for the O( N) models based on multiple embedded Z2 spin components and/or correlated projections. Topological features are discussed for the XY model and numerical simulations presented for d=2, d=3 and mean field theory lattices.

  18. Embedded Operating System for MicroBlaze

    OpenAIRE

    2006-01-01

    This paper presents a work in progress on experiments with embedded operating systems for the MicroBlaze processor. Modern embedded systems based on a configurable platform incorporating a similar processor core are gaining importance with the ongoing effort to minimize cost and development time. After an overview of the configurable platform based on this processor core, we devote our attention to uClinux OS. This OS has been successfully ported for the MicroBlaze processor, and we present o...

  19. Embedded Lattice and Properties of Gram Matrix

    Directory of Open Access Journals (Sweden)

    Futa Yuichi

    2017-03-01

    Full Text Available In this article, we formalize in Mizar [14] the definition of embedding of lattice and its properties. We formally define an inner product on an embedded module. We also formalize properties of Gram matrix. We formally prove that an inverse of Gram matrix for a rational lattice exists. Lattice of Z-module is necessary for lattice problems, LLL (Lenstra, Lenstra and Lov´asz base reduction algorithm [16] and cryptographic systems with lattice [17].

  20. Recurring sequence-structure motifs in (βα)8-barrel proteins and experimental optimization of a chimeric protein designed based on such motifs.

    Science.gov (United States)

    Wang, Jichao; Zhang, Tongchuan; Liu, Ruicun; Song, Meilin; Wang, Juncheng; Hong, Jiong; Chen, Quan; Liu, Haiyan

    2017-02-01

    An interesting way of generating novel artificial proteins is to combine sequence motifs from natural proteins, mimicking the evolutionary path suggested by natural proteins comprising recurring motifs. We analyzed the βα and αβ modules of TIM barrel proteins by structure alignment-based sequence clustering. A number of preferred motifs were identified. A chimeric TIM was designed by using recurring elements as mutually compatible interfaces. The foldability of the designed TIM protein was then significantly improved by six rounds of directed evolution. The melting temperature has been improved by more than 20°C. A variety of characteristics suggested that the resulting protein is well-folded. Our analysis provided a library of peptide motifs that is potentially useful for different protein engineering studies. The protein engineering strategy of using recurring motifs as interfaces to connect partial natural proteins may be applied to other protein folds. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Is chondroitin sulfate responsible for the biological effects attributed to the GC protein-derived Macrophage Activating Factor (GcMAF)?

    Science.gov (United States)

    Ruggiero, Marco; Reinwald, Heinz; Pacini, Stefania

    2016-09-01

    We hypothesize that a plasma glycosaminoglycan, chondroitin sulfate, may be responsible for the biological and clinical effects attributed to the Gc protein-derived Macrophage Activating Factor (GcMAF), a protein that is extracted from human blood. Thus, Gc protein binds chondroitin sulfate on the cell surface and such an interaction may occur also in blood, colostrum and milk. This interpretation would solve the inconsistencies encountered in explaining the effects of GcMAF in vitro and in vivo. According to our model, the Gc protein or the GcMAF bind to chondroitin sulfate both on the cell surface and in bodily fluids, and the resulting multimolecular complexes, under the form of oligomers trigger a transmembrane signal or, alternatively, are internalized and convey the signal directly to the nucleus thus eliciting the diverse biological effects observed for both GcMAF and chondroitin sulfate.

  2. Embedding capacity estimation of reversible watermarking schemes

    Indian Academy of Sciences (India)

    Rishabh Iyer; Rushikesh Borse; Subhasis Chaudhuri

    2014-12-01

    Estimation of the embedding capacity is an important problem specifically in reversible multi-pass watermarking and is required for analysis before any image can be watermarked. In this paper, we propose an efficient method for estimating the embedding capacity of a given cover image under multi-pass embedding, without actually embedding the watermark. We demonstrate this for a class of reversible watermarking schemes which operate on a disjoint group of pixels, specifically for pixel pairs. The proposed algorithm iteratively updates the co-occurrence matrix at every stage to estimate the multi-pass embedding capacity, and is much more efficient vis-a-vis actual watermarking. We also suggest an extremely efficient, pre-computable tree based implementation which is conceptually similar to the cooccurrence based method, but provides the estimates in a single iteration, requiring a complexity akin to that of single pass capacity estimation. We also provide upper bounds on the embedding capacity.We finally evaluate performance of our algorithms on recent watermarking algorithms.

  3. Arm To Arm Interface Using Embedded C

    Directory of Open Access Journals (Sweden)

    Mohanraj.C

    2013-02-01

    Full Text Available Embedded systems are the most emerging field in these recent years. In this paper a different number of ARM processors (LPC2148 and LPC2378 are interconnected using C for distributed services. N numbers of processors are connected as the network and each processing devices are interlinked with each other, so that the each data that is processed by the devices and it can be used by the other device to activate their entire process. All the processed data’s are communicated to other device through Xbee interface card. LPC2148 and LPC2378 ARM processors are used in this prototype and winXtalk is used as a software terminal window. In this paper, the ultimate benefits of multiple processor interactions related to the embedded applications and design issues of processor interconnection are discussed. The features of multiple processor interaction in inter process communication and executions of embedded multitasking are also discussed. In modern embedded computing platform, embedded processor used in various applications like home automation, industrial control, medical system, access control, etc. In this paper, using embedded processor interactions, the several data communication is established.

  4. 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.

  5. Fast and Accurate Discovery of Degenerate Linear Motifs in Protein Sequences

    Science.gov (United States)

    Levy, Emmanuel D.; Michnick, Stephen W.

    2014-01-01

    Linear motifs mediate a wide variety of cellular functions, which makes their characterization in protein sequences crucial to understanding cellular systems. However, the short length and degenerate nature of linear motifs make their discovery a difficult problem. Here, we introduce MotifHound, an algorithm particularly suited for the discovery of small and degenerate linear motifs. MotifHound performs an exact and exhaustive enumeration of all motifs present in proteins of interest, including all of their degenerate forms, and scores the overrepresentation of each motif based on its occurrence in proteins of interest relative to a background (e.g., proteome) using the hypergeometric distribution. To assess MotifHound, we benchmarked it together with state-of-the-art algorithms. The benchmark consists of 11,880 sets of proteins from S. cerevisiae; in each set, we artificially spiked-in one motif varying in terms of three key parameters, (i) number of occurrences, (ii) length and (iii) the number of degenerate or “wildcard” positions. The benchmark enabled the evaluation of the impact of these three properties on the performance of the different algorithms. The results showed that MotifHound and SLiMFinder were the most accurate in detecting degenerate linear motifs. Interestingly, MotifHound was 15 to 20 times faster at comparable accuracy and performed best in the discovery of highly degenerate motifs. We complemented the benchmark by an analysis of proteins experimentally shown to bind the FUS1 SH3 domain from S. cerevisiae. Using the full-length protein partners as sole information, MotifHound recapitulated most experimentally determined motifs binding to the FUS1 SH3 domain. Moreover, these motifs exhibited properties typical of SH3 binding peptides, e.g., high intrinsic disorder and evolutionary conservation, despite the fact that none of these properties were used as prior information. MotifHound is available (http://michnick.bcm.umontreal.ca or http

  6. Odor-active compounds in cooked rice cultivars from Camargue (France) analyzed by GC-O and GC-MS.

    Science.gov (United States)

    Maraval, Isabelle; Mestres, Christian; Pernin, Karine; Ribeyre, Fabienne; Boulanger, Renaud; Guichard, Elisabeth; Gunata, Ziya

    2008-07-09

    Volatile compounds of cooked rice from scented (Aychade, Fidji) and nonscented (Ruille) cultivars grown in the Camargue area in France were compared to that of a marketed Asian scented one (Thai) by gas chromatography-olfactometry (GC-O) and gas chromatography-mass spectrometry (GC-MS). GC-O analyses of the organic extracts resulted in the perception of 40 odorous compounds. Only two compounds, oct-1-en-3-one and 2-acetyl-1-pyrroline, were almost always perceived. Hierarchical cluster analysis showed that most of the difference between rice odors was linked to quantitative differences with only 11 compounds being specific to some of the rice. Sixty compounds were identified and quantified by GC-MS, including a few new odor-active components. Principal component analysis enabled us to differentiate scented cultivars from a nonscented one, and scented rice cultivars from Camargue from a Thai sample. Calculated odor-active values evidenced that the Thai sample odor differed from that of scented Camargue cultivars because of the degradation of lipids and of cinnamic acid compounds.

  7. Exponentially many maximum genus embeddings and genus embeddings for complete graphs

    Institute of Scientific and Technical Information of China (English)

    REN Han; BAI Yun

    2008-01-01

    There are many results on the maximum genus,among which most are written for the existence of values of such embeddings,and few attention has been paid to the estimation of such embeddings and their applications.In this paper we study the number of maximum genus embeddings for a graph and find an exponential lower bound for such numbers.Our results show that in general case,a simple connected graph has exponentially many distinct maximum genus embeddings.In particular,a connected cubie graph G of order n always has at least (√2)m+n+α/2 distinct maximum genus embeddings,where α and m denote,respectively,the number of inner vertices and odd compo-nents of an optimal tree T.What surprise us most is that such two extremal embeddings (i.e.,the maximum genus embeddings and the genus embeddings) are sometimes closely related with each other.In fact,as applications,we show that for a sufficient large natural number n,there are at least C2n/4 many genus embeddings for complete graph Kn with n=4,7,10 (mod12),where C is a constance depending on the Value of n of residue 12.These results improve the bounds obtained by Korzhik and Voss and the methods used here are much simpler and straight.

  8. Transcription factor motif quality assessment requires systematic comparative analysis [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Caleb Kipkurui Kibet

    2016-03-01

    Full Text Available Transcription factor (TF binding site prediction remains a challenge in gene regulatory research due to degeneracy and potential variability in binding sites in the genome. Dozens of algorithms designed to learn binding models (motifs have generated many motifs available in research papers with a subset making it to databases like JASPAR, UniPROBE and Transfac. The presence of many versions of motifs from the various databases for a single TF and the lack of a standardized assessment technique makes it difficult for biologists to make an appropriate choice of binding model and for algorithm developers to benchmark, test and improve on their models. In this study, we review and evaluate the approaches in use, highlight differences and demonstrate the difficulty of defining a standardized motif assessment approach. We review scoring functions, motif length, test data and the type of performance metrics used in prior studies as some of the factors that influence the outcome of a motif assessment. We show that the scoring functions and statistics used in motif assessment influence ranking of motifs in a TF-specific manner. We also show that TF binding specificity can vary by source of genomic binding data. We also demonstrate that information content of a motif is not in isolation a measure of motif quality but is influenced by TF binding behaviour. We conclude that there is a need for an easy-to-use tool that presents all available evidence for a comparative analysis.

  9. HIGEDA: a hierarchical gene-set genetics based algorithm for finding subtle motifs in biological sequences.

    Science.gov (United States)

    Le, Thanh; Altman, Tom; Gardiner, Katheleen

    2010-02-01

    Identification of motifs in biological sequences is a challenging problem because such motifs are often short, degenerate, and may contain gaps. Most algorithms that have been developed for motif-finding use the expectation-maximization (EM) algorithm iteratively. Although EM algorithms can converge quickly, they depend strongly on initialization parameters and can converge to local sub-optimal solutions. In addition, they cannot generate gapped motifs. The effectiveness of EM algorithms in motif finding can be improved by incorporating methods that choose different sets of initial parameters to enable escape from local optima, and that allow gapped alignments within motif models. We have developed HIGEDA, an algorithm that uses the hierarchical gene-set genetic algorithm (HGA) with EM to initiate and search for the best parameters for the motif model. In addition, HIGEDA can identify gapped motifs using a position weight matrix and dynamic programming to generate an optimal gapped alignment of the motif model with sequences from the dataset. We show that HIGEDA outperforms MEME and other motif-finding algorithms on both DNA and protein sequences. Source code and test datasets are available for download at http://ouray.cudenver.edu/~tnle/, implemented in C++ and supported on Linux and MS Windows.

  10. Finding a Leucine in a Haystack: Searching the Proteome for ambigous Leucine-Aspartic Acid motifs

    KAUST Repository

    Arold, Stefan T.

    2016-01-25

    Leucine-aspartic acid (LD) motifs are short helical protein-protein interaction motifs involved in cell motility, survival and communication. LD motif interactions are also implicated in cancer metastasis and are targeted by several viruses. LD motifs are notoriously difficult to detect because sequence pattern searches lead to an excessively high number of false positives. Hence, despite 20 years of research, only six LD motif–containing proteins are known in humans, three of which are close homologues of the paxillin family. To enable the proteome-wide discovery of LD motifs, we developed LD Motif Finder (LDMF), a web tool based on machine learning that combines sequence information with structural predictions to detect LD motifs with high accuracy. LDMF predicted 13 new LD motifs in humans. Using biophysical assays, we experimentally confirmed in vitro interactions for four novel LD motif proteins. Thus, LDMF allows proteome-wide discovery of LD motifs, despite a highly ambiguous sequence pattern. Functional implications will be discussed.

  11. Motif Discovery in Tissue-Specific Regulatory Sequences Using Directed Information

    Directory of Open Access Journals (Sweden)

    States David

    2007-01-01

    Full Text Available Motif discovery for the identification of functional regulatory elements underlying gene expression is a challenging problem. Sequence inspection often leads to discovery of novel motifs (including transcription factor sites with previously uncharacterized function in gene expression. Coupled with the complexity underlying tissue-specific gene expression, there are several motifs that are putatively responsible for expression in a certain cell type. This has important implications in understanding fundamental biological processes such as development and disease progression. In this work, we present an approach to the identification of motifs (not necessarily transcription factor sites and examine its application to some questions in current bioinformatics research. These motifs are seen to discriminate tissue-specific gene promoter or regulatory regions from those that are not tissue-specific. There are two main contributions of this work. Firstly, we propose the use of directed information for such classification constrained motif discovery, and then use the selected features with a support vector machine (SVM classifier to find the tissue specificity of any sequence of interest. Such analysis yields several novel interesting motifs that merit further experimental characterization. Furthermore, this approach leads to a principled framework for the prospective examination of any chosen motif to be discriminatory motif for a group of coexpressed/coregulated genes, thereby integrating sequence and expression perspectives. We hypothesize that the discovery of these motifs would enable the large-scale investigation for the tissue-specific regulatory role of any conserved sequence element identified from genome-wide studies.

  12. Transduction motif analysis of gastric cancer based on a human signaling network

    Energy Technology Data Exchange (ETDEWEB)

    Liu, G.; Li, D.Z.; Jiang, C.S.; Wang, W. [Fuzhou General Hospital of Nanjing Command, Department of Gastroenterology, Fuzhou, China, Department of Gastroenterology, Fuzhou General Hospital of Nanjing Command, Fuzhou (China)

    2014-04-04

    To investigate signal regulation models of gastric cancer, databases and literature were used to construct the signaling network in humans. Topological characteristics of the network were analyzed by CytoScape. After marking gastric cancer-related genes extracted from the CancerResource, GeneRIF, and COSMIC databases, the FANMOD software was used for the mining of gastric cancer-related motifs in a network with three vertices. The significant motif difference method was adopted to identify significantly different motifs in the normal and cancer states. Finally, we conducted a series of analyses of the significantly different motifs, including gene ontology, function annotation of genes, and model classification. A human signaling network was constructed, with 1643 nodes and 5089 regulating interactions. The network was configured to have the characteristics of other biological networks. There were 57,942 motifs marked with gastric cancer-related genes out of a total of 69,492 motifs, and 264 motifs were selected as significantly different motifs by calculating the significant motif difference (SMD) scores. Genes in significantly different motifs were mainly enriched in functions associated with cancer genesis, such as regulation of cell death, amino acid phosphorylation of proteins, and intracellular signaling cascades. The top five significantly different motifs were mainly cascade and positive feedback types. Almost all genes in the five motifs were cancer related, including EPOR, MAPK14, BCL2L1, KRT18, PTPN6, CASP3, TGFBR2, AR, and CASP7. The development of cancer might be curbed by inhibiting signal transductions upstream and downstream of the selected motifs.

  13. Transduction motif analysis of gastric cancer based on a human signaling network

    Directory of Open Access Journals (Sweden)

    G. Liu

    2014-05-01

    Full Text Available To investigate signal regulation models of gastric cancer, databases and literature were used to construct the signaling network in humans. Topological characteristics of the network were analyzed by CytoScape. After marking gastric cancer-related genes extracted from the CancerResource, GeneRIF, and COSMIC databases, the FANMOD software was used for the mining of gastric cancer-related motifs in a network with three vertices. The significant motif difference method was adopted to identify significantly different motifs in the normal and cancer states. Finally, we conducted a series of analyses of the significantly different motifs, including gene ontology, function annotation of genes, and model classification. A human signaling network was constructed, with 1643 nodes and 5089 regulating interactions. The network was configured to have the characteristics of other biological networks. There were 57,942 motifs marked with gastric cancer-related genes out of a total of 69,492 motifs, and 264 motifs were selected as significantly different motifs by calculating the significant motif difference (SMD scores. Genes in significantly different motifs were mainly enriched in functions associated with cancer genesis, such as regulation of cell death, amino acid phosphorylation of proteins, and intracellular signaling cascades. The top five significantly different motifs were mainly cascade and positive feedback types. Almost all genes in the five motifs were cancer related, including EPOR, MAPK14, BCL2L1, KRT18, PTPN6, CASP3, TGFBR2, AR, and CASP7. The development of cancer might be curbed by inhibiting signal transductions upstream and downstream of the selected motifs.

  14. Phosphotyrosine Substrate Sequence Motifs for Dual Specificity Phosphatases.

    Directory of Open Access Journals (Sweden)

    Bryan M Zhao

    Full Text Available Protein tyrosine phosphatases dephosphorylate tyrosine residues of proteins, whereas, dual specificity phosphatases (DUSPs are a subgroup of protein tyrosine phosphatases that dephosphorylate not only Tyr(P residue, but also the Ser(P and Thr(P residues of proteins. The DUSPs are linked to the regulation of many cellular functions and signaling pathways. Though many cellular targets of DUSPs are known, the relationship between catalytic activity and substrate specificity is poorly defined. We investigated the interactions of peptide substrates with select DUSPs of four types: MAP kinases (DUSP1 and DUSP7, atypical (DUSP3, DUSP14, DUSP22 and DUSP27, viral (variola VH1, and Cdc25 (A-C. Phosphatase recognition sites were experimentally determined by measuring dephosphorylation of 6,218 microarrayed Tyr(P peptides representing confirmed and theoretical phosphorylation motifs from the cellular proteome. A broad continuum of dephosphorylation was observed across the microarrayed peptide substrates for all phosphatases, suggesting a complex relationship between substrate sequence recognition and optimal activity. Further analysis of peptide dephosphorylation by hierarchical clustering indicated that DUSPs could be organized by substrate sequence motifs, and peptide-specificities by phylogenetic relationships among the catalytic domains. The most highly dephosphorylated peptides represented proteins from 29 cell-signaling pathways, greatly expanding the list of potential targets of DUSPs. These newly identified DUSP substrates will be important for examining structure-activity relationships with physiologically relevant targets.

  15. The discodermolide hairpin structure flows from conformationally stable modular motifs.

    Science.gov (United States)

    Jogalekar, Ashutosh S; Kriel, Frederik H; Shi, Qi; Cornett, Ben; Cicero, Daniel; Snyder, James P

    2010-01-14

    (+)-Discodermolide (DDM), a polyketide macrolide from marine sponge, is a potent microtubule assembly promoter. Reported solid-state, solution, and protein-bound DDM conformations reveal the unusual result that a common hairpin conformational motif exists in all three microenvironments. No other flexible microtubule binding agent exhibits such constancy of conformation. In the present study, we combine force-field conformational searches with NMR deconvolution in different solvents to compare DDM conformers with those observed in other environments. While several conformational families are perceived, the hairpin form dominates. The stability of this motif is dictated primarily by steric factors arising from repeated modular segments in DDM composed of the C(Me)-CHX-C(Me) fragment. Furthermore, docking protocols were utilized to probe the DDM binding mode in beta-tubulin. A previously suggested pose is substantiated (Pose-1), while an alternative (Pose-2) has been identified. SAR analysis for DDM analogues differentiates the two poses and suggests that Pose-2 is better able to accommodate the biodata.

  16. A simple motif for protein recognition in DNA secondary structures.

    Science.gov (United States)

    Landt, Stephen G; Ramirez, Alejandro; Daugherty, Matthew D; Frankel, Alan D

    2005-09-02

    DNA in a single-stranded form (ssDNA) exists transiently within the cell and comprises the telomeres of linear chromosomes and the genomes of some DNA viruses. As with RNA, in the single-stranded state, some DNA sequences are able to fold into complex secondary and tertiary structures that may be recognized by proteins and participate in gene regulation. To better understand how such DNA elements might fold and interact with proteins, and to compare recognition features to those of a structured RNA, we used in vitro selection to identify ssDNAs that bind an RNA-binding peptide from the HIV Rev protein with high affinity and specificity. The large majority of selected binders contain a non-Watson-Crick G.T base-pair and an adjacent C:G base-pair and both are essential for binding. This GT motif can be presented in different DNA contexts, including a nearly perfect duplex and a branched three-helix structure, and appears to be recognized in large part by arginine residues separated by one turn of an alpha-helix. Interestingly, a very similar GT motif is necessary also for protein binding and function of a well-characterized model ssDNA regulatory element from the proenkephalin promoter.

  17. The Origin of Motif Families in Food Webs

    CERN Document Server

    Klaise, Janis

    2016-01-01

    Food webs have been found to exhibit remarkable motif profiles, patterns in the relative prevalences of all possible three-species sub-graphs, and this has been related to ecosystem properties such as stability and robustness. Analysing 46 food webs of various kinds, we find that most food webs fall into one of two distinct motif families. The separation between the families is well predicted by a global measure of hierarchical order in directed networks - trophic coherence. We find that trophic coherence is also a good predictor for the extent of omnivory, defined as the tendency of species to feed on multiple trophic levels. We compare our results to a network assembly model that admits tunable trophic coherence via a single free parameter. The model is able to generate food webs in either of the two families by varying this parameter, and correctly classifies almost all the food webs in our database. This establishes a link between global order and local preying patterns in food webs.

  18. Synchronization patterns: from network motifs to hierarchical networks

    Science.gov (United States)

    Krishnagopal, Sanjukta; Lehnert, Judith; Poel, Winnie; Zakharova, Anna; Schöll, Eckehard

    2017-03-01

    We investigate complex synchronization patterns such as cluster synchronization and partial amplitude death in networks of coupled Stuart-Landau oscillators with fractal connectivities. The study of fractal or self-similar topology is motivated by the network of neurons in the brain. This fractal property is well represented in hierarchical networks, for which we present three different models. In addition, we introduce an analytical eigensolution method and provide a comprehensive picture of the interplay of network topology and the corresponding network dynamics, thus allowing us to predict the dynamics of arbitrarily large hierarchical networks simply by analysing small network motifs. We also show that oscillation death can be induced in these networks, even if the coupling is symmetric, contrary to previous understanding of oscillation death. Our results show that there is a direct correlation between topology and dynamics: hierarchical networks exhibit the corresponding hierarchical dynamics. This helps bridge the gap between mesoscale motifs and macroscopic networks. This article is part of the themed issue 'Horizons of cybernetical physics'.

  19. Graph animals, subgraph sampling and motif search in large networks

    CERN Document Server

    Baskerville, Kim; Paczuski, Maya

    2007-01-01

    We generalize a sampling algorithm for lattice animals (connected clusters on a regular lattice) to a Monte Carlo algorithm for `graph animals', i.e. connected subgraphs in arbitrary networks. As with the algorithm in [N. Kashtan et al., Bioinformatics 20, 1746 (2004)], it provides a weighted sample, but the computation of the weights is much faster (linear in the size of subgraphs, instead of super-exponential). This allows subgraphs with up to ten or more nodes to be sampled with very high statistics, from arbitrarily large networks. Using this together with a heuristic algorithm for rapidly classifying isomorphic graphs, we present results for two protein interaction networks obtained using the TAP high throughput method: one of Escherichia coli with 230 nodes and 695 links, and one for yeast (Saccharomyces cerevisiae) with roughly ten times more nodes and links. We find in both cases that most connected subgraphs are strong motifs (Z-scores >10) or anti-motifs (Z-scores <-10) when the null model is the...

  20. Prevalent RNA recognition motif duplication in the human genome.

    Science.gov (United States)

    Tsai, Yihsuan S; Gomez, Shawn M; Wang, Zefeng

    2014-05-01

    The sequence-specific recognition of RNA by proteins is mediated through various RNA binding domains, with the RNA recognition motif (RRM) being the most frequent and present in >50% of RNA-binding proteins (RBPs). Many RBPs contain multiple RRMs, and it is unclear how each RRM contributes to the binding specificity of the entire protein. We found that RRMs within the same RBP (i.e., sibling RRMs) tend to have significantly higher similarity than expected by chance. Sibling RRM pairs from RBPs shared by multiple species tend to have lower similarity than those found only in a single species, suggesting that multiple RRMs within the same protein might arise from domain duplication followed by divergence through random mutations. This finding is exemplified by a recent RRM domain duplication in DAZ proteins and an ancient duplication in PABP proteins. Additionally, we found that different similarities between sibling RRMs are associated with distinct functions of an RBP and that the RBPs tend to contain repetitive sequences with low complexity. Taken together, this study suggests that the number of RBPs with multiple RRMs has expanded in mammals and that the multiple sibling RRMs may recognize similar target motifs in a cooperative manner.

  1. A new type of GC-MS with advanced capabilities

    Science.gov (United States)

    Fialkov, Alexander B.; Steiner, Urs; Jones, Larry; Amirav, Aviv

    2006-03-01

    We have combined the benefits of supersonic molecular beam interface and its related fly-through electron ionization (EI) ion source with the advanced features of the Varian 1200L gas chromatography-mass spectrometry (GC-MS) and mass spectrometry-mass spectrometry (MS-MS), resulting in a new and powerful GC-MS platform with record setting performance. Electron ionization of vibrationally cold molecules in the supersonic molecular beams (SMB) (cold EI) provided mass spectra with enhanced molecular ion, yet with good library search results and superior identification probabilities. We found that high GC column flow rates lower the elution temperature for any given compounds. This allows much larger molecules to elute at the maximum temperature of standard columns. We analyzed a mixture of heavy linear chain hydrocarbons all the way to C84H170 with a molecular weight of 1179.3 amu, using a 4 m 0.25 mm i.d. column and 32 ml/min He flow rate. Furthermore, we obtained a dominant molecular ion to all these compounds. The lower elution temperatures also greatly enhance the ability to analyze very thermally labile compounds such as carbamate pesticides. The experimental 1200 system is capable of triple quadrupole based MS-MS. We found that MS-MS on the molecular ion is much more effective than on fragment ions, and thus, the enhancement of the molecular ion directly improves the MS-MS sensitivity. Fast GC-MS analysis was also explored, based on very high column flow rate for fast splitless injections without affecting the sensitivity, and on the high system selectivity due to the combination of enhanced molecular ion and MS-MS. We demonstrate a few seconds long GC-MS-MS analysis of diazinon, spiked at 10 ng/g in a mixed fruit and vegetable extract. The feature of enhanced molecular ion provides significant enhancement in the detection sensitivity via SIM and RSIM on the molecular ion. While octafluoronaphthalene (OFN) detection limit of below 1 fg in SIM mode is shown, the

  2. Results of de-novo and Motif activity analyses - FANTOM5 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us FANTOM5 Results of de-novo and Motif activity analyses Data detail Data name Results of de-n...S motif near TSS de-novo motif analysis with HOMER etc. Significance of the corre.../extra/Motifs/ File size: 6.2 GB Simple search URL - Data acquisition method - Data anal...ysis method JASPER motif search HOMER motif analysis Number of data entries 400 files - About This Da...tabase Database Description Download License Update History of This Database Site Policy | Contact Us Results of de-novo and Motif activity analyses - FANTOM5 | LSDB Archive ...

  3. Comparison Between Three Chromatographic (GC-ECD, GC-PFPD and GC-ITD-MS) Methods and a UV-Vis Spectrophotometric Method for the Determination of Dithiocarbamates in Lettuce

    OpenAIRE

    Pizzutti,Ionara R.; Kok,André de; Silva,Rosselei C. da; Rohers,Graciele N.

    2017-01-01

    The purpose of this study was to compare the performance of gas chromatographic with electron capture detector, pulsed flame photometric detector and mass spectrometry (GC-ECD, GC-PFPD and GC-MS) and UV-Vis spectrophotometric methods, based on acidic hydrolysis with tin(II) chloride of dithiocarbamate and analysis of the evolved CS2. For the validation studies were assessed linearity, limit of detection (LOD), limit of quantification (LOQ), accuracy and precision. Recovery experiments were pe...

  4. Effects of GC bias in next-generation-sequencing data on de novo genome assembly.

    Science.gov (United States)

    Chen, Yen-Chun; Liu, Tsunglin; Yu, Chun-Hui; Chiang, Tzen-Yuh; Hwang, Chi-Chuan

    2013-01-01

    Next-generation-sequencing (NGS) has revolutionized the field of genome assembly because of its much higher data throughput and much lower cost compared with traditional Sanger sequencing. However, NGS poses new computational challenges to de novo genome assembly. Among the challenges, GC bias in NGS data is known to aggravate genome assembly. However, it is not clear to what extent GC bias affects genome assembly in general. In this work, we conduct a systematic analysis on the effects of GC bias on genome assembly. Our analyses reveal that GC bias only lowers assembly completeness when the degree of GC bias is above a threshold. At a strong GC bias, the assembly fragmentation due to GC bias can be explained by the low coverage of reads in the GC-poor or GC-rich regions of a genome. This effect is observed for all the assemblers under study. Increasing the total amount of NGS data thus rescues the assembly fragmentation because of GC bias. However, the amount of data needed for a full rescue depends on the distribution of GC contents. Both low and high coverage depths due to GC bias lower the accuracy of assembly. These pieces of information provide guidance toward a better de novo genome assembly in the presence of GC bias.

  5. Sequence Length Limits for Controlling False Positives in Discovering Nucleotide Sequence Motifs

    Institute of Scientific and Technical Information of China (English)

    CHEN Lei; QiAN Zi-liang

    2008-01-01

    In the study of motif discovery, especially the transcription factor DNA binding sites discovery, a too long input sequence would return non-informative motifs rather than those biological functional motifs. This paper gave theoretical analyses and computational experiments to suggest the length limits of the input sequence. When the sequence length exceeds a certain critical point, the probability of discovering the motif decreases sharply. The work not only gave an explanation on the unsatisfying results of the existed motif discovery problems that the input sequence length might be too long and exceed the point, but also provided an estimation of input sequence length we should accept to get more meaningful and reliable results in motif discovery.

  6. Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder

    Science.gov (United States)

    Sharov, Alexei A.; Ko, Minoru S.H.

    2009-01-01

    We present CisFinder software, which generates a comprehensive list of motifs enriched in a set of DNA sequences and describes them with position frequency matrices (PFMs). A new algorithm was designed to estimate PFMs directly from counts of n-mer words with and without gaps; then PFMs are extended over gaps and flanking regions and clustered to generate non-redundant sets of motifs. The algorithm successfully identified binding motifs for 12 transcription factors (TFs) in embryonic stem cells based on published chromatin immunoprecipitation sequencing data. Furthermore, CisFinder successfully identified alternative binding motifs of TFs (e.g. POU5F1, ESRRB, and CTCF) and motifs for known and unknown co-factors of genes associated with the pluripotent state of ES cells. CisFinder also showed robust performance in the identification of motifs that were only slightly enriched in a set of DNA sequences. PMID:19740934

  7. Runtime support for reconfigurable real-time embedded systems

    NARCIS (Netherlands)

    Papp, Z.

    2001-01-01

    As the embedding environment becomes more and more complex so does the embedded system itself. An aspect of the complexity, the demand for robust and fault tolerant embedded solutions is ever increasing. Consequently the embedded system design and development face new challenges including modeling,

  8. Lipid-Mediated Regulation of Embedded Receptor Kinases via Parallel Allosteric Relays.

    Science.gov (United States)

    Ghosh, Madhubrata; Wang, Loo Chien; Ramesh, Ranita; Morgan, Leslie K; Kenney, Linda J; Anand, Ganesh S

    2017-02-28

    Membrane-anchored receptors are essential cellular signaling elements for stimulus sensing, propagation, and transmission inside cells. However, the contributions of lipid interactions to the function and dynamics of embedded receptor kinases have not been described in detail. In this study, we used amide hydrogen/deuterium exchange mass spectrometry, a sensitive biophysical approach, to probe the dynamics of a membrane-embedded receptor kinase, EnvZ, together with functional assays to describe the role of lipids in receptor kinase function. Our results reveal that lipids play an important role in regulating receptor function through interactions with transmembrane segments, as well as through peripheral interactions with nonembedded domains. Specifically, the lipid membrane allosterically modulates the activity of the embedded kinase by altering the dynamics of a glycine-rich motif that is critical for phosphotransfer from ATP. This allostery in EnvZ is independent of membrane composition and involves direct interactions with transmembrane and periplasmic segments, as well as peripheral interactions with nonembedded domains of the protein. In the absence of the membrane-spanning regions, lipid allostery is propagated entirely through peripheral interactions. Whereas lipid allostery impacts the phosphotransferase function of the kinase, extracellular stimulus recognition is mediated via a four-helix bundle subdomain located in the cytoplasm, which functions as the osmosensing core through osmolality-dependent helical stabilization. Our findings emphasize the functional modularity in a membrane-embedded kinase, separated into membrane association, phosphotransferase function, and stimulus recognition. These components are integrated through long-range communication relays, with lipids playing an essential role in regulation.

  9. GC/MS DETERMINATION OF BIOACTIVE COMPONENTS OF PLEUROTUS OSTREATUS

    Directory of Open Access Journals (Sweden)

    V.Priya

    2012-03-01

    Full Text Available In this study, the bioactive components of Pleurotus ostreatus have been evaluated using GC/MS. The chemical compositions of the hydroalcholic extract of Pleurotus ostreatus were investigated using Perkin-Elmer Chromatography–Mass Spectrometry, while the mass spectra of the compounds found in the extract was matched with the National Institute of Standards and Technology (NIST library. GC/MS analysis of hydroalcholic extract of Pleurotus ostreatus revealed the existence of Cholestane-3,7,1,25-tetrol tetraacetate,(3a,5a,7a,12 a-55.20, 9,12-Octadecadienoic acid,methyl ester(E,E-18.55,14,17- Octadecadienoic acid,methyl ester(E,E-5.59,Pentadecanoic acid, ethyl ester-3.84.. The results of this study offer a platform for using Pleurotus ostreatus as herbal alternative for the current synthetic antimicrobial agents.

  10. GC/MS Analysis of the Aromatic Composition of Gasoline

    Science.gov (United States)

    Kostecka, Keith S.; Rabah, Ashraf; Palmer, Charles F., Jr.

    1995-09-01

    The gas chromatography/mass spectrometry (GC/MS) analysis of three brands of regular unleaded gasoline was conducted as part of the independent project of an undergraduate journalism major. In his work, samples of each gasoline were diluted down to part per million (ppm) levels with dichloromethane and then one microliter injections were made onto a Hewlett-Packard GC (5890 Series II unit). Mass spectra were also obtained on each sample through use of a 5971A mass selective detector (MSD). Subsequent characterization was consequently effected through utilization of the standard mass spectra available in a 49,000 compound National Bureau of Standards reference library. Comparison of the obtained and standard spectra revealed that the same aromatic hydrocarbons (including, in part: benzene, the xylenes, naphthalene, and methylated naphthalenes) were present in all three samples. Percentage values for these and other aromatic hydrocarbons were then generated and tabulated.

  11. Analysis of Volatile Compounds in Foie Gras by SDE,GC-MS and GC-O%SDE联合GC-MS与GC-O分析鹅肥肝挥发性风味物质

    Institute of Scientific and Technical Information of China (English)

    谢章斌; 范亚苇; 邓泽元; 刘蓉; 李静; 胡蒋宁; 杜金平

    2011-01-01

    The volatile compounds in foie gras was extracted by simultaneous distillation extraction(SDE) and analyzed by gas chromatography-mass spectrometry(GC-MS) and gas chromatography-olfactometry(GC-O).Totally 41 volatile flavor compounds were identified including 8 hydrocarbons,4 alcohols,2 phenols 7 aldehydes,5 ketones,1 acids,7 ester,7 other compounds and 3 unknown compounds.Among these compounds,hexanal,2-ethylcyclohexanol,nonanal,2-pentadecanone,6,10,14-trimethyl-tetradecanal,di-n-octyl phthalate made a greater contribution to the flavor of foie gras.%采用同时蒸馏萃取法(simultaneous distillation extraction,SDE)提取鹅肥肝的挥发性风味物质,结合气质联用技术(gas chromatography-mass spectrometry,GC-MS)和气相色谱-嗅闻技术(gas chromatography-olfactometry,GC-O)对其挥发性风味物质和主体风味物质进行分析。鉴定出41种风味成分,其中烃类8种、醇类4种、酚类2种、醛类7种、酮类5种、酸类1种、酯类7种、其他7种,3种未鉴定出。同时6种物质对鹅肥肝的风味有较大贡献,分别是己醛、2-乙基环己醇、壬醛、6,10,14-三甲基-2-十五烷酮、十四烷醛和邻苯二甲酸二正辛酯。

  12. Model GC1312S Multifunction Integrated Optical Circuit Devices

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Model GC1312S multifunction integrated optical circuit device (MIOC) used in inertial-grade interferometric fiber optics gyroscopes (IFOGs) is fabricated by annealing and proton exchange process (APE). The unique feature of the device is the incorporation of the beat detection circuit besides all the features the conventional single Y-branch multifunction integrated optical circuit devices have. The device structure, operation principle and typical characteristics, etc., are briefly presented in this paper.

  13. Diverse Power Iteration Embeddings and Its Applications

    Energy Technology Data Exchange (ETDEWEB)

    Huang H.; Yoo S.; Yu, D.; Qin, H.

    2014-12-14

    Abstract—Spectral Embedding is one of the most effective dimension reduction algorithms in data mining. However, its computation complexity has to be mitigated in order to apply it for real-world large scale data analysis. Many researches have been focusing on developing approximate spectral embeddings which are more efficient, but meanwhile far less effective. This paper proposes Diverse Power Iteration Embeddings (DPIE), which not only retains the similar efficiency of power iteration methods but also produces a series of diverse and more effective embedding vectors. We test this novel method by applying it to various data mining applications (e.g. clustering, anomaly detection and feature selection) and evaluating their performance improvements. The experimental results show our proposed DPIE is more effective than popular spectral approximation methods, and obtains the similar quality of classic spectral embedding derived from eigen-decompositions. Moreover it is extremely fast on big data applications. For example in terms of clustering result, DPIE achieves as good as 95% of classic spectral clustering on the complex datasets but 4000+ times faster in limited memory environment.

  14. Autonomous Multicamera Tracking on Embedded Smart Cameras

    Directory of Open Access Journals (Sweden)

    Bischof Horst

    2007-01-01

    Full Text Available There is currently a strong trend towards the deployment of advanced computer vision methods on embedded systems. This deployment is very challenging since embedded platforms often provide limited resources such as computing performance, memory, and power. In this paper we present a multicamera tracking method on distributed, embedded smart cameras. Smart cameras combine video sensing, processing, and communication on a single embedded device which is equipped with a multiprocessor computation and communication infrastructure. Our multicamera tracking approach focuses on a fully decentralized handover procedure between adjacent cameras. The basic idea is to initiate a single tracking instance in the multicamera system for each object of interest. The tracker follows the supervised object over the camera network, migrating to the camera which observes the object. Thus, no central coordination is required resulting in an autonomous and scalable tracking approach. We have fully implemented this novel multicamera tracking approach on our embedded smart cameras. Tracking is achieved by the well-known CamShift algorithm; the handover procedure is realized using a mobile agent system available on the smart camera network. Our approach has been successfully evaluated on tracking persons at our campus.

  15. Group Theory for Embedded Random Matrix Ensembles

    CERN Document Server

    Kota, V K B

    2014-01-01

    Embedded random matrix ensembles are generic models for describing statistical properties of finite isolated quantum many-particle systems. For the simplest spinless fermion (or boson) systems with say $m$ fermions (or bosons) in $N$ single particle states and interacting with say $k$-body interactions, we have EGUE($k$) [embedded GUE of $k$-body interactions) with GUE embedding and the embedding algebra is $U(N)$. In this paper, using EGUE($k$) representation for a Hamiltonian that is $k$-body and an independent EGUE($t$) representation for a transition operator that is $t$-body and employing the embedding $U(N)$ algebra, finite-$N$ formulas for moments up to order four are derived, for the first time, for the transition strength densities (transition strengths multiplied by the density of states at the initial and final energies). In the asymptotic limit, these formulas reduce to those derived for the EGOE version and establish that in general bivariate transition strength densities take bivariate Gaussian ...

  16. Embedded Web Technology: Applying World Wide Web Standards to Embedded Systems

    Science.gov (United States)

    Ponyik, Joseph G.; York, David W.

    2002-01-01

    Embedded Systems have traditionally been developed in a highly customized manner. The user interface hardware and software along with the interface to the embedded system are typically unique to the system for which they are built, resulting in extra cost to the system in terms of development time and maintenance effort. World Wide Web standards have been developed in the passed ten years with the goal of allowing servers and clients to intemperate seamlessly. The client and server systems can consist of differing hardware and software platforms but the World Wide Web standards allow them to interface without knowing about the details of system at the other end of the interface. Embedded Web Technology is the merging of Embedded Systems with the World Wide Web. Embedded Web Technology decreases the cost of developing and maintaining the user interface by allowing the user to interface to the embedded system through a web browser running on a standard personal computer. Embedded Web Technology can also be used to simplify an Embedded System's internal network.

  17. Orthogonality of embedded wave functions for different states in frozen-density embedding theory

    Energy Technology Data Exchange (ETDEWEB)

    Zech, Alexander; Wesolowski, Tomasz A. [Département de Chimie Physique, Université de Genève, 30 quai Ernest-Ansermet, CH-1211 Genève 4 (Switzerland); Aquilante, Francesco [Dipartimento di Chimica “G. Ciamician,” Università di Bologna, Via Selmi 2, IT-40126 Bologna (Italy)

    2015-10-28

    Other than lowest-energy stationary embedded wave functions obtained in Frozen-Density Embedding Theory (FDET) [T. A. Wesolowski, Phys. Rev. A 77, 012504 (2008)] can be associated with electronic excited states but they can be mutually non-orthogonal. Although this does not violate any physical principles — embedded wave functions are only auxiliary objects used to obtain stationary densities — working with orthogonal functions has many practical advantages. In the present work, we show numerically that excitation energies obtained using conventional FDET calculations (allowing for non-orthogonality) can be obtained using embedded wave functions which are strictly orthogonal. The used method preserves the mathematical structure of FDET and self-consistency between energy, embedded wave function, and the embedding potential (they are connected through the Euler-Lagrange equations). The orthogonality is built-in through the linearization in the embedded density of the relevant components of the total energy functional. Moreover, we show formally that the differences between the expectation values of the embedded Hamiltonian are equal to the excitation energies, which is the exact result within linearized FDET. Linearized FDET is shown to be a robust approximation for a large class of reference densities.

  18. Exponentially many maximum genus embeddings and genus embeddings for complete graphs

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    There are many results on the maximum genus, among which most are written for the existence of values of such embeddings, and few attention has been paid to the estimation of such embeddings and their applications. In this paper we study the number of maximum genus embeddings for a graph and find an exponential lower bound for such numbers. Our results show that in gen-eral case, a simple connected graph has exponentially many distinct maximum genus embeddings. In particular, a connected cubic graph G of order n always has at least 2~1/2m+n+ α2 distinct maximum genus embeddings, where α and m denote, respectively, the number of inner vertices and odd compo-nents of an optimal tree T . What surprise us most is that such two extremal embeddings (i.e., the maximum genus embeddings and the genus embeddings) are sometimes closely related with each other. In fact, as applications, we show that for a suffcient large natural number n, there are at least C2 n4 dmeapneyn dgienngu os ne mthbee vdadliuneg soffonrocf ormespidleutee 1g2r.a pThh eKsen rwesiuthlt sn i m≡p r4o,v 7e, 1th0e ( mbooudn1d2)s, owbthaeirnee dC b iys Ka ocroznhsikta anncde Voss and the methods used here are much simpler and straight.

  19. IMB3-Miner: Mining Induced/Embedded Subtrees by Constraining the Level of Embedding

    NARCIS (Netherlands)

    Tan, H.; Dillon, T.S.; Hadzic, F.; Chang, E.; Feng, L.

    Tree mining has recently attracted a lot of interest in areas such as Bioinformatics, XML mining, Web mining, etc. We are mainly concerned with mining frequent induced and embedded subtrees. While more interesting patterns can be obtained when mining embedded subtrees, unfortunately mining such

  20. An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes.

    Science.gov (United States)

    Liu, Bingqiang; Zhang, Hanyuan; Zhou, Chuan; Li, Guojun; Fennell, Anne; Wang, Guanghui; Kang, Yu; Liu, Qi; Ma, Qin

    2016-08-09

    Phylogenetic footprinting is an important computational technique for identifying cis-regulatory motifs in orthologous regulatory regions from multiple genomes, as motifs tend to evolve slower than their surrounding non-functional sequences. Its application, however, has several difficulties for optimizing the selection of orthologous data and reducing the false positives in motif prediction. Here we present an integrative phylogenetic footprinting framework for accurate motif predictions in prokaryotic genomes (MP(3)). The framework includes a new orthologous data preparation procedure, an additional promoter scoring and pruning method and an integration of six existing motif finding algorithms as basic motif search engines. Specifically, we collected orthologous genes from available prokaryotic genomes and built the orthologous regulatory regions based on sequence similarity of promoter regions. This procedure made full use of the large-scale genomic data and taxonomy information and filtered out the promoters with limited contribution to produce a high quality orthologous promoter set. The promoter scoring and pruning is implemented through motif voting by a set of complementary predicting tools that mine as many motif candidates as possible and simultaneously eliminate the effect of random noise. We have applied the framework to Escherichia coli k12 genome and evaluated the prediction performance through comparison with seven existing programs. This evaluation was systematically carried out at the nucleotide and binding site level, and the results showed that MP(3) consistently outperformed other popular motif finding tools. We have integrated MP(3) into our motif identification and analysis server DMINDA, allowing users to efficiently identify and analyze motifs in 2,072 completely sequenced prokaryotic genomes. The performance evaluation indicated that MP(3) is effective for predicting regulatory motifs in prokaryotic genomes. Its application may enhance

  1. NestedMICA as an ab initio protein motif discovery tool

    Directory of Open Access Journals (Sweden)

    Down Thomas A

    2008-01-01

    Full Text Available Abstract Background Discovering overrepresented patterns in amino acid sequences is an important step in protein functional element identification. We adapted and extended NestedMICA, an ab initio motif finder originally developed for finding transcription binding site motifs, to find short protein signals, and compared its performance with another popular protein motif finder, MEME. NestedMICA, an open source protein motif discovery tool written in Java, is driven by a Monte Carlo technique called Nested Sampling. It uses multi-class sequence background models to represent different "uninteresting" parts of sequences that do not contain motifs of interest. In order to assess NestedMICA as a protein motif finder, we have tested it on synthetic datasets produced by spiking instances of known motifs into a randomly selected set of protein sequences. NestedMICA was also tested using a biologically-authentic test set, where we evaluated its performance with respect to varying sequence length. Results Generally NestedMICA recovered most of the short (3–9 amino acid long test protein motifs spiked into a test set of sequences at different frequencies. We showed that it can be used to find multiple motifs at the same time, too. In all the assessment experiments we carried out, its overall motif discovery performance was better than that of MEME. Conclusion NestedMICA proved itself to be a robust and sensitive ab initio protein motif finder, even for relatively short motifs that exist in only a small fraction of sequences. Availability NestedMICA is available under the Lesser GPL open-source license from: http://www.sanger.ac.uk/Software/analysis/nmica/

  2. The value of position-specific priors in motif discovery using MEME.

    Science.gov (United States)

    Bailey, Timothy L; Bodén, Mikael; Whitington, Tom; Machanick, Philip

    2010-04-09

    Position-specific priors have been shown to be a flexible and elegant way to extend the power of Gibbs sampler-based motif discovery algorithms. Information of many types-including sequence conservation, nucleosome positioning, and negative examples-can be converted into a prior over the location of motif sites, which then guides the sequence motif discovery algorithm. This approach has been shown to confer many of the benefits of conservation-based and discriminative motif discovery approaches on Gibbs sampler-based motif discovery methods, but has not previously been studied with methods based on expectation maximization (EM). We extend the popular EM-based MEME algorithm to utilize position-specific priors and demonstrate their effectiveness for discovering transcription factor (TF) motifs in yeast and mouse DNA sequences. Utilizing a discriminative, conservation-based prior dramatically improves MEME's ability to discover motifs in 156 yeast TF ChIP-chip datasets, more than doubling the number of datasets where it finds the correct motif. On these datasets, MEME using the prior has a higher success rate than eight other conservation-based motif discovery approaches. We also show that the same type of prior improves the accuracy of motifs discovered by MEME in mouse TF ChIP-seq data, and that the motifs tend to be of slightly higher quality those found by a Gibbs sampling algorithm using the same prior. We conclude that using position-specific priors can substantially increase the power of EM-based motif discovery algorithms such as MEME algorithm.

  3. The value of position-specific priors in motif discovery using MEME

    Directory of Open Access Journals (Sweden)

    Whitington Tom

    2010-04-01

    Full Text Available Abstract Background Position-specific priors have been shown to be a flexible and elegant way to extend the power of Gibbs sampler-based motif discovery algorithms. Information of many types–including sequence conservation, nucleosome positioning, and negative examples–can be converted into a prior over the location of motif sites, which then guides the sequence motif discovery algorithm. This approach has been shown to confer many of the benefits of conservation-based and discriminative motif discovery approaches on Gibbs sampler-based motif discovery methods, but has not previously been studied with methods based on expectation maximization (EM. Results We extend the popular EM-based MEME algorithm to utilize position-specific priors and demonstrate their effectiveness for discovering transcription factor (TF motifs in yeast and mouse DNA sequences. Utilizing a discriminative, conservation-based prior dramatically improves MEME's ability to discover motifs in 156 yeast TF ChIP-chip datasets, more than doubling the number of datasets where it finds the correct motif. On these datasets, MEME using the prior has a higher success rate than eight other conservation-based motif discovery approaches. We also show that the same type of prior improves the accuracy of motifs discovered by MEME in mouse TF ChIP-seq data, and that the motifs tend to be of slightly higher quality those found by a Gibbs sampling algorithm using the same prior. Conclusions We conclude that using position-specific priors can substantially increase the power of EM-based motif discovery algorithms such as MEME algorithm.

  4. Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder

    OpenAIRE

    Sharov, Alexei A; Minoru S.H. Ko

    2009-01-01

    We present CisFinder software, which generates a comprehensive list of motifs enriched in a set of DNA sequences and describes them with position frequency matrices (PFMs). A new algorithm was designed to estimate PFMs directly from counts of n-mer words with and without gaps; then PFMs are extended over gaps and flanking regions and clustered to generate non-redundant sets of motifs. The algorithm successfully identified binding motifs for 12 transcription factors (TFs) in embryonic stem cel...

  5. Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins.

    Science.gov (United States)

    Foulk, Michael S; Urban, John M; Casella, Cinzia; Gerbi, Susan A

    2015-05-01

    Nascent strand sequencing (NS-seq) is used to discover DNA replication origins genome-wide, allowing identification of features for their specification. NS-seq depends on the ability of lambda exonuclease (λ-exo) to efficiently digest parental DNA while leaving RNA-primer protected nascent strands intact. We used genomics and biochemical approaches to determine if λ-exo digests all parental DNA sequences equally. We report that λ-exo does not efficiently digest G-quadruplex (G4) structures in a plasmid. Moreover, λ-exo digestion of nonreplicating genomic DNA (LexoG0) enriches GC-rich DNA and G4 motifs genome-wide. We used LexoG0 data to control for nascent strand-independent λ-exo biases in NS-seq and validated this approach at the rDNA locus. The λ-exo-controlled NS-seq peaks are not GC-rich, and only 35.5% overlap with 6.8% of all G4s, suggesting that G4s are not general determinants for origin specification but may play a role for a subset. Interestingly, we observed a periodic spacing of G4 motifs and nucleosomes around the peak summits, suggesting that G4s may position nucleosomes at this subset of origins. Finally, we demonstrate that use of Na(+) instead of K(+) in the λ-exo digestion buffer reduced the effect of G4s on λ-exo digestion and discuss ways to increase both the sensitivity and specificity of NS-seq.

  6. Photoconductive ZnO films with embedded quantum dot or ruthenium dye sensitizers

    Directory of Open Access Journals (Sweden)

    Michael A. White

    2013-09-01

    Full Text Available We report a new type of solution-processed photoconductive film based on embedding photosensitizers (semiconductor nanocrystals or ruthenium dye molecules within conductive ZnO sol-gel matrices. Mixing photosensitizers directly with sol-gel precursors prior to film deposition yields highly colored ZnO films containing well-dispersed sensitizers. These films show internal photoconductivity quantum efficiencies up to ∼50% and photoresponses over 100 mA/W with visible photoexcitation, competitive with other more complex photodetectors reported recently. This simple motif is attractive for the development of robust sensitized-oxide photodetectors and for fundamental studies of photoinduced charge separation from a variety of molecular or quantum dot sensitizers into conductive oxides.

  7. Comparison of GC-FPD and GC-FID in determining ethanethiol in air of workplace%GC-FPD与GC-FID用于测定工作场所空气中乙硫醇的方法比较

    Institute of Scientific and Technical Information of China (English)

    李颜岩; 史立新

    2013-01-01

    目的 比较工作场所空气中乙硫醇采用FPD(火焰光度检测器)与FID(氢焰离子化检测器)气相色谱测定的方法.方法 空气中以分子或蒸汽态存在的乙硫醇用浸渍玻璃纤维滤纸采集,经洗脱与提取后进样,弱极性色谱柱分离,分别采用FPD、FID进行检测,比较方法学技术指标.结果 FID测定乙硫醇在0.2μg/ml ~ 8.4 μg/ml范围内线性关系良好,r=0.9999,检出限为0.2μg/nnl,与FPD的测定结果基本相当.结论 采用GC-FID测定空气中的乙硫醇的技术参数与用GC-FPD基本等效;GC-FID较为常见,使用与推广更具有实际意义.

  8. Phytochemical studies on Allamanda cathartica L. using GC-MS

    Institute of Scientific and Technical Information of China (English)

    Prabhadevi V; Sahaya Sathish S; Johnson M; Venkatramani B; Janakiraman N

    2012-01-01

    Objective: To explore the phytochemical constituents present in Allamanda cathartica (A. cathartica) L. using GC-MS. Methods: 20 g of the powdered leaf and stem sample of A. cathartica was equilibrated with 200 d/m of A. cathartica ethanol for 24 h, separately. The volume of the supernatant was later reduced by heating to 2 d/m. The concentrated ethanolic extracts were further subjected to GC-MS analysis. Results: The GC-MS analyses determined the presence of 28 different phytochemical compounds in the ethanolic leaf extract of A. cathartica. The major phytoconstituents were 9,12,15-octadecatrienoic acid (Z,Z,Z)- (16.39%), n-hexadecanoic acid (14.08%), 3-O-methyl-d-glucose (11.03%) and 9,12,15-octadecatrienoic acid ethyl ester (Z,Z,Z)-(10.58%). The ethanolic stem extract of A. cathartica showed the presence of 26 different bioactive compounds. The major ones are 3-O-methyl-d-glucose (29.86%), 2-furancarboxaldehyde 5-(hydroxymethyl)- (14.87%), n-hexadecanoic acid (9.13%) and 9,12,15-octadecatrienoic acid (Z,Z,Z)- (7.34%). Conclusions: This study helps to predict the formula and structure of biomolecules which can be used as drugs and further investigation may lead to the development of drug formulation.

  9. Detection of the Spermicide Nonoxynol-9 Via GC-MS

    Science.gov (United States)

    Musah, Rabi A.; Vuong, Angela L.; Henck, Colin; Shepard, Jason R. E.

    2012-05-01

    The spermicide nonoxynol-9 is actually a complex mixture of dozens of closely related amphiphilic compounds, and the chemical properties of this assortment significantly hamper its characterization by GC-MS. The inability to perform routine GC-MS testing on nonoxynol-9 has limited its evidentiary value in forensic casework, which relies heavily on this technique for analysis. A disturbing trend in sexual assault is the use of condoms by assailants, to avoid leaving behind DNA evidence that can connect a perpetrator to a victim. This observation necessitates the development of alternative methods for the analysis of trace evidence that can show causal links between a victim and a suspect. Detection of lubricants associated with sexual assault is one such way to establish this connection. The development of GC-MS methods that permit facile detection of both nonoxynol-9 alone and nonoxynol-9 extracted from other complex matrices that have potential as trace evidence in sexual assault is reported. A detection limit of 2.14 μg of nonoxynol-9 is demonstrated, and a detailed mass spectral profile that elaborates on what is known of its structure is provided.

  10. Potential deleterious role of anti-Neu5Gc antibodies in xenotransplantation.

    Science.gov (United States)

    Salama, Apolline; Evanno, Gwénaëlle; Harb, Jean; Soulillou, Jean-Paul

    2015-01-01

    Human beings do not synthesize the glycolyl form of the sialic acid (Neu5Gc) and only express the acetylated form of the sugar, whereas a diet-based intake of Neu5Gc provokes a natural immunization and production of anti-Neu5Gc antibodies in human serum. However, Neu5Gc is expressed on mammal glycoproteins and glycolipids in most organs and cells. We review here the relevance of Neu5Gc and anti-Neu5Gc antibodies in the context of xenotransplantation and the use of animal-derived molecules and products, as well as the possible consequences of a long-term exposure to anti-Neu5Gc antibodies in recipients of xenografts. In addition, the importance of an accurate estimation of the anti-Neu5Gc response following xenotransplantation and the future contribution of knockout animals mimicking the human situation are also assessed.

  11. Mapping network motif tunability and robustness in the design of synthetic signaling circuits.

    Directory of Open Access Journals (Sweden)

    Sergio Iadevaia

    Full Text Available Cellular networks are highly dynamic in their function, yet evolutionarily conserved in their core network motifs or topologies. Understanding functional tunability and robustness of network motifs to small perturbations in function and structure is vital to our ability to synthesize controllable circuits. In establishing core sets of network motifs, we selected topologies that are overrepresented in mammalian networks, including the linear, feedback, feed-forward, and bifan circuits. Static and dynamic tunability of network motifs were defined as the motif ability to respectively attain steady-state or transient outputs in response to pre-defined input stimuli. Detailed computational analysis suggested that static tunability is insensitive to the circuit topology, since all of the motifs displayed similar ability to attain predefined steady-state outputs in response to constant inputs. Dynamic tunability, in contrast, was tightly dependent on circuit topology, with some motifs performing superiorly in achieving observed time-course outputs. Finally, we mapped dynamic tunability onto motif topologies to determine robustness of motif structures to changes in topology and identify design principles for the rational assembly of robust synthetic networks.

  12. A motif extraction algorithm based on hashing and modulo-4 arithmetic.

    Science.gov (United States)

    Sheng, Huitao; Mehrotra, Kishan; Mohan, Chilukuri; Raina, Ramesh

    2008-01-01

    We develop an algorithm to identify cis-elements in promoter regions of coregulated genes. This algorithm searches for subsequences of desired length whose frequency of occurrence is relatively high, while accounting for slightly perturbed variants using hash table and modulo arithmetic. Motifs are evaluated using profile matrices and higher-order Markov background model. Simulation results show that our algorithm discovers more motifs present in the test sequences, when compared with two well-known motif-discovery tools (MDScan and AlignACE). The algorithm produces very promising results on real data set; the output of the algorithm contained many known motifs.

  13. Analysis and Synthesis of Distributed Real-Time Embedded Systems

    DEFF Research Database (Denmark)

    Pop, Paul; Eles, Petru; Peng, Zebo

    Embedded computer systems are now everywhere: from alarm clocks to PDAs, from mobile phones to cars, almost all the devices we use are controlled by embedded computers. An important class of embedded computer systems is that of hard real-time systems, which have to fulfill strict timing...... in important reductions of design costs. Analysis and Synthesis of Distributed Real-Time Embedded Systems will be of interest to advanced undergraduates, graduate students, researchers and designers involved in the field of embedded systems....

  14. A new type of Na(+-driven ATP synthase membrane rotor with a two-carboxylate ion-coupling motif.

    Directory of Open Access Journals (Sweden)

    Sarah Schulz

    Full Text Available The anaerobic bacterium Fusobacterium nucleatum uses glutamate decarboxylation to generate a transmembrane gradient of Na⁺. Here, we demonstrate that this ion-motive force is directly coupled to ATP synthesis, via an F₁F₀-ATP synthase with a novel Na⁺ recognition motif, shared by other human pathogens. Molecular modeling and free-energy simulations of the rotary element of the enzyme, the c-ring, indicate Na⁺ specificity in physiological settings. Consistently, activity measurements showed Na⁺ stimulation of the enzyme, either membrane-embedded or isolated, and ATP synthesis was sensitive to the Na⁺ ionophore monensin. Furthermore, Na⁺ has a protective effect against inhibitors targeting the ion-binding sites, both in the complete ATP synthase and the isolated c-ring. Definitive evidence of Na⁺ coupling is provided by two identical crystal structures of the c₁₁ ring, solved by X-ray crystallography at 2.2 and 2.6 Å resolution, at pH 5.3 and 8.7, respectively. Na⁺ ions occupy all binding sites, each coordinated by four amino acids and a water molecule. Intriguingly, two carboxylates instead of one mediate ion binding. Simulations and experiments demonstrate that this motif implies that a proton is concurrently bound to all sites, although Na⁺ alone drives the rotary mechanism. The structure thus reveals a new mode of ion coupling in ATP synthases and provides a basis for drug-design efforts against this opportunistic pathogen.

  15. Group-specific component (GC) polymorphism in Cádiz (southern Spain).

    Science.gov (United States)

    Vizcaya, M A; Romero, J L; Gamero, J J; Arufe, M I

    1992-01-01

    The genetic polymorphism of group-specific component (GC) was analysed in a sample of 443 healthy unrelated subjects of both sexes resident in the province of Cádiz (Southern Spain). Isoelectric focusing was carried out in polyacrylamide gels followed by staining with coomassie blue R 250. The estimated gene frequencies were as follows: GC*1S = 0.6185; GC*1F = 0.1162; GC*2 = 0.2652.

  16. Expression of human AID in yeast induces mutations in context similar to the context of somatic hypermutation at G-C pairs in immunoglobulin genes

    Directory of Open Access Journals (Sweden)

    Kunkel Thomas A

    2005-06-01

    Full Text Available Abstract Background Antibody genes are diversified by somatic hypermutation (SHM, gene conversion and class-switch recombination. All three processes are initiated by the activation-induced deaminase (AID. According to a DNA deamination model of SHM, AID converts cytosine to uracil in DNA sequences. The initial deamination of cytosine leads to mutation and recombination in pathways involving replication, DNA mismatch repair and possibly base excision repair. The DNA sequence context of mutation hotspots at G-C pairs during SHM is DGYW/WRCH (G-C is a hotspot position, R = A/G, Y = T/C, W = A/T, D = A/G/T. Results To investigate the mechanisms of AID-induced mutagenesis in a model system, we studied the genetic consequences of AID expression in yeast. We constructed a yeast vector with an artificially synthesized human AID gene insert using codons common to highly expressed yeast genes. We found that expression of the artificial hAIDSc gene was moderately mutagenic in a wild-type strain and highly mutagenic in an ung1 uracil-DNA glycosylase-deficient strain. A majority of mutations were at G-C pairs. In the ung1 strain, C-G to T-A transitions were found almost exclusively, while a mixture of transitions with 12% transversions was characteristic in the wild-type strain. In the ung1 strain mutations that could have originated from deamination of the transcribed stand were found more frequently. In the wild-type strain, the strand bias was reversed. DGYW/WRCH motifs were preferential sites of mutations. Conclusion The results are consistent with the hypothesis that AID-mediated deamination of DNA is a major cause of mutations at G-C base pairs in immunoglobulin genes during SHM. The sequence contexts of mutations in yeast induced by AID and those of somatic mutations at G-C pairs in immunoglobulin genes are significantly similar. This indicates that the intrinsic substrate specificity of AID itself is a primary determinant of mutational hotspots at G-C

  17. On the embedding of Weyl manifolds

    Science.gov (United States)

    Avalos, R.; Dahia, F.; Romero, C.

    2017-01-01

    We discuss the possibility of extending different versions of the Campbell-Magaard theorem, which have already been established in the context of semi-Riemannian geometry, to the context of Weyl's geometry. We show that some of the known results can be naturally extended to the new geometric scenario, although new difficulties arise. In pursuit of solving the embedding problem, we have obtained some no-go theorems. We also highlight some of the difficulties that appear in the embedding problem, which are typical of the Weylian character of the geometry. The establishing of these new results may be viewed as part of a program that highlights the possible significance of embedding theorems of increasing degrees of generality in the context of modern higher-dimensional space-time theories.

  18. Embedded and real-time operating systems

    CERN Document Server

    Wang, K C

    2017-01-01

    This book covers the basic concepts and principles of operating systems, showing how to apply them to the design and implementation of complete operating systems for embedded and real-time systems. It includes all the foundational and background information on ARM architecture, ARM instructions and programming, toolchain for developing programs, virtual machines for software implementation and testing, program execution image, function call conventions, run-time stack usage and link C programs with assembly code. It describes the design and implementation of a complete OS for embedded systems in incremental steps, explaining the design principles and implementation techniques. For Symmetric Multiprocessing (SMP) embedded systems, the author examines the ARM MPcore processors, which include the SCU and GIC for interrupts routing and interprocessor communication and synchronization by Software Generated Interrupts (SGIs). Throughout the book, complete working sample systems demonstrate the design principles and...

  19. Design Technology for Heterogeneous Embedded Systems

    CERN Document Server

    O'Connor, Ian; Piguet, Christian

    2012-01-01

    Designing technology to address the problem of heterogeneous embedded systems, while remaining compatible with standard “More Moore” flows, i.e. capable of handling simultaneously both silicon complexity and system complexity, represents one of the most important challenges facing the semiconductor industry today. While the micro-electronics industry has built its own specific design methods to focus mainly on the management of complexity through the establishment of abstraction levels, the emergence of device heterogeneity requires new approaches enabling the satisfactory design of physically heterogeneous embedded systems for the widespread deployment of such systems. This book, compiled largely from a set of contributions from participants of past editions of the Winter School on Heterogeneous Embedded Systems Design Technology (FETCH), proposes a broad and holistic overview of design techniques used to tackle the various facets of heterogeneity in terms of technology and opportunities at the physical ...

  20. Locally Linear Discriminate Embedding for Face Recognition

    Directory of Open Access Journals (Sweden)

    Eimad E. Abusham

    2009-01-01

    Full Text Available A novel method based on the local nonlinear mapping is presented in this research. The method is called Locally Linear Discriminate Embedding (LLDE. LLDE preserves a local linear structure of a high-dimensional space and obtains a compact data representation as accurately as possible in embedding space (low dimensional before recognition. For computational simplicity and fast processing, Radial Basis Function (RBF classifier is integrated with the LLDE. RBF classifier is carried out onto low-dimensional embedding with reference to the variance of the data. To validate the proposed method, CMU-PIE database has been used and experiments conducted in this research revealed the efficiency of the proposed methods in face recognition, as compared to the linear and non-linear approaches.