combinatorial pattern matching: Topics by Science.gov

Sample records for combinatorial pattern matching

Sin(x)**2 + cos(x)**2 = 1. [programming identities using comparative combinatorial substitutions

NASA Technical Reports Server (NTRS)

Stoutemyer, D. R.

1977-01-01

Attempts to achieve tasteful automatic employment of the identities sin sq x + cos sq x = 1 and cos sq h x -sin sq h x = 1 in a manner which truly minimizes the complexity of the resulting expression are described. The disappointments of trigonometric reduction, trigonometric expansion, pattern matching, Poisson series, and Demoivre's theorem are related. The advantages of using the method of comparative combinatorial substitutions are illustrated.
cGRNB: a web server for building combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets.

PubMed

Xu, Huayong; Yu, Hui; Tu, Kang; Shi, Qianqian; Wei, Chaochun; Li, Yuan-Yuan; Li, Yi-Xue

2013-01-01

We are witnessing rapid progress in the development of methodologies for building the combinatorial gene regulatory networks involving both TFs (Transcription Factors) and miRNAs (microRNAs). There are a few tools available to do these jobs but most of them are not easy to use and not accessible online. A web server is especially needed in order to allow users to upload experimental expression datasets and build combinatorial regulatory networks corresponding to their particular contexts. In this work, we compiled putative TF-gene, miRNA-gene and TF-miRNA regulatory relationships from forward-engineering pipelines and curated them as built-in data libraries. We streamlined the R codes of our two separate forward-and-reverse engineering algorithms for combinatorial gene regulatory network construction and formalized them as two major functional modules. As a result, we released the cGRNB (combinatorial Gene Regulatory Networks Builder): a web server for constructing combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets. The cGRNB enables two major network-building modules, one for MPGE (miRNA-perturbed gene expression) datasets and the other for parallel miRNA/mRNA expression datasets. A miRNA-centered two-layer combinatorial regulatory cascade is the output of the first module and a comprehensive genome-wide network involving all three types of combinatorial regulations (TF-gene, TF-miRNA, and miRNA-gene) are the output of the second module. In this article we propose cGRNB, a web server for building combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets. Since parallel miRNA/mRNA expression datasets are rapidly accumulated by the advance of next-generation sequencing techniques, cGRNB will be very useful tool for researchers to build combinatorial gene regulatory networks based on expression datasets. The cGRNB web-server is free and available online at http://www.scbit.org/cgrnb.
MARCC (Matrix-Assisted Reader Chromatin Capture): an antibody-free method to enrich and analyze combinatorial nucleosome modifications

PubMed Central

Su, Zhangli

2016-01-01

Combinatorial patterns of histone modifications are key indicators of different chromatin states. Most of the current approaches rely on the usage of antibodies to analyze combinatorial histone modifications. Here we detail an antibody-free method named MARCC (Matrix-Assisted Reader Chromatin Capture) to enrich combinatorial histone modifications. The combinatorial patterns are enriched on native nucleosomes extracted from cultured mammalian cells and prepared by micrococcal nuclease digestion. Such enrichment is achieved by recombinant chromatin-interacting protein modules, or so-called reader domains, which can bind in a combinatorial modification-dependent manner. The enriched chromatin can be quantified by western blotting or mass spectrometry for the co-existence of histone modifications, while the associated DNA content can be analyzed by qPCR or next-generation sequencing. Altogether, MARCC provides a reproducible, efficient and customizable solution to enrich and analyze combinatorial histone modifications. PMID:26131849
Research on parallel combinatory spread spectrum communication system with double information matching

NASA Astrophysics Data System (ADS)

Xue, Wei; Wang, Qi; Wang, Tianyu

2018-04-01

This paper presents an improved parallel combinatory spread spectrum (PC/SS) communication system with the method of double information matching (DIM). Compared with conventional PC/SS system, the new model inherits the advantage of high transmission speed, large information capacity and high security. Besides, the problem traditional system will face is the high bit error rate (BER) and since its data-sequence mapping algorithm. Hence the new model presented shows lower BER and higher efficiency by its optimization of mapping algorithm.
A Bioinformatics Approach for Detecting Repetitive Nested Motifs using Pattern Matching.

PubMed

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.
Combinatorial techniques to efficiently investigate and optimize organic thin film processing and properties.

PubMed

Wieberger, Florian; Kolb, Tristan; Neuber, Christian; Ober, Christopher K; Schmidt, Hans-Werner

2013-04-08

In this article we present several developed and improved combinatorial techniques to optimize processing conditions and material properties of organic thin films. The combinatorial approach allows investigations of multi-variable dependencies and is the perfect tool to investigate organic thin films regarding their high performance purposes. In this context we develop and establish the reliable preparation of gradients of material composition, temperature, exposure, and immersion time. Furthermore we demonstrate the smart application of combinations of composition and processing gradients to create combinatorial libraries. First a binary combinatorial library is created by applying two gradients perpendicular to each other. A third gradient is carried out in very small areas and arranged matrix-like over the entire binary combinatorial library resulting in a ternary combinatorial library. Ternary combinatorial libraries allow identifying precise trends for the optimization of multi-variable dependent processes which is demonstrated on the lithographic patterning process. Here we verify conclusively the strong interaction and thus the interdependency of variables in the preparation and properties of complex organic thin film systems. The established gradient preparation techniques are not limited to lithographic patterning. It is possible to utilize and transfer the reported combinatorial techniques to other multi-variable dependent processes and to investigate and optimize thin film layers and devices for optical, electro-optical, and electronic applications.
Comprehensive human transcription factor binding site map for combinatory binding motifs discovery.

PubMed

Müller-Molina, Arnoldo J; Schöler, Hans R; Araúzo-Bravo, Marcos J

2012-01-01

To know the map between transcription factors (TFs) and their binding sites is essential to reverse engineer the regulation process. Only about 10%-20% of the transcription factor binding motifs (TFBMs) have been reported. This lack of data hinders understanding gene regulation. To address this drawback, we propose a computational method that exploits never used TF properties to discover the missing TFBMs and their sites in all human gene promoters. The method starts by predicting a dictionary of regulatory "DNA words." From this dictionary, it distills 4098 novel predictions. To disclose the crosstalk between motifs, an additional algorithm extracts TF combinatorial binding patterns creating a collection of TF regulatory syntactic rules. Using these rules, we narrowed down a list of 504 novel motifs that appear frequently in syntax patterns. We tested the predictions against 509 known motifs confirming that our system can reliably predict ab initio motifs with an accuracy of 81%-far higher than previous approaches. We found that on average, 90% of the discovered combinatorial binding patterns target at least 10 genes, suggesting that to control in an independent manner smaller gene sets, supplementary regulatory mechanisms are required. Additionally, we discovered that the new TFBMs and their combinatorial patterns convey biological meaning, targeting TFs and genes related to developmental functions. Thus, among all the possible available targets in the genome, the TFs tend to regulate other TFs and genes involved in developmental functions. We provide a comprehensive resource for regulation analysis that includes a dictionary of "DNA words," newly predicted motifs and their corresponding combinatorial patterns. Combinatorial patterns are a useful filter to discover TFBMs that play a major role in orchestrating other factors and thus, are likely to lock/unlock cellular functional clusters.
Comprehensive Human Transcription Factor Binding Site Map for Combinatory Binding Motifs Discovery

PubMed Central

Müller-Molina, Arnoldo J.; Schöler, Hans R.; Araúzo-Bravo, Marcos J.

2012-01-01

To know the map between transcription factors (TFs) and their binding sites is essential to reverse engineer the regulation process. Only about 10%–20% of the transcription factor binding motifs (TFBMs) have been reported. This lack of data hinders understanding gene regulation. To address this drawback, we propose a computational method that exploits never used TF properties to discover the missing TFBMs and their sites in all human gene promoters. The method starts by predicting a dictionary of regulatory “DNA words.” From this dictionary, it distills 4098 novel predictions. To disclose the crosstalk between motifs, an additional algorithm extracts TF combinatorial binding patterns creating a collection of TF regulatory syntactic rules. Using these rules, we narrowed down a list of 504 novel motifs that appear frequently in syntax patterns. We tested the predictions against 509 known motifs confirming that our system can reliably predict ab initio motifs with an accuracy of 81%—far higher than previous approaches. We found that on average, 90% of the discovered combinatorial binding patterns target at least 10 genes, suggesting that to control in an independent manner smaller gene sets, supplementary regulatory mechanisms are required. Additionally, we discovered that the new TFBMs and their combinatorial patterns convey biological meaning, targeting TFs and genes related to developmental functions. Thus, among all the possible available targets in the genome, the TFs tend to regulate other TFs and genes involved in developmental functions. We provide a comprehensive resource for regulation analysis that includes a dictionary of “DNA words,” newly predicted motifs and their corresponding combinatorial patterns. Combinatorial patterns are a useful filter to discover TFBMs that play a major role in orchestrating other factors and thus, are likely to lock/unlock cellular functional clusters. PMID:23209563
An Alternate Approach to Alternating Sums: A Method to DIE for

ERIC Educational Resources Information Center

Benjamin, Arthur T.; Quinn, Jennifer J.

2008-01-01

Positive sums count. Alternating sums match. Alternating sums of binomial coefficients, Fibonacci numbers, and other combinatorial quantities are analyzed using sign-reversing involutions. In particular, we describe the quantity being considered, match positive and negative terms through an Involution, and count the Exceptions to the matching rule…
A combinatorial code for pattern formation in Drosophila oogenesis.

PubMed

Yakoby, Nir; Bristow, Christopher A; Gong, Danielle; Schafer, Xenia; Lembong, Jessica; Zartman, Jeremiah J; Halfon, Marc S; Schüpbach, Trudi; Shvartsman, Stanislav Y

2008-11-01

Two-dimensional patterning of the follicular epithelium in Drosophila oogenesis is required for the formation of three-dimensional eggshell structures. Our analysis of a large number of published gene expression patterns in the follicle cells suggests that they follow a simple combinatorial code based on six spatial building blocks and the operations of union, difference, intersection, and addition. The building blocks are related to the distribution of inductive signals, provided by the highly conserved epidermal growth factor receptor and bone morphogenetic protein signaling pathways. We demonstrate the validity of the code by testing it against a set of patterns obtained in a large-scale transcriptional profiling experiment. Using the proposed code, we distinguish 36 distinct patterns for 81 genes expressed in the follicular epithelium and characterize their joint dynamics over four stages of oogenesis. The proposed combinatorial framework allows systematic analysis of the diversity and dynamics of two-dimensional transcriptional patterns and guides future studies of gene regulation.
Morphological Constraints on Cerebellar Granule Cell Combinatorial Diversity.

PubMed

Gilmer, Jesse I; Person, Abigail L

2017-12-13

Combinatorial expansion by the cerebellar granule cell layer (GCL) is fundamental to theories of cerebellar contributions to motor control and learning. Granule cells (GrCs) sample approximately four mossy fiber inputs and are thought to form a combinatorial code useful for pattern separation and learning. We constructed a spatially realistic model of the cerebellar GCL and examined how GCL architecture contributes to GrC combinatorial diversity. We found that GrC combinatorial diversity saturates quickly as mossy fiber input diversity increases, and that this saturation is in part a consequence of short dendrites, which limit access to diverse inputs and favor dense sampling of local inputs. This local sampling also produced GrCs that were combinatorially redundant, even when input diversity was extremely high. In addition, we found that mossy fiber clustering, which is a common anatomical pattern, also led to increased redundancy of GrC input combinations. We related this redundancy to hypothesized roles of temporal expansion of GrC information encoding in service of learned timing, and we show that GCL architecture produces GrC populations that support both temporal and combinatorial expansion. Finally, we used novel anatomical measurements from mice of either sex to inform modeling of sparse and filopodia-bearing mossy fibers, finding that these circuit features uniquely contribute to enhancing GrC diversification and redundancy. Our results complement information theoretic studies of granule layer structure and provide insight into the contributions of granule layer anatomical features to afferent mixing. SIGNIFICANCE STATEMENT Cerebellar granule cells are among the simplest neurons, with tiny somata and, on average, just four dendrites. These characteristics, along with their dense organization, inspired influential theoretical work on the granule cell layer as a combinatorial expander, where each granule cell represents a unique combination of inputs. Despite the centrality of these theories to cerebellar physiology, the degree of expansion supported by anatomically realistic patterns of inputs is unknown. Using modeling and anatomy, we show that realistic input patterns constrain combinatorial diversity by producing redundant combinations, which nevertheless could support temporal diversification of like combinations, suitable for learned timing. Our study suggests a neural substrate for producing high levels of both combinatorial and temporal diversity in the granule cell layer. Copyright © 2017 the authors 0270-6474/17/3712153-14$15.00/0.
Combinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions.

PubMed

Blasi, Thomas; Feller, Christian; Feigelman, Justin; Hasenauer, Jan; Imhof, Axel; Theis, Fabian J; Becker, Peter B; Marr, Carsten

2016-01-27

Post-translational modifications (PTMs) are pivotal to cellular information processing, but how combinatorial PTM patterns ("motifs") are set remains elusive. We develop a computational framework, which we provide as open source code, to investigate the design principles generating the combinatorial acetylation patterns on histone H4 in Drosophila melanogaster. We find that models assuming purely unspecific or lysine site-specific acetylation rates were insufficient to explain the experimentally determined motif abundances. Rather, these abundances were best described by an ensemble of models with acetylation rates that were specific to motifs. The model ensemble converged upon four acetylation pathways; we validated three of these using independent data from a systematic enzyme depletion study. Our findings suggest that histone acetylation patterns originate through specific pathways involving motif-specific acetylation activity. Copyright © 2016 Elsevier Inc. All rights reserved.
Scaffold architecture and pharmacophoric properties of natural products and trade drugs: application in the design of natural product-based combinatorial libraries.

PubMed

Lee, M L; Schneider, G

2001-01-01

Natural products were analyzed to determine whether they contain appealing novel scaffold architectures for potential use in combinatorial chemistry. Ring systems were extracted and clustered on the basis of structural similarity. Several such potential scaffolds for combinatorial chemistry were identified that are not present in current trade drugs. For one of these scaffolds a virtual combinatorial library was generated. Pharmacophoric properties of natural products, trade drugs, and the virtual combinatorial library were assessed using a self-organizing map. Obviously, current trade drugs and natural products have several topological pharmacophore patterns in common. These features can be systematically explored with selected combinatorial libraries based on a combination of natural product-derived and synthetic molecular building blocks.
Balancing focused combinatorial libraries based on multiple GPCR ligands

NASA Astrophysics Data System (ADS)

Soltanshahi, Farhad; Mansley, Tamsin E.; Choi, Sun; Clark, Robert D.

2006-08-01

G-Protein coupled receptors (GPCRs) are important targets for drug discovery, and combinatorial chemistry is an important tool for pharmaceutical development. The absence of detailed structural information, however, limits the kinds of combinatorial design techniques that can be applied to GPCR targets. This is particularly problematic given the current emphasis on focused combinatorial libraries. By linking an incremental construction method (OptDesign) to the very fast shape-matching capability of ChemSpace, we have created an efficient method for designing targeted sublibraries that are topomerically similar to known actives. Multi-objective scoring allows consideration of multiple queries (actives) simultaneously. This can lead to a distribution of products skewed towards one particular query structure, however, particularly when the ligands of interest are quite dissimilar to one another. A novel pivoting technique is described which makes it possible to generate promising designs even under those circumstances. The approach is illustrated by application to some serotonergic agonists and chemokine antagonists.
Signal dimensionality and the emergence of combinatorial structure.

PubMed

Little, Hannah; Eryılmaz, Kerem; de Boer, Bart

2017-11-01

In language, a small number of meaningless building blocks can be combined into an unlimited set of meaningful utterances. This is known as combinatorial structure. One hypothesis for the initial emergence of combinatorial structure in language is that recombining elements of signals solves the problem of overcrowding in a signal space. Another hypothesis is that iconicity may impede the emergence of combinatorial structure. However, how these two hypotheses relate to each other is not often discussed. In this paper, we explore how signal space dimensionality relates to both overcrowding in the signal space and iconicity. We use an artificial signalling experiment to test whether a signal space and a meaning space having similar topologies will generate an iconic system and whether, when the topologies differ, the emergence of combinatorially structured signals is facilitated. In our experiments, signals are created from participants' hand movements, which are measured using an infrared sensor. We found that participants take advantage of iconic signal-meaning mappings where possible. Further, we use trajectory predictability, measures of variance, and Hidden Markov Models to measure the use of structure within the signals produced and found that when topologies do not match, then there is more evidence of combinatorial structure. The results from these experiments are interpreted in the context of the differences between the emergence of combinatorial structure in different linguistic modalities (speech and sign). Copyright © 2017 Elsevier B.V. All rights reserved.
Morphological priming by itself: a study of Portuguese conjugations.

PubMed

Veríssimo, João; Clahsen, Harald

2009-07-01

Does the language processing system make use of abstract grammatical categories and representations that are not directly visible from the surface form of a linguistic expression? This study examines stem-formation processes and conjugation classes, a case of 'pure' morphology that provides insight into the role of grammatical structure in language processing. We report results from a cross-modal priming experiment examining 1st and 3rd conjugation verb forms in Portuguese. Although items were closely matched with respect to a range of non-morphological factors, distinct priming patterns were found for 1st and 3rd conjugation stems. We attribute the observed priming patterns to different representations of conjugational stems, combinatorial morphologically structured ones for 1st conjugation and un-analyzed morphologically unstructured ones for 3rd conjugation stems. Our findings underline the importance of morphology for language comprehension indicating that morphological analysis goes beyond the identification of grammatical morphemes.
Beyond Aztec Castles: Toric Cascades in the dP 3 Quiver

NASA Astrophysics Data System (ADS)

Lai, Tri; Musiker, Gregg

2017-12-01

Given one of an infinite class of supersymmetric quiver gauge theories, string theorists can associate a corresponding toric variety (which is a Calabi-Yau 3-fold) as well as an associated combinatorial model known as a brane tiling. In combinatorial language, a brane tiling is a bipartite graph on a torus and its perfect matchings are of interest to both combinatorialists and physicists alike. A cluster algebra may also be associated to such quivers and in this paper we study the generators of this algebra, known as cluster variables, for the quiver associated to the cone over the del Pezzo surface d P 3. In particular, mutation sequences involving mutations exclusively at vertices with two in-coming arrows and two out-going arrows are referred to as toric cascades in the string theory literature. Such toric cascades give rise to interesting discrete integrable systems on the level of cluster variable dynamics. We provide an explicit algebraic formula for all cluster variables that are reachable by toric cascades as well as a combinatorial interpretation involving perfect matchings of subgraphs of the d P 3 brane tiling for these formulas in most cases.
ChIP-less analysis of chromatin states.

PubMed

Su, Zhangli; Boersma, Melissa D; Lee, Jin-Hee; Oliver, Samuel S; Liu, Shichong; Garcia, Benjamin A; Denu, John M

2014-01-01

Histone post-translational modifications (PTMs) are key epigenetic regulators in chromatin-based processes. Increasing evidence suggests that vast combinations of PTMs exist within chromatin histones. These complex patterns, rather than individual PTMs, are thought to define functional chromatin states. However, the ability to interrogate combinatorial histone PTM patterns at the nucleosome level has been limited by the lack of direct molecular tools. Here we demonstrate an efficient, quantitative, antibody-free, chromatin immunoprecipitation-less (ChIP-less) method for interrogating diverse epigenetic states. At the heart of the workflow are recombinant chromatin reader domains, which target distinct chromatin states with combinatorial PTM patterns. Utilizing a newly designed combinatorial histone peptide microarray, we showed that three reader domains (ATRX-ADD, ING2-PHD and AIRE-PHD) displayed greater specificity towards combinatorial PTM patterns than corresponding commercial histone antibodies. Such specific recognitions were employed to develop a chromatin reader-based affinity enrichment platform (matrix-assisted reader chromatin capture, or MARCC). We successfully applied the reader-based platform to capture unique chromatin states, which were quantitatively profiled by mass spectrometry to reveal interconnections between nucleosomal histone PTMs. Specifically, a highly enriched signature that harbored H3K4me0, H3K9me2/3, H3K79me0 and H4K20me2/3 within the same nucleosome was identified from chromatin enriched by ATRX-ADD. This newly reported PTM combination was enriched in heterochromatin, as revealed by the associated DNA. Our results suggest the broad utility of recombinant reader domains as an enrichment tool specific to combinatorial PTM patterns, which are difficult to probe directly by antibody-based approaches. The reader affinity platform is compatible with several downstream analyses to investigate the physical coexistence of nucleosomal PTM states associated with specific genomic loci. Collectively, the reader-based workflow will greatly facilitate our understanding of how distinct chromatin states and reader domains function in gene regulatory mechanisms.
A Functional Analytic Approach To Computer-Interactive Mathematics

PubMed Central

2005-01-01

Following a pretest, 11 participants who were naive with regard to various algebraic and trigonometric transformations received an introductory lecture regarding the fundamentals of the rectangular coordinate system. Following the lecture, they took part in a computer-interactive matching-to-sample procedure in which they received training on particular formula-to-formula and formula-to-graph relations as these formulas pertain to reflections and vertical and horizontal shifts. In training A-B, standard formulas served as samples and factored formulas served as comparisons. In training B-C, factored formulas served as samples and graphs served as comparisons. Subsequently, the program assessed for mutually entailed B-A and C-B relations as well as combinatorially entailed C-A and A-C relations. After all participants demonstrated mutual entailment and combinatorial entailment, we employed a test of novel relations to assess 40 different and complex variations of the original training formulas and their respective graphs. Six of 10 participants who completed training demonstrated perfect or near-perfect performance in identifying novel formula-to-graph relations. Three of the 4 participants who made more than three incorrect responses during the assessment of novel relations showed some commonality among their error patterns. Derived transfer of stimulus control using mathematical relations is discussed. PMID:15898471
A functional analytic approach to computer-interactive mathematics.

PubMed

Ninness, Chris; Rumph, Robin; McCuller, Glen; Harrison, Carol; Ford, Angela M; Ninness, Sharon K

2005-01-01

Following a pretest, 11 participants who were naive with regard to various algebraic and trigonometric transformations received an introductory lecture regarding the fundamentals of the rectangular coordinate system. Following the lecture, they took part in a computer-interactive matching-to-sample procedure in which they received training on particular formula-to-formula and formula-to-graph relations as these formulas pertain to reflections and vertical and horizontal shifts. In training A-B, standard formulas served as samples and factored formulas served as comparisons. In training B-C, factored formulas served as samples and graphs served as comparisons. Subsequently, the program assessed for mutually entailed B-A and C-B relations as well as combinatorially entailed C-A and A-C relations. After all participants demonstrated mutual entailment and combinatorial entailment, we employed a test of novel relations to assess 40 different and complex variations of the original training formulas and their respective graphs. Six of 10 participants who completed training demonstrated perfect or near-perfect performance in identifying novel formula-to-graph relations. Three of the 4 participants who made more than three incorrect responses during the assessment of novel relations showed some commonality among their error patterns. Derived transfer of stimulus control using mathematical relations is discussed.

Small area estimation of obesity prevalence and dietary patterns: a model applied to Rio de Janeiro city, Brazil.

PubMed

Cataife, Guido

2014-03-01

We propose the use of previously developed small area estimation techniques to monitor obesity and dietary habits in developing countries and apply the model to Rio de Janeiro city. We estimate obesity prevalence rates at the Census Tract through a combinatorial optimization spatial microsimulation model that matches body mass index and socio-demographic data in Brazil's 2008-9 family expenditure survey with Census 2010 socio-demographic data. Obesity ranges from 8% to 25% in most areas and affects the poor almost as much as the rich. Male and female obesity rates are uncorrelated at the small area level. The model is an effective tool to understand the complexity of the problem and to aid in policy design. © 2013 Published by Elsevier Ltd.
Combinatorial Algorithms to Enable Computational Science and Engineering: Work from the CSCAPES Institute

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boman, Erik G.; Catalyurek, Umit V.; Chevalier, Cedric

2015-01-16

This final progress report summarizes the work accomplished at the Combinatorial Scientific Computing and Petascale Simulations Institute. We developed Zoltan, a parallel mesh partitioning library that made use of accurate hypergraph models to provide load balancing in mesh-based computations. We developed several graph coloring algorithms for computing Jacobian and Hessian matrices and organized them into a software package called ColPack. We developed parallel algorithms for graph coloring and graph matching problems, and also designed multi-scale graph algorithms. Three PhD students graduated, six more are continuing their PhD studies, and four postdoctoral scholars were advised. Six of these students and Fellowsmore » have joined DOE Labs (Sandia, Berkeley), as staff scientists or as postdoctoral scientists. We also organized the SIAM Workshop on Combinatorial Scientific Computing (CSC) in 2007, 2009, and 2011 to continue to foster the CSC community.« less
Design of combinatorial libraries for the exploration of virtual hits from fragment space searches with LoFT.

PubMed

Lessel, Uta; Wellenzohn, Bernd; Fischer, J Robert; Rarey, Matthias

2012-02-27

A case study is presented illustrating the design of a focused CDK2 library. The scaffold of the library was detected by a feature trees search in a fragment space based on reactions from combinatorial chemistry. For the design the software LoFT (Library optimizer using Feature Trees) was used. The special feature called FTMatch was applied to restrict the parts of the queries where the reagents are permitted to match. This way a 3D scoring function could be simulated. Results were compared with alternative designs by GOLD docking and ROCS 3D alignments.
One-dimensional Euclidean matching problem: exact solutions, correlation functions, and universality.

PubMed

Caracciolo, Sergio; Sicuro, Gabriele

2014-10-01

We discuss the equivalence relation between the Euclidean bipartite matching problem on the line and on the circumference and the Brownian bridge process on the same domains. The equivalence allows us to compute the correlation function and the optimal cost of the original combinatorial problem in the thermodynamic limit; moreover, we solve also the minimax problem on the line and on the circumference. The properties of the average cost and correlation functions are discussed.
On Stable Marriages and Greedy Matchings

DOE Office of Scientific and Technical Information (OSTI.GOV)

Manne, Fredrik; Naim, Md; Lerring, Hakon

2016-12-11

Research on stable marriage problems has a long and mathematically rigorous history, while that of exploiting greedy matchings in combinatorial scientific computing is a younger and less developed research field. In this paper we consider the relationships between these two areas. In particular we show that several problems related to computing greedy matchings can be formulated as stable marriage problems and as a consequence several recently proposed algorithms for computing greedy matchings are in fact special cases of well known algorithms for the stable marriage problem. However, in terms of implementations and practical scalable solutions on modern hardware, the greedymore » matching community has made considerable progress. We show that due to the strong relationship between these two fields many of these results are also applicable for solving stable marriage problems.« less
Maps and streams in the auditory cortex: nonhuman primates illuminate human speech processing

PubMed Central

Rauschecker, Josef P; Scott, Sophie K

2010-01-01

Speech and language are considered uniquely human abilities: animals have communication systems, but they do not match human linguistic skills in terms of recursive structure and combinatorial power. Yet, in evolution, spoken language must have emerged from neural mechanisms at least partially available in animals. In this paper, we will demonstrate how our understanding of speech perception, one important facet of language, has profited from findings and theory in nonhuman primate studies. Chief among these are physiological and anatomical studies showing that primate auditory cortex, across species, shows patterns of hierarchical structure, topographic mapping and streams of functional processing. We will identify roles for different cortical areas in the perceptual processing of speech and review functional imaging work in humans that bears on our understanding of how the brain decodes and monitors speech. A new model connects structures in the temporal, frontal and parietal lobes linking speech perception and production. PMID:19471271
It looks easy! Heuristics for combinatorial optimization problems.

PubMed

Chronicle, Edward P; MacGregor, James N; Ormerod, Thomas C; Burr, Alistair

2006-04-01

Human performance on instances of computationally intractable optimization problems, such as the travelling salesperson problem (TSP), can be excellent. We have proposed a boundary-following heuristic to account for this finding. We report three experiments with TSPs where the capacity to employ this heuristic was varied. In Experiment 1, participants free to use the heuristic produced solutions significantly closer to optimal than did those prevented from doing so. Experiments 2 and 3 together replicated this finding in larger problems and demonstrated that a potential confound had no effect. In all three experiments, performance was closely matched by a boundary-following model. The results implicate global rather than purely local processes. Humans may have access to simple, perceptually based, heuristics that are suited to some combinatorial optimization tasks.
Spread the word: MMN brain response reveals whole-form access of discontinuous particle verbs.

PubMed

Hanna, Jeff; Cappelle, Bert; Pulvermüller, Friedemann

2017-12-01

The status of particle verbs such as rise (…) up as either lexically stored or combinatorially assembled is an issue which so far has not been settled decisively. In this study, we use the mismatch negativity (MMN) brain response to observe neurophysiological responses to discontinuous particle verbs. The MMN can be used to distinguish between whole-form storage and combinatorial processes, as it is enhanced to stored words compared to unknown pseudowords, whereas combinatorially legal strings elicit a reduced MMN relative to ungrammatical ones. Earlier work had found larger MMNs to congruent than to incongruent verb-particle combinations when particle and verb appeared as adjacent elements, thus suggesting whole-form storage at least in this case. However, it is still possible that particle verbs discontinuously spread out across a sentence would elicit the combinatorial, grammar-violation response pattern instead. Here, we tested the brain signatures of discontinuous verb-particle combinations, orthogonally varying congruence and semantic transparency. The results show for the first time brain indices of whole-form storage for discontinuous constituents, thus arguing in favour of access to whole-form-stored lexical elements in the processing of particle verbs, irrespective of their semantic opacity. Results are discussed in the context of linguistic debates about the status of particle verbs as words, lexical elements or syntactically generated combinations. The explanation of the pattern of results within a neurobiological language model is highlighted. Copyright © 2017 Elsevier Inc. All rights reserved.
Neural correlates of implicit and explicit combinatorial semantic processing

PubMed Central

Graves, William W.; Binder, Jeffrey R.; Desai, Rutvik H.; Conant, Lisa L.; Seidenberg, Mark S.

2010-01-01

Language consists of sequences of words, but comprehending phrases involves more than concatenating meanings: A boat house is a shelter for boats, whereas a summer house is a house used during summer, and a ghost house is typically uninhabited. Little is known about the brain bases of combinatorial semantic processes. We performed two fMRI experiments using familiar, highly meaningful phrases (LAKE HOUSE) and unfamiliar phrases with minimal meaning created by reversing the word order of the familiar items (HOUSE LAKE). The first experiment used a 1-back matching task to assess implicit semantic processing, and the second used a classification task to engage explicit semantic processing. These conditions required processing of the same words, but with more effective combinatorial processing in the meaningful condition. The contrast of meaningful versus reversed phrases revealed activation primarily during the classification task, to a greater extent in the right hemisphere, including right angular gyrus, dorsomedial prefrontal cortex, and bilateral posterior cingulate/precuneus, areas previously implicated in semantic processing. Positive correlations of fMRI signal with lexical (word-level) frequency occurred exclusively with the 1-back task and to a greater spatial extent on the left, including left posterior middle temporal gyrus and bilateral parahippocampus. These results reveal strong effects of task demands on engagement of lexical versus combinatorial processing and suggest a hemispheric dissociation between these levels of semantic representation. PMID:20600969
High-throughput characterization of film thickness in thin film materials libraries by digital holographic microscopy.

PubMed

Lai, Yiu Wai; Krause, Michael; Savan, Alan; Thienhaus, Sigurd; Koukourakis, Nektarios; Hofmann, Martin R; Ludwig, Alfred

2011-10-01

A high-throughput characterization technique based on digital holography for mapping film thickness in thin-film materials libraries was developed. Digital holographic microscopy is used for fully automatic measurements of the thickness of patterned films with nanometer resolution. The method has several significant advantages over conventional stylus profilometry: it is contactless and fast, substrate bending is compensated, and the experimental setup is simple. Patterned films prepared by different combinatorial thin-film approaches were characterized to investigate and demonstrate this method. The results show that this technique is valuable for the quick, reliable and high-throughput determination of the film thickness distribution in combinatorial materials research. Importantly, it can also be applied to thin films that have been structured by shadow masking.
Combinatorial programming of human neuronal progenitors using magnetically-guided stoichiometric mRNA delivery.

PubMed

Azimi, Sayyed M; Sheridan, Steven D; Ghannad-Rezaie, Mostafa; Eimon, Peter M; Yanik, Mehmet Fatih

2018-05-01

Identification of optimal transcription-factor expression patterns to direct cellular differentiation along a desired pathway presents significant challenges. We demonstrate massively combinatorial screening of temporally-varying mRNA transcription factors to direct differentiation of neural progenitor cells using a dynamically-reconfigurable magnetically-guided spotting technology for localizing mRNA, enabling experiments on millimetre size spots. In addition, we present a time-interleaved delivery method that dramatically reduces fluctuations in the delivered transcription-factor copy-numbers per cell. We screened combinatorial and temporal delivery of a pool of midbrain-specific transcription factors to augment the generation of dopaminergic neurons. We show that the combinatorial delivery of LMX1A, FOXA2 and PITX3 is highly effective in generating dopaminergic neurons from midbrain progenitors. We show that LMX1A significantly increases TH -expression levels when delivered to neural progenitor cells either during proliferation or after induction of neural differentiation, while FOXA2 and PITX3 increase expression only when delivered prior to induction, demonstrating temporal dependence of factor addition. © 2018, Azimi et al.
Optimum Design of PIλDμ Controller for an Automatic Voltage Regulator System Using Combinatorial Test Design

PubMed Central

Sahib, Mouayad A.; Gambardella, Luca M.; Afzal, Wasif; Zamli, Kamal Z.

2016-01-01

Combinatorial test design is a plan of test that aims to reduce the amount of test cases systematically by choosing a subset of the test cases based on the combination of input variables. The subset covers all possible combinations of a given strength and hence tries to match the effectiveness of the exhaustive set. This mechanism of reduction has been used successfully in software testing research with t-way testing (where t indicates the interaction strength of combinations). Potentially, other systems may exhibit many similarities with this approach. Hence, it could form an emerging application in different areas of research due to its usefulness. To this end, more recently it has been applied in a few research areas successfully. In this paper, we explore the applicability of combinatorial test design technique for Fractional Order (FO), Proportional-Integral-Derivative (PID) parameter design controller, named as FOPID, for an automatic voltage regulator (AVR) system. Throughout the paper, we justify this new application theoretically and practically through simulations. In addition, we report on first experiments indicating its practical use in this field. We design different algorithms and adapted other strategies to cover all the combinations with an optimum and effective test set. Our findings indicate that combinatorial test design can find the combinations that lead to optimum design. Besides this, we also found that by increasing the strength of combination, we can approach to the optimum design in a way that with only 4-way combinatorial set, we can get the effectiveness of an exhaustive test set. This significantly reduced the number of tests needed and thus leads to an approach that optimizes design of parameters quickly. PMID:27829025
Using Optimal Dependency-Trees for Combinatorial Optimization: Learning the Structure of the Search Space.

DTIC Science & Technology

1997-01-01

create a dependency tree containing an optimum set of n-1 first-order dependencies. To do this, first, we select an arbitrary bit Xroot to place at the...the root to an arbitrary bit Xroot -For all other bits Xi, set bestMatchingBitInTree[Xi] to Xroot . -While not all bits have been
ChromBiSim: Interactive chromatin biclustering using a simple approach.

PubMed

Noureen, Nighat; Zohaib, Hafiz Muhammad; Qadir, Muhammad Abdul; Fazal, Sahar

2017-10-01

Combinatorial patterns of histone modifications sketch the epigenomic locale. Specific positions of these modifications in the genome are marked by the presence of such signals. Various methods highlight such patterns on global scale hence missing the local patterns which are the actual hidden combinatorics. We present ChromBiSim, an interactive tool for mining subsets of modifications from epigenomic profiles. ChromBiSim efficiently extracts biclusters with their genomic locations. It is the very first user interface based and multiple cell type handling tool for decoding the interplay of subsets of histone modifications combinations along their genomic locations. It displays the results in the forms of charts and heat maps in accordance with saving them in files which could be used for post analysis. ChromBiSim tested on multiple cell types produced in total 803 combinatorial patterns. It could be used to highlight variations among diseased versus normal cell types of any species. ChromBiSim is available at (http://sourceforge.net/projects/chrombisim) in C-sharp and python languages. Copyright © 2017 Elsevier Inc. All rights reserved.
Differential regulation of transcription through distinct Suppressor of Hairless DNA binding site architectures during Notch signaling in proneural clusters.

PubMed

Cave, John W; Xia, Li; Caudy, Michael

2011-01-01

In Drosophila melanogaster, achaete (ac) and m8 are model basic helix-loop-helix activator (bHLH A) and repressor genes, respectively, that have the opposite cell expression pattern in proneural clusters during Notch signaling. Previous studies have shown that activation of m8 transcription in specific cells within proneural clusters by Notch signaling is programmed by a "combinatorial" and "architectural" DNA transcription code containing binding sites for the Su(H) and proneural bHLH A proteins. Here we show the novel result that the ac promoter contains a similar combinatorial code of Su(H) and bHLH A binding sites but contains a different Su(H) site architectural code that does not mediate activation during Notch signaling, thus programming a cell expression pattern opposite that of m8 in proneural clusters.
Template-based combinatorial enumeration of virtual compound libraries for lipids

PubMed Central

2012-01-01

A variety of software packages are available for the combinatorial enumeration of virtual libraries for small molecules, starting from specifications of core scaffolds with attachments points and lists of R-groups as SMILES or SD files. Although SD files include atomic coordinates for core scaffolds and R-groups, it is not possible to control 2-dimensional (2D) layout of the enumerated structures generated for virtual compound libraries because different packages generate different 2D representations for the same structure. We have developed a software package called LipidMapsTools for the template-based combinatorial enumeration of virtual compound libraries for lipids. Virtual libraries are enumerated for the specified lipid abbreviations using matching lists of pre-defined templates and chain abbreviations, instead of core scaffolds and lists of R-groups provided by the user. 2D structures of the enumerated lipids are drawn in a specific and consistent fashion adhering to the framework for representing lipid structures proposed by the LIPID MAPS consortium. LipidMapsTools is lightweight, relatively fast and contains no external dependencies. It is an open source package and freely available under the terms of the modified BSD license. PMID:23006594
Template-based combinatorial enumeration of virtual compound libraries for lipids.

PubMed

Sud, Manish; Fahy, Eoin; Subramaniam, Shankar

2012-09-25

A variety of software packages are available for the combinatorial enumeration of virtual libraries for small molecules, starting from specifications of core scaffolds with attachments points and lists of R-groups as SMILES or SD files. Although SD files include atomic coordinates for core scaffolds and R-groups, it is not possible to control 2-dimensional (2D) layout of the enumerated structures generated for virtual compound libraries because different packages generate different 2D representations for the same structure. We have developed a software package called LipidMapsTools for the template-based combinatorial enumeration of virtual compound libraries for lipids. Virtual libraries are enumerated for the specified lipid abbreviations using matching lists of pre-defined templates and chain abbreviations, instead of core scaffolds and lists of R-groups provided by the user. 2D structures of the enumerated lipids are drawn in a specific and consistent fashion adhering to the framework for representing lipid structures proposed by the LIPID MAPS consortium. LipidMapsTools is lightweight, relatively fast and contains no external dependencies. It is an open source package and freely available under the terms of the modified BSD license.
Experimental Design for Combinatorial and High Throughput Materials Development

NASA Astrophysics Data System (ADS)

Cawse, James N.

2002-12-01

In the past decade, combinatorial and high throughput experimental methods have revolutionized the pharmaceutical industry, allowing researchers to conduct more experiments in a week than was previously possible in a year. Now high throughput experimentation is rapidly spreading from its origins in the pharmaceutical world to larger industrial research establishments such as GE and DuPont, and even to smaller companies and universities. Consequently, researchers need to know the kinds of problems, desired outcomes, and appropriate patterns for these new strategies. Editor James Cawse's far-reaching study identifies and applies, with specific examples, these important new principles and techniques. Experimental Design for Combinatorial and High Throughput Materials Development progresses from methods that are now standard, such as gradient arrays, to mathematical developments that are breaking new ground. The former will be particularly useful to researchers entering the field, while the latter should inspire and challenge advanced practitioners. The book's contents are contributed by leading researchers in their respective fields. Chapters include: -High Throughput Synthetic Approaches for the Investigation of Inorganic Phase Space -Combinatorial Mapping of Polymer Blends Phase Behavior -Split-Plot Designs -Artificial Neural Networks in Catalyst Development -The Monte Carlo Approach to Library Design and Redesign This book also contains over 200 useful charts and drawings. Industrial chemists, chemical engineers, materials scientists, and physicists working in combinatorial and high throughput chemistry will find James Cawse's study to be an invaluable resource.
GRADIENT: Graph Analytic Approach for Discovering Irregular Events, Nascent and Temporal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hogan, Emilie

2015-03-31

Finding a time-ordered signature within large graphs is a computationally complex problem due to the combinatorial explosion of potential patterns. GRADIENT is designed to search and understand that problem space.
GRADIENT: Graph Analytic Approach for Discovering Irregular Events, Nascent and Temporal

ScienceCinema

Hogan, Emilie

2018-01-16

Finding a time-ordered signature within large graphs is a computationally complex problem due to the combinatorial explosion of potential patterns. GRADIENT is designed to search and understand that problem space.

Pattern recognition with composite correlation filters designed with multi-object combinatorial optimization

DOE PAGES

Awwal, Abdul; Diaz-Ramirez, Victor H.; Cuevas, Andres; ...

2014-10-23

Composite correlation filters are used for solving a wide variety of pattern recognition problems. These filters are given by a combination of several training templates chosen by a designer in an ad hoc manner. In this work, we present a new approach for the design of composite filters based on multi-objective combinatorial optimization. Given a vast search space of training templates, an iterative algorithm is used to synthesize a filter with an optimized performance in terms of several competing criteria. Furthermore, by employing a suggested binary-search procedure a filter bank with a minimum number of filters can be constructed, formore » a prespecified trade-off of performance metrics. Computer simulation results obtained with the proposed method in recognizing geometrically distorted versions of a target in cluttered and noisy scenes are discussed and compared in terms of recognition performance and complexity with existing state-of-the-art filters.« less
Pattern recognition with composite correlation filters designed with multi-object combinatorial optimization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Awwal, Abdul; Diaz-Ramirez, Victor H.; Cuevas, Andres

Composite correlation filters are used for solving a wide variety of pattern recognition problems. These filters are given by a combination of several training templates chosen by a designer in an ad hoc manner. In this work, we present a new approach for the design of composite filters based on multi-objective combinatorial optimization. Given a vast search space of training templates, an iterative algorithm is used to synthesize a filter with an optimized performance in terms of several competing criteria. Furthermore, by employing a suggested binary-search procedure a filter bank with a minimum number of filters can be constructed, formore » a prespecified trade-off of performance metrics. Computer simulation results obtained with the proposed method in recognizing geometrically distorted versions of a target in cluttered and noisy scenes are discussed and compared in terms of recognition performance and complexity with existing state-of-the-art filters.« less
Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH.

PubMed

Volk, Jochen; Herrmann, Torsten; Wüthrich, Kurt

2008-07-01

MATCH (Memetic Algorithm and Combinatorial Optimization Heuristics) is a new memetic algorithm for automated sequence-specific polypeptide backbone NMR assignment of proteins. MATCH employs local optimization for tracing partial sequence-specific assignments within a global, population-based search environment, where the simultaneous application of local and global optimization heuristics guarantees high efficiency and robustness. MATCH thus makes combined use of the two predominant concepts in use for automated NMR assignment of proteins. Dynamic transition and inherent mutation are new techniques that enable automatic adaptation to variable quality of the experimental input data. The concept of dynamic transition is incorporated in all major building blocks of the algorithm, where it enables switching between local and global optimization heuristics at any time during the assignment process. Inherent mutation restricts the intrinsically required randomness of the evolutionary algorithm to those regions of the conformation space that are compatible with the experimental input data. Using intact and artificially deteriorated APSY-NMR input data of proteins, MATCH performed sequence-specific resonance assignment with high efficiency and robustness.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Braunstein, Samuel L.; Ghosh, Sibasish; Severini, Simone

We reconsider density matrices of graphs as defined in quant-ph/0406165. The density matrix of a graph is the combinatorial Laplacian of the graph normalized to have unit trace. We describe a simple combinatorial condition (the 'degree condition') to test the separability of density matrices of graphs. The condition is directly related to the Peres-Horodecki partial transposition condition. We prove that the degree condition is necessary for separability, and we conjecture that it is also sufficient. We prove special cases of the conjecture involving nearest-point graphs and perfect matchings. We observe that the degree condition appears to have a value beyondmore » the density matrices of graphs. In fact, we point out that circulant density matrices and other matrices constructed from groups always satisfy the condition and indeed are separable with respect to any split. We isolate a number of problems and delineate further generalizations.« less
Inference of combinatorial Boolean rules of synergistic gene sets from cancer microarray datasets.

PubMed

Park, Inho; Lee, Kwang H; Lee, Doheon

2010-06-15

Gene set analysis has become an important tool for the functional interpretation of high-throughput gene expression datasets. Moreover, pattern analyses based on inferred gene set activities of individual samples have shown the ability to identify more robust disease signatures than individual gene-based pattern analyses. Although a number of approaches have been proposed for gene set-based pattern analysis, the combinatorial influence of deregulated gene sets on disease phenotype classification has not been studied sufficiently. We propose a new approach for inferring combinatorial Boolean rules of gene sets for a better understanding of cancer transcriptome and cancer classification. To reduce the search space of the possible Boolean rules, we identify small groups of gene sets that synergistically contribute to the classification of samples into their corresponding phenotypic groups (such as normal and cancer). We then measure the significance of the candidate Boolean rules derived from each group of gene sets; the level of significance is based on the class entropy of the samples selected in accordance with the rules. By applying the present approach to publicly available prostate cancer datasets, we identified 72 significant Boolean rules. Finally, we discuss several identified Boolean rules, such as the rule of glutathione metabolism (down) and prostaglandin synthesis regulation (down), which are consistent with known prostate cancer biology. Scripts written in Python and R are available at http://biosoft.kaist.ac.kr/~ihpark/. The refined gene sets and the full list of the identified Boolean rules are provided in the Supplementary Material. Supplementary data are available at Bioinformatics online.
Toxicity and Detoxification Effects of Herbal Caowu via Ultra Performance Liquid Chromatography/Mass Spectrometry Metabolomics Analyzed using Pattern Recognition Method

PubMed Central

Yan, Yan; Zhang, Aihua; Dong, Hui; Yan, Guangli; Sun, Hui; Wu, Xiuhong; Han, Ying; Wang, Xijun

2017-01-01

Background: Caowu (Radix Aconiti kusnezoffii, CW), the root of Aconitum kusnezoffii Reichb., has widely used clinically in rheumatic arthritis, painful joints, and tumors for thousands of years. However, the toxicity of heart and central nervous system induced by CW still limited the application. Materials and Methods: Metabolomics was performed to identify the sensitive and reliable biomarkers and to characterize the phenotypically biochemical perturbations and potential mechanisms of CW-induced toxicity, and the detoxification by combinatorial intervention of CW with Gancao (Radix Glycyrrhizae) (CG), Baishao (Radix Paeoniae Alba) (CB), and Renshen (Radix Ginseng) (CR) was also analyzed by pattern recognition methods. Results: As a result, the metabolites were characterized and responsible for pentose and glucuronate interconversions, tryptophan metabolism, amino sugar and nucleotide sugar metabolism, taurine and hypotaurine metabolism, fructose and mannose metabolism, and starch and sucrose metabolism, six networks of which were the same to the metabolic pathways of Chuanwu (Radix Aconiti, CHW) group. The ascorbate and aldarate metabolism was also characterized by CW group. The urinary metabolomics also revealed CW-induced serious toxicity to heart and liver. Thirteen significant metabolites were identified and had validated as phenotypic toxicity biomarkers of CW, five biomarkers of which were commonly owned in Aconitum. The changes of toxicity metabolites obtained from combinatorial intervention of CG, CB, and CR also were analyzed to investigate the regulation degree of toxicity biomarkers adjusted by different combinatorial interventions at 6th month. Conclusion: Metabolomics analyses coupled with pattern recognition methods in the evaluation of drug toxicity and finding detoxification methods were highlighted in this work. SUMMARY Metabolomics was performed to characterize the biochemical potential mechanisms of Caowu toxicityThirteen significant metabolites were identified and validated as phenotypic toxicity biomarkers of CaowuMetabolite changes of toxicity obtained can be adjusted by different combinatorial interventions.Pattern recognition plot reflects the toxicity effects tendency of the urine metabolic fluctuations according to time after treatment of herbal Caowu. Abbreviations used: CW: Caowu (Radix Aconiti kusnezoffii); CHW: Chuanwu (Radix Aconiti); TCM: Traditional Chinese Medicine; CG: Caowu and Gancao; CB: Caowu and Baishao; CR: Caowu and Renshen; QC: Quality control; UPLC: Ultra performance liquid chromatography; MS: Mass spectrometry; PCA: Principal component analysis; PLS-DA: Partial least squares-discriminant analysis; OPLS: Orthogonal projection to latent structures analysis. PMID:29200734
A path following algorithm for the graph matching problem.

PubMed

Zaslavskiy, Mikhail; Bach, Francis; Vert, Jean-Philippe

2009-12-01

We propose a convex-concave programming approach for the labeled weighted graph matching problem. The convex-concave programming formulation is obtained by rewriting the weighted graph matching problem as a least-square problem on the set of permutation matrices and relaxing it to two different optimization problems: a quadratic convex and a quadratic concave optimization problem on the set of doubly stochastic matrices. The concave relaxation has the same global minimum as the initial graph matching problem, but the search for its global minimum is also a hard combinatorial problem. We, therefore, construct an approximation of the concave problem solution by following a solution path of a convex-concave problem obtained by linear interpolation of the convex and concave formulations, starting from the convex relaxation. This method allows to easily integrate the information on graph label similarities into the optimization problem, and therefore, perform labeled weighted graph matching. The algorithm is compared with some of the best performing graph matching methods on four data sets: simulated graphs, QAPLib, retina vessel images, and handwritten Chinese characters. In all cases, the results are competitive with the state of the art.
Energy Landscapes for the Self-Assembly of Supramolecular Polyhedra

NASA Astrophysics Data System (ADS)

Russell, Emily R.; Menon, Govind

2016-06-01

We develop a mathematical model for the energy landscape of polyhedral supramolecular cages recently synthesized by self-assembly (Sun et al. in Science 328:1144-1147, 2010). Our model includes two essential features of the experiment: (1) geometry of the organic ligands and metallic ions; and (2) combinatorics. The molecular geometry is used to introduce an energy that favors square-planar vertices (modeling {Pd}^{2+} ions) and bent edges with one of two preferred opening angles (modeling boomerang-shaped ligands of two types). The combinatorics of the model involve two-colorings of edges of polyhedra with four-valent vertices. The set of such two-colorings, quotiented by the octahedral symmetry group, has a natural graph structure and is called the combinatorial configuration space. The energy landscape of our model is the energy of each state in the combinatorial configuration space. The challenge in the computation of the energy landscape is a combinatorial explosion in the number of two-colorings of edges. We describe sampling methods based on the symmetries of the configurations and connectivity of the configuration graph. When the two preferred opening angles encompass the geometrically ideal angle, the energy landscape exhibits a very low-energy minimum for the most symmetric configuration at equal mixing of the two angles, even when the average opening angle does not match the ideal angle.
High-flexibility combinatorial peptide synthesis with laser-based transfer of monomers in solid matrix material.

PubMed

Loeffler, Felix F; Foertsch, Tobias C; Popov, Roman; Mattes, Daniela S; Schlageter, Martin; Sedlmayr, Martyna; Ridder, Barbara; Dang, Florian-Xuan; von Bojničić-Kninski, Clemens; Weber, Laura K; Fischer, Andrea; Greifenstein, Juliane; Bykovskaya, Valentina; Buliev, Ivan; Bischoff, F Ralf; Hahn, Lothar; Meier, Michael A R; Bräse, Stefan; Powell, Annie K; Balaban, Teodor Silviu; Breitling, Frank; Nesterov-Mueller, Alexander

2016-06-14

Laser writing is used to structure surfaces in many different ways in materials and life sciences. However, combinatorial patterning applications are still limited. Here we present a method for cost-efficient combinatorial synthesis of very-high-density peptide arrays with natural and synthetic monomers. A laser automatically transfers nanometre-thin solid material spots from different donor slides to an acceptor. Each donor bears a thin polymer film, embedding one type of monomer. Coupling occurs in a separate heating step, where the matrix becomes viscous and building blocks diffuse and couple to the acceptor surface. Furthermore, we can consecutively deposit two material layers of activation reagents and amino acids. Subsequent heat-induced mixing facilitates an in situ activation and coupling of the monomers. This allows us to incorporate building blocks with click chemistry compatibility or a large variety of commercially available non-activated, for example, posttranslationally modified building blocks into the array's peptides with >17,000 spots per cm(2).
High-throughput flow injection analysis mass spectroscopy with networked delivery of color-rendered results. 2. Three-dimensional spectral mapping of 96-well combinatorial chemistry racks.

PubMed

Görlach, E; Richmond, R; Lewis, I

1998-08-01

For the last two years, the mass spectroscopy section of the Novartis Pharma Research Core Technology group has analyzed tens of thousands of multiple parallel synthesis samples from the Novartis Pharma Combinatorial Chemistry program, using an in-house developed automated high-throughput flow injection analysis electrospray ionization mass spectroscopy system. The electrospray spectra of these samples reflect the many structures present after the cleavage step from the solid support. The overall success of the sequential synthesis is mirrored in the purity of the expected end product, but the partial success of individual synthesis steps is evident in the impurities in the mass spectrum. However this latter reaction information, which is of considerable utility to the combinatorial chemist, is effectively hidden from view by the very large number of analyzed samples. This information is now revealed at the workbench of the combinatorial chemist by a novel three-dimensional display of each rack's complete mass spectral ion current using the in-house RackViewer Visual Basic application. Colorization of "forbidden loss" and "forbidden gas-adduct" zones, normalization to expected monoisotopic molecular weight, colorization of ionization intensity, and sorting by row or column were used in combination to highlight systematic patterns in the mass spectroscopy data.
Space communications scheduler: A rule-based approach to adaptive deadline scheduling

NASA Technical Reports Server (NTRS)

Straguzzi, Nicholas

1990-01-01

Job scheduling is a deceptively complex subfield of computer science. The highly combinatorial nature of the problem, which is NP-complete in nearly all cases, requires a scheduling program to intelligently transverse an immense search tree to create the best possible schedule in a minimal amount of time. In addition, the program must continually make adjustments to the initial schedule when faced with last-minute user requests, cancellations, unexpected device failures, quests, cancellations, unexpected device failures, etc. A good scheduler must be quick, flexible, and efficient, even at the expense of generating slightly less-than-optimal schedules. The Space Communication Scheduler (SCS) is an intelligent rule-based scheduling system. SCS is an adaptive deadline scheduler which allocates modular communications resources to meet an ordered set of user-specified job requests on board the NASA Space Station. SCS uses pattern matching techniques to detect potential conflicts through algorithmic and heuristic means. As a result, the system generates and maintains high density schedules without relying heavily on backtracking or blind search techniques. SCS is suitable for many common real-world applications.
On Parallel Push-Relabel based Algorithms for Bipartite Maximum Matching

DOE Office of Scientific and Technical Information (OSTI.GOV)

Langguth, Johannes; Azad, Md Ariful; Halappanavar, Mahantesh

2014-07-01

We study multithreaded push-relabel based algorithms for computing maximum cardinality matching in bipartite graphs. Matching is a fundamental combinatorial (graph) problem with applications in a wide variety of problems in science and engineering. We are motivated by its use in the context of sparse linear solvers for computing maximum transversal of a matrix. We implement and test our algorithms on several multi-socket multicore systems and compare their performance to state-of-the-art augmenting path-based serial and parallel algorithms using a testset comprised of a wide range of real-world instances. Building on several heuristics for enhancing performance, we demonstrate good scaling for themore » parallel push-relabel algorithm. We show that it is comparable to the best augmenting path-based algorithms for bipartite matching. To the best of our knowledge, this is the first extensive study of multithreaded push-relabel based algorithms. In addition to a direct impact on the applications using matching, the proposed algorithmic techniques can be extended to preflow-push based algorithms for computing maximum flow in graphs.« less
Patterns of Hierarchy in Formal and Principled Moral Reasoning.

ERIC Educational Resources Information Center

Zeidler, Dana Lewis

Measurements of formal reasoning and principled moral reasoning ability were obtained from a sample of 99 tenth grade students. Specific modes of formal reasoning (proportional reasoning, controlling variables, probabilistic, correlational and combinatorial reasoning) were first examined. Findings support the notion of hierarchical relationships…
Cuisenaire Rods Go to College.

ERIC Educational Resources Information Center

Chinn, Phyllis; And Others

1992-01-01

Presents examples of questions and answers arising from a hands-on and exploratory approach to discrete mathematics using cuisenaire rods. Combinatorial questions about trains formed of cuisenaire rods provide the setting for discovering numerical patterns by experimentation and organizing the results using induction and successive differences.…
Counting in Lattices: Combinatorial Problems from Statistical Mechanics.

NASA Astrophysics Data System (ADS)

Randall, Dana Jill

In this thesis we consider two classical combinatorial problems arising in statistical mechanics: counting matchings and self-avoiding walks in lattice graphs. The first problem arises in the study of the thermodynamical properties of monomers and dimers (diatomic molecules) in crystals. Fisher, Kasteleyn and Temperley discovered an elegant technique to exactly count the number of perfect matchings in two dimensional lattices, but it is not applicable for matchings of arbitrary size, or in higher dimensional lattices. We present the first efficient approximation algorithm for computing the number of matchings of any size in any periodic lattice in arbitrary dimension. The algorithm is based on Monte Carlo simulation of a suitable Markov chain and has rigorously derived performance guarantees that do not rely on any assumptions. In addition, we show that these results generalize to counting matchings in any graph which is the Cayley graph of a finite group. The second problem is counting self-avoiding walks in lattices. This problem arises in the study of the thermodynamics of long polymer chains in dilute solution. While there are a number of Monte Carlo algorithms used to count self -avoiding walks in practice, these are heuristic and their correctness relies on unproven conjectures. In contrast, we present an efficient algorithm which relies on a single, widely-believed conjecture that is simpler than preceding assumptions and, more importantly, is one which the algorithm itself can test. Thus our algorithm is reliable, in the sense that it either outputs answers that are guaranteed, with high probability, to be correct, or finds a counterexample to the conjecture. In either case we know we can trust our results and the algorithm is guaranteed to run in polynomial time. This is the first algorithm for counting self-avoiding walks in which the error bounds are rigorously controlled. This work was supported in part by an AT&T graduate fellowship, a University of California dissertation year fellowship and Esprit working group "RAND". Part of this work was done while visiting ICSI and the University of Edinburgh.
Landmark matching based retinal image alignment by enforcing sparsity in correspondence matrix.

PubMed

Zheng, Yuanjie; Daniel, Ebenezer; Hunter, Allan A; Xiao, Rui; Gao, Jianbin; Li, Hongsheng; Maguire, Maureen G; Brainard, David H; Gee, James C

2014-08-01

Retinal image alignment is fundamental to many applications in diagnosis of eye diseases. In this paper, we address the problem of landmark matching based retinal image alignment. We propose a novel landmark matching formulation by enforcing sparsity in the correspondence matrix and offer its solutions based on linear programming. The proposed formulation not only enables a joint estimation of the landmark correspondences and a predefined transformation model but also combines the benefits of the softassign strategy (Chui and Rangarajan, 2003) and the combinatorial optimization of linear programming. We also introduced a set of reinforced self-similarities descriptors which can better characterize local photometric and geometric properties of the retinal image. Theoretical analysis and experimental results with both fundus color images and angiogram images show the superior performances of our algorithms to several state-of-the-art techniques. Copyright © 2013 Elsevier B.V. All rights reserved.
Emergent latent symbol systems in recurrent neural networks

NASA Astrophysics Data System (ADS)

Monner, Derek; Reggia, James A.

2012-12-01

Fodor and Pylyshyn [(1988). Connectionism and cognitive architecture: A critical analysis. Cognition, 28(1-2), 3-71] famously argued that neural networks cannot behave systematically short of implementing a combinatorial symbol system. A recent response from Frank et al. [(2009). Connectionist semantic systematicity. Cognition, 110(3), 358-379] claimed to have trained a neural network to behave systematically without implementing a symbol system and without any in-built predisposition towards combinatorial representations. We believe systems like theirs may in fact implement a symbol system on a deeper and more interesting level: one where the symbols are latent - not visible at the level of network structure. In order to illustrate this possibility, we demonstrate our own recurrent neural network that learns to understand sentence-level language in terms of a scene. We demonstrate our model's learned understanding by testing it on novel sentences and scenes. By paring down our model into an architecturally minimal version, we demonstrate how it supports combinatorial computation over distributed representations by using the associative memory operations of Vector Symbolic Architectures. Knowledge of the model's memory scheme gives us tools to explain its errors and construct superior future models. We show how the model designs and manipulates a latent symbol system in which the combinatorial symbols are patterns of activation distributed across the layers of a neural network, instantiating a hybrid of classical symbolic and connectionist representations that combines advantages of both.
A simple protocol for combinatorial cyclic depsipeptide libraries sequencing by matrix-assisted laser desorption/ionisation mass spectrometry.

PubMed

Gurevich-Messina, Juan M; Giudicessi, Silvana L; Martínez-Ceron, María C; Acosta, Gerardo; Erra-Balsells, Rosa; Cascone, Osvaldo; Albericio, Fernando; Camperi, Silvia A

2015-01-01

Short cyclic peptides have a great interest in therapeutic, diagnostic and affinity chromatography applications. The screening of 'one-bead-one-peptide' combinatorial libraries combined with mass spectrometry (MS) is an excellent tool to find peptides with affinity for any target protein. The fragmentation patterns of cyclic peptides are quite more complex than those of their linear counterparts, and the elucidation of the resulting tandem mass spectra is rather more difficult. Here, we propose a simple protocol for combinatorial cyclic libraries synthesis and ring opening before MS analysis. In this strategy, 4-hydroxymethylbenzoic acid, which forms a benzyl ester with the first amino acid, was used as the linker. A glycolamidic ester group was incorporated after the combinatorial positions by adding glycolic acid. The library synthesis protocol consisted in the following: (i) incorporation of Fmoc-Asp[2-phenylisopropyl (OPp)]-OH to Ala-Gly-oxymethylbenzamide-ChemMatrix, (ii) synthesis of the combinatorial library, (iii) assembly of a glycolic acid, (iv) couple of an Ala residue in the N-terminal, (v) removal of OPp, (vi) peptide cyclisation through side chain Asp and N-Ala amino terminus and (vii) removal of side chain protecting groups. In order to simultaneously open the ring and release each peptide, benzyl and glycolamidic esters were cleaved with ammonia. Peptide sequences could be deduced from the tandem mass spectra of each single bead evaluated. The strategy herein proposed is suitable for the preparation of one-bead-one-cyclic depsipeptide libraries that can be easily open for its sequencing by matrix-assisted laser desorption/ionisation MS. It employs techniques and reagents frequently used in a broad range of laboratories without special expertise in organic synthesis. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.
The AMchip04 and the processing unit prototype for the FastTracker

NASA Astrophysics Data System (ADS)

Andreani, A.; Annovi, A.; Beretta, M.; Bogdan, M.; Citterio, M.; Alberti, F.; Giannetti, P.; Lanza, A.; Magalotti, D.; Piendibene, M.; Shochet, M.; Stabile, A.; Tang, J.; Tompkins, L.; Volpi, G.

2012-08-01

Modern experiments search for extremely rare processes hidden in much larger background levels. As the experiment`s complexity, the accelerator backgrounds and luminosity increase we need increasingly complex and exclusive event selection. We present the first prototype of a new Processing Unit (PU), the core of the FastTracker processor (FTK). FTK is a real time tracking device for the ATLAS experiment`s trigger upgrade. The computing power of the PU is such that a few hundred of them will be able to reconstruct all the tracks with transverse momentum above 1 GeV/c in ATLAS events up to Phase II instantaneous luminosities (3 × 1034 cm-2 s-1) with an event input rate of 100 kHz and a latency below a hundred microseconds. The PU provides massive computing power to minimize the online execution time of complex tracking algorithms. The time consuming pattern recognition problem, generally referred to as the ``combinatorial challenge'', is solved by the Associative Memory (AM) technology exploiting parallelism to the maximum extent; it compares the event to all pre-calculated ``expectations'' or ``patterns'' (pattern matching) simultaneously, looking for candidate tracks called ``roads''. This approach reduces to a linear behavior the typical exponential complexity of the CPU based algorithms. Pattern recognition is completed by the time data are loaded into the AM devices. We report on the design of the first Processing Unit prototypes. The design had to address the most challenging aspects of this technology: a huge number of detector clusters (``hits'') must be distributed at high rate with very large fan-out to all patterns (10 Million patterns will be located on 128 chips placed on a single board) and a huge number of roads must be collected and sent back to the FTK post-pattern-recognition functions. A network of high speed serial links is used to solve the data distribution problem.
Probabilistic Analysis of Combinatorial Optimization Problems on Hypergraph Matchings

DTIC Science & Technology

2012-02-01

per dimension” ( recall that d is equal to the number of independent subsets of vertices Vk in the hypergraph Hd jn, and n denotes the number of...disjoint solutions whose costs are iid random variables. First, recalling the interpretation of feasible MAP solu- tions as paths in the index graph G, we...elements. On the other hand, recall that a (feasible) path G can be described as a set of n vectors D f.i .1/ 1 ; : : : ; i .1/ d /; : : : ; .i .n

Generalized Correlation Coefficient for Non-Parametric Analysis of Microarray Time-Course Data.

PubMed

Tan, Qihua; Thomassen, Mads; Burton, Mark; Mose, Kristian Fredløv; Andersen, Klaus Ejner; Hjelmborg, Jacob; Kruse, Torben

2017-06-06

Modeling complex time-course patterns is a challenging issue in microarray study due to complex gene expression patterns in response to the time-course experiment. We introduce the generalized correlation coefficient and propose a combinatory approach for detecting, testing and clustering the heterogeneous time-course gene expression patterns. Application of the method identified nonlinear time-course patterns in high agreement with parametric analysis. We conclude that the non-parametric nature in the generalized correlation analysis could be an useful and efficient tool for analyzing microarray time-course data and for exploring the complex relationships in the omics data for studying their association with disease and health.
Effect of the Implicit Combinatorial Model on Combinatorial Reasoning in Secondary School Pupils.

ERIC Educational Resources Information Center

Batanero, Carmen; And Others

1997-01-01

Elementary combinatorial problems may be classified into three different combinatorial models: (1) selection; (2) partition; and (3) distribution. The main goal of this research was to determine the effect of the implicit combinatorial model on pupils' combinatorial reasoning before and after instruction. Gives an analysis of variance of the…
Shibboleth: An Automated Foreign Accent Identification Program

ERIC Educational Resources Information Center

Frost, Wende

2013-01-01

The speech of non-native (L2) speakers of a language contains phonological rules that differentiate them from native speakers. These phonological rules characterize or distinguish accents in an L2. The Shibboleth program creates combinatorial rule-sets to describe the phonological pattern of these accents and classifies L2 speakers into their…
Past tense in the brain's time: neurophysiological evidence for dual-route processing of past-tense verbs.

PubMed

Bakker, Iske; Macgregor, Lucy J; Pulvermüller, Friedemann; Shtyrov, Yury

2013-05-01

A controversial issue in neuro- and psycholinguistics is whether regular past-tense forms of verbs are stored lexically or generated productively by the application of abstract combinatorial schemas, for example affixation rules. The success or failure of models in accounting for this particular issue can be used to draw more general conclusions about cognition and the degree to which abstract, symbolic representations and rules are psychologically and neurobiologically real. This debate can potentially be resolved using a neurophysiological paradigm, in which alternative predictions of the brain response patterns for lexical and syntactic processing are put to the test. We used magnetoencephalography (MEG) to record neural responses to spoken monomorphemic words ('hide'), pseudowords ('smide'), regular past-tense forms ('cried') and ungrammatical (overregularised) past-tense forms ('flied') in a passive listening oddball paradigm, in which lexically and syntactically modulated stimuli are known to elicit distinct patterns of the mismatch negativity (MMN) brain response. We observed an enhanced ('lexical') MMN to monomorphemic words relative to pseudowords, but a reversed ('syntactic') MMN to ungrammatically inflected past tenses relative to grammatical forms. This dissociation between responses to monomorphemic and bimorphemic stimuli indicates that regular past tenses are processed more similarly to syntactic sequences than to lexically stored monomorphemic words, suggesting that regular past tenses are generated productively by the application of a combinatorial scheme to their separately represented stems and affixes. We suggest discrete combinatorial neuronal assemblies, which bind classes of sequentially occurring lexical elements into morphologically complex units, as the neurobiological basis of regular past tense inflection. Copyright © 2013 Elsevier Inc. All rights reserved.
Viral morphogenesis is the dominant source of sequence censorship in M13 combinatorial peptide phage display.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rodi, D. J.; Soares, A. S.; Makowski, L.

Novel statistical methods have been developed and used to quantitate and annotate the sequence diversity within combinatorial peptide libraries on the basis of small numbers (1-200) of sequences selected at random from commercially available M13 p3-based phage display libraries. These libraries behave statistically as though they correspond to populations containing roughly 4.0{+-}1.6% of the random dodecapeptides and 7.9{+-}2.6% of the random constrained heptapeptides that are theoretically possible within the phage populations. Analysis of amino acid residue occurrence patterns shows no demonstrable influence on sequence censorship by Escherichia coli tRNA isoacceptor profiles or either overall codon or Class II codon usagemore » patterns, suggesting no metabolic constraints on recombinant p3 synthesis. There is an overall depression in the occurrence of cysteine, arginine and glycine residues and an overabundance of proline, threonine and histidine residues. The majority of position-dependent amino acid sequence bias is clustered at three positions within the inserted peptides of the dodecapeptide library, +1, +3 and +12 downstream from the signal peptidase cleavage site. Conformational tendency measures of the peptides indicate a significant preference for inserts favoring a {beta}-turn conformation. The observed protein sequence limitations can primarily be attributed to genetic codon degeneracy and signal peptidase cleavage preferences. These data suggest that for applications in which maximal sequence diversity is essential, such as epitope mapping or novel receptor identification, combinatorial peptide libraries should be constructed using codon-corrected trinucleotide cassettes within vector-host systems designed to minimize morphogenesis-related censorship.« less
Breast cancer prognosis by combinatorial analysis of gene expression data.

PubMed

Alexe, Gabriela; Alexe, Sorin; Axelrod, David E; Bonates, Tibérius O; Lozina, Irina I; Reiss, Michael; Hammer, Peter L

2006-01-01

The potential of applying data analysis tools to microarray data for diagnosis and prognosis is illustrated on the recent breast cancer dataset of van 't Veer and coworkers. We re-examine that dataset using the novel technique of logical analysis of data (LAD), with the double objective of discovering patterns characteristic for cases with good or poor outcome, using them for accurate and justifiable predictions; and deriving novel information about the role of genes, the existence of special classes of cases, and other factors. Data were analyzed using the combinatorics and optimization-based method of LAD, recently shown to provide highly accurate diagnostic and prognostic systems in cardiology, cancer proteomics, hematology, pulmonology, and other disciplines. LAD identified a subset of 17 of the 25,000 genes, capable of fully distinguishing between patients with poor, respectively good prognoses. An extensive list of 'patterns' or 'combinatorial biomarkers' (that is, combinations of genes and limitations on their expression levels) was generated, and 40 patterns were used to create a prognostic system, shown to have 100% and 92.9% weighted accuracy on the training and test sets, respectively. The prognostic system uses fewer genes than other methods, and has similar or better accuracy than those reported in other studies. Out of the 17 genes identified by LAD, three (respectively, five) were shown to play a significant role in determining poor (respectively, good) prognosis. Two new classes of patients (described by similar sets of covering patterns, gene expression ranges, and clinical features) were discovered. As a by-product of the study, it is shown that the training and the test sets of van 't Veer have differing characteristics. The study shows that LAD provides an accurate and fully explanatory prognostic system for breast cancer using genomic data (that is, a system that, in addition to predicting good or poor prognosis, provides an individualized explanation of the reasons for that prognosis for each patient). Moreover, the LAD model provides valuable insights into the roles of individual and combinatorial biomarkers, allows the discovery of new classes of patients, and generates a vast library of biomedical research hypotheses.
A New Model for a Carpool Matching Service.

PubMed

Xia, Jizhe; Curtin, Kevin M; Li, Weihong; Zhao, Yonglong

2015-01-01

Carpooling is an effective means of reducing traffic. A carpool team shares a vehicle for their commute, which reduces the number of vehicles on the road during rush hour periods. Carpooling is officially sanctioned by most governments, and is supported by the construction of high-occupancy vehicle lanes. A number of carpooling services have been designed in order to match commuters into carpool teams, but it known that the determination of optimal carpool teams is a combinatorially complex problem, and therefore technological solutions are difficult to achieve. In this paper, a model for carpool matching services is proposed, and both optimal and heuristic approaches are tested to find solutions for that model. The results show that different solution approaches are preferred over different ranges of problem instances. Most importantly, it is demonstrated that a new formulation and associated solution procedures can permit the determination of optimal carpool teams and routes. An instantiation of the model is presented (using the street network of Guangzhou city, China) to demonstrate how carpool teams can be determined.
A New Model for a Carpool Matching Service

PubMed Central

Xia, Jizhe; Curtin, Kevin M.; Li, Weihong; Zhao, Yonglong

2015-01-01

Carpooling is an effective means of reducing traffic. A carpool team shares a vehicle for their commute, which reduces the number of vehicles on the road during rush hour periods. Carpooling is officially sanctioned by most governments, and is supported by the construction of high-occupancy vehicle lanes. A number of carpooling services have been designed in order to match commuters into carpool teams, but it known that the determination of optimal carpool teams is a combinatorially complex problem, and therefore technological solutions are difficult to achieve. In this paper, a model for carpool matching services is proposed, and both optimal and heuristic approaches are tested to find solutions for that model. The results show that different solution approaches are preferred over different ranges of problem instances. Most importantly, it is demonstrated that a new formulation and associated solution procedures can permit the determination of optimal carpool teams and routes. An instantiation of the model is presented (using the street network of Guangzhou city, China) to demonstrate how carpool teams can be determined. PMID:26125552
PROBABILISTIC CROSS-IDENTIFICATION IN CROWDED FIELDS AS AN ASSIGNMENT PROBLEM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Budavári, Tamás; Basu, Amitabh, E-mail: budavari@jhu.edu, E-mail: basu.amitabh@jhu.edu

2016-10-01

One of the outstanding challenges of cross-identification is multiplicity: detections in crowded regions of the sky are often linked to more than one candidate associations of similar likelihoods. We map the resulting maximum likelihood partitioning to the fundamental assignment problem of discrete mathematics and efficiently solve the two-way catalog-level matching in the realm of combinatorial optimization using the so-called Hungarian algorithm. We introduce the method, demonstrate its performance in a mock universe where the true associations are known, and discuss the applicability of the new procedure to large surveys.
Probabilistic Cross-identification in Crowded Fields as an Assignment Problem

NASA Astrophysics Data System (ADS)

Budavári, Tamás; Basu, Amitabh

2016-10-01

One of the outstanding challenges of cross-identification is multiplicity: detections in crowded regions of the sky are often linked to more than one candidate associations of similar likelihoods. We map the resulting maximum likelihood partitioning to the fundamental assignment problem of discrete mathematics and efficiently solve the two-way catalog-level matching in the realm of combinatorial optimization using the so-called Hungarian algorithm. We introduce the method, demonstrate its performance in a mock universe where the true associations are known, and discuss the applicability of the new procedure to large surveys.
The disadvantage of combinatorial communication.

PubMed Central

Lachmann, Michael; Bergstrom, Carl T.

2004-01-01

Combinatorial communication allows rapid and efficient transfer of detailed information, yet combinatorial communication is used by few, if any, non-human species. To complement recent studies illustrating the advantages of combinatorial communication, we highlight a critical disadvantage. We use the concept of information value to show that deception poses a greater and qualitatively different threat to combinatorial signalling than to non-combinatorial systems. This additional potential for deception may represent a strategic barrier that has prevented widespread evolution of combinatorial communication. Our approach has the additional benefit of drawing clear distinctions among several types of deception that can occur in communication systems. PMID:15556886
The disadvantage of combinatorial communication.

PubMed

Lachmann, Michael; Bergstrom, Carl T

2004-11-22

Combinatorial communication allows rapid and efficient transfer of detailed information, yet combinatorial communication is used by few, if any, non-human species. To complement recent studies illustrating the advantages of combinatorial communication, we highlight a critical disadvantage. We use the concept of information value to show that deception poses a greater and qualitatively different threat to combinatorial signalling than to non-combinatorial systems. This additional potential for deception may represent a strategic barrier that has prevented widespread evolution of combinatorial communication. Our approach has the additional benefit of drawing clear distinctions among several types of deception that can occur in communication systems.
The combinatorial control of alternative splicing in C. elegans

PubMed Central

2017-01-01

Normal development requires the right splice variants to be made in the right tissues at the right time. The core splicing machinery is engaged in all splicing events, but which precise splice variant is made requires the choice between alternative splice sites—for this to occur, a set of splicing factors (SFs) must recognize and bind to short RNA motifs in the pre-mRNA. In C. elegans, there is known to be extensive variation in splicing patterns across development, but little is known about the targets of each SF or how multiple SFs combine to regulate splicing. Here we combine RNA-seq with in vitro binding assays to study how 4 different C. elegans SFs, ASD-1, FOX-1, MEC-8, and EXC-7, regulate splicing. The 4 SFs chosen all have well-characterised biology and well-studied loss-of-function genetic alleles, and all contain RRM domains. Intriguingly, while the SFs we examined have varied roles in C. elegans development, they show an unexpectedly high overlap in their targets. We also find that binding sites for these SFs occur on the same pre-mRNAs more frequently than expected suggesting extensive combinatorial control of splicing. We confirm that regulation of splicing by multiple SFs is often combinatorial and show that this is functionally significant. We also find that SFs appear to combine to affect splicing in two modes—they either bind in close proximity within the same intron or they appear to bind to separate regions of the intron in a conserved order. Finally, we find that the genes whose splicing are regulated by multiple SFs are highly enriched for genes involved in the cytoskeleton and in ion channels that are key for neurotransmission. Together, this shows that specific classes of genes have complex combinatorial regulation of splicing and that this combinatorial regulation is critical for normal development to occur. PMID:29121637
Why is combinatorial communication rare in the natural world, and why is language an exception to this trend?

PubMed

Scott-Phillips, Thomas C; Blythe, Richard A

2013-11-06

In a combinatorial communication system, some signals consist of the combinations of other signals. Such systems are more efficient than equivalent, non-combinatorial systems, yet despite this they are rare in nature. Why? Previous explanations have focused on the adaptive limits of combinatorial communication, or on its purported cognitive difficulties, but neither of these explains the full distribution of combinatorial communication in the natural world. Here, we present a nonlinear dynamical model of the emergence of combinatorial communication that, unlike previous models, considers how initially non-communicative behaviour evolves to take on a communicative function. We derive three basic principles about the emergence of combinatorial communication. We hence show that the interdependence of signals and responses places significant constraints on the historical pathways by which combinatorial signals might emerge, to the extent that anything other than the most simple form of combinatorial communication is extremely unlikely. We also argue that these constraints can be bypassed if individuals have the socio-cognitive capacity to engage in ostensive communication. Humans, but probably no other species, have this ability. This may explain why language, which is massively combinatorial, is such an extreme exception to nature's general trend for non-combinatorial communication.
Quantum Matching Theory (with new complexity-theoretic, combinatorial and topical insights on the nature of the quantum entanglement)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gurvits, L.

2002-01-01

Classical matching theory can be defined in terms of matrices with nonnegative entries. The notion of Positive operator, central in Quantum Theory, is a natural generalization of matrices with non-negative entries. Based on this point of view, we introduce a definition of perfect Quantum (operator) matching. We show that the new notion inherits many 'classical' properties, but not all of them. This new notion goes somewhere beyound matroids. For separable bipartite quantum states this new notion coinsides with the full rank property of the intersection of two corresponding geometric matroids. In the classical situation, permanents are naturally associated with perfectsmore » matchings. We introduce an analog of permanents for positive operators, called Quantum Permanent and show how this generalization of the permanent is related to the Quantum Entanglement. Besides many other things, Quantum Permanents provide new rational inequalities necessary for the separability of bipartite quantum states. Using Quantum Permanents, we give deterministic poly-time algorithm to solve Hidden Matroids Intersection Problem and indicate some 'classical' complexity difficulties associated with the Quantum Entanglement. Finally, we prove that the weak membership problem for the convex set of separable bipartite density matrices is NP-HARD.« less
Combinatorial wetting in colour: an optofluidic nose.

PubMed

Raymond, Kevin P; Burgess, Ian B; Kinney, Mackenzie H; Lončar, Marko; Aizenberg, Joanna

2012-10-07

We present a colourimetric litmus test for simple differentiation of organic liquids based on wetting, which achieves chemical specificity without a significant sacrifice in portability or ease-of-use. Chemical specificity is derived from the combination of colourimetric wetting patterns produced by liquids in an array of inverse opal films, each having a graded wettability, but using different surface groups to define that gradient.
Synthesis of Chemiluminescent Esters: A Combinatorial Synthesis Experiment for Organic Chemistry Students

ERIC Educational Resources Information Center

Duarte, Robert; Nielson, Janne T.; Dragojlovic, Veljko

2004-01-01

A group of techniques aimed at synthesizing a large number of structurally diverse compounds is called combinatorial synthesis. Synthesis of chemiluminescence esters using parallel combinatorial synthesis and mix-and-split combinatorial synthesis is experimented.
The Role of Left Occipitotemporal Cortex in Reading: Reconciling Stimulus, Task, and Lexicality Effects

PubMed Central

Humphries, Colin; Desai, Rutvik H.; Seidenberg, Mark S.; Osmon, David C.; Stengel, Ben C.; Binder, Jeffrey R.

2013-01-01

Although the left posterior occipitotemporal sulcus (pOTS) has been called a visual word form area, debate persists over the selectivity of this region for reading relative to general nonorthographic visual object processing. We used high-resolution functional magnetic resonance imaging to study left pOTS responses to combinatorial orthographic and object shape information. Participants performed naming and visual discrimination tasks designed to encourage or suppress phonological encoding. During the naming task, all participants showed subregions within left pOTS that were more sensitive to combinatorial orthographic information than to object information. This difference disappeared, however, when phonological processing demands were removed. Responses were stronger to pseudowords than to words, but this effect also disappeared when phonological processing demands were removed. Subregions within the left pOTS are preferentially activated when visual input must be mapped to a phonological representation (i.e., a name) and particularly when component parts of the visual input must be mapped to corresponding phonological elements (consonant or vowel phonemes). Results indicate a specialized role for subregions within the left pOTS in the isomorphic mapping of familiar combinatorial visual patterns to phonological forms. This process distinguishes reading from picture naming and accounts for a wide range of previously reported stimulus and task effects in left pOTS. PMID:22505661
Causal gene identification using combinatorial V-structure search.

PubMed

Cai, Ruichu; Zhang, Zhenjie; Hao, Zhifeng

2013-07-01

With the advances of biomedical techniques in the last decade, the costs of human genomic sequencing and genomic activity monitoring are coming down rapidly. To support the huge genome-based business in the near future, researchers are eager to find killer applications based on human genome information. Causal gene identification is one of the most promising applications, which may help the potential patients to estimate the risk of certain genetic diseases and locate the target gene for further genetic therapy. Unfortunately, existing pattern recognition techniques, such as Bayesian networks, cannot be directly applied to find the accurate causal relationship between genes and diseases. This is mainly due to the insufficient number of samples and the extremely high dimensionality of the gene space. In this paper, we present the first practical solution to causal gene identification, utilizing a new combinatorial formulation over V-Structures commonly used in conventional Bayesian networks, by exploring the combinations of significant V-Structures. We prove the NP-hardness of the combinatorial search problem under a general settings on the significance measure on the V-Structures, and present a greedy algorithm to find sub-optimal results. Extensive experiments show that our proposal is both scalable and effective, particularly with interesting findings on the causal genes over real human genome data. Copyright © 2013 Elsevier Ltd. All rights reserved.
Novel In Vivo Model for Combinatorial Fluorescence Labeling in Mouse Prostate

PubMed Central

Fang, Xiaolan; Gyabaah, Kenneth; Nickkholgh, Bita; Cline, J. Mark; Balaji, K.C.

2015-01-01

BACKGROUND The epithelial layer of prostate glands contains several types of cells, including luminal and basal cells. Yet there is paucity of animal models to study the cellular origin of normal or neoplastic development in the prostate to facilitate the treatment of heterogenous prostate diseases by targeting individual cell lineages. METHODS We developed a mouse model that expresses different types of fluorescent proteins (XFPs) specifically in prostatic cells. Using an in vivo stochastic fluorescent protein combinatorial strategy, XFP signals were expressed specifically in prostate of Protein Kinase D1 (PKD1) knock-out, K-RasG12D knock-in, and Phosphatase and tensin homolog (PTEN) and PKD1 double knock-out mice under the control of PB-Cre promoter. RESULTS In vivo XFP signals were observed in prostate of PKD1 knock-out, K-RasG12D knock-in, and PTEN PKD1 double knock-out mice, which developed normal, hyperplastic, and neoplastic prostate, respectively. The patchy expression pattern of XFPs in neoplasia tissue indicated the clonal origin of cancer cells in the prostate. CONCLUSIONS The transgenic mouse models demonstrate combinatorial fluorescent protein expression in normal and cancerous prostatic tissues. This novel prostate-specific fluorescent labeled mouse model, which we named Prorainbow, could be useful in studying benign and malignant pathology of prostate. PMID:25753731

Novel In Vivo model for combinatorial fluorescence labeling in mouse prostate.

PubMed

Fang, Xiaolan; Gyabaah, Kenneth; Nickkholgh, Bita; Cline, J Mark; Balaji, K C

2015-06-15

The epithelial layer of prostate glands contains several types of cells, including luminal and basal cells. Yet there is paucity of animal models to study the cellular origin of normal or neoplastic development in the prostate to facilitate the treatment of heterogenous prostate diseases by targeting individual cell lineages. We developed a mouse model that expresses different types of fluorescent proteins (XFPs) specifically in prostatic cells. Using an in vivo stochastic fluorescent protein combinatorial strategy, XFP signals were expressed specifically in prostate of Protein Kinase D1 (PKD1) knock-out, K-Ras(G) (12) (D) knock-in, and Phosphatase and tensin homolog (PTEN) and PKD1 double knock-out mice under the control of PB-Cre promoter. In vivo XFP signals were observed in prostate of PKD1 knock-out, K-Ras(G) (12) (D) knock-in, and PTEN PKD1 double knock-out mice, which developed normal, hyperplastic, and neoplastic prostate, respectively. The patchy expression pattern of XFPs in neoplasia tissue indicated the clonal origin of cancer cells in the prostate. The transgenic mouse models demonstrate combinatorial fluorescent protein expression in normal and cancerous prostatic tissues. This novel prostate-specific fluorescent labeled mouse model, which we named Prorainbow, could be useful in studying benign and malignant pathology of prostate. © 2015 Wiley Periodicals, Inc.
Combinatorial pattern discovery approach for the folding trajectory analysis of a beta-hairpin.

PubMed

Parida, Laxmi; Zhou, Ruhong

2005-06-01

The study of protein folding mechanisms continues to be one of the most challenging problems in computational biology. Currently, the protein folding mechanism is often characterized by calculating the free energy landscape versus various reaction coordinates, such as the fraction of native contacts, the radius of gyration, RMSD from the native structure, and so on. In this paper, we present a combinatorial pattern discovery approach toward understanding the global state changes during the folding process. This is a first step toward an unsupervised (and perhaps eventually automated) approach toward identification of global states. The approach is based on computing biclusters (or patterned clusters)-each cluster is a combination of various reaction coordinates, and its signature pattern facilitates the computation of the Z-score for the cluster. For this discovery process, we present an algorithm of time complexity c in RO((N + nm) log n), where N is the size of the output patterns and (n x m) is the size of the input with n time frames and m reaction coordinates. To date, this is the best time complexity for this problem. We next apply this to a beta-hairpin folding trajectory and demonstrate that this approach extracts crucial information about protein folding intermediate states and mechanism. We make three observations about the approach: (1) The method recovers states previously obtained by visually analyzing free energy surfaces. (2) It also succeeds in extracting meaningful patterns and structures that had been overlooked in previous works, which provides a better understanding of the folding mechanism of the beta-hairpin. These new patterns also interconnect various states in existing free energy surfaces versus different reaction coordinates. (3) The approach does not require calculating the free energy values, yet it offers an analysis comparable to, and sometimes better than, the methods that use free energy landscapes, thus validating the choice of reaction coordinates. (An abstract version of this work was presented at the 2005 Asia Pacific Bioinformatics Conference [1].).
Logical analysis of diffuse large B-cell lymphomas.

PubMed

Alexe, G; Alexe, S; Axelrod, D E; Hammer, P L; Weissmann, D

2005-07-01

The goal of this study is to re-examine the oligonucleotide microarray dataset of Shipp et al., which contains the intensity levels of 6817 genes of 58 patients with diffuse large B-cell lymphoma (DLBCL) and 19 with follicular lymphoma (FL), by means of the combinatorics, optimisation, and logic-based methodology of logical analysis of data (LAD). The motivations for this new analysis included the previously demonstrated capabilities of LAD and its expected potential (1) to identify different informative genes than those discovered by conventional statistical methods, (2) to identify combinations of gene expression levels capable of characterizing different types of lymphoma, and (3) to assemble collections of such combinations that if considered jointly are capable of accurately distinguishing different types of lymphoma. The central concept of LAD is a pattern or combinatorial biomarker, a concept that resembles a rule as used in decision tree methods. LAD is able to exhaustively generate the collection of all those patterns which satisfy certain quality constraints, through a systematic combinatorial process guided by clear optimization criteria. Then, based on a set covering approach, LAD aggregates the collection of patterns into classification models. In addition, LAD is able to use the information provided by large collections of patterns in order to extract subsets of variables, which collectively are able to distinguish between different types of disease. For the differential diagnosis of DLBCL versus FL, a model based on eight significant genes is constructed and shown to have a sensitivity of 94.7% and a specificity of 100% on the test set. For the prognosis of good versus poor outcome among the DLBCL patients, a model is constructed on another set consisting also of eight significant genes, and shown to have a sensitivity of 87.5% and a specificity of 90% on the test set. The genes selected by LAD also work well as a basis for other kinds of statistical analysis, indicating their robustness. These two models exhibit accuracies that compare favorably to those in the original study. In addition, the current study also provides a ranking by importance of the genes in the selected significant subsets as well as a library of dozens of combinatorial biomarkers (i.e. pairs or triplets of genes) that can serve as a source of mathematically generated, statistically significant research hypotheses in need of biological explanation.
High performance embedded system for real-time pattern matching

NASA Astrophysics Data System (ADS)

Sotiropoulou, C.-L.; Luciano, P.; Gkaitatzis, S.; Citraro, S.; Giannetti, P.; Dell'Orso, M.

2017-02-01

In this paper we present an innovative and high performance embedded system for real-time pattern matching. This system is based on the evolution of hardware and algorithms developed for the field of High Energy Physics and more specifically for the execution of extremely fast pattern matching for tracking of particles produced by proton-proton collisions in hadron collider experiments. A miniaturized version of this complex system is being developed for pattern matching in generic image processing applications. The system works as a contour identifier able to extract the salient features of an image. It is based on the principles of cognitive image processing, which means that it executes fast pattern matching and data reduction mimicking the operation of the human brain. The pattern matching can be executed by a custom designed Associative Memory chip. The reference patterns are chosen by a complex training algorithm implemented on an FPGA device. Post processing algorithms (e.g. pixel clustering) are also implemented on the FPGA. The pattern matching can be executed on a 2D or 3D space, on black and white or grayscale images, depending on the application and thus increasing exponentially the processing requirements of the system. We present the firmware implementation of the training and pattern matching algorithm, performance and results on a latest generation Xilinx Kintex Ultrascale FPGA device.
Asessing for Structural Understanding in Childrens' Combinatorial Problem Solving.

ERIC Educational Resources Information Center

English, Lyn

1999-01-01

Assesses children's structural understanding of combinatorial problems when presented in a variety of task situations. Provides an explanatory model of students' combinatorial understandings that informs teaching and assessment. Addresses several components of children's structural understanding of elementary combinatorial problems. (Contains 50…
Fuel management optimization using genetic algorithms and code independence

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeChaine, M.D.; Feltus, M.A.

1994-12-31

Fuel management optimization is a hard problem for traditional optimization techniques. Loading pattern optimization is a large combinatorial problem without analytical derivative information. Therefore, methods designed for continuous functions, such as linear programming, do not always work well. Genetic algorithms (GAs) address these problems and, therefore, appear ideal for fuel management optimization. They do not require derivative information and work well with combinatorial. functions. The GAs are a stochastic method based on concepts from biological genetics. They take a group of candidate solutions, called the population, and use selection, crossover, and mutation operators to create the next generation of bettermore » solutions. The selection operator is a {open_quotes}survival-of-the-fittest{close_quotes} operation and chooses the solutions for the next generation. The crossover operator is analogous to biological mating, where children inherit a mixture of traits from their parents, and the mutation operator makes small random changes to the solutions.« less
Optofluidic wavelength division multiplexing for single-virus detection

PubMed Central

Ozcelik, Damla; Parks, Joshua W.; Wall, Thomas A.; Stott, Matthew A.; Cai, Hong; Parks, Joseph W.; Hawkins, Aaron R.; Schmidt, Holger

2015-01-01

Optical waveguides simultaneously transport light at different colors, forming the basis of fiber-optic telecommunication networks that shuttle data in dozens of spectrally separated channels. Here, we reimagine this wavelength division multiplexing (WDM) paradigm in a novel context––the differentiated detection and identification of single influenza viruses on a chip. We use a single multimode interference (MMI) waveguide to create wavelength-dependent spot patterns across the entire visible spectrum and enable multiplexed single biomolecule detection on an optofluidic chip. Each target is identified by its time-dependent fluorescence signal without the need for spectral demultiplexing upon detection. We demonstrate detection of individual fluorescently labeled virus particles of three influenza A subtypes in two implementations: labeling of each virus using three different colors and two-color combinatorial labeling. By extending combinatorial multiplexing to three or more colors, MMI-based WDM provides the multiplexing power required for differentiated clinical tests and the growing field of personalized medicine. PMID:26438840
Design of self-coded combinatorial libraries to facilitate direct analysis of ligands by mass spectrometry.

PubMed

Hughes, I

1998-09-24

The direct analysis of selected components from combinatorial libraries by sensitive methods such as mass spectrometry is potentially more efficient than deconvolution and tagging strategies since additional steps of resynthesis or introduction of molecular tags are avoided. A substituent selection procedure is described that eliminates the mass degeneracy commonly observed in libraries prepared by "split-and-mix" methods, without recourse to high-resolution mass measurements. A set of simple rules guides the choice of substituents such that all components of the library have unique nominal masses. Additional rules extend the scope by ensuring that characteristic isotopic mass patterns distinguish isobaric components. The method is applicable to libraries having from two to four varying substituent groups and can encode from a few hundred to several thousand components. No restrictions are imposed on the manner in which the "self-coded" library is synthesized or screened.
Geometry Helps to Compare Persistence Diagrams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kerber, Michael; Morozov, Dmitriy; Nigmetov, Arnur

2015-11-16

Exploiting geometric structure to improve the asymptotic complexity of discrete assignment problems is a well-studied subject. In contrast, the practical advantages of using geometry for such problems have not been explored. We implement geometric variants of the Hopcroft--Karp algorithm for bottleneck matching (based on previous work by Efrat el al.), and of the auction algorithm by Bertsekas for Wasserstein distance computation. Both implementations use k-d trees to replace a linear scan with a geometric proximity query. Our interest in this problem stems from the desire to compute distances between persistence diagrams, a problem that comes up frequently in topological datamore » analysis. We show that our geometric matching algorithms lead to a substantial performance gain, both in running time and in memory consumption, over their purely combinatorial counterparts. Moreover, our implementation significantly outperforms the only other implementation available for comparing persistence diagrams.« less
Hypergraph-Based Combinatorial Optimization of Matrix-Vector Multiplication

ERIC Educational Resources Information Center

Wolf, Michael Maclean

2009-01-01

Combinatorial scientific computing plays an important enabling role in computational science, particularly in high performance scientific computing. In this thesis, we will describe our work on optimizing matrix-vector multiplication using combinatorial techniques. Our research has focused on two different problems in combinatorial scientific…
Combinatorial structures to modeling simple games and applications

NASA Astrophysics Data System (ADS)

Molinero, Xavier

2017-09-01

We connect three different topics: combinatorial structures, game theory and chemistry. In particular, we establish the bases to represent some simple games, defined as influence games, and molecules, defined from atoms, by using combinatorial structures. First, we characterize simple games as influence games using influence graphs. It let us to modeling simple games as combinatorial structures (from the viewpoint of structures or graphs). Second, we formally define molecules as combinations of atoms. It let us to modeling molecules as combinatorial structures (from the viewpoint of combinations). It is open to generate such combinatorial structures using some specific techniques as genetic algorithms, (meta-)heuristics algorithms and parallel programming, among others.
Nanostructured Ti-Ta thin films synthesized by combinatorial glancing angle sputter deposition

NASA Astrophysics Data System (ADS)

Motemani, Yahya; Khare, Chinmay; Savan, Alan; Hans, Michael; Paulsen, Alexander; Frenzel, Jan; Somsen, Christoph; Mücklich, Frank; Eggeler, Gunther; Ludwig, Alfred

2016-12-01

Ti-Ta alloys are attractive materials for applications in actuators as well as biomedical implants. When fabricated as thin films, these alloys can potentially be employed as microactuators, components for micro-implantable devices and coatings on surgical implants. In this study, Ti100-x Ta x (x = 21, 30) nanocolumnar thin films are fabricated by glancing angle deposition (GLAD) at room temperature using Ti73Ta27 and Ta sputter targets. Crystal structure, morphology and microstructure of the nanostructured thin films are systematically investigated by XRD, SEM and TEM, respectively. Nanocolumns of ˜150-160 nm in width are oriented perpendicular to the substrate for both Ti79Ta21 and Ti70Ta30 compositions. The disordered α″ martensite phase with orthorhombic structure is formed in room temperature as-deposited thin films. The columns are found to be elongated small single crystals which are aligned perpendicular to the (20\\bar{4}) and (204) planes of α″ martensite, indicating that the films’ growth orientation is mainly dominated by these crystallographic planes. Laser pre-patterned substrates are utilized to obtain periodic nanocolumnar arrays. The differences in seed pattern, and inter-seed distances lead to growth of multi-level porous nanostructures. Using a unique sputter deposition geometry consisting of Ti73Ta27 and Ta sputter sources, a nanocolumnar Ti-Ta materials library was fabricated on a static substrate by a co-deposition process (combinatorial-GLAD approach). In this library, a composition spread developed between Ti72.8Ta27.2 and Ti64.4Ta35.6, as confirmed by high-throughput EDX analysis. The morphology over the materials library varies from well-isolated nanocolumns to fan-like nanocolumnar structures. The influence of two sputter sources is investigated by studying the resulting column angle on the materials library. The presented nanostructuring methods including the use of the GLAD technique along with pre-patterning and a combinatorial materials library fabrication strategy offer a promising technological approach for investigating Ti-Ta thin films for a range of applications. The proposed approaches can be similarly implemented for other materials systems which can benefit from the formation of a nanocolumnar morphology.
Fast Combinatorial Algorithm for the Solution of Linearly Constrained Least Squares Problems

DOEpatents

Van Benthem, Mark H.; Keenan, Michael R.

2008-11-11

A fast combinatorial algorithm can significantly reduce the computational burden when solving general equality and inequality constrained least squares problems with large numbers of observation vectors. The combinatorial algorithm provides a mathematically rigorous solution and operates at great speed by reorganizing the calculations to take advantage of the combinatorial nature of the problems to be solved. The combinatorial algorithm exploits the structure that exists in large-scale problems in order to minimize the number of arithmetic operations required to obtain a solution.
Disease clusters, exact distributions of maxima, and P-values.

PubMed

Grimson, R C

1993-10-01

This paper presents combinatorial (exact) methods that are useful in the analysis of disease cluster data obtained from small environments, such as buildings and neighbourhoods. Maxwell-Boltzmann and Fermi-Dirac occupancy models are compared in terms of appropriateness of representation of disease incidence patterns (space and/or time) in these environments. The methods are illustrated by a statistical analysis of the incidence pattern of bone fractures in a setting wherein fracture clustering was alleged to be occurring. One of the methodological results derived in this paper is the exact distribution of the maximum cell frequency in occupancy models.
A New Approach for Proving or Generating Combinatorial Identities

ERIC Educational Resources Information Center

Gonzalez, Luis

2010-01-01

A new method for proving, in an immediate way, many combinatorial identities is presented. The method is based on a simple recursive combinatorial formula involving n + 1 arbitrary real parameters. Moreover, this formula enables one not only to prove, but also generate many different combinatorial identities (not being required to know them "a…
An efficient way of layout processing based on calibre DRC and pattern matching for defects inspection application

NASA Astrophysics Data System (ADS)

Li, Helen; Lee, Robben; Lee, Tyzy; Xue, Teddy; Liu, Hermes; Wu, Hall; Wan, Qijian; Du, Chunshan; Hu, Xinyi; Liu, Zhengfang

2018-03-01

As technology advances, escalating layout design complexity and chip size make defect inspection becomes more challenging than ever before. The YE (Yield Enhancement) engineers are seeking for an efficient strategy to ensure accuracy without suffering running time. A smart way is to set different resolutions for different pattern structures, for examples, logic pattern areas have a higher scan resolution while the dummy areas have a lower resolution, SRAM area may have another different resolution. This can significantly reduce the scan processing time meanwhile the accuracy does not suffer. Due to the limitation of the inspection equipment, the layout must be processed in order to output the Care Area marker in line with the requirement of the equipment, for instance, the marker shapes must be rectangle and the number of the rectangle shapes should be as small as possible. The challenge is how to select the different Care Areas by pattern structures, merge the areas efficiently and then partition them into pieces of rectangle shapes. This paper presents a solution based on Calibre DRC and Pattern Matching. Calibre equation-based DRC is a powerful layout processing engine and Calibre Pattern Matching's automated visual capture capability enables designers to define these geometries as layout patterns and store them in libraries which can be re-used in multiple design layouts. Pattern Matching simplifies the description of very complex relationships between pattern shapes efficiently and accurately. Pattern matching's true power is on display when it is integrated with normal DRC deck. In this application of defects inspection, we first run Calibre DRC to get rule based Care Area then use Calibre Pattern Matching's automated pattern capture capability to capture Care Area shapes which need a higher scan resolution with a tune able pattern halo. In the pattern matching step, when the patterns are matched, a bounding box marker will be output to identify the high resolution area. The equation-based DRC and Pattern Matching effectively work together for different scan phases.
Dynamic combinatorial libraries: new opportunities in systems chemistry.

PubMed

Hunt, Rosemary A R; Otto, Sijbren

2011-01-21

Combinatorial chemistry is a tool for selecting molecules with special properties. Dynamic combinatorial chemistry started off aiming to be just that. However, unlike ordinary combinatorial chemistry, the interconnectedness of dynamic libraries gives them an extra dimension. An understanding of these molecular networks at systems level is essential for their use as a selection tool and creates exciting new opportunities in systems chemistry. In this feature article we discuss selected examples and considerations related to the advanced exploitation of dynamic combinatorial libraries for their originally conceived purpose of identifying strong binding interactions. Also reviewed are examples illustrating a trend towards increasing complexity in terms of network behaviour and reversible chemistry. Finally, new applications of dynamic combinatorial chemistry in self-assembly, transport and self-replication are discussed.
Cephalopod dynamic camouflage: bridging the continuum between background matching and disruptive coloration

PubMed Central

Hanlon, R.T.; Chiao, C.-C.; Mäthger, L.M.; Barbosa, A.; Buresch, K.C.; Chubb, C.

2008-01-01

Individual cuttlefish, octopus and squid have the versatile capability to use body patterns for background matching and disruptive coloration. We define—qualitatively and quantitatively—the chief characteristics of the three major body pattern types used for camouflage by cephalopods: uniform and mottle patterns for background matching, and disruptive patterns that primarily enhance disruptiveness but aid background matching as well. There is great variation within each of the three body pattern types, but by defining their chief characteristics we lay the groundwork to test camouflage concepts by correlating background statistics with those of the body pattern. We describe at least three ways in which background matching can be achieved in cephalopods. Disruptive patterns in cuttlefish possess all four of the basic components of ‘disruptiveness’, supporting Cott's hypotheses, and we provide field examples of disruptive coloration in which the body pattern contrast exceeds that of the immediate surrounds. Based upon laboratory testing as well as thousands of images of camouflaged cephalopods in the field (a sample is provided on a web archive), we note that size, contrast and edges of background objects are key visual cues that guide cephalopod camouflage patterning. Mottle and disruptive patterns are frequently mixed, suggesting that background matching and disruptive mechanisms are often used in the same pattern. PMID:19008200
Automated phase mapping with AgileFD and its application to light absorber discovery in the V–Mn–Nb oxide system

DOE PAGES

Suram, Santosh K.; Xue, Yexiang; Bai, Junwen; ...

2016-11-21

Rapid construction of phase diagrams is a central tenet of combinatorial materials science with accelerated materials discovery efforts often hampered by challenges in interpreting combinatorial X-ray diffraction data sets, which we address by developing AgileFD, an artificial intelligence algorithm that enables rapid phase mapping from a combinatorial library of X-ray diffraction patterns. AgileFD models alloying-based peak shifting through a novel expansion of convolutional nonnegative matrix factorization, which not only improves the identification of constituent phases but also maps their concentration and lattice parameter as a function of composition. By incorporating Gibbs’ phase rule into the algorithm, physically meaningful phase mapsmore » are obtained with unsupervised operation, and more refined solutions are attained by injecting expert knowledge of the system. The algorithm is demonstrated through investigation of the V–Mn–Nb oxide system where decomposition of eight oxide phases, including two with substantial alloying, provides the first phase map for this pseudoternary system. This phase map enables interpretation of high-throughput band gap data, leading to the discovery of new solar light absorbers and the alloying-based tuning of the direct-allowed band gap energy of MnV 2O 6. Lastly, the open-source family of AgileFD algorithms can be implemented into a broad range of high throughput workflows to accelerate materials discovery.« less
Automated phase mapping with AgileFD and its application to light absorber discovery in the V–Mn–Nb oxide system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suram, Santosh K.; Xue, Yexiang; Bai, Junwen

Rapid construction of phase diagrams is a central tenet of combinatorial materials science with accelerated materials discovery efforts often hampered by challenges in interpreting combinatorial X-ray diffraction data sets, which we address by developing AgileFD, an artificial intelligence algorithm that enables rapid phase mapping from a combinatorial library of X-ray diffraction patterns. AgileFD models alloying-based peak shifting through a novel expansion of convolutional nonnegative matrix factorization, which not only improves the identification of constituent phases but also maps their concentration and lattice parameter as a function of composition. By incorporating Gibbs’ phase rule into the algorithm, physically meaningful phase mapsmore » are obtained with unsupervised operation, and more refined solutions are attained by injecting expert knowledge of the system. The algorithm is demonstrated through investigation of the V–Mn–Nb oxide system where decomposition of eight oxide phases, including two with substantial alloying, provides the first phase map for this pseudoternary system. This phase map enables interpretation of high-throughput band gap data, leading to the discovery of new solar light absorbers and the alloying-based tuning of the direct-allowed band gap energy of MnV 2O 6. Lastly, the open-source family of AgileFD algorithms can be implemented into a broad range of high throughput workflows to accelerate materials discovery.« less

A Combinatorial Approach to Detecting Gene-Gene and Gene-Environment Interactions in Family Studies

PubMed Central

Lou, Xiang-Yang; Chen, Guo-Bo; Yan, Lei; Ma, Jennie Z.; Mangold, Jamie E.; Zhu, Jun; Elston, Robert C.; Li, Ming D.

2008-01-01

Widespread multifactor interactions present a significant challenge in determining risk factors of complex diseases. Several combinatorial approaches, such as the multifactor dimensionality reduction (MDR) method, have emerged as a promising tool for better detecting gene-gene (G × G) and gene-environment (G × E) interactions. We recently developed a general combinatorial approach, namely the generalized multifactor dimensionality reduction (GMDR) method, which can entertain both qualitative and quantitative phenotypes and allows for both discrete and continuous covariates to detect G × G and G × E interactions in a sample of unrelated individuals. In this article, we report the development of an algorithm that can be used to study G × G and G × E interactions for family-based designs, called pedigree-based GMDR (PGMDR). Compared to the available method, our proposed method has several major improvements, including allowing for covariate adjustments and being applicable to arbitrary phenotypes, arbitrary pedigree structures, and arbitrary patterns of missing marker genotypes. Our Monte Carlo simulations provide evidence that the PGMDR method is superior in performance to identify epistatic loci compared to the MDR-pedigree disequilibrium test (PDT). Finally, we applied our proposed approach to a genetic data set on tobacco dependence and found a significant interaction between two taste receptor genes (i.e., TAS2R16 and TAS2R38) in affecting nicotine dependence. PMID:18834969
HnRNP L and L-like cooperate in multiple-exon regulation of CD45 alternative splicing

PubMed Central

Preußner, Marco; Schreiner, Silke; Hung, Lee-Hsueh; Porstner, Martina; Jäck, Hans-Martin; Benes, Vladimir; Rätsch, Gunnar; Bindereif, Albrecht

2012-01-01

CD45 encodes a trans-membrane protein-tyrosine phosphatase expressed in diverse cells of the immune system. By combinatorial use of three variable exons 4–6, isoforms are generated that differ in their extracellular domain, thereby modulating phosphatase activity and immune response. Alternative splicing of these CD45 exons involves two heterogeneous ribonucleoproteins, hnRNP L and its cell-type specific paralog hnRNP L-like (LL). To address the complex combinatorial splicing of exons 4–6, we investigated hnRNP L/LL protein expression in human B-cells in relation to CD45 splicing patterns, applying RNA-Seq. In addition, mutational and RNA-binding analyses were carried out in HeLa cells. We conclude that hnRNP LL functions as the major CD45 splicing repressor, with two CA elements in exon 6 as its primary target. In exon 4, one element is targeted by both hnRNP L and LL. In contrast, exon 5 was never repressed on its own and only co-regulated with exons 4 and 6. Stable L/LL interaction requires CD45 RNA, specifically exons 4 and 6. We propose a novel model of combinatorial alternative splicing: HnRNP L and LL cooperate on the CD45 pre-mRNA, bridging exons 4 and 6 and looping out exon 5, thereby achieving full repression of the three variable exons. PMID:22402488
Breeding novel solutions in the brain: a model of Darwinian neurodynamics.

PubMed

Szilágyi, András; Zachar, István; Fedor, Anna; de Vladar, Harold P; Szathmáry, Eörs

2016-01-01

Background : The fact that surplus connections and neurons are pruned during development is well established. We complement this selectionist picture by a proof-of-principle model of evolutionary search in the brain, that accounts for new variations in theory space. We present a model for Darwinian evolutionary search for candidate solutions in the brain. Methods : We combine known components of the brain - recurrent neural networks (acting as attractors), the action selection loop and implicit working memory - to provide the appropriate Darwinian architecture. We employ a population of attractor networks with palimpsest memory. The action selection loop is employed with winners-share-all dynamics to select for candidate solutions that are transiently stored in implicit working memory. Results : We document two processes: selection of stored solutions and evolutionary search for novel solutions. During the replication of candidate solutions attractor networks occasionally produce recombinant patterns, increasing variation on which selection can act. Combinatorial search acts on multiplying units (activity patterns) with hereditary variation and novel variants appear due to (i) noisy recall of patterns from the attractor networks, (ii) noise during transmission of candidate solutions as messages between networks, and, (iii) spontaneously generated, untrained patterns in spurious attractors. Conclusions : Attractor dynamics of recurrent neural networks can be used to model Darwinian search. The proposed architecture can be used for fast search among stored solutions (by selection) and for evolutionary search when novel candidate solutions are generated in successive iterations. Since all the suggested components are present in advanced nervous systems, we hypothesize that the brain could implement a truly evolutionary combinatorial search system, capable of generating novel variants.
cDREM: inferring dynamic combinatorial gene regulation.

PubMed

Wise, Aaron; Bar-Joseph, Ziv

2015-04-01

Genes are often combinatorially regulated by multiple transcription factors (TFs). Such combinatorial regulation plays an important role in development and facilitates the ability of cells to respond to different stresses. While a number of approaches have utilized sequence and ChIP-based datasets to study combinational regulation, these have often ignored the combinational logic and the dynamics associated with such regulation. Here we present cDREM, a new method for reconstructing dynamic models of combinatorial regulation. cDREM integrates time series gene expression data with (static) protein interaction data. The method is based on a hidden Markov model and utilizes the sparse group Lasso to identify small subsets of combinatorially active TFs, their time of activation, and the logical function they implement. We tested cDREM on yeast and human data sets. Using yeast we show that the predicted combinatorial sets agree with other high throughput genomic datasets and improve upon prior methods developed to infer combinatorial regulation. Applying cDREM to study human response to flu, we were able to identify several combinatorial TF sets, some of which were known to regulate immune response while others represent novel combinations of important TFs.
Use of combinatorial chemistry to speed drug discovery.

PubMed

Rádl, S

1998-10-01

IBC's International Conference on Integrating Combinatorial Chemistry into the Discovery Pipeline was held September 14-15, 1998. The program started with a pre-conference workshop on High-Throughput Compound Characterization and Purification. The agenda of the main conference was divided into sessions of Synthesis, Automation and Unique Chemistries; Integrating Combinatorial Chemistry, Medicinal Chemistry and Screening; Combinatorial Chemistry Applications for Drug Discovery; and Information and Data Management. This meeting was an excellent opportunity to see how big pharma, biotech and service companies are addressing the current bottlenecks in combinatorial chemistry to speed drug discovery. (c) 1998 Prous Science. All rights reserved.
A multi-pattern hash-binary hybrid algorithm for URL matching in the HTTP protocol.

PubMed

Zeng, Ping; Tan, Qingping; Meng, Xiankai; Shao, Zeming; Xie, Qinzheng; Yan, Ying; Cao, Wei; Xu, Jianjun

2017-01-01

In this paper, based on our previous multi-pattern uniform resource locator (URL) binary-matching algorithm called HEM, we propose an improved multi-pattern matching algorithm called MH that is based on hash tables and binary tables. The MH algorithm can be applied to the fields of network security, data analysis, load balancing, cloud robotic communications, and so on-all of which require string matching from a fixed starting position. Our approach effectively solves the performance problems of the classical multi-pattern matching algorithms. This paper explores ways to improve string matching performance under the HTTP protocol by using a hash method combined with a binary method that transforms the symbol-space matching problem into a digital-space numerical-size comparison and hashing problem. The MH approach has a fast matching speed, requires little memory, performs better than both the classical algorithms and HEM for matching fields in an HTTP stream, and it has great promise for use in real-world applications.
A multi-pattern hash-binary hybrid algorithm for URL matching in the HTTP protocol

PubMed Central

Tan, Qingping; Meng, Xiankai; Shao, Zeming; Xie, Qinzheng; Yan, Ying; Cao, Wei; Xu, Jianjun

2017-01-01

In this paper, based on our previous multi-pattern uniform resource locator (URL) binary-matching algorithm called HEM, we propose an improved multi-pattern matching algorithm called MH that is based on hash tables and binary tables. The MH algorithm can be applied to the fields of network security, data analysis, load balancing, cloud robotic communications, and so on—all of which require string matching from a fixed starting position. Our approach effectively solves the performance problems of the classical multi-pattern matching algorithms. This paper explores ways to improve string matching performance under the HTTP protocol by using a hash method combined with a binary method that transforms the symbol-space matching problem into a digital-space numerical-size comparison and hashing problem. The MH approach has a fast matching speed, requires little memory, performs better than both the classical algorithms and HEM for matching fields in an HTTP stream, and it has great promise for use in real-world applications. PMID:28399157
Microbatteries for Combinatorial Studies of Conventional Lithium-Ion Batteries

NASA Technical Reports Server (NTRS)

West, William; Whitacre, Jay; Bugga, Ratnakumar

2003-01-01

Integrated arrays of microscopic solid-state batteries have been demonstrated in a continuing effort to develop microscopic sources of power and of voltage reference circuits to be incorporated into low-power integrated circuits. Perhaps even more importantly, arrays of microscopic batteries can be fabricated and tested in combinatorial experiments directed toward optimization and discovery of battery materials. The value of the combinatorial approach to optimization and discovery has been proven in the optoelectronic, pharmaceutical, and bioengineering industries. Depending on the specific application, the combinatorial approach can involve the investigation of hundreds or even thousands of different combinations; hence, it is time-consuming and expensive to attempt to implement the combinatorial approach by building and testing full-size, discrete cells and batteries. The conception of microbattery arrays makes it practical to bring the advantages of the combinatorial approach to the development of batteries.
The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature.

PubMed

Özgür, Arzucan; Hur, Junguk; He, Yongqun

2016-01-01

The Interaction Network Ontology (INO) logically represents biological interactions, pathways, and networks. INO has been demonstrated to be valuable in providing a set of structured ontological terms and associated keywords to support literature mining of gene-gene interactions from biomedical literature. However, previous work using INO focused on single keyword matching, while many interactions are represented with two or more interaction keywords used in combination. This paper reports our extension of INO to include combinatory patterns of two or more literature mining keywords co-existing in one sentence to represent specific INO interaction classes. Such keyword combinations and related INO interaction type information could be automatically obtained via SPARQL queries, formatted in Excel format, and used in an INO-supported SciMiner, an in-house literature mining program. We studied the gene interaction sentences from the commonly used benchmark Learning Logic in Language (LLL) dataset and one internally generated vaccine-related dataset to identify and analyze interaction types containing multiple keywords. Patterns obtained from the dependency parse trees of the sentences were used to identify the interaction keywords that are related to each other and collectively represent an interaction type. The INO ontology currently has 575 terms including 202 terms under the interaction branch. The relations between the INO interaction types and associated keywords are represented using the INO annotation relations: 'has literature mining keywords' and 'has keyword dependency pattern'. The keyword dependency patterns were generated via running the Stanford Parser to obtain dependency relation types. Out of the 107 interactions in the LLL dataset represented with two-keyword interaction types, 86 were identified by using the direct dependency relations. The LLL dataset contained 34 gene regulation interaction types, each of which associated with multiple keywords. A hierarchical display of these 34 interaction types and their ancestor terms in INO resulted in the identification of specific gene-gene interaction patterns from the LLL dataset. The phenomenon of having multi-keyword interaction types was also frequently observed in the vaccine dataset. By modeling and representing multiple textual keywords for interaction types, the extended INO enabled the identification of complex biological gene-gene interactions represented with multiple keywords.
A Strategic Design of an Opto-Chemical Security Device with Resettable and Reconfigurable Password Based Upon Dual Channel Two-in-One Chemosensor Molecule.

PubMed

Majumdar, Tapas; Haldar, Basudeb; Mallick, Arabinda

2017-02-20

A simple strategy is proposed to design and develop an intelligent device based on dual channel ion responsive spectral properties of a commercially available molecule, harmine (HM). The system can process different sets of opto-chemical inputs generating different patterns as fluorescence outputs at specific wavelengths which can provide an additional level of protection exploiting both password and pattern recognitions. The proposed system could have the potential to come up with highly secured combinatorial locks at the molecular level that could pose valuable real time and on-site applications for user authentication.
A Strategic Design of an Opto-Chemical Security Device with Resettable and Reconfigurable Password Based Upon Dual Channel Two-in-One Chemosensor Molecule

NASA Astrophysics Data System (ADS)

Majumdar, Tapas; Haldar, Basudeb; Mallick, Arabinda

2017-02-01

A simple strategy is proposed to design and develop an intelligent device based on dual channel ion responsive spectral properties of a commercially available molecule, harmine (HM). The system can process different sets of opto-chemical inputs generating different patterns as fluorescence outputs at specific wavelengths which can provide an additional level of protection exploiting both password and pattern recognitions. The proposed system could have the potential to come up with highly secured combinatorial locks at the molecular level that could pose valuable real time and on-site applications for user authentication.
MIFT: GIFT Combinatorial Geometry Input to VCS Code

DTIC Science & Technology

1977-03-01

r-w w-^ H ^ß0318is CQ BRL °RCUMr REPORT NO. 1967 —-S: ... MIFT: GIFT COMBINATORIAL GEOMETRY INPUT TO VCS CODE Albert E...TITLE (and Subtitle) MIFT: GIFT Combinatorial Geometry Input to VCS Code S. TYPE OF REPORT & PERIOD COVERED FINAL 6. PERFORMING ORG. REPORT NUMBER...Vehicle Code System (VCS) called MORSE was modified to accept the GIFT combinatorial geometry package. GIFT , as opposed to the geometry package
Neural Meta-Memes Framework for Combinatorial Optimization

NASA Astrophysics Data System (ADS)

Song, Li Qin; Lim, Meng Hiot; Ong, Yew Soon

In this paper, we present a Neural Meta-Memes Framework (NMMF) for combinatorial optimization. NMMF is a framework which models basic optimization algorithms as memes and manages them dynamically when solving combinatorial problems. NMMF encompasses neural networks which serve as the overall planner/coordinator to balance the workload between memes. We show the efficacy of the proposed NMMF through empirical study on a class of combinatorial problem, the quadratic assignment problem (QAP).
Clothing Matching for Visually Impaired Persons

PubMed Central

Yuan, Shuai; Tian, YingLi; Arditi, Aries

2012-01-01

Matching clothes is a challenging task for many blind people. In this paper, we present a proof of concept system to solve this problem. The system consists of 1) a camera connected to a computer to perform pattern and color matching process; 2) speech commands for system control and configuration; and 3) audio feedback to provide matching results for both color and patterns of clothes. This system can handle clothes in deficient color without any pattern, as well as clothing with multiple colors and complex patterns to aid both blind and color deficient people. Furthermore, our method is robust to variations of illumination, clothing rotation and wrinkling. To evaluate the proposed prototype, we collect two challenging databases including clothes without any pattern, or with multiple colors and different patterns under different conditions of lighting and rotation. Results reported here demonstrate the robustness and effectiveness of the proposed clothing matching system. PMID:22523465
Clothing Matching for Visually Impaired Persons.

PubMed

Yuan, Shuai; Tian, Yingli; Arditi, Aries

2011-01-01

Matching clothes is a challenging task for many blind people. In this paper, we present a proof of concept system to solve this problem. The system consists of 1) a camera connected to a computer to perform pattern and color matching process; 2) speech commands for system control and configuration; and 3) audio feedback to provide matching results for both color and patterns of clothes. This system can handle clothes in deficient color without any pattern, as well as clothing with multiple colors and complex patterns to aid both blind and color deficient people. Furthermore, our method is robust to variations of illumination, clothing rotation and wrinkling. To evaluate the proposed prototype, we collect two challenging databases including clothes without any pattern, or with multiple colors and different patterns under different conditions of lighting and rotation. Results reported here demonstrate the robustness and effectiveness of the proposed clothing matching system.
A transcription factor network coordinates attraction, repulsion, and adhesion combinatorially to control motor axon pathway selection.

PubMed

Zarin, Aref Arzan; Asadzadeh, Jamshid; Hokamp, Karsten; McCartney, Daniel; Yang, Long; Bashaw, Greg J; Labrador, Juan-Pablo

2014-03-19

Combinations of transcription factors (TFs) instruct precise wiring patterns in the developing nervous system; however, how these factors impinge on surface molecules that control guidance decisions is poorly understood. Using mRNA profiling, we identified the complement of membrane molecules regulated by the homeobox TF Even-skipped (Eve), the major determinant of dorsal motor neuron (dMN) identity in Drosophila. Combinatorial loss- and gain-of-function genetic analyses of Eve target genes indicate that the integrated actions of attractive, repulsive, and adhesive molecules direct eve-dependent dMN axon guidance. Furthermore, combined misexpression of Eve target genes is sufficient to partially restore CNS exit and can convert the guidance behavior of interneurons to that of dMNs. Finally, we show that a network of TFs, comprised of eve, zfh1, and grain, induces the expression of the Unc5 and Beaten-path guidance receptors and the Fasciclin 2 and Neuroglian adhesion molecules to guide individual dMN axons. Copyright © 2014 Elsevier Inc. All rights reserved.
A Transcription Factor Network Coordinates Attraction, Repulsion, and Adhesion Combinatorially to Control Motor Axon Pathway Selection

PubMed Central

Zarin, Aref Arzan; Asadzadeh, Jamshid; Hokamp, Karsten; McCartney, Daniel; Yang, Long; Bashaw, Greg J.; Labrador, Juan-Pablo

2014-01-01

SUMMARY Combinations of transcription factors (TFs) instruct precise wiring patterns in the developing nervous system; however, how these factors impinge on surface molecules that control guidance decisions is poorly understood. Using mRNA profiling, we identified the complement of membrane molecules regulated by the homeobox TF Even-skipped (Eve), the major determinant of dorsal motor neuron (dMN) identity in Drosophila. Combinatorial loss- and gain-of-function genetic analyses of Eve target genes indicate that the integrated actions of attractive, repulsive, and adhesive molecules direct eve-dependent dMN axon guidance. Furthermore, combined misexpression of Eve target genes is sufficient to partially restore CNS exit and can convert the guidance behavior of interneurons to that of dMNs. Finally, we show that a network of TFs, comprised of eve, zfh1, and grain, induces the expression of the Unc5 and Beaten-path guidance receptors and the Fasciclin 2 and Neuroglian adhesion molecules to guide individual dMN axons. PMID:24560702
Structator: fast index-based search for RNA sequence-structure patterns

PubMed Central

2011-01-01

Background The secondary structure of RNA molecules is intimately related to their function and often more conserved than the sequence. Hence, the important task of searching databases for RNAs requires to match sequence-structure patterns. Unfortunately, current tools for this task have, in the best case, a running time that is only linear in the size of sequence databases. Furthermore, established index data structures for fast sequence matching, like suffix trees or arrays, cannot benefit from the complementarity constraints introduced by the secondary structure of RNAs. Results We present a novel method and readily applicable software for time efficient matching of RNA sequence-structure patterns in sequence databases. Our approach is based on affix arrays, a recently introduced index data structure, preprocessed from the target database. Affix arrays support bidirectional pattern search, which is required for efficiently handling the structural constraints of the pattern. Structural patterns like stem-loops can be matched inside out, such that the loop region is matched first and then the pairing bases on the boundaries are matched consecutively. This allows to exploit base pairing information for search space reduction and leads to an expected running time that is sublinear in the size of the sequence database. The incorporation of a new chaining approach in the search of RNA sequence-structure patterns enables the description of molecules folding into complex secondary structures with multiple ordered patterns. The chaining approach removes spurious matches from the set of intermediate results, in particular of patterns with little specificity. In benchmark experiments on the Rfam database, our method runs up to two orders of magnitude faster than previous methods. Conclusions The presented method's sublinear expected running time makes it well suited for RNA sequence-structure pattern matching in large sequence databases. RNA molecules containing several stem-loop substructures can be described by multiple sequence-structure patterns and their matches are efficiently handled by a novel chaining method. Beyond our algorithmic contributions, we provide with Structator a complete and robust open-source software solution for index-based search of RNA sequence-structure patterns. The Structator software is available at http://www.zbh.uni-hamburg.de/Structator. PMID:21619640
Rotation and scale change invariant point pattern relaxation matching by the Hopfield neural network

NASA Astrophysics Data System (ADS)

Sang, Nong; Zhang, Tianxu

1997-12-01

Relaxation matching is one of the most relevant methods for image matching. The original relaxation matching technique using point patterns is sensitive to rotations and scale changes. We improve the original point pattern relaxation matching technique to be invariant to rotations and scale changes. A method that makes the Hopfield neural network perform this matching process is discussed. An advantage of this is that the relaxation matching process can be performed in real time with the neural network's massively parallel capability to process information. Experimental results with large simulated images demonstrate the effectiveness and feasibility of the method to perform point patten relaxation matching invariant to rotations and scale changes and the method to perform this matching by the Hopfield neural network. In addition, we show that the method presented can be tolerant to small random error.
Combinatorial Labeling Method for Improving Peptide Fragmentation in Mass Spectrometry

NASA Astrophysics Data System (ADS)

Kuchibhotla, Bhanuramanand; Kola, Sankara Rao; Medicherla, Jagannadham V.; Cherukuvada, Swamy V.; Dhople, Vishnu M.; Nalam, Madhusudhana Rao

2017-06-01

Annotation of peptide sequence from tandem mass spectra constitutes the central step of mass spectrometry-based proteomics. Peptide mass spectra are obtained upon gas-phase fragmentation. Identification of the protein from a set of experimental peptide spectral matches is usually referred as protein inference. Occurrence and intensity of these fragment ions in the MS/MS spectra are dependent on many factors such as amino acid composition, peptide basicity, activation mode, protease, etc. Particularly, chemical derivatizations of peptides were known to alter their fragmentation. In this study, the influence of acetylation, guanidinylation, and their combination on peptide fragmentation was assessed initially on a lipase (LipA) from Bacillus subtilis followed by a bovine six protein mix digest. The dual modification resulted in improved fragment ion occurrence and intensity changes, and this resulted in the equivalent representation of b- and y-type fragment ions in an ion trap MS/MS spectrum. The improved representation has allowed us to accurately annotate the peptide sequences de novo. Dual labeling has significantly reduced the false positive protein identifications in standard bovine six peptide digest. Our study suggests that the combinatorial labeling of peptides is a useful method to validate protein identifications for high confidence protein inference. [Figure not available: see fulltext.

Tailoring gas sensor arrays via the design of short peptides sequences as binding elements.

PubMed

Mascini, Marcello; Pizzoni, Daniel; Perez, German; Chiarappa, Emilio; Di Natale, Corrado; Pittia, Paola; Compagnone, Dario

2017-07-15

A semi-combinatorial virtual approach was used to prepare peptide-based gas sensors with binding properties towards five different chemical classes (alcohols, aldehydes, esters, hydrocarbons and ketones). Molecular docking simulations were conducted for a complete tripeptide library (8000 elements) versus 58 volatile compounds belonging to those five chemical classes. By maximizing the differences between chemical classes, a subset of 120 tripeptides was extracted and used as scaffolds for generating a combinatorial library of 7912 tetrapeptides. This library was processed in an analogous way to the former. Five tetrapeptides (IHRI, KSDS, LGFD, TGKF and WHVS) were chosen depending on their virtual affinity and cross-reactivity for the experimental step. The five peptides were covalently bound to gold nanoparticles by adding a terminal cysteine to each tetrapeptide and deposited onto 20MHz quartz crystal microbalances to construct the gas sensors. The behavior of peptides after this chemical modification was simulated at the pH range used in the immobilization step. ΔF signals analyzed by principal component analysis matched the virtually screened data. The array was able to clearly discriminate the 13 volatile compounds tested based on their hydrophobicity and hydrophilicity molecules as well as the molecular weight. Copyright © 2016 Elsevier B.V. All rights reserved.
FOREWORD: Focus on Combinatorial Materials Science Focus on Combinatorial Materials Science

NASA Astrophysics Data System (ADS)

Chikyo, Toyohiro

2011-10-01

About 15 years have passed since the introduction of modern combinatorial synthesis and high-throughput techniques for the development of novel inorganic materials; however, similar methods existed before. The most famous was reported in 1970 by Hanak who prepared composition-spread films of metal alloys by sputtering mixed-material targets. Although this method was innovative, it was rarely used because of the large amount of data to be processed. This problem is solved in the modern combinatorial material research, which is strongly related to computer data analysis and robotics. This field is still at the developing stage and may be enriched by new methods. Nevertheless, given the progress in measurement equipment and procedures, we believe the combinatorial approach will become a major and standard tool of materials screening and development. The first article of this journal, published in 2000, was titled 'Combinatorial solid state materials science and technology', and this focus issue aims to reintroduce this topic to the Science and Technology of Advanced Materials audience. It covers recent progress in combinatorial materials research describing new results in catalysis, phosphors, polymers and metal alloys for shape memory materials. Sophisticated high-throughput characterization schemes and innovative synthesis tools are also presented, such as spray deposition using nanoparticles or ion plating. On a technical note, data handling systems are introduced to familiarize researchers with the combinatorial methodology. We hope that through this focus issue a wide audience of materials scientists can learn about recent and future trends in combinatorial materials science and high-throughput experimentation.
Estimating meme fitness in adaptive memetic algorithms for combinatorial problems.

PubMed

Smith, J E

2012-01-01

Among the most promising and active research areas in heuristic optimisation is the field of adaptive memetic algorithms (AMAs). These gain much of their reported robustness by adapting the probability with which each of a set of local improvement operators is applied, according to an estimate of their current value to the search process. This paper addresses the issue of how the current value should be estimated. Assuming the estimate occurs over several applications of a meme, we consider whether the extreme or mean improvements should be used, and whether this aggregation should be global, or local to some part of the solution space. To investigate these issues, we use the well-established COMA framework that coevolves the specification of a population of memes (representing different local search algorithms) alongside a population of candidate solutions to the problem at hand. Two very different memetic algorithms are considered: the first using adaptive operator pursuit to adjust the probabilities of applying a fixed set of memes, and a second which applies genetic operators to dynamically adapt and create memes and their functional definitions. For the latter, especially on combinatorial problems, credit assignment mechanisms based on historical records, or on notions of landscape locality, will have limited application, and it is necessary to estimate the value of a meme via some form of sampling. The results on a set of binary encoded combinatorial problems show that both methods are very effective, and that for some problems it is necessary to use thousands of variables in order to tease apart the differences between different reward schemes. However, for both memetic algorithms, a significant pattern emerges that reward based on mean improvement is better than that based on extreme improvement. This contradicts recent findings from adapting the parameters of operators involved in global evolutionary search. The results also show that local reward schemes outperform global reward schemes in combinatorial spaces, unlike in continuous spaces. An analysis of evolving meme behaviour is used to explain these findings.
Evaluation of the Optimum Composition of Low-Temperature Fuel Cell Electrocatalysts for Methanol Oxidation by Combinatorial Screening.

PubMed

Antolini, Ermete

2017-02-13

Combinatorial chemistry and high-throughput screening represent an innovative and rapid tool to prepare and evaluate a large number of new materials, saving time and expense for research and development. Considering that the activity and selectivity of catalysts depend on complex kinetic phenomena, making their development largely empirical in practice, they are prime candidates for combinatorial discovery and optimization. This review presents an overview of recent results of combinatorial screening of low-temperature fuel cell electrocatalysts for methanol oxidation. Optimum catalyst compositions obtained by combinatorial screening were compared with those of bulk catalysts, and the effect of the library geometry on the screening of catalyst composition is highlighted.
Combinatorial Nano-Bio Interfaces.

PubMed

Cai, Pingqiang; Zhang, Xiaoqian; Wang, Ming; Wu, Yun-Long; Chen, Xiaodong

2018-06-08

Nano-bio interfaces are emerging from the convergence of engineered nanomaterials and biological entities. Despite rapid growth, clinical translation of biomedical nanomaterials is heavily compromised by the lack of comprehensive understanding of biophysicochemical interactions at nano-bio interfaces. In the past decade, a few investigations have adopted a combinatorial approach toward decoding nano-bio interfaces. Combinatorial nano-bio interfaces comprise the design of nanocombinatorial libraries and high-throughput bioevaluation. In this Perspective, we address challenges in combinatorial nano-bio interfaces and call for multiparametric nanocombinatorics (composition, morphology, mechanics, surface chemistry), multiscale bioevaluation (biomolecules, organelles, cells, tissues/organs), and the recruitment of computational modeling and artificial intelligence. Leveraging combinatorial nano-bio interfaces will shed light on precision nanomedicine and its potential applications.
Combinatorial computational chemistry approach for materials design: applications in deNOx catalysis, Fischer-Tropsch synthesis, lanthanoid complex, and lithium ion secondary battery.

PubMed

Koyama, Michihisa; Tsuboi, Hideyuki; Endou, Akira; Takaba, Hiromitsu; Kubo, Momoji; Del Carpio, Carlos A; Miyamoto, Akira

2007-02-01

Computational chemistry can provide fundamental knowledge regarding various aspects of materials. While its impact in scientific research is greatly increasing, its contributions to industrially important issues are far from satisfactory. In order to realize industrial innovation by computational chemistry, a new concept "combinatorial computational chemistry" has been proposed by introducing the concept of combinatorial chemistry to computational chemistry. This combinatorial computational chemistry approach enables theoretical high-throughput screening for materials design. In this manuscript, we review the successful applications of combinatorial computational chemistry to deNO(x) catalysts, Fischer-Tropsch catalysts, lanthanoid complex catalysts, and cathodes of the lithium ion secondary battery.
Dynamic pattern matcher using incomplete data

NASA Technical Reports Server (NTRS)

Johnson, Gordon G. (Inventor); Wang, Lui (Inventor)

1993-01-01

This invention relates generally to pattern matching systems, and more particularly to a method for dynamically adapting the system to enhance the effectiveness of a pattern match. Apparatus and methods for calculating the similarity between patterns are known. There is considerable interest, however, in the storage and retrieval of data, particularly, when the search is called or initiated by incomplete information. For many search algorithms, a query initiating a data search requires exact information, and the data file is searched for an exact match. Inability to find an exact match thus results in a failure of the system or method.
Optimization of self-aligned double patterning (SADP)-compliant layout designs using pattern matching for sub-20nm metal routing

NASA Astrophysics Data System (ADS)

Wang, Lynn T.-N.; Schroeder, Uwe Paul; Madhavan, Sriram

2017-03-01

A pattern-based methodology for optimizing SADP-compliant layout designs is developed based on identifying cut mask patterns and replacing them with pre-characterized fixing solutions. A pattern-based library of difficult-tomanufacture cut patterns with pre-characterized fixing solutions is built. A pattern-based engine searches for matching patterns in the decomposed layouts. When a match is found, the engine opportunistically replaces the detected pattern with a pre-characterized fixing solution. The methodology was demonstrated on a 7nm routed metal2 block. A small library of 30 cut patterns increased the number of more manufacturable cuts by 38% and metal-via enclosure by 13% with a small parasitic capacitance impact of 0.3%.
Chemoinformatic Analysis of Combinatorial Libraries, Drugs, Natural Products and Molecular Libraries Small Molecule Repository

PubMed Central

Singh, Narender; Guha, Rajarshi; Giulianotti, Marc; Pinilla, Clemencia; Houghten, Richard; Medina-Franco, Jose L.

2009-01-01

A multiple criteria approach is presented, that is used to perform a comparative analysis of four recently developed combinatorial libraries to drugs, Molecular Libraries Small Molecule Repository (MLSMR) and natural products. The compound databases were assessed in terms of physicochemical properties, scaffolds and fingerprints. The approach enables the analysis of property space coverage, degree of overlap between collections, scaffold and structural diversity and overall structural novelty. The degree of overlap between combinatorial libraries and drugs was assessed using the R-NN curve methodology, which measures the density of chemical space around a query molecule embedded in the chemical space of a target collection. The combinatorial libraries studied in this work exhibit scaffolds that were not observed in the drug, MLSMR and natural products collections. The fingerprint-based comparisons indicate that these combinatorial libraries are structurally different to current drugs. The R-NN curve methodology revealed that a proportion of molecules in the combinatorial libraries are located within the property space of the drugs. However, the R-NN analysis also showed that there are a significant number of molecules in several combinatorial libraries that are located in sparse regions of the drug space. PMID:19301827
Smooth Constrained Heuristic Optimization of a Combinatorial Chemical Space

DTIC Science & Technology

2015-05-01

ARL-TR-7294•MAY 2015 US Army Research Laboratory Smooth ConstrainedHeuristic Optimization of a Combinatorial Chemical Space by Berend Christopher...7294•MAY 2015 US Army Research Laboratory Smooth ConstrainedHeuristic Optimization of a Combinatorial Chemical Space by Berend Christopher...
Preparation of cherry-picked combinatorial libraries by string synthesis.

PubMed

Furka, Arpád; Dibó, Gábor; Gombosuren, Naran

2005-03-01

String synthesis [1-3] is an efficient and cheap manual method for preparation of combinatorial libraries by using macroscopic solid support units. Sorting the units between two synthetic steps is an important operation of the procedure. The software developed to guide sorting can be used only when complete combinatorial libraries are prepared. Since very often only selected components of the full libraries are needed, new software was constructed that guides sorting in preparation of non-complete combinatorial libraries. Application of the software is described in details.
Betting on Illusory Patterns: Probability Matching in Habitual Gamblers.

PubMed

Gaissmaier, Wolfgang; Wilke, Andreas; Scheibehenne, Benjamin; McCanney, Paige; Barrett, H Clark

2016-03-01

Why do people gamble? A large body of research suggests that cognitive distortions play an important role in pathological gambling. Many of these distortions are specific cases of a more general misperception of randomness, specifically of an illusory perception of patterns in random sequences. In this article, we provide further evidence for the assumption that gamblers are particularly prone to perceiving illusory patterns. In particular, we compared habitual gamblers to a matched sample of community members with regard to how much they exhibit the choice anomaly 'probability matching'. Probability matching describes the tendency to match response proportions to outcome probabilities when predicting binary outcomes. It leads to a lower expected accuracy than the maximizing strategy of predicting the most likely event on each trial. Previous research has shown that an illusory perception of patterns in random sequences fuels probability matching. So does impulsivity, which is also reported to be higher in gamblers. We therefore hypothesized that gamblers will exhibit more probability matching than non-gamblers, which was confirmed in a controlled laboratory experiment. Additionally, gamblers scored much lower than community members on the cognitive reflection task, which indicates higher impulsivity. This difference could account for the difference in probability matching between the samples. These results suggest that gamblers are more willing to bet impulsively on perceived illusory patterns.
Validation of an Instrument and Testing Protocol for Measuring the Combinatorial Analysis Schema.

ERIC Educational Resources Information Center

Staver, John R.; Harty, Harold

1979-01-01

Designs a testing situation to examine the presence of combinatorial analysis, to establish construct validity in the use of an instrument, Combinatorial Analysis Behavior Observation Scheme (CABOS), and to investigate the presence of the schema in young adolescents. (Author/GA)
Optimizing Muscle Parameters in Musculoskeletal Modeling Using Monte Carlo Simulations

NASA Technical Reports Server (NTRS)

Hanson, Andrea; Reed, Erik; Cavanagh, Peter

2011-01-01

Astronauts assigned to long-duration missions experience bone and muscle atrophy in the lower limbs. The use of musculoskeletal simulation software has become a useful tool for modeling joint and muscle forces during human activity in reduced gravity as access to direct experimentation is limited. Knowledge of muscle and joint loads can better inform the design of exercise protocols and exercise countermeasure equipment. In this study, the LifeModeler(TM) (San Clemente, CA) biomechanics simulation software was used to model a squat exercise. The initial model using default parameters yielded physiologically reasonable hip-joint forces. However, no activation was predicted in some large muscles such as rectus femoris, which have been shown to be active in 1-g performance of the activity. Parametric testing was conducted using Monte Carlo methods and combinatorial reduction to find a muscle parameter set that more closely matched physiologically observed activation patterns during the squat exercise. Peak hip joint force using the default parameters was 2.96 times body weight (BW) and increased to 3.21 BW in an optimized, feature-selected test case. The rectus femoris was predicted to peak at 60.1% activation following muscle recruitment optimization, compared to 19.2% activation with default parameters. These results indicate the critical role that muscle parameters play in joint force estimation and the need for exploration of the solution space to achieve physiologically realistic muscle activation.
Bifurcation-based approach reveals synergism and optimal combinatorial perturbation.

PubMed

Liu, Yanwei; Li, Shanshan; Liu, Zengrong; Wang, Ruiqi

2016-06-01

Cells accomplish the process of fate decisions and form terminal lineages through a series of binary choices in which cells switch stable states from one branch to another as the interacting strengths of regulatory factors continuously vary. Various combinatorial effects may occur because almost all regulatory processes are managed in a combinatorial fashion. Combinatorial regulation is crucial for cell fate decisions because it may effectively integrate many different signaling pathways to meet the higher regulation demand during cell development. However, whether the contribution of combinatorial regulation to the state transition is better than that of a single one and if so, what the optimal combination strategy is, seem to be significant issue from the point of view of both biology and mathematics. Using the approaches of combinatorial perturbations and bifurcation analysis, we provide a general framework for the quantitative analysis of synergism in molecular networks. Different from the known methods, the bifurcation-based approach depends only on stable state responses to stimuli because the state transition induced by combinatorial perturbations occurs between stable states. More importantly, an optimal combinatorial perturbation strategy can be determined by investigating the relationship between the bifurcation curve of a synergistic perturbation pair and the level set of a specific objective function. The approach is applied to two models, i.e., a theoretical multistable decision model and a biologically realistic CREB model, to show its validity, although the approach holds for a general class of biological systems.
Combinatorial enzyme technology for the conversion of agricultural fibers to functional properties

USDA-ARS?s Scientific Manuscript database

The concept of combinatorial chemistry has received little attention in agriculture and food research, although its applications in this area were described more than fifteen years ago (1, 2). More recently, interest in the use of combinatorial chemistry in agrochemical discovery has been revitalize...
An Investigation into Post-Secondary Students' Understanding of Combinatorial Questions

ERIC Educational Resources Information Center

Bulone, Vincent William

2017-01-01

The purpose of this dissertation was to study aspects of how post-secondary students understand combinatorial problems. Within this dissertation, I considered understanding through two different lenses: i) student connections to previous problems; and ii) common combinatorial distinctions such as ordered versus unordered and repetitive versus…
VRPD Novel Combinatory Approaches to Repair Visual System After Optic Nerve Damage

DTIC Science & Technology

2015-05-01

At 4 and 8 weeks after injury, retinas were immunostained with an antibody against beta III tubulin (TUJ1) to estimate RGC survival. The degree of...Optic chiasm presentation of Semaphorin6D in the context of Plexin-A1 and Nr- CAM promotes retinal axon midline crossing. Neuron 74, 676–690. Leaver...for Nr- CAM in the patterning of binocular visual pathways. Neuron 50, 535–547. Williams, S.E., Mann, F., Erskine, L., Sakurai, T., Wei, S., Rossi, D.J
Efficient feature subset selection with probabilistic distance criteria. [pattern recognition

NASA Technical Reports Server (NTRS)

Chittineni, C. B.

1979-01-01

Recursive expressions are derived for efficiently computing the commonly used probabilistic distance measures as a change in the criteria both when a feature is added to and when a feature is deleted from the current feature subset. A combinatorial algorithm for generating all possible r feature combinations from a given set of s features in (s/r) steps with a change of a single feature at each step is presented. These expressions can also be used for both forward and backward sequential feature selection.
Fan fault diagnosis based on symmetrized dot pattern analysis and image matching

NASA Astrophysics Data System (ADS)

Xu, Xiaogang; Liu, Haixiao; Zhu, Hao; Wang, Songling

2016-07-01

To detect the mechanical failure of fans, a new diagnostic method based on the symmetrized dot pattern (SDP) analysis and image matching is proposed. Vibration signals of 13 kinds of running states are acquired on a centrifugal fan test bed and reconstructed by the SDP technique. The SDP pattern templates of each running state are established. An image matching method is performed to diagnose the fault. In order to improve the diagnostic accuracy, the single template, multiple templates and clustering fault templates are used to perform the image matching.

Combinatorial effects on clumped isotopes and their significance in biogeochemistry

NASA Astrophysics Data System (ADS)

Yeung, Laurence Y.

2016-01-01

The arrangement of isotopes within a collection of molecules records their physical and chemical histories. Clumped-isotope analysis interrogates these arrangements, i.e., how often rare isotopes are bound together, which in many cases can be explained by equilibrium and/or kinetic isotope fractionation. However, purely combinatorial effects, rooted in the statistics of pairing atoms in a closed system, are also relevant, and not well understood. Here, I show that combinatorial isotope effects are most important when two identical atoms are neighbors on the same molecule (e.g., O2, N2, and D-D clumping in CH4). When the two halves of an atom pair are either assembled with different isotopic preferences or drawn from different reservoirs, combinatorial effects cause depletions in clumped-isotope abundance that are most likely between zero and -1‰, although they could potentially be -10‰ or larger for D-D pairs. These depletions are of similar magnitude, but of opposite sign, to low-temperature equilibrium clumped-isotope effects for many small molecules. Enzymatic isotope-pairing reactions, which can have site-specific isotopic fractionation factors and atom reservoirs, should express this class of combinatorial isotope effect, although it is not limited to biological reactions. Chemical-kinetic isotope effects, which are related to a bond-forming transition state, arise independently and express second-order combinatorial effects related to the abundance of the rare isotope. Heteronuclear moeties (e.g., Csbnd O and Csbnd H), are insensitive to direct combinatorial influences, but secondary combinatorial influences are evident. In general, both combinatorial and chemical-kinetic factors are important for calculating and interpreting clumped-isotope signatures of kinetically controlled reactions. I apply this analytical framework to isotope-pairing reactions relevant to geochemical oxygen, carbon, and nitrogen cycling that may be influenced by combinatorial clumped-isotope effects. These isotopic signatures, manifest as either directly bound isotope ;clumps; or as features of a molecule's isotopic anatomy, are linked to molecular mechanisms and may eventually provide additional information about biogeochemical cycling on environmentally relevant spatial scales.
COPS: Detecting Co-Occurrence and Spatial Arrangement of Transcription Factor Binding Motifs in Genome-Wide Datasets

PubMed Central

Lohmann, Ingrid

2012-01-01

In multi-cellular organisms, spatiotemporal activity of cis-regulatory DNA elements depends on their occupancy by different transcription factors (TFs). In recent years, genome-wide ChIP-on-Chip, ChIP-Seq and DamID assays have been extensively used to unravel the combinatorial interaction of TFs with cis-regulatory modules (CRMs) in the genome. Even though genome-wide binding profiles are increasingly becoming available for different TFs, single TF binding profiles are in most cases not sufficient for dissecting complex regulatory networks. Thus, potent computational tools detecting statistically significant and biologically relevant TF-motif co-occurrences in genome-wide datasets are essential for analyzing context-dependent transcriptional regulation. We have developed COPS (Co-Occurrence Pattern Search), a new bioinformatics tool based on a combination of association rules and Markov chain models, which detects co-occurring TF binding sites (BSs) on genomic regions of interest. COPS scans DNA sequences for frequent motif patterns using a Frequent-Pattern tree based data mining approach, which allows efficient performance of the software with respect to both data structure and implementation speed, in particular when mining large datasets. Since transcriptional gene regulation very often relies on the formation of regulatory protein complexes mediated by closely adjoining TF binding sites on CRMs, COPS additionally detects preferred short distance between co-occurring TF motifs. The performance of our software with respect to biological significance was evaluated using three published datasets containing genomic regions that are independently bound by several TFs involved in a defined biological process. In sum, COPS is a fast, efficient and user-friendly tool mining statistically and biologically significant TFBS co-occurrences and therefore allows the identification of TFs that combinatorially regulate gene expression. PMID:23272209
Growth of Ca{sub 2}MnO{sub 4} Ruddlesden-Popper structured thin films using combinatorial substrate epitaxy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lacotte, M.; David, A.; Pravarthana, D.

2014-12-28

The local epitaxial growth of pulsed laser deposited Ca{sub 2}MnO{sub 4} films on polycrystalline spark plasma sintered Sr{sub 2}TiO{sub 4} substrates was investigated to determine phase formation and preferred epitaxial orientation relationships (ORs) for isostructural Ruddlesden-Popper (RP) heteroepitaxy, further developing the high-throughput synthetic approach called Combinatorial Substrate Epitaxy (CSE). Both grazing incidence X-ray diffraction and electron backscatter diffraction patterns of the film and substrate were indexable as single-phase RP-structured compounds. The optimal growth temperature (between 650 °C and 800 °C) was found to be 750 °C using the maximum value of the average image quality of the backscattered diffraction patterns. Films grew inmore » a grain-over-grain pattern such that each Ca{sub 2}MnO{sub 4} grain had a single OR with the Sr{sub 2}TiO{sub 4} grain on which it grew. Three primary ORs described 47 out of 49 grain pairs that covered nearly all of RP orientation space. The first OR, found for 20 of the 49, was the expected RP unit-cell over RP unit-cell OR, expressed as [100][001]{sub film}||[100][001]{sub sub}. The other two ORs were essentially rotated from the first by 90°, with one (observed for 17 of 49 pairs) being rotated about the [100] and the other (observed for 10 of 49 pairs) being rotated about the [110] (and not exactly by 90°). These results indicate that only a small number of ORs are needed to describe isostructural RP heteroepitaxy and further demonstrate the potential of CSE in the design and growth of a wide range of complex functional oxides.« less
Hyperspectral imaging of cuttlefish camouflage indicates good color match in the eyes of fish predators.

PubMed

Chiao, Chuan-Chin; Wickiser, J Kenneth; Allen, Justine J; Genter, Brock; Hanlon, Roger T

2011-05-31

Camouflage is a widespread phenomenon throughout nature and an important antipredator tactic in natural selection. Many visual predators have keen color perception, and thus camouflage patterns should provide some degree of color matching in addition to other visual factors such as pattern, contrast, and texture. Quantifying camouflage effectiveness in the eyes of the predator is a challenge from the perspectives of both biology and optical imaging technology. Here we take advantage of hyperspectral imaging (HSI), which records full-spectrum light data, to simultaneously visualize color match and pattern match in the spectral and the spatial domains, respectively. Cuttlefish can dynamically camouflage themselves on any natural substrate and, despite their colorblindness, produce body patterns that appear to have high-fidelity color matches to the substrate when viewed directly by humans or with RGB images. Live camouflaged cuttlefish on natural backgrounds were imaged using HSI, and subsequent spectral analysis revealed that most reflectance spectra of individual cuttlefish and substrates were similar, rendering the color match possible. Modeling color vision of potential di- and trichromatic fish predators of cuttlefish corroborated the spectral match analysis and demonstrated that camouflaged cuttlefish show good color match as well as pattern match in the eyes of fish predators. These findings (i) indicate the strong potential of HSI technology to enhance studies of biological coloration and (ii) provide supporting evidence that cuttlefish can produce color-coordinated camouflage on natural substrates despite lacking color vision.
Context-Sensitive Grammar Transform: Compression and Pattern Matching

NASA Astrophysics Data System (ADS)

Maruyama, Shirou; Tanaka, Youhei; Sakamoto, Hiroshi; Takeda, Masayuki

A framework of context-sensitive grammar transform for speeding-up compressed pattern matching (CPM) is proposed. A greedy compression algorithm with the transform model is presented as well as a Knuth-Morris-Pratt (KMP)-type compressed pattern matching algorithm. The compression ratio is a match for gzip and Re-Pair, and the search speed of our CPM algorithm is almost twice faster than the KMP-type CPM algorithm on Byte-Pair-Encoding by Shibata et al.[18], and in the case of short patterns, faster than the Boyer-Moore-Horspool algorithm with the stopper encoding by Rautio et al.[14], which is regarded as one of the best combinations that allows a practically fast search.
The construction of combinatorial manifolds with prescribed sets of links of vertices

NASA Astrophysics Data System (ADS)

Gaifullin, A. A.

2008-10-01

To every oriented closed combinatorial manifold we assign the set (with repetitions) of isomorphism classes of links of its vertices. The resulting transformation \\mathcal{L} is the main object of study in this paper. We pose an inversion problem for \\mathcal{L} and show that this problem is closely related to Steenrod's problem on the realization of cycles and to the Rokhlin-Schwartz-Thom construction of combinatorial Pontryagin classes. We obtain a necessary condition for a set of isomorphism classes of combinatorial spheres to belong to the image of \\mathcal{L}. (Sets satisfying this condition are said to be balanced.) We give an explicit construction showing that every balanced set of isomorphism classes of combinatorial spheres falls into the image of \\mathcal{L} after passing to a multiple set and adding several pairs of the form (Z,-Z), where -Z is the sphere Z with the orientation reversed. Given any singular simplicial cycle \\xi of a space X, this construction enables us to find explicitly a combinatorial manifold M and a map \\varphi\\colon M\\to X such that \\varphi_* \\lbrack M \\rbrack =r[\\xi] for some positive integer r. The construction is based on resolving singularities of \\xi. We give applications of the main construction to cobordisms of manifolds with singularities and cobordisms of simple cells. In particular, we prove that every rational additive invariant of cobordisms of manifolds with singularities admits a local formula. Another application is the construction of explicit (though inefficient) local combinatorial formulae for polynomials in the rational Pontryagin classes of combinatorial manifolds.
Training and Transfer in Combinatorial Problem Solving: The Development of Formal Reasoning During Early Adolescence

ERIC Educational Resources Information Center

Barratt, Barnaby B.

1975-01-01

This study investigated the emergence of combinatorial competence in early adolescence and the effectiveness of a programmed discovery training procedure. Significant increases in combinatorial skill with age were shown; it was found that the expression of this skill was significantly facilitated if problems involved concrete material of low…
Invention as a combinatorial process: evidence from US patents

PubMed Central

Youn, Hyejin; Strumsky, Deborah; Bettencourt, Luis M. A.; Lobo, José

2015-01-01

Invention has been commonly conceptualized as a search over a space of combinatorial possibilities. Despite the existence of a rich literature, spanning a variety of disciplines, elaborating on the recombinant nature of invention, we lack a formal and quantitative characterization of the combinatorial process underpinning inventive activity. Here, we use US patent records dating from 1790 to 2010 to formally characterize invention as a combinatorial process. To do this, we treat patented inventions as carriers of technologies and avail ourselves of the elaborate system of technology codes used by the United States Patent and Trademark Office to classify the technologies responsible for an invention's novelty. We find that the combinatorial inventive process exhibits an invariant rate of ‘exploitation’ (refinements of existing combinations of technologies) and ‘exploration’ (the development of new technological combinations). This combinatorial dynamic contrasts sharply with the creation of new technological capabilities—the building blocks to be combined—that has significantly slowed down. We also find that, notwithstanding the very reduced rate at which new technologies are introduced, the generation of novel technological combinations engenders a practically infinite space of technological configurations. PMID:25904530
Combinatorial application of two aldehyde oxidoreductases on isobutanol production in the presence of furfural.

PubMed

Seo, Hyung-Min; Jeon, Jong-Min; Lee, Ju Hee; Song, Hun-Suk; Joo, Han-Byul; Park, Sung-Hee; Choi, Kwon-Young; Kim, Yong Hyun; Park, Kyungmoon; Ahn, Jungoh; Lee, Hongweon; Yang, Yung-Hun

2016-01-01

Furfural is a toxic by-product formulated from pretreatment processes of lignocellulosic biomass. In order to utilize the lignocellulosic biomass on isobutanol production, inhibitory effect of the furfural on isobutanol production was investigated and combinatorial application of two oxidoreductases, FucO and YqhD, was suggested as an alternative strategy. Furfural decreased cell growth and isobutanol production when only YqhD or FucO was employed as an isobutyraldehyde oxidoreductase. However, combinatorial overexpression of FucO and YqhD could overcome the inhibitory effect of furfural giving higher isobutanol production by 110% compared with overexpression of YqhD. The combinatorial oxidoreductases increased furfural detoxification rate 2.1-fold and also accelerated glucose consumption 1.4-fold. When it compares to another known system increasing furfural tolerance, membrane-bound transhydrogenase (pntAB), the combinatorial aldehyde oxidoreductases were better on cell growth and production. Thus, to control oxidoreductases is important to produce isobutanol using furfural-containing biomass and the combinatorial overexpression of FucO and YqhD can be an alternative strategy.
Combinatorial Methods for Exploring Complex Materials

NASA Astrophysics Data System (ADS)

Amis, Eric J.

2004-03-01

Combinatorial and high-throughput methods have changed the paradigm of pharmaceutical synthesis and have begun to have a similar impact on materials science research. Already there are examples of combinatorial methods used for inorganic materials, catalysts, and polymer synthesis. For many investigations the primary goal has been discovery of new material compositions that optimize properties such as phosphorescence or catalytic activity. In the midst of the excitement generated to "make things", another opportunity arises for materials science to "understand things" by using the efficiency of combinatorial methods. We have shown that combinatorial methods hold potential for rapid and systematic generation of experimental data over the multi-parameter space typical of investigations in polymer physics. We have applied the combinatorial approach to studies of polymer thin films, biomaterials, polymer blends, filled polymers, and semicrystalline polymers. By combining library fabrication, high-throughput measurements, informatics, and modeling we can demonstrate validation of the methodology, new observations, and developments toward predictive models. This talk will present some of our latest work with applications to coating stability, multi-component formulations, and nanostructure assembly.
Tumor-targeting peptides from combinatorial libraries*

PubMed Central

Liu, Ruiwu; Li, Xiaocen; Xiao, Wenwu; Lam, Kit S.

2018-01-01

Cancer is one of the major and leading causes of death worldwide. Two of the greatest challenges infighting cancer are early detection and effective treatments with no or minimum side effects. Widespread use of targeted therapies and molecular imaging in clinics requires high affinity, tumor-specific agents as effective targeting vehicles to deliver therapeutics and imaging probes to the primary or metastatic tumor sites. Combinatorial libraries such as phage-display and one-bead one-compound (OBOC) peptide libraries are powerful approaches in discovering tumor-targeting peptides. This review gives an overview of different combinatorial library technologies that have been used for the discovery of tumor-targeting peptides. Examples of tumor-targeting peptides identified from each combinatorial library method will be discussed. Published tumor-targeting peptide ligands and their applications will also be summarized by the combinatorial library methods and their corresponding binding receptors. PMID:27210583
Identification of combinatorial drug regimens for treatment of Huntington's disease using Drosophila

NASA Astrophysics Data System (ADS)

Agrawal, Namita; Pallos, Judit; Slepko, Natalia; Apostol, Barbara L.; Bodai, Laszlo; Chang, Ling-Wen; Chiang, Ann-Shyn; Michels Thompson, Leslie; Marsh, J. Lawrence

2005-03-01

We explore the hypothesis that pathology of Huntington's disease involves multiple cellular mechanisms whose contributions to disease are incrementally additive or synergistic. We provide evidence that the photoreceptor neuron degeneration seen in flies expressing mutant human huntingtin correlates with widespread degenerative events in the Drosophila CNS. We use a Drosophila Huntington's disease model to establish dose regimens and protocols to assess the effectiveness of drug combinations used at low threshold concentrations. These proof of principle studies identify at least two potential combinatorial treatment options and illustrate a rapid and cost-effective paradigm for testing and optimizing combinatorial drug therapies while reducing side effects for patients with neurodegenerative disease. The potential for using prescreening in Drosophila to inform combinatorial therapies that are most likely to be effective for testing in mammals is discussed. combinatorial treatments | neurodegeneration
Nonparametric Combinatorial Sequence Models

NASA Astrophysics Data System (ADS)

Wauthier, Fabian L.; Jordan, Michael I.; Jojic, Nebojsa

This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This paper presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three sequence datasets which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution induced by the prior. By integrating out the posterior our method compares favorably to leading binding predictors.
Dynamic combinatorial libraries: from exploring molecular recognition to systems chemistry.

PubMed

Li, Jianwei; Nowak, Piotr; Otto, Sijbren

2013-06-26

Dynamic combinatorial chemistry (DCC) is a subset of combinatorial chemistry where the library members interconvert continuously by exchanging building blocks with each other. Dynamic combinatorial libraries (DCLs) are powerful tools for discovering the unexpected and have given rise to many fascinating molecules, ranging from interlocked structures to self-replicators. Furthermore, dynamic combinatorial molecular networks can produce emergent properties at systems level, which provide exciting new opportunities in systems chemistry. In this perspective we will highlight some new methodologies in this field and analyze selected examples of DCLs that are under thermodynamic control, leading to synthetic receptors, catalytic systems, and complex self-assembled supramolecular architectures. Also reviewed are extensions of the principles of DCC to systems that are not at equilibrium and may therefore harbor richer functional behavior. Examples include self-replication and molecular machines.
Synergistic Effect of Combinatorial Treatment with Curcumin and Mitomycin C on the Induction of Apoptosis of Breast Cancer Cells: A cDNA Microarray Analysis

PubMed Central

Zhou, Qian-Mei; Chen, Qi-Long; Du, Jia; Wang, Xiu-Feng; Lu, Yi-Yu; Zhang, Hui; Su, Shi-Bing

2014-01-01

In order to explore the synergistic mechanisms of combinatorial treatment using curcumin and mitomycin C (MMC) for breast cancer, MCF-7 breast cancer xenografts were conducted to observe the synergistic effect of combinatorial treatment using curcumin and MMC at various dosages. The synergistic mechanisms of combinatorial treatment using curcumin and MMC on the inhibition of tumor growth were explored by differential gene expression profile, gene ontology (GO), ingenuity pathway analysis (IPA) and Signal–Net network analysis. The expression levels of selected genes identified by cDNA microarray expression profiling were validated by quantitative RT-PCR (qRT-PCR) and Western blot analysis. Effect of combinatorial treatment on the inhibition of cell growth was observed by MTT assay. Apoptosis was detected by flow cytometric analysis and Hoechst 33258 staining. The combinatorial treatment of 100 mg/kg curcumin and 1.5 mg/kg MMC revealed synergistic inhibition on tumor growth. Among 1501 differentially expressed genes, the expression of 25 genes exhibited an obvious change and a significant difference in 27 signal pathways was observed (p < 0.05). In addition, Mapk1 (ERK) and Mapk14 (MAPK p38) had more cross-interactions with other genes and revealed an increase in expression by 8.14- and 11.84-fold, respectively during the combinatorial treatment by curcumin and MMC when compared with the control. Moreover, curcumin can synergistically improve tumoricidal effect of MMC in another human breast cancer MDA-MB-231 cells. Apoptosis was significantly induced by the combinatorial treatment (p < 0.05) and significantly inhibited by ERK inhibitor (PD98059) in MCF-7 cells (p < 0.05). The synergistic effect of combinatorial treatment by curcumin and MMC on the induction of apoptosis in breast cancer cells may be via the ERK pathway. PMID:25226537
A combinatorial model for dentate gyrus sparse coding

DOE PAGES

Severa, William; Parekh, Ojas; James, Conrad D.; ...

2016-12-29

The dentate gyrus forms a critical link between the entorhinal cortex and CA3 by providing a sparse version of the signal. Concurrent with this increase in sparsity, a widely accepted theory suggests the dentate gyrus performs pattern separation—similar inputs yield decorrelated outputs. Although an active region of study and theory, few logically rigorous arguments detail the dentate gyrus’s (DG) coding. We suggest a theoretically tractable, combinatorial model for this action. The model provides formal methods for a highly redundant, arbitrarily sparse, and decorrelated output signal.To explore the value of this model framework, we assess how suitable it is for twomore » notable aspects of DG coding: how it can handle the highly structured grid cell representation in the input entorhinal cortex region and the presence of adult neurogenesis, which has been proposed to produce a heterogeneous code in the DG. We find tailoring the model to grid cell input yields expansion parameters consistent with the literature. In addition, the heterogeneous coding reflects activity gradation observed experimentally. Lastly, we connect this approach with more conventional binary threshold neural circuit models via a formal embedding.« less
Mixed-up trees: the structure of phylogenetic mixtures.

PubMed

Matsen, Frederick A; Mossel, Elchanan; Steel, Mike

2008-05-01

In this paper, we apply new geometric and combinatorial methods to the study of phylogenetic mixtures. The focus of the geometric approach is to describe the geometry of phylogenetic mixture distributions for the two state random cluster model, which is a generalization of the two state symmetric (CFN) model. In particular, we show that the set of mixture distributions forms a convex polytope and we calculate its dimension; corollaries include a simple criterion for when a mixture of branch lengths on the star tree can mimic the site pattern frequency vector of a resolved quartet tree. Furthermore, by computing volumes of polytopes we can clarify how "common" non-identifiable mixtures are under the CFN model. We also present a new combinatorial result which extends any identifiability result for a specific pair of trees of size six to arbitrary pairs of trees. Next we present a positive result showing identifiability of rates-across-sites models. Finally, we answer a question raised in a previous paper concerning "mixed branch repulsion" on trees larger than quartet trees under the CFN model.
Optimization and quantization in gradient symbol systems: a framework for integrating the continuous and the discrete in cognition.

PubMed

Smolensky, Paul; Goldrick, Matthew; Mathis, Donald

2014-08-01

Mental representations have continuous as well as discrete, combinatorial properties. For example, while predominantly discrete, phonological representations also vary continuously; this is reflected by gradient effects in instrumental studies of speech production. Can an integrated theoretical framework address both aspects of structure? The framework we introduce here, Gradient Symbol Processing, characterizes the emergence of grammatical macrostructure from the Parallel Distributed Processing microstructure (McClelland, Rumelhart, & The PDP Research Group, 1986) of language processing. The mental representations that emerge, Distributed Symbol Systems, have both combinatorial and gradient structure. They are processed through Subsymbolic Optimization-Quantization, in which an optimization process favoring representations that satisfy well-formedness constraints operates in parallel with a distributed quantization process favoring discrete symbolic structures. We apply a particular instantiation of this framework, λ-Diffusion Theory, to phonological production. Simulations of the resulting model suggest that Gradient Symbol Processing offers a way to unify accounts of grammatical competence with both discrete and continuous patterns in language performance. Copyright © 2013 Cognitive Science Society, Inc.
Decoupling Polymer Properties to Elucidate Mechanisms Governing Cell Behavior

PubMed Central

Wang, Xintong; Boire, Timothy C.; Bronikowski, Christine; Zachman, Angela L.; Crowder, Spencer W.

2012-01-01

Determining how a biomaterial interacts with cells (“structure-function relationship”) reflects its eventual clinical applicability. Therefore, a fundamental understanding of how individual material properties modulate cell-biomaterial interactions is pivotal to improving the efficacy and safety of clinically translatable biomaterial systems. However, due to the coupled nature of material properties, their individual effects on cellular responses are difficult to understand. Structure-function relationships can be more clearly understood by the effective decoupling of each individual parameter. In this article, we discuss three basic decoupling strategies: (1) surface modification, (2) cross-linking, and (3) combinatorial approaches (i.e., copolymerization and polymer blending). Relevant examples of coupled material properties are briefly reviewed in each section to highlight the need for improved decoupling methods. This follows with examples of more effective decoupling techniques, mainly from the perspective of three primary classes of synthetic materials: polyesters, polyethylene glycol, and polyacrylamide. Recent strides in decoupling methodologies, especially surface-patterning and combinatorial techniques, offer much promise in further understanding the structure-function relationships that largely govern the success of future advancements in biomaterials, tissue engineering, and drug delivery. PMID:22536977
Combinatorial theory of Macdonald polynomials I: proof of Haglund's formula.

PubMed

Haglund, J; Haiman, M; Loehr, N

2005-02-22

Haglund recently proposed a combinatorial interpretation of the modified Macdonald polynomials H(mu). We give a combinatorial proof of this conjecture, which establishes the existence and integrality of H(mu). As corollaries, we obtain the cocharge formula of Lascoux and Schutzenberger for Hall-Littlewood polynomials, a formula of Sahi and Knop for Jack's symmetric functions, a generalization of this result to the integral Macdonald polynomials J(mu), a formula for H(mu) in terms of Lascoux-Leclerc-Thibon polynomials, and combinatorial expressions for the Kostka-Macdonald coefficients K(lambda,mu) when mu is a two-column shape.

HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets

PubMed Central

De Kumar, Bony; Parker, Hugo J.; Paulson, Ariel; Parrish, Mark E.; Pushel, Irina; Singh, Narendra Pratap; Zhang, Ying; Slaughter, Brian D.; Unruh, Jay R.; Florens, Laurence; Zeitlinger, Julia; Krumlauf, Robb

2017-01-01

Hoxa1 has diverse functional roles in differentiation and development. We identify and characterize properties of regions bound by HOXA1 on a genome-wide basis in differentiating mouse ES cells. HOXA1-bound regions are enriched for clusters of consensus binding motifs for HOX, PBX, and MEIS, and many display co-occupancy of PBX and MEIS. PBX and MEIS are members of the TALE family and genome-wide analysis of multiple TALE members (PBX, MEIS, TGIF, PREP1, and PREP2) shows that nearly all HOXA1 targets display occupancy of one or more TALE members. The combinatorial binding patterns of TALE proteins define distinct classes of HOXA1 targets, which may create functional diversity. Transgenic reporter assays in zebrafish confirm enhancer activities for many HOXA1-bound regions and the importance of HOX-PBX and TGIF motifs for their regulation. Proteomic analyses show that HOXA1 physically interacts on chromatin with PBX, MEIS, and PREP family members, but not with TGIF, suggesting that TGIF may have an independent input into HOXA1-bound regions. Therefore, TALE proteins appear to represent a wide repertoire of HOX cofactors, which may coregulate enhancers through distinct mechanisms. We also discover extensive auto- and cross-regulatory interactions among the Hoxa1 and TALE genes, indicating that the specificity of HOXA1 during development may be regulated though a complex cross-regulatory network of HOXA1 and TALE proteins. This study provides new insight into a regulatory network involving combinatorial interactions between HOXA1 and TALE proteins. PMID:28784834
To Think without Thinking: The Implications of Combinatory Play and the Creative Process for Neuroaesthetics

ERIC Educational Resources Information Center

Stevens, Victoria

2014-01-01

The author considers combinatory play as an intersection between creativity, play, and neuroaesthetics. She discusses combinatory play as vital to the creative process in art and science, particularly with regard to the incubation of new ideas. She reviews findings from current neurobiological research and outlines the way that the brain activates…
Combinatorial genetic perturbation to refine metabolic circuits for producing biofuels and biochemicals.

PubMed

Kim, Hyo Jin; Turner, Timothy Lee; Jin, Yong-Su

2013-11-01

Recent advances in metabolic engineering have enabled microbial factories to compete with conventional processes for producing fuels and chemicals. Both rational and combinatorial approaches coupled with synthetic and systematic tools play central roles in metabolic engineering to create and improve a selected microbial phenotype. Compared to knowledge-based rational approaches, combinatorial approaches exploiting biological diversity and high-throughput screening have been demonstrated as more effective tools for improving various phenotypes of interest. In particular, identification of unprecedented targets to rewire metabolic circuits for maximizing yield and productivity of a target chemical has been made possible. This review highlights general principles and the features of the combinatorial approaches using various libraries to implement desired phenotypes for strain improvement. In addition, recent applications that harnessed the combinatorial approaches to produce biofuels and biochemicals will be discussed. Copyright © 2013 Elsevier Inc. All rights reserved.
Tumor-targeting peptides from combinatorial libraries.

PubMed

Liu, Ruiwu; Li, Xiaocen; Xiao, Wenwu; Lam, Kit S

2017-02-01

Cancer is one of the major and leading causes of death worldwide. Two of the greatest challenges in fighting cancer are early detection and effective treatments with no or minimum side effects. Widespread use of targeted therapies and molecular imaging in clinics requires high affinity, tumor-specific agents as effective targeting vehicles to deliver therapeutics and imaging probes to the primary or metastatic tumor sites. Combinatorial libraries such as phage-display and one-bead one-compound (OBOC) peptide libraries are powerful approaches in discovering tumor-targeting peptides. This review gives an overview of different combinatorial library technologies that have been used for the discovery of tumor-targeting peptides. Examples of tumor-targeting peptides identified from each combinatorial library method will be discussed. Published tumor-targeting peptide ligands and their applications will also be summarized by the combinatorial library methods and their corresponding binding receptors. Copyright © 2017. Published by Elsevier B.V.
Towards a computational- and algorithmic-level account of concept blending using analogies and amalgams

NASA Astrophysics Data System (ADS)

Besold, Tarek R.; Kühnberger, Kai-Uwe; Plaza, Enric

2017-10-01

Concept blending - a cognitive process which allows for the combination of certain elements (and their relations) from originally distinct conceptual spaces into a new unified space combining these previously separate elements, and enables reasoning and inference over the combination - is taken as a key element of creative thought and combinatorial creativity. In this article, we summarise our work towards the development of a computational-level and algorithmic-level account of concept blending, combining approaches from computational analogy-making and case-based reasoning (CBR). We present the theoretical background, as well as an algorithmic proposal integrating higher-order anti-unification matching and generalisation from analogy with amalgams from CBR. The feasibility of the approach is then exemplified in two case studies.
Alignment of Tractograms As Graph Matching.

PubMed

Olivetti, Emanuele; Sharmin, Nusrat; Avesani, Paolo

2016-01-01

The white matter pathways of the brain can be reconstructed as 3D polylines, called streamlines, through the analysis of diffusion magnetic resonance imaging (dMRI) data. The whole set of streamlines is called tractogram and represents the structural connectome of the brain. In multiple applications, like group-analysis, segmentation, or atlasing, tractograms of different subjects need to be aligned. Typically, this is done with registration methods, that transform the tractograms in order to increase their similarity. In contrast with transformation-based registration methods, in this work we propose the concept of tractogram correspondence, whose aim is to find which streamline of one tractogram corresponds to which streamline in another tractogram, i.e., a map from one tractogram to another. As a further contribution, we propose to use the relational information of each streamline, i.e., its distances from the other streamlines in its own tractogram, as the building block to define the optimal correspondence. We provide an operational procedure to find the optimal correspondence through a combinatorial optimization problem and we discuss its similarity to the graph matching problem. In this work, we propose to represent tractograms as graphs and we adopt a recent inexact sub-graph matching algorithm to approximate the solution of the tractogram correspondence problem. On tractograms generated from the Human Connectome Project dataset, we report experimental evidence that tractogram correspondence, implemented as graph matching, provides much better alignment than affine registration and comparable if not better results than non-linear registration of volumes.
Intrinsic information carriers in combinatorial dynamical systems

NASA Astrophysics Data System (ADS)

Harmer, Russ; Danos, Vincent; Feret, Jérôme; Krivine, Jean; Fontana, Walter

2010-09-01

Many proteins are composed of structural and chemical features—"sites" for short—characterized by definite interaction capabilities, such as noncovalent binding or covalent modification of other proteins. This modularity allows for varying degrees of independence, as the behavior of a site might be controlled by the state of some but not all sites of the ambient protein. Independence quickly generates a startling combinatorial complexity that shapes most biological networks, such as mammalian signaling systems, and effectively prevents their study in terms of kinetic equations—unless the complexity is radically trimmed. Yet, if combinatorial complexity is key to the system's behavior, eliminating it will prevent, not facilitate, understanding. A more adequate representation of a combinatorial system is provided by a graph-based framework of rewrite rules where each rule specifies only the information that an interaction mechanism depends on. Unlike reactions, which deal with molecular species, rules deal with patterns, i.e., multisets of molecular species. Although the stochastic dynamics induced by a collection of rules on a mixture of molecules can be simulated, it appears useful to capture the system's average or deterministic behavior by means of differential equations. However, expansion of the rules into kinetic equations at the level of molecular species is not only impractical, but conceptually indefensible. If rules describe bona fide patterns of interaction, molecular species are unlikely to constitute appropriate units of dynamics. Rather, we must seek aggregate variables reflective of the causal structure laid down by the rules. We call these variables "fragments" and the process of identifying them "fragmentation." Ideally, fragments are aspects of the system's microscopic population that the set of rules can actually distinguish on average; in practice, it may only be feasible to identify an approximation to this. Most importantly, fragments are self-consistent descriptors of system dynamics in that their time-evolution is governed by a closed system of kinetic equations. Taken together, fragments are endogenous distinctions that matter for the dynamics of a system, which warrants viewing them as the carriers of information. Although fragments can be thought of as multisets of molecular species (an extensional view), their self-consistency suggests treating them as autonomous aspects cut off from their microscopic realization (an intensional view). Fragmentation is a seeded process that depends on the choice of observables whose dynamics one insists to describe. Different observables can cause distinct fragmentations, in effect altering the set of information carriers that govern the behavior of a system, even though nothing has changed in its microscopic constitution. In this contribution, we present a mathematical specification of fragments, but not an algorithmic implementation. We have described the latter elsewhere in rather technical terms that, although effective, were lacking an embedding into a more general conceptual framework, which we here provide.
Intrinsic information carriers in combinatorial dynamical systems.

PubMed

Harmer, Russ; Danos, Vincent; Feret, Jérôme; Krivine, Jean; Fontana, Walter

2010-09-01

Many proteins are composed of structural and chemical features--"sites" for short--characterized by definite interaction capabilities, such as noncovalent binding or covalent modification of other proteins. This modularity allows for varying degrees of independence, as the behavior of a site might be controlled by the state of some but not all sites of the ambient protein. Independence quickly generates a startling combinatorial complexity that shapes most biological networks, such as mammalian signaling systems, and effectively prevents their study in terms of kinetic equations-unless the complexity is radically trimmed. Yet, if combinatorial complexity is key to the system's behavior, eliminating it will prevent, not facilitate, understanding. A more adequate representation of a combinatorial system is provided by a graph-based framework of rewrite rules where each rule specifies only the information that an interaction mechanism depends on. Unlike reactions, which deal with molecular species, rules deal with patterns, i.e., multisets of molecular species. Although the stochastic dynamics induced by a collection of rules on a mixture of molecules can be simulated, it appears useful to capture the system's average or deterministic behavior by means of differential equations. However, expansion of the rules into kinetic equations at the level of molecular species is not only impractical, but conceptually indefensible. If rules describe bona fide patterns of interaction, molecular species are unlikely to constitute appropriate units of dynamics. Rather, we must seek aggregate variables reflective of the causal structure laid down by the rules. We call these variables "fragments" and the process of identifying them "fragmentation." Ideally, fragments are aspects of the system's microscopic population that the set of rules can actually distinguish on average; in practice, it may only be feasible to identify an approximation to this. Most importantly, fragments are self-consistent descriptors of system dynamics in that their time-evolution is governed by a closed system of kinetic equations. Taken together, fragments are endogenous distinctions that matter for the dynamics of a system, which warrants viewing them as the carriers of information. Although fragments can be thought of as multisets of molecular species (an extensional view), their self-consistency suggests treating them as autonomous aspects cut off from their microscopic realization (an intensional view). Fragmentation is a seeded process that depends on the choice of observables whose dynamics one insists to describe. Different observables can cause distinct fragmentations, in effect altering the set of information carriers that govern the behavior of a system, even though nothing has changed in its microscopic constitution. In this contribution, we present a mathematical specification of fragments, but not an algorithmic implementation. We have described the latter elsewhere in rather technical terms that, although effective, were lacking an embedding into a more general conceptual framework, which we here provide.
rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison.

PubMed

Hahn, Lars; Leimeister, Chris-André; Ounit, Rachid; Lonardi, Stefano; Morgenstern, Burkhard

2016-10-01

Many algorithms for sequence analysis rely on word matching or word statistics. Often, these approaches can be improved if binary patterns representing match and don't-care positions are used as a filter, such that only those positions of words are considered that correspond to the match positions of the patterns. The performance of these approaches, however, depends on the underlying patterns. Herein, we show that the overlap complexity of a pattern set that was introduced by Ilie and Ilie is closely related to the variance of the number of matches between two evolutionarily related sequences with respect to this pattern set. We propose a modified hill-climbing algorithm to optimize pattern sets for database searching, read mapping and alignment-free sequence comparison of nucleic-acid sequences; our implementation of this algorithm is called rasbhari. Depending on the application at hand, rasbhari can either minimize the overlap complexity of pattern sets, maximize their sensitivity in database searching or minimize the variance of the number of pattern-based matches in alignment-free sequence comparison. We show that, for database searching, rasbhari generates pattern sets with slightly higher sensitivity than existing approaches. In our Spaced Words approach to alignment-free sequence comparison, pattern sets calculated with rasbhari led to more accurate estimates of phylogenetic distances than the randomly generated pattern sets that we previously used. Finally, we used rasbhari to generate patterns for short read classification with CLARK-S. Here too, the sensitivity of the results could be improved, compared to the default patterns of the program. We integrated rasbhari into Spaced Words; the source code of rasbhari is freely available at http://rasbhari.gobics.de/.
Sleep patterns and match performance in elite Australian basketball athletes.

PubMed

Staunton, Craig; Gordon, Brett; Custovic, Edhem; Stanger, Jonathan; Kingsley, Michael

2017-08-01

To assess sleep patterns and associations between sleep and match performance in elite Australian female basketball players. Prospective cohort study. Seventeen elite female basketball players were monitored across two consecutive in-season competitions (30 weeks). Total sleep time and sleep efficiency were determined using triaxial accelerometers for Baseline, Pre-match, Match-day and Post-match timings. Match performance was determined using the basketball efficiency statistic (EFF). The effects of match schedule (Regular versus Double-Header; Home versus Away) and sleep on EFF were assessed. The Double-Header condition changed the pattern of sleep when compared with the Regular condition (F (3,48) =3.763, P=0.017), where total sleep time Post-match was 11% less for Double-Header (mean±SD; 7.2±1.4h) compared with Regular (8.0±1.3h; P=0.007). Total sleep time for Double-Header was greater Pre-match (8.2±1.7h) compared with Baseline (7.1±1.6h; P=0.022) and Match-day (7.3±1.5h; P=0.007). Small correlations existed between sleep metrics at Pre-match and EFF for pooled data (r=-0.39 to -0.22; P≥0.238). Relationships between total sleep time and EFF ranged from moderate negative to large positive correlations for individual players (r=-0.37 to 0.62) and reached significance for one player (r=0.60; P=0.025). Match schedule can affect the sleep patterns of elite female basketball players. A large degree of inter-individual variability existed in the relationship between sleep and match performance; nevertheless, sleep monitoring might assist in the optimisation of performance for some athletes. Copyright © 2017 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.
Application of computer assisted combinatorial chemistry in antivirial, antimalarial and anticancer agents design

NASA Astrophysics Data System (ADS)

Burello, E.; Bologa, C.; Frecer, V.; Miertus, S.

Combinatorial chemistry and technologies have been developed to a stage where synthetic schemes are available for generation of a large variety of organic molecules. The innovative concept of combinatorial design assumes that screening of a large and diverse library of compounds will increase the probability of finding an active analogue among the compounds tested. Since the rate at which libraries are screened for activity currently constitutes a limitation to the use of combinatorial technologies, it is important to be selective about the number of compounds to be synthesized. Early experience with combinatorial chemistry indicated that chemical diversity alone did not result in a significant increase in the number of generated lead compounds. Emphasis has therefore been increasingly put on the use of computer assisted combinatorial chemical techniques. Computational methods are valuable in the design of virtual libraries of molecular models. Selection strategies based on computed physicochemical properties of the models or of a target compound are introduced to reduce the time and costs of library synthesis and screening. In addition, computational structure-based library focusing methods can be used to perform in silico screening of the activity of compounds against a target receptor by docking the ligands into the receptor model. Three case studies are discussed dealing with the design of targeted combinatorial libraries of inhibitors of HIV-1 protease, P. falciparum plasmepsin and human urokinase as potential antivirial, antimalarial and anticancer drugs. These illustrate library focusing strategies.
Automatic ground control point recognition with parallel associative memory

NASA Technical Reports Server (NTRS)

Al-Tahir, Raid; Toth, Charles K.; Schenck, Anton F.

1990-01-01

The basic principle of the associative memory is to match the unknown input pattern against a stored training set, and responding with the 'closest match' and the corresponding label. Generally, an associative memory system requires two preparatory steps: selecting attributes of the pattern class, and training the system by associating patterns with labels. Experimental results gained from using Parallel Associative Memory are presented. The primary concern is an automatic search for ground control points in aerial photographs. Synthetic patterns are tested followed by real data. The results are encouraging as a relatively high level of correct matches is reached.
Geometrical study of phyllotactic patterns by Bernoulli spiral lattices.

PubMed

Sushida, Takamichi; Yamagishi, Yoshikazu

2017-06-01

Geometrical studies of phyllotactic patterns deal with the centric or cylindrical models produced by ideal lattices. van Iterson (Mathematische und mikroskopisch - anatomische Studien über Blattstellungen nebst Betrachtungen über den Schalenbau der Miliolinen, Verlag von Gustav Fischer, Jena, 1907) suggested a centric model representing ideal phyllotactic patterns as disk packings of Bernoulli spiral lattices and presented a phase diagram now called Van Iterson's diagram explaining the bifurcation processes of their combinatorial structures. Geometrical properties on disk packings were shown by Rothen & Koch (J. Phys France, 50(13), 1603-1621, 1989). In contrast, as another centric model, we organized a mathematical framework of Voronoi tilings of Bernoulli spiral lattices and showed mathematically that the phase diagram of a Voronoi tiling is graph-theoretically dual to Van Iterson's diagram. This paper gives a review of two centric models for disk packings and Voronoi tilings of Bernoulli spiral lattices. © 2017 Japanese Society of Developmental Biologists.
Signaling mechanisms underlying the robustness and tunability of the plant immune network

PubMed Central

Kim, Yungil; Tsuda, Kenichi; Igarashi, Daisuke; Hillmer, Rachel A.; Sakakibara, Hitoshi; Myers, Chad L.; Katagiri, Fumiaki

2014-01-01

Summary How does robust and tunable behavior emerge in a complex biological network? We sought to understand this for the signaling network controlling pattern-triggered immunity (PTI) in Arabidopsis. A dynamic network model containing four major signaling sectors, the jasmonate, ethylene, PAD4, and salicylate sectors, which together explain up to 80% of the PTI level, was built using data for dynamic sector activities and PTI levels under exhaustive combinatorial sector perturbations. Our regularized multiple regression model had a high level of predictive power and captured known and unexpected signal flows in the network. The sole inhibitory sector in the model, the ethylene sector, was central to the network robustness via its inhibition of the jasmonate sector. The model's multiple input sites linked specific signal input patterns varying in strength and timing to different network response patterns, indicating a mechanism enabling tunability. PMID:24439900
The Oncoprotein BRD4-NUT Generates Aberrant Histone Modification Patterns.

PubMed

Zee, Barry M; Dibona, Amy B; Alekseyenko, Artyom A; French, Christopher A; Kuroda, Mitzi I

2016-01-01

Defects in chromatin proteins frequently manifest in diseases. A striking case of a chromatin-centric disease is NUT-midline carcinoma (NMC), which is characterized by expression of NUT as a fusion partner most frequently with BRD4. ChIP-sequencing studies from NMC patients revealed that BRD4-NUT (B4N) covers large genomic regions and elevates transcription within these domains. To investigate how B4N modulates chromatin, we performed affinity purification of B4N when ectopically expressed in 293-TREx cells and quantified the associated histone posttranslational modifications (PTM) using proteomics. We observed significant enrichment of acetylation particularly on H3 K18 and of combinatorial patterns such as H3 K27 acetylation paired with K36 methylation. We postulate that B4N complexes override the preexisting histone code with new PTM patterns that reflect aberrant transcription and that epigenetically modulate the nucleosome environment toward the NMC state.
The Oncoprotein BRD4-NUT Generates Aberrant Histone Modification Patterns

PubMed Central

Zee, Barry M.; Dibona, Amy B.; Alekseyenko, Artyom A.; French, Christopher A.; Kuroda, Mitzi I.

2016-01-01

Defects in chromatin proteins frequently manifest in diseases. A striking case of a chromatin-centric disease is NUT-midline carcinoma (NMC), which is characterized by expression of NUT as a fusion partner most frequently with BRD4. ChIP-sequencing studies from NMC patients revealed that BRD4-NUT (B4N) covers large genomic regions and elevates transcription within these domains. To investigate how B4N modulates chromatin, we performed affinity purification of B4N when ectopically expressed in 293-TREx cells and quantified the associated histone posttranslational modifications (PTM) using proteomics. We observed significant enrichment of acetylation particularly on H3 K18 and of combinatorial patterns such as H3 K27 acetylation paired with K36 methylation. We postulate that B4N complexes override the preexisting histone code with new PTM patterns that reflect aberrant transcription and that epigenetically modulate the nucleosome environment toward the NMC state. PMID:27698495
Examining the relationship between comprehension and production processes in code-switched language

PubMed Central

Guzzardo Tamargo, Rosa E.; Valdés Kroff, Jorge R.; Dussias, Paola E.

2016-01-01

We employ code-switching (the alternation of two languages in bilingual communication) to test the hypothesis, derived from experience-based models of processing (e.g., Boland, Tanenhaus, Carlson, & Garnsey, 1989; Gennari & MacDonald, 2009), that bilinguals are sensitive to the combinatorial distributional patterns derived from production and that they use this information to guide processing during the comprehension of code-switched sentences. An analysis of spontaneous bilingual speech confirmed the existence of production asymmetries involving two auxiliary + participle phrases in Spanish–English code-switches. A subsequent eye-tracking study with two groups of bilingual code-switchers examined the consequences of the differences in distributional patterns found in the corpus study for comprehension. Participants’ comprehension costs mirrored the production patterns found in the corpus study. Findings are discussed in terms of the constraints that may be responsible for the distributional patterns in code-switching production and are situated within recent proposals of the links between production and comprehension. PMID:28670049
Examining the relationship between comprehension and production processes in code-switched language.

PubMed

Guzzardo Tamargo, Rosa E; Valdés Kroff, Jorge R; Dussias, Paola E

2016-08-01

We employ code-switching (the alternation of two languages in bilingual communication) to test the hypothesis, derived from experience-based models of processing (e.g., Boland, Tanenhaus, Carlson, & Garnsey, 1989; Gennari & MacDonald, 2009), that bilinguals are sensitive to the combinatorial distributional patterns derived from production and that they use this information to guide processing during the comprehension of code-switched sentences. An analysis of spontaneous bilingual speech confirmed the existence of production asymmetries involving two auxiliary + participle phrases in Spanish-English code-switches. A subsequent eye-tracking study with two groups of bilingual code-switchers examined the consequences of the differences in distributional patterns found in the corpus study for comprehension. Participants' comprehension costs mirrored the production patterns found in the corpus study. Findings are discussed in terms of the constraints that may be responsible for the distributional patterns in code-switching production and are situated within recent proposals of the links between production and comprehension.
Smart sensor for terminal homing

NASA Astrophysics Data System (ADS)

Panda, D.; Aggarwal, R.; Hummel, R.

1980-01-01

The practical scene matching problem is considered to present certain complications which must extend classical image processing capabilities. Certain aspects of the scene matching problem which must be addressed by a smart sensor for terminal homing are discussed. First a philosophy for treating the matching problem for the terminal homing scenario is outlined. Then certain aspects of the feature extraction process and symbolic pattern matching are considered. It is thought that in the future general ideas from artificial intelligence will be more useful for terminal homing requirements of fast scene recognition and pattern matching.
Combinatorial chemistry has matured in the last three decades: dedicated to Professor Árpád Furka on the occasion of his 80th birthday.

PubMed

Dibó, Gábor

2012-02-01

Combinatorial chemistry was introduced in the 1980s. It provided the possibility to produce new compounds in practically unlimited number. New strategies and technologies have also been developed that made it possible to screen very large number of compounds and to identify useful components in mixtures containing millions of different substances. This dramatically changed the drug discovery process and the way of thinking of synthetic chemists. In addition, combinatorial strategies became useful in areas such as pharmaceutical research, agrochemistry, catalyst design, and materials research. Prof. Árpád Furka is one of the pioneers of combinatorial chemistry.

Construction of a virtual combinatorial library using SMILES strings to discover potential structure-diverse PPAR modulators.

PubMed

Liao, Chenzhong; Liu, Bing; Shi, Leming; Zhou, Jiaju; Lu, Xian-Ping

2005-07-01

Based on the structural characters of PPAR modulators, a virtual combinatorial library containing 1226,625 compounds was constructed using SMILES strings. Selected ADME filters were employed to compel compounds having poor drug-like properties from this library. This library was converted to sdf and mol2 files by CONCORD 4.0, and was then docked to PPARgamma by DOCK 4.0 to identify new chemical entities that may be potential drug leads against type 2 diabetes and other metabolic diseases. The method to construct virtual combinatorial library using SMILES strings was further visualized by Visual Basic.net that can facilitate the needs of generating other type virtual combinatorial libraries.
Systematic Identification of Combinatorial Drivers and Targets in Cancer Cell Lines

PubMed Central

Tabchy, Adel; Eltonsy, Nevine; Housman, David E.; Mills, Gordon B.

2013-01-01

There is an urgent need to elicit and validate highly efficacious targets for combinatorial intervention from large scale ongoing molecular characterization efforts of tumors. We established an in silico bioinformatic platform in concert with a high throughput screening platform evaluating 37 novel targeted agents in 669 extensively characterized cancer cell lines reflecting the genomic and tissue-type diversity of human cancers, to systematically identify combinatorial biomarkers of response and co-actionable targets in cancer. Genomic biomarkers discovered in a 141 cell line training set were validated in an independent 359 cell line test set. We identified co-occurring and mutually exclusive genomic events that represent potential drivers and combinatorial targets in cancer. We demonstrate multiple cooperating genomic events that predict sensitivity to drug intervention independent of tumor lineage. The coupling of scalable in silico and biologic high throughput cancer cell line platforms for the identification of co-events in cancer delivers rational combinatorial targets for synthetic lethal approaches with a high potential to pre-empt the emergence of resistance. PMID:23577104
Systematic identification of combinatorial drivers and targets in cancer cell lines.

PubMed

Tabchy, Adel; Eltonsy, Nevine; Housman, David E; Mills, Gordon B

2013-01-01

There is an urgent need to elicit and validate highly efficacious targets for combinatorial intervention from large scale ongoing molecular characterization efforts of tumors. We established an in silico bioinformatic platform in concert with a high throughput screening platform evaluating 37 novel targeted agents in 669 extensively characterized cancer cell lines reflecting the genomic and tissue-type diversity of human cancers, to systematically identify combinatorial biomarkers of response and co-actionable targets in cancer. Genomic biomarkers discovered in a 141 cell line training set were validated in an independent 359 cell line test set. We identified co-occurring and mutually exclusive genomic events that represent potential drivers and combinatorial targets in cancer. We demonstrate multiple cooperating genomic events that predict sensitivity to drug intervention independent of tumor lineage. The coupling of scalable in silico and biologic high throughput cancer cell line platforms for the identification of co-events in cancer delivers rational combinatorial targets for synthetic lethal approaches with a high potential to pre-empt the emergence of resistance.
An evaluation of methods for estimating the number of local optima in combinatorial optimization problems.

PubMed

Hernando, Leticia; Mendiburu, Alexander; Lozano, Jose A

2013-01-01

The solution of many combinatorial optimization problems is carried out by metaheuristics, which generally make use of local search algorithms. These algorithms use some kind of neighborhood structure over the search space. The performance of the algorithms strongly depends on the properties that the neighborhood imposes on the search space. One of these properties is the number of local optima. Given an instance of a combinatorial optimization problem and a neighborhood, the estimation of the number of local optima can help not only to measure the complexity of the instance, but also to choose the most convenient neighborhood to solve it. In this paper we review and evaluate several methods to estimate the number of local optima in combinatorial optimization problems. The methods reviewed not only come from the combinatorial optimization literature, but also from the statistical literature. A thorough evaluation in synthetic as well as real problems is given. We conclude by providing recommendations of methods for several scenarios.
Combinatorial materials approach to accelerate materials discovery for transportation (Conference Presentation)

NASA Astrophysics Data System (ADS)

Tong, Wei

2017-04-01

Combinatorial material research offers fast and efficient solutions to identify promising and advanced materials. It has revolutionized the pharmaceutical industry and now is being applied to accelerate the discovery of other new compounds, e.g. superconductors, luminescent materials, catalysts etc. Differing from the traditional trial-and-error process, this approach allows for the synthesis of a large number of compositionally diverse compounds by varying the combinations of the components and adjusting the ratios. It largely reduces the cost of single-sample synthesis/characterization, along with the turnaround time in the material discovery process, therefore, could dramatically change the existing paradigm for discovering and commercializing new materials. This talk outlines the use of combinatorial materials approach in the material discovery in transportation sector. It covers the general introduction to the combinatorial material concept, state of art for its application in energy-related research. At the end, LBNL capabilities in combinatorial materials synthesis and high throughput characterization that are applicable for material discovery research will be highlighted.
Kangaroo – A pattern-matching program for biological sequences

PubMed Central

2002-01-01

Background Biologists are often interested in performing a simple database search to identify proteins or genes that contain a well-defined sequence pattern. Many databases do not provide straightforward or readily available query tools to perform simple searches, such as identifying transcription binding sites, protein motifs, or repetitive DNA sequences. However, in many cases simple pattern-matching searches can reveal a wealth of information. We present in this paper a regular expression pattern-matching tool that was used to identify short repetitive DNA sequences in human coding regions for the purpose of identifying potential mutation sites in mismatch repair deficient cells. Results Kangaroo is a web-based regular expression pattern-matching program that can search for patterns in DNA, protein, or coding region sequences in ten different organisms. The program is implemented to facilitate a wide range of queries with no restriction on the length or complexity of the query expression. The program is accessible on the web at http://bioinfo.mshri.on.ca/kangaroo/ and the source code is freely distributed at http://sourceforge.net/projects/slritools/. Conclusion A low-level simple pattern-matching application can prove to be a useful tool in many research settings. For example, Kangaroo was used to identify potential genetic targets in a human colorectal cancer variant that is characterized by a high frequency of mutations in coding regions containing mononucleotide repeats. PMID:12150718
Discovery of the leinamycin family of natural products by mining actinobacterial genomes

PubMed Central

Xu, Zhengren; Guo, Zhikai; Hindra; Ma, Ming; Zhou, Hao; Gansemans, Yannick; Zhu, Xiangcheng; Huang, Yong; Zhao, Li-Xing; Jiang, Yi; Cheng, Jinhua; Van Nieuwerburgh, Filip; Suh, Joo-Won; Duan, Yanwen

2017-01-01

Nature’s ability to generate diverse natural products from simple building blocks has inspired combinatorial biosynthesis. The knowledge-based approach to combinatorial biosynthesis has allowed the production of designer analogs by rational metabolic pathway engineering. While successful, structural alterations are limited, with designer analogs often produced in compromised titers. The discovery-based approach to combinatorial biosynthesis complements the knowledge-based approach by exploring the vast combinatorial biosynthesis repertoire found in Nature. Here we showcase the discovery-based approach to combinatorial biosynthesis by targeting the domain of unknown function and cysteine lyase domain (DUF–SH) didomain, specific for sulfur incorporation from the leinamycin (LNM) biosynthetic machinery, to discover the LNM family of natural products. By mining bacterial genomes from public databases and the actinomycetes strain collection at The Scripps Research Institute, we discovered 49 potential producers that could be grouped into 18 distinct clades based on phylogenetic analysis of the DUF–SH didomains. Further analysis of the representative genomes from each of the clades identified 28 lnm-type gene clusters. Structural diversities encoded by the LNM-type biosynthetic machineries were predicted based on bioinformatics and confirmed by in vitro characterization of selected adenylation proteins and isolation and structural elucidation of the guangnanmycins and weishanmycins. These findings demonstrate the power of the discovery-based approach to combinatorial biosynthesis for natural product discovery and structural diversity and highlight Nature’s rich biosynthetic repertoire. Comparative analysis of the LNM-type biosynthetic machineries provides outstanding opportunities to dissect Nature’s biosynthetic strategies and apply these findings to combinatorial biosynthesis for natural product discovery and structural diversity. PMID:29229819
Discovery of the leinamycin family of natural products by mining actinobacterial genomes.

PubMed

Pan, Guohui; Xu, Zhengren; Guo, Zhikai; Hindra; Ma, Ming; Yang, Dong; Zhou, Hao; Gansemans, Yannick; Zhu, Xiangcheng; Huang, Yong; Zhao, Li-Xing; Jiang, Yi; Cheng, Jinhua; Van Nieuwerburgh, Filip; Suh, Joo-Won; Duan, Yanwen; Shen, Ben

2017-12-26

Nature's ability to generate diverse natural products from simple building blocks has inspired combinatorial biosynthesis. The knowledge-based approach to combinatorial biosynthesis has allowed the production of designer analogs by rational metabolic pathway engineering. While successful, structural alterations are limited, with designer analogs often produced in compromised titers. The discovery-based approach to combinatorial biosynthesis complements the knowledge-based approach by exploring the vast combinatorial biosynthesis repertoire found in Nature. Here we showcase the discovery-based approach to combinatorial biosynthesis by targeting the domain of unknown function and cysteine lyase domain (DUF-SH) didomain, specific for sulfur incorporation from the leinamycin (LNM) biosynthetic machinery, to discover the LNM family of natural products. By mining bacterial genomes from public databases and the actinomycetes strain collection at The Scripps Research Institute, we discovered 49 potential producers that could be grouped into 18 distinct clades based on phylogenetic analysis of the DUF-SH didomains. Further analysis of the representative genomes from each of the clades identified 28 lnm -type gene clusters. Structural diversities encoded by the LNM-type biosynthetic machineries were predicted based on bioinformatics and confirmed by in vitro characterization of selected adenylation proteins and isolation and structural elucidation of the guangnanmycins and weishanmycins. These findings demonstrate the power of the discovery-based approach to combinatorial biosynthesis for natural product discovery and structural diversity and highlight Nature's rich biosynthetic repertoire. Comparative analysis of the LNM-type biosynthetic machineries provides outstanding opportunities to dissect Nature's biosynthetic strategies and apply these findings to combinatorial biosynthesis for natural product discovery and structural diversity.
Combinatorial pretreatment and fermentation optimization enabled a record yield on lignin bioconversion.

PubMed

Liu, Zhi-Hua; Xie, Shangxian; Lin, Furong; Jin, Mingjie; Yuan, Joshua S

2018-01-01

Lignin valorization has recently been considered to be an essential process for sustainable and cost-effective biorefineries. Lignin represents a potential new feedstock for value-added products. Oleaginous bacteria such as Rhodococcus opacus can produce intracellular lipids from biodegradation of aromatic substrates. These lipids can be used for biofuel production, which can potentially replace petroleum-derived chemicals. However, the low reactivity of lignin produced from pretreatment and the underdeveloped fermentation technology hindered lignin bioconversion to lipids. In this study, combinatorial pretreatment with an optimized fermentation strategy was evaluated to improve lignin valorization into lipids using R. opacus PD630. As opposed to single pretreatment, combinatorial pretreatment produced a 12.8-75.6% higher lipid concentration in fermentation using lignin as the carbon source. Gas chromatography-mass spectrometry analysis showed that combinatorial pretreatment released more aromatic monomers, which could be more readily utilized by lignin-degrading strains. Three detoxification strategies were used to remove potential inhibitors produced from pretreatment. After heating detoxification of the lignin stream, the lipid concentration further increased by 2.9-9.7%. Different fermentation strategies were evaluated in scale-up lipid fermentation using a 2.0-l fermenter. With laccase treatment of the lignin stream produced from combinatorial pretreatment, the highest cell dry weight and lipid concentration were 10.1 and 1.83 g/l, respectively, in fed-batch fermentation, with a total soluble substrate concentration of 40 g/l. The improvement of the lipid fermentation performance may have resulted from lignin depolymerization by the combinatorial pretreatment and laccase treatment, reduced inhibition effects by fed-batch fermentation, adequate oxygen supply, and an accurate pH control in the fermenter. Overall, these results demonstrate that combinatorial pretreatment, together with fermentation optimization, favorably improves lipid production using lignin as the carbon source. Combinatorial pretreatment integrated with fed-batch fermentation was an effective strategy to improve the bioconversion of lignin into lipids, thus facilitating lignin valorization in biorefineries.
Neural representations of the sense of self

PubMed Central

Klemm, William R.

2011-01-01

The brain constructs representations of what is sensed and thought about in the form of nerve impulses that propagate in circuits and network assemblies (Circuit Impulse Patterns, CIPs). CIP representations of which humans are consciously aware occur in the context of a sense of self. Thus, research on mechanisms of consciousness might benefit from a focus on how a conscious sense of self is represented in brain. Like all senses, the sense of self must be contained in patterns of nerve impulses. Unlike the traditional senses that are registered by impulse flow in relatively simple, pauci-synaptic projection pathways, the sense of self is a system- level phenomenon that may be generated by impulse patterns in widely distributed complex and interacting circuits. The problem for researchers then is to identify the CIPs that are unique to conscious experience. Also likely to be of great relevance to constructing the representation of self are the coherence shifts in activity timing relations among the circuits. Consider that an embodied sense of self is generated and contained as unique combinatorial temporal patterns across multiple neurons in each circuit that contributes to constructing the sense of self. As with other kinds of CIPs, those representing the sense of self can be learned from experience, stored in memory, modified by subsequent experiences, and expressed in the form of decisions, choices, and commands. These CIPs are proposed here to be the actual physical basis for conscious thought and the sense of self. When active in wakefulness or dream states, the CIP representations of self act as an agent of the brain, metaphorically as an avatar. Because the selfhood CIP patterns may only have to represent the self and not directly represent the inner and outer worlds of embodied brain, the self representation should have more degrees of freedom than subconscious mind and may therefore have some capacity for a free-will mind of its own. S everal lines of evidence for this theory are reviewed. Suggested new research includes identifying distinct combinatorially coded impulse patterns and their temporal coherence shifts in defined circuitry, such as neocortical microcolumns. This task might be facilitated by identifying the micro-topography of field-potential oscillatory coherences among various regions and between different frequencies associated with specific conscious mentation. Other approaches can include identifying the changes in discrete conscious operations produced by focal trans-cranial magnetic stimulation. PMID:21826192
Synthesis of small combinatorial libraries of natural products: identification and quantification of new long-chain 3-methyl-2-alkanones from the root essential oil of Inula helenium L. (Asteraceae).

PubMed

Radulović, Niko S; Denić, Marija S; Stojanović-Radić, Zorica Z

2014-01-01

Recently, a potent anti-staphylococcal activity of Inula helenium L. (Asteraceae) root essential oil was reported. Also, bioassay guided fractionation of the oil pointed to eudesmane sesquiterpene lactones and a series of unidentified constituents as the main carriers of the observed activity. To identify nine new constituents (long-chain 3-methyl-2-alkanones) from a fraction of this root essential oil with a low minimum inhibitory concentration value (0.8 µg/mL) by employing a synthetic methodology that leads to the formation of a small combinatorial library of these compounds. The identity of these constituents was inferred from mass spectral fragmentation patterns and GC retention data. A library of 3-methyl-2-alkanones (C11 -C19 homologous series) was synthesised in three steps starting from methyl acetoacetate and the corresponding alkyl halides. The synthetic library was also screened for in vitro anti-microbial activity. Gas chromatographic analyses of I. helenium essential oil samples with spiked compounds from the synthesised library corroborated the tentative identifications of the long-chain 3-methyl-2-alkanones. The availability of these anti-microbial compounds from this library made it possible to construct GC/FID calibration curves and determine their content in the plant material: 0.08 - 24.2 mg/100 g of dry roots. The small combinatorial library approach enabled the first unequivocal identification of long-chain 3-methyl-2-alkanones as plant secondary metabolites, and, also, allowed determination of not only a single compound and biological properties, but those of a group of structurally related compounds. Copyright © 2013 John Wiley & Sons, Ltd.
HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets.

PubMed

De Kumar, Bony; Parker, Hugo J; Paulson, Ariel; Parrish, Mark E; Pushel, Irina; Singh, Narendra Pratap; Zhang, Ying; Slaughter, Brian D; Unruh, Jay R; Florens, Laurence; Zeitlinger, Julia; Krumlauf, Robb

2017-09-01

Hoxa1 has diverse functional roles in differentiation and development. We identify and characterize properties of regions bound by HOXA1 on a genome-wide basis in differentiating mouse ES cells. HOXA1-bound regions are enriched for clusters of consensus binding motifs for HOX, PBX, and MEIS, and many display co-occupancy of PBX and MEIS. PBX and MEIS are members of the TALE family and genome-wide analysis of multiple TALE members (PBX, MEIS, TGIF, PREP1, and PREP2) shows that nearly all HOXA1 targets display occupancy of one or more TALE members. The combinatorial binding patterns of TALE proteins define distinct classes of HOXA1 targets, which may create functional diversity. Transgenic reporter assays in zebrafish confirm enhancer activities for many HOXA1-bound regions and the importance of HOX-PBX and TGIF motifs for their regulation. Proteomic analyses show that HOXA1 physically interacts on chromatin with PBX, MEIS, and PREP family members, but not with TGIF, suggesting that TGIF may have an independent input into HOXA1-bound regions. Therefore, TALE proteins appear to represent a wide repertoire of HOX cofactors, which may coregulate enhancers through distinct mechanisms. We also discover extensive auto- and cross-regulatory interactions among the Hoxa1 and TALE genes, indicating that the specificity of HOXA1 during development may be regulated though a complex cross-regulatory network of HOXA1 and TALE proteins. This study provides new insight into a regulatory network involving combinatorial interactions between HOXA1 and TALE proteins. © 2017 De Kumar et al.; Published by Cold Spring Harbor Laboratory Press.
Rule-based spatial modeling with diffusing, geometrically constrained molecules.

PubMed

Gruenert, Gerd; Ibrahim, Bashar; Lenser, Thorsten; Lohel, Maiko; Hinze, Thomas; Dittrich, Peter

2010-06-07

We suggest a new type of modeling approach for the coarse grained, particle-based spatial simulation of combinatorially complex chemical reaction systems. In our approach molecules possess a location in the reactor as well as an orientation and geometry, while the reactions are carried out according to a list of implicitly specified reaction rules. Because the reaction rules can contain patterns for molecules, a combinatorially complex or even infinitely sized reaction network can be defined. For our implementation (based on LAMMPS), we have chosen an already existing formalism (BioNetGen) for the implicit specification of the reaction network. This compatibility allows to import existing models easily, i.e., only additional geometry data files have to be provided. Our simulations show that the obtained dynamics can be fundamentally different from those simulations that use classical reaction-diffusion approaches like Partial Differential Equations or Gillespie-type spatial stochastic simulation. We show, for example, that the combination of combinatorial complexity and geometric effects leads to the emergence of complex self-assemblies and transportation phenomena happening faster than diffusion (using a model of molecular walkers on microtubules). When the mentioned classical simulation approaches are applied, these aspects of modeled systems cannot be observed without very special treatment. Further more, we show that the geometric information can even change the organizational structure of the reaction system. That is, a set of chemical species that can in principle form a stationary state in a Differential Equation formalism, is potentially unstable when geometry is considered, and vice versa. We conclude that our approach provides a new general framework filling a gap in between approaches with no or rigid spatial representation like Partial Differential Equations and specialized coarse-grained spatial simulation systems like those for DNA or virus capsid self-assembly.
Rule-based spatial modeling with diffusing, geometrically constrained molecules

PubMed Central

2010-01-01

Background We suggest a new type of modeling approach for the coarse grained, particle-based spatial simulation of combinatorially complex chemical reaction systems. In our approach molecules possess a location in the reactor as well as an orientation and geometry, while the reactions are carried out according to a list of implicitly specified reaction rules. Because the reaction rules can contain patterns for molecules, a combinatorially complex or even infinitely sized reaction network can be defined. For our implementation (based on LAMMPS), we have chosen an already existing formalism (BioNetGen) for the implicit specification of the reaction network. This compatibility allows to import existing models easily, i.e., only additional geometry data files have to be provided. Results Our simulations show that the obtained dynamics can be fundamentally different from those simulations that use classical reaction-diffusion approaches like Partial Differential Equations or Gillespie-type spatial stochastic simulation. We show, for example, that the combination of combinatorial complexity and geometric effects leads to the emergence of complex self-assemblies and transportation phenomena happening faster than diffusion (using a model of molecular walkers on microtubules). When the mentioned classical simulation approaches are applied, these aspects of modeled systems cannot be observed without very special treatment. Further more, we show that the geometric information can even change the organizational structure of the reaction system. That is, a set of chemical species that can in principle form a stationary state in a Differential Equation formalism, is potentially unstable when geometry is considered, and vice versa. Conclusions We conclude that our approach provides a new general framework filling a gap in between approaches with no or rigid spatial representation like Partial Differential Equations and specialized coarse-grained spatial simulation systems like those for DNA or virus capsid self-assembly. PMID:20529264
Wafer-Fused Orientation-Patterned GaAs

DTIC Science & Technology

2008-02-13

frequencies utilizing existing industrial foundries. 15. SUBJECT TERMS Orientation-patterned Gallium Arsenide, hydride vapor phase epitaxy, quasi-phase... Gallium Arsenide, hydride vapor phase epitaxy, quasi-phase-matching, nonlinear frequency conversion 1. INTRODUCTION Quasi-phase-matching (QPM)1...and E. Lallier, “Second harmonic generation of CO2 laser using thick quasi-phase-matched GaAs layer grown by hydride vapour phase epitaxy
An Indexed Combinatorial Library: The Synthesis and Testing of Insect Repellents

NASA Astrophysics Data System (ADS)

Miles, William H.; Gelato, Kathy A.; Pompizzi, Kristen M.; Scarbinsky, Aislinn M.; Albrecht, Brian K.; Reynolds, Elaine R.

2001-04-01

An indexed combinatorial library of amides was prepared by the reaction of amines and acid chlorides. A simple test for insect repellency using fruit flies (Drosophila melanogaster) allowed the determination of the most repellent sublibraries. The student-generated data were collected and analyzed to determine the most active amide(s) in the library. This experiment illustrates the fundamentals of combinatorial chemistry, a field that has undergone explosive growth in the last decade.
Control of Multilayer Networks

PubMed Central

Menichetti, Giulia; Dall’Asta, Luca; Bianconi, Ginestra

2016-01-01

The controllability of a network is a theoretical problem of relevance in a variety of contexts ranging from financial markets to the brain. Until now, network controllability has been characterized only on isolated networks, while the vast majority of complex systems are formed by multilayer networks. Here we build a theoretical framework for the linear controllability of multilayer networks by mapping the problem into a combinatorial matching problem. We found that correlating the external signals in the different layers can significantly reduce the multiplex network robustness to node removal, as it can be seen in conjunction with a hybrid phase transition occurring in interacting Poisson networks. Moreover we observe that multilayer networks can stabilize the fully controllable multiplex network configuration that can be stable also when the full controllability of the single network is not stable. PMID:26869210
Multiple-variable neighbourhood search for the single-machine total weighted tardiness problem

NASA Astrophysics Data System (ADS)

Chung, Tsui-Ping; Fu, Qunjie; Liao, Ching-Jong; Liu, Yi-Ting

2017-07-01

The single-machine total weighted tardiness (SMTWT) problem is a typical discrete combinatorial optimization problem in the scheduling literature. This problem has been proved to be NP hard and thus provides a challenging area for metaheuristics, especially the variable neighbourhood search algorithm. In this article, a multiple variable neighbourhood search (m-VNS) algorithm with multiple neighbourhood structures is proposed to solve the problem. Special mechanisms named matching and strengthening operations are employed in the algorithm, which has an auto-revising local search procedure to explore the solution space beyond local optimality. Two aspects, searching direction and searching depth, are considered, and neighbourhood structures are systematically exchanged. Experimental results show that the proposed m-VNS algorithm outperforms all the compared algorithms in solving the SMTWT problem.
A smart way to identify and extract repeated patterns of a layout

NASA Astrophysics Data System (ADS)

Wei, Fang; Gu, Tingting; Chu, Zhihao; Zhang, Chenming; Chen, Han; Zhu, Jun; Hu, Xinyi; Du, Chunshan; Wan, Qijian; Liu, Zhengfang

2018-03-01

As integrated circuits (IC) technology moves forward, manufacturing process is facing more and more challenges. Optical proximity correction (OPC) has been playing an important role in the whole manufacturing process. In the deep sub-micron technology, OPC engineers not only need to guarantee the layout designs to be manufacturable but also take a more precise control of the critical patterns to ensure a high performance circuit. One of the tasks that would like to be performed is the consistency checking as the identical patterns under identical context should have identical OPC results in theory, like SRAM regions. Consistency checking is essentially a technique of repeated patterns identification, extraction and derived patterns (i.e. OPC results) comparison. The layout passing to the OPC team may not have enough design hierarchical information either because the original designs may have undergone several layout processing steps or some other unknown reasons. This paper presents a generic way to identify and extract repeated layout structures in SRAM regions purely based on layout pattern analysis through Calibre Pattern Matching and Calibre equation-based DRC (eqDRC). Without Pattern Matching and eqDRC, it will take lots of effort to manually get it done by trial and error, it is almost impossible to automate the pattern analysis process. Combining Pattern Matching and eqDRC opens a new way to implement this flow. The repeated patterns must have some fundamental features for measurement of pitches in the horizontal and vertical direction separately by Calibre eqDRC and meanwhile can be a helper to generate some anchor points which will be the starting points for Pattern Matching to capture patterns. The informative statistical report from the pattern search tells the match counts individually for each patterns captured. Experiment shows that this is a smart way of identifying and extracting repeated structures effectively. The OPC results are the derived layers on these repeated structures, by running pattern search using design layers as pattern layers and OPC results as marker layers, it is an easy job to compare the consistency.
Practical relevance of pattern uniqueness in forensic science.

PubMed

Jayaprakash, Paul T

2013-09-10

Uniqueness being unprovable, it has recently been argued that individualization in forensic science is irrelevant and, probability, as applied for DNA profiles, should be applied for all identifications. Critiques against uniqueness have omitted physical matching, a realistic and tangible individualization that supports uniqueness. Describing case examples illustrating pattern matches including physical matching, it is indicated that individualizations are practically relevant for forensic science as they establish facts on a definitive basis providing firm leads benefitting criminal investigation. As a tenet of forensic identification, uniqueness forms a fundamental paradigm relevant for individualization. Evidence on the indeterministic and stochastic causal pathways of characteristics in patterns available in the related fields of science sufficiently supports the proposition of uniqueness. Characteristics involved in physical matching and matching achieved in patterned evidence existing in the state of nature are not events amenable for counting; instead these are ensemble of visible units occupying the entire pattern area stretching the probability of re-occurrence of a verisimilitude pattern into infinity offering epistemic support to uniqueness. Observational methods are as respectable as instrumental or statistical methods since they are capable of generating results that are tangible and obviously valid as in physical matching. Applying the probabilistic interpretation used for DNA profiles to the other patterns would be unbefitting since these two are disparate, the causal pathways of the events, the loci, in the manipulated DNA profiles being determinable. While uniqueness enables individualizations, it does not vouch for eliminating errors. Instead of dismissing uniqueness and individualization, accepting errors as human or system failures and seeking remedial measures would benefit forensic science practice and criminal investigation. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Evolutionary combinatorial chemistry, a novel tool for SAR studies on peptide transport across the blood-brain barrier. Part 2. Design, synthesis and evaluation of a first generation of peptides.

PubMed

Teixidó, Meritxell; Belda, Ignasi; Zurita, Esther; Llorà, Xavier; Fabre, Myriam; Vilaró, Senén; Albericio, Fernando; Giralt, Ernest

2005-12-01

The use of high-throughput methods in drug discovery allows the generation and testing of a large number of compounds, but at the price of providing redundant information. Evolutionary combinatorial chemistry combines the selection and synthesis of biologically active compounds with artificial intelligence optimization methods, such as genetic algorithms (GA). Drug candidates for the treatment of central nervous system (CNS) disorders must overcome the blood-brain barrier (BBB). This paper reports a new genetic algorithm that searches for the optimal physicochemical properties for peptide transport across the blood-brain barrier. A first generation of peptides has been generated and synthesized. Due to the high content of N-methyl amino acids present in most of these peptides, their syntheses were especially challenging due to over-incorporations, deletions and DKP formations. Distinct fragmentation patterns during peptide cleavage have been identified. The first generation of peptides has been studied by evaluation techniques such as immobilized artificial membrane chromatography (IAMC), a cell-based assay, log Poctanol/water calculations, etc. Finally, a second generation has been proposed. (c) 2005 European Peptide Society and John Wiley & Sons, Ltd.
Laser direct writing of combinatorial libraries of idealized cellular constructs: Biomedical applications

NASA Astrophysics Data System (ADS)

Schiele, Nathan R.; Koppes, Ryan A.; Corr, David T.; Ellison, Karen S.; Thompson, Deanna M.; Ligon, Lee A.; Lippert, Thomas K. M.; Chrisey, Douglas B.

2009-03-01

The ability to control cell placement and to produce idealized cellular constructs is essential for understanding and controlling intercellular processes and ultimately for producing engineered tissue replacements. We have utilized a novel intra-cavity variable aperture excimer laser operated at 193 nm to reproducibly direct write mammalian cells with micrometer resolution to form a combinatorial array of idealized cellular constructs. We deposited patterns of human dermal fibroblasts, mouse myoblasts, rat neural stem cells, human breast cancer cells, and bovine pulmonary artery endothelial cells to study aspects of collagen network formation, breast cancer progression, and neural stem cell proliferation, respectively. Mammalian cells were deposited by matrix assisted pulsed laser evaporation direct write from ribbons comprised of a UV transparent quartz coated with either a thin layer of extracellular matrix or triazene as a dynamic release layer using CAD/CAM control. We demonstrate that through optical imaging and incorporation of a machine vision algorithm, specific cells on the ribbon can be laser deposited in spatial coherence with respect to geometrical arrays and existing cells on the receiving substrate. Having the ability to direct write cells into idealized cellular constructs can help to answer many biomedical questions and advance tissue engineering and cancer research.
Effect of Composition on the Voltage Fade Phenomenon in Lithium-, Manganese-Rich xLiMnO 3•(1-x)LiNi aMn bCo cO 2: A Combinatorial Synthesis Approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vu, Anh; Qin, Yan; Bareno, Javier

2015-10-30

The effect of composition on the voltage fade phenomenon was probed using combinatorial synthesis methods. In compositions that have the general formula, (Li 2MnO 3) a(LiNiO 2) b(LiMnO 2) c(LiCoO 2) d, where 0 ≤ a≤0.83, 0.15 ≤ b ≤ 0.42, 0 ≤ c ≤ 0.85, and 0 ≤ d ≤ 0.30 (a + b + c + d = 1), the dependence of features in the x-ray diffraction pattern and of voltage fade on composition were identified and mapped. The observed values of voltage fade indicated that it displayed some sensitivity to composition, but that the sensitivity was notmore » large. The values of voltage fade were found to be amenable to statistical modeling. The model indicated that it may be possible to lower the value of voltage fade below 0.01% by adjusting the composition of the system; however, the composition is not expected to have the layered–layered structure.« less
Expediting Combinatorial Data Set Analysis by Combining Human and Algorithmic Analysis.

PubMed

Stein, Helge Sören; Jiao, Sally; Ludwig, Alfred

2017-01-09

A challenge in combinatorial materials science remains the efficient analysis of X-ray diffraction (XRD) data and its correlation to functional properties. Rapid identification of phase-regions and proper assignment of corresponding crystal structures is necessary to keep pace with the improved methods for synthesizing and characterizing materials libraries. Therefore, a new modular software called htAx (high-throughput analysis of X-ray and functional properties data) is presented that couples human intelligence tasks used for "ground-truth" phase-region identification with subsequent unbiased verification by an algorithm to efficiently analyze which phases are present in a materials library. Identified phases and phase-regions may then be correlated to functional properties in an expedited manner. For the functionality of htAx to be proven, two previously published XRD benchmark data sets of the materials systems Al-Cr-Fe-O and Ni-Ti-Cu are analyzed by htAx. The analysis of ∼1000 XRD patterns takes less than 1 day with htAx. The proposed method reliably identifies phase-region boundaries and robustly identifies multiphase structures. The method also addresses the problem of identifying regions with previously unpublished crystal structures using a special daisy ternary plot.
A combinatorial approach to angiosperm pollen morphology.

PubMed

Mander, Luke

2016-11-30

Angiosperms (flowering plants) are strikingly diverse. This is clearly expressed in the morphology of their pollen grains, which are characterized by enormous variety in their shape and patterning. In this paper, I approach angiosperm pollen morphology from the perspective of enumerative combinatorics. This involves generating angiosperm pollen morphotypes by algorithmically combining character states and enumerating the results of these combinations. I use this approach to generate 3 643 200 pollen morphotypes, which I visualize using a parallel-coordinates plot. This represents a raw morphospace. To compare real-world and theoretical morphologies, I map the pollen of 1008 species of Neotropical angiosperms growing on Barro Colorado Island (BCI), Panama, onto this raw morphospace. This highlights that, in addition to their well-documented taxonomic diversity, Neotropical rainforests also represent an enormous reservoir of morphological diversity. Angiosperm pollen morphospace at BCI has been filled mostly by pollen morphotypes that are unique to single plant species. Repetition of pollen morphotypes among higher taxa at BCI reflects both constraint and convergence. This combinatorial approach to morphology addresses the complexity that results from large numbers of discrete character combinations and could be employed in any situation where organismal form can be captured by discrete morphological characters. © 2016 The Author(s).
A combinatorial approach to angiosperm pollen morphology

PubMed Central

2016-01-01

Angiosperms (flowering plants) are strikingly diverse. This is clearly expressed in the morphology of their pollen grains, which are characterized by enormous variety in their shape and patterning. In this paper, I approach angiosperm pollen morphology from the perspective of enumerative combinatorics. This involves generating angiosperm pollen morphotypes by algorithmically combining character states and enumerating the results of these combinations. I use this approach to generate 3 643 200 pollen morphotypes, which I visualize using a parallel-coordinates plot. This represents a raw morphospace. To compare real-world and theoretical morphologies, I map the pollen of 1008 species of Neotropical angiosperms growing on Barro Colorado Island (BCI), Panama, onto this raw morphospace. This highlights that, in addition to their well-documented taxonomic diversity, Neotropical rainforests also represent an enormous reservoir of morphological diversity. Angiosperm pollen morphospace at BCI has been filled mostly by pollen morphotypes that are unique to single plant species. Repetition of pollen morphotypes among higher taxa at BCI reflects both constraint and convergence. This combinatorial approach to morphology addresses the complexity that results from large numbers of discrete character combinations and could be employed in any situation where organismal form can be captured by discrete morphological characters. PMID:27881756
Searching for substructures in fragment spaces.

PubMed

Ehrlich, Hans-Christian; Volkamer, Andrea; Rarey, Matthias

2012-12-21

A common task in drug development is the selection of compounds fulfilling specific structural features from a large data pool. While several methods that iteratively search through such data sets exist, their application is limited compared to the infinite character of molecular space. The introduction of the concept of fragment spaces (FSs), which are composed of molecular fragments and their connection rules, made the representation of large combinatorial data sets feasible. At the same time, search algorithms face the problem of structural features spanning over multiple fragments. Due to the combinatorial nature of FSs, an enumeration of all products is impossible. In order to overcome these time and storage issues, we present a method that is able to find substructures in FSs without explicit product enumeration. This is accomplished by splitting substructures into subsubstructures and mapping them onto fragments with respect to fragment connectivity rules. The method has been evaluated on three different drug discovery scenarios considering the exploration of a molecule class, the elaboration of decoration patterns for a molecular core, and the exhaustive query for peptides in FSs. FSs can be searched in seconds, and found products contain novel compounds not present in the PubChem database which may serve as hints for new lead structures.
Learning graph matching.

PubMed

Caetano, Tibério S; McAuley, Julian J; Cheng, Li; Le, Quoc V; Smola, Alex J

2009-06-01

As a fundamental problem in pattern recognition, graph matching has applications in a variety of fields, from computer vision to computational biology. In graph matching, patterns are modeled as graphs and pattern recognition amounts to finding a correspondence between the nodes of different graphs. Many formulations of this problem can be cast in general as a quadratic assignment problem, where a linear term in the objective function encodes node compatibility and a quadratic term encodes edge compatibility. The main research focus in this theme is about designing efficient algorithms for approximately solving the quadratic assignment problem, since it is NP-hard. In this paper we turn our attention to a different question: how to estimate compatibility functions such that the solution of the resulting graph matching problem best matches the expected solution that a human would manually provide. We present a method for learning graph matching: the training examples are pairs of graphs and the 'labels' are matches between them. Our experimental results reveal that learning can substantially improve the performance of standard graph matching algorithms. In particular, we find that simple linear assignment with such a learning scheme outperforms Graduated Assignment with bistochastic normalisation, a state-of-the-art quadratic assignment relaxation algorithm.
The Interglomerular Circuit Potently Inhibits Olfactory Bulb Output Neurons by Both Direct and Indirect Pathways.

PubMed

Liu, Shaolin; Puche, Adam C; Shipley, Michael T

2016-09-14

Sensory processing shapes our perception. In mammals, odor information is encoded by combinatorial activity patterns of olfactory bulb (OB) glomeruli. Glomeruli are richly interconnected by short axon cells (SACs), which form the interglomerular circuit (IGC). It is unclear how the IGC impacts OB output to downstream neural circuits. We combined in vitro and in vivo electrophysiology with optogenetics in mice and found the following: (1) the IGC potently and monosynaptically inhibits the OB output neurons mitral/tufted cells (MTCs) by GABA release from SACs: (2) gap junction-mediated electrical coupling is strong for the SAC→MTC synapse, but negligible for the SAC→ETC synapse; (3) brief IGC-mediated inhibition is temporally prolonged by the intrinsic properties of MTCs; and (4) sniff frequency IGC activation in vivo generates persistent MTC inhibition. These findings suggest that the temporal sequence of glomerular activation by sensory input determines which stimulus features are transmitted to downstream olfactory networks and those filtered by lateral inhibition. Odor identity is encoded by combinatorial patterns of activated glomeruli, the initial signal transformation site of the olfactory system. Lateral circuit processing among activated glomeruli modulates olfactory signal transformation before transmission to higher brain centers. Using a combination of in vitro and in vivo optogenetics, this work demonstrates that interglomerular circuitry produces potent inhibition of olfactory bulb output neurons via direct chemical and electrical synapses as well as by indirect pathways. The direct inhibitory synaptic input engages mitral cell intrinsic membrane properties to generate inhibition that outlasts the initial synaptic action. Copyright © 2016 the authors 0270-6474/16/369604-14$15.00/0.
Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development

PubMed Central

Kazemian, Majid; Pham, Hannah; Wolfe, Scot A.; Brodsky, Michael H.; Sinha, Saurabh

2013-01-01

Regulation of eukaryotic gene transcription is often combinatorial in nature, with multiple transcription factors (TFs) regulating common target genes, often through direct or indirect mutual interactions. Many individual examples of cooperative binding by directly interacting TFs have been identified, but it remains unclear how pervasive this mechanism is during animal development. Cooperative TF binding should be manifest in genomic sequences as biased arrangements of TF-binding sites. Here, we explore the extent and diversity of such arrangements related to gene regulation during Drosophila embryogenesis. We used the DNA-binding specificities of 322 TFs along with chromatin accessibility information to identify enriched spacing and orientation patterns of TF-binding site pairs. We developed a new statistical approach for this task, specifically designed to accurately assess inter-site spacing biases while accounting for the phenomenon of homotypic site clustering commonly observed in developmental regulatory regions. We observed a large number of short-range distance preferences between TF-binding site pairs, including examples where the preference depends on the relative orientation of the binding sites. To test whether these binding site patterns reflect physical interactions between the corresponding TFs, we analyzed 27 TF pairs whose binding sites exhibited short distance preferences. In vitro protein–protein binding experiments revealed that >65% of these TF pairs can directly interact with each other. For five pairs, we further demonstrate that they bind cooperatively to DNA if both sites are present with the preferred spacing. This study demonstrates how DNA-binding motifs can be used to produce a comprehensive map of sequence signatures for different mechanisms of combinatorial TF action. PMID:23847101
Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development.

PubMed

Kazemian, Majid; Pham, Hannah; Wolfe, Scot A; Brodsky, Michael H; Sinha, Saurabh

2013-09-01

Regulation of eukaryotic gene transcription is often combinatorial in nature, with multiple transcription factors (TFs) regulating common target genes, often through direct or indirect mutual interactions. Many individual examples of cooperative binding by directly interacting TFs have been identified, but it remains unclear how pervasive this mechanism is during animal development. Cooperative TF binding should be manifest in genomic sequences as biased arrangements of TF-binding sites. Here, we explore the extent and diversity of such arrangements related to gene regulation during Drosophila embryogenesis. We used the DNA-binding specificities of 322 TFs along with chromatin accessibility information to identify enriched spacing and orientation patterns of TF-binding site pairs. We developed a new statistical approach for this task, specifically designed to accurately assess inter-site spacing biases while accounting for the phenomenon of homotypic site clustering commonly observed in developmental regulatory regions. We observed a large number of short-range distance preferences between TF-binding site pairs, including examples where the preference depends on the relative orientation of the binding sites. To test whether these binding site patterns reflect physical interactions between the corresponding TFs, we analyzed 27 TF pairs whose binding sites exhibited short distance preferences. In vitro protein-protein binding experiments revealed that >65% of these TF pairs can directly interact with each other. For five pairs, we further demonstrate that they bind cooperatively to DNA if both sites are present with the preferred spacing. This study demonstrates how DNA-binding motifs can be used to produce a comprehensive map of sequence signatures for different mechanisms of combinatorial TF action.
Comparison of dissimilarity measures for cluster analysis of X-ray diffraction data from combinatorial libraries

NASA Astrophysics Data System (ADS)

Iwasaki, Yuma; Kusne, A. Gilad; Takeuchi, Ichiro

2017-12-01

Machine learning techniques have proven invaluable to manage the ever growing volume of materials research data produced as developments continue in high-throughput materials simulation, fabrication, and characterization. In particular, machine learning techniques have been demonstrated for their utility in rapidly and automatically identifying potential composition-phase maps from structural data characterization of composition spread libraries, enabling rapid materials fabrication-structure-property analysis and functional materials discovery. A key issue in development of an automated phase-diagram determination method is the choice of dissimilarity measure, or kernel function. The desired measure reduces the impact of confounding structural data issues on analysis performance. The issues include peak height changes and peak shifting due to lattice constant change as a function of composition. In this work, we investigate the choice of dissimilarity measure in X-ray diffraction-based structure analysis and the choice of measure's performance impact on automatic composition-phase map determination. Nine dissimilarity measures are investigated for their impact in analyzing X-ray diffraction patterns for a Fe-Co-Ni ternary alloy composition spread. The cosine, Pearson correlation coefficient, and Jensen-Shannon divergence measures are shown to provide the best performance in the presence of peak height change and peak shifting (due to lattice constant change) when the magnitude of peak shifting is unknown. With prior knowledge of the maximum peak shifting, dynamic time warping in a normalized constrained mode provides the best performance. This work also serves to demonstrate a strategy for rapid analysis of a large number of X-ray diffraction patterns in general beyond data from combinatorial libraries.
The Interglomerular Circuit Potently Inhibits Olfactory Bulb Output Neurons by Both Direct and Indirect Pathways

PubMed Central

Puche, Adam C.; Shipley, Michael T.

2016-01-01

Sensory processing shapes our perception. In mammals, odor information is encoded by combinatorial activity patterns of olfactory bulb (OB) glomeruli. Glomeruli are richly interconnected by short axon cells (SACs), which form the interglomerular circuit (IGC). It is unclear how the IGC impacts OB output to downstream neural circuits. We combined in vitro and in vivo electrophysiology with optogenetics in mice and found the following: (1) the IGC potently and monosynaptically inhibits the OB output neurons mitral/tufted cells (MTCs) by GABA release from SACs: (2) gap junction-mediated electrical coupling is strong for the SAC→MTC synapse, but negligible for the SAC→ETC synapse; (3) brief IGC-mediated inhibition is temporally prolonged by the intrinsic properties of MTCs; and (4) sniff frequency IGC activation in vivo generates persistent MTC inhibition. These findings suggest that the temporal sequence of glomerular activation by sensory input determines which stimulus features are transmitted to downstream olfactory networks and those filtered by lateral inhibition. SIGNIFICANCE STATEMENT Odor identity is encoded by combinatorial patterns of activated glomeruli, the initial signal transformation site of the olfactory system. Lateral circuit processing among activated glomeruli modulates olfactory signal transformation before transmission to higher brain centers. Using a combination of in vitro and in vivo optogenetics, this work demonstrates that interglomerular circuitry produces potent inhibition of olfactory bulb output neurons via direct chemical and electrical synapses as well as by indirect pathways. The direct inhibitory synaptic input engages mitral cell intrinsic membrane properties to generate inhibition that outlasts the initial synaptic action. PMID:27629712
A mass action model of a Fibroblast Growth Factor signaling pathway and its simplification.

PubMed

Gaffney, E A; Heath, J K; Kwiatkowska, M Z

2008-11-01

We consider a kinetic law of mass action model for Fibroblast Growth Factor (FGF) signaling, focusing on the induction of the RAS-MAP kinase pathway via GRB2 binding. Our biologically simple model suffers a combinatorial explosion in the number of differential equations required to simulate the system. In addition to numerically solving the full model, we show that it can be accurately simplified. This requires combining matched asymptotics, the quasi-steady state hypothesis, and the fact subsets of the equations decouple asymptotically. Both the full and simplified models reproduce the qualitative dynamics observed experimentally and in previous stochastic models. The simplified model also elucidates both the qualitative features of GRB2 binding and the complex relationship between SHP2 levels, the rate SHP2 induces dephosphorylation and levels of bound GRB2. In addition to providing insight into the important and redundant features of FGF signaling, such work further highlights the usefulness of numerous simplification techniques in the study of mass action models of signal transduction, as also illustrated recently by Borisov and co-workers (Borisov et al. in Biophys. J. 89, 951-966, 2005, Biosystems 83, 152-166, 2006; Kiyatkin et al. in J. Biol. Chem. 281, 19925-19938, 2006). These developments will facilitate the construction of tractable models of FGF signaling, incorporating further biological realism, such as spatial effects or realistic binding stoichiometries, despite a more severe combinatorial explosion associated with the latter.
Combinatorial fabrication and screening of organic light-emitting device arrays

NASA Astrophysics Data System (ADS)

Shinar, Joseph; Shinar, Ruth; Zhou, Zhaoqun

2007-11-01

The combinatorial fabrication and screening of 2-dimensional (2-d) small molecular UV-violet organic light-emitting device (OLED) arrays, 1-d blue-to-red arrays, 1-d intense white OLED libraries, 1-d arrays to study Förster energy transfer in guest-host OLEDs, and 2-d arrays to study exciplex emission from OLEDs is described. The results demonstrate the power of combinatorial approaches for screening OLED materials and configurations, and for studying their basic properties.
Combinatorial Dyson-Schwinger equations and inductive data types

NASA Astrophysics Data System (ADS)

Kock, Joachim

2016-06-01

The goal of this contribution is to explain the analogy between combinatorial Dyson-Schwinger equations and inductive data types to a readership of mathematical physicists. The connection relies on an interpretation of combinatorial Dyson-Schwinger equations as fixpoint equations for polynomial functors (established elsewhere by the author, and summarised here), combined with the now-classical fact that polynomial functors provide semantics for inductive types. The paper is expository, and comprises also a brief introduction to type theory.
Combinatorial chemistry on solid support in the search for central nervous system agents.

PubMed

Zajdel, Paweł; Pawłowski, Maciej; Martinez, Jean; Subra, Gilles

2009-08-01

The advent of combinatorial chemistry was one of the most important developments, that has significantly contributed to the drug discovery process. Within just a few years, its initial concept aimed at production of libraries containing huge number of compounds (thousands to millions), so called screening libraries, has shifted towards preparation of small and medium-sized rationally designed libraries. When applicable, the use of solid supports for the generation of libraries has been a real breakthrough in enhancing productivity. With a limited amount of resin and simple manual workups, the split/mix procedure may generate thousands of bead-tethered compounds. Beads can be chemically or physically encoded to facilitate the identification of a hit after the biological assay. Compartmentalization of solid supports using small reactors like teabags, kans or pellicular discrete supports like Lanterns resulted in powerful sort and combine technologies, relying on codes 'written' on the reactor, and thus reducing the need for automation and improving the number of compounds synthesized. These methods of solid-phase combinatorial chemistry have been recently supported by introduction of solid-supported reagents and scavenger resins. The first part of this review discusses the general premises of combinatorial chemistry and some methods used in the design of primary and focused combinatorial libraries. The aim of the second part is to present combinatorial chemistry methodologies aimed at discovering bioactive compounds acting on diverse GPCR involved in central nervous system disorders.
Combinatorial stresses kill pathogenic Candida species

PubMed Central

Kaloriti, Despoina; Tillmann, Anna; Cook, Emily; Jacobsen, Mette; You, Tao; Lenardon, Megan; Ames, Lauren; Barahona, Mauricio; Chandrasekaran, Komelapriya; Coghill, George; Goodman, Daniel; Gow, Neil A. R.; Grebogi, Celso; Ho, Hsueh-Lui; Ingram, Piers; McDonagh, Andrew; De Moura, Alessandro P. S.; Pang, Wei; Puttnam, Melanie; Radmaneshfar, Elahe; Romano, Maria Carmen; Silk, Daniel; Stark, Jaroslav; Stumpf, Michael; Thiel, Marco; Thorne, Thomas; Usher, Jane; Yin, Zhikang; Haynes, Ken; Brown, Alistair J. P.

2012-01-01

Pathogenic microbes exist in dynamic niches and have evolved robust adaptive responses to promote survival in their hosts. The major fungal pathogens of humans, Candida albicans and Candida glabrata, are exposed to a range of environmental stresses in their hosts including osmotic, oxidative and nitrosative stresses. Significant efforts have been devoted to the characterization of the adaptive responses to each of these stresses. In the wild, cells are frequently exposed simultaneously to combinations of these stresses and yet the effects of such combinatorial stresses have not been explored. We have developed a common experimental platform to facilitate the comparison of combinatorial stress responses in C. glabrata and C. albicans. This platform is based on the growth of cells in buffered rich medium at 30°C, and was used to define relatively low, medium and high doses of osmotic (NaCl), oxidative (H 2O2) and nitrosative stresses (e.g., dipropylenetriamine (DPTA)-NONOate). The effects of combinatorial stresses were compared with the corresponding individual stresses under these growth conditions. We show for the first time that certain combinations of combinatorial stress are especially potent in terms of their ability to kill C. albicans and C. glabrata and/or inhibit their growth. This was the case for combinations of osmotic plus oxidative stress and for oxidative plus nitrosative stress. We predict that combinatorial stresses may be highly signif cant in host defences against these pathogenic yeasts. PMID:22463109
Steam explosion and its combinatorial pretreatment refining technology of plant biomass to bio-based products.

PubMed

Chen, Hong-Zhang; Liu, Zhi-Hua

2015-06-01

Pretreatment is a key unit operation affecting the refinery efficiency of plant biomass. However, the poor efficiency of pretreatment and the lack of basic theory are the main challenges to the industrial implementation of the plant biomass refinery. The purpose of this work is to review steam explosion and its combinatorial pretreatment as a means of overcoming the intrinsic characteristics of plant biomass, including recalcitrance, heterogeneity, multi-composition, and diversity. The main advantages of the selective use of steam explosion and other combinatorial pretreatments across the diversity of raw materials are introduced. Combinatorial pretreatment integrated with other unit operations is proposed as a means to exploit the high-efficiency production of bio-based products from plant biomass. Finally, several pilot- and demonstration-scale operations of the plant biomass refinery are described. Based on the principle of selective function and structure fractionation, and multi-level and directional composition conversion, an integrated process with the combinatorial pretreatments of steam explosion and other pretreatments as the core should be feasible and conform to the plant biomass refinery concept. Combinatorial pretreatments of steam explosion and other pretreatments should be further exploited based on the type and intrinsic characteristics of the plant biomass used, the bio-based products to be made, and the complementarity of the processes. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
LateBiclustering: Efficient Heuristic Algorithm for Time-Lagged Bicluster Identification.

PubMed

Gonçalves, Joana P; Madeira, Sara C

2014-01-01

Identifying patterns in temporal data is key to uncover meaningful relationships in diverse domains, from stock trading to social interactions. Also of great interest are clinical and biological applications, namely monitoring patient response to treatment or characterizing activity at the molecular level. In biology, researchers seek to gain insight into gene functions and dynamics of biological processes, as well as potential perturbations of these leading to disease, through the study of patterns emerging from gene expression time series. Clustering can group genes exhibiting similar expression profiles, but focuses on global patterns denoting rather broad, unspecific responses. Biclustering reveals local patterns, which more naturally capture the intricate collaboration between biological players, particularly under a temporal setting. Despite the general biclustering formulation being NP-hard, considering specific properties of time series has led to efficient solutions for the discovery of temporally aligned patterns. Notably, the identification of biclusters with time-lagged patterns, suggestive of transcriptional cascades, remains a challenge due to the combinatorial explosion of delayed occurrences. Herein, we propose LateBiclustering, a sensible heuristic algorithm enabling a polynomial rather than exponential time solution for the problem. We show that it identifies meaningful time-lagged biclusters relevant to the response of Saccharomyces cerevisiae to heat stress.

RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps

PubMed Central

Drory Retwitzer, Matan; Polishchuk, Maya; Churkin, Elena; Kifer, Ilona; Yakhini, Zohar; Barash, Danny

2015-01-01

Searching for RNA sequence-structure patterns is becoming an essential tool for RNA practitioners. Novel discoveries of regulatory non-coding RNAs in targeted organisms and the motivation to find them across a wide range of organisms have prompted the use of computational RNA pattern matching as an enhancement to sequence similarity. State-of-the-art programs differ by the flexibility of patterns allowed as queries and by their simplicity of use. In particular—no existing method is available as a user-friendly web server. A general program that searches for RNA sequence-structure patterns is RNA Structator. However, it is not available as a web server and does not provide the option to allow flexible gap pattern representation with an upper bound of the gap length being specified at any position in the sequence. Here, we introduce RNAPattMatch, a web-based application that is user friendly and makes sequence/structure RNA queries accessible to practitioners of various background and proficiency. It also extends RNA Structator and allows a more flexible variable gaps representation, in addition to analysis of results using energy minimization methods. RNAPattMatch service is available at http://www.cs.bgu.ac.il/rnapattmatch. A standalone version of the search tool is also available to download at the site. PMID:25940619
On the uniqueness of color patterns in raptor feathers

USGS Publications Warehouse

Ellis, D.H.

2009-01-01

For this study, I compared sequentially molted feathers for a few captive raptors from year to year and symmetrically matched feathers (left/right pairs) for many raptors to see if color patterns of sequential feather pairs were identical or if symmetrical pairs were mirror-image identical. Feather pairs were found to be identical only when without color pattern (e.g., the all-white rectrices of Bald Eagles [Haliaeetus leucocephalus]). Complex patterns were not closely matched, but some simple patterns were sometimes closely matched, although not identical. Previous claims that complex color patterns in feather pairs are fingerprint-identical (and therefore that molted feathers from wild raptors can be used to identify breeding adults from year to year with certainty) were found to be untrue: each feather is unique. Although it is unwise to be certain of bird of origin using normal feathers, abnormal feathers can often be so used. ?? 2009 The Raptor Research Foundation, Inc.
Evaluation of the Current Status of the Combinatorial Approach for the Study of Phase Diagrams

PubMed Central

Wong-Ng, W.

2012-01-01

This paper provides an evaluation of the effectiveness of using the high throughput combinatorial approach for preparing phase diagrams of thin film and bulk materials. Our evaluation is based primarily on examples of combinatorial phase diagrams that have been reported in the literature as well as based on our own laboratory experiments. Various factors that affect the construction of these phase diagrams are examined. Instrumentation and analytical approaches needed to improve data acquisition and data analysis are summarized. PMID:26900530
Research on thermal protection mechanism of forward-facing cavity and opposing jet combinatorial thermal protection system

NASA Astrophysics Data System (ADS)

Lu, Hai-Bo; Liu, Wei-Qiang

2014-04-01

Validated by the correlated experiments, a nose-tip with forward-facing cavity/opposing jet/the combinatorial configuration of forward-facing cavity and opposing jet thermal protection system (TPS) are investigated numerically. The physical mechanism of these TPS is discussed, and the cooling efficiency of them is compared. The combinatorial system is more suitable to be the TPS for the high speed vehicles which need fly under various flow conditions with long-range and long time.
Combinatorial approach to the representation of the Schur-Weyl duality in one-dimensional spin systems

NASA Astrophysics Data System (ADS)

Jakubczyk, Dorota; Jakubczyk, Paweł

2018-02-01

We propose combinatorial approach to the representation of Schur-Weyl duality in physical systems on the example of one-dimensional spin chains. Exploiting the Robinson-Schensted-Knuth algorithm, we perform decomposition of the dual group representations into irreducible representations in a fully combinatorial way. As representation space, we choose the Hilbert space of the spin chains, but this approach can be easily generalized to an arbitrary physical system where the Schur-Weyl duality works.
Massively multiplex single-cell Hi-C

PubMed Central

Ramani, Vijay; Deng, Xinxian; Qiu, Ruolan; Gunderson, Kevin L; Steemers, Frank J; Disteche, Christine M; Noble, William S; Duan, Zhijun; Shendure, Jay

2016-01-01

We present single-cell combinatorial indexed Hi-C (sciHi-C), which applies the concept of combinatorial cellular indexing to chromosome conformation capture. In this proof-of-concept, we generate and sequence six sciHi-C libraries comprising a total of 10,696 single cells. We use sciHi-C data to separate cells by karytoypic and cell-cycle state differences and identify cell-to-cell heterogeneity in mammalian chromosomal conformation. Our results demonstrate that combinatorial indexing is a generalizable strategy for single-cell genomics. PMID:28135255
Optimized stereo matching in binocular three-dimensional measurement system using structured light.

PubMed

Liu, Kun; Zhou, Changhe; Wei, Shengbin; Wang, Shaoqing; Fan, Xin; Ma, Jianyong

2014-09-10

In this paper, we develop an optimized stereo-matching method used in an active binocular three-dimensional measurement system. A traditional dense stereo-matching algorithm is time consuming due to a long search range and the high complexity of a similarity evaluation. We project a binary fringe pattern in combination with a series of N binary band limited patterns. In order to prune the search range, we execute an initial matching before exhaustive matching and evaluate a similarity measure using logical comparison instead of a complicated floating-point operation. Finally, an accurate point cloud can be obtained by triangulation methods and subpixel interpolation. The experiment results verify the computational efficiency and matching accuracy of the method.
Combinatorial Interdependence in Lottery

ERIC Educational Resources Information Center

Helman, Danny

2005-01-01

This paper examines a real life question of gamble facing lottery players. Combinatorial dependence plays a central role in shaping the game probabilistic structure, but might not carry the merited weight in punters' considerations.
Neural-network-based system for recognition of partially occluded shapes and patterns

NASA Astrophysics Data System (ADS)

Mital, Dinesh P.; Teoh, Eam-Khwang; Amarasinghe, S. K.; Suganthan, P. N.

1996-10-01

The purpose of this paper is to demonstrate how a structural matching approach can be used to perfonn effective rotational invariant fingerprint identification. In this approach, each of the exiracted features is correlated with Live of its nearest neighbouring features to form a local feature gmup for a first-stage matching. After that, the feature with the highest match is used as a central feature whereby all the other features are correlated to form a global feature group for a second.stage matching. The correlation between the features is in terms of distance and relative angle. This approach actually make the matching method rotational invariant A substantial amount of testing was carried out and it shows that this matching technique is capable of matching the four basic fingerprint patterns with an average matching time of4 seconds on a 66Mhz, 486 DX personal computer.
Ta2O5-memristor synaptic array with winner-take-all method for neuromorphic pattern matching

NASA Astrophysics Data System (ADS)

Truong, Son Ngoc; Van Pham, Khoa; Yang, Wonsun; Min, Kyeong-Sik; Abbas, Yawar; Kang, Chi Jung; Shin, Sangho; Pedrotti, Ken

2016-08-01

Pattern matching or pattern recognition is one of the elemental components that constitute the very complicated recalling and remembering process in human's brain. To realize this neuromorphic pattern matching, we fabricated and tested a 3 × 3 memristor synaptic array with the winner-take-all method in this research. In the measurement, first, the 3 × 3 Ta2O5 memristor array is programmed to store [LLL], [LHH], and [HLH], where L is a low-resistance state and H is a high-resistance state, at the 1st, 2nd, and 3rd columns, respectively. After the programming, three input patterns, [111], [100], and [010], are applied to the memristor synaptic array. From the measurement results, we confirm that all three input patterns can be recognized well by using a twin memristor crossbar with synaptic arrays. This measurement can be thought of as the first real verification of the twin memristor crossbar with memristive synaptic arrays for neuromorphic pattern recognition.
X-ray Moiré deflectometry using synthetic reference images

DOE PAGES

Stutman, Dan; Valdivia, Maria Pia; Finkenthal, Michael

2015-06-25

Moiré fringe deflectometry with grating interferometers is a technique that enables refraction-based x-ray imaging using a single exposure of an object. To obtain the refraction image, the method requires a reference fringe pattern (without the object). Our study shows that, in order to avoid artifacts, the reference pattern must be exactly matched in phase with the object fringe pattern. In experiments, however, it is difficult to produce a perfectly matched reference pattern due to unavoidable interferometer drifts. We present a simple method to obtain matched reference patterns using a phase-scan procedure to generate synthetic Moiré images. As a result, themore » method will enable deflectometric diagnostics of transient phenomena such as laser-produced plasmas and could improve the sensitivity and accuracy of medical phase-contrast imaging.« less
Datagram: Results of the NRMP for 1983.

ERIC Educational Resources Information Center

Graettinger, John S.

1983-01-01

Results of the National Resident Matching Program are discussed, including changes in enrollment, withdrawal, and matching patterns, data on foreign medical graduates, ratio of positions per applicant, specialization patterns, and program participation. Tabulations for each specialty are presented in numerical and percentage forms. (MSE)
Defect-free atomic array formation using the Hungarian matching algorithm

NASA Astrophysics Data System (ADS)

Lee, Woojun; Kim, Hyosub; Ahn, Jaewook

2017-05-01

Deterministic loading of single atoms onto arbitrary two-dimensional lattice points has recently been demonstrated, where by dynamically controlling the optical-dipole potential, atoms from a probabilistically loaded lattice were relocated to target lattice points to form a zero-entropy atomic lattice. In this atom rearrangement, how to pair atoms with the target sites is a combinatorial optimization problem: brute-force methods search all possible combinations so the process is slow, while heuristic methods are time efficient but optimal solutions are not guaranteed. Here, we use the Hungarian matching algorithm as a fast and rigorous alternative to this problem of defect-free atomic lattice formation. Our approach utilizes an optimization cost function that restricts collision-free guiding paths so that atom loss due to collision is minimized during rearrangement. Experiments were performed with cold rubidium atoms that were trapped and guided with holographically controlled optical-dipole traps. The result of atom relocation from a partially filled 7 ×7 lattice to a 3 ×3 target lattice strongly agrees with the theoretical analysis: using the Hungarian algorithm minimizes the collisional and trespassing paths and results in improved performance, with over 50% higher success probability than the heuristic shortest-move method.
A Systematic Study of Simple Combinatorial Configurations.

ERIC Educational Resources Information Center

Dubois, Jean-Guy

1984-01-01

A classification of the simple combinatorial configurations which correspond to various cases of distribution and ordering of objects into boxes is given (in French). Concrete descriptions, structured relations, translations, and formalizations are discussed. (MNS)
Combinatorial Mathematics: Research into Practice

ERIC Educational Resources Information Center

Sriraman, Bharath; English, Lyn D.

2004-01-01

Implications and suggestions for using combinatorial mathematics in the classroom through a survey and synthesis of numerous research studies are presented. The implications revolve around five major themes that emerge from analysis of these studies.
Enabling techniques in the search for new antibiotics: Combinatorial biosynthesis of sugar-containing antibiotics.

PubMed

Park, Je Won; Nam, Sang-Jip; Yoon, Yeo Joon

2017-06-15

Nature has a talent for inventing a vast number of natural products, including hybrids generated by blending different scaffolds, resulting in a myriad of bioactive chemical entities. Herein, we review the highlights and recent trends (2010-2016) in the combinatorial biosynthesis of sugar-containing antibiotics where nature's structural diversification capabilities are exploited to enable the creation of new anti-infective and anti-proliferative drugs. In this review, we describe the modern combinatorial biosynthetic approaches for polyketide synthase-derived complex and aromatic polyketides, non-ribosomal peptide synthetase-directed lipo-/glycopeptides, aminoglycosides, nucleoside antibiotics, and alkaloids, along with their therapeutic potential. Finally, we present the feasible nexus between combinatorial biosynthesis, systems biology, and synthetic biology as a toolbox to provide new antibiotics that will be indispensable in the post-antibiotic era. Copyright © 2016 Elsevier Inc. All rights reserved.
Combinatorial vector fields and the valley structure of fitness landscapes.

PubMed

Stadler, Bärbel M R; Stadler, Peter F

2010-12-01

Adaptive (downhill) walks are a computationally convenient way of analyzing the geometric structure of fitness landscapes. Their inherently stochastic nature has limited their mathematical analysis, however. Here we develop a framework that interprets adaptive walks as deterministic trajectories in combinatorial vector fields and in return associate these combinatorial vector fields with weights that measure their steepness across the landscape. We show that the combinatorial vector fields and their weights have a product structure that is governed by the neutrality of the landscape. This product structure makes practical computations feasible. The framework presented here also provides an alternative, and mathematically more convenient, way of defining notions of valleys, saddle points, and barriers in landscape. As an application, we propose a refined approximation for transition rates between macrostates that are associated with the valleys of the landscape.
Measuring and Specifying Combinatorial Coverage of Test Input Configurations

PubMed Central

Kuhn, D. Richard; Kacker, Raghu N.; Lei, Yu

2015-01-01

A key issue in testing is how many tests are needed for a required level of coverage or fault detection. Estimates are often based on error rates in initial testing, or on code coverage. For example, tests may be run until a desired level of statement or branch coverage is achieved. Combinatorial methods present an opportunity for a different approach to estimating required test set size, using characteristics of the test set. This paper describes methods for estimating the coverage of, and ability to detect, t-way interaction faults of a test set based on a covering array. We also develop a connection between (static) combinatorial coverage and (dynamic) code coverage, such that if a specific condition is satisfied, 100% branch coverage is assured. Using these results, we propose practical recommendations for using combinatorial coverage in specifying test requirements. PMID:28133442
Combinatorial chemical bath deposition of CdS contacts for chalcogenide photovoltaics

DOE PAGES

Mokurala, Krishnaiah; Baranowski, Lauryn L.; de Souza Lucas, Francisco W.; ...

2016-08-01

Contact layers play an important role in thin film solar cells, but new material development and optimization of its thickness is usually a long and tedious process. A high-throughput experimental approach has been used to accelerate the rate of research in photovoltaic (PV) light absorbers and transparent conductive electrodes, however the combinatorial research on contact layers is less common. Here, we report on the chemical bath deposition (CBD) of CdS thin films by combinatorial dip coating technique and apply these contact layers to Cu(In,Ga)Se 2 (CIGSe) and Cu 2ZnSnSe 4 (CZTSe) light absorbers in PV devices. Combinatorial thickness steps ofmore » CdS thin films were achieved by removal of the substrate from the chemical bath, at regular intervals of time, and in equal distance increments. The trends in the photoconversion efficiency and in the spectral response of the PV devices as a function of thickness of CdS contacts were explained with the help of optical and morphological characterization of the CdS thin films. The maximum PV efficiency achieved for the combinatorial dip-coating CBD was similar to that for the PV devices processed using conventional CBD. Finally, the results of this study lead to the conclusion that combinatorial dip-coating can be used to accelerate the optimization of PV device performance of CdS and other candidate contact layers for a wide range of emerging absorbers.« less
Polynomial functors and combinatorial Dyson-Schwinger equations

NASA Astrophysics Data System (ADS)

Kock, Joachim

2017-04-01

We present a general abstract framework for combinatorial Dyson-Schwinger equations, in which combinatorial identities are lifted to explicit bijections of sets, and more generally equivalences of groupoids. Key features of combinatorial Dyson-Schwinger equations are revealed to follow from general categorical constructions and universal properties. Rather than beginning with an equation inside a given Hopf algebra and referring to given Hochschild 1-cocycles, our starting point is an abstract fixpoint equation in groupoids, shown canonically to generate all the algebraic structures. Precisely, for any finitary polynomial endofunctor P defined over groupoids, the system of combinatorial Dyson-Schwinger equations X = 1 + P(X) has a universal solution, namely the groupoid of P-trees. The isoclasses of P-trees generate naturally a Connes-Kreimer-like bialgebra, in which the abstract Dyson-Schwinger equation can be internalised in terms of canonical B+-operators. The solution to this equation is a series (the Green function), which always enjoys a Faà di Bruno formula, and hence generates a sub-bialgebra isomorphic to the Faà di Bruno bialgebra. Varying P yields different bialgebras, and cartesian natural transformations between various P yield bialgebra homomorphisms and sub-bialgebras, corresponding for example to truncation of Dyson-Schwinger equations. Finally, all constructions can be pushed inside the classical Connes-Kreimer Hopf algebra of trees by the operation of taking core of P-trees. A byproduct of the theory is an interpretation of combinatorial Green functions as inductive data types in the sense of Martin-Löf type theory (expounded elsewhere).

The 3of5 web application for complex and comprehensive pattern matching in protein sequences.

PubMed

Seiler, Markus; Mehrle, Alexander; Poustka, Annemarie; Wiemann, Stefan

2006-03-16

The identification of patterns in biological sequences is a key challenge in genome analysis and in proteomics. Frequently such patterns are complex and highly variable, especially in protein sequences. They are frequently described using terms of regular expressions (RegEx) because of the user-friendly terminology. Limitations arise for queries with the increasing complexity of patterns and are accompanied by requirements for enhanced capabilities. This is especially true for patterns containing ambiguous characters and positions and/or length ambiguities. We have implemented the 3of5 web application in order to enable complex pattern matching in protein sequences. 3of5 is named after a special use of its main feature, the novel n-of-m pattern type. This feature allows for an extensive specification of variable patterns where the individual elements may vary in their position, order, and content within a defined stretch of sequence. The number of distinct elements can be constrained by operators, and individual characters may be excluded. The n-of-m pattern type can be combined with common regular expression terms and thus also allows for a comprehensive description of complex patterns. 3of5 increases the fidelity of pattern matching and finds ALL possible solutions in protein sequences in cases of length-ambiguous patterns instead of simply reporting the longest or shortest hits. Grouping and combined search for patterns provides a hierarchical arrangement of larger patterns sets. The algorithm is implemented as internet application and freely accessible. The application is available at http://dkfz.de/mga2/3of5/3of5.html. The 3of5 application offers an extended vocabulary for the definition of search patterns and thus allows the user to comprehensively specify and identify peptide patterns with variable elements. The n-of-m pattern type offers an improved accuracy for pattern matching in combination with the ability to find all solutions, without compromising the user friendliness of regular expression terms.
Development of a microbial high-throughput screening instrument based on elastic light scatter patterns

NASA Astrophysics Data System (ADS)

Bae, Euiwon; Patsekin, Valery; Rajwa, Bartek; Bhunia, Arun K.; Holdman, Cheryl; Davisson, V. Jo; Hirleman, E. Daniel; Robinson, J. Paul

2012-04-01

A microbial high-throughput screening (HTS) system was developed that enabled high-speed combinatorial studies directly on bacterial colonies. The system consists of a forward scatterometer for elastic light scatter (ELS) detection, a plate transporter for sample handling, and a robotic incubator for automatic incubation. To minimize the ELS pattern-capturing time, a new calibration plate and correction algorithms were both designed, which dramatically reduced correction steps during acquisition of the circularly symmetric ELS patterns. Integration of three different control software programs was implemented, and the performance of the system was demonstrated with single-species detection for library generation and with time-resolved measurement for understanding ELS colony growth correlation, using Escherichia coli and Listeria. An in-house colony-tracking module enabled researchers to easily understand the time-dependent variation of the ELS from identical colony, which enabled further analysis in other biochemical experiments. The microbial HTS system provided an average scan time of 4.9 s per colony and the capability of automatically collecting more than 4000 ELS patterns within a 7-h time span.
Document Image Parsing and Understanding using Neuromorphic Architecture

DTIC Science & Technology

2015-03-01

processing speed at different layers. In the pattern matching layer, the computing power of multicore processors is explored to reduce the processing...developed to reduce the processing speed at different layers. In the pattern matching layer, the computing power of multicore processors is explored... cortex where the complex data is reduced to abstract representations. The abstract representation is compared to stored patterns in massively parallel
Study and response time for the visual recognition of 'similarity' and identity

NASA Technical Reports Server (NTRS)

Derks, P. L.; Bauer, T. M.

1974-01-01

Four subjects compared successively presented pairs of line patterns for a match between any lines in the pattern (similarity) and for a match between all lines (identity). The encoding or study times for pattern recognition from immediate memory and the latency in responses to comparison stimuli were examined. Qualitative differences within and between subjects were most evident in study times.
Hypothesis Support Mechanism for Mid-Level Visual Pattern Recognition

NASA Technical Reports Server (NTRS)

Amador, Jose J (Inventor)

2007-01-01

A method of mid-level pattern recognition provides for a pose invariant Hough Transform by parametrizing pairs of points in a pattern with respect to at least two reference points, thereby providing a parameter table that is scale- or rotation-invariant. A corresponding inverse transform may be applied to test hypothesized matches in an image and a distance transform utilized to quantify the level of match.
Discovering gene annotations in biomedical text databases

PubMed Central

Cakmak, Ali; Ozsoyoglu, Gultekin

2008-01-01

Background Genes and gene products are frequently annotated with Gene Ontology concepts based on the evidence provided in genomics articles. Manually locating and curating information about a genomic entity from the biomedical literature requires vast amounts of human effort. Hence, there is clearly a need forautomated computational tools to annotate the genes and gene products with Gene Ontology concepts by computationally capturing the related knowledge embedded in textual data. Results In this article, we present an automated genomic entity annotation system, GEANN, which extracts information about the characteristics of genes and gene products in article abstracts from PubMed, and translates the discoveredknowledge into Gene Ontology (GO) concepts, a widely-used standardized vocabulary of genomic traits. GEANN utilizes textual "extraction patterns", and a semantic matching framework to locate phrases matching to a pattern and produce Gene Ontology annotations for genes and gene products. In our experiments, GEANN has reached to the precision level of 78% at therecall level of 61%. On a select set of Gene Ontology concepts, GEANN either outperforms or is comparable to two other automated annotation studies. Use of WordNet for semantic pattern matching improves the precision and recall by 24% and 15%, respectively, and the improvement due to semantic pattern matching becomes more apparent as the Gene Ontology terms become more general. Conclusion GEANN is useful for two distinct purposes: (i) automating the annotation of genomic entities with Gene Ontology concepts, and (ii) providing existing annotations with additional "evidence articles" from the literature. The use of textual extraction patterns that are constructed based on the existing annotations achieve high precision. The semantic pattern matching framework provides a more flexible pattern matching scheme with respect to "exactmatching" with the advantage of locating approximate pattern occurrences with similar semantics. Relatively low recall performance of our pattern-based approach may be enhanced either by employing a probabilistic annotation framework based on the annotation neighbourhoods in textual data, or, alternatively, the statistical enrichment threshold may be adjusted to lower values for applications that put more value on achieving higher recall values. PMID:18325104
Discovering gene annotations in biomedical text databases.

PubMed

Cakmak, Ali; Ozsoyoglu, Gultekin

2008-03-06

Genes and gene products are frequently annotated with Gene Ontology concepts based on the evidence provided in genomics articles. Manually locating and curating information about a genomic entity from the biomedical literature requires vast amounts of human effort. Hence, there is clearly a need forautomated computational tools to annotate the genes and gene products with Gene Ontology concepts by computationally capturing the related knowledge embedded in textual data. In this article, we present an automated genomic entity annotation system, GEANN, which extracts information about the characteristics of genes and gene products in article abstracts from PubMed, and translates the discoveredknowledge into Gene Ontology (GO) concepts, a widely-used standardized vocabulary of genomic traits. GEANN utilizes textual "extraction patterns", and a semantic matching framework to locate phrases matching to a pattern and produce Gene Ontology annotations for genes and gene products. In our experiments, GEANN has reached to the precision level of 78% at therecall level of 61%. On a select set of Gene Ontology concepts, GEANN either outperforms or is comparable to two other automated annotation studies. Use of WordNet for semantic pattern matching improves the precision and recall by 24% and 15%, respectively, and the improvement due to semantic pattern matching becomes more apparent as the Gene Ontology terms become more general. GEANN is useful for two distinct purposes: (i) automating the annotation of genomic entities with Gene Ontology concepts, and (ii) providing existing annotations with additional "evidence articles" from the literature. The use of textual extraction patterns that are constructed based on the existing annotations achieve high precision. The semantic pattern matching framework provides a more flexible pattern matching scheme with respect to "exactmatching" with the advantage of locating approximate pattern occurrences with similar semantics. Relatively low recall performance of our pattern-based approach may be enhanced either by employing a probabilistic annotation framework based on the annotation neighbourhoods in textual data, or, alternatively, the statistical enrichment threshold may be adjusted to lower values for applications that put more value on achieving higher recall values.
Data-Driven Engineering of Social Dynamics: Pattern Matching and Profit Maximization

PubMed Central

Peng, Huan-Kai; Lee, Hao-Chih; Pan, Jia-Yu; Marculescu, Radu

2016-01-01

In this paper, we define a new problem related to social media, namely, the data-driven engineering of social dynamics. More precisely, given a set of observations from the past, we aim at finding the best short-term intervention that can lead to predefined long-term outcomes. Toward this end, we propose a general formulation that covers two useful engineering tasks as special cases, namely, pattern matching and profit maximization. By incorporating a deep learning model, we derive a solution using convex relaxation and quadratic-programming transformation. Moreover, we propose a data-driven evaluation method in place of the expensive field experiments. Using a Twitter dataset, we demonstrate the effectiveness of our dynamics engineering approach for both pattern matching and profit maximization, and study the multifaceted interplay among several important factors of dynamics engineering, such as solution validity, pattern-matching accuracy, and intervention cost. Finally, the method we propose is general enough to work with multi-dimensional time series, so it can potentially be used in many other applications. PMID:26771830
Data-Driven Engineering of Social Dynamics: Pattern Matching and Profit Maximization.

PubMed

Peng, Huan-Kai; Lee, Hao-Chih; Pan, Jia-Yu; Marculescu, Radu

2016-01-01

In this paper, we define a new problem related to social media, namely, the data-driven engineering of social dynamics. More precisely, given a set of observations from the past, we aim at finding the best short-term intervention that can lead to predefined long-term outcomes. Toward this end, we propose a general formulation that covers two useful engineering tasks as special cases, namely, pattern matching and profit maximization. By incorporating a deep learning model, we derive a solution using convex relaxation and quadratic-programming transformation. Moreover, we propose a data-driven evaluation method in place of the expensive field experiments. Using a Twitter dataset, we demonstrate the effectiveness of our dynamics engineering approach for both pattern matching and profit maximization, and study the multifaceted interplay among several important factors of dynamics engineering, such as solution validity, pattern-matching accuracy, and intervention cost. Finally, the method we propose is general enough to work with multi-dimensional time series, so it can potentially be used in many other applications.
Stepwise molding, etching, and imprinting to form libraries of nanopatterned substrates.

PubMed

Zhao, Zhi; Cai, Yangjun; Liao, Wei-Ssu; Cremer, Paul S

2013-06-04

Herein, we describe a novel colloidal lithographic strategy for the stepwise patterning of planar substrates with numerous complex and unique designs. In conjunction with colloidal self-assembly, imprint molding, and capillary force lithography, reactive ion etching was used to create complex libraries of nanoscale features. This combinatorial strategy affords the ability to develop an exponentially increasing number of two-dimensional nanoscale patterns with each sequential step in the process. Specifically, dots, triangles, circles, and lines could be assembled on the surface separately and in combination with each other. Numerous architectures are obtained for the first time with high uniformity and reproducibility. These hexagonal arrays were made from polystyrene and gold features, whereby each surface element could be tuned from the micrometer size scale down to line widths of ~35 nm. The patterned area could be 1 cm(2) or even larger. The techniques described herein can be combined with further steps to make even larger libraries. Moreover, these polymer and metal features may prove useful in optical, sensing, and electronic applications.
Embryonic expression of the transforming growth factor beta ligand and receptor genes in chicken.

PubMed

Cooley, James R; Yatskievych, Tatiana A; Antin, Parker B

2014-03-01

Transforming growth factor-beta (TGFβ) signaling regulates a myriad of biological processes during embryogenesis, in the adult, and during the manifestation of disease. TGFβ signaling is propagated through one of three TGFβ ligands interacting with Type I and Type II receptors, and Type III co-receptors. Although TGFβ signaling is regulated partly by the combinatorial expression patterns of TGFβ receptors and ligands, a comprehensive gene expression analysis has not been published. Here we report the embryonic mRNA expression patterns in chicken embryos of the canonical TGFβ ligands (TGFB1, TGFB2, and TGFB3) and receptors (TGFBR1, TGFBR2, TGFBR3), plus the Activin A receptor, type 1 (ACVR1) and co receptor Endoglin (ENG) that also transduce TGFβ signaling. TGFB ligands and receptors show dynamic and frequently overlapping expression patterns in numerous embryonic cell layers and structures. Integrating expression information identifies combinations of ligands and receptors that are involved in specific developmental processes including somitogenesis, cardiogenesis and vasculogenesis. Copyright © 2013 Wiley Periodicals, Inc.
Combinatorial invariants and covariants as tools for conical intersections.

PubMed

Ryb, Itai; Baer, Roi

2004-12-01

The combinatorial invariant and covariant are introduced as practical tools for analysis of conical intersections in molecules. The combinatorial invariant is a quantity depending on adiabatic electronic states taken at discrete nuclear configuration points. It is invariant to the phase choice (gauge) of these states. In the limit that the points trace a loop in nuclear configuration space, the value of the invariant approaches the corresponding Berry phase factor. The Berry phase indicates the presence of an odd or even number of conical intersections on surfaces bounded by these loops. Based on the combinatorial invariant, we develop a computationally simple and efficient method for locating conical intersections. The method is robust due to its use of gauge invariant nature. It does not rely on the landscape of intersecting potential energy surfaces nor does it require the computation of nonadiabatic couplings. We generalize the concept to open paths and combinatorial covariants for higher dimensions obtaining a technique for the construction of the gauge-covariant adiabatic-diabatic transformation matrix. This too does not make use of nonadiabatic couplings. The importance of using gauge-covariant expressions is underlined throughout. These techniques can be readily implemented by standard quantum chemistry codes. (c) 2004 American Institute of Physics.
On the suitability of different representations of solid catalysts for combinatorial library design by genetic algorithms.

PubMed

Gobin, Oliver C; Schüth, Ferdi

2008-01-01

Genetic algorithms are widely used to solve and optimize combinatorial problems and are more often applied for library design in combinatorial chemistry. Because of their flexibility, however, their implementation can be challenging. In this study, the influence of the representation of solid catalysts on the performance of genetic algorithms was systematically investigated on the basis of a new, constrained, multiobjective, combinatorial test problem with properties common to problems in combinatorial materials science. Constraints were satisfied by penalty functions, repair algorithms, or special representations. The tests were performed using three state-of-the-art evolutionary multiobjective algorithms by performing 100 optimization runs for each algorithm and test case. Experimental data obtained during the optimization of a noble metal-free solid catalyst system active in the selective catalytic reduction of nitric oxide with propene was used to build up a predictive model to validate the results of the theoretical test problem. A significant influence of the representation on the optimization performance was observed. Binary encodings were found to be the preferred encoding in most of the cases, and depending on the experimental test unit, repair algorithms or penalty functions performed best.
Direct Profiling the Post-Translational Modification Codes of a Single Protein Immobilized on a Surface Using Cu-free Click Chemistry.

PubMed

Kim, Kyung Lock; Park, Kyeng Min; Murray, James; Kim, Kimoon; Ryu, Sung Ho

2018-05-23

Combinatorial post-translational modifications (PTMs), which can serve as dynamic "molecular barcodes", have been proposed to regulate distinct protein functions. However, studies of combinatorial PTMs on single protein molecules have been hindered by a lack of suitable analytical methods. Here, we describe erasable single-molecule blotting (eSiMBlot) for combinatorial PTM profiling. This assay is performed in a highly multiplexed manner and leverages the benefits of covalent protein immobilization, cyclic probing with different antibodies, and single molecule fluorescence imaging. Especially, facile and efficient covalent immobilization on a surface using Cu-free click chemistry permits multiple rounds (>10) of antibody erasing/reprobing without loss of antigenicity. Moreover, cumulative detection of coregistered multiple data sets for immobilized single-epitope molecules, such as HA peptide, can be used to increase the antibody detection rate. Finally, eSiMBlot enables direct visualization and quantitative profiling of combinatorial PTM codes at the single-molecule level, as we demonstrate by revealing the novel phospho-codes of ligand-induced epidermal growth factor receptor. Thus, eSiMBlot provides an unprecedentedly simple, rapid, and versatile platform for analyzing the vast number of combinatorial PTMs in biological pathways.
Direct Profiling the Post-Translational Modification Codes of a Single Protein Immobilized on a Surface Using Cu-free Click Chemistry

PubMed Central

2018-01-01

Combinatorial post-translational modifications (PTMs), which can serve as dynamic “molecular barcodes”, have been proposed to regulate distinct protein functions. However, studies of combinatorial PTMs on single protein molecules have been hindered by a lack of suitable analytical methods. Here, we describe erasable single-molecule blotting (eSiMBlot) for combinatorial PTM profiling. This assay is performed in a highly multiplexed manner and leverages the benefits of covalent protein immobilization, cyclic probing with different antibodies, and single molecule fluorescence imaging. Especially, facile and efficient covalent immobilization on a surface using Cu-free click chemistry permits multiple rounds (>10) of antibody erasing/reprobing without loss of antigenicity. Moreover, cumulative detection of coregistered multiple data sets for immobilized single-epitope molecules, such as HA peptide, can be used to increase the antibody detection rate. Finally, eSiMBlot enables direct visualization and quantitative profiling of combinatorial PTM codes at the single-molecule level, as we demonstrate by revealing the novel phospho-codes of ligand-induced epidermal growth factor receptor. Thus, eSiMBlot provides an unprecedentedly simple, rapid, and versatile platform for analyzing the vast number of combinatorial PTMs in biological pathways.
Lexicographic goal programming and assessment tools for a combinatorial production problem.

DOT National Transportation Integrated Search

2008-01-01

NP-complete combinatorial problems often necessitate the use of near-optimal solution techniques including : heuristics and metaheuristics. The addition of multiple optimization criteria can further complicate : comparison of these solution technique...
Phase transition in the countdown problem

NASA Astrophysics Data System (ADS)

Lacasa, Lucas; Luque, Bartolo

2012-07-01

We present a combinatorial decision problem, inspired by the celebrated quiz show called Countdown, that involves the computation of a given target number T from a set of k randomly chosen integers along with a set of arithmetic operations. We find that the probability of winning the game evidences a threshold phenomenon that can be understood in the terms of an algorithmic phase transition as a function of the set size k. Numerical simulations show that such probability sharply transitions from zero to one at some critical value of the control parameter, hence separating the algorithm's parameter space in different phases. We also find that the system is maximally efficient close to the critical point. We derive analytical expressions that match the numerical results for finite size and permit us to extrapolate the behavior in the thermodynamic limit.
Combinatorial Enzyme Design Probes Allostery and Cooperativity in the Trypsin Fold

DOE Office of Scientific and Technical Information (OSTI.GOV)

Page, Michael J.; Di Cera, Enrico; St. Louis-MED)

2010-06-14

Converting one enzyme into another is challenging due to the uneven distribution of important amino acids for function in both protein sequence and structure. We report a strategy for protein engineering allowing an organized mixing and matching of genetic material that leverages lower throughput with increased quality of screens. Our approach successfully tested the contribution of each surface-exposed loop in the trypsin fold alone and the cooperativity of their combinations towards building the substrate selectivity and Na{sup +}-dependent allosteric activation of the protease domain of human coagulation factor Xa into a bacterial trypsin. As the created proteases lack additional proteinmore » domains and protein co-factor activation mechanism requisite for the complexity of blood coagulation, they are stepping-stones towards further understanding and engineering of artificial clotting factors.« less
"Anticlumping" and Other Combinatorial Effects on Clumped Isotopes: Implications for Tracing Biogeochemical Cycling

NASA Astrophysics Data System (ADS)

Yeung, L.

2015-12-01

I present a mode of isotopic ordering that has purely combinatorial origins. It can be important when identical rare isotopes are paired by coincidence (e.g., they are neighbors on the same molecule), or when extrinsic factors govern the isotopic composition of the two atoms that share a chemical bond. By itself, combinatorial isotope pairing yields products with isotopes either randomly distributed or with a deficit relative to a random distribution of isotopes. These systematics arise because of an unconventional coupling between the formation of singly- and multiply-substituted isotopic moieties. In a random distribution, rare isotopes are symmetrically distributed: Single isotopic substitutions (e.g., H‒D and D‒H in H2) occur with equal probability, and double isotopic substitutions (e.g., D2) occur according to random chance. The absence of symmetry in a bond-making complex can yield unequal numbers of singly-substituted molecules (e.g., more H‒D than D‒H in H2), which is recorded in the product molecule as a deficit in doubly-substituted moieties and an "anticlumped" isotope distribution (i.e., Δn < 0). Enzymatic isotope pairing reactions, which can have site-specific isotopic fractionation factors and atom reservoirs, should express this class of combinatorial isotope effect. Chemical-kinetic isotope effects, which are related to the bond-forming transition state, arise independently and express second-order combinatorial effects. In general, both combinatorial and chemical factors are important for calculating and interpreting clumped-isotope signatures of individual reactions. In many reactions relevant to geochemical oxygen, carbon, and nitrogen cycling, combinatorial isotope pairing likely plays a strong role in the clumped isotope distribution of the products. These isotopic signatures, manifest as either directly bound isotope clumps or as features of a molecule's isotopic anatomy, could be exploited as tracers of biogeochemistry that can relate molecular mechanisms to signals observable at environmentally relevant spatial scales.
Implementation of Multipattern String Matching Accelerated with GPU for Intrusion Detection System

NASA Astrophysics Data System (ADS)

Nehemia, Rangga; Lim, Charles; Galinium, Maulahikmah; Rinaldi Widianto, Ahmad

2017-04-01

As Internet-related security threats continue to increase in terms of volume and sophistication, existing Intrusion Detection System is also being challenged to cope with the current Internet development. Multi Pattern String Matching algorithm accelerated with Graphical Processing Unit is being utilized to improve the packet scanning performance of the IDS. This paper implements a Multi Pattern String Matching algorithm, also called Parallel Failureless Aho Corasick accelerated with GPU to improve the performance of IDS. OpenCL library is used to allow the IDS to support various GPU, including popular GPU such as NVIDIA and AMD, used in our research. The experiment result shows that the application of Multi Pattern String Matching using GPU accelerated platform provides a speed up, by up to 141% in term of throughput compared to the previous research.

Creative thought as blind-variation and selective-retention: Combinatorial models of exceptional creativity

NASA Astrophysics Data System (ADS)

Simonton, Dean Keith

2010-06-01

Campbell (1960) proposed that creative thought should be conceived as a blind-variation and selective-retention process (BVSR). This article reviews the developments that have taken place in the half century that has elapsed since his proposal, with special focus on the use of combinatorial models as formal representations of the general theory. After defining the key concepts of blind variants, creative thought, and disciplinary context, the combinatorial models are specified in terms of individual domain samples, variable field size, ideational combination, and disciplinary communication. Empirical implications are then derived with respect to individual, domain, and field systems. These abstract combinatorial models are next provided substantive reinforcement with respect to findings concerning the cognitive processes, personality traits, developmental factors, and social contexts that contribute to creativity. The review concludes with some suggestions regarding future efforts to explicate creativity according to BVSR theory.
Combinatorial Color Space Models for Skin Detection in Sub-continental Human Images

NASA Astrophysics Data System (ADS)

Khaled, Shah Mostafa; Saiful Islam, Md.; Rabbani, Md. Golam; Tabassum, Mirza Rehenuma; Gias, Alim Ul; Kamal, Md. Mostafa; Muctadir, Hossain Muhammad; Shakir, Asif Khan; Imran, Asif; Islam, Saiful

Among different color models HSV, HLS, YIQ, YCbCr, YUV, etc. have been most popular for skin detection. Most of the research done in the field of skin detection has been trained and tested on human images of African, Mongolian and Anglo-Saxon ethnic origins, skin colors of Indian sub-continentals have not been focused separately. Combinatorial algorithms, without affecting asymptotic complexity can be developed using the skin detection concepts of these color models for boosting detection performance. In this paper a comparative study of different combinatorial skin detection algorithms have been made. For training and testing 200 images (skin and non skin) containing pictures of sub-continental male and females have been used to measure the performance of the combinatorial approaches, and considerable development in success rate with True Positive of 99.5% and True Negative of 93.3% have been observed.
Optimized Reaction Conditions for Amide Bond Formation in DNA-Encoded Combinatorial Libraries.

PubMed

Li, Yizhou; Gabriele, Elena; Samain, Florent; Favalli, Nicholas; Sladojevich, Filippo; Scheuermann, Jörg; Neri, Dario

2016-08-08

DNA-encoded combinatorial libraries are increasingly being used as tools for the discovery of small organic binding molecules to proteins of biological or pharmaceutical interest. In the majority of cases, synthetic procedures for the formation of DNA-encoded combinatorial libraries incorporate at least one step of amide bond formation between amino-modified DNA and a carboxylic acid. We investigated reaction conditions and established a methodology by using 1-ethyl-3-(3-(dimethylamino)propyl)carbodiimide, 1-hydroxy-7-azabenzotriazole and N,N'-diisopropylethylamine (EDC/HOAt/DIPEA) in combination, which provided conversions greater than 75% for 423/543 (78%) of the carboxylic acids tested. These reaction conditions were efficient with a variety of primary and secondary amines, as well as with various types of amino-modified oligonucleotides. The reaction conditions, which also worked efficiently over a broad range of DNA concentrations and reaction scales, should facilitate the synthesis of novel DNA-encoded combinatorial libraries.
Combinatorial games with a pass: a dynamical systems approach.

PubMed

Morrison, Rebecca E; Friedman, Eric J; Landsberg, Adam S

2011-12-01

By treating combinatorial games as dynamical systems, we are able to address a longstanding open question in combinatorial game theory, namely, how the introduction of a "pass" move into a game affects its behavior. We consider two well known combinatorial games, 3-pile Nim and 3-row Chomp. In the case of Nim, we observe that the introduction of the pass dramatically alters the game's underlying structure, rendering it considerably more complex, while for Chomp, the pass move is found to have relatively minimal impact. We show how these results can be understood by recasting these games as dynamical systems describable by dynamical recursion relations. From these recursion relations, we are able to identify underlying structural connections between these "games with passes" and a recently introduced class of "generic (perturbed) games." This connection, together with a (non-rigorous) numerical stability analysis, allows one to understand and predict the effect of a pass on a game.
Mixture-based combinatorial libraries from small individual peptide libraries: a case study on α1-antitrypsin deficiency.

PubMed

Chang, Yi-Pin; Chu, Yen-Ho

2014-05-16

The design, synthesis and screening of diversity-oriented peptide libraries using a "libraries from libraries" strategy for the development of inhibitors of α1-antitrypsin deficiency are described. The major buttress of the biochemical approach presented here is the use of well-established solid-phase split-and-mix method for the generation of mixture-based libraries. The combinatorial technique iterative deconvolution was employed for library screening. While molecular diversity is the general consideration of combinatorial libraries, exquisite design through systematic screening of small individual libraries is a prerequisite for effective library screening and can avoid potential problems in some cases. This review will also illustrate how large peptide libraries were designed, as well as how a conformation-sensitive assay was developed based on the mechanism of the conformational disease. Finally, the combinatorially selected peptide inhibitor capable of blocking abnormal protein aggregation will be characterized by biophysical, cellular and computational methods.
Diversity of Salmonella isolates from central Florida surface waters.

PubMed

McEgan, Rachel; Chandler, Jeffrey C; Goodridge, Lawrence D; Danyluk, Michelle D

2014-11-01

Identification of Salmonella serotypes is important for understanding the environmental diversity of the genus Salmonella. This study evaluates the diversity of Salmonella isolates recovered from 165 of 202 Central Florida surface water samples and investigates whether the serotype of the environmental Salmonella isolates can be predicted by a previously published multiplex PCR assay (S. Kim, J. G. Frye, J. Hu, P. J. Fedorka-Cray, R. Gautom, and D. S. Boyle, J. Clin. Microbiol. 44:3608-3615, 2006, http://dx.doi.org/10.1128/JCM.00701-06). Multiplex PCR was performed on 562 Salmonella isolates (as many as 36 isolates per water sample) to predict serotypes. Kauffmann-White serogrouping was used to confirm multiplex PCR pattern groupings before isolates were serotyped, analyzed by pulsed-field gel electrophoresis, and assayed for antimicrobial susceptibility. In 41.2% of the Salmonella-positive water samples, all Salmonella isolates had identical multiplex PCR patterns; in the remaining 58.8%, two or more multiplex PCR patterns were identified. Within each sample, isolates with matching multiplex PCR patterns had matching serogroups. The multiplex patterns of 495 isolates (88.1%) did not match any previously reported pattern. The remaining 68 isolates matched reported patterns but did not match the serotypes for those patterns. The use of the multiplex PCR allowed the number of isolates requiring further analysis to be reduced to 223. Thirty-three Salmonella enterica serotypes were identified; the most frequent included serotypes Muenchen, Rubislaw, Anatum, Gaminara, and IV_50:z4,z23:-. A majority (141/223) of Salmonella isolates clustered into one genotypic group. Salmonella isolates in Central Florida surface waters are serotypically, genotypically, and phenotypically (in terms of antimicrobial susceptibility) diverse. While isolates could be grouped as different or potentially the same using multiplex PCR, the multiplex PCR pattern did not predict the Salmonella serotype. Copyright © 2014, American Society for Microbiology. All Rights Reserved.
Diversity of Salmonella Isolates from Central Florida Surface Waters

PubMed Central

McEgan, Rachel; Chandler, Jeffrey C.; Goodridge, Lawrence D.

2014-01-01

Identification of Salmonella serotypes is important for understanding the environmental diversity of the genus Salmonella. This study evaluates the diversity of Salmonella isolates recovered from 165 of 202 Central Florida surface water samples and investigates whether the serotype of the environmental Salmonella isolates can be predicted by a previously published multiplex PCR assay (S. Kim, J. G. Frye, J. Hu, P. J. Fedorka-Cray, R. Gautom, and D. S. Boyle, J. Clin. Microbiol. 44:3608–3615, 2006, http://dx.doi.org/10.1128/JCM.00701-06). Multiplex PCR was performed on 562 Salmonella isolates (as many as 36 isolates per water sample) to predict serotypes. Kauffmann-White serogrouping was used to confirm multiplex PCR pattern groupings before isolates were serotyped, analyzed by pulsed-field gel electrophoresis, and assayed for antimicrobial susceptibility. In 41.2% of the Salmonella-positive water samples, all Salmonella isolates had identical multiplex PCR patterns; in the remaining 58.8%, two or more multiplex PCR patterns were identified. Within each sample, isolates with matching multiplex PCR patterns had matching serogroups. The multiplex patterns of 495 isolates (88.1%) did not match any previously reported pattern. The remaining 68 isolates matched reported patterns but did not match the serotypes for those patterns. The use of the multiplex PCR allowed the number of isolates requiring further analysis to be reduced to 223. Thirty-three Salmonella enterica serotypes were identified; the most frequent included serotypes Muenchen, Rubislaw, Anatum, Gaminara, and IV_50:z4,z23:−. A majority (141/223) of Salmonella isolates clustered into one genotypic group. Salmonella isolates in Central Florida surface waters are serotypically, genotypically, and phenotypically (in terms of antimicrobial susceptibility) diverse. While isolates could be grouped as different or potentially the same using multiplex PCR, the multiplex PCR pattern did not predict the Salmonella serotype. PMID:25172861
Structure-based design of combinatorial mutagenesis libraries

PubMed Central

Verma, Deeptak; Grigoryan, Gevorg; Bailey-Kellogg, Chris

2015-01-01

The development of protein variants with improved properties (thermostability, binding affinity, catalytic activity, etc.) has greatly benefited from the application of high-throughput screens evaluating large, diverse combinatorial libraries. At the same time, since only a very limited portion of sequence space can be experimentally constructed and tested, an attractive possibility is to use computational protein design to focus libraries on a productive portion of the space. We present a general-purpose method, called “Structure-based Optimization of Combinatorial Mutagenesis” (SOCoM), which can optimize arbitrarily large combinatorial mutagenesis libraries directly based on structural energies of their constituents. SOCoM chooses both positions and substitutions, employing a combinatorial optimization framework based on library-averaged energy potentials in order to avoid explicitly modeling every variant in every possible library. In case study applications to green fluorescent protein, β-lactamase, and lipase A, SOCoM optimizes relatively small, focused libraries whose variants achieve energies comparable to or better than previous library design efforts, as well as larger libraries (previously not designable by structure-based methods) whose variants cover greater diversity while still maintaining substantially better energies than would be achieved by representative random library approaches. By allowing the creation of large-scale combinatorial libraries based on structural calculations, SOCoM promises to increase the scope of applicability of computational protein design and improve the hit rate of discovering beneficial variants. While designs presented here focus on variant stability (predicted by total energy), SOCoM can readily incorporate other structure-based assessments, such as the energy gap between alternative conformational or bound states. PMID:25611189
Structure-based design of combinatorial mutagenesis libraries.

PubMed

Verma, Deeptak; Grigoryan, Gevorg; Bailey-Kellogg, Chris

2015-05-01

The development of protein variants with improved properties (thermostability, binding affinity, catalytic activity, etc.) has greatly benefited from the application of high-throughput screens evaluating large, diverse combinatorial libraries. At the same time, since only a very limited portion of sequence space can be experimentally constructed and tested, an attractive possibility is to use computational protein design to focus libraries on a productive portion of the space. We present a general-purpose method, called "Structure-based Optimization of Combinatorial Mutagenesis" (SOCoM), which can optimize arbitrarily large combinatorial mutagenesis libraries directly based on structural energies of their constituents. SOCoM chooses both positions and substitutions, employing a combinatorial optimization framework based on library-averaged energy potentials in order to avoid explicitly modeling every variant in every possible library. In case study applications to green fluorescent protein, β-lactamase, and lipase A, SOCoM optimizes relatively small, focused libraries whose variants achieve energies comparable to or better than previous library design efforts, as well as larger libraries (previously not designable by structure-based methods) whose variants cover greater diversity while still maintaining substantially better energies than would be achieved by representative random library approaches. By allowing the creation of large-scale combinatorial libraries based on structural calculations, SOCoM promises to increase the scope of applicability of computational protein design and improve the hit rate of discovering beneficial variants. While designs presented here focus on variant stability (predicted by total energy), SOCoM can readily incorporate other structure-based assessments, such as the energy gap between alternative conformational or bound states. © 2015 The Protein Society.
Fractional Programming for Communication Systems—Part II: Uplink Scheduling via Matching

NASA Astrophysics Data System (ADS)

Shen, Kaiming; Yu, Wei

2018-05-01

This two-part paper develops novel methodologies for using fractional programming (FP) techniques to design and optimize communication systems. Part I of this paper proposes a new quadratic transform for FP and treats its application for continuous optimization problems. In this Part II of the paper, we study discrete problems, such as those involving user scheduling, which are considerably more difficult to solve. Unlike the continuous problems, discrete or mixed discrete-continuous problems normally cannot be recast as convex problems. In contrast to the common heuristic of relaxing the discrete variables, this work reformulates the original problem in an FP form amenable to distributed combinatorial optimization. The paper illustrates this methodology by tackling the important and challenging problem of uplink coordinated multi-cell user scheduling in wireless cellular systems. Uplink scheduling is more challenging than downlink scheduling, because uplink user scheduling decisions significantly affect the interference pattern in nearby cells. Further, the discrete scheduling variable needs to be optimized jointly with continuous variables such as transmit power levels and beamformers. The main idea of the proposed FP approach is to decouple the interaction among the interfering links, thereby permitting a distributed and joint optimization of the discrete and continuous variables with provable convergence. The paper shows that the well-known weighted minimum mean-square-error (WMMSE) algorithm can also be derived from a particular use of FP; but our proposed FP-based method significantly outperforms WMMSE when discrete user scheduling variables are involved, both in term of run-time efficiency and optimizing results.
Transport of calcium ions through a bulk membrane by use of a dynamic combinatorial library.

PubMed

Saggiomo, Vittorio; Lüning, Ulrich

2009-07-07

In a bulk membrane transport experiment, a dynamic combinatorial library (DCL) has been used to transport calcium ions; the calcium ions amplify the formation of a macrocyclic carrier which results in transport.
Counting Pizza Pieces and Other Combinatorial Problems.

ERIC Educational Resources Information Center

Maier, Eugene

1988-01-01

The general combinatorial problem of counting the number of regions into which the interior of a circle is divided by a family of lines is considered. A general formula is developed and its use is illustrated in two situations. (PK)
On the existence of binary simplex codes. [using combinatorial construction

NASA Technical Reports Server (NTRS)

Taylor, H.

1977-01-01

Using a simple combinatorial construction, the existence of a binary simplex code with m codewords for all m is greater than or equal to 1 is proved. The problem of the shortest possible length is left open.
Application of combinatorial biocatalysis for a unique ring expansion of dihydroxymethylzearalenone

USDA-ARS?s Scientific Manuscript database

Combinatorial biocatalysis was applied to generate a diverse set of dihydroxymethylzearalenone derivatives with modified ring structure. In one chemoenzymatic reaction sequence, dihydroxymethylzearalenone was first subjected to a unique enzyme-catalyzed oxidative ring opening reaction that creates ...
Rapid evolution of regulatory element libraries for tunable transcriptional and translational control of gene expression.

PubMed

Jin, Erqing; Wong, Lynn; Jiao, Yun; Engel, Jake; Holdridge, Benjamin; Xu, Peng

2017-12-01

Engineering cell factories for producing biofuels and pharmaceuticals has spurred great interests to develop rapid and efficient synthetic biology tools customized for modular pathway engineering. Along the way, combinatorial gene expression control through modification of regulatory element offered tremendous opportunity for fine-tuning gene expression and generating digital-like genetic circuits. In this report, we present an efficient evolutionary approach to build a range of regulatory control elements. The reported method allows for rapid construction of promoter, 5'UTR, terminator and trans -activating RNA libraries. Synthetic overlapping oligos with high portion of degenerate nucleotides flanking the regulatory element could be efficiently assembled to a vector expressing fluorescence reporter. This approach combines high mutation rate of the synthetic DNA with the high assembly efficiency of Gibson Mix. Our constructed library demonstrates broad range of transcriptional or translational gene expression dynamics. Specifically, both the promoter library and 5'UTR library exhibits gene expression dynamics spanning across three order of magnitude. The terminator library and trans -activating RNA library displays relatively narrowed gene expression pattern. The reported study provides a versatile toolbox for rapidly constructing a large family of prokaryotic regulatory elements. These libraries also facilitate the implementation of combinatorial pathway engineering principles and the engineering of more efficient microbial cell factory for various biomanufacturing applications.
Virtual screening using combinatorial cyclic peptide libraries reveals protein interfaces readily targetable by cyclic peptides.

PubMed

Duffy, Fergal J; O'Donovan, Darragh; Devocelle, Marc; Moran, Niamh; O'Connell, David J; Shields, Denis C

2015-03-23

Protein-protein and protein-peptide interactions are responsible for the vast majority of biological functions in vivo, but targeting these interactions with small molecules has historically been difficult. What is required are efficient combined computational and experimental screening methods to choose among a number of potential protein interfaces worthy of targeting lead macrocyclic compounds for further investigation. To achieve this, we have generated combinatorial 3D virtual libraries of short disulfide-bonded peptides and compared them to pharmacophore models of important protein-protein and protein-peptide structures, including short linear motifs (SLiMs), protein-binding peptides, and turn structures at protein-protein interfaces, built from 3D models available in the Protein Data Bank. We prepared a total of 372 reference pharmacophores, which were matched against 108,659 multiconformer cyclic peptides. After normalization to exclude nonspecific cyclic peptides, the top hits notably are enriched for mimetics of turn structures, including a turn at the interaction surface of human α thrombin, and also feature several protein-binding peptides. The top cyclic peptide hits also cover the critical "hot spot" interaction sites predicted from the interaction crystal structure. We have validated our method by testing cyclic peptides predicted to inhibit thrombin, a key protein in the blood coagulation pathway of important therapeutic interest, identifying a cyclic peptide inhibitor with lead-like activity. We conclude that protein interfaces most readily targetable by cyclic peptides and related macrocyclic drugs may be identified computationally among a set of candidate interfaces, accelerating the choice of interfaces against which lead compounds may be screened.
Genes@Work: an efficient algorithm for pattern discovery and multivariate feature selection in gene expression data.

PubMed

Lepre, Jorge; Rice, J Jeremy; Tu, Yuhai; Stolovitzky, Gustavo

2004-05-01

Despite the growing literature devoted to finding differentially expressed genes in assays probing different tissues types, little attention has been paid to the combinatorial nature of feature selection inherent to large, high-dimensional gene expression datasets. New flexible data analysis approaches capable of searching relevant subgroups of genes and experiments are needed to understand multivariate associations of gene expression patterns with observed phenotypes. We present in detail a deterministic algorithm to discover patterns of multivariate gene associations in gene expression data. The patterns discovered are differential with respect to a control dataset. The algorithm is exhaustive and efficient, reporting all existent patterns that fit a given input parameter set while avoiding enumeration of the entire pattern space. The value of the pattern discovery approach is demonstrated by finding a set of genes that differentiate between two types of lymphoma. Moreover, these genes are found to behave consistently in an independent dataset produced in a different laboratory using different arrays, thus validating the genes selected using our algorithm. We show that the genes deemed significant in terms of their multivariate statistics will be missed using other methods. Our set of pattern discovery algorithms including a user interface is distributed as a package called Genes@Work. This package is freely available to non-commercial users and can be downloaded from our website (http://www.research.ibm.com/FunGen).
Regulatory sequence analysis tools.

PubMed

van Helden, Jacques

2003-07-01

The web resource Regulatory Sequence Analysis Tools (RSAT) (http://rsat.ulb.ac.be/rsat) offers a collection of software tools dedicated to the prediction of regulatory sites in non-coding DNA sequences. These tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Alternative formats are supported for the representation of regulatory motifs (strings or position-specific scoring matrices) and several algorithms are proposed for pattern discovery. RSAT currently holds >100 fully sequenced genomes and these data are regularly updated from GenBank.
Criticism of EFSA's scientific opinion on combinatorial effects of 'stacked' GM plants.

PubMed

Bøhn, Thomas

2018-01-01

Recent genetically modified plants tend to include both insect resistance and herbicide tolerance traits. Some of these 'stacked' GM plants have multiple Cry-toxins expressed as well as tolerance to several herbicides. This means that non-target organisms in the environment (biodiversity) will be co-exposed to multiple stressors simultaneously. A similar co-exposure may happen to consumers through chemical residues in the food chain. EFSA, the responsible unit for minimizing risk of harm in European food chains, has expressed its scientific interest in combinatorial effects. However, when new data showed how two Cry-toxins acted in combination (added toxicity), and that the same Cry-toxins showed combinatorial effects when co-exposed with Roundup (Bøhn et al., 2016), EFSA dismissed these new peer-reviewed results. In effect, EFSA claimed that combinatorial effects are not relevant for itself. EFSA was justifying this by referring to a policy question, and by making invalid assumptions, which could have been checked directly with the lead-author. With such approach, EFSA may miss the opportunity to improve its environmental and health risk assessment of toxins and pesticides in the food chain. Failure to follow its own published requests for combinatorial effects research, may also risk jeopardizing EFSA's scientific and public reputation. Copyright © 2017. Published by Elsevier Ltd.
A Dictionary Approach to Electron Backscatter Diffraction Indexing.

PubMed

Chen, Yu H; Park, Se Un; Wei, Dennis; Newstadt, Greg; Jackson, Michael A; Simmons, Jeff P; De Graef, Marc; Hero, Alfred O

2015-06-01

We propose a framework for indexing of grain and subgrain structures in electron backscatter diffraction patterns of polycrystalline materials. We discretize the domain of a dynamical forward model onto a dense grid of orientations, producing a dictionary of patterns. For each measured pattern, we identify the most similar patterns in the dictionary, and identify boundaries, detect anomalies, and index crystal orientations. The statistical distribution of these closest matches is used in an unsupervised binary decision tree (DT) classifier to identify grain boundaries and anomalous regions. The DT classifies a pattern as an anomaly if it has an abnormally low similarity to any pattern in the dictionary. It classifies a pixel as being near a grain boundary if the highly ranked patterns in the dictionary differ significantly over the pixel's neighborhood. Indexing is accomplished by computing the mean orientation of the closest matches to each pattern. The mean orientation is estimated using a maximum likelihood approach that models the orientation distribution as a mixture of Von Mises-Fisher distributions over the quaternionic three sphere. The proposed dictionary matching approach permits segmentation, anomaly detection, and indexing to be performed in a unified manner with the additional benefit of uncertainty quantification.

Post-decomposition optimizations using pattern matching and rule-based clustering for multi-patterning technology

NASA Astrophysics Data System (ADS)

Wang, Lynn T.-N.; Madhavan, Sriram

2018-03-01

A pattern matching and rule-based polygon clustering methodology with DFM scoring is proposed to detect decomposition-induced manufacturability detractors and fix the layout designs prior to manufacturing. A pattern matcher scans the layout for pre-characterized patterns from a library. If a pattern were detected, rule-based clustering identifies the neighboring polygons that interact with those captured by the pattern. Then, DFM scores are computed for the possible layout fixes: the fix with the best score is applied. The proposed methodology was applied to two 20nm products with a chip area of 11 mm2 on the metal 2 layer. All the hotspots were resolved. The number of DFM spacing violations decreased by 7-15%.
Automated CD-SEM recipe creation technology for mass production using CAD data

NASA Astrophysics Data System (ADS)

Kawahara, Toshikazu; Yoshida, Masamichi; Tanaka, Masashi; Ido, Sanyu; Nakano, Hiroyuki; Adachi, Naokaka; Abe, Yuichi; Nagatomo, Wataru

2011-03-01

Critical Dimension Scanning Electron Microscope (CD-SEM) recipe creation needs sample preparation necessary for matching pattern registration, and recipe creation on CD-SEM using the sample, which hinders the reduction in test production cost and time in semiconductor manufacturing factories. From the perspective of cost reduction and improvement of the test production efficiency, automated CD-SEM recipe creation without the sample preparation and the manual operation has been important in the production lines. For the automated CD-SEM recipe creation, we have introduced RecipeDirector (RD) that enables the recipe creation by using Computer-Aided Design (CAD) data and text data that includes measurement information. We have developed a system that automatically creates the CAD data and the text data necessary for the recipe creation on RD; and, for the elimination of the manual operation, we have enhanced RD so that all measurement information can be specified in the text data. As a result, we have established an automated CD-SEM recipe creation system without the sample preparation and the manual operation. For the introduction of the CD-SEM recipe creation system using RD to the production lines, the accuracy of the pattern matching was an issue. The shape of design templates for the matching created from the CAD data was different from that of SEM images in vision. Thus, a development of robust pattern matching algorithm that considers the shape difference was needed. The addition of image processing of the templates for the matching and shape processing of the CAD patterns in the lower layer has enabled the robust pattern matching. This paper describes the automated CD-SEM recipe creation technology for the production lines without the sample preparation and the manual operation using RD applied in Sony Semiconductor Kyusyu Corporation Kumamoto Technology Center (SCK Corporation Kumamoto TEC).
Running Clubs--A Combinatorial Investigation.

ERIC Educational Resources Information Center

Nissen, Phillip; Taylor, John

1991-01-01

Presented is a combinatorial problem based on the Hash House Harriers rule which states that the route of the run should not have previously been traversed by the club. Discovered is how many weeks the club can meet before the rule has to be broken. (KR)
Quantum Resonance Approach to Combinatorial Optimization

NASA Technical Reports Server (NTRS)

Zak, Michail

1997-01-01

It is shown that quantum resonance can be used for combinatorial optimization. The advantage of the approach is in independence of the computing time upon the dimensionality of the problem. As an example, the solution to a constraint satisfaction problem of exponential complexity is demonstrated.
Whole organism lineage tracing by combinatorial and cumulative genome editing

PubMed Central

McKenna, Aaron; Findlay, Gregory M.; Gagnon, James A.; Horwitz, Marshall S.; Schier, Alexander F.; Shendure, Jay

2016-01-01

Multicellular systems develop from single cells through distinct lineages. However, current lineage tracing approaches scale poorly to whole, complex organisms. Here we use genome editing to progressively introduce and accumulate diverse mutations in a DNA barcode over multiple rounds of cell division. The barcode, an array of CRISPR/Cas9 target sites, marks cells and enables the elucidation of lineage relationships via the patterns of mutations shared between cells. In cell culture and zebrafish, we show that rates and patterns of editing are tunable, and that thousands of lineage-informative barcode alleles can be generated. By sampling hundreds of thousands of cells from individual zebrafish, we find that most cells in adult organs derive from relatively few embryonic progenitors. In future analyses, genome editing of synthetic target arrays for lineage tracing (GESTALT) can be used to generate large-scale maps of cell lineage in multicellular systems for normal development and disease. PMID:27229144
Nutritional Status and Daytime Pattern of Protein Intake on Match, Post-Match, Rest and Training Days in Senior Professional and Youth Elite Soccer Players.

PubMed

Bettonviel A, E O; Brinkmans N, Y J; Russcher, Kris; Wardenaar, Floris C; Witard, Oliver C

2016-06-01

The nutritional status of elite soccer players across match, postmatch, training and rest days has not been defined. Recent evidence suggests the pattern of dietary protein intake impacts the daytime turnover of muscle proteins and, as such, influences muscle recovery. We assessed the nutritional status and daytime pattern of protein intake in senior professional and elite youth soccer players and compared findings against published recommendations. Fourteen senior professional (SP) and 15 youth elite (YP) soccer players from the Dutch premier division completed nutritional assessments using a 24-hr web-based recall method. Recall days consisted of a match, postmatch, rest, and training day. Daily energy intake over the 4-day period was similar between SP (2988 ± 583 kcal/day) and YP (2938 ± 465 kcal/day; p = .800). Carbohydrate intake over the combined 4-day period was lower in SP (4.7 ± 0.7 g·kg-1 BM·day-1) vs. YP (6.0 ± 1.5 g·kg-1 BM·day-1, p = .006) and SP failed to meet recommended carbohydrate intakes on match and training days. Conversely, recommended protein intakes were met for SP (1.9 ± 0.3 g·kg-1 BM·day-1) and YP (1.7 ± 0.4 g·kg-1 BM·day-1), with no differences between groups (p = .286). Accordingly, both groups met or exceeded recommended daily protein intakes on individual match, postmatch, rest and training days. A similar "balanced" daytime pattern of protein intake was observed in SP and YP. To conclude, SP increased protein intake on match and training days to a greater extent than YP, however at the expense of carbohydrate intake. The daytime distribution of protein intake for YP and SP aligned with current recommendations of a balanced protein meal pattern.
On matching the anode ring with the magnetic field in an ATON-type Hall effect thruster

NASA Astrophysics Data System (ADS)

Liu, Jinwen; Li, Hong; Zhang, Xu; Ding, Yongjie; Wei, Liqiu; Li, Jianzhi; Yu, Daren; Wang, Xiaogang

2018-06-01

In an ATON-type Hall effect thruster, a ring-shaped anode and a cusped magnetic field intersect the match between the anode shape and the field topology thus must be clarified to optimize the electron transport to the anode and consequently the design of a high-efficiency thruster. By changing the match pattern with both the change in the length of the anode ring and the axial displacement of the cusp magnetic field, this study experimentally investigated the influence of the match pattern on the discharge characteristics of an ATON-type thruster—P100—under the condition of a moderate discharge voltage. The experimental results show that there is a match pattern that always optimizes the performance of the P100 thruster. At the rated operation parameters (300 V of discharge voltage and 5 mg/s of propellant mass flow rate) and the rated magnetic field strength, the observed improvements on thrust (˜79 mN to ˜85 mN) and anode efficiency (˜46% to ˜55%) are significant. Through further theoretical analysis, this study revealed that the change in the characteristics of electron momentum and energy transfer in the near-anode region, induced by the change of the match pattern, is the basic reason. The findings of this work are instructive for both understanding the electron motion in a cusp magnetic field and guiding the design of the anode ring intersecting with a cusp magnetic field in an ATON-type Hall effect thruster.
Random vs. Combinatorial Methods for Discrete Event Simulation of a Grid Computer Network

NASA Technical Reports Server (NTRS)

Kuhn, D. Richard; Kacker, Raghu; Lei, Yu

2010-01-01

This study compared random and t-way combinatorial inputs of a network simulator, to determine if these two approaches produce significantly different deadlock detection for varying network configurations. Modeling deadlock detection is important for analyzing configuration changes that could inadvertently degrade network operations, or to determine modifications that could be made by attackers to deliberately induce deadlock. Discrete event simulation of a network may be conducted using random generation, of inputs. In this study, we compare random with combinatorial generation of inputs. Combinatorial (or t-way) testing requires every combination of any t parameter values to be covered by at least one test. Combinatorial methods can be highly effective because empirical data suggest that nearly all failures involve the interaction of a small number of parameters (1 to 6). Thus, for example, if all deadlocks involve at most 5-way interactions between n parameters, then exhaustive testing of all n-way interactions adds no additional information that would not be obtained by testing all 5-way interactions. While the maximum degree of interaction between parameters involved in the deadlocks clearly cannot be known in advance, covering all t-way interactions may be more efficient than using random generation of inputs. In this study we tested this hypothesis for t = 2, 3, and 4 for deadlock detection in a network simulation. Achieving the same degree of coverage provided by 4-way tests would have required approximately 3.2 times as many random tests; thus combinatorial methods were more efficient for detecting deadlocks involving a higher degree of interactions. The paper reviews explanations for these results and implications for modeling and simulation.
Advanced optical correlation and digital methods for pattern matching—50th anniversary of Vander Lugt matched filter

NASA Astrophysics Data System (ADS)

Millán, María S.

2012-10-01

On the verge of the 50th anniversary of Vander Lugt’s formulation for pattern matching based on matched filtering and optical correlation, we acknowledge the very intense research activity developed in the field of correlation-based pattern recognition during this period of time. The paper reviews some domains that appeared as emerging fields in the last years of the 20th century and have been developed later on in the 21st century. Such is the case of three-dimensional (3D) object recognition, biometric pattern matching, optical security and hybrid optical-digital processors. 3D object recognition is a challenging case of multidimensional image recognition because of its implications in the recognition of real-world objects independent of their perspective. Biometric recognition is essentially pattern recognition for which the personal identification is based on the authentication of a specific physiological characteristic possessed by the subject (e.g. fingerprint, face, iris, retina, and multifactor combinations). Biometric recognition often appears combined with encryption-decryption processes to secure information. The optical implementations of correlation-based pattern recognition processes still rely on the 4f-correlator, the joint transform correlator, or some of their variants. But the many applications developed in the field have been pushing the systems for a continuous improvement of their architectures and algorithms, thus leading towards merged optical-digital solutions.
Formal Operations and Ego Identity in Adolescence.

ERIC Educational Resources Information Center

Wagner, Janis A.

1987-01-01

Investigated the relationship between the development of formal operations and the formation of ego identity in adolescence. Obtained significant positive correlations between combinatorial ability and degree of identity, suggesting that high identity may facilitate the application of combinatorial operations. Found some gender differences in task…
Manipulating Combinatorial Structures.

ERIC Educational Resources Information Center

Labelle, Gilbert

This set of transparencies shows how the manipulation of combinatorial structures in the context of modern combinatorics can easily lead to interesting teaching and learning activities at every level of education from elementary school to university. The transparencies describe: (1) the importance and relations of combinatorics to science and…
Gian-Carlos Rota and Combinatorial Math.

ERIC Educational Resources Information Center

Kolata, Gina Bari

1979-01-01

Presents the first of a series of occasional articles about mathematics as seen through the eyes of its prominent scholars. In an interview with Gian-Carlos Rota of the Massachusetts Institute of Technology he discusses how combinatorial mathematics began as a field and its future. (HM)
A Model of Students' Combinatorial Thinking

ERIC Educational Resources Information Center

Lockwood, Elise

2013-01-01

Combinatorial topics have become increasingly prevalent in K-12 and undergraduate curricula, yet research on combinatorics education indicates that students face difficulties when solving counting problems. The research community has not yet addressed students' ways of thinking at a level that facilitates deeper understanding of how students…
The LATL as locus of composition: MEG evidence from English and Arabic.

PubMed

Westerlund, Masha; Kastner, Itamar; Al Kaabi, Meera; Pylkkänen, Liina

2015-02-01

Neurolinguistic investigations into the processing of structured sentences as well as simple adjective-noun phrases point to the left anterior temporal lobe (LATL) as a leading candidate for basic linguistic composition. Here, we characterized the combinatory profile of the LATL over a variety of syntactic and semantic environments, and across two languages, English and Arabic. The contribution of the LATL was investigated across two types of composition: the optional modification of a predicate (modification) and the satisfaction of a predicate's argument position (argument saturation). Target words were presented during MEG recordings, either in combinatory contexts (e.g. "eats meat") or in non-combinatory contexts (preceded by an unpronounceable consonant string, e.g. "xqkr meat"). Across both languages, the LATL showed increased responses to words in combinatory contexts, an effect that was robust to composition type and word order. Together with related findings, these results solidify the role of the LATL in basic semantic composition. Copyright © 2014 Elsevier Inc. All rights reserved.
DNA Assembly Techniques for Next Generation Combinatorial Biosynthesis of Natural Products

PubMed Central

Cobb, Ryan E.; Ning, Jonathan C.; Zhao, Huimin

2013-01-01

Natural product scaffolds remain important leads for pharmaceutical development. However, transforming a natural product into a drug entity often requires derivatization to enhance the compound’s therapeutic properties. A powerful method by which to perform this derivatization is combinatorial biosynthesis, the manipulation of the genes in the corresponding pathway to divert synthesis towards novel derivatives. While these manipulations have traditionally been carried out via restriction digestion/ligation-based cloning, the shortcomings of such techniques limit their throughput and thus the scope of corresponding combinatorial biosynthesis experiments. In the burgeoning field of synthetic biology, the demand for facile DNA assembly techniques has promoted the development of a host of novel DNA assembly strategies. Here we describe the advantages of these recently-developed tools for rapid, efficient synthesis of large DNA constructs. We also discuss their potential to facilitate the simultaneous assembly of complete libraries of natural product biosynthetic pathways, ushering in the next generation of combinatorial biosynthesis. PMID:24127070
Novel Design Strategy for Checkpoint Kinase 2 Inhibitors Using Pharmacophore Modeling, Combinatorial Fusion, and Virtual Screening

PubMed Central

Wang, Yen-Ling

2014-01-01

Checkpoint kinase 2 (Chk2) has a great effect on DNA-damage and plays an important role in response to DNA double-strand breaks and related lesions. In this study, we will concentrate on Chk2 and the purpose is to find the potential inhibitors by the pharmacophore hypotheses (PhModels), combinatorial fusion, and virtual screening techniques. Applying combinatorial fusion into PhModels and virtual screening techniques is a novel design strategy for drug design. We used combinatorial fusion to analyze the prediction results and then obtained the best correlation coefficient of the testing set (r test) with the value 0.816 by combining the BesttrainBesttest and FasttrainFasttest prediction results. The potential inhibitors were selected from NCI database by screening according to BesttrainBesttest + FasttrainFasttest prediction results and molecular docking with CDOCKER docking program. Finally, the selected compounds have high interaction energy between a ligand and a receptor. Through these approaches, 23 potential inhibitors for Chk2 are retrieved for further study. PMID:24864236
A methodology to find the elementary landscape decomposition of combinatorial optimization problems.

PubMed

Chicano, Francisco; Whitley, L Darrell; Alba, Enrique

2011-01-01

A small number of combinatorial optimization problems have search spaces that correspond to elementary landscapes, where the objective function f is an eigenfunction of the Laplacian that describes the neighborhood structure of the search space. Many problems are not elementary; however, the objective function of a combinatorial optimization problem can always be expressed as a superposition of multiple elementary landscapes if the underlying neighborhood used is symmetric. This paper presents theoretical results that provide the foundation for algebraic methods that can be used to decompose the objective function of an arbitrary combinatorial optimization problem into a sum of subfunctions, where each subfunction is an elementary landscape. Many steps of this process can be automated, and indeed a software tool could be developed that assists the researcher in finding a landscape decomposition. This methodology is then used to show that the subset sum problem is a superposition of two elementary landscapes, and to show that the quadratic assignment problem is a superposition of three elementary landscapes.
Manta Matcher: automated photographic identification of manta rays using keypoint features.

PubMed

Town, Christopher; Marshall, Andrea; Sethasathien, Nutthaporn

2013-07-01

For species which bear unique markings, such as natural spot patterning, field work has become increasingly more reliant on visual identification to recognize and catalog particular specimens or to monitor individuals within populations. While many species of interest exhibit characteristic markings that in principle allow individuals to be identified from photographs, scientists are often faced with the task of matching observations against databases of hundreds or thousands of images. We present a novel technique for automated identification of manta rays (Manta alfredi and Manta birostris) by means of a pattern-matching algorithm applied to images of their ventral surface area. Automated visual identification has recently been developed for several species. However, such methods are typically limited to animals that can be photographed above water, or whose markings exhibit high contrast and appear in regular constellations. While manta rays bear natural patterning across their ventral surface, these patterns vary greatly in their size, shape, contrast, and spatial distribution. Our method is the first to have proven successful at achieving high matching accuracies on a large corpus of manta ray images taken under challenging underwater conditions. Our method is based on automated extraction and matching of keypoint features using the Scale-Invariant Feature Transform (SIFT) algorithm. In order to cope with the considerable variation in quality of underwater photographs, we also incorporate preprocessing and image enhancement steps. Furthermore, we use a novel pattern-matching approach that results in better accuracy than the standard SIFT approach and other alternative methods. We present quantitative evaluation results on a data set of 720 images of manta rays taken under widely different conditions. We describe a novel automated pattern representation and matching method that can be used to identify individual manta rays from photographs. The method has been incorporated into a website (mantamatcher.org) which will serve as a global resource for ecological and conservation research. It will allow researchers to manage and track sightings data to establish important life-history parameters as well as determine other ecological data such as abundance, range, movement patterns, and structure of manta ray populations across the world.
Manta Matcher: automated photographic identification of manta rays using keypoint features

PubMed Central

Town, Christopher; Marshall, Andrea; Sethasathien, Nutthaporn

2013-01-01

For species which bear unique markings, such as natural spot patterning, field work has become increasingly more reliant on visual identification to recognize and catalog particular specimens or to monitor individuals within populations. While many species of interest exhibit characteristic markings that in principle allow individuals to be identified from photographs, scientists are often faced with the task of matching observations against databases of hundreds or thousands of images. We present a novel technique for automated identification of manta rays (Manta alfredi and Manta birostris) by means of a pattern-matching algorithm applied to images of their ventral surface area. Automated visual identification has recently been developed for several species. However, such methods are typically limited to animals that can be photographed above water, or whose markings exhibit high contrast and appear in regular constellations. While manta rays bear natural patterning across their ventral surface, these patterns vary greatly in their size, shape, contrast, and spatial distribution. Our method is the first to have proven successful at achieving high matching accuracies on a large corpus of manta ray images taken under challenging underwater conditions. Our method is based on automated extraction and matching of keypoint features using the Scale-Invariant Feature Transform (SIFT) algorithm. In order to cope with the considerable variation in quality of underwater photographs, we also incorporate preprocessing and image enhancement steps. Furthermore, we use a novel pattern-matching approach that results in better accuracy than the standard SIFT approach and other alternative methods. We present quantitative evaluation results on a data set of 720 images of manta rays taken under widely different conditions. We describe a novel automated pattern representation and matching method that can be used to identify individual manta rays from photographs. The method has been incorporated into a website (mantamatcher.org) which will serve as a global resource for ecological and conservation research. It will allow researchers to manage and track sightings data to establish important life-history parameters as well as determine other ecological data such as abundance, range, movement patterns, and structure of manta ray populations across the world. PMID:23919138
Topological Classification of Crystalline Insulators through Band Structure Combinatorics

NASA Astrophysics Data System (ADS)

Kruthoff, Jorrit; de Boer, Jan; van Wezel, Jasper; Kane, Charles L.; Slager, Robert-Jan

2017-10-01

We present a method for efficiently enumerating all allowed, topologically distinct, electronic band structures within a given crystal structure in all physically relevant dimensions. The algorithm applies to crystals without time-reversal, particle-hole, chiral, or any other anticommuting or anti-unitary symmetries. The results presented match the mathematical structure underlying the topological classification of these crystals in terms of K -theory and therefore elucidate this abstract mathematical framework from a simple combinatorial perspective. Using a straightforward counting procedure, we classify all allowed topological phases of spinless particles in crystals in class A . Employing this classification, we study transitions between topological phases within class A that are driven by band inversions at high-symmetry points in the first Brillouin zone. This enables us to list all possible types of phase transitions within a given crystal structure and to identify whether or not they give rise to intermediate Weyl semimetallic phases.

Method and apparatus for digitally based high speed x-ray spectrometer

DOEpatents

Warburton, W.K.; Hubbard, B.

1997-11-04

A high speed, digitally based, signal processing system which accepts input data from a detector-preamplifier and produces a spectral analysis of the x-rays illuminating the detector. The system achieves high throughputs at low cost by dividing the required digital processing steps between a ``hardwired`` processor implemented in combinatorial digital logic, which detects the presence of the x-ray signals in the digitized data stream and extracts filtered estimates of their amplitudes, and a programmable digital signal processing computer, which refines the filtered amplitude estimates and bins them to produce the desired spectral analysis. One set of algorithms allow this hybrid system to match the resolution of analog systems while operating at much higher data rates. A second set of algorithms implemented in the processor allow the system to be self calibrating as well. The same processor also handles the interface to an external control computer. 19 figs.
Method and apparatus for digitally based high speed x-ray spectrometer

DOEpatents

Warburton, William K.; Hubbard, Bradley

1997-01-01

A high speed, digitally based, signal processing system which accepts input data from a detector-preamplifier and produces a spectral analysis of the x-rays illuminating the detector. The system achieves high throughputs at low cost by dividing the required digital processing steps between a "hardwired" processor implemented in combinatorial digital logic, which detects the presence of the x-ray signals in the digitized data stream and extracts filtered estimates of their amplitudes, and a programmable digital signal processing computer, which refines the filtered amplitude estimates and bins them to produce the desired spectral analysis. One set of algorithms allow this hybrid system to match the resolution of analog systems while operating at much higher data rates. A second set of algorithms implemented in the processor allow the system to be self calibrating as well. The same processor also handles the interface to an external control computer.
Key aspects of the Novartis compound collection enhancement project for the compilation of a comprehensive chemogenomics drug discovery screening collection.

PubMed

Jacoby, Edgar; Schuffenhauer, Ansgar; Popov, Maxim; Azzaoui, Kamal; Havill, Benjamin; Schopfer, Ulrich; Engeloch, Caroline; Stanek, Jaroslav; Acklin, Pierre; Rigollier, Pascal; Stoll, Friederike; Koch, Guido; Meier, Peter; Orain, David; Giger, Rudolph; Hinrichs, Jürgen; Malagu, Karine; Zimmermann, Jürg; Roth, Hans-Joerg

2005-01-01

The NIBR (Novartis Institutes for BioMedical Research) compound collection enrichment and enhancement project integrates corporate internal combinatorial compound synthesis and external compound acquisition activities in order to build up a comprehensive screening collection for a modern drug discovery organization. The main purpose of the screening collection is to supply the Novartis drug discovery pipeline with hit-to-lead compounds for today's and the future's portfolio of drug discovery programs, and to provide tool compounds for the chemogenomics investigation of novel biological pathways and circuits. As such, it integrates designed focused and diversity-based compound sets from the synthetic and natural paradigms able to cope with druggable and currently deemed undruggable targets and molecular interaction modes. Herein, we will summarize together with new trends published in the literature, scientific challenges faced and key approaches taken at NIBR to match the chemical and biological spaces.
Combinatorial biomatrix/cell-based therapies for restoration of host tissue architecture and function

PubMed Central

Cantu, David Antonio; Kao, W. John

2014-01-01

This Progress Report reviews recent advances in the utility of extracellular matrix (ECM)-mimic biomaterials in presenting and delivering therapeutic cells to promote tissue healing. This overview gives a brief introduction of different cell types being used in regenerative medicine and tissue engineering while addressing critical issues that must be overcome before cell-based approaches can be routinely employed in the clinic. A selection of 5 commonly used cell-associated, biomaterial platforms (collagen, hyaluronic acid, fibrin, alginate, and poly(ethylene glycol)) are reviewed for treatment of a number of acute injury or diseases with emphasis on animal models and clinical trials. This article concludes with current challenges and future perspectives regarding foreign body host response to biomaterials and immunological reactions to allogeneic or xenogeneic cells, vascularization and angiogenesis, matching mechanical strength and anisotropy of native tissues, as well as other non-technical issues regarding the clinical translation of biomatrix/cell-based therapies. PMID:23828863
Efficient Aho-Corasick String Matching on Emerging Multicore Architectures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tumeo, Antonino; Villa, Oreste; Secchi, Simone

String matching algorithms are critical to several scientific fields. Beside text processing and databases, emerging applications such as DNA protein sequence analysis, data mining, information security software, antivirus, ma- chine learning, all exploit string matching algorithms [3]. All these applica- tions usually process large quantity of textual data, require high performance and/or predictable execution times. Among all the string matching algorithms, one of the most studied, especially for text processing and security applica- tions, is the Aho-Corasick algorithm. 1 2 Book title goes here Aho-Corasick is an exact, multi-pattern string matching algorithm which performs the search in a time linearlymore » proportional to the length of the input text independently from pattern set size. However, depending on the imple- mentation, when the number of patterns increase, the memory occupation may raise drastically. In turn, this can lead to significant variability in the performance, due to the memory access times and the caching effects. This is a significant concern for many mission critical applications and modern high performance architectures. For example, security applications such as Network Intrusion Detection Systems (NIDS), must be able to scan network traffic against very large dictionaries in real time. Modern Ethernet links reach up to 10 Gbps, and malicious threats are already well over 1 million, and expo- nentially growing [28]. When performing the search, a NIDS should not slow down the network, or let network packets pass unchecked. Nevertheless, on the current state-of-the-art cache based processors, there may be a large per- formance variability when dealing with big dictionaries and inputs that have different frequencies of matching patterns. In particular, when few patterns are matched and they are all in the cache, the procedure is fast. Instead, when they are not in the cache, often because many patterns are matched and the caches are continuously thrashed, they should be retrieved from the system memory and the procedure is slowed down by the increased latency. Efficient implementations of string matching algorithms have been the fo- cus of several works, targeting Field Programmable Gate Arrays [4, 25, 15, 5], highly multi-threaded solutions like the Cray XMT [34], multicore proces- sors [19] or heterogeneous processors like the Cell Broadband Engine [35, 22]. Recently, several researchers have also started to investigate the use Graphic Processing Units (GPUs) for string matching algorithms in security applica- tions [20, 10, 32, 33]. Most of these approaches mainly focus on reaching high peak performance, or try to optimize the memory occupation, rather than looking at performance stability. However, hardware solutions supports only small dictionary sizes due to lack of memory and are difficult to customize, while platforms such as the Cell/B.E. are very complex to program.« less
A weak pattern random creation and scoring method for lithography process tuning

NASA Astrophysics Data System (ADS)

Zhang, Meili; Deng, Guogui; Wang, Mudan; Yu, Shirui; Hu, Xinyi; Du, Chunshan; Wan, Qijian; Liu, Zhengfang; Gao, Gensheng; Kabeel, Aliaa; Madkour, Kareem; ElManhawy, Wael; Kwan, Joe

2018-03-01

As the IC technology node moves forward, critical dimension becomes smaller and smaller, which brings huge challenge to IC manufacturing. Lithography is one of the most important steps during the whole manufacturing process and litho hotspots become a big source of yield detractors. Thus tuning lithographic recipes to cover a big range of litho hotspots is very essential to yield enhancing. During early technology developing stage, foundries only have limited customer layout data for recipe tuning. So collecting enough patterns is significant for process optimization. After accumulating enough patterns, a general way to treat them is not precise and applicable. Instead, an approach to scoring these patterns could provide a priority and reference to address different patterns more effectively. For example, the weakest group of patterns could be applied the most limited specs to ensure process robustness. This paper presents a new method of creation of real design alike patterns of multiple layers based on design rules using Layout Schema Generator (LSG) utility and a pattern scoring flow using Litho-friendly Design (LFD) and Pattern Matching. Through LSG, plenty of new unknown patterns could be created for further exploration. Then, litho simulation through LFD and topological matches by using Pattern Matching is applied on the output patterns of LSG. Finally, lithographical severity, printability properties and topological distribution of every pattern are collected. After a statistical analysis of pattern data, every pattern is given a relative score representing the pattern's yield detracting level. By sorting the output pattern score tables, weak patterns could be filtered out for further research and process tuning. This pattern generation and scoring flow is demonstrated on 28nm logic technology node. A weak pattern library is created and scored to help improve recipe coverage of litho hotspots and enhance the reliability of process.
In vitro and direct in vivo testing of mixture-based combinatorial libraries for the identification of highly active and specific opiate ligands.

PubMed

Houghten, Richard A; Dooley, Colette T; Appel, Jon R

2006-05-26

The use of combinatorial libraries for the identification of novel opiate and related ligands in opioid receptor assays is reviewed. Case studies involving opioid assays used to demonstrate the viability of combinatorial libraries are described. The identification of new opioid peptides composed of L-amino acids, D-amino acids, or L-, D-, and unnatural amino acids is reviewed. New opioid compounds have also been identified from peptidomimetic libraries, such as peptoids and alkylated dipeptides, and those identified from acyclic (eg, polyamine, urea) and heterocyclic (eg, bicyclic guanidine) libraries are reviewed.
Sentence Processing in an Artificial Language: Learning and Using Combinatorial Constraints

ERIC Educational Resources Information Center

Amato, Michael S.; MacDonald, Maryellen C.

2010-01-01

A study combining artificial grammar and sentence comprehension methods investigated the learning and online use of probabilistic, nonadjacent combinatorial constraints. Participants learned a small artificial language describing cartoon monsters acting on objects. Self-paced reading of sentences in the artificial language revealed comprehenders'…
A nonlinear dynamics approach for incorporating wind-speed patterns into wind-power project evaluation.

PubMed

Huffaker, Ray; Bittelli, Marco

2015-01-01

Wind-energy production may be expanded beyond regions with high-average wind speeds (such as the Midwest U.S.A.) to sites with lower-average speeds (such as the Southeast U.S.A.) by locating favorable regional matches between natural wind-speed and energy-demand patterns. A critical component of wind-power evaluation is to incorporate wind-speed dynamics reflecting documented diurnal and seasonal behavioral patterns. Conventional probabilistic approaches remove patterns from wind-speed data. These patterns must be restored synthetically before they can be matched with energy-demand patterns. How to accurately restore wind-speed patterns is a vexing problem spurring an expanding line of papers. We propose a paradigm shift in wind power evaluation that employs signal-detection and nonlinear-dynamics techniques to empirically diagnose whether synthetic pattern restoration can be avoided altogether. If the complex behavior of observed wind-speed records is due to nonlinear, low-dimensional, and deterministic system dynamics, then nonlinear dynamics techniques can reconstruct wind-speed dynamics from observed wind-speed data without recourse to conventional probabilistic approaches. In the first study of its kind, we test a nonlinear dynamics approach in an application to Sugarland Wind-the first utility-scale wind project proposed in Florida, USA. We find empirical evidence of a low-dimensional and nonlinear wind-speed attractor characterized by strong temporal patterns that match up well with regular daily and seasonal electricity demand patterns.
Quantum Efficiency and Bandgap Analysis for Combinatorial Photovoltaics: Sorting Activity of Cu–O Compounds in All-Oxide Device Libraries

PubMed Central

2014-01-01

All-oxide-based photovoltaics (PVs) encompass the potential for extremely low cost solar cells, provided they can obtain an order of magnitude improvement in their power conversion efficiencies. To achieve this goal, we perform a combinatorial materials study of metal oxide based light absorbers, charge transporters, junctions between them, and PV devices. Here we report the development of a combinatorial internal quantum efficiency (IQE) method. IQE measures the efficiency associated with the charge separation and collection processes, and thus is a proxy for PV activity of materials once placed into devices, discarding optical properties that cause uncontrolled light harvesting. The IQE is supported by high-throughput techniques for bandgap fitting, composition analysis, and thickness mapping, which are also crucial parameters for the combinatorial investigation cycle of photovoltaics. As a model system we use a library of 169 solar cells with a varying thickness of sprayed titanium dioxide (TiO2) as the window layer, and covarying thickness and composition of binary compounds of copper oxides (Cu–O) as the light absorber, fabricated by Pulsed Laser Deposition (PLD). The analysis on the combinatorial devices shows the correlation between compositions and bandgap, and their effect on PV activity within several device configurations. The analysis suggests that the presence of Cu4O3 plays a significant role in the PV activity of binary Cu–O compounds. PMID:24410367
On the Number of Non-equivalent Ancestral Configurations for Matching Gene Trees and Species Trees.

PubMed

Disanto, Filippo; Rosenberg, Noah A

2017-09-14

An ancestral configuration is one of the combinatorially distinct sets of gene lineages that, for a given gene tree, can reach a given node of a specified species tree. Ancestral configurations have appeared in recursive algebraic computations of the conditional probability that a gene tree topology is produced under the multispecies coalescent model for a given species tree. For matching gene trees and species trees, we study the number of ancestral configurations, considered up to an equivalence relation introduced by Wu (Evolution 66:763-775, 2012) to reduce the complexity of the recursive probability computation. We examine the largest number of non-equivalent ancestral configurations possible for a given tree size n. Whereas the smallest number of non-equivalent ancestral configurations increases polynomially with n, we show that the largest number increases with [Formula: see text], where k is a constant that satisfies [Formula: see text]. Under a uniform distribution on the set of binary labeled trees with a given size n, the mean number of non-equivalent ancestral configurations grows exponentially with n. The results refine an earlier analysis of the number of ancestral configurations considered without applying the equivalence relation, showing that use of the equivalence relation does not alter the exponential nature of the increase with tree size.
Searching social networks for subgraph patterns

NASA Astrophysics Data System (ADS)

Ogaard, Kirk; Kase, Sue; Roy, Heather; Nagi, Rakesh; Sambhoos, Kedar; Sudit, Moises

2013-06-01

Software tools for Social Network Analysis (SNA) are being developed which support various types of analysis of social networks extracted from social media websites (e.g., Twitter). Once extracted and stored in a database such social networks are amenable to analysis by SNA software. This data analysis often involves searching for occurrences of various subgraph patterns (i.e., graphical representations of entities and relationships). The authors have developed the Graph Matching Toolkit (GMT) which provides an intuitive Graphical User Interface (GUI) for a heuristic graph matching algorithm called the Truncated Search Tree (TruST) algorithm. GMT is a visual interface for graph matching algorithms processing large social networks. GMT enables an analyst to draw a subgraph pattern by using a mouse to select categories and labels for nodes and links from drop-down menus. GMT then executes the TruST algorithm to find the top five occurrences of the subgraph pattern within the social network stored in the database. GMT was tested using a simulated counter-insurgency dataset consisting of cellular phone communications within a populated area of operations in Iraq. The results indicated GMT (when executing the TruST graph matching algorithm) is a time-efficient approach to searching large social networks. GMT's visual interface to a graph matching algorithm enables intelligence analysts to quickly analyze and summarize the large amounts of data necessary to produce actionable intelligence.
Combinatorial enzyme technology: Conversion of pectin to oligo species and its effect on microbial growth

USDA-ARS?s Scientific Manuscript database

Plant cell wall polysaccharides, which consist of polymeric backbones with various types of substitution, were studied using the concept of combinatorial enzyme technology for conversion of agricultural fibers to functional products. Using citrus pectin as the starting substrate, an active oligo spe...
Students' Verification Strategies for Combinatorial Problems

ERIC Educational Resources Information Center

Mashiach Eizenberg, Michal; Zaslavsky, Orit

2004-01-01

We focus on a major difficulty in solving combinatorial problems, namely, on the verification of a solution. Our study aimed at identifying undergraduate students' tendencies to verify their solutions, and the verification strategies that they employ when solving these problems. In addition, an attempt was made to evaluate the level of efficiency…
Applications of Combinatorial Programming to Data Analysis: The Traveling Salesman and Related Problems

ERIC Educational Resources Information Center

Hubert, Lawrence J.; Baker, Frank B.

1978-01-01

The "Traveling Salesman" and similar combinatorial programming tasks encountered in operations research are discussed as possible data analysis models in psychology, for example, in developmental scaling, Guttman scaling, profile smoothing, and data array clustering. A short overview of various computational approaches from this area of…
Mesopause Horizontal wind estimates based on AIM CIPS polar mesospheric cloud pattern matching

NASA Astrophysics Data System (ADS)

Rong, P.; Yue, J.; Russell, J. M.; Gong, J.; Wu, D. L.; Randall, C. E.

2013-12-01

A cloud pattern matching approach is used to estimate horizontal winds in the mesopause region using Polar Mesospheric Cloud (PMC) albedo data measured by the Cloud Imaging and Particle Size instrument on the AIM satellite. Measurements for all 15 orbits per day throughout July 2007 are used to achieve statistical significance. For each orbit, eighteen out of the twenty-seven scenes are used for the pattern matching operation. Some scenes at the lower latitudes are not included because there is barely any cloud coverage for these scenes. The frame-size chosen is about 12 degrees in longitude and 3 degrees in latitude. There is no strict criterion in choosing the frame size since PMCs are widespread in the polar region and most local patterns do not have a clearly defined boundary. The frame moves at a step of 1/6th of the frame size in both the longitudinal and latitudinal directions to achieve as many 'snap-shots' as possible. A 70% correlation is used as a criterion to define an acceptable match between two patterns at two time frames; in this case the time difference is about 3.6 minutes that spans every 5 'bowtie' scenes. A 70% criterion appears weak if the chosen pattern is expected to act like a tracer. It is known that PMC brightness varies rapidly with a changing temperature and water vapor environment or changing nucleation conditions, especially on smaller spatial scales; therefore PMC patterns are not ideal tracers. Nevertheless, within a short time span such as 3.6 minutes a 70% correlation is sufficient to identify two cloud patterns that come from the same source region, although the two patterns may exhibit a significant difference in the actual brightness. Analysis of a large number of matched cloud patterns indicates that over the 3.6-minute time span about 70% of the patterns remain in the same locations. Given the 25-km2 horizontal resolution of CIPS data, this suggests that the overall magnitude of horizontal wind at PMC altitudes (~80-87 km) in the polar summer cannot exceed 25 m/s. In other words, the wind detection resolution is no better than 25 m/s. There are about 10% of cases in which it appears that an easterly prevails, with a peak value at about 80-100m/s. In another 5% of cases a westerly appears to prevail. The remaining 15% cases are related to either invalid cloud features with poor background correction or the situation in which the matching occurs at the corners of the bowties. The AIM CIPS cloud pattern matching results overall suggest that higher wind speed (25-200 m/s) can be reached occasionally, while in a majority of cases the wind advection caused albedo change is much smaller than the in-situ albedo change. However, we must note that this analysis was a feasibility study and the short period analyzed may not be representative of the winds over a seasonal time scale or the multiple-year average.
How Game Location Affects Soccer Performance: T-Pattern Analysis of Attack Actions in Home and Away Matches.

PubMed

Diana, Barbara; Zurloni, Valentino; Elia, Massimiliano; Cavalera, Cesare M; Jonsson, Gudberg K; Anguera, M Teresa

2017-01-01

The influence of game location on performance has been widely examined in sport contexts. Concerning soccer, game-location affects positively the secondary and tertiary level of performance; however, there are fewer evidences about its effect on game structure (primary level of performance). This study aimed to detect the effect of game location on a primary level of performance in soccer. In particular, the objective was to reveal the hidden structures underlying the attack actions, in both home and away matches played by a top club (Serie A 2012/2013-First Leg). The methodological approach was based on systematic observation, supported by digital recordings and T-pattern analysis. Data were analyzed with THEME 6.0 software. A quantitative analysis, with nonparametric Mann-Whitney test and descriptive statistics, was carried out to test the hypotheses. A qualitative analysis on complex patterns was performed to get in-depth information on the game structure. This study showed that game tactics were significantly different, with home matches characterized by a more structured and varied game than away matches. In particular, a higher number of different patterns, with a higher level of complexity and including more unique behaviors was detected in home matches than in the away ones. No significant differences were found in the number of events coded per game between the two conditions. THEME software, and the corresponding T-pattern detection algorithm, enhance research opportunities by going further than frequency-based analyses, making this method an effective tool in supporting sport performance analysis and training.
How Game Location Affects Soccer Performance: T-Pattern Analysis of Attack Actions in Home and Away Matches

PubMed Central

Diana, Barbara; Zurloni, Valentino; Elia, Massimiliano; Cavalera, Cesare M.; Jonsson, Gudberg K.; Anguera, M. Teresa

2017-01-01

The influence of game location on performance has been widely examined in sport contexts. Concerning soccer, game-location affects positively the secondary and tertiary level of performance; however, there are fewer evidences about its effect on game structure (primary level of performance). This study aimed to detect the effect of game location on a primary level of performance in soccer. In particular, the objective was to reveal the hidden structures underlying the attack actions, in both home and away matches played by a top club (Serie A 2012/2013—First Leg). The methodological approach was based on systematic observation, supported by digital recordings and T-pattern analysis. Data were analyzed with THEME 6.0 software. A quantitative analysis, with nonparametric Mann–Whitney test and descriptive statistics, was carried out to test the hypotheses. A qualitative analysis on complex patterns was performed to get in-depth information on the game structure. This study showed that game tactics were significantly different, with home matches characterized by a more structured and varied game than away matches. In particular, a higher number of different patterns, with a higher level of complexity and including more unique behaviors was detected in home matches than in the away ones. No significant differences were found in the number of events coded per game between the two conditions. THEME software, and the corresponding T-pattern detection algorithm, enhance research opportunities by going further than frequency-based analyses, making this method an effective tool in supporting sport performance analysis and training. PMID:28878712
Computing quality scores and uncertainty for approximate pattern matching in geospatial semantic graphs

DOE PAGES

Stracuzzi, David John; Brost, Randolph C.; Phillips, Cynthia A.; ...

2015-09-26

Geospatial semantic graphs provide a robust foundation for representing and analyzing remote sensor data. In particular, they support a variety of pattern search operations that capture the spatial and temporal relationships among the objects and events in the data. However, in the presence of large data corpora, even a carefully constructed search query may return a large number of unintended matches. This work considers the problem of calculating a quality score for each match to the query, given that the underlying data are uncertain. As a result, we present a preliminary evaluation of three methods for determining both match qualitymore » scores and associated uncertainty bounds, illustrated in the context of an example based on overhead imagery data.« less
Combining on-chip synthesis of a focused combinatorial library with computational target prediction reveals imidazopyridine GPCR ligands.

PubMed

Reutlinger, Michael; Rodrigues, Tiago; Schneider, Petra; Schneider, Gisbert

2014-01-07

Using the example of the Ugi three-component reaction we report a fast and efficient microfluidic-assisted entry into the imidazopyridine scaffold, where building block prioritization was coupled to a new computational method for predicting ligand-target associations. We identified an innovative GPCR-modulating combinatorial chemotype featuring ligand-efficient adenosine A1/2B and adrenergic α1A/B receptor antagonists. Our results suggest the tight integration of microfluidics-assisted synthesis with computer-based target prediction as a viable approach to rapidly generate bioactivity-focused combinatorial compound libraries with high success rates. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Generation of Dynamic Combinatorial Libraries Using Hydrazone‐Functionalized Surface Mimetics

PubMed Central

Hewitt, Sarah H.

2018-01-01

Dynamic combinatorial chemistry (DCC) represents an approach, whereby traditional supramolecular scaffolds used for protein surface recognition might be exploited to achieve selective high affinity target recognition. Synthesis, in situ screening and amplification under selection pressure allows the generation of ligands, which bear different moieties capable of making multivalent non‐covalent interactions with target proteins. Generic tetracarboxyphenyl porphyrin scaffolds bearing four hydrazide moieties have been used to form dynamic combinatorial libraries (DCLs) using aniline‐catalyzed reversible hydrazone exchange reactions, in 10 % DMSO, 5 mm NH4OAc, at pH 6.75. High resolution mass spectrometry (HRMS) was used to monitor library composition and establish conditions under which equilibria were established.
Escape Distance in Ground-Nesting Birds Differs with Individual Level of Camouflage.

PubMed

Wilson-Aggarwal, Jared K; Troscianko, Jolyon T; Stevens, Martin; Spottiswoode, Claire N

2016-08-01

Camouflage is one of the most widespread antipredator strategies in the animal kingdom, yet no animal can match its background perfectly in a complex environment. Therefore, selection should favor individuals that use information on how effective their camouflage is in their immediate habitat when responding to an approaching threat. In a field study of African ground-nesting birds (plovers, coursers, and nightjars), we tested the hypothesis that individuals adaptively modulate their escape behavior in relation to their degree of background matching. We used digital imaging and models of predator vision to quantify differences in color, luminance, and pattern between eggs and their background, as well as the plumage of incubating adult nightjars. We found that plovers and coursers showed greater escape distances when their eggs were a poorer pattern match to the background. Nightjars sit on their eggs until a potential threat is nearby, and, correspondingly, they showed greater escape distances when the pattern and color match of the incubating adult's plumage-rather than its eggs-was a poorer match to the background. Finally, escape distances were shorter in the middle of the day, suggesting that escape behavior is mediated by both camouflage and thermoregulation.
Patterns of Movement in Foster Care: An Optimal Matching Analysis

PubMed Central

Havlicek, Judy

2011-01-01

Placement instability remains a vexing problem for child welfare agencies across the country. This study uses child welfare administrative data to retrospectively follow the entire placement histories (birth to age 17.5) of 474 foster youth who reached the age of majority in the state of Illinois and to search for patterns in their movement through the child welfare system. Patterns are identified through optimal matching and hierarchical cluster analyses. Multiple logistic regression is used to analyze administrative and survey data in order to examine covariates related to patterns. Five distinct patterns of movement are differentiated: Late Movers, Settled with Kin, Community Care, Institutionalized, and Early Entry. These patterns suggest high but variable rates of movement. Implications for child welfare policy and service provision are discussed. PMID:20873020
Automated Combinatorial Chemistry in the Organic Chemistry Majors Laboratory

ERIC Educational Resources Information Center

Nichols, Christopher J.; Hanne, Larry F.

2010-01-01

A multidisciplinary experiment has been developed in which students each synthesize a combinatorial library of 48 hydrazones with the aid of a liquid-handling robot. Each product is then subjected to a Kirby-Bauer disk diffusion assay to assess its antibacterial activity. Students gain experience working with automation and at the…
More Combinatorial Proofs via Flagpole Arrangements

ERIC Educational Resources Information Center

DeTemple, Duane; Reynolds, H. David, II

2006-01-01

Combinatorial identities are proved by counting the number of arrangements of a flagpole and guy wires on a row of blocks that satisfy a set of conditions. An identity is proved by first deriving and then equating two expressions that each count the number of permissible arrangements. Identities for binomial coefficients and recursion relations…
Using Combinatorial Approach to Improve Students' Learning of the Distributive Law and Multiplicative Identities

ERIC Educational Resources Information Center

Tsai, Yu-Ling; Chang, Ching-Kuch

2009-01-01

This article reports an alternative approach, called the combinatorial model, to learning multiplicative identities, and investigates the effects of implementing results for this alternative approach. Based on realistic mathematics education theory, the new instructional materials or modules of the new approach were developed by the authors. From…
Children's Strategies for Solving Two- and Three-Dimensional Combinatorial Problems.

ERIC Educational Resources Information Center

English, Lyn D.

1993-01-01

Investigated strategies that 7- to 12-year-old children (n=96) spontaneously applied in solving novel combinatorial problems. With experience in solving two-dimensional problems, children were able to refine their strategies and adapt them to three dimensions. Results on some problems indicated significant effects of age. (Contains 32 references.)…
Identities for Generalized Fibonacci Numbers: A Combinatorial Approach

ERIC Educational Resources Information Center

Plaza, A.; Falcon, S.

2008-01-01

This note shows a combinatorial approach to some identities for generalized Fibonacci numbers. While it is a straightforward task to prove these identities with induction, and also by arithmetical manipulations such as rearrangements, the approach used here is quite simple to follow and eventually reduces the proof to a counting problem. (Contains…
Combinatorial Partial Hydrogenation Reactions of 4-Nitroacetophenone: An Undergraduate Organic Laboratory

ERIC Educational Resources Information Center

Kittredge, Kevin W.; Marine, Susan S.; Taylor, Richard T.

2004-01-01

A molecule possessing other functional groups that could be hydrogenerated is examined, where a variety of metal catalysts are evaluated under similar reaction conditions. Optimizing organic reactions is both time and labor intensive, and the use of a combinatorial parallel synthesis reactor was great time saving device, as per summary.
Human Performance on the Traveling Salesman and Related Problems: A Review

ERIC Educational Resources Information Center

MacGregor, James N.; Chu, Yun

2011-01-01

The article provides a review of recent research on human performance on the traveling salesman problem (TSP) and related combinatorial optimization problems. We discuss what combinatorial optimization problems are, why they are important, and why they may be of interest to cognitive scientists. We next describe the main characteristics of human…
Heuristic Implementation of Dynamic Programming for Matrix Permutation Problems in Combinatorial Data Analysis

ERIC Educational Resources Information Center

Brusco, Michael J.; Kohn, Hans-Friedrich; Stahl, Stephanie

2008-01-01

Dynamic programming methods for matrix permutation problems in combinatorial data analysis can produce globally-optimal solutions for matrices up to size 30x30, but are computationally infeasible for larger matrices because of enormous computer memory requirements. Branch-and-bound methods also guarantee globally-optimal solutions, but computation…
Iconicity and the Emergence of Combinatorial Structure in Language

ERIC Educational Resources Information Center

Verhoef, Tessa; Kirby, Simon; de Boer, Bart

2016-01-01

In language, recombination of a discrete set of meaningless building blocks forms an unlimited set of possible utterances. How such combinatorial structure emerged in the evolution of human language is increasingly being studied. It has been shown that it can emerge when languages culturally evolve and adapt to human cognitive biases. How the…
Crossover versus mutation: a comparative analysis of the evolutionary strategy of genetic algorithms applied to combinatorial optimization problems.

PubMed

Osaba, E; Carballedo, R; Diaz, F; Onieva, E; de la Iglesia, I; Perallos, A

2014-01-01

Since their first formulation, genetic algorithms (GAs) have been one of the most widely used techniques to solve combinatorial optimization problems. The basic structure of the GAs is known by the scientific community, and thanks to their easy application and good performance, GAs are the focus of a lot of research works annually. Although throughout history there have been many studies analyzing various concepts of GAs, in the literature there are few studies that analyze objectively the influence of using blind crossover operators for combinatorial optimization problems. For this reason, in this paper a deep study on the influence of using them is conducted. The study is based on a comparison of nine techniques applied to four well-known combinatorial optimization problems. Six of the techniques are GAs with different configurations, and the remaining three are evolutionary algorithms that focus exclusively on the mutation process. Finally, to perform a reliable comparison of these results, a statistical study of them is made, performing the normal distribution z-test.
Crossover versus Mutation: A Comparative Analysis of the Evolutionary Strategy of Genetic Algorithms Applied to Combinatorial Optimization Problems

PubMed Central

Osaba, E.; Carballedo, R.; Diaz, F.; Onieva, E.; de la Iglesia, I.; Perallos, A.

2014-01-01

Since their first formulation, genetic algorithms (GAs) have been one of the most widely used techniques to solve combinatorial optimization problems. The basic structure of the GAs is known by the scientific community, and thanks to their easy application and good performance, GAs are the focus of a lot of research works annually. Although throughout history there have been many studies analyzing various concepts of GAs, in the literature there are few studies that analyze objectively the influence of using blind crossover operators for combinatorial optimization problems. For this reason, in this paper a deep study on the influence of using them is conducted. The study is based on a comparison of nine techniques applied to four well-known combinatorial optimization problems. Six of the techniques are GAs with different configurations, and the remaining three are evolutionary algorithms that focus exclusively on the mutation process. Finally, to perform a reliable comparison of these results, a statistical study of them is made, performing the normal distribution z-test. PMID:25165731
Novel design strategy for checkpoint kinase 2 inhibitors using pharmacophore modeling, combinatorial fusion, and virtual screening.

PubMed

Lin, Chun-Yuan; Wang, Yen-Ling

2014-01-01

Checkpoint kinase 2 (Chk2) has a great effect on DNA-damage and plays an important role in response to DNA double-strand breaks and related lesions. In this study, we will concentrate on Chk2 and the purpose is to find the potential inhibitors by the pharmacophore hypotheses (PhModels), combinatorial fusion, and virtual screening techniques. Applying combinatorial fusion into PhModels and virtual screening techniques is a novel design strategy for drug design. We used combinatorial fusion to analyze the prediction results and then obtained the best correlation coefficient of the testing set (r test) with the value 0.816 by combining the Best(train)Best(test) and Fast(train)Fast(test) prediction results. The potential inhibitors were selected from NCI database by screening according to Best(train)Best(test) + Fast(train)Fast(test) prediction results and molecular docking with CDOCKER docking program. Finally, the selected compounds have high interaction energy between a ligand and a receptor. Through these approaches, 23 potential inhibitors for Chk2 are retrieved for further study.
A combinatorial filtering method for magnetotelluric time-series based on Hilbert-Huang transform

NASA Astrophysics Data System (ADS)

Cai, Jianhua

2014-11-01

Magnetotelluric (MT) time-series are often contaminated with noise from natural or man-made processes. A substantial improvement is possible when the time-series are presented as clean as possible for further processing. A combinatorial method is described for filtering of MT time-series based on the Hilbert-Huang transform that requires a minimum of human intervention and leaves good data sections unchanged. Good data sections are preserved because after empirical mode decomposition the data are analysed through hierarchies, morphological filtering, adaptive threshold and multi-point smoothing, allowing separation of noise from signals. The combinatorial method can be carried out without any assumption about the data distribution. Simulated data and the real measured MT time-series from three different regions, with noise caused by baseline drift, high frequency noise and power-line contribution, are processed to demonstrate the application of the proposed method. Results highlight the ability of the combinatorial method to pick out useful signals, and the noise is suppressed greatly so that their deleterious influence is eliminated for the MT transfer function estimation.
Combinatorial discovery of new methanol-tolerant non-noble metal cathode electrocatalysts for direct methanol fuel cells.

PubMed

Yu, Jong-Sung; Kim, Min-Sik; Kim, Jung Ho

2010-12-14

Combinatorial synthesis and screening were used to identify methanol-tolerant non-platinum cathode electrocatalysts for use in direct methanol fuel cells (DMFCs). Oxygen reduction consumes protons at the surface of DMFC cathode catalysts. In combinatorial screening, this pH change allows one to differentiate active catalysts using fluorescent acid-base indicators. Combinatorial libraries of carbon-supported catalyst compositions containing Ru, Mo, W, Sn, and Se were screened. Ternary and quaternary compositions containing Ru, Sn, Mo, Se were more active than the "standard" Alonso-Vante catalyst, Ru(3)Mo(0.08)Se(2), when tested in liquid-feed DMFCs. Physical characterization of the most active catalysts by powder X-ray diffraction, gas adsorption, and X-ray photoelectron spectroscopy revealed that the predominant crystalline phase was hexagonal close-packed (hcp) ruthenium, and showed a surface mostly covered with oxide. The best new catalyst, Ru(7.0)Sn(1.0)Se(1.0), was significantly more active than Ru(3)Se(2)Mo(0.08), even though the latter contained smaller particles.
Combinatorial Characterization of TiO2 Chemical Vapor Deposition Utilizing Titanium Isopropoxide.

PubMed

Reinke, Michael; Ponomarev, Evgeniy; Kuzminykh, Yury; Hoffmann, Patrik

2015-07-13

The combinatorial characterization of the growth kinetics in chemical vapor deposition processes is challenging because precise information about the local precursor flow is usually difficult to access. In consequence, combinatorial chemical vapor deposition techniques are utilized more to study functional properties of thin films as a function of chemical composition, growth rate or crystallinity than to study the growth process itself. We present an experimental procedure which allows the combinatorial study of precursor surface kinetics during the film growth using high vacuum chemical vapor deposition. As consequence of the high vacuum environment, the precursor transport takes place in the molecular flow regime, which allows predicting and modifying precursor impinging rates on the substrate with comparatively little experimental effort. In this contribution, we study the surface kinetics of titanium dioxide formation using titanium tetraisopropoxide as precursor molecule over a large parameter range. We discuss precursor flux and temperature dependent morphology, crystallinity, growth rates, and precursor deposition efficiency. We conclude that the surface reaction of the adsorbed precursor molecules comprises a higher order reaction component with respect to precursor surface coverage.
Particle-Based Microarrays of Oligonucleotides and Oligopeptides.

PubMed

Nesterov-Mueller, Alexander; Maerkle, Frieder; Hahn, Lothar; Foertsch, Tobias; Schillo, Sebastian; Bykovskaya, Valentina; Sedlmayr, Martyna; Weber, Laura K; Ridder, Barbara; Soehindrijo, Miriam; Muenster, Bastian; Striffler, Jakob; Bischoff, F Ralf; Breitling, Frank; Loeffler, Felix F

2014-10-28

In this review, we describe different methods of microarray fabrication based on the use of micro-particles/-beads and point out future tendencies in the development of particle-based arrays. First, we consider oligonucleotide bead arrays, where each bead is a carrier of one specific sequence of oligonucleotides. This bead-based array approach, appearing in the late 1990s, enabled high-throughput oligonucleotide analysis and had a large impact on genome research. Furthermore, we consider particle-based peptide array fabrication using combinatorial chemistry. In this approach, particles can directly participate in both the synthesis and the transfer of synthesized combinatorial molecules to a substrate. Subsequently, we describe in more detail the synthesis of peptide arrays with amino acid polymer particles, which imbed the amino acids inside their polymer matrix. By heating these particles, the polymer matrix is transformed into a highly viscous gel, and thereby, imbedded monomers are allowed to participate in the coupling reaction. Finally, we focus on combinatorial laser fusing of particles for the synthesis of high-density peptide arrays. This method combines the advantages of particles and combinatorial lithographic approaches.
Particle-Based Microarrays of Oligonucleotides and Oligopeptides

PubMed Central

Nesterov-Mueller, Alexander; Maerkle, Frieder; Hahn, Lothar; Foertsch, Tobias; Schillo, Sebastian; Bykovskaya, Valentina; Sedlmayr, Martyna; Weber, Laura K.; Ridder, Barbara; Soehindrijo, Miriam; Muenster, Bastian; Striffler, Jakob; Bischoff, F. Ralf; Breitling, Frank; Loeffler, Felix F.

2014-01-01

In this review, we describe different methods of microarray fabrication based on the use of micro-particles/-beads and point out future tendencies in the development of particle-based arrays. First, we consider oligonucleotide bead arrays, where each bead is a carrier of one specific sequence of oligonucleotides. This bead-based array approach, appearing in the late 1990s, enabled high-throughput oligonucleotide analysis and had a large impact on genome research. Furthermore, we consider particle-based peptide array fabrication using combinatorial chemistry. In this approach, particles can directly participate in both the synthesis and the transfer of synthesized combinatorial molecules to a substrate. Subsequently, we describe in more detail the synthesis of peptide arrays with amino acid polymer particles, which imbed the amino acids inside their polymer matrix. By heating these particles, the polymer matrix is transformed into a highly viscous gel, and thereby, imbedded monomers are allowed to participate in the coupling reaction. Finally, we focus on combinatorial laser fusing of particles for the synthesis of high-density peptide arrays. This method combines the advantages of particles and combinatorial lithographic approaches. PMID:27600347

Combinatorially-generated library of 6-fluoroquinolone analogs as potential novel antitubercular agents: a chemometric and molecular modeling assessment.

PubMed

Minovski, Nikola; Perdih, Andrej; Solmajer, Tom

2012-05-01

The virtual combinatorial chemistry approach as a methodology for generating chemical libraries of structurally-similar analogs in a virtual environment was employed for building a general mixed virtual combinatorial library with a total of 53.871 6-FQ structural analogs, introducing the real synthetic pathways of three well known 6-FQ inhibitors. The druggability properties of the generated combinatorial 6-FQs were assessed using an in-house developed drug-likeness filter integrating the Lipinski/Veber rule-sets. The compounds recognized as drug-like were used as an external set for prediction of the biological activity values using a neural-networks (NN) model based on an experimentally-determined set of active 6-FQs. Furthermore, a subset of compounds was extracted from the pool of drug-like 6-FQs, with predicted biological activity, and subsequently used in virtual screening (VS) campaign combining pharmacophore modeling and molecular docking studies. This complex scheme, a powerful combination of chemometric and molecular modeling approaches provided novel QSAR guidelines that could aid in the further lead development of 6-FQs agents.
Prosody and alignment: a sequential perspective

NASA Astrophysics Data System (ADS)

Szczepek Reed, Beatrice

2010-12-01

In their analysis of a corpus of classroom interactions in an inner city high school, Roth and Tobin describe how teachers and students accomplish interactional alignment by prosodically matching each other's turns. Prosodic matching, and specific prosodic patterns are interpreted as signs of, and contributions to successful interactional outcomes and positive emotions. Lack of prosodic matching, and other specific prosodic patterns are interpreted as features of unsuccessful interactions, and negative emotions. This forum focuses on the article's analysis of the relation between interpersonal alignment, emotion and prosody. It argues that prosodic matching, and other prosodic linking practices, play a primarily sequential role, i.e. one that displays the way in which participants place and design their turns in relation to other participants' turns. Prosodic matching, rather than being a conversational action in itself, is argued to be an interactional practice (Schegloff 1997), which is not always employed for the accomplishment of `positive', or aligning actions.
Fuzzy logic of Aristotelian forms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perlovsky, L.I.

1996-12-31

Model-based approaches to pattern recognition and machine vision have been proposed to overcome the exorbitant training requirements of earlier computational paradigms. However, uncertainties in data were found to lead to a combinatorial explosion of the computational complexity. This issue is related here to the roles of a priori knowledge vs. adaptive learning. What is the a-priori knowledge representation that supports learning? I introduce Modeling Field Theory (MFT), a model-based neural network whose adaptive learning is based on a priori models. These models combine deterministic, fuzzy, and statistical aspects to account for a priori knowledge, its fuzzy nature, and data uncertainties.more » In the process of learning, a priori fuzzy concepts converge to crisp or probabilistic concepts. The MFT is a convergent dynamical system of only linear computational complexity. Fuzzy logic turns out to be essential for reducing the combinatorial complexity to linear one. I will discuss the relationship of the new computational paradigm to two theories due to Aristotle: theory of Forms and logic. While theory of Forms argued that the mind cannot be based on ready-made a priori concepts, Aristotelian logic operated with just such concepts. I discuss an interpretation of MFT suggesting that its fuzzy logic, combining a-priority and adaptivity, implements Aristotelian theory of Forms (theory of mind). Thus, 2300 years after Aristotle, a logic is developed suitable for his theory of mind.« less
Screening of a Combinatorial Library of Organic Polymers for the Solid-Phase Extraction of Patulin from Apple Juice

PubMed Central

Giovannoli, Cristina; Spano, Giulia; Di Nardo, Fabio; Anfossi, Laura; Baggiani, Claudio

2017-01-01

Patulin is a water-soluble mycotoxin produced by several species of fungi. Governmental bodies have placed it under scrutiny for its potential negative health effects, and maximum residue limits are fixed in specific food matrices to protect consumers’ health. Confirmatory analysis of patulin in complex food matrices can be a difficult task, and sample clean-up treatments are frequently necessary before instrumental analyses. With the aim of simplifying the clean-up step, we prepared a 256-member combinatorial polymeric library based on 16 functional monomers, four cross-linkers and four different porogenic solvents. The library was screened for the binding towards patulin in different media (acetonitrile and citrate buffer at pH 3.2), with the goal of identifying polymer formulations with good binding properties towards the target compound. As a proof of concept, a methacrylic acid-co-pentaerithrytole tetraacrylate polymer prepared in chloroform was successfully used as a solid-phase extraction material for the clean-up and extraction of patulin from apple juice. Clean chromatographic patterns and acceptable recoveries were obtained for juice spiked with patulin at concentration levels of 25 (64 ± 12%), 50 (83 ± 5.6%) and 100 μg L−1 (76 ± 4.5%). The within-day and between-day reproducibility evaluated at a concentration level of 25 μg L−1 were 5.6 and 7.6%, respectively. PMID:28531103
Pitch Adaptation Patterns in Bimodal Cochlear Implant Users: Over Time and After Experience

PubMed Central

Reiss, Lina A.J.; Ito, Rindy A.; Eggleston, Jessica L.; Liao, Selena; Becker, Jillian J.; Lakin, Carrie E.; Warren, Frank M.; McMenomey, Sean O.

2014-01-01

Background Pitch plasticity has been observed in Hybrid cochlear implant (CI) users. Does pitch plasticity also occur in bimodal CI users with traditional long-electrode CIs, and is pitch adaptation pattern associated with electrode discrimination or speech recognition performance? Objective Characterize pitch adaptation patterns in long-electrode CI users, correlate these patterns with electrode discrimination and speech perception outcomes, and analyze which subject factors are associated with the different patterns. Methods Electric-to-acoustic pitch matches were obtained in 19 subjects over time from CI activation to at least 12 months after activation, and in a separate group of 18 subjects in a single visit after at least 24 months of CI experience. Audiometric thresholds, electrode discrimination performance, and speech perception scores were also measured. Results Subjects measured over time had pitch adaptation patterns that fit one of the following categories: 1) “Pitch-adapting”, i.e. the mismatch between perceived electrode pitch and the corresponding frequency-to-electrode allocations decreased; 2) “Pitch-dropping”, i.e. the pitches of multiple electrodes dropped and converged to a similar low pitch; 3) “Pitch-unchanging”, i.e. electrode pitches did not change. Subjects measured after CI experience had a parallel set of adaptation patterns: 1) “Matched-pitch”, i.e. the electrode pitch was matched to the frequency allocation; 2) “Low-pitch”, i.e. the pitches of multiple electrodes were all around the lowest frequency allocation; 3) “Nonmatched-pitch”, i.e. the pitch patterns were compressed relative to the frequency allocations and did not fit either the matched-pitch or low-pitch categories. Unlike Hybrid CI users which were mostly in the pitch-adapting/matched-pitch category, the majority of bimodal CI users were in the latter two categories, pitch-dropping/low-pitch or pitch-unchanging/nonmatched-pitch. Subjects with pitch-adapting or matched-pitch patterns tended to have better low-frequency thresholds than subjects in the latter categories. Changes in electrode discrimination over time were not associated with changes in pitch differences between electrodes. Reductions in speech perception scores over time showed a weak but nonsignificant association with dropping-pitch patterns. Conclusions Bimodal CI users with more residual hearing may have somewhat greater similarity to Hybrid CI users and be more likely to adapt pitch perception to reduce mismatch with the frequencies allocated to the electrodes and the acoustic hearing. In contrast, bimodal CI users with less residual hearing exhibit either no adaptation, or surprisingly, a third pattern in which the pitches of the basal electrodes drop to match the frequency range allocated to the most apical electrode. The lack of association of electrode discrimination changes with pitch changes suggests that electrode discrimination does not depend on perceived pitch differences between electrodes, but rather on some other characteristics such as timbre. In contrast, speech perception may depend more on pitch perception and the ability to distinguish pitch between electrodes, especially since during multi-electrode stimulation, cues such as timbre may be less useful for discrimination. PMID:25319401
Probabilistic multi-catalogue positional cross-match

NASA Astrophysics Data System (ADS)

Pineau, F.-X.; Derriere, S.; Motch, C.; Carrera, F. J.; Genova, F.; Michel, L.; Mingo, B.; Mints, A.; Nebot Gómez-Morán, A.; Rosen, S. R.; Ruiz Camuñas, A.

2017-01-01

Context. Catalogue cross-correlation is essential to building large sets of multi-wavelength data, whether it be to study the properties of populations of astrophysical objects or to build reference catalogues (or timeseries) from survey observations. Nevertheless, resorting to automated processes with limited sets of information available on large numbers of sources detected at different epochs with various filters and instruments inevitably leads to spurious associations. We need both statistical criteria to select detections to be merged as unique sources, and statistical indicators helping in achieving compromises between completeness and reliability of selected associations. Aims: We lay the foundations of a statistical framework for multi-catalogue cross-correlation and cross-identification based on explicit simplified catalogue models. A proper identification process should rely on both astrometric and photometric data. Under some conditions, the astrometric part and the photometric part can be processed separately and merged a posteriori to provide a single global probability of identification. The present paper addresses almost exclusively the astrometrical part and specifies the proper probabilities to be merged with photometric likelihoods. Methods: To select matching candidates in n catalogues, we used the Chi (or, indifferently, the Chi-square) test with 2(n-1) degrees of freedom. We thus call this cross-match a χ-match. In order to use Bayes' formula, we considered exhaustive sets of hypotheses based on combinatorial analysis. The volume of the χ-test domain of acceptance - a 2(n-1)-dimensional acceptance ellipsoid - is used to estimate the expected numbers of spurious associations. We derived priors for those numbers using a frequentist approach relying on simple geometrical considerations. Likelihoods are based on standard Rayleigh, χ and Poisson distributions that we normalized over the χ-test acceptance domain. We validated our theoretical results by generating and cross-matching synthetic catalogues. Results: The results we obtain do not depend on the order used to cross-correlate the catalogues. We applied the formalism described in the present paper to build the multi-wavelength catalogues used for the science cases of the Astronomical Resource Cross-matching for High Energy Studies (ARCHES) project. Our cross-matching engine is publicly available through a multi-purpose web interface. In a longer term, we plan to integrate this tool into the CDS XMatch Service.
Integrating an object system into CLIPS: Language design and implementation issues

NASA Technical Reports Server (NTRS)

Auburn, Mark

1990-01-01

This paper describes the reasons why an object system with integrated pattern-matching and object-oriented programming facilities is desirable for CLIPS and how it is possible to integrate such a system into CLIPS while maintaining the run-time performance and the low memory usage for which CLIPS is known. The requirements for an object system in CLIPS that includes object-oriented programming and integrated pattern-matching are discussed and various techniques for optimizing the object system and its integration with the pattern-matcher are presented.
A Nonlinear Dynamics Approach for Incorporating Wind-Speed Patterns into Wind-Power Project Evaluation

PubMed Central

Huffaker, Ray; Bittelli, Marco

2015-01-01

Wind-energy production may be expanded beyond regions with high-average wind speeds (such as the Midwest U.S.A.) to sites with lower-average speeds (such as the Southeast U.S.A.) by locating favorable regional matches between natural wind-speed and energy-demand patterns. A critical component of wind-power evaluation is to incorporate wind-speed dynamics reflecting documented diurnal and seasonal behavioral patterns. Conventional probabilistic approaches remove patterns from wind-speed data. These patterns must be restored synthetically before they can be matched with energy-demand patterns. How to accurately restore wind-speed patterns is a vexing problem spurring an expanding line of papers. We propose a paradigm shift in wind power evaluation that employs signal-detection and nonlinear-dynamics techniques to empirically diagnose whether synthetic pattern restoration can be avoided altogether. If the complex behavior of observed wind-speed records is due to nonlinear, low-dimensional, and deterministic system dynamics, then nonlinear dynamics techniques can reconstruct wind-speed dynamics from observed wind-speed data without recourse to conventional probabilistic approaches. In the first study of its kind, we test a nonlinear dynamics approach in an application to Sugarland Wind—the first utility-scale wind project proposed in Florida, USA. We find empirical evidence of a low-dimensional and nonlinear wind-speed attractor characterized by strong temporal patterns that match up well with regular daily and seasonal electricity demand patterns. PMID:25617767
Combinatorial effect of substratum properties on mesenchymal stem cell sheet engineering and subsequent multi-lineage differentiation.

PubMed

Chuah, Yon Jin; Zhang, Ying; Wu, Yingnan; Menon, Nishanth V; Goh, Ghim Hian; Lee, Ann Charlene; Chan, Vincent; Zhang, Yilei; Kang, Yuejun

2015-09-01

Cell sheet engineering has been exploited as an alternative approach in tissue regeneration and the use of stem cells to generate cell sheets has further showed its potential in stem cell-mediated tissue regeneration. There exist vast interests in developing strategies to enhance the formation of stem cell sheets for downstream applications. It has been proved that stem cells are sensitive to the biophysical cues of the microenvironment. Therefore we hypothesized that the combinatorial substratum properties could be tailored to modulate the development of cell sheet formation and further influence its multipotency. For validation, polydimethylsiloxane (PDMS) of different combinatorial substratum properties (including stiffness, roughness and wettability) were created, on which the human bone marrow derived mesenchymal stem cells (BMSCs) were cultured to form cell sheets with their multipotency evaluated after induced differentiation. The results showed that different combinatorial effects of these substratum properties were able to influence BMSC behavior such as adhesion, spreading and proliferation during cell sheet development. Collagen formation within the cell sheet was enhanced on substrates with lower stiffness, higher hydrophobicity and roughness, which further assisted the induced chondrogenesis and osteogenesis, respectively. These findings suggested that combinatorial substratum properties had profound effects on BMSC cell sheet integrity and multipotency, which had significant implications for future biomaterials and scaffold designs in the field of BMSC-mediated tissue regeneration. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
High-throughput combinatorial chemical bath deposition: The case of doping Cu (In, Ga) Se film with antimony

NASA Astrophysics Data System (ADS)

Yan, Zongkai; Zhang, Xiaokun; Li, Guang; Cui, Yuxing; Jiang, Zhaolian; Liu, Wen; Peng, Zhi; Xiang, Yong

2018-01-01

The conventional methods for designing and preparing thin film based on wet process remain a challenge due to disadvantages such as time-consuming and ineffective, which hinders the development of novel materials. Herein, we present a high-throughput combinatorial technique for continuous thin film preparation relied on chemical bath deposition (CBD). The method is ideally used to prepare high-throughput combinatorial material library with low decomposition temperatures and high water- or oxygen-sensitivity at relatively high-temperature. To check this system, a Cu(In, Ga)Se (CIGS) thin films library doped with 0-19.04 at.% of antimony (Sb) was taken as an example to evaluate the regulation of varying Sb doping concentration on the grain growth, structure, morphology and electrical properties of CIGS thin film systemically. Combined with the Energy Dispersive Spectrometer (EDS), X-ray Photoelectron Spectroscopy (XPS), automated X-ray Diffraction (XRD) for rapid screening and Localized Electrochemical Impedance Spectroscopy (LEIS), it was confirmed that this combinatorial high-throughput system could be used to identify the composition with the optimal grain orientation growth, microstructure and electrical properties systematically, through accurately monitoring the doping content and material composition. According to the characterization results, a Sb2Se3 quasi-liquid phase promoted CIGS film-growth model has been put forward. In addition to CIGS thin film reported here, the combinatorial CBD also could be applied to the high-throughput screening of other sulfide thin film material systems.
A Statistical Procedure for Testing Unusually Frequent Exactly Matching Responses and Nearly Matching Responses. Research Report. ETS RR-17-23

ERIC Educational Resources Information Center

Haberman, Shelby J.; Lee, Yi-Hsuan

2017-01-01

In investigations of unusual testing behavior, a common question is whether a specific pattern of responses occurs unusually often within a group of examinees. In many current tests, modern communication techniques can permit quite large numbers of examinees to share keys, or common response patterns, to the entire test. To address this issue,…
Patterns of Somatic Diagnoses in Older People with Intellectual Disability: A Swedish Eleven Year Case-Control Study of Inpatient Data

ERIC Educational Resources Information Center

Sandberg, Magnus; Ahlström, Gerd; Kristensson, Jimmie

2017-01-01

Background: Knowledge about diagnoses patterns in older people with intellectual disabilities is limited. Methods: The case group (n = 7936) comprised people with intellectual disabilities aged 55 years and older. The control group (n = 7936) was age matched and sex matched. Somatic inpatient diagnoses (2002-2012) were collected retrospectively.…
Combination Across Domains: An MEG Investigation into the Relationship between Mathematical, Pictorial, and Linguistic Processing

PubMed Central

Bemis, Douglas K.; Pylkkänen, Liina

2013-01-01

Debates surrounding the evolution of language often hinge upon its relationship to cognition more generally and many investigations have attempted to demark the boundary between the two. Though results from these studies suggest that language may recruit domain-general mechanisms during certain types of complex processing, the domain-generality of basic combinatorial mechanisms that lie at the core of linguistic processing is still unknown. Our previous work (Bemis and Pylkkänen, 2011, 2012) used magnetoencephalography to isolate neural activity associated with the simple composition of an adjective and a noun (“red boat”) and found increased activity during this processing localized to the left anterior temporal lobe (lATL), ventro-medial prefrontal cortex (vmPFC), and left angular gyrus (lAG). The present study explores the domain-generality of these effects and their associated combinatorial mechanisms through two parallel non-linguistic combinatorial tasks designed to be as minimal and natural as the linguistic paradigm. In the first task, we used pictures of colored shapes to elicit combinatorial conceptual processing similar to that evoked by the linguistic expressions and find increased activity again localized to the vmPFC during combinatorial processing. This result suggests that a domain-general semantic combinatorial mechanism operates during basic linguistic composition, and that activity generated by its processing localizes to the vmPFC. In the second task, we recorded neural activity as subjects performed simple addition between two small numerals. Consistent with a wide array of recent results, we find no effects related to basic addition that coincide with our linguistic effects and instead find increased activity localized to the intraparietal sulcus. This result suggests that the scope of the previously identified linguistic effects is restricted to compositional operations and does not extend generally to all tasks that are merely similar in form. PMID:23293621
How communication changes when we cannot mime the world: Experimental evidence for the effect of iconicity on combinatoriality.

PubMed

Roberts, Gareth; Lewandowski, Jirka; Galantucci, Bruno

2015-08-01

Communication systems are exposed to two different pressures: a pressure for transmission efficiency, such that messages are simple to produce and perceive, and a pressure for referential efficiency, such that messages are easy to understand with their intended meaning. A solution to the first pressure is combinatoriality--the recombination of a few basic meaningless forms to express an infinite number of meanings. A solution to the second is iconicity--the use of forms that resemble what they refer to. These two solutions appear to be incompatible with each other, as iconic forms are ill-suited for use as meaningless combinatorial units. Furthermore, in the early stages of a communication system, when basic referential forms are in the process of being established, the pressure for referential efficiency is likely to be particularly strong, which may lead it to trump the pressure for transmission efficiency. This means that, where iconicity is available as a strategy, it is likely to impede the emergence of combinatoriality. Although this hypothesis seems consistent with some observations of natural language, it was unclear until recently how it could be soundly tested. This has changed thanks to the development of a line of research, known as Experimental Semiotics, in which participants construct novel communication systems in the laboratory using an unfamiliar medium. We conducted an Experimental Semiotic study in which we manipulated the opportunity for iconicity by varying the kind of referents to be communicated, while keeping the communication medium constant. We then measured the combinatoriality and transmission efficiency of the communication systems. We found that, where iconicity was available, it provided scaffolding for the construction of communication systems and was overwhelmingly adopted. Where it was not available, however, the resulting communication systems were more combinatorial and their forms more efficient to produce. This study enriches our understanding of the fundamental design principles of human communication and contributes tools to enrich it further. Copyright © 2015 Elsevier B.V. All rights reserved.
Applications of high throughput (combinatorial) methodologies to electronic, magnetic, optical, and energy-related materials

NASA Astrophysics Data System (ADS)

Green, Martin L.; Takeuchi, Ichiro; Hattrick-Simpers, Jason R.

2013-06-01

High throughput (combinatorial) materials science methodology is a relatively new research paradigm that offers the promise of rapid and efficient materials screening, optimization, and discovery. The paradigm started in the pharmaceutical industry but was rapidly adopted to accelerate materials research in a wide variety of areas. High throughput experiments are characterized by synthesis of a "library" sample that contains the materials variation of interest (typically composition), and rapid and localized measurement schemes that result in massive data sets. Because the data are collected at the same time on the same "library" sample, they can be highly uniform with respect to fixed processing parameters. This article critically reviews the literature pertaining to applications of combinatorial materials science for electronic, magnetic, optical, and energy-related materials. It is expected that high throughput methodologies will facilitate commercialization of novel materials for these critically important applications. Despite the overwhelming evidence presented in this paper that high throughput studies can effectively inform commercial practice, in our perception, it remains an underutilized research and development tool. Part of this perception may be due to the inaccessibility of proprietary industrial research and development practices, but clearly the initial cost and availability of high throughput laboratory equipment plays a role. Combinatorial materials science has traditionally been focused on materials discovery, screening, and optimization to combat the extremely high cost and long development times for new materials and their introduction into commerce. Going forward, combinatorial materials science will also be driven by other needs such as materials substitution and experimental verification of materials properties predicted by modeling and simulation, which have recently received much attention with the advent of the Materials Genome Initiative. Thus, the challenge for combinatorial methodology will be the effective coupling of synthesis, characterization and theory, and the ability to rapidly manage large amounts of data in a variety of formats.
Performance evaluation of the multiple root node approach to the Rete pattern matcher for production systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sohn, A.; Gaudiot, J.-L.

1991-12-31

Much effort has been expanded on special architectures and algorithms dedicated to efficient processing of the pattern matching step of production systems. In this paper, the authors investigate the possible improvement on the Rete pattern matcher for production systems. Inefficiencies in the Rete match algorithm have been identified, based on which they introduce a pattern matcher with multiple root nodes. A complete implementation of the multiple root node-based production system interpreter is presented to investigate its relative algorithmic behavior over the Rete-based Ops5 production system interpreter. Benchmark production system programs are executed (not simulated) on a sequential machine Sun 4/490more » by using both interpreters and various experimental results are presented. Their investigation indicates that the multiple root node-based production system interpreter would give a maximum of up to 6-fold improvement over the Lisp implementation of the Rete-based Ops5 for the match step.« less
Moving Object Detection Using a Parallax Shift Vector Algorithm

NASA Astrophysics Data System (ADS)

Gural, Peter S.; Otto, Paul R.; Tedesco, Edward F.

2018-07-01

There are various algorithms currently in use to detect asteroids from ground-based observatories, but they are generally restricted to linear or mildly curved movement of the target object across the field of view. Space-based sensors in high inclination, low Earth orbits can induce significant parallax in a collected sequence of images, especially for objects at the typical distances of asteroids in the inner solar system. This results in a highly nonlinear motion pattern of the asteroid across the sensor, which requires a more sophisticated search pattern for detection processing. Both the classical pattern matching used in ground-based asteroid search and the more sensitive matched filtering and synthetic tracking techniques, can be adapted to account for highly complex parallax motion. A new shift vector generation methodology is discussed along with its impacts on commonly used detection algorithms, processing load, and responsiveness to asteroid track reporting. The matched filter, template generator, and pattern matcher source code for the software described herein are available via GitHub.
Integrating Monetary and Non-monetary Reenlistment Incentives Utilizing the Combinatorial Retention Auction Mechanism (CRAM)

DTIC Science & Technology

2008-12-01

NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS INTEGRATING MONETARY AND NON-MONETARY REENLISTMENT INCENTIVES UTILIZING THE...Monetary and Non- monetary Reenlistment Incentives Utilizing the Combinatorial Retention Auction Mechanism (CRAM) 6. AUTHOR(S) Brooke Zimmerman 5...iii Approved for public release; distribution is unlimited INTEGRATING MONETARY AND NON-MONETARY REENLISTMENT INCENTIVES UTILIZING THE
Combinatorial Solid-Phase Synthesis of Aromatic Oligoamides: A Research-Based Laboratory Module for Undergraduate Organic Chemistry

ERIC Educational Resources Information Center

Fuller, Amelia A.

2016-01-01

A five-week, research-based experiment suitable for second-semester introductory organic laboratory students is described. Each student designs, prepares, and analyzes a combinatorial array of six aromatic oligoamides. Molecules are prepared on solid phase via a six-step synthetic sequence, and purities and identities are determined by analysis of…
Two-dimensional combinatorial screening enables the bottom-up design of a microRNA-10b inhibitor.

PubMed

Velagapudi, Sai Pradeep; Disney, Matthew D

2014-03-21

The RNA motifs that bind guanidinylated kanamycin A (G Kan A) and guanidinylated neomycin B (G Neo B) were identified via two-dimensional combinatorial screening (2DCS). The results of these studies enabled the "bottom-up" design of a small molecule inhibitor of oncogenic microRNA-10b.

The Classicist and the Frequentist Approach to Probability within a "TinkerPlots2" Combinatorial Problem

ERIC Educational Resources Information Center

Prodromou, Theodosia

2012-01-01

This article seeks to address a pedagogical theory of introducing the classicist and the frequentist approach to probability, by investigating important elements in 9th grade students' learning process while working with a "TinkerPlots2" combinatorial problem. Results from this research study indicate that, after the students had seen…
An Onto-Semiotic Analysis of Combinatorial Problems and the Solving Processes by University Students

ERIC Educational Resources Information Center

Godino, Juan D.; Batanero, Carmen; Roa, Rafael

2005-01-01

In this paper we describe an ontological and semiotic model for mathematical knowledge, using elementary combinatorics as an example. We then apply this model to analyze the solving process of some combinatorial problems by students with high mathematical training, and show its utility in providing a semiotic explanation for the difficulty of…
Combinatorial synthesis of ceramic materials

DOEpatents

Lauf, Robert J [Oak Ridge, TN; Walls, Claudia A [Oak Ridge, TN; Boatner, Lynn A [Oak Ridge, TN

2010-02-23

A combinatorial library includes a gelcast substrate defining a plurality of cavities in at least one surface thereof; and a plurality of gelcast test materials in the cavities, at least two of the test materials differing from the substrate in at least one compositional characteristic, the two test materials differing from each other in at least one compositional characteristic.
Combinatorial synthesis of ceramic materials

DOEpatents

Lauf, Robert J.; Walls, Claudia A.; Boatner, Lynn A.

2006-11-14

A combinatorial library includes a gelcast substrate defining a plurality of cavities in at least one surface thereof; and a plurality of gelcast test materials in the cavities, at least two of the test materials differing from the substrate in at least one compositional characteristic, the two test materials differing from each other in at least one compositional characteristic.
The Shape of Things to Come: The Computational Pictograph as a Bridge from Combinatorial Space to Outcome Distribution

ERIC Educational Resources Information Center

Abrahamson, Dor

2006-01-01

This snapshot introduces a computer-based representation and activity that enables students to simultaneously "see" the combinatorial space of a stochastic device (e.g., dice, spinner, coins) and its outcome distribution. The author argues that the "ambiguous" representation fosters student insight into probability. [Snapshots are subject to peer…
Phase Transitions in Combinatorial Optimization Problems: Basics, Algorithms and Statistical Mechanics

NASA Astrophysics Data System (ADS)

Hartmann, Alexander K.; Weigt, Martin

2005-10-01

A concise, comprehensive introduction to the topic of statistical physics of combinatorial optimization, bringing together theoretical concepts and algorithms from computer science with analytical methods from physics. The result bridges the gap between statistical physics and combinatorial optimization, investigating problems taken from theoretical computing, such as the vertex-cover problem, with the concepts and methods of theoretical physics. The authors cover rapid developments and analytical methods that are both extremely complex and spread by word-of-mouth, providing all the necessary basics in required detail. Throughout, the algorithms are shown with examples and calculations, while the proofs are given in a way suitable for graduate students, post-docs, and researchers. Ideal for newcomers to this young, multidisciplinary field.
Combinatorial complexity of pathway analysis in metabolic networks.

PubMed

Klamt, Steffen; Stelling, Jörg

2002-01-01

Elementary flux mode analysis is a promising approach for a pathway-oriented perspective of metabolic networks. However, in larger networks it is hampered by the combinatorial explosion of possible routes. In this work we give some estimations on the combinatorial complexity including theoretical upper bounds for the number of elementary flux modes in a network of a given size. In a case study, we computed the elementary modes in the central metabolism of Escherichia coli while utilizing four different substrates. Interestingly, although the number of modes occurring in this complex network can exceed half a million, it is still far below the upper bound. Hence, to a certain extent, pathway analysis of central catabolism is feasible to assess network properties such as flexibility and functionality.
Building synthetic gene circuits from combinatorial libraries: screening and selection strategies.

PubMed

Schaerli, Yolanda; Isalan, Mark

2013-07-01

The promise of wide-ranging biotechnology applications inspires synthetic biologists to design novel genetic circuits. However, building such circuits rationally is still not straightforward and often involves painstaking trial-and-error. Mimicking the process of natural selection can help us to bridge the gap between our incomplete understanding of nature's design rules and our desire to build functional networks. By adopting the powerful method of directed evolution, which is usually applied to protein engineering, functional networks can be obtained through screening or selecting from randomised combinatorial libraries. This review first highlights the practical options to introduce combinatorial diversity into gene circuits and then examines strategies for identifying the potentially rare library members with desired functions, either by screening or selection.
The Effect of Timbre, Pitch, and Vibrato on Vocal Pitch-Matching Accuracy.

PubMed

Duvvuru, Sirisha; Erickson, Molly

2016-05-01

This study seeks to examine how target stimulus timbre, vibrato, pitch, and singer classification affect pitch-matching accuracy. This is a repeated-measures factorial design. Source signals were synthesized with a source slope of -12 dB/octave with and without vibrato at each of the pitches, C4, B4, and F5. These source signals were filtered using five formant patterns (A-E) constituting a total of 30 stimuli (5 formant patterns × 3 pitches × 2 vibrato conditions). Twelve sopranos and 11 mezzo-sopranos with at least 3 years of individual voice training were recruited from the University Of Tennessee, Knoxville, School of Music and the Knoxville Opera Company. Each singer attempted to match the pitch of all 30 stimuli presented twice in a random order. Results indicated that there was no significant effect of formant pattern on pitch-matching accuracy. With increasing pitch from C4 to F5, pitch-matching accuracy increased in midpoint of the vowel condition but not in prephonatory set condition. Mezzo-sopranos moved toward being in tune from prephonatory to midpoint of the vowel. However, sopranos at C4 sang closer to being in tune at prephonatory but lowered the pitch at the midpoint of the vowel. Presence or absence of vibrato did not affect the pitch-matching accuracy. However, the interesting finding of the study was that singers attempted to match the timbre of stimuli with vibrato. The results of this study show that pitch matching is a complex process affected by many parameters. Copyright © 2016 The Voice Foundation. Published by Elsevier Inc. All rights reserved.
Application of Approximate Pattern Matching in Two Dimensional Spaces to Grid Layout for Biochemical Network Maps

PubMed Central

Inoue, Kentaro; Shimozono, Shinichi; Yoshida, Hideaki; Kurata, Hiroyuki

2012-01-01

Background For visualizing large-scale biochemical network maps, it is important to calculate the coordinates of molecular nodes quickly and to enhance the understanding or traceability of them. The grid layout is effective in drawing compact, orderly, balanced network maps with node label spaces, but existing grid layout algorithms often require a high computational cost because they have to consider complicated positional constraints through the entire optimization process. Results We propose a hybrid grid layout algorithm that consists of a non-grid, fast layout (preprocessor) algorithm and an approximate pattern matching algorithm that distributes the resultant preprocessed nodes on square grid points. To demonstrate the feasibility of the hybrid layout algorithm, it is characterized in terms of the calculation time, numbers of edge-edge and node-edge crossings, relative edge lengths, and F-measures. The proposed algorithm achieves outstanding performances compared with other existing grid layouts. Conclusions Use of an approximate pattern matching algorithm quickly redistributes the laid-out nodes by fast, non-grid algorithms on the square grid points, while preserving the topological relationships among the nodes. The proposed algorithm is a novel use of the pattern matching, thereby providing a breakthrough for grid layout. This application program can be freely downloaded from http://www.cadlive.jp/hybridlayout/hybridlayout.html. PMID:22679486
Three-dimensional particle tracking in concave structures made by ultraviolet nanoimprint via total internal reflection fluorescence microscopy and refractive-index-matching method

NASA Astrophysics Data System (ADS)

Fujinami, Taku; Kigami, Hiroshi; Unno, Noriyuki; Taniguchi, Jun; Satake, Shin-ichi

2018-06-01

Total internal reflection fluorescence microscopy (TIRFM) is a promising method for measuring fluid flow close to a wall with nanoscale resolution in a process that is termed "multilayer nanoparticle image velocimetry" (MnPIV). TIRFM uses evanescent light that is generated on a substrate (typically a glass slide) by total internal reflection of light. Many researchers have previously studied x- y- z (3D) flows of water close to flat glass slides using MnPIV. On the other hand, a fluid flow close to a structured surface is also important. To measure flows of water near micro-patterns, we previously developed an MnPIV technique that uses a refractive-index-matching method. In previous study, the micropattern is made of a thermoplastic material with a refractive index that closely matches that of water. In this study, ultraviolet nanoimprint lithography was used for fabricating the appropriate micro-patterns because this technique can fabricate a pattern with a high resolution. As a result, we succeeded in performing MnPIV in water with a circular hole array pattern made by ultraviolet nanoimprint using a refractive-index-matching method. We believe that this technique will be helpful in elucidating fluid flows around microstructures.
Application of approximate pattern matching in two dimensional spaces to grid layout for biochemical network maps.

PubMed

Inoue, Kentaro; Shimozono, Shinichi; Yoshida, Hideaki; Kurata, Hiroyuki

2012-01-01

For visualizing large-scale biochemical network maps, it is important to calculate the coordinates of molecular nodes quickly and to enhance the understanding or traceability of them. The grid layout is effective in drawing compact, orderly, balanced network maps with node label spaces, but existing grid layout algorithms often require a high computational cost because they have to consider complicated positional constraints through the entire optimization process. We propose a hybrid grid layout algorithm that consists of a non-grid, fast layout (preprocessor) algorithm and an approximate pattern matching algorithm that distributes the resultant preprocessed nodes on square grid points. To demonstrate the feasibility of the hybrid layout algorithm, it is characterized in terms of the calculation time, numbers of edge-edge and node-edge crossings, relative edge lengths, and F-measures. The proposed algorithm achieves outstanding performances compared with other existing grid layouts. Use of an approximate pattern matching algorithm quickly redistributes the laid-out nodes by fast, non-grid algorithms on the square grid points, while preserving the topological relationships among the nodes. The proposed algorithm is a novel use of the pattern matching, thereby providing a breakthrough for grid layout. This application program can be freely downloaded from http://www.cadlive.jp/hybridlayout/hybridlayout.html.
Three-dimensional particle tracking in concave structures made by ultraviolet nanoimprint via total internal reflection fluorescence microscopy and refractive-index-matching method

NASA Astrophysics Data System (ADS)

Fujinami, Taku; Kigami, Hiroshi; Unno, Noriyuki; Taniguchi, Jun; Satake, Shin-ichi

2018-03-01

Total internal reflection fluorescence microscopy (TIRFM) is a promising method for measuring fluid flow close to a wall with nanoscale resolution in a process that is termed "multilayer nanoparticle image velocimetry" (MnPIV). TIRFM uses evanescent light that is generated on a substrate (typically a glass slide) by total internal reflection of light. Many researchers have previously studied x-y-z (3D) flows of water close to flat glass slides using MnPIV. On the other hand, a fluid flow close to a structured surface is also important. To measure flows of water near micro-patterns, we previously developed an MnPIV technique that uses a refractive-index-matching method. In previous study, the micropattern is made of a thermoplastic material with a refractive index that closely matches that of water. In this study, ultraviolet nanoimprint lithography was used for fabricating the appropriate micro-patterns because this technique can fabricate a pattern with a high resolution. As a result, we succeeded in performing MnPIV in water with a circular hole array pattern made by ultraviolet nanoimprint using a refractive-index-matching method. We believe that this technique will be helpful in elucidating fluid flows around microstructures.
Soft-assembled Multilevel Dynamics of Tactical Behaviors in Soccer

PubMed Central

Ric, Angel; Torrents, Carlota; Gonçalves, Bruno; Sampaio, Jaime; Hristovski, Robert

2016-01-01

This study aimed to identify the tactical patterns and the timescales of variables during a soccer match, allowing understanding the multilevel organization of tactical behaviors, and to determine the similarity of patterns performed by different groups of teammates during the first and second halves. Positional data from 20 professional male soccer players from the same team were collected using high frequency global positioning systems (5 Hz). Twenty-nine categories of tactical behaviors were determined from eight positioning-derived variables creating multivariate binary (Boolean) time-series matrices. Hierarchical principal component analysis (PCA) was used to identify the multilevel structure of tactical behaviors. The sequential reduction of each set level of principal components revealed a sole principal component as the slowest collective variable, forming the global basin of attraction of tactical patterns during each half of the match. In addition, the mean dwell time of each positioning-derived variable helped to understand the multilevel organization of collective tactical behavior during a soccer match. This approach warrants further investigations to analyze the influence of task constraints on the emergence of tactical behavior. Furthermore, PCA can help coaches to design representative training tasks according to those tactical patterns captured during match competitions and to compare them depending on situational variables. PMID:27761120
Lip movements affect infants' audiovisual speech perception.

PubMed

Yeung, H Henny; Werker, Janet F

2013-05-01

Speech is robustly audiovisual from early in infancy. Here we show that audiovisual speech perception in 4.5-month-old infants is influenced by sensorimotor information related to the lip movements they make while chewing or sucking. Experiment 1 consisted of a classic audiovisual matching procedure, in which two simultaneously displayed talking faces (visual [i] and [u]) were presented with a synchronous vowel sound (audio /i/ or /u/). Infants' looking patterns were selectively biased away from the audiovisual matching face when the infants were producing lip movements similar to those needed to produce the heard vowel. Infants' looking patterns returned to those of a baseline condition (no lip movements, looking longer at the audiovisual matching face) when they were producing lip movements that did not match the heard vowel. Experiment 2 confirmed that these sensorimotor effects interacted with the heard vowel, as looking patterns differed when infants produced these same lip movements while seeing and hearing a talking face producing an unrelated vowel (audio /a/). These findings suggest that the development of speech perception and speech production may be mutually informative.
Combinatorial explosion in model gene networks

NASA Astrophysics Data System (ADS)

Edwards, R.; Glass, L.

2000-09-01

The explosive growth in knowledge of the genome of humans and other organisms leaves open the question of how the functioning of genes in interacting networks is coordinated for orderly activity. One approach to this problem is to study mathematical properties of abstract network models that capture the logical structures of gene networks. The principal issue is to understand how particular patterns of activity can result from particular network structures, and what types of behavior are possible. We study idealized models in which the logical structure of the network is explicitly represented by Boolean functions that can be represented by directed graphs on n-cubes, but which are continuous in time and described by differential equations, rather than being updated synchronously via a discrete clock. The equations are piecewise linear, which allows significant analysis and facilitates rapid integration along trajectories. We first give a combinatorial solution to the question of how many distinct logical structures exist for n-dimensional networks, showing that the number increases very rapidly with n. We then outline analytic methods that can be used to establish the existence, stability and periods of periodic orbits corresponding to particular cycles on the n-cube. We use these methods to confirm the existence of limit cycles discovered in a sample of a million randomly generated structures of networks of 4 genes. Even with only 4 genes, at least several hundred different patterns of stable periodic behavior are possible, many of them surprisingly complex. We discuss ways of further classifying these periodic behaviors, showing that small mutations (reversal of one or a few edges on the n-cube) need not destroy the stability of a limit cycle. Although these networks are very simple as models of gene networks, their mathematical transparency reveals relationships between structure and behavior, they suggest that the possibilities for orderly dynamics in such networks are extremely rich and they offer novel ways to think about how mutations can alter dynamics.
Combinatorial explosion in model gene networks.

PubMed

Edwards, R.; Glass, L.

2000-09-01

The explosive growth in knowledge of the genome of humans and other organisms leaves open the question of how the functioning of genes in interacting networks is coordinated for orderly activity. One approach to this problem is to study mathematical properties of abstract network models that capture the logical structures of gene networks. The principal issue is to understand how particular patterns of activity can result from particular network structures, and what types of behavior are possible. We study idealized models in which the logical structure of the network is explicitly represented by Boolean functions that can be represented by directed graphs on n-cubes, but which are continuous in time and described by differential equations, rather than being updated synchronously via a discrete clock. The equations are piecewise linear, which allows significant analysis and facilitates rapid integration along trajectories. We first give a combinatorial solution to the question of how many distinct logical structures exist for n-dimensional networks, showing that the number increases very rapidly with n. We then outline analytic methods that can be used to establish the existence, stability and periods of periodic orbits corresponding to particular cycles on the n-cube. We use these methods to confirm the existence of limit cycles discovered in a sample of a million randomly generated structures of networks of 4 genes. Even with only 4 genes, at least several hundred different patterns of stable periodic behavior are possible, many of them surprisingly complex. We discuss ways of further classifying these periodic behaviors, showing that small mutations (reversal of one or a few edges on the n-cube) need not destroy the stability of a limit cycle. Although these networks are very simple as models of gene networks, their mathematical transparency reveals relationships between structure and behavior, they suggest that the possibilities for orderly dynamics in such networks are extremely rich and they offer novel ways to think about how mutations can alter dynamics. (c) 2000 American Institute of Physics.
Ligand design by a combinatorial approach based on modeling and experiment: application to HLA-DR4

NASA Astrophysics Data System (ADS)

Evensen, Erik; Joseph-McCarthy, Diane; Weiss, Gregory A.; Schreiber, Stuart L.; Karplus, Martin

2007-07-01

Combinatorial synthesis and large scale screening methods are being used increasingly in drug discovery, particularly for finding novel lead compounds. Although these "random" methods sample larger areas of chemical space than traditional synthetic approaches, only a relatively small percentage of all possible compounds are practically accessible. It is therefore helpful to select regions of chemical space that have greater likelihood of yielding useful leads. When three-dimensional structural data are available for the target molecule this can be achieved by applying structure-based computational design methods to focus the combinatorial library. This is advantageous over the standard usage of computational methods to design a small number of specific novel ligands, because here computation is employed as part of the combinatorial design process and so is required only to determine a propensity for binding of certain chemical moieties in regions of the target molecule. This paper describes the application of the Multiple Copy Simultaneous Search (MCSS) method, an active site mapping and de novo structure-based design tool, to design a focused combinatorial library for the class II MHC protein HLA-DR4. Methods for the synthesizing and screening the computationally designed library are presented; evidence is provided to show that binding was achieved. Although the structure of the protein-ligand complex could not be determined, experimental results including cross-exclusion of a known HLA-DR4 peptide ligand (HA) by a compound from the library. Computational model building suggest that at least one of the ligands designed and identified by the methods described binds in a mode similar to that of native peptides.
MiYA, an efficient machine-learning workflow in conjunction with the YeastFab assembly strategy for combinatorial optimization of heterologous metabolic pathways in Saccharomyces cerevisiae.

PubMed

Zhou, Yikang; Li, Gang; Dong, Junkai; Xing, Xin-Hui; Dai, Junbiao; Zhang, Chong

2018-05-01

Facing boosting ability to construct combinatorial metabolic pathways, how to search the metabolic sweet spot has become the rate-limiting step. We here reported an efficient Machine-learning workflow in conjunction with YeastFab Assembly strategy (MiYA) for combinatorial optimizing the large biosynthetic genotypic space of heterologous metabolic pathways in Saccharomyces cerevisiae. Using β-carotene biosynthetic pathway as example, we first demonstrated that MiYA has the power to search only a small fraction (2-5%) of combinatorial space to precisely tune the expression level of each gene with a machine-learning algorithm of an artificial neural network (ANN) ensemble to avoid over-fitting problem when dealing with a small number of training samples. We then applied MiYA to improve the biosynthesis of violacein. Feed with initial data from a colorimetric plate-based, pre-screened pool of 24 strains producing violacein, MiYA successfully predicted, and verified experimentally, the existence of a strain that showed a 2.42-fold titer improvement in violacein production among 3125 possible designs. Furthermore, MiYA was able to largely avoid the branch pathway of violacein biosynthesis that makes deoxyviolacein, and produces very pure violacein. Together, MiYA combines the advantages of standardized building blocks and machine learning to accelerate the Design-Build-Test-Learn (DBTL) cycle for combinatorial optimization of metabolic pathways, which could significantly accelerate the development of microbial cell factories. Copyright © 2018 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.
Receptive fields of locust brain neurons are matched to polarization patterns of the sky.

PubMed

Bech, Miklós; Homberg, Uwe; Pfeiffer, Keram

2014-09-22

Many animals, including insects, are able to use celestial cues as a reference for spatial orientation and long-distance navigation [1]. In addition to direct sunlight, the chromatic gradient of the sky and its polarization pattern are suited to serve as orientation cues [2-5]. Atmospheric scattering of sunlight causes a regular pattern of E vectors in the sky, which are arranged along concentric circles around the sun [5, 6]. Although certain insects rely predominantly on sky polarization for spatial orientation [7], it has been argued that detection of celestial E vector orientation may not suffice to differentiate between solar and antisolar directions [8, 9]. We show here that polarization-sensitive (POL) neurons in the brain of the desert locust Schistocerca gregaria can overcome this ambiguity. Extracellular recordings from POL units in the central complex and lateral accessory lobes revealed E vector tunings arranged in concentric circles within large receptive fields, matching the sky polarization pattern at certain solar positions. Modeling of neuronal responses under an idealized sky polarization pattern (Rayleigh sky) suggests that these "matched filter" properties allow locusts to unambiguously determine the solar azimuth by relying solely on the sky polarization pattern for compass navigation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Employee Turnover: Evidence from a Case Study.

ERIC Educational Resources Information Center

Borland, Jeff

1997-01-01

Patterns of employee turnover from a medium-sized law firm in Australia were examined in regard to theories of worker mobility (matching, sectoral shift, and incentive). Results support a role for matching effects, but personnel practices affect the timing of turnover. Matching and incentive-based theories do not explain the high rates of turnover…
Body Weight and Matching with a Physically Attractive Romantic Partner

ERIC Educational Resources Information Center

Carmalt, Julie H.; Cawley, John; Joyner, Kara; Sobal, Jeffery

2008-01-01

Matching and attribute trade are two perspectives used to explain mate selection. We investigated patterns of matching and trade, focusing on obesity, using Add Health Romantic Pair data (N = 1,405 couples). Obese individuals, relative to healthy weight individuals, were less likely to have physically attractive partners, with this disadvantage…
The Combinatorial Trace Method in Action

ERIC Educational Resources Information Center

Krebs, Mike; Martinez, Natalie C.

2013-01-01

On any finite graph, the number of closed walks of length k is equal to the sum of the kth powers of the eigenvalues of any adjacency matrix. This simple observation is the basis for the combinatorial trace method, wherein we attempt to count (or bound) the number of closed walks of a given length so as to obtain information about the graph's…
Transcriptional Architecture of Synaptic Communication Delineates GABAergic Neuron Identity.

PubMed

Paul, Anirban; Crow, Megan; Raudales, Ricardo; He, Miao; Gillis, Jesse; Huang, Z Josh

2017-10-19

Understanding the organizational logic of neural circuits requires deciphering the biological basis of neuronal diversity and identity, but there is no consensus on how neuron types should be defined. We analyzed single-cell transcriptomes of a set of anatomically and physiologically characterized cortical GABAergic neurons and conducted a computational genomic screen for transcriptional profiles that distinguish them from one another. We discovered that cardinal GABAergic neuron types are delineated by a transcriptional architecture that encodes their synaptic communication patterns. This architecture comprises 6 categories of ∼40 gene families, including cell-adhesion molecules, transmitter-modulator receptors, ion channels, signaling proteins, neuropeptides and vesicular release components, and transcription factors. Combinatorial expression of select members across families shapes a multi-layered molecular scaffold along the cell membrane that may customize synaptic connectivity patterns and input-output signaling properties. This molecular genetic framework of neuronal identity integrates cell phenotypes along multiple axes and provides a foundation for discovering and classifying neuron types. Copyright © 2017 Elsevier Inc. All rights reserved.
Self-organized adaptation of a simple neural circuit enables complex robot behaviour

NASA Astrophysics Data System (ADS)

Steingrube, Silke; Timme, Marc; Wörgötter, Florentin; Manoonpong, Poramate

2010-03-01

Controlling sensori-motor systems in higher animals or complex robots is a challenging combinatorial problem, because many sensory signals need to be simultaneously coordinated into a broad behavioural spectrum. To rapidly interact with the environment, this control needs to be fast and adaptive. Present robotic solutions operate with limited autonomy and are mostly restricted to few behavioural patterns. Here we introduce chaos control as a new strategy to generate complex behaviour of an autonomous robot. In the presented system, 18 sensors drive 18 motors by means of a simple neural control circuit, thereby generating 11 basic behavioural patterns (for example, orienting, taxis, self-protection and various gaits) and their combinations. The control signal quickly and reversibly adapts to new situations and also enables learning and synaptic long-term storage of behaviourally useful motor responses. Thus, such neural control provides a powerful yet simple way to self-organize versatile behaviours in autonomous agents with many degrees of freedom.
Combining robotic training and inactivation of the healthy hemisphere restores pre-stroke motor patterns in mice

PubMed Central

Spalletti, Cristina; Alia, Claudia; Lai, Stefano; Panarese, Alessandro; Conti, Sara

2017-01-01

Focal cortical stroke often leads to persistent motor deficits, prompting the need for more effective interventions. The efficacy of rehabilitation can be increased by ‘plasticity-stimulating’ treatments that enhance experience-dependent modifications in spared areas. Transcallosal pathways represent a promising therapeutic target, but their role in post-stroke recovery remains controversial. Here, we demonstrate that the contralesional cortex exerts an enhanced interhemispheric inhibition over the perilesional tissue after focal cortical stroke in mouse forelimb motor cortex. Accordingly, we designed a rehabilitation protocol combining intensive, repeatable exercises on a robotic platform with reversible inactivation of the contralesional cortex. This treatment promoted recovery in general motor tests and in manual dexterity with remarkable restoration of pre-lesion movement patterns, evaluated by kinematic analysis. Recovery was accompanied by a reduction of transcallosal inhibition and ‘plasticity brakes’ over the perilesional tissue. Our data support the use of combinatorial clinical therapies exploiting robotic devices and modulation of interhemispheric connectivity. PMID:29280732
Association between dietary patterns and metabolic syndrome in Chinese adults: a propensity score-matched case-control study.

PubMed

Xia, Yang; Gu, Yeqing; Yu, Fei; Zhang, Qing; Liu, Li; Meng, Ge; Wu, Hongmei; Du, Huanmin; Shi, Hongbin; Guo, Xiaoyan; Liu, Xing; Li, Chunlei; Han, Peipei; Dong, Renwei; Wang, Xiuyang; Bao, Xue; Su, Qian; Fang, Liyun; Liu, Fangfang; Yang, Huijun; Kang, Li; Ma, Yixuan; Yu, Bin; Sun, Shaomei; Wang, Xing; Zhou, Ming; Jia, Qiyu; Guo, Qi; Wu, Yuntang; Song, Kun; Huang, Guowei; Wang, Guolin; Niu, Kaijun

2016-10-06

Previous studies indicated that dietary patterns were associated with metabolic syndrome (MS), but little is known in Chinese. We design this case-control study to evaluate the associations between dietary patterns and MS in Chinese adults. In this study, 1492 participants with MS were matched with 1492 controls using the 1:1 ratio propensity score matching methods. Dietary intake was assessed using a valid self-administered food frequency questionnaire, and MS was defined in accordance with the criteria of the American Heart Association scientific statement of 2009. Higher scores for the high-protein/cholesterol pattern were associated with higher prevalence of MS. Compared with the participants in the lowest quartile, the odds ratio (OR) for the extreme quartile was 1.36 (95% confidence interval (CI), 1.10-1.68) and the P for trend <0.01 after adjusted for the other two dietary pattern scores. We also found a moderate consumption of the balanced pattern was associated with the lowest prevalence of MS. The ORs across quartiles of the balanced pattern were 1 (reference), 0.83 (95% CI, 0.68-1.02), 0.69 (95% CI, 0.56-0.85), and 0.84 (95% CI, 0.68-1.04) after adjustment. Our study demonstrates that there is a strong association between a diet rich in animal offal, animal blood, meat, and sausage and a higher prevalence of MS.
Gas phase electrodeposition: a programmable multimaterial deposition method for combinatorial nanostructured device discovery.

PubMed

Lin, En-Chiang; Cole, Jesse J; Jacobs, Heiko O

2010-11-10

This article reports and applies a recently discovered programmable multimaterial deposition process to the formation and combinatorial improvement of 3D nanostructured devices. The gas-phase deposition process produces charged <5 nm particles of silver, tungsten, and platinum and uses externally biased electrodes to control the material flux and to turn deposition ON/OFF in selected domains. Domains host nanostructured dielectrics to define arrays of electrodynamic 10 × nanolenses to further control the flux to form <100 nm resolution deposits. The unique feature of the process is that material type, amount, and sequence can be altered from one domain to the next leading to different types of nanostructures including multimaterial bridges, interconnects, or nanowire arrays with 20 nm positional accuracy. These features enable combinatorial nanostructured materials and device discovery. As a first demonstration, we produce and identify in a combinatorial way 3D nanostructured electrode designs that improve light scattering, absorption, and minority carrier extraction of bulk heterojunction photovoltaic cells. Photovoltaic cells from domains with long and dense nanowire arrays improve the relative power conversion efficiency by 47% when compared to flat domains on the same substrate.
An Acupuncture Research Protocol Developed from Historical Writings by Mathematical Reflections: A Rational Individualized Acupoint Selection Method for Immediate Pain Relief

PubMed Central

Schroeder, Sven; Meyer-Hamme, Gesa; Zhang, Jianwei; Epplée, Susanne; Friedemann, Thomas; Hu, Weiguo

2013-01-01

While balancing yin and yang is one basic principle of Chinese medicine, balancing methods for combination of meridians and acupoints had been described throughout the history of Chinese medicine. We have identified six historical systems for combinations of acupuncture points in historical writings. All of them represent symmetrical combinations which are defined by the steps in the Chinese Clock. Taking the historical systems as a basis, we calculated the possible combinations that fit into these systems they revealed, leading to a total of 19 systems offering new balancing combinations. Merging the data of these 19 systems, there are 7 combinatorial options for every meridian. On the basis of this data, we calculated 4-meridian combinations with an ideal balance pattern, which is given when all meridians balance each other. We identified 5 of these patterns for every meridian, so we end up with 60 patterns for all the 12 meridians but we find multiple overlapping. Finally, 15 distinct patterns remain. By combining this theoretical concept with the Image and Mirror Concept, we developed an acupuncture research protocol. This protocol potentially solves some problems of acupuncture trials because it represents a rational reproducible procedure independent of examiner experience, but the resulting treatment is individualized. PMID:23431334
Optimizing countershading camouflage.

PubMed

Cuthill, Innes C; Sanghera, N Simon; Penacchio, Olivier; Lovell, Paul George; Ruxton, Graeme D; Harris, Julie M

2016-11-15

Countershading, the widespread tendency of animals to be darker on the side that receives strongest illumination, has classically been explained as an adaptation for camouflage: obliterating cues to 3D shape and enhancing background matching. However, there have only been two quantitative tests of whether the patterns observed in different species match the optimal shading to obliterate 3D cues, and no tests of whether optimal countershading actually improves concealment or survival. We use a mathematical model of the light field to predict the optimal countershading for concealment that is specific to the light environment and then test this prediction with correspondingly patterned model "caterpillars" exposed to avian predation in the field. We show that the optimal countershading is strongly illumination-dependent. A relatively sharp transition in surface patterning from dark to light is only optimal under direct solar illumination; if there is diffuse illumination from cloudy skies or shade, the pattern provides no advantage over homogeneous background-matching coloration. Conversely, a smoother gradation between dark and light is optimal under cloudy skies or shade. The demonstration of these illumination-dependent effects of different countershading patterns on predation risk strongly supports the comparative evidence showing that the type of countershading varies with light environment.
Modularity in protein structures: study on all-alpha proteins.

PubMed

Khan, Taushif; Ghosh, Indira

2015-01-01

Modularity is known as one of the most important features of protein's robust and efficient design. The architecture and topology of proteins play a vital role by providing necessary robust scaffolds to support organism's growth and survival in constant evolutionary pressure. These complex biomolecules can be represented by several layers of modular architecture, but it is pivotal to understand and explore the smallest biologically relevant structural component. In the present study, we have developed a component-based method, using protein's secondary structures and their arrangements (i.e. patterns) in order to investigate its structural space. Our result on all-alpha protein shows that the known structural space is highly populated with limited set of structural patterns. We have also noticed that these frequently observed structural patterns are present as modules or "building blocks" in large proteins (i.e. higher secondary structure content). From structural descriptor analysis, observed patterns are found to be within similar deviation; however, frequent patterns are found to be distinctly occurring in diverse functions e.g. in enzymatic classes and reactions. In this study, we are introducing a simple approach to explore protein structural space using combinatorial- and graph-based geometry methods, which can be used to describe modularity in protein structures. Moreover, analysis indicates that protein function seems to be the driving force that shapes the known structure space.
Construction of a scFv Library with Synthetic, Non-combinatorial CDR Diversity.

PubMed

Bai, Xuelian; Shim, Hyunbo

2017-01-01

Many large synthetic antibody libraries have been designed, constructed, and successfully generated high-quality antibodies suitable for various demanding applications. While synthetic antibody libraries have many advantages such as optimized framework sequences and a broader sequence landscape than natural antibodies, their sequence diversities typically are generated by random combinatorial synthetic processes which cause the incorporation of many undesired CDR sequences. Here, we describe the construction of a synthetic scFv library using oligonucleotide mixtures that contain predefined, non-combinatorially synthesized CDR sequences. Each CDR is first inserted to a master scFv framework sequence and the resulting single-CDR libraries are subjected to a round of proofread panning. The proofread CDR sequences are assembled to produce the final scFv library with six diversified CDRs.
Natural products and combinatorial chemistry: back to the future.

PubMed

Ortholand, Jean-Yves; Ganesan, A

2004-06-01

The introduction of high-throughput synthesis and combinatorial chemistry has precipitated a global decline in the screening of natural products by the pharmaceutical industry. Some companies terminated their natural products program, despite the unproven success of the new technologies. This was a premature decision, as natural products have a long history of providing important medicinal agents. Furthermore, they occupy a complementary region of chemical space compared with the typical synthetic compound library. For these reasons, the interest in natural products has been rekindled. Various approaches have evolved that combine the power of natural products and organic chemistry, ranging from the combinatorial total synthesis of analogues to the exploration of natural product scaffolds and the design of completely unnatural molecules that resemble natural products in their molecular characteristics.
Two is better than one; toward a rational design of combinatorial therapy.

PubMed

Chen, Sheng-Hong; Lahav, Galit

2016-12-01

Drug combination is an appealing strategy for combating the heterogeneity of tumors and evolution of drug resistance. However, the rationale underlying combinatorial therapy is often not well established due to lack of understandings of the specific pathways responding to the drugs, and their temporal dynamics following each treatment. Here we present several emerging trends in harnessing properties of biological systems for the optimal design of drug combinations, including the type of drugs, specific concentration, sequence of addition and the temporal schedule of treatments. We highlight recent studies showing different approaches for efficient design of drug combinations including single-cell signaling dynamics, adaption and pathway crosstalk. Finally, we discuss novel and feasible approaches that can facilitate the optimal design of combinatorial therapy. Copyright © 2016 Elsevier Ltd. All rights reserved.
SO2 and NH3 gas adsorption on a ternary ZnO/CuO/CuCl2 impregnated activated carbon evaluated using combinatorial methods.

PubMed

Romero, Jennifer V; Smith, Jock W H; Sullivan, Braden M; Croll, Lisa M; Dahn, J R

2012-01-09

Ternary libraries of 64 ZnO/CuO/CuCl(2) impregnated activated carbon samples were prepared on untreated or HNO(3)-treated carbon and evaluated for their SO(2) and NH(3) gas adsorption properties gravimetrically using a combinatorial method. CuCl(2) is shown to be a viable substitute for HNO(3) and some compositions of ternary ZnO/CuO/CuCl(2) impregnated carbon samples prepared on untreated carbon provided comparable SO(2) and NH(3) gas removal capacities to the materials prepared on HNO(3)-treated carbon. Through combinatorial methods, it was determined that the use of HNO(3) in this multigas adsorbent formulation can be avoided.
High-throughput screening for combinatorial thin-film library of thermoelectric materials.

PubMed

Watanabe, Masaki; Kita, Takuji; Fukumura, Tomoteru; Ohtomo, Akira; Ueno, Kazunori; Kawasaki, Masashi

2008-01-01

A high-throughput method has been developed to evaluate the Seebeck coefficient and electrical resistivity of combinatorial thin-film libraries of thermoelectric materials from room temperature to 673 K. Thin-film samples several millimeters in size were deposited on an integrated Al2O3 substrate with embedded lead wires and local heaters for measurement of the thermopower under a controlled temperature gradient. An infrared camera was used for real-time observation of the temperature difference Delta T between two electrical contacts on the sample to obtain the Seebeck coefficient. The Seebeck coefficient and electrical resistivity of constantan thin films were shown to be almost identical to standard data for bulk constantan. High-throughput screening was demonstrated for a thermoelectric Mg-Si-Ge combinatorial library.
Library fingerprints: a novel approach to the screening of virtual libraries.

PubMed

Klon, Anthony E; Diller, David J

2007-01-01

We propose a novel method to prioritize libraries for combinatorial synthesis and high-throughput screening that assesses the viability of a particular library on the basis of the aggregate physical-chemical properties of the compounds using a naïve Bayesian classifier. This approach prioritizes collections of related compounds according to the aggregate values of their physical-chemical parameters in contrast to single-compound screening. The method is also shown to be useful in screening existing noncombinatorial libraries when the compounds in these libraries have been previously clustered according to their molecular graphs. We show that the method used here is comparable or superior to the single-compound virtual screening of combinatorial libraries and noncombinatorial libraries and is superior to the pairwise Tanimoto similarity searching of a collection of combinatorial libraries.
Patterns across multiple memories are identified over time.

PubMed

Richards, Blake A; Xia, Frances; Santoro, Adam; Husse, Jana; Woodin, Melanie A; Josselyn, Sheena A; Frankland, Paul W

2014-07-01

Memories are not static but continue to be processed after encoding. This is thought to allow the integration of related episodes via the identification of patterns. Although this idea lies at the heart of contemporary theories of systems consolidation, it has yet to be demonstrated experimentally. Using a modified water-maze paradigm in which platforms are drawn stochastically from a spatial distribution, we found that mice were better at matching platform distributions 30 d compared to 1 d after training. Post-training time-dependent improvements in pattern matching were associated with increased sensitivity to new platforms that conflicted with the pattern. Increased sensitivity to pattern conflict was reduced by pharmacogenetic inhibition of the medial prefrontal cortex (mPFC). These results indicate that pattern identification occurs over time, which can lead to conflicts between new information and existing knowledge that must be resolved, in part, by computations carried out in the mPFC.
Measuring the Rarity of Fingerprint Patterns in the Dutch Population Using an Extended Classification Set.

PubMed

de Jongh, Arent; Lubach, Anko R; Lie Kwie, Sheryl L; Alberink, Ivo

2018-06-11

Latent print examiners often use their experience and knowledge to reach a conclusion on the identity of the source. Their conclusion is primarily based on their personal opinion on the rarity of the matching fingerprint features. Fingerprint patterns, if present, can play a significant role in the final assessment of a match. The authors believe that statistical data on the rarity of fingerprint patterns strengthens the subjective evaluation of the corresponding information. In order to provide fingerprint examiners with additional numerical support, fingerprint patterns were manually classified in a set of 24,104 fingerprints. In this study the frequencies of occurrence of 35 different fingerprint patterns have been obtained. The frequency data presented in this study can be used in the ACE-V process applied in forensic casework, allowing for the assessment of the evidential strength related to a specific fingerprint pattern type. © 2018 American Academy of Forensic Sciences.
Generalised Spin Dynamics and Induced Bounds of Automorphic [A]nX, [AX]n NMR Systems via Dual Tensorial Sets: An Invariant Cardinality Role for CFP

NASA Astrophysics Data System (ADS)

Temme, Francis P.

For uniform spins and their indistinguishable point sets of tensorial bases defining automorphic group-based Liouvillian NMR spin dynamics, the role of recursively-derived coefficients of fractional parentage (CFP) bijections and Schur duality-defined CFP(0)(n) ≡ ¦GI¦(n) group invariant cardinality is central both to understanding the impact of time-reversal invariance(TRI) spin physics, and to analysis as density-matrix formalisms over democratic recoupled (DR) dual tensorial sets, {T{ṽ}k(11.1)(SU2 × ln)}. Over abstract spin space, these tensorial sets are (ṽ) invariant-theoretic forms which lie beyond the Liouvillian graph recoupling and Racah-forms envisaged by Sanctuary [1]. This is a direct consequence of the dominance of the ln group. It leads to new views on the value of projective group actions as mappings over specialised Liouvillian carrier spaces, and on the need for the replacement of Racah-Wigner (R-W) orthogonality for distinct point sets, by criteria based on explicit properties of invariants [J. Phys.: Math. & Theor. A 41, 015210 (2008)] for multiple invariant systems. Ũ × P group actions over disjoint (L) carrier subspaces, leading to exclusively combinatorial views of the nature of quantal completeness for indistinguishable point-based tensorial sets. Such generalised invariant-theoretic approaches lie beyond the range of Lévi-Civitá generator views, or of Lévy-Leblond and Lévy-Nahas [9] with its additional cyclic-commutators defining mono-invariant DR forms. Comparison of the latter with generalised multiple-invariant techniques provides an answer to the question of precisely why [A]n≥4(X) and [AX]n≥4 NMR system spin dynamics are not ameniable to conventional R-W analysis of recoupled discrete-point tensorial systems. Our work augments earlier Hilbert space views, both of Louck and Biedenharn [21] on boson pattern projective mapping, and of Corio [19]. The roles of recent ln group action and (λ ⊢ n)-Schur combinatorial concepts, as well as of polyhedral-combinatorial modelling over invariance algebras, contribute significantly to our understanding of invariant-based techniques of Liouville dual tensorial sets for automorphic NMR spin physics.1

Impact of Fatigue on Positional Movements During Professional Rugby Union Match Play.

PubMed

Tee, Jason C; Lambert, Mike I; Coopoo, Yoga

2017-04-01

In team sports, fatigue is manifested by a self-regulated decrease in movement distance and intensity. There is currently limited information on the effect of fatigue on movement patterns in rugby union match play, particularly for players in different position groups (backs vs forwards). This study investigated the effect of different match periods on movement patterns of professional rugby union players. Global positioning system (GPS) data were collected from 46 professional match participations to determine temporal effects on movement patterns. Total relative distance (m/min) was decreased in the 2nd half for both forwards (-13%, ±8%, ES = very likely large) and backs (-9%, ±7%, ES = very likely large). A larger reduction in high-intensity-running distance in the 2nd half was observed for forwards (-27%, ±16%, ES = very likely medium) than for backs (-10%, ±15%; ES = unclear). Similar patterns were observed for sprint (>6 m/s) frequency (forwards -29%, ±29%, ES = likely small vs backs -13% ±18%, ES = possibly small) and acceleration (>2.75 m/s 2 ) frequency (forwards -27%, ±24%, ES = likely medium vs backs -5%, ±46%, ES = unclear). Analysis of 1st- and 2nd-half quartiles revealed differing pacing strategies for forwards and backs. Forwards display a "slow-positive" pacing strategy, while the pacing strategy of backs is "flat." Forwards suffered progressively greater performance decrements over the course of the match, while backs were able to maintain performance intensity. These findings reflect differing physical demands, notably contact and running loads, of players in different positions.
Fast and simple character classes and bounded gaps pattern matching, with applications to protein searching.

PubMed

Navarro, Gonzalo; Raffinot, Mathieu

2003-01-01

The problem of fast exact and approximate searching for a pattern that contains classes of characters and bounded size gaps (CBG) in a text has a wide range of applications, among which a very important one is protein pattern matching (for instance, one PROSITE protein site is associated with the CBG [RK] - x(2,3) - [DE] - x(2,3) - Y, where the brackets match any of the letters inside, and x(2,3) a gap of length between 2 and 3). Currently, the only way to search for a CBG in a text is to convert it into a full regular expression (RE). However, a RE is more sophisticated than a CBG, and searching for it with a RE pattern matching algorithm complicates the search and makes it slow. This is the reason why we design in this article two new practical CBG matching algorithms that are much simpler and faster than all the RE search techniques. The first one looks exactly once at each text character. The second one does not need to consider all the text characters, and hence it is usually faster than the first one, but in bad cases may have to read the same text character more than once. We then propose a criterion based on the form of the CBG to choose a priori the fastest between both. We also show how to search permitting a few mistakes in the occurrences. We performed many practical experiments using the PROSITE database, and all of them show that our algorithms are the fastest in virtually all cases.
Accurate Identification of Unknown and Known Metabolic Mixture Components by Combining 3D NMR with Fourier Transform Ion Cyclotron Resonance Tandem Mass Spectrometry.

PubMed

Wang, Cheng; He, Lidong; Li, Da-Wei; Bruschweiler-Li, Lei; Marshall, Alan G; Brüschweiler, Rafael

2017-10-06

Metabolite identification in metabolomics samples is a key step that critically impacts downstream analysis. We recently introduced the SUMMIT NMR/mass spectrometry (MS) hybrid approach for the identification of the molecular structure of unknown metabolites based on the combination of NMR, MS, and combinatorial cheminformatics. Here, we demonstrate the feasibility of the approach for an untargeted analysis of both a model mixture and E. coli cell lysate based on 2D/3D NMR experiments in combination with Fourier transform ion cyclotron resonance MS and MS/MS data. For 19 of the 25 model metabolites, SUMMIT yielded complete structures that matched those in the mixture independent of database information. Of those, seven top-ranked structures matched those in the mixture, and four of those were further validated by positive ion MS/MS. For five metabolites, not part of the 19 metabolites, correct molecular structural motifs could be identified. For E. coli, SUMMIT MS/NMR identified 20 previously known metabolites with three or more 1 H spins independent of database information. Moreover, for 15 unknown metabolites, molecular structural fragments were determined consistent with their spin systems and chemical shifts. By providing structural information for entire metabolites or molecular fragments, SUMMIT MS/NMR greatly assists the targeted or untargeted analysis of complex mixtures of unknown compounds.
Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns

PubMed Central

2013-01-01

Background It is well known that the search for homologous RNAs is more effective if both sequence and structure information is incorporated into the search. However, current tools for searching with RNA sequence-structure patterns cannot fully handle mutations occurring on both these levels or are simply not fast enough for searching large sequence databases because of the high computational costs of the underlying sequence-structure alignment problem. Results We present new fast index-based and online algorithms for approximate matching of RNA sequence-structure patterns supporting a full set of edit operations on single bases and base pairs. Our methods efficiently compute semi-global alignments of structural RNA patterns and substrings of the target sequence whose costs satisfy a user-defined sequence-structure edit distance threshold. For this purpose, we introduce a new computing scheme to optimally reuse the entries of the required dynamic programming matrices for all substrings and combine it with a technique for avoiding the alignment computation of non-matching substrings. Our new index-based methods exploit suffix arrays preprocessed from the target database and achieve running times that are sublinear in the size of the searched sequences. To support the description of RNA molecules that fold into complex secondary structures with multiple ordered sequence-structure patterns, we use fast algorithms for the local or global chaining of approximate sequence-structure pattern matches. The chaining step removes spurious matches from the set of intermediate results, in particular of patterns with little specificity. In benchmark experiments on the Rfam database, our improved online algorithm is faster than the best previous method by up to factor 45. Our best new index-based algorithm achieves a speedup of factor 560. Conclusions The presented methods achieve considerable speedups compared to the best previous method. This, together with the expected sublinear running time of the presented index-based algorithms, allows for the first time approximate matching of RNA sequence-structure patterns in large sequence databases. Beyond the algorithmic contributions, we provide with RaligNAtor a robust and well documented open-source software package implementing the algorithms presented in this manuscript. The RaligNAtor software is available at http://www.zbh.uni-hamburg.de/ralignator. PMID:23865810
Heterogeneity across the dorso-ventral axis in zebrafish EVL is regulated by a novel module consisting of sox, snail1a and max genes.

PubMed

Chen, Yi-Yen; Harris, Matthew P; Levesque, Mitchell P; Nüsslein-Volhard, Christiane; Sonawane, Mahendra

2012-01-01

In vertebrates, the dorso-ventral (DV) axis is defined by the combinatorial action of localised Wnt, FGF and Nodal signalling along with the antagonizing activities of Chordin and BMP pathways. Our knowledge of the factors that may act in concert with these core pathways to regulate early embryonic patterning is far from complete. Furthermore, while all three germ layers respond to these patterning cues, it is not clear whether in zebrafish the outermost protective epithelium, the enveloping layer (EVL), is also patterned along the DV axis. Here, we have identified a transgenic line driving GFP under a crestin promoter, which specifically labels the dorsal domain of the EVL suggesting heterogeneity in the EVL across the DV axis. Our attempts to understand how the expression from this promoter fragment is regulated specifically in the dorsal domain, have unravelled potential novel players involved in early EVL and embryonic patterning. We show that along with Nodal signalling components, four proteins Sox11b, Sox19b, Snail1a and Max are involved in regulating the size of this EVL domain. However, Chordin-BMP signalling might be dispensable for the dorso-ventral patterning of the EVL. For the first time, this transgenic line unravels the heterogeneity in the EVL and will serve as an important tool in understanding the molecular basis of the DV patterning of the EVL. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.
Graph rigidity, cyclic belief propagation, and point pattern matching.

PubMed

McAuley, Julian J; Caetano, Tibério S; Barbosa, Marconi S

2008-11-01

A recent paper [1] proposed a provably optimal polynomial time method for performing near-isometric point pattern matching by means of exact probabilistic inference in a chordal graphical model. Its fundamental result is that the chordal graph in question is shown to be globally rigid, implying that exact inference provides the same matching solution as exact inference in a complete graphical model. This implies that the algorithm is optimal when there is no noise in the point patterns. In this paper, we present a new graph that is also globally rigid but has an advantage over the graph proposed in [1]: Its maximal clique size is smaller, rendering inference significantly more efficient. However, this graph is not chordal, and thus, standard Junction Tree algorithms cannot be directly applied. Nevertheless, we show that loopy belief propagation in such a graph converges to the optimal solution. This allows us to retain the optimality guarantee in the noiseless case, while substantially reducing both memory requirements and processing time. Our experimental results show that the accuracy of the proposed solution is indistinguishable from that in [1] when there is noise in the point patterns.
Specific Patterns of Emotion Recognition from Faces in Children with ASD: Results of a Cross-Modal Matching Paradigm

ERIC Educational Resources Information Center

Golan, Ofer; Gordon, Ilanit; Fichman, Keren; Keinan, Giora

2018-01-01

Children with ASD show emotion recognition difficulties, as part of their social communication deficits. We examined facial emotion recognition (FER) in intellectually disabled children with ASD and in younger typically developing (TD) controls, matched on mental age. Our emotion-matching paradigm employed three different modalities: facial, vocal…
Variability of Valuation of Non-Monetary Incentives: Motivating and Implementing the Combinatorial Retention Auction Mechanism

DTIC Science & Technology

2009-03-01

homeport, geographic stability for two tours and compressed work week; homeport, lump sum SRB, and telecommuting ). The Monte Carlo simulation...Geographic stability 2 tours, and compressed work week). The Add 2 combination includes home port choice, lump sum SRB, and telecommuting ...VALUATION OF NON-MONETARY INCENTIVES: MOTIVATING AND IMPLEMENTING THE COMBINATORIAL RETENTION AUCTION MECHANISM by Jason Blake Ellis March 2009
Combinatorial Targeting of Prostate Carcinoma Cells and Tumor Associated Pericytes with Antibody-Based Immunotherapy and Metronomic Chemotherapy

DTIC Science & Technology

2011-03-01

Carcinoma Cells and Tumor Associated Pericytes with Antibody-Based Immunotherapy and Metronomic Chemotherapy. PRINCIPAL INVESTIGATOR: Soldano...Combinatorial Targeting of Prostate Carcinoma Cells and Tumor Associated Pericytes with Antibody-Based Immunotherapy and Metronomic Chemotherapy. 5b. GRANT...SUPPLEMENTARY NOTES 14. ABSTRACT Seventy seven 10 week old TRAMP mice were enrolled in the study. Administration of metronomic chemotherapy with
Computer Description of Black Hawk Helicopter

DTIC Science & Technology

1979-06-01

Model Combinatorial Geometry Models Black Hawk Helicopter Helicopter GIFT Computer Code Geometric Description of Targets 20. ABSTRACT...description was made using the technique of combinatorial geometry (COM-GEOM) and will be used as input to the GIFT computer code which generates Tliic...rnHp The data used bv the COVART comtmter code was eenerated bv the Geometric Information for Targets ( GIFT )Z computer code. This report documents
Designed Electroresponsive Biomaterials: Sequence-Controlled Behavior

DTIC Science & Technology

2010-06-29

protein of the M13 . Traditional phage and yeast display methodologies indicate that peptide sequences with high affinities for electrode materials...drug delivery. The original vision for this work was to employ combinatorial tools such as phage and yeast display under electrical selection pressure...and drug delivery. The original vision for this work was to employ combinatorial tools such as phage and yeast display under electrical selection
Nonlinear Multidimensional Assignment Problems Efficient Conic Optimization Methods and Applications

DTIC Science & Technology

2015-06-24

WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) Arizona State University School of Mathematical & Statistical Sciences 901 S...SUPPLEMENTARY NOTES 14. ABSTRACT The major goals of this project were completed: the exact solution of previously unsolved challenging combinatorial optimization... combinatorial optimization problem, the Directional Sensor Problem, was solved in two ways. First, heuristically in an engineering fashion and second, exactly
TARCMO: Theory and Algorithms for Robust, Combinatorial, Multicriteria Optimization

DTIC Science & Technology

2016-11-28

objective 9 4.6 On The Recoverable Robust Traveling Salesman Problem . . . . . 11 4.7 A Bicriteria Approach to Robust Optimization...be found. 4.6 On The Recoverable Robust Traveling Salesman Problem The traveling salesman problem (TSP) is a well-known combinatorial optimiza- tion...procedure for the robust traveling salesman problem . While this iterative algorithms results in an optimal solution to the robust TSP, computation
Functional autonomy of distant-acting human enhancers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Visel, Axel; Akiyama, Jennifer A.; Shoukry, Malak

2009-02-19

Many human genes are associated with dispersed arrays of transcriptional enhancers that regulate their expression in time and space. Studies in invertebrate model systems have suggested that these elements function as discrete and independent regulatory units, but the in vivo combinatorial properties of vertebrate enhancers remain poorly understood. To explore the modularity and regulatory autonomy of human developmental enhancers, we experimentally concatenated up to four enhancers from different genes and used a transgenic mouse assay to compare the in vivo activity of these compound elements with that of the single modules. In all of the six different combinations of elementsmore » tested, the reporter gene activity patterns were additive without signs of interference between the individual modules, indicating that regulatory specificity was maintained despite the presence of closely-positioned heterologous enhancers. Even in cases where two elements drove expression in close anatomical proximity, such as within neighboring subregions of the developing limb bud, the compound patterns did not show signs of cross-inhibition between individual elements or novel expression sites. These data indicate that human developmental enhancers are highly modular and functionally autonomous and suggest that genomic enhancer shuffling may have contributed to the evolution of complex gene expression patterns in vertebrates« less
Optimal Control Surface Layout for an Aeroservoelastic Wingbox

NASA Technical Reports Server (NTRS)

Stanford, Bret K.

2017-01-01

This paper demonstrates a technique for locating the optimal control surface layout of an aeroservoelastic Common Research Model wingbox, in the context of maneuver load alleviation and active utter suppression. The combinatorial actuator layout design is solved using ideas borrowed from topology optimization, where the effectiveness of a given control surface is tied to a layout design variable, which varies from zero (the actuator is removed) to one (the actuator is retained). These layout design variables are optimized concurrently with a large number of structural wingbox sizing variables and control surface actuation variables, in order to minimize the sum of structural weight and actuator weight. Results are presented that demonstrate interdependencies between structural sizing patterns and optimal control surface layouts, for both static and dynamic aeroelastic physics.
The ALK receptor in sympathetic neuron development and neuroblastoma.

PubMed

Janoueix-Lerosey, Isabelle; Lopez-Delisle, Lucille; Delattre, Olivier; Rohrer, Hermann

2018-05-01

The ALK gene encodes a tyrosine kinase receptor characterized by an expression pattern mainly restricted to the developing central and peripheral nervous systems. In 2008, the discovery of ALK activating mutations in neuroblastoma, a tumor of the sympathetic nervous system, represented a breakthrough in the understanding of the pathogenesis of this pediatric cancer and established mutated ALK as a tractable therapeutic target for precision medicine. Subsequent studies addressed the identity of ALK ligands, as well as its physiological function in the sympathoadrenal lineage, its role in neuroblastoma development and the signaling pathways triggered by mutated ALK. This review focuses on these different aspects of the ALK biology and summarizes the various therapeutic strategies relying on ALK inhibition in neuroblastoma, either as monotherapies or combinatory treatments.
What can we learn from fitness landscapes?

PubMed

Hartl, Daniel L

2014-10-01

A combinatorially complete data set consists of studies of all possible combinations of a set of mutant sites in a gene or mutant alleles in a genome. Among the most robust conclusions from these studies is that epistasis between beneficial mutations often shows a pattern of diminishing returns, in which favorable mutations are less fit when combined than would be expected. Another robust inference is that the number of adaptive evolutionary paths is often limited to a relatively small fraction of the theoretical possibilities, owing largely to sign epistasis requiring evolutionary steps that would entail a decrease in fitness. Here we summarize these and other results while also examining issues that remain unresolved and future directions that seem promising. Copyright © 2014 Elsevier Ltd. All rights reserved.
Alignment of RNA molecules: Binding energy and statistical properties of random sequences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valba, O. V., E-mail: valbaolga@gmail.com; Nechaev, S. K., E-mail: sergei.nechaev@gmail.com; Tamm, M. V., E-mail: thumm.m@gmail.com

2012-02-15

A new statistical approach to the problem of pairwise alignment of RNA sequences is proposed. The problem is analyzed for a pair of interacting polymers forming an RNA-like hierarchical cloverleaf structures. An alignment is characterized by the numbers of matches, mismatches, and gaps. A weight function is assigned to each alignment; this function is interpreted as a free energy taking into account both direct monomer-monomer interactions and a combinatorial contribution due to formation of various cloverleaf secondary structures. The binding free energy is determined for a pair of RNA molecules. Statistical properties are discussed, including fluctuations of the binding energymore » between a pair of RNA molecules and loop length distribution in a complex. Based on an analysis of the free energy per nucleotide pair complexes of random RNAs as a function of the number of nucleotide types c, a hypothesis is put forward about the exclusivity of the alphabet c = 4 used by nature.« less
Cross-Identification of Astronomical Catalogs on Multiple GPUs

NASA Astrophysics Data System (ADS)

Lee, M. A.; Budavári, T.

2013-10-01

One of the most fundamental problems in observational astronomy is the cross-identification of sources. Observations are made in different wavelengths, at different times, and from different locations and instruments, resulting in a large set of independent observations. The scientific outcome is often limited by our ability to quickly perform meaningful associations between detections. The matching, however, is difficult scientifically, statistically, as well as computationally. The former two require detailed physical modeling and advanced probabilistic concepts; the latter is due to the large volumes of data and the problem's combinatorial nature. In order to tackle the computational challenge and to prepare for future surveys, whose measurements will be exponentially increasing in size past the scale of feasible CPU-based solutions, we developed a new implementation which addresses the issue by performing the associations on multiple Graphics Processing Units (GPUs). Our implementation utilizes up to 6 GPUs in combination with the Thrust library to achieve an over 40x speed up verses the previous best implementation running on a multi-CPU SQL Server.
Distance-Based Phylogenetic Methods Around a Polytomy.

PubMed

Davidson, Ruth; Sullivant, Seth

2014-01-01

Distance-based phylogenetic algorithms attempt to solve the NP-hard least-squares phylogeny problem by mapping an arbitrary dissimilarity map representing biological data to a tree metric. The set of all dissimilarity maps is a Euclidean space properly containing the space of all tree metrics as a polyhedral fan. Outputs of distance-based tree reconstruction algorithms such as UPGMA and neighbor-joining are points in the maximal cones in the fan. Tree metrics with polytomies lie at the intersections of maximal cones. A phylogenetic algorithm divides the space of all dissimilarity maps into regions based upon which combinatorial tree is reconstructed by the algorithm. Comparison of phylogenetic methods can be done by comparing the geometry of these regions. We use polyhedral geometry to compare the local nature of the subdivisions induced by least-squares phylogeny, UPGMA, and neighbor-joining when the true tree has a single polytomy with exactly four neighbors. Our results suggest that in some circumstances, UPGMA and neighbor-joining poorly match least-squares phylogeny.

Statistical mechanics of letters in words

PubMed Central

Stephens, Greg J.; Bialek, William

2013-01-01

We consider words as a network of interacting letters, and approximate the probability distribution of states taken on by this network. Despite the intuition that the rules of English spelling are highly combinatorial and arbitrary, we find that maximum entropy models consistent with pairwise correlations among letters provide a surprisingly good approximation to the full statistics of words, capturing ~92% of the multi-information in four-letter words and even “discovering” words that were not represented in the data. These maximum entropy models incorporate letter interactions through a set of pairwise potentials and thus define an energy landscape on the space of possible words. Guided by the large letter redundancy we seek a lower-dimensional encoding of the letter distribution and show that distinctions between local minima in the landscape account for ~68% of the four-letter entropy. We suggest that these states provide an effective vocabulary which is matched to the frequency of word use and much smaller than the full lexicon. PMID:20866490
Effects of musical training on sound pattern processing in high-school students.

PubMed

Wang, Wenjung; Staffaroni, Laura; Reid, Errold; Steinschneider, Mitchell; Sussman, Elyse

2009-05-01

Recognizing melody in music involves detection of both the pitch intervals and the silence between sequentially presented sounds. This study tested the hypothesis that active musical training in adolescents facilitates the ability to passively detect sequential sound patterns compared to musically non-trained age-matched peers. Twenty adolescents, aged 15-18 years, were divided into groups according to their musical training and current experience. A fixed order tone pattern was presented at various stimulus rates while electroencephalogram was recorded. The influence of musical training on passive auditory processing of the sound patterns was assessed using components of event-related brain potentials (ERPs). The mismatch negativity (MMN) ERP component was elicited in different stimulus onset asynchrony (SOA) conditions in non-musicians than musicians, indicating that musically active adolescents were able to detect sound patterns across longer time intervals than age-matched peers. Musical training facilitates detection of auditory patterns, allowing the ability to automatically recognize sequential sound patterns over longer time periods than non-musical counterparts.
A hierarchical graph neuron scheme for real-time pattern recognition.

PubMed

Nasution, B B; Khan, A I

2008-02-01

The hierarchical graph neuron (HGN) implements a single cycle memorization and recall operation through a novel algorithmic design. The HGN is an improvement on the already published original graph neuron (GN) algorithm. In this improved approach, it recognizes incomplete/noisy patterns. It also resolves the crosstalk problem, which is identified in the previous publications, within closely matched patterns. To accomplish this, the HGN links multiple GN networks for filtering noise and crosstalk out of pattern data inputs. Intrinsically, the HGN is a lightweight in-network processing algorithm which does not require expensive floating point computations; hence, it is very suitable for real-time applications and tiny devices such as the wireless sensor networks. This paper describes that the HGN's pattern matching capability and the small response time remain insensitive to the increases in the number of stored patterns. Moreover, the HGN does not require definition of rules or setting of thresholds by the operator to achieve the desired results nor does it require heuristics entailing iterative operations for memorization and recall of patterns.
"One-sample concept" micro-combinatory for high throughput TEM of binary films.

PubMed

Sáfrán, György

2018-04-01

Phases of thin films may remarkably differ from that of bulk. Unlike to the comprehensive data files of Binary Phase Diagrams [1] available for bulk, complete phase maps for thin binary layers do not exist. This is due to both the diverse metastable, non-equilibrium or instable phases feasible in thin films and the required volume of characterization work with analytical techniques like TEM, SAED and EDS. The aim of the present work was to develop a method that remarkably facilitates the TEM study of the diverse binary phases of thin films, or the creation of phase maps. A micro-combinatorial method was worked out that enables both preparation and study of a gradient two-component film within a single TEM specimen. For a demonstration of the technique thin Mn x Al 1- x binary samples with evolving concentration from x = 0 to x = 1 have been prepared so that the transition from pure Mn to pure Al covers a 1.5 mm long track within the 3 mm diameter TEM grid. The proposed method enables the preparation and study of thin combinatorial samples including all feasible phases as a function of composition or other deposition parameters. Contrary to known "combinatorial chemistry", in which a series of different samples are deposited in one run, and investigated, one at a time, the present micro-combinatorial method produces a single specimen condensing a complete library of a binary system that can be studied, efficiently, within a single TEM session. That provides extremely high throughput for TEM characterization of composition-dependent phases, exploration of new materials, or the construction of phase diagrams of binary films. Copyright © 2018 Elsevier B.V. All rights reserved.
Combinatorial anticancer effects of curcumin and 5-fluorouracil loaded thiolated chitosan nanoparticles towards colon cancer treatment.

PubMed

Anitha, A; Deepa, N; Chennazhi, K P; Lakshmanan, Vinoth-Kumar; Jayakumar, R

2014-09-01

Evaluation of the combinatorial anticancer effects of curcumin/5-fluorouracil loaded thiolated chitosan nanoparticles (CRC-TCS-NPs/5-FU-TCS-NPs) on colon cancer cells and the analysis of pharmacokinetics and biodistribution of CRC-TCS-NPs/5-FU-TCS-NPs in a mouse model. CRC-TCS-NPs/5-FU-TCS-NPs were developed by ionic cross-linking. The in vitro combinatorial anticancer effect of the nanomedicine was proven by different assays. Further the pharmacokinetics and biodistribution analyses were performed in Swiss Albino mouse using HPLC. The 5-FU-TCS-NPs (size: 150±40nm, zeta potential: +48.2±5mV) and CRC-TCS-NPs (size: 150±20nm, zeta potential: +35.7±3mV) were proven to be compatible with blood. The in vitro drug release studies at pH4.5 and 7.4 showed a sustained release profile over a period of 4 days, where both the systems exhibited a higher release in acidic pH. The in vitro combinatorial anticancer effects in colon cancer (HT29) cells using MTT, live/dead, mitochondrial membrane potential and cell cycle analysis measurements confirmed the enhanced anticancer effects (2.5 to 3 fold). The pharmacokinetic studies confirmed the improved plasma concentrations of 5-FU and CRC up to 72h, unlike bare CRC and 5-FU. To conclude, the combination of 5-FU-TCS-NPs and CRC-TCS-NPs showed enhanced anticancer effects on colon cancer cells in vitro and improved the bioavailability of the drugs in vivo. The enhanced anticancer effects of combinatorial nanomedicine are advantageous in terms of reduction in the dosage of 5-FU, thereby improving the chemotherapeutic efficacy and patient compliance of colorectal cancer cases. Copyright © 2014 Elsevier B.V. All rights reserved.
A dynamical systems model for combinatorial cancer therapy enhances oncolytic adenovirus efficacy by MEK-inhibition.

PubMed

Bagheri, Neda; Shiina, Marisa; Lauffenburger, Douglas A; Korn, W Michael

2011-02-01

Oncolytic adenoviruses, such as ONYX-015, have been tested in clinical trials for currently untreatable tumors, but have yet to demonstrate adequate therapeutic efficacy. The extent to which viruses infect targeted cells determines the efficacy of this approach but many tumors down-regulate the Coxsackievirus and Adenovirus Receptor (CAR), rendering them less susceptible to infection. Disrupting MAPK pathway signaling by pharmacological inhibition of MEK up-regulates CAR expression, offering possible enhanced adenovirus infection. MEK inhibition, however, interferes with adenovirus replication due to resulting G1-phase cell cycle arrest. Therefore, enhanced efficacy will depend on treatment protocols that productively balance these competing effects. Predictive understanding of how to attain and enhance therapeutic efficacy of combinatorial treatment is difficult since the effects of MEK inhibitors, in conjunction with adenovirus/cell interactions, are complex nonlinear dynamic processes. We investigated combinatorial treatment strategies using a mathematical model that predicts the impact of MEK inhibition on tumor cell proliferation, ONYX-015 infection, and oncolysis. Specifically, we fit a nonlinear differential equation system to dedicated experimental data and analyzed the resulting simulations for favorable treatment strategies. Simulations predicted enhanced combinatorial therapy when both treatments were applied simultaneously; we successfully validated these predictions in an ensuing explicit test study. Further analysis revealed that a CAR-independent mechanism may be responsible for amplified virus production and cell death. We conclude that integrated computational and experimental analysis of combinatorial therapy provides a useful means to identify treatment/infection protocols that yield clinically significant oncolysis. Enhanced oncolytic therapy has the potential to dramatically improve non-surgical cancer treatment, especially in locally advanced or metastatic cases where treatment options remain limited.
Novel drug metabolism indices for pharmacogenetic functional status based on combinatory genotyping of CYP2C9, CYP2C19 and CYP2D6 genes

PubMed Central

Villagra, David; Goethe, John; Schwartz, Harold I; Szarek, Bonnie; Kocherla, Mohan; Gorowski, Krystyna; Windemuth, Andreas; Ruaño, Gualberto

2011-01-01

Aims We aim to demonstrate clinical relevance and utility of four novel drug-metabolism indices derived from a combinatory (multigene) approach to CYP2C9, CYP2C19 and CYP2D6 allele scoring. Each index considers all three genes as complementary components of a liver enzyme drug metabolism system and uniquely benchmarks innate hepatic drug metabolism reserve or alteration through CYP450 combinatory genotype scores. Methods A total of 1199 psychiatric referrals were genotyped for polymorphisms in the CYP2C9, CYP2C19 and CYP2D6 gene loci and were scored on each of the four indices. The data were used to create distributions and rankings of innate drug metabolism capacity to which individuals can be compared. Drug-specific indices are a combination of the drug metabolism indices with substrate-specific coefficients. Results The combinatory drug metabolism indices proved useful in positioning individuals relative to a population with regard to innate drug metabolism capacity prior to pharmacotherapy. Drug-specific indices generate pharmacogenetic guidance of immediate clinical relevance, and can be further modified to incorporate covariates in particular clinical cases. Conclusions We believe that this combinatory approach represents an improvement over the current gene-by-gene reporting by providing greater scope while still allowing for the resolution of a single-gene index when needed. This method will result in novel clinical and research applications, facilitating the translation from pharmacogenomics to personalized medicine, particularly in psychiatry where many drugs are metabolized or activated by multiple CYP450 isoenzymes. PMID:21861665
Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data

PubMed Central

Zhao, Zheng; Bai, Jing; Wu, Aiwei; Wang, Yuan; Zhang, Jinwen; Wang, Zishan; Li, Yongsheng; Xu, Juan; Li, Xia

2015-01-01

Long non-coding RNAs (lncRNAs) are emerging as key regulators of diverse biological processes and diseases. However, the combinatorial effects of these molecules in a specific biological function are poorly understood. Identifying co-expressed protein-coding genes of lncRNAs would provide ample insight into lncRNA functions. To facilitate such an effort, we have developed Co-LncRNA, which is a web-based computational tool that allows users to identify GO annotations and KEGG pathways that may be affected by co-expressed protein-coding genes of a single or multiple lncRNAs. LncRNA co-expressed protein-coding genes were first identified in publicly available human RNA-Seq datasets, including 241 datasets across 6560 total individuals representing 28 tissue types/cell lines. Then, the lncRNA combinatorial effects in a given GO annotations or KEGG pathways are taken into account by the simultaneous analysis of multiple lncRNAs in user-selected individual or multiple datasets, which is realized by enrichment analysis. In addition, this software provides a graphical overview of pathways that are modulated by lncRNAs, as well as a specific tool to display the relevant networks between lncRNAs and their co-expressed protein-coding genes. Co-LncRNA also supports users in uploading their own lncRNA and protein-coding gene expression profiles to investigate the lncRNA combinatorial effects. It will be continuously updated with more human RNA-Seq datasets on an annual basis. Taken together, Co-LncRNA provides a web-based application for investigating lncRNA combinatorial effects, which could shed light on their biological roles and could be a valuable resource for this community. Database URL: http://www.bio-bigdata.com/Co-LncRNA/ PMID:26363020
Combinatorial Study of a Novel Poly (ADP-ribose) Polymerase Inhibitor and an HDAC Inhibitor, SAHA, in Leukemic Cell Lines.

PubMed

Hegde, Mahesh; Mantelingu, Kempegowda; Pandey, Monica; Pavankumar, Chottanahalli S; Rangappa, Kanchugarakoppal S; Raghavan, Sathees C

2016-10-01

Cancer is a multifactorial disease, which makes it difficult to cure. Since more than one defective cellular component is often involved during oncogenesis, combination therapy is gaining prominence in the field of cancer therapeutics. The purpose of this study was to investigate the combinatorial effects of a novel PARP inhibitor, P10, and HDAC inhibitor, SAHA, in leukemic cells. Combinatorial effects of P10 and SAHA were tested using propidium iodide staining in different leukemic cells. Further, flowcytometry-based assays such as calcein-AM/ethidium homodimer staining, annexin-FITC/PI staining, and JC-1 staining were carried out to elucidate the mechanism of cell death. In addition, cell-cycle analysis, immunocytochemistry studies, and western blotting analysis were conducted to check the combinatorial effect in Nalm6 cells. Propidium iodide staining showed that P10 in combination with SAHA induced cell death in Nalm6 cells, in which PARP expression and activity is high with a combination index of <0.2. Annexin-FITC/PI staining, JC-1 staining, and other biochemical assays revealed that P10 in combination with SAHA induced apoptosis by causing a change in mitochondrial membrane potential in >65 % cells. Importantly, combinatorial treatment induced S phase arrest in 40-45 % cells due to DNA damage and plausible replicative stress. Finally, we demonstrated that treatment with P10 led to DNA strand breaks, which were further potentiated by SAHA (p < 0.01), leading to activation of apoptosis and increased cell death in PARP-positive leukemic cells. Our study reveals that coadministration of PARP inhibitor with SAHA could be used as a combination therapy against leukemic cells that possess high levels of intrinsic PARP activity.
Hospital daily outpatient visits forecasting using a combinatorial model based on ARIMA and SES models.

PubMed

Luo, Li; Luo, Le; Zhang, Xinli; He, Xiaoli

2017-07-10

Accurate forecasting of hospital outpatient visits is beneficial for the reasonable planning and allocation of healthcare resource to meet the medical demands. In terms of the multiple attributes of daily outpatient visits, such as randomness, cyclicity and trend, time series methods, ARIMA, can be a good choice for outpatient visits forecasting. On the other hand, the hospital outpatient visits are also affected by the doctors' scheduling and the effects are not pure random. Thinking about the impure specialty, this paper presents a new forecasting model that takes cyclicity and the day of the week effect into consideration. We formulate a seasonal ARIMA (SARIMA) model on a daily time series and then a single exponential smoothing (SES) model on the day of the week time series, and finally establish a combinatorial model by modifying them. The models are applied to 1 year of daily visits data of urban outpatients in two internal medicine departments of a large hospital in Chengdu, for forecasting the daily outpatient visits about 1 week ahead. The proposed model is applied to forecast the cross-sectional data for 7 consecutive days of daily outpatient visits over an 8-weeks period based on 43 weeks of observation data during 1 year. The results show that the two single traditional models and the combinatorial model are simplicity of implementation and low computational intensiveness, whilst being appropriate for short-term forecast horizons. Furthermore, the combinatorial model can capture the comprehensive features of the time series data better. Combinatorial model can achieve better prediction performance than the single model, with lower residuals variance and small mean of residual errors which needs to be optimized deeply on the next research step.
Expression and Protein Interaction Analyses Reveal Combinatorial Interactions of LBD Transcription Factors During Arabidopsis Pollen Development.

PubMed

Kim, Mirim; Kim, Min-Jung; Pandey, Shashank; Kim, Jungmook

2016-11-01

LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factor gene family members play key roles in diverse aspects of plant development. LBD10 and LBD27 have been shown to be essential for pollen development in Arabidopsis thaliana. From the previous RNA sequencing (RNA-Seq) data set of Arabidopsis pollen, we identified the mRNAs of LBD22, LBD25 and LBD36 in addition to LBD10 and LBD27 in Arabidopsis pollen. Here we conducted expression and cellular analysis using GFP:GUS (green fluorescent protein:β-glucuronidase) reporter gene and subcellular localization assays using LBD:GFP fusion proteins expressed under the control of their own promoters in Arabidopsis. We found that these LBD proteins display spatially and temporally distinct and overlapping expression patterns during pollen development. Bimolecular fluorescence complementation and GST (glutathione S-transferase) pull-down assays demonstrated that protein-protein interactions occur among the LBDs exhibiting overlapping expression during pollen development. We further showed that LBD10, LBD22, LBD25, LBD27 and LBD36 interact with each other to form heterodimers, which are localized to the nucleus in Arabidopsis protoplasts. Taken together, these results suggest that combinatorial interactions among LBD proteins may be important for their function in pollen development in Arabidopsis. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.
Leveraging Modeling Approaches: Reaction Networks and Rules

PubMed Central

Blinov, Michael L.; Moraru, Ion I.

2012-01-01

We have witnessed an explosive growth in research involving mathematical models and computer simulations of intracellular molecular interactions, ranging from metabolic pathways to signaling and gene regulatory networks. Many software tools have been developed to aid in the study of such biological systems, some of which have a wealth of features for model building and visualization, and powerful capabilities for simulation and data analysis. Novel high resolution and/or high throughput experimental techniques have led to an abundance of qualitative and quantitative data related to the spatio-temporal distribution of molecules and complexes, their interactions kinetics, and functional modifications. Based on this information, computational biology researchers are attempting to build larger and more detailed models. However, this has proved to be a major challenge. Traditionally, modeling tools require the explicit specification of all molecular species and interactions in a model, which can quickly become a major limitation in the case of complex networks – the number of ways biomolecules can combine to form multimolecular complexes can be combinatorially large. Recently, a new breed of software tools has been created to address the problems faced when building models marked by combinatorial complexity. These have a different approach for model specification, using reaction rules and species patterns. Here we compare the traditional modeling approach with the new rule-based methods. We make a case for combining the capabilities of conventional simulation software with the unique features and flexibility of a rule-based approach in a single software platform for building models of molecular interaction networks. PMID:22161349
Leveraging modeling approaches: reaction networks and rules.

PubMed

Blinov, Michael L; Moraru, Ion I

2012-01-01

We have witnessed an explosive growth in research involving mathematical models and computer simulations of intracellular molecular interactions, ranging from metabolic pathways to signaling and gene regulatory networks. Many software tools have been developed to aid in the study of such biological systems, some of which have a wealth of features for model building and visualization, and powerful capabilities for simulation and data analysis. Novel high-resolution and/or high-throughput experimental techniques have led to an abundance of qualitative and quantitative data related to the spatiotemporal distribution of molecules and complexes, their interactions kinetics, and functional modifications. Based on this information, computational biology researchers are attempting to build larger and more detailed models. However, this has proved to be a major challenge. Traditionally, modeling tools require the explicit specification of all molecular species and interactions in a model, which can quickly become a major limitation in the case of complex networks - the number of ways biomolecules can combine to form multimolecular complexes can be combinatorially large. Recently, a new breed of software tools has been created to address the problems faced when building models marked by combinatorial complexity. These have a different approach for model specification, using reaction rules and species patterns. Here we compare the traditional modeling approach with the new rule-based methods. We make a case for combining the capabilities of conventional simulation software with the unique features and flexibility of a rule-based approach in a single software platform for building models of molecular interaction networks.
Lattice-Matched Epitaxial Graphene Grown on Boron Nitride.

PubMed

Davies, Andrew; Albar, Juan D; Summerfield, Alex; Thomas, James C; Cheng, Tin S; Korolkov, Vladimir V; Stapleton, Emily; Wrigley, James; Goodey, Nathan L; Mellor, Christopher J; Khlobystov, Andrei N; Watanabe, Kenji; Taniguchi, Takashi; Foxon, C Thomas; Eaves, Laurence; Novikov, Sergei V; Beton, Peter H

2018-01-10

Lattice-matched graphene on hexagonal boron nitride is expected to lead to the formation of a band gap but requires the formation of highly strained material and has not hitherto been realized. We demonstrate that aligned, lattice-matched graphene can be grown by molecular beam epitaxy using substrate temperatures in the range 1600-1710 °C and coexists with a topologically modified moiré pattern with regions of strained graphene which have giant moiré periods up to ∼80 nm. Raman spectra reveal narrow red-shifted peaks due to isotropic strain, while the giant moiré patterns result in complex splitting of Raman peaks due to strain variations across the moiré unit cell. The lattice-matched graphene has a lower conductance than both the Frenkel-Kontorova-type domain walls and also the topological defects where they terminate. We relate these results to theoretical models of band gap formation in graphene/boron nitride heterostructures.
An improved principal component analysis based region matching method for fringe direction estimation

NASA Astrophysics Data System (ADS)

He, A.; Quan, C.

2018-04-01

The principal component analysis (PCA) and region matching combined method is effective for fringe direction estimation. However, its mask construction algorithm for region matching fails in some circumstances, and the algorithm for conversion of orientation to direction in mask areas is computationally-heavy and non-optimized. We propose an improved PCA based region matching method for the fringe direction estimation, which includes an improved and robust mask construction scheme, and a fast and optimized orientation-direction conversion algorithm for the mask areas. Along with the estimated fringe direction map, filtered fringe pattern by automatic selective reconstruction modification and enhanced fast empirical mode decomposition (ASRm-EFEMD) is used for Hilbert spiral transform (HST) to demodulate the phase. Subsequently, windowed Fourier ridge (WFR) method is used for the refinement of the phase. The robustness and effectiveness of proposed method are demonstrated by both simulated and experimental fringe patterns.
Discovery of Cationic Polymers for Non-viral Gene Delivery using Combinatorial Approaches

PubMed Central

Barua, Sutapa; Ramos, James; Potta, Thrimoorthy; Taylor, David; Huang, Huang-Chiao; Montanez, Gabriela; Rege, Kaushal

2015-01-01

Gene therapy is an attractive treatment option for diseases of genetic origin, including several cancers and cardiovascular diseases. While viruses are effective vectors for delivering exogenous genes to cells, concerns related to insertional mutagenesis, immunogenicity, lack of tropism, decay and high production costs necessitate the discovery of non-viral methods. Significant efforts have been focused on cationic polymers as non-viral alternatives for gene delivery. Recent studies have employed combinatorial syntheses and parallel screening methods for enhancing the efficacy of gene delivery, biocompatibility of the delivery vehicle, and overcoming cellular level barriers as they relate to polymer-mediated transgene uptake, transport, transcription, and expression. This review summarizes and discusses recent advances in combinatorial syntheses and parallel screening of cationic polymer libraries for the discovery of efficient and safe gene delivery systems. PMID:21843141
Combinatorial Optimization in Project Selection Using Genetic Algorithm

NASA Astrophysics Data System (ADS)

Dewi, Sari; Sawaluddin

2018-01-01

This paper discusses the problem of project selection in the presence of two objective functions that maximize profit and minimize cost and the existence of some limitations is limited resources availability and time available so that there is need allocation of resources in each project. These resources are human resources, machine resources, raw material resources. This is treated as a consideration to not exceed the budget that has been determined. So that can be formulated mathematics for objective function (multi-objective) with boundaries that fulfilled. To assist the project selection process, a multi-objective combinatorial optimization approach is used to obtain an optimal solution for the selection of the right project. It then described a multi-objective method of genetic algorithm as one method of multi-objective combinatorial optimization approach to simplify the project selection process in a large scope.
Programming gene expression with combinatorial promoters

PubMed Central

Cox, Robert Sidney; Surette, Michael G; Elowitz, Michael B

2007-01-01

Promoters control the expression of genes in response to one or more transcription factors (TFs). The architecture of a promoter is the arrangement and type of binding sites within it. To understand natural genetic circuits and to design promoters for synthetic biology, it is essential to understand the relationship between promoter function and architecture. We constructed a combinatorial library of random promoter architectures. We characterized 288 promoters in Escherichia coli, each containing up to three inputs from four different TFs. The library design allowed for multiple −10 and −35 boxes, and we observed varied promoter strength over five decades. To further analyze the functional repertoire, we defined a representation of promoter function in terms of regulatory range, logic type, and symmetry. Using these results, we identified heuristic rules for programming gene expression with combinatorial promoters. PMID:18004278
Analytical validation of a psychiatric pharmacogenomic test.

PubMed

Jablonski, Michael R; King, Nina; Wang, Yongbao; Winner, Joel G; Watterson, Lucas R; Gunselman, Sandra; Dechairo, Bryan M

2018-05-01

The aim of this study was to validate the analytical performance of a combinatorial pharmacogenomics test designed to aid in the appropriate medication selection for neuropsychiatric conditions. Genomic DNA was isolated from buccal swabs. Twelve genes (65 variants/alleles) associated with psychotropic medication metabolism, side effects, and mechanisms of actions were evaluated by bead array, MALDI-TOF mass spectrometry, and/or capillary electrophoresis methods (GeneSight Psychotropic, Assurex Health, Inc.). The combinatorial pharmacogenomics test has a dynamic range of 2.5-20 ng/μl of input genomic DNA, with comparable performance for all assays included in the test. Both the precision and accuracy of the test were >99.9%, with individual gene components between 99.4 and 100%. This study demonstrates that the combinatorial pharmacogenomics test is robust and reproducible, making it suitable for clinical use.
Simulating the component counts of combinatorial structures.

PubMed

Arratia, Richard; Barbour, A D; Ewens, W J; Tavaré, Simon

2018-02-09

This article describes and compares methods for simulating the component counts of random logarithmic combinatorial structures such as permutations and mappings. We exploit the Feller coupling for simulating permutations to provide a very fast method for simulating logarithmic assemblies more generally. For logarithmic multisets and selections, this approach is replaced by an acceptance/rejection method based on a particular conditioning relationship that represents the distribution of the combinatorial structure as that of independent random variables conditioned on a weighted sum. We show how to improve its acceptance rate. We illustrate the method by estimating the probability that a random mapping has no repeated component sizes, and establish the asymptotic distribution of the difference between the number of components and the number of distinct component sizes for a very general class of logarithmic structures. Copyright © 2018. Published by Elsevier Inc.

Single cell systems biology by super-resolution imaging and combinatorial labeling

PubMed Central

Lubeck, Eric; Cai, Long

2012-01-01

Fluorescence microscopy is a powerful quantitative tool for exploring regulatory networks in single cells. However, the number of molecular species that can be measured simultaneously is limited by the spectral separability of fluorophores. Here we demonstrate a simple but general strategy to drastically increase the capacity for multiplex detection of molecules in single cells by using optical super-resolution microscopy (SRM) and combinatorial labeling. As a proof of principle, we labeled mRNAs with unique combinations of fluorophores using Fluorescence in situ Hybridization (FISH), and resolved the sequences and combinations of fluorophores with SRM. We measured the mRNA levels of 32 genes simultaneously in single S. cerevisiae cells. These experiments demonstrate that combinatorial labeling and super-resolution imaging of single cells provides a natural approach to bring systems biology into single cells. PMID:22660740
What Performance Analysts Need to Know About Research Trends in Association Football (2012-2016): A Systematic Review.

PubMed

Sarmento, Hugo; Clemente, Filipe Manuel; Araújo, Duarte; Davids, Keith; McRobert, Allistair; Figueiredo, António

2018-04-01

Evolving patterns of match analysis research need to be systematically reviewed regularly since this area of work is burgeoning rapidly and studies can offer new insights to performance analysts if theoretically and coherently organized. The purpose of this paper was to conduct a systematic review of published articles on match analysis in adult male football, identify and organize common research topics, and synthesize the emerging patterns of work between 2012 and 2016, according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines. The Web of Science database was searched for relevant published studies using the following keywords: 'football' and 'soccer', each one associated with the terms 'match analysis', 'performance analysis', 'notational analysis', 'game analysis', 'tactical analysis' and 'patterns of play'. Of 483 studies initially identified, 77 were fully reviewed and their outcome measures extracted and analyzed. Results showed that research mainly focused on (1) performance at set pieces, i.e. corner kicks, free kicks, penalty kicks; (2) collective system behaviours, captured by established variables such as team centroid (geometrical centre of a set of players) and team dispersion (quantification of how far players are apart), as well as tendencies for team communication (establishing networks based on passing sequences), sequential patterns (predicting future passing sequences), and group outcomes (relationships between match-related statistics and final match scores); and (3) activity profile of players, i.e. playing roles, effects of fatigue, substitutions during matches, and the effects of environmental constraints on performance, such as heat and altitude. From the previous review, novel variables were identified that require new measurement techniques. It is evident that the complexity engendered during performance in competitive soccer requires an integrated approach that considers multiple aspects. A challenge for researchers is to align these new measures with the needs of the coaches through a more integrated relationship between coaches and researchers, to produce practical and usable information that improves player performance and coach activity.
Is a High Tone Pointy? Speakers of Different Languages Match Mandarin Chinese Tones to Visual Shapes Differently

PubMed Central

Shang, Nan; Styles, Suzy J.

2017-01-01

Studies investigating cross-modal correspondences between auditory pitch and visual shapes have shown children and adults consistently match high pitch to pointy shapes and low pitch to curvy shapes, yet no studies have investigated linguistic-uses of pitch. In the present study, we used a bouba/kiki style task to investigate the sound/shape mappings for Tones of Mandarin Chinese, for three groups of participants with different language backgrounds. We recorded the vowels [i] and [u] articulated in each of the four tones of Mandarin Chinese. In Study 1 a single auditory stimulus was presented with two images (one curvy, one spiky). In Study 2 a single image was presented with two auditory stimuli differing only in tone. Participants were asked to select the best match in an online ‘Quiz.’ Across both studies, we replicated the previously observed ‘u-curvy, i-pointy’ sound/shape cross-modal correspondence in all groups. However, Tones were mapped differently by people with different language backgrounds: speakers of Mandarin Chinese classified as Chinese-dominant systematically matched Tone 1 (high, steady) to the curvy shape and Tone 4 (falling) to the pointy shape, while English speakers with no knowledge of Chinese preferred to match Tone 1 (high, steady) to the pointy shape and Tone 3 (low, dipping) to the curvy shape. These effects were observed most clearly in Study 2 where tone-pairs were contrasted explicitly. These findings are in line with the dominant patterns of linguistic pitch perception for speakers of these languages (pitch-change, and pitch height, respectively). Chinese English balanced bilinguals showed a bivalent pattern, swapping between the Chinese pitch-change pattern and the English pitch-height pattern depending on the task. These findings show for that the supposedly universal pattern of mapping linguistic sounds to shape is modulated by the sensory properties of a speaker’s language system, and that people with high functioning in more than one language can dynamically shift between patterns. PMID:29270147
Obfuscation Framework Based on Functionally Equivalent Combinatorial Logic Families

DTIC Science & Technology

2008-03-01

of Defense, or the United States Government . AFIT/GCS/ENG/08-12 Obfuscation Framework Based on Functionally Equivalent Combinatorial Logic Families...time, United States policy strongly encourages the sale and transfer of some military equipment to foreign governments and makes it easier for...Proceedings of the International Conference on Availability, Reliability and Security, 2007. 14. McDonald, J. Todd and Alec Yasinsac. “Of unicorns and random
Combinatorial study of degree assortativity in networks.

PubMed

Estrada, Ernesto

2011-10-01

Why are some networks degree-degree correlated (assortative), while most of the real-world ones are anticorrelated (disassortative)? Here, we prove, by combinatorial methods, that the assortativity of a network depends only on three structural factors: transitivity (clustering coefficient), intermodular connectivity, and branching. Then, a network is assortative if the contributions of the first two factors are larger than that of the third. Highly branched networks are likely to be disassortative.
Development of combinatorial chemistry methods for coatings: high-throughput adhesion evaluation and scale-up of combinatorial leads.

PubMed

Potyrailo, Radislav A; Chisholm, Bret J; Morris, William G; Cawse, James N; Flanagan, William P; Hassib, Lamyaa; Molaison, Chris A; Ezbiansky, Karin; Medford, George; Reitz, Hariklia

2003-01-01

Coupling of combinatorial chemistry methods with high-throughput (HT) performance testing and measurements of resulting properties has provided a powerful set of tools for the 10-fold accelerated discovery of new high-performance coating materials for automotive applications. Our approach replaces labor-intensive steps with automated systems for evaluation of adhesion of 8 x 6 arrays of coating elements that are discretely deposited on a single 9 x 12 cm plastic substrate. Performance of coatings is evaluated with respect to their resistance to adhesion loss, because this parameter is one of the primary considerations in end-use automotive applications. Our HT adhesion evaluation provides previously unavailable capabilities of high speed and reproducibility of testing by using a robotic automation, an expanded range of types of tested coatings by using the coating tagging strategy, and an improved quantitation by using high signal-to-noise automatic imaging. Upon testing, the coatings undergo changes that are impossible to quantitatively predict using existing knowledge. Using our HT methodology, we have developed several coatings leads. These HT screening results for the best coating compositions have been validated on the traditional scales of coating formulation and adhesion loss testing. These validation results have confirmed the superb performance of combinatorially developed coatings over conventional coatings on the traditional scale.
Enhancement of Bone-Marrow-Derived Mesenchymal Stem Cell Angiogenic Capacity by NPWT for a Combinatorial Therapy to Promote Wound Healing with Large Defect

PubMed Central

Ma, Zhanjun

2017-01-01

Poor viability of engrafted bone marrow mesenchymal stem cells (BMSCs) often hinders their application for wound healing, and the strategy of how to take full advantage of their angiogenic capacity within wounds still remains unclear. Negative pressure wound therapy (NPWT) has been demonstrated to be effective for enhancing wound healing, especially for the promotion of angiogenesis within wounds. Here we utilized combinatory strategy using the transplantation of BMSCs and NPWT to investigate whether this combinatory therapy could accelerate angiogenesis in wounds. In vitro, after 9-day culture, BMSCs proliferation significantly increased in NPWT group. Furthermore, NPWT induced their differentiation into the angiogenic related cells, which are indispensable for wound angiogenesis. In vivo, rat full-thickness cutaneous wounds treated with BMSCs combined with NPWT exhibited better viability of the cells and enhanced angiogenesis and maturation of functional blood vessels than did local BMSC injection or NPWT alone. Expression of angiogenesis markers (NG2, VEGF, CD31, and α-SMA) was upregulated in wounds treated with combined BMSCs with NPWT. Our data suggest that NPWT may act as an inductive role to enhance BMSCs angiogenic capacity and this combinatorial therapy may serve as a simple but efficient clinical solution for complex wounds with large defects. PMID:28243602
Coupled Phases and Combinatorial Selection in Fluctuating Hydrothermal Pools: A Scenario to Guide Experimental Approaches to the Origin of Cellular Life

PubMed Central

Damer, Bruce; Deamer, David

2015-01-01

Hydrothermal fields on the prebiotic Earth are candidate environments for biogenesis. We propose a model in which molecular systems driven by cycles of hydration and dehydration in such sites undergo chemical evolution in dehydrated films on mineral surfaces followed by encapsulation and combinatorial selection in a hydrated bulk phase. The dehydrated phase can consist of concentrated eutectic mixtures or multilamellar liquid crystalline matrices. Both conditions organize and concentrate potential monomers and thereby promote polymerization reactions that are driven by reduced water activity in the dehydrated phase. In the case of multilamellar lipid matrices, polymers that have been synthesized are captured in lipid vesicles upon rehydration to produce a variety of molecular systems. Each vesicle represents a protocell, an “experiment” in a natural version of combinatorial chemistry. Two kinds of selective processes can then occur. The first is a physical process in which relatively stable molecular systems will be preferentially selected. The second is a chemical process in which rare combinations of encapsulated polymers form systems capable of capturing energy and nutrients to undergo growth by catalyzed polymerization. Given continued cycling over extended time spans, such combinatorial processes will give rise to molecular systems having the fundamental properties of life. PMID:25780958
A combinatorial perspective of the protein inference problem.

PubMed

Yang, Chao; He, Zengyou; Yu, Weichuan

2013-01-01

In a shotgun proteomics experiment, proteins are the most biologically meaningful output. The success of proteomics studies depends on the ability to accurately and efficiently identify proteins. Many methods have been proposed to facilitate the identification of proteins from peptide identification results. However, the relationship between protein identification and peptide identification has not been thoroughly explained before. In this paper, we devote ourselves to a combinatorial perspective of the protein inference problem. We employ combinatorial mathematics to calculate the conditional protein probabilities (protein probability means the probability that a protein is correctly identified) under three assumptions, which lead to a lower bound, an upper bound, and an empirical estimation of protein probabilities, respectively. The combinatorial perspective enables us to obtain an analytical expression for protein inference. Our method achieves comparable results with ProteinProphet in a more efficient manner in experiments on two data sets of standard protein mixtures and two data sets of real samples. Based on our model, we study the impact of unique peptides and degenerate peptides (degenerate peptides are peptides shared by at least two proteins) on protein probabilities. Meanwhile, we also study the relationship between our model and ProteinProphet. We name our program ProteinInfer. Its Java source code, our supplementary document and experimental results are available at: >http://bioinformatics.ust.hk/proteininfer.
Integrative Analysis of Transcription Factor Combinatorial Interactions Using a Bayesian Tensor Factorization Approach

PubMed Central

Ye, Yusen; Gao, Lin; Zhang, Shihua

2017-01-01

Transcription factors play a key role in transcriptional regulation of genes and determination of cellular identity through combinatorial interactions. However, current studies about combinatorial regulation is deficient due to lack of experimental data in the same cellular environment and extensive existence of data noise. Here, we adopt a Bayesian CANDECOMP/PARAFAC (CP) factorization approach (BCPF) to integrate multiple datasets in a network paradigm for determining precise TF interaction landscapes. In our first application, we apply BCPF to integrate three networks built based on diverse datasets of multiple cell lines from ENCODE respectively to predict a global and precise TF interaction network. This network gives 38 novel TF interactions with distinct biological functions. In our second application, we apply BCPF to seven types of cell type TF regulatory networks and predict seven cell lineage TF interaction networks, respectively. By further exploring the dynamics and modularity of them, we find cell lineage-specific hub TFs participate in cell type or lineage-specific regulation by interacting with non-specific TFs. Furthermore, we illustrate the biological function of hub TFs by taking those of cancer lineage and blood lineage as examples. Taken together, our integrative analysis can reveal more precise and extensive description about human TF combinatorial interactions. PMID:29033978
Integrative Analysis of Transcription Factor Combinatorial Interactions Using a Bayesian Tensor Factorization Approach.

PubMed

Ye, Yusen; Gao, Lin; Zhang, Shihua

2017-01-01

Transcription factors play a key role in transcriptional regulation of genes and determination of cellular identity through combinatorial interactions. However, current studies about combinatorial regulation is deficient due to lack of experimental data in the same cellular environment and extensive existence of data noise. Here, we adopt a Bayesian CANDECOMP/PARAFAC (CP) factorization approach (BCPF) to integrate multiple datasets in a network paradigm for determining precise TF interaction landscapes. In our first application, we apply BCPF to integrate three networks built based on diverse datasets of multiple cell lines from ENCODE respectively to predict a global and precise TF interaction network. This network gives 38 novel TF interactions with distinct biological functions. In our second application, we apply BCPF to seven types of cell type TF regulatory networks and predict seven cell lineage TF interaction networks, respectively. By further exploring the dynamics and modularity of them, we find cell lineage-specific hub TFs participate in cell type or lineage-specific regulation by interacting with non-specific TFs. Furthermore, we illustrate the biological function of hub TFs by taking those of cancer lineage and blood lineage as examples. Taken together, our integrative analysis can reveal more precise and extensive description about human TF combinatorial interactions.
A Key Pre-Distribution Scheme Based on µ-PBIBD for Enhancing Resilience in Wireless Sensor Networks.

PubMed

Yuan, Qi; Ma, Chunguang; Yu, Haitao; Bian, Xuefen

2018-05-12

Many key pre-distribution (KPD) schemes based on combinatorial design were proposed for secure communication of wireless sensor networks (WSNs). Due to complexity of constructing the combinatorial design, it is infeasible to generate key rings using the corresponding combinatorial design in large scale deployment of WSNs. In this paper, we present a definition of new combinatorial design, termed “µ-partially balanced incomplete block design (µ-PBIBD)”, which is a refinement of partially balanced incomplete block design (PBIBD), and then describe a 2-D construction of µ-PBIBD which is mapped to KPD in WSNs. Our approach is of simple construction which provides a strong key connectivity and a poor network resilience. To improve the network resilience of KPD based on 2-D µ-PBIBD, we propose a KPD scheme based on 3-D Ex-µ-PBIBD which is a construction of µ-PBIBD from 2-D space to 3-D space. Ex-µ-PBIBD KPD scheme improves network scalability and resilience while has better key connectivity. Theoretical analysis and comparison with the related schemes show that key pre-distribution scheme based on Ex-µ-PBIBD provides high network resilience and better key scalability, while it achieves a trade-off between network resilience and network connectivity.
Diversity-oriented combinatorial biosynthesis of benzenediol lactone scaffolds by subunit shuffling of fungal polyketide synthases.

PubMed

Xu, Yuquan; Zhou, Tong; Zhang, Shuwei; Espinosa-Artiles, Patricia; Wang, Luoyi; Zhang, Wei; Lin, Min; Gunatilaka, A A Leslie; Zhan, Jixun; Molnár, István

2014-08-26

Combinatorial biosynthesis aspires to exploit the promiscuity of microbial anabolic pathways to engineer the synthesis of new chemical entities. Fungal benzenediol lactone (BDL) polyketides are important pharmacophores with wide-ranging bioactivities, including heat shock response and immune system modulatory effects. Their biosynthesis on a pair of sequentially acting iterative polyketide synthases (iPKSs) offers a test case for the modularization of secondary metabolic pathways into "build-couple-pair" combinatorial synthetic schemes. Expression of random pairs of iPKS subunits from four BDL model systems in a yeast heterologous host created a diverse library of BDL congeners, including a polyketide with an unnatural skeleton and heat shock response-inducing activity. Pairwise heterocombinations of the iPKS subunits also helped to illuminate the innate, idiosyncratic programming of these enzymes. Even in combinatorial contexts, these biosynthetic programs remained largely unchanged, so that the iPKSs built their cognate biosynthons, coupled these building blocks into chimeric polyketide intermediates, and catalyzed intramolecular pairing to release macrocycles or α-pyrones. However, some heterocombinations also provoked stuttering, i.e., the relaxation of iPKSs chain length control to assemble larger homologous products. The success of such a plug and play approach to biosynthesize novel chemical diversity bodes well for bioprospecting unnatural polyketides for drug discovery.
Successful application of the dual-vector system II in creating a reliable phage-displayed combinatorial Fab library.

PubMed

Song, Suk-yoon; Hur, Byung-ung; Lee, Kyung-woo; Choi, Hyo-jung; Kim, Sung-soo; Kang, Goo; Cha, Sang-hoon

2009-03-31

The dual-vector system-II (DVS-II), which allows efficient display of Fab antibodies on phage, has been reported previously, but its practical applicability in a phage-displayed antibody library has not been verified. To resolve this issue, we created two small combinatorial human Fab antibody libraries using the DVS-II, and isolation of target-specific antibodies was attempted. Biopanning of one antibody library, termed DVFAB-1L library, which has a 1.3 x 10(7) combinatorial antibody complexity, against fluorescein-BSA resulted in successful isolation of human Fab clones specific for the antigen despite the presence of only a single light chain in the library. By using the unique feature of the DVS-II, an antibody library of a larger size, named DVFAB-131L, which has a 1.5 x 10(9) combinatorial antibody complexity, was also generated in a rapid manner by combining 1.3 x 10(7) heavy chains and 131 light chains and more diverse anti-fluorescein-BSA Fab antibody clones were successfully obtained. Our results demonstrate that the DVS-II can be applied readily in creating phage-displayed antibody libraries with much less effort, and target-specific antibody clones can be isolated reliably via light chain promiscuity of antibody molecule.
A Key Pre-Distribution Scheme Based on µ-PBIBD for Enhancing Resilience in Wireless Sensor Networks

PubMed Central

Yuan, Qi; Ma, Chunguang; Yu, Haitao; Bian, Xuefen

2018-01-01

Many key pre-distribution (KPD) schemes based on combinatorial design were proposed for secure communication of wireless sensor networks (WSNs). Due to complexity of constructing the combinatorial design, it is infeasible to generate key rings using the corresponding combinatorial design in large scale deployment of WSNs. In this paper, we present a definition of new combinatorial design, termed “µ-partially balanced incomplete block design (µ-PBIBD)”, which is a refinement of partially balanced incomplete block design (PBIBD), and then describe a 2-D construction of µ-PBIBD which is mapped to KPD in WSNs. Our approach is of simple construction which provides a strong key connectivity and a poor network resilience. To improve the network resilience of KPD based on 2-D µ-PBIBD, we propose a KPD scheme based on 3-D Ex-µ-PBIBD which is a construction of µ-PBIBD from 2-D space to 3-D space. Ex-µ-PBIBD KPD scheme improves network scalability and resilience while has better key connectivity. Theoretical analysis and comparison with the related schemes show that key pre-distribution scheme based on Ex-µ-PBIBD provides high network resilience and better key scalability, while it achieves a trade-off between network resilience and network connectivity. PMID:29757244
Iconicity and the Emergence of Combinatorial Structure in Language.

PubMed

Verhoef, Tessa; Kirby, Simon; de Boer, Bart

2016-11-01

In language, recombination of a discrete set of meaningless building blocks forms an unlimited set of possible utterances. How such combinatorial structure emerged in the evolution of human language is increasingly being studied. It has been shown that it can emerge when languages culturally evolve and adapt to human cognitive biases. How the emergence of combinatorial structure interacts with the existence of holistic iconic form-meaning mappings in a language is still unknown. The experiment presented in this paper studies the role of iconicity and human cognitive learning biases in the emergence of combinatorial structure in artificial whistled languages. Participants learned and reproduced whistled words for novel objects with the use of a slide whistle. Their reproductions were used as input for the next participant, to create transmission chains and simulate cultural transmission. Two conditions were studied: one in which the persistence of iconic form-meaning mappings was possible and one in which this was experimentally made impossible. In both conditions, cultural transmission caused the whistled languages to become more learnable and more structured, but this process was slightly delayed in the first condition. Our findings help to gain insight into when and how words may lose their iconic origins when they become part of an organized linguistic system. Copyright © 2015 Cognitive Science Society, Inc.
Single-frequency oscillation of thin-disk lasers due to phase-matched pumping.

PubMed

Vorholt, Christian; Wittrock, Ulrich

2017-09-04

We present a novel pump concept that should lead to single-frequency operation of thin-disk lasers without the need for etalons or other spectral filters. The single-frequency operation is due to matching the standing wave pattern of partially coherent pump light to the standing wave pattern of the laser light inside the disk. The output power and the optical efficiency of our novel pump concept are compared with conventional pumping. The feasibility of our pump concept was shown in previous experiments.
Using pattern based layout comparison for a quick analysis of design changes

NASA Astrophysics Data System (ADS)

Huang, Lucas; Yang, Legender; Kan, Huan; Zou, Elain; Wan, Qijian; Du, Chunshan; Hu, Xinyi; Liu, Zhengfang

2018-03-01

A design usually goes through several versions until achieving a most successful one. These changes between versions are not a complete substitution but a continual improvement, either fixing the known issues of its prior versions (engineering change order) or a more optimized design substitution of a portion of the design. On the manufacturing side, process engineers care more about the design pattern changes because any new pattern occurrence may be a killer of the yield. An effective and efficient way to narrow down the diagnosis scope appeals to the engineers. What is the best approach of comparing two layouts? A direct overlay of two layouts may not always work as even though most of the design instances will be kept in the layout from version to version, the actual placements may be different. An alternative way, pattern based layout comparison, comes to play. By expanding this application, it makes it possible to transfer the learning in one cycle to another and accelerate the process of failure analysis. This paper presents a solution to compare two layouts by using Calibre DRC and Pattern Matching. The key step in this flow is layout decomposition. In theory, with a fixed pattern size, a layout can always be decomposed into limited number of patterns by moving the pattern center around the layout, the number is limited but may be huge if the layout is not processed smartly! A mathematical answer is not what we are looking for but an engineering solution is more desired. Layouts must be decomposed into patterns with physical meaning in a smart way. When a layout is decomposed and patterns are classified, a pattern library with unique patterns inside is created for that layout. After individual pattern libraries for each layout are created, run pattern comparison utility provided by Calibre Pattern Matching to compare the pattern libraries, unique patterns will come out for each layout. This paper illustrates this flow in details and demonstrates the advantage of combining Calibre DRC and Calibre Pattern Matching.
Transparent Electrochemical Gratings from a Patterned Bistable Silver Mirror.

PubMed

Park, Chihyun; Na, Jongbeom; Han, Minsu; Kim, Eunkyoung

2017-07-25

Silver mirror patterns were formed reversibly on a polystyrene (PS)-patterned electrode to produce gratings through the electrochemical reduction of silver ions. The electrochemical gratings exhibited high transparency (T > 95%), similar to a see-through window, by matching the refractive index of the grating pattern with the surrounding medium. The gratings switch to a diffractive state upon the formation of a mirror pattern (T < 5%) with a high diffraction efficiency up to 40%, providing reversible diffractive gratings. The diffraction state was maintained in the voltage-off state (V-off) for 40 min, which demonstrated bistable reversible electrochemical grating (BREG) behavior. By carefully combining the BREGs through period matching, dual-color switching was achieved within the full color region, which exhibited three distinct optical switching states between -2.5, 0, and +2.5 V. The wide range of light tenability using the metallic BREGs developed herein enabled IR modulation, NIR light reflection, and on-demand heat transfer.
Mixed Pattern Matching-Based Traffic Abnormal Behavior Recognition

PubMed Central

Cui, Zhiming; Zhao, Pengpeng

2014-01-01

A motion trajectory is an intuitive representation form in time-space domain for a micromotion behavior of moving target. Trajectory analysis is an important approach to recognize abnormal behaviors of moving targets. Against the complexity of vehicle trajectories, this paper first proposed a trajectory pattern learning method based on dynamic time warping (DTW) and spectral clustering. It introduced the DTW distance to measure the distances between vehicle trajectories and determined the number of clusters automatically by a spectral clustering algorithm based on the distance matrix. Then, it clusters sample data points into different clusters. After the spatial patterns and direction patterns learned from the clusters, a recognition method for detecting vehicle abnormal behaviors based on mixed pattern matching was proposed. The experimental results show that the proposed technical scheme can recognize main types of traffic abnormal behaviors effectively and has good robustness. The real-world application verified its feasibility and the validity. PMID:24605045

Signal detection by means of orthogonal decomposition

NASA Astrophysics Data System (ADS)

Hajdu, C. F.; Dabóczi, T.; Péceli, G.; Zamantzas, C.

2018-03-01

Matched filtering is a well-known method frequently used in digital signal processing to detect the presence of a pattern in a signal. In this paper, we suggest a time variant matched filter, which, unlike a regular matched filter, maintains a given alignment between the input signal and the template carrying the pattern, and can be realized recursively. We introduce a method to synchronize the two signals for presence detection, usable in case direct synchronization between the signal generator and the receiver is not possible or not practical. We then propose a way of realizing and extending the same filter by modifying a recursive spectral observer, which gives rise to orthogonal filter channels and also leads to another way to synchronize the two signals.
The within-match patterns of locomotor efficiency during professional soccer match play: Implications for injury risk?

PubMed

Barrett, Steve; Midgley, Adrian; Reeves, Matt; Joel, Tom; Franklin, Ed; Heyworth, Rob; Garrett, Andrew; Lovell, Ric

2016-10-01

The principle aim of the current study was to examine within-match patterns of locomotor efficiency in professional soccer, determined as the ratio between tri-axial accelerometer data (PlayerLoad™) and locomotor activities. Between match variability and determinants of PlayerLoad™ during match play were also assessed. A single cohort, observational study. Tri-axial accelerometer data (PlayerLoad™) was recorded during 86 competitive soccer matches in 63 English championship players (574 match observations). Accelerometer data accumulated (PlayerLoad Vector Magnitude [PLVM]) from the individual-component planes of PlayerLoad™ (anterior-posterior PlayerLoad™ [PLAP], medial-lateral PlayerLoad™ [PLML] and vertical PlayerLoad™ [PLV]), together with locomotor activity (Total Distance Covered [TDC]) were determined in 15-min segments. Locomotor efficiency was calculated using the ratio of PLVM and TDC (PlayerLoad™ per metre). The proportion of variance explaining the within-match trends in PLVM, PLAP, APML, APv, and TDC was determined owing to matches, individual players, and positional role. PLVM, PLAP, APML, APv and TDC reduced after the initial 15-min match period (p=0.001; η(2)=0.22-0.43, large effects). PL:TDC increased in the last 15min of each half (p=0.001; η(2)=0.25, large effect). The variance in PLVM during soccer match-play was explained by individual players (63.9%; p=0.001) and between-match variation (21.6%; p=0.001), but not positional role (14.1%; p=0.364). Locomotor efficiency is lower during the latter stages of each half of competitive soccer match-play, a trend synonymous with observations of increased injury incidence and fatigue in these periods. Locomotor efficiency may be a valuable metric to identify fatigue and heightened injury risk during soccer training and match-play. Copyright © 2015 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.
Wheat gliadin: digital imaging and database construction using a 4-band reference system of agarose isoelectric focusing patterns.

PubMed

Black, J A; Waggamon, K A

1992-01-01

An isoelectric focusing method using thin-layer agarose gel has been developed for wheat gliadin. Using flat-bed units with a third electrode, up to 72 samples per gel may be analyzed. Advantages over traditional acid polyacrylamide gel electrophoresis methodology include: faster run times, nontoxic media, and greater sample capacity. The method is suitable for fingerprinting or purity testing of wheat varieties. Using digital images captured by a flat-bed scanner, a 4-band reference system using isoelectric points was devised. Software enables separated bands to be assigned pI values based upon reference tracks. Precision of assigned isoelectric points is shown to be on the order of 0.02 pH units. Captured images may be stored in a computer database and compared to unknown patterns to enable an identification. Parameters for a match with a stored pattern may be adjusted for pI interval required for a match, and number of best matches.
Oscillatory neural network for pattern recognition: trajectory based classification and supervised learning.

PubMed

Miller, Vonda H; Jansen, Ben H

2008-12-01

Computer algorithms that match human performance in recognizing written text or spoken conversation remain elusive. The reasons why the human brain far exceeds any existing recognition scheme to date in the ability to generalize and to extract invariant characteristics relevant to category matching are not clear. However, it has been postulated that the dynamic distribution of brain activity (spatiotemporal activation patterns) is the mechanism by which stimuli are encoded and matched to categories. This research focuses on supervised learning using a trajectory based distance metric for category discrimination in an oscillatory neural network model. Classification is accomplished using a trajectory based distance metric. Since the distance metric is differentiable, a supervised learning algorithm based on gradient descent is demonstrated. Classification of spatiotemporal frequency transitions and their relation to a priori assessed categories is shown along with the improved classification results after supervised training. The results indicate that this spatiotemporal representation of stimuli and the associated distance metric is useful for simple pattern recognition tasks and that supervised learning improves classification results.
Ideal Standards, Acceptance, and Relationship Satisfaction: Latitudes of Differential Effects

PubMed Central

Buyukcan-Tetik, Asuman; Campbell, Lorne; Finkenauer, Catrin; Karremans, Johan C.; Kappen, Gesa

2017-01-01

We examined whether the relations of consistency between ideal standards and perceptions of a current romantic partner with partner acceptance and relationship satisfaction level off, or decelerate, above a threshold. We tested our hypothesis using a 3-year longitudinal data set collected from heterosexual newlywed couples. We used two indicators of consistency: pattern correspondence (within-person correlation between ideal standards and perceived partner ratings) and mean-level match (difference between ideal standards score and perceived partner score). Our results revealed that pattern correspondence had no relation with partner acceptance, but a positive linear/exponential association with relationship satisfaction. Mean-level match had a significant positive association with actor’s acceptance and relationship satisfaction up to the point where perceived partner score equaled ideal standards score. Partner effects did not show a consistent pattern. The results suggest that the consistency between ideal standards and perceived partner attributes has a non-linear association with acceptance and relationship satisfaction, although the results were more conclusive for mean-level match. PMID:29033876
A tiger cannot change its stripes: using a three-dimensional model to match images of living tigers and tiger skins.

PubMed

Hiby, Lex; Lovell, Phil; Patil, Narendra; Kumar, N Samba; Gopalaswamy, Arjun M; Karanth, K Ullas

2009-06-23

The tiger is one of many species in which individuals can be identified by surface patterns. Camera traps can be used to record individual tigers moving over an array of locations and provide data for monitoring and studying populations and devising conservation strategies. We suggest using a combination of algorithms to calculate similarity scores between pattern samples scanned from the images to automate the search for a match to a new image. We show how using a three-dimensional surface model of a tiger to scan the pattern samples allows comparison of images that differ widely in camera angles and body posture. The software, which is free to download, considerably reduces the effort required to maintain an image catalogue and we suggest it could be used to trace the origin of a tiger skin by searching a central database of living tigers' images for matches to an image of the skin.
A tiger cannot change its stripes: using a three-dimensional model to match images of living tigers and tiger skins

PubMed Central

Hiby, Lex; Lovell, Phil; Patil, Narendra; Kumar, N. Samba; Gopalaswamy, Arjun M.; Karanth, K. Ullas

2009-01-01

The tiger is one of many species in which individuals can be identified by surface patterns. Camera traps can be used to record individual tigers moving over an array of locations and provide data for monitoring and studying populations and devising conservation strategies. We suggest using a combination of algorithms to calculate similarity scores between pattern samples scanned from the images to automate the search for a match to a new image. We show how using a three-dimensional surface model of a tiger to scan the pattern samples allows comparison of images that differ widely in camera angles and body posture. The software, which is free to download, considerably reduces the effort required to maintain an image catalogue and we suggest it could be used to trace the origin of a tiger skin by searching a central database of living tigers' images for matches to an image of the skin. PMID:19324633
PepPat, a pattern-based oligopeptide homology search method and the identification of a novel tachykinin-like peptide.

PubMed

Jiang, Ying; Gao, Ge; Fang, Gang; Gustafson, Eric L; Laverty, Maureen; Yin, Yanbin; Zhang, Yong; Luo, Jingchu; Greene, Jonathan R; Bayne, Marvin L; Hedrick, Joseph A; Murgolo, Nicholas J

2003-05-01

PepPat, a hybrid method that combines pattern matching with similarity scoring, is described. We also report PepPat's application in the identification of a novel tachykinin-like peptide. PepPat takes as input a query peptide and a user-specified regular expression pattern within the peptide. It first performs a database pattern match and then ranks candidates on the basis of their similarity to the query peptide. PepPat calculates similarity over the pattern spanning region, enhancing PepPat's sensitivity for short query peptides. PepPat can also search for a user-specified number of occurrences of a repeated pattern within the target sequence. We illustrate PepPat's application in short peptide ligand mining. As a validation example, we report the identification of a novel tachykinin-like peptide, C14TKL-1, and show it is an NK1 (neuokinin receptor 1) agonist whose message is widely expressed in human periphery. PepPat is offered online at: http://peppat.cbi.pku.edu.cn.
Computer Description of the Field Artillery Ammunition Supply Vehicle

DTIC Science & Technology

1983-04-01

Combinatorial Geometry (COM-GEOM) GIFT Computer Code Computer Target Description 2& AfTNACT (Cmne M feerve shb N ,neemssalyan ify by block number) A...input to the GIFT computer code to generate target vulnerability data. F.a- 4 ono OF I NOV 5S OLETE UNCLASSIFIED SECUOITY CLASSIFICATION OF THIS PAGE...Combinatorial Geometry (COM-GEOM) desrription. The "Geometric Information for Tarqets" ( GIFT ) computer code accepts the CO!-GEOM description and
Optimization of Highway Work Zone Decisions Considering Short-Term and Long-Term Impacts

DTIC Science & Technology

2010-01-01

strategies which can minimize the one-time work zone cost. Considering the complex and combinatorial nature of this optimization problem, a heuristic...combination of lane closure and traffic control strategies which can minimize the one-time work zone cost. Considering the complex and combinatorial nature ...zone) NV # the number of vehicle classes NPV $ Net Present Value p’(t) % Adjusted traffic diversion rate at time t p(t) % Natural diversion rate
Thermal analysis of combinatorial solid geometry models using SINDA

NASA Technical Reports Server (NTRS)

Gerencser, Diane; Radke, George; Introne, Rob; Klosterman, John; Miklosovic, Dave

1993-01-01

Algorithms have been developed using Monte Carlo techniques to determine the thermal network parameters necessary to perform a finite difference analysis on Combinatorial Solid Geometry (CSG) models. Orbital and laser fluxes as well as internal heat generation are modeled to facilitate satellite modeling. The results of the thermal calculations are used to model the infrared (IR) images of targets and assess target vulnerability. Sample analyses and validation are presented which demonstrate code products.
Combinatorial study of Ni-Ti-Pt ternary metal gate electrodes on HfO{sub 2} for the advanced gate stack

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, K.-S.; Green, M. L.; Suehle, J.

2006-10-02

The authors have fabricated combinatorial Ni-Ti-Pt ternary metal gate thin film libraries on HfO{sub 2} using magnetron co-sputtering to investigate flatband voltage shift ({delta}V{sub fb}), work function ({phi}{sub m}), and leakage current density (J{sub L}) variations. A more negative {delta}V{sub fb} is observed close to the Ti-rich corner than at the Ni- and Pt-rich corners, implying smaller {phi}{sub m} near the Ti-rich corners and higher {phi}{sub m} near the Ni- and Pt-rich corners. In addition, measured J{sub L} values can be explained consistently with the observed {phi}{sub m} variations. Combinatorial methodologies prove to be useful in surveying the large compositionalmore » space of ternary alloy metal gate electrode systems.« less
DNA-Encoded Dynamic Combinatorial Chemical Libraries.

PubMed

Reddavide, Francesco V; Lin, Weilin; Lehnert, Sarah; Zhang, Yixin

2015-06-26

Dynamic combinatorial chemistry (DCC) explores the thermodynamic equilibrium of reversible reactions. Its application in the discovery of protein binders is largely limited by difficulties in the analysis of complex reaction mixtures. DNA-encoded chemical library (DECL) technology allows the selection of binders from a mixture of up to billions of different compounds; however, experimental results often show low a signal-to-noise ratio and poor correlation between enrichment factor and binding affinity. Herein we describe the design and application of DNA-encoded dynamic combinatorial chemical libraries (EDCCLs). Our experiments have shown that the EDCCL approach can be used not only to convert monovalent binders into high-affinity bivalent binders, but also to cause remarkably enhanced enrichment of potent bivalent binders by driving their in situ synthesis. We also demonstrate the application of EDCCLs in DNA-templated chemical reactions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Learning to Predict Combinatorial Structures

NASA Astrophysics Data System (ADS)

Vembu, Shankar

2009-12-01

The major challenge in designing a discriminative learning algorithm for predicting structured data is to address the computational issues arising from the exponential size of the output space. Existing algorithms make different assumptions to ensure efficient, polynomial time estimation of model parameters. For several combinatorial structures, including cycles, partially ordered sets, permutations and other graph classes, these assumptions do not hold. In this thesis, we address the problem of designing learning algorithms for predicting combinatorial structures by introducing two new assumptions: (i) The first assumption is that a particular counting problem can be solved efficiently. The consequence is a generalisation of the classical ridge regression for structured prediction. (ii) The second assumption is that a particular sampling problem can be solved efficiently. The consequence is a new technique for designing and analysing probabilistic structured prediction models. These results can be applied to solve several complex learning problems including but not limited to multi-label classification, multi-category hierarchical classification, and label ranking.
Discovery of Antibiotics-derived Polymers for Gene Delivery using Combinatorial Synthesis and Cheminformatics Modeling

PubMed Central

Potta, Thrimoorthy; Zhen, Zhuo; Grandhi, Taraka Sai Pavan; Christensen, Matthew D.; Ramos, James; Breneman, Curt M.; Rege, Kaushal

2014-01-01

We describe the combinatorial synthesis and cheminformatics modeling of aminoglycoside antibiotics-derived polymers for transgene delivery and expression. Fifty-six polymers were synthesized by polymerizing aminoglycosides with diglycidyl ether cross-linkers. Parallel screening resulted in identification of several lead polymers that resulted in high transgene expression levels in cells. The role of polymer physicochemical properties in determining efficacy of transgene expression was investigated using Quantitative Structure-Activity Relationship (QSAR) cheminformatics models based on Support Vector Regression (SVR) and ‘building block’ polymer structures. The QSAR model exhibited high predictive ability, and investigation of descriptors in the model, using molecular visualization and correlation plots, indicated that physicochemical attributes related to both, aminoglycosides and diglycidyl ethers facilitated transgene expression. This work synergistically combines combinatorial synthesis and parallel screening with cheminformatics-based QSAR models for discovery and physicochemical elucidation of effective antibiotics-derived polymers for transgene delivery in medicine and biotechnology. PMID:24331709
Optimal weighted combinatorial forecasting model of QT dispersion of ECGs in Chinese adults.

PubMed

Wen, Zhang; Miao, Ge; Xinlei, Liu; Minyi, Cen

2016-07-01

This study aims to provide a scientific basis for unifying the reference value standard of QT dispersion of ECGs in Chinese adults. Three predictive models including regression model, principal component model, and artificial neural network model are combined to establish the optimal weighted combination model. The optimal weighted combination model and single model are verified and compared. Optimal weighted combinatorial model can reduce predicting risk of single model and improve the predicting precision. The reference value of geographical distribution of Chinese adults' QT dispersion was precisely made by using kriging methods. When geographical factors of a particular area are obtained, the reference value of QT dispersion of Chinese adults in this area can be estimated by using optimal weighted combinatorial model and reference value of the QT dispersion of Chinese adults anywhere in China can be obtained by using geographical distribution figure as well.
Development of New Sensing Materials Using Combinatorial and High-Throughput Experimentation

NASA Astrophysics Data System (ADS)

Potyrailo, Radislav A.; Mirsky, Vladimir M.

New sensors with improved performance characteristics are needed for applications as diverse as bedside continuous monitoring, tracking of environmental pollutants, monitoring of food and water quality, monitoring of chemical processes, and safety in industrial, consumer, and automotive settings. Typical requirements in sensor improvement are selectivity, long-term stability, sensitivity, response time, reversibility, and reproducibility. Design of new sensing materials is the important cornerstone in the effort to develop new sensors. Often, sensing materials are too complex to predict their performance quantitatively in the design stage. Thus, combinatorial and high-throughput experimentation methodologies provide an opportunity to generate new required data to discover new sensing materials and/or to optimize existing material compositions. The goal of this chapter is to provide an overview of the key concepts of experimental development of sensing materials using combinatorial and high-throughput experimentation tools, and to promote additional fruitful interactions between computational scientists and experimentalists.
Fast Modeling of Binding Affinities by Means of Superposing Significant Interaction Rules (SSIR) Method

PubMed Central

Besalú, Emili

2016-01-01

The Superposing Significant Interaction Rules (SSIR) method is described. It is a general combinatorial and symbolic procedure able to rank compounds belonging to combinatorial analogue series. The procedure generates structure-activity relationship (SAR) models and also serves as an inverse SAR tool. The method is fast and can deal with large databases. SSIR operates from statistical significances calculated from the available library of compounds and according to the previously attached molecular labels of interest or non-interest. The required symbolic codification allows dealing with almost any combinatorial data set, even in a confidential manner, if desired. The application example categorizes molecules as binding or non-binding, and consensus ranking SAR models are generated from training and two distinct cross-validation methods: leave-one-out and balanced leave-two-out (BL2O), the latter being suited for the treatment of binary properties. PMID:27240346
Review of high-throughput techniques for detecting solid phase Transformation from material libraries produced by combinatorial methods

NASA Technical Reports Server (NTRS)

Lee, Jonathan A.

2005-01-01

High-throughput measurement techniques are reviewed for solid phase transformation from materials produced by combinatorial methods, which are highly efficient concepts to fabricate large variety of material libraries with different compositional gradients on a single wafer. Combinatorial methods hold high potential for reducing the time and costs associated with the development of new materials, as compared to time-consuming and labor-intensive conventional methods that test large batches of material, one- composition at a time. These high-throughput techniques can be automated to rapidly capture and analyze data, using the entire material library on a single wafer, thereby accelerating the pace of materials discovery and knowledge generation for solid phase transformations. The review covers experimental techniques that are applicable to inorganic materials such as shape memory alloys, graded materials, metal hydrides, ferric materials, semiconductors and industrial alloys.
Exploiting Quantum Resonance to Solve Combinatorial Problems

NASA Technical Reports Server (NTRS)

Zak, Michail; Fijany, Amir

2006-01-01

Quantum resonance would be exploited in a proposed quantum-computing approach to the solution of combinatorial optimization problems. In quantum computing in general, one takes advantage of the fact that an algorithm cannot be decoupled from the physical effects available to implement it. Prior approaches to quantum computing have involved exploitation of only a subset of known quantum physical effects, notably including parallelism and entanglement, but not including resonance. In the proposed approach, one would utilize the combinatorial properties of tensor-product decomposability of unitary evolution of many-particle quantum systems for physically simulating solutions to NP-complete problems (a class of problems that are intractable with respect to classical methods of computation). In this approach, reinforcement and selection of a desired solution would be executed by means of quantum resonance. Classes of NP-complete problems that are important in practice and could be solved by the proposed approach include planning, scheduling, search, and optimal design.

Combinatorial studies of (1-x)Na0.5Bi0.5TiO3-xBaTiO3 thin-film chips

NASA Astrophysics Data System (ADS)

Cheng, Hong-Wei; Zhang, Xue-Jin; Zhang, Shan-Tao; Feng, Yan; Chen, Yan-Feng; Liu, Zhi-Guo; Cheng, Guang-Xi

2004-09-01

Applying a combinatorial methodology, (1-x)Na0.5Bi0.5TiO3-xBaTiO3 (NBT-BT) thin-film chips were fabricated on (001)-LaAlO3 substrates by pulsed laser deposition with a few quaternary masks. A series of NBT-BT library with the composition of BT ranged from 0 to 44% was obtained with uniform composition and well crystallinity. The relation between the concentration of NBT-BT and their structural and dielectric properties were investigated by x-ray diffraction (XRD), evanescent microwave probe, atomic force microscopy, and Raman spectroscopy. An obvious morphotropic phase boundary (MPB) was established to be about 9% BT by XRD, Raman frequency shift, and dielectric anomaly, different from the well-known MPB of the materials. The result shows the high efficiency of combinatorial method in searching new relaxor ferroelectrics.
A noisy chaotic neural network for solving combinatorial optimization problems: stochastic chaotic simulated annealing.

PubMed

Wang, Lipo; Li, Sa; Tian, Fuyu; Fu, Xiuju

2004-10-01

Recently Chen and Aihara have demonstrated both experimentally and mathematically that their chaotic simulated annealing (CSA) has better search ability for solving combinatorial optimization problems compared to both the Hopfield-Tank approach and stochastic simulated annealing (SSA). However, CSA may not find a globally optimal solution no matter how slowly annealing is carried out, because the chaotic dynamics are completely deterministic. In contrast, SSA tends to settle down to a global optimum if the temperature is reduced sufficiently slowly. Here we combine the best features of both SSA and CSA, thereby proposing a new approach for solving optimization problems, i.e., stochastic chaotic simulated annealing, by using a noisy chaotic neural network. We show the effectiveness of this new approach with two difficult combinatorial optimization problems, i.e., a traveling salesman problem and a channel assignment problem for cellular mobile communications.
Temporal-pattern similarity analysis reveals the beneficial and detrimental effects of context reinstatement on human memory.

PubMed

Staudigl, Tobias; Vollmar, Christian; Noachtar, Soheyl; Hanslmayr, Simon

2015-04-01

A powerful force in human memory is the context in which memories are encoded (Tulving and Thomson, 1973). Several studies suggest that the reinstatement of neural encoding patterns is beneficial for memory retrieval (Manning et al., 2011; Staresina et al., 2012; Jafarpour et al., 2014). However, reinstatement of the original encoding context is not always helpful, for instance, when retrieving a memory in a different contextual situation (Smith and Vela, 2001). It is an open question whether such context-dependent memory effects can be captured by the reinstatement of neural patterns. We investigated this question by applying temporal and spatial pattern similarity analysis in MEG and intracranial EEG in a context-match paradigm. Items (words) were tagged by individual dynamic context stimuli (movies). The results show that beta oscillatory phase in visual regions and the parahippocampal cortex tracks the incidental reinstatement of individual context trajectories on a single-trial level. Crucially, memory benefitted from reinstatement when the encoding and retrieval contexts matched but suffered from reinstatement when the contexts did not match. Copyright © 2015 the authors 0270-6474/15/355373-12$15.00/0.
Fast alignment-free sequence comparison using spaced-word frequencies.

PubMed

Leimeister, Chris-Andre; Boden, Marcus; Horwege, Sebastian; Lindner, Sebastian; Morgenstern, Burkhard

2014-07-15

Alignment-free methods for sequence comparison are increasingly used for genome analysis and phylogeny reconstruction; they circumvent various difficulties of traditional alignment-based approaches. In particular, alignment-free methods are much faster than pairwise or multiple alignments. They are, however, less accurate than methods based on sequence alignment. Most alignment-free approaches work by comparing the word composition of sequences. A well-known problem with these methods is that neighbouring word matches are far from independent. To reduce the statistical dependency between adjacent word matches, we propose to use 'spaced words', defined by patterns of 'match' and 'don't care' positions, for alignment-free sequence comparison. We describe a fast implementation of this approach using recursive hashing and bit operations, and we show that further improvements can be achieved by using multiple patterns instead of single patterns. To evaluate our approach, we use spaced-word frequencies as a basis for fast phylogeny reconstruction. Using real-world and simulated sequence data, we demonstrate that our multiple-pattern approach produces better phylogenies than approaches relying on contiguous words. Our program is freely available at http://spaced.gobics.de/. © The Author 2014. Published by Oxford University Press.
Meta-image navigation augmenters for GPS denied mountain navigation of small UAS

NASA Astrophysics Data System (ADS)

Wang, Teng; ćelik, Koray; Somani, Arun K.

2014-06-01

We present a novel approach to use mountain drainage patterns for GPS-Denied navigation of small unmanned aerial systems (UAS) such as the ScanEagle, utilizing a down-looking fixed focus monocular imager. Our proposal allows extension of missions to GPS-denied mountain areas, with no assumption of human-made geographic objects. We leverage the analogy between mountain drainage patterns, human arteriograms, and human fingerprints, to match local drainage patterns to Graphics Processing Unit (GPU) rendered parallax occlusion maps of geo-registered radar returns (GRRR). Details of our actual GPU algorithm is beyond the subject of this paper, and is planned as a future paper. The matching occurs in real-time, while GRRR data is loaded on-board the aircraft pre-mission, so as not to require a scanning aperture radar during the mission. For recognition purposes, we represent a given mountain area with a set of spatially distributed mountain minutiae, i.e., details found in the drainage patterns, so that conventional minutiae-based fingerprint matching approaches can be used to match real-time camera image against template images in the training set. We use medical arteriography processing techniques to extract the patterns. The minutiae-based representation of mountains is achieved by first exposing mountain ridges and valleys with a series of filters and then extracting mountain minutiae from these ridges/valleys. Our results are experimentally validated on actual terrain data and show the effectiveness of minutiae-based mountain representation method. Furthermore, we study how to select landmarks for UAS navigation based on the proposed mountain representation and give a set of examples to show its feasibility. This research was in part funded by Rockwell Collins Inc.
Mean-field message-passing equations in the Hopfield model and its generalizations

NASA Astrophysics Data System (ADS)

Mézard, Marc

2017-02-01

Motivated by recent progress in using restricted Boltzmann machines as preprocessing algorithms for deep neural network, we revisit the mean-field equations [belief-propagation and Thouless-Anderson Palmer (TAP) equations] in the best understood of such machines, namely the Hopfield model of neural networks, and we explicit how they can be used as iterative message-passing algorithms, providing a fast method to compute the local polarizations of neurons. In the "retrieval phase", where neurons polarize in the direction of one memorized pattern, we point out a major difference between the belief propagation and TAP equations: The set of belief propagation equations depends on the pattern which is retrieved, while one can use a unique set of TAP equations. This makes the latter method much better suited for applications in the learning process of restricted Boltzmann machines. In the case where the patterns memorized in the Hopfield model are not independent, but are correlated through a combinatorial structure, we show that the TAP equations have to be modified. This modification can be seen either as an alteration of the reaction term in TAP equations or, more interestingly, as the consequence of message passing on a graphical model with several hidden layers, where the number of hidden layers depends on the depth of the correlations in the memorized patterns. This layered structure is actually necessary when one deals with more general restricted Boltzmann machines.
Punctuated evolution and robustness in morphogenesis

PubMed Central

Grigoriev, D.; Reinitz, J.; Vakulenko, S.; Weber, A.

2014-01-01

This paper presents an analytic approach to the pattern stability and evolution problem in morphogenesis. The approach used here is based on the ideas from the gene and neural network theory. We assume that gene networks contain a number of small groups of genes (called hubs) controlling morphogenesis process. Hub genes represent an important element of gene network architecture and their existence is empirically confirmed. We show that hubs can stabilize morphogenetic pattern and accelerate the morphogenesis. The hub activity exhibits an abrupt change depending on the mutation frequency. When the mutation frequency is small, these hubs suppress all mutations and gene product concentrations do not change, thus, the pattern is stable. When the environmental pressure increases and the population needs new genotypes, the genetic drift and other effects increase the mutation frequency. For the frequencies that are larger than a critical amount the hubs turn off; and as a result, many mutations can affect phenotype. This effect can serve as an engine for evolution. We show that this engine is very effective: the evolution acceleration is an exponential function of gene redundancy. Finally, we show that the Eldredge-Gould concept of punctuated evolution results from the network architecture, which provides fast evolution, control of evolvability, and pattern robustness. To describe analytically the effect of exponential acceleration, we use mathematical methods developed recently for hard combinatorial problems, in particular, for so-called k-SAT problem, and numerical simulations. PMID:24996115
The use of network analysis to study complex animal communication systems: a study on nightingale song.

PubMed

Weiss, Michael; Hultsch, Henrike; Adam, Iris; Scharff, Constance; Kipper, Silke

2014-06-22

The singing of song birds can form complex signal systems comprised of numerous subunits sung with distinct combinatorial properties that have been described as syntax-like. This complexity has inspired inquiries into similarities of bird song to human language; but the quantitative analysis and description of song sequences is a challenging task. In this study, we analysed song sequences of common nightingales (Luscinia megarhynchos) by means of a network analysis. We translated long nocturnal song sequences into networks of song types with song transitions as connectors. As network measures, we calculated shortest path length and transitivity and identified the 'small-world' character of nightingale song networks. Besides comparing network measures with conventional measures of song complexity, we also found a correlation between network measures and age of birds. Furthermore, we determined the numbers of in-coming and out-going edges of each song type, characterizing transition patterns. These transition patterns were shared across males for certain song types. Playbacks with different transition patterns provided first evidence that these patterns are responded to differently and thus play a role in singing interactions. We discuss potential functions of the network properties of song sequences in the framework of vocal leadership. Network approaches provide biologically meaningful parameters to describe the song structure of species with extremely large repertoires and complex rules of song retrieval.
The use of network analysis to study complex animal communication systems: a study on nightingale song

PubMed Central

Weiss, Michael; Hultsch, Henrike; Adam, Iris; Scharff, Constance; Kipper, Silke

2014-01-01

The singing of song birds can form complex signal systems comprised of numerous subunits sung with distinct combinatorial properties that have been described as syntax-like. This complexity has inspired inquiries into similarities of bird song to human language; but the quantitative analysis and description of song sequences is a challenging task. In this study, we analysed song sequences of common nightingales (Luscinia megarhynchos) by means of a network analysis. We translated long nocturnal song sequences into networks of song types with song transitions as connectors. As network measures, we calculated shortest path length and transitivity and identified the ‘small-world’ character of nightingale song networks. Besides comparing network measures with conventional measures of song complexity, we also found a correlation between network measures and age of birds. Furthermore, we determined the numbers of in-coming and out-going edges of each song type, characterizing transition patterns. These transition patterns were shared across males for certain song types. Playbacks with different transition patterns provided first evidence that these patterns are responded to differently and thus play a role in singing interactions. We discuss potential functions of the network properties of song sequences in the framework of vocal leadership. Network approaches provide biologically meaningful parameters to describe the song structure of species with extremely large repertoires and complex rules of song retrieval. PMID:24807258
Microfluidic impact printer with interchangeable cartridges for versatile non-contact multiplexed micropatterning

PubMed Central

Ding, Yuzhe; Huang, Eric; Lam, Kit S.; Pan, Tingrui

2015-01-01

Biopatterning has been increasingly used for well-defined cellular microenvironment, patterned surface topology, and guided biological cues; however, it meets additional challenges on biocompatibility, temperature and chemical sensitivity and limited reagent volume. In this paper, we target at combining the desired features from the non-contact inkjet printing and the dot-matrix impact printing to establish a versatile multiplexed micropatterning platform, referred to as Microfluidic Impact Printer (MI-Printer), for emerging biomedical applications. Using this platform, we can achieve the distinct features of no cross-contamination, minute volume manipulation with minimal dead volume, high-throughput and biocompatible printing process, multiplexed patterning with automatic alignment, printing availability for complex medium (cell suspension or colloidal solutions), interchangeable/disposable microfluidic cartridge design with out-of-cleanroom microfabrication, simple printing system assembly and configuration, all highly desirable towards biological applications. Specifically, the printing resolution of the MI-printer platform has been experimentally characterized and theoretically analyzed. Printed droplets with 80µm in diameter have been repeatedly obtained. Furthermore, two unique features of MI-printer platform, multiplexed printing and self-alignment printing, have been successfully experimentally demonstrated (less than 10µm misalignment). In addition, combinatorial patterning and biological patterning, which utilizes the multiplexed and self-alignment printing nature of the MI-printer, have been devised to demonstrate the applicability of this robust printing technique for emerging biomedical applications. PMID:23525299
The spatiotemporal order of signaling events unveils the logic of development signaling.

PubMed

Zhu, Hao; Owen, Markus R; Mao, Yanlan

2016-08-01

Animals from worms and insects to birds and mammals show distinct body plans; however, the embryonic development of diverse body plans with tissues and organs within is controlled by a surprisingly few signaling pathways. It is well recognized that combinatorial use of and dynamic interactions among signaling pathways follow specific logic to control complex and accurate developmental signaling and patterning, but it remains elusive what such logic is, or even, what it looks like. We have developed a computational model for Drosophila eye development with innovated methods to reveal how interactions among multiple pathways control the dynamically generated hexagonal array of R8 cells. We obtained two novel findings. First, the coupling between the long-range inductive signals produced by the proneural Hh signaling and the short-range restrictive signals produced by the antineural Notch and EGFR signaling is essential for generating accurately spaced R8s. Second, the spatiotemporal orders of key signaling events reveal a robust pattern of lateral inhibition conducted by Ato-coordinated Notch and EGFR signaling to collectively determine R8 patterning. This pattern, stipulating the orders of signaling and comparable to the protocols of communication, may help decipher the well-appreciated but poorly defined logic of developmental signaling. The model is available upon request. hao.zhu@ymail.com Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.
The spatiotemporal order of signaling events unveils the logic of development signaling

PubMed Central

Zhu, Hao; Owen, Markus R.; Mao, Yanlan

2016-01-01

Motivation: Animals from worms and insects to birds and mammals show distinct body plans; however, the embryonic development of diverse body plans with tissues and organs within is controlled by a surprisingly few signaling pathways. It is well recognized that combinatorial use of and dynamic interactions among signaling pathways follow specific logic to control complex and accurate developmental signaling and patterning, but it remains elusive what such logic is, or even, what it looks like. Results: We have developed a computational model for Drosophila eye development with innovated methods to reveal how interactions among multiple pathways control the dynamically generated hexagonal array of R8 cells. We obtained two novel findings. First, the coupling between the long-range inductive signals produced by the proneural Hh signaling and the short-range restrictive signals produced by the antineural Notch and EGFR signaling is essential for generating accurately spaced R8s. Second, the spatiotemporal orders of key signaling events reveal a robust pattern of lateral inhibition conducted by Ato-coordinated Notch and EGFR signaling to collectively determine R8 patterning. This pattern, stipulating the orders of signaling and comparable to the protocols of communication, may help decipher the well-appreciated but poorly defined logic of developmental signaling. Availability and implementation: The model is available upon request. Contact: hao.zhu@ymail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153573
Enhanced visual processing contributes to matrix reasoning in autism

PubMed Central

Soulières, Isabelle; Dawson, Michelle; Samson, Fabienne; Barbeau, Elise B.; Sahyoun, Cherif; Strangman, Gary E.; Zeffiro, Thomas A.; Mottron, Laurent

2009-01-01

Recent behavioral investigations have revealed that autistics perform more proficiently on Raven's Standard Progressive Matrices (RSPM) than would be predicted by their Wechsler intelligence scores. A widely-used test of fluid reasoning and intelligence, the RSPM assays abilities to flexibly infer rules, manage goal hierarchies, and perform high-level abstractions. The neural substrates for these abilities are known to encompass a large frontoparietal network, with different processing models placing variable emphasis on the specific roles of the prefrontal or posterior regions. We used functional magnetic resonance imaging to explore the neural bases of autistics' RSPM problem solving. Fifteen autistic and eighteen non-autistic participants, matched on age, sex, manual preference and Wechsler IQ, completed 60 self-paced randomly-ordered RSPM items along with a visually similar 60-item pattern matching comparison task. Accuracy and response times did not differ between groups in the pattern matching task. In the RSPM task, autistics performed with similar accuracy, but with shorter response times, compared to their non-autistic controls. In both the entire sample and a subsample of participants additionally matched on RSPM performance to control for potential response time confounds, neural activity was similar in both groups for the pattern matching task. However, for the RSPM task, autistics displayed relatively increased task-related activity in extrastriate areas (BA18), and decreased activity in the lateral prefrontal cortex (BA9) and the medial posterior parietal cortex (BA7). Visual processing mechanisms may therefore play a more prominent role in reasoning in autistics. PMID:19530215
Behavioral and Temporal Pattern Detection Within Financial Data With Hidden Information

DTIC Science & Technology

2012-02-01

probabilistic pattern detector to monitor the pattern. 15. SUBJECT TERMS Runtime verification, Hidden data, Hidden Markov models, Formal specifications...sequences in many other fields besides financial systems [L, TV, LC, LZ ]. Rather, the technique suggested in this paper is positioned as a hybrid...operation of the pattern detector . Section 7 describes the operation of the probabilistic pattern-matching monitor, and section 8 describes three
Empirical tests of the role of disruptive coloration in reducing detectability

PubMed Central

Fraser, Stewart; Callahan, Alison; Klassen, Dana; Sherratt, Thomas N

2007-01-01

Disruptive patterning is a potentially universal camouflage technique that is thought to enhance concealment by rendering the detection of body shapes more difficult. In a recent series of field experiments, artificial moths with markings that extended to the edges of their ‘wings’ survived at higher rates than moths with the same edge patterns inwardly displaced. While this result seemingly indicates a benefit to obscuring edges, it is possible that the higher density markings of the inwardly displaced patterns concomitantly reduced their extent of background matching. Likewise, it has been suggested that the mealworm baits placed on the artificial moths could have created differential contrasts with different moth patterns. To address these concerns, we conducted controlled trials in which human subjects searched for computer-generated moth images presented against images of oak trees. Moths with edge-extended disruptive markings survived at higher rates, and took longer to find, than all other moth types, whether presented sequentially or simultaneously. However, moths with no edge markings and reduced interior pattern density survived better than their high-density counterparts, indicating that background matching may have played a so-far unrecognized role in the earlier experiments. Our disruptively patterned non-background-matching moths also had the lowest overall survivorship, indicating that disruptive coloration alone may not provide significant protection from predators. Collectively, our results provide independent support for the survival value of disruptive markings and demonstrate that there are common features in human and avian perception of camouflage. PMID:17360282
A spot-matching method using cumulative frequency matrix in 2D gel images

PubMed Central

Han, Chan-Myeong; Park, Joon-Ho; Chang, Chu-Seok; Ryoo, Myung-Chun

2014-01-01

A new method for spot matching in two-dimensional gel electrophoresis images using a cumulative frequency matrix is proposed. The method improves on the weak points of the previous method called ‘spot matching by topological patterns of neighbour spots’. It accumulates the frequencies of neighbour spot pairs produced through the entire matching process and determines spot pairs one by one in order of higher frequency. Spot matching by frequencies of neighbour spot pairs shows a fairly better performance. However, it can give researchers a hint for whether the matching results can be trustworthy or not, which can save researchers a lot of effort for verification of the results. PMID:26019609
Engineering of routes to heparin and related polysaccharides.

PubMed

Bhaskar, Ujjwal; Sterner, Eric; Hickey, Anne Marie; Onishi, Akihiro; Zhang, Fuming; Dordick, Jonathan S; Linhardt, Robert J

2012-01-01

Anticoagulant heparin has been shown to possess important biological functions that vary according to its fine structure. Variability within heparin's structure occurs owing to its biosynthesis and animal tissue-based recovery and adds another dimension to its complex polymeric structure. The structural variations in chain length and sulfation patterns mediate its interaction with many heparin-binding proteins, thereby eliciting complex biological responses. The advent of novel chemical and enzymatic approaches for polysaccharide synthesis coupled with high throughput combinatorial approaches for drug discovery have facilitated an increased effort to understand heparin's structure-activity relationships. An improved understanding would offer potential for new therapeutic development through the engineering of polysaccharides. Such a bioengineering approach requires the amalgamation of several different disciplines, including carbohydrate synthesis, applied enzymology, metabolic engineering, and process biochemistry.
The successively temporal error concealment algorithm using error-adaptive block matching principle

NASA Astrophysics Data System (ADS)

Lee, Yu-Hsuan; Wu, Tsai-Hsing; Chen, Chao-Chyun

2014-09-01

Generally, the temporal error concealment (TEC) adopts the blocks around the corrupted block (CB) as the search pattern to find the best-match block in previous frame. Once the CB is recovered, it is referred to as the recovered block (RB). Although RB can be the search pattern to find the best-match block of another CB, RB is not the same as its original block (OB). The error between the RB and its OB limits the performance of TEC. The successively temporal error concealment (STEC) algorithm is proposed to alleviate this error. The STEC procedure consists of tier-1 and tier-2. The tier-1 divides a corrupted macroblock into four corrupted 8 × 8 blocks and generates a recovering order for them. The corrupted 8 × 8 block with the first place of recovering order is recovered in tier-1, and remaining 8 × 8 CBs are recovered in tier-2 along the recovering order. In tier-2, the error-adaptive block matching principle (EA-BMP) is proposed for the RB as the search pattern to recover remaining corrupted 8 × 8 blocks. The proposed STEC outperforms sophisticated TEC algorithms on average PSNR by 0.3 dB on the packet error rate of 20% at least.
Changeable camouflage: how well can flounder resemble the colour and spatial scale of substrates in their natural habitats?

PubMed Central

Akkaynak, Derya; Siemann, Liese A.; Barbosa, Alexandra

2017-01-01

Flounder change colour and pattern for camouflage. We used a spectrometer to measure reflectance spectra and a digital camera to capture body patterns of two flounder species camouflaged on four natural backgrounds of different spatial scale (sand, small gravel, large gravel and rocks). We quantified the degree of spectral match between flounder and background relative to the situation of perfect camouflage in which flounder and background were assumed to have identical spectral distribution. Computations were carried out for three biologically relevant observers: monochromatic squid, dichromatic crab and trichromatic guitarfish. Our computations present a new approach to analysing datasets with multiple spectra that have large variance. Furthermore, to investigate the spatial match between flounder and background, images of flounder patterns were analysed using a custom program originally developed to study cuttlefish camouflage. Our results show that all flounder and background spectra fall within the same colour gamut and that, in terms of different observer visual systems, flounder matched most substrates in luminance and colour contrast. Flounder matched the spatial scales of all substrates except for rocks. We discuss findings in terms of flounder biology; furthermore, we discuss our methodology in light of hyperspectral technologies that combine high-resolution spectral and spatial imaging. PMID:28405370
Changeable camouflage: how well can flounder resemble the colour and spatial scale of substrates in their natural habitats?

PubMed

Akkaynak, Derya; Siemann, Liese A; Barbosa, Alexandra; Mäthger, Lydia M

2017-03-01

Flounder change colour and pattern for camouflage. We used a spectrometer to measure reflectance spectra and a digital camera to capture body patterns of two flounder species camouflaged on four natural backgrounds of different spatial scale (sand, small gravel, large gravel and rocks). We quantified the degree of spectral match between flounder and background relative to the situation of perfect camouflage in which flounder and background were assumed to have identical spectral distribution. Computations were carried out for three biologically relevant observers: monochromatic squid, dichromatic crab and trichromatic guitarfish. Our computations present a new approach to analysing datasets with multiple spectra that have large variance. Furthermore, to investigate the spatial match between flounder and background, images of flounder patterns were analysed using a custom program originally developed to study cuttlefish camouflage. Our results show that all flounder and background spectra fall within the same colour gamut and that, in terms of different observer visual systems, flounder matched most substrates in luminance and colour contrast. Flounder matched the spatial scales of all substrates except for rocks. We discuss findings in terms of flounder biology; furthermore, we discuss our methodology in light of hyperspectral technologies that combine high-resolution spectral and spatial imaging.

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