Directory of Open Access Journals (Sweden)
Armand Paauw
Full Text Available Horizontal gene transfer is a key step in the evolution of Enterobacteriaceae. By acquiring virulence determinants of foreign origin, commensals can evolve into pathogens. In Enterobacteriaceae, horizontal transfer of these virulence determinants is largely dependent on transfer by plasmids, phages, genomic islands (GIs and genomic modules (GMs. The High Pathogenicity Island (HPI is a GI encoding virulence genes that can be transferred between different Enterobacteriaceae. We investigated the HPI because it was present in an Enterobacter hormaechei outbreak strain (EHOS. Genome sequence analysis showed that the EHOS contained an integration site for mobile elements and harbored two GIs and three putative GMs, including a new variant of the HPI (HPI-ICEEh1. We demonstrate, for the first time, that combinatorial transfers of GIs and GMs between Enterobacter cloacae complex isolates must have occurred. Furthermore, the excision and circularization of several combinations of the GIs and GMs was demonstrated. Because of its flexibility, the multiple integration site of mobile DNA can be considered an integration hotspot (IHS that increases the genomic plasticity of the bacterium. Multiple combinatorial transfers of diverse combinations of the HPI and other genomic elements among Enterobacteriaceae may accelerate the generation of new pathogenic strains.
Balancing focused combinatorial libraries based on multiple GPCR ligands
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.
Regnier, David; Lacroix, Denis; Scamps, Guillaume; Hashimoto, Yukio
2018-03-01
In a mean-field description of superfluidity, particle number and gauge angle are treated as quasiclassical conjugated variables. This level of description was recently used to describe nuclear reactions around the Coulomb barrier. Important effects of the relative gauge angle between two identical superfluid nuclei (symmetric collisions) on transfer probabilities and fusion barrier have been uncovered. A theory making contact with experiments should at least average over different initial relative gauge-angles. In the present work, we propose a new approach to obtain the multiple pair transfer probabilities between superfluid systems. This method, called phase-space combinatorial (PSC) technique, relies both on phase-space averaging and combinatorial arguments to infer the full pair transfer probability distribution at the cost of multiple mean-field calculations only. After benchmarking this approach in a schematic model, we apply it to the collision 20O+20O at various energies below the Coulomb barrier. The predictions for one pair transfer are similar to results obtained with an approximated projection method, whereas significant differences are found for two pairs transfer. Finally, we investigated the applicability of the PSC method to the contact between nonidentical superfluid systems. A generalization of the method is proposed and applied to the schematic model showing that the pair transfer probabilities are reasonably reproduced. The applicability of the PSC method to asymmetric nuclear collisions is investigated for the 14O+20O collision and it turns out that unrealistically small single- and multiple pair transfer probabilities are obtained. This is explained by the fact that relative gauge angle play in this case a minor role in the particle transfer process compared to other mechanisms, such as equilibration of the charge/mass ratio. We conclude that the best ground for probing gauge-angle effects in nuclear reaction and/or for applying the proposed
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…
Integrating Multiple Data Sources for Combinatorial Marker Discovery: A Study in Tumorigenesis.
Bandyopadhyay, Sanghamitra; Mallik, Saurav
2018-01-01
Identification of combinatorial markers from multiple data sources is a challenging task in bioinformatics. Here, we propose a novel computational framework for identifying significant combinatorial markers ( s) using both gene expression and methylation data. The gene expression and methylation data are integrated into a single continuous data as well as a (post-discretized) boolean data based on their intrinsic (i.e., inverse) relationship. A novel combined score of methylation and expression data (viz., ) is introduced which is computed on the integrated continuous data for identifying initial non-redundant set of genes. Thereafter, (maximal) frequent closed homogeneous genesets are identified using a well-known biclustering algorithm applied on the integrated boolean data of the determined non-redundant set of genes. A novel sample-based weighted support ( ) is then proposed that is consecutively calculated on the integrated boolean data of the determined non-redundant set of genes in order to identify the non-redundant significant genesets. The top few resulting genesets are identified as potential s. Since our proposed method generates a smaller number of significant non-redundant genesets than those by other popular methods, the method is much faster than the others. Application of the proposed technique on an expression and a methylation data for Uterine tumor or Prostate Carcinoma produces a set of significant combination of markers. We expect that such a combination of markers will produce lower false positives than individual markers.
27 CFR 24.282 - Multiple transfers.
2010-04-01
... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Multiple transfers. 24.282 Section 24.282 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT... transfer record for all wine (including distilling material and vinegar stock) transferred by pipeline to...
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).
DEFF Research Database (Denmark)
Nielsen, John
1994-01-01
An overview of combinatorial chemistry is presented. Combinatorial chemistry, sometimes referred to as `irrational drug design,' involves the generation of molecular diversity. The resulting chemical library is then screened for biologically active compounds.......An overview of combinatorial chemistry is presented. Combinatorial chemistry, sometimes referred to as `irrational drug design,' involves the generation of molecular diversity. The resulting chemical library is then screened for biologically active compounds....
Single-embryo transfer versus multiple-embryo transfer.
Gerris, Jan
2009-01-01
Despite the progress made in assisted reproductive technology, live birth rates remain disappointingly low. Multiple-embryo transfer has been an accepted practice with which to increase the success rate. This has led to a higher incidence of multiple-order births compared with natural conception, which not only increase the risk of mortality and morbidity to both mother and children but are also associated with social and economic consequences. Elective single-embryo transfer (eSET) was developed in an effort to increase singleton pregnancies in assisted reproduction. Studies comparing eSET with multiple-embryo transfer highlight the benefit of this approach and suggest that, with careful patient selection and the transfer of good-quality embryos, the risk of a multiple-order pregnancy can be reduced without significantly decreasing live birth rates. Although the use of eSET has gradually increased in clinical practice, its acceptance has been limited by factors such as availability of funding and awareness of the procedure. An open discussion of eSET is warranted in an effort to enable a broader understanding by physicians and patients of the merits of this approach. Ultimately, eSET may provide a more cost-effective, potentially safer approach to patients undergoing assisted reproduction technology.
Wang, Xiong; Zheng, Kai; Zheng, Huayu; Nie, Hongli; Yang, Zujun; Tang, Lixia
2014-12-20
Iterative saturation mutagenesis (ISM) has been shown to be a powerful method for directed evolution. In this study, the approach was modified (termed M-ISM) by combining the single-site saturation mutagenesis method with a DC-Analyzer-facilitated combinatorial strategy, aiming to evolve novel biocatalysts efficiently in the case where multiple sites are targeted simultaneously. Initially, all target sites were explored individually by constructing single-site saturation mutagenesis libraries. Next, the top two to four variants in each library were selected and combined using the DC-Analyzer-facilitated combinatorial strategy. In addition to site-saturation mutagenesis, iterative saturation mutagenesis also needed to be performed. The advantages of M-ISM over ISM were that the screening effort is greatly reduced, and the entire M-ISM procedure was less time-consuming. The M-ISM strategy was successfully applied to the randomization of halohydrin dehalogenase from Agrobacterium radiobacter AD1 (HheC) when five interesting sites were targeted simultaneously. After screening 900 clones in total, six positive mutants were obtained. These mutants exhibited 4.0- to 9.3-fold higher k(cat) values than did the wild-type HheC toward 1,3-dichloro-2-propanol. However, with the ISM strategy, the best hit showed a 5.9-fold higher k(cat) value toward 1,3-DCP than the wild-type HheC, which was obtained after screening 4000 clones from four rounds of mutagenesis. Therefore, M-ISM could serve as a simple and efficient version of ISM for the randomization of target genes with multiple positions of interest.
High performance multiple stream data transfer
International Nuclear Information System (INIS)
Rademakers, F.; Saiz, P.
2001-01-01
The ALICE detector at LHC (CERN), will record raw data at a rate of 1.2 Gigabytes per second. Trying to analyse all this data at CERN will not be feasible. As originally proposed by the MONARC project, data collected at CERN will be transferred to remote centres to use their computing infrastructure. The remote centres will reconstruct and analyse the events, and make available the results. Therefore high-rate data transfer between computing centres (Tiers) will become of paramount importance. The authors will present several tests that have been made between CERN and remote centres in Padova (Italy), Torino (Italy), Catania (Italy), Lyon (France), Ohio (United States), Warsaw (Poland) and Calcutta (India). These tests consisted, in a first stage, of sending raw data from CERN to the remote centres and back, using a ftp method that allows connections of several streams at the same time. Thanks to these multiple streams, it is possible to increase the rate at which the data is transferred. While several 'multiple stream ftp solutions' already exist, the authors' method is based on a parallel socket implementation which allows, besides files, also objects (or any large message) to be send in parallel. A prototype will be presented able to manage different transfers. This is the first step of a system to be implemented that will be able to take care of the connections with the remote centres to exchange data and monitor the status of the transfer
Nonparametric combinatorial sequence models.
Wauthier, Fabian L; Jordan, Michael I; Jojic, Nebojsa
2011-11-01
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 article 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 biological sequence families 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 over sequence representations induced by the prior. By integrating out the posterior, our method compares favorably to leading binding predictors.
Weyl Group Multiple Dirichlet Series Type A Combinatorial Theory (AM-175)
Brubaker, Ben; Friedberg, Solomon
2011-01-01
Weyl group multiple Dirichlet series are generalizations of the Riemann zeta function. Like the Riemann zeta function, they are Dirichlet series with analytic continuation and functional equations, having applications to analytic number theory. By contrast, these Weyl group multiple Dirichlet series may be functions of several complex variables and their groups of functional equations may be arbitrary finite Weyl groups. Furthermore, their coefficients are multiplicative up to roots of unity, generalizing the notion of Euler products. This book proves foundational results about these series an
A Quantitative and Combinatorial Approach to Non-Linear Meanings of Multiplication
Tillema, Erik; Gatza, Andrew
2016-01-01
We provide a conceptual analysis of how combinatorics problems have the potential to support students to establish non-linear meanings of multiplication (NLMM). The problems we analyze we have used in a series of studies with 6th, 8th, and 10th grade students. We situate the analysis in prior work on students' quantitative and multiplicative…
Kodali, Anuradha
In this thesis, we develop dynamic multiple fault diagnosis (DMFD) algorithms to diagnose faults that are sporadic and coupled. Firstly, we formulate a coupled factorial hidden Markov model-based (CFHMM) framework to diagnose dependent faults occurring over time (dynamic case). Here, we implement a mixed memory Markov coupling model to determine the most likely sequence of (dependent) fault states, the one that best explains the observed test outcomes over time. An iterative Gauss-Seidel coordinate ascent optimization method is proposed for solving the problem. A soft Viterbi algorithm is also implemented within the framework for decoding dependent fault states over time. We demonstrate the algorithm on simulated and real-world systems with coupled faults; the results show that this approach improves the correct isolation rate as compared to the formulation where independent fault states are assumed. Secondly, we formulate a generalization of set-covering, termed dynamic set-covering (DSC), which involves a series of coupled set-covering problems over time. The objective of the DSC problem is to infer the most probable time sequence of a parsimonious set of failure sources that explains the observed test outcomes over time. The DSC problem is NP-hard and intractable due to the fault-test dependency matrix that couples the failed tests and faults via the constraint matrix, and the temporal dependence of failure sources over time. Here, the DSC problem is motivated from the viewpoint of a dynamic multiple fault diagnosis problem, but it has wide applications in operations research, for e.g., facility location problem. Thus, we also formulated the DSC problem in the context of a dynamically evolving facility location problem. Here, a facility can be opened, closed, or can be temporarily unavailable at any time for a given requirement of demand points. These activities are associated with costs or penalties, viz., phase-in or phase-out for the opening or closing of a
Napolitano, Roberta; Soesbe, Todd C; De León-Rodríguez, Luis M; Sherry, A Dean; Udugamasooriya, D Gomika
2011-08-24
The sensitivity of magnetic resonance imaging (MRI) contrast agents is highly dependent on the rate of water exchange between the inner sphere of a paramagnetic ion and bulk water. Normally, identifying a paramagnetic complex that has optimal water exchange kinetics is done by synthesizing and testing one compound at a time. We report here a rapid, economical on-bead combinatorial synthesis of a library of imaging agents. Eighty different 1,4,7,10-tetraazacyclododecan-1,4,7,10-tetraacetic acid (DOTA)-tetraamide peptoid derivatives were prepared on beads using a variety of charged, uncharged but polar, hydrophobic, and variably sized primary amines. A single chemical exchange saturation transfer image of the on-bead library easily distinguished those compounds having the most favorable water exchange kinetics. This combinatorial approach will allow rapid screening of libraries of imaging agents to identify the chemical characteristics of a ligand that yield the most sensitive imaging agents. This technique could be automated and readily adapted to other types of MRI or magnetic resonance/positron emission tomography agents as well.
Applications of combinatorial optimization
Paschos, Vangelis Th
2013-01-01
Combinatorial optimization is a multidisciplinary scientific area, lying in the interface of three major scientific domains: mathematics, theoretical computer science and management. The three volumes of the Combinatorial Optimization series aims to cover a wide range of topics in this area. These topics also deal with fundamental notions and approaches as with several classical applications of combinatorial optimization. "Applications of Combinatorial Optimization" is presenting a certain number among the most common and well-known applications of Combinatorial Optimization.
Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species.
Baker, Kate S; Dallman, Timothy J; Field, Nigel; Childs, Tristan; Mitchell, Holly; Day, Martin; Weill, François-Xavier; Lefèvre, Sophie; Tourdjman, Mathieu; Hughes, Gwenda; Jenkins, Claire; Thomson, Nicholas
2018-04-13
Horizontal gene transfer has played a role in developing the global public health crisis of antimicrobial resistance (AMR). However, the dynamics of AMR transfer through bacterial populations and its direct impact on human disease is poorly elucidated. Here, we study parallel epidemic emergences of multiple Shigella species, a priority AMR organism, in men who have sex with men to gain insight into AMR emergence and spread. Using genomic epidemiology, we show that repeated horizontal transfer of a single AMR plasmid among Shigella enhanced existing and facilitated new epidemics. These epidemic patterns contrasted with slighter, slower increases in disease caused by organisms with vertically inherited (chromosomally encoded) AMR. This demonstrates that horizontal transfer of AMR directly affects epidemiological outcomes of globally important AMR pathogens and highlights the need for integration of genomic analyses into all areas of AMR research, surveillance and management.
Laplace transform analysis of a multiplicative asset transfer model
Sokolov, Andrey; Melatos, Andrew; Kieu, Tien
2010-07-01
We analyze a simple asset transfer model in which the transfer amount is a fixed fraction f of the giver’s wealth. The model is analyzed in a new way by Laplace transforming the master equation, solving it analytically and numerically for the steady-state distribution, and exploring the solutions for various values of f∈(0,1). The Laplace transform analysis is superior to agent-based simulations as it does not depend on the number of agents, enabling us to study entropy and inequality in regimes that are costly to address with simulations. We demonstrate that Boltzmann entropy is not a suitable (e.g. non-monotonic) measure of disorder in a multiplicative asset transfer system and suggest an asymmetric stochastic process that is equivalent to the asset transfer model.
Combinatorial microelectrochemistry
International Nuclear Information System (INIS)
Maerkle, Wolfgang; Speiser, Bernd
2005-01-01
Microelectrode steady-state voltammetry is used to monitor on-line the progress of preparative electrolyses. This allows to follow educt and product concentrations as a function of the advance of the electrolysis, end-point detection, calculation of the number of electrons transferred per molecule, and determination of diffusion coefficient ratios for redox couples. The technique is demonstrated by numerical simulation, experiments with mixtures of redox partners, electrolyses in macrocells, and miniaturized electrolyses in vials or the wells of microtiter plates
Concepts of combinatorial optimization
Paschos, Vangelis Th
2014-01-01
Combinatorial optimization is a multidisciplinary scientific area, lying in the interface of three major scientific domains: mathematics, theoretical computer science and management. The three volumes of the Combinatorial Optimization series aim to cover a wide range of topics in this area. These topics also deal with fundamental notions and approaches as with several classical applications of combinatorial optimization.Concepts of Combinatorial Optimization, is divided into three parts:- On the complexity of combinatorial optimization problems, presenting basics about worst-case and randomi
Hu, T C
2002-01-01
Newly enlarged, updated second edition of a valuable text presents algorithms for shortest paths, maximum flows, dynamic programming and backtracking. Also discusses binary trees, heuristic and near optimums, matrix multiplication, and NP-complete problems. 153 black-and-white illus. 23 tables.Newly enlarged, updated second edition of a valuable, widely used text presents algorithms for shortest paths, maximum flows, dynamic programming and backtracking. Also discussed are binary trees, heuristic and near optimums, matrix multiplication, and NP-complete problems. New to this edition: Chapter 9
Multiple scattering theory of radiative transfer in inhomogeneous atmospheres.
Kanal, M.
1973-01-01
In this paper we treat the multiple scattering theory of radiative transfer in plane-parallel inhomogeneous atmospheres. The treatment presented here may be adopted to model atmospheres characterized by an optical depth dependent coherent scattering phase function. For the purpose of illustration we consider the semi-infinite medium in which the absorption property of the atmosphere is characterized by an exponential function. The methodology employed here is the extension of the case treated previously by the author for homogeneous atmospheres.
Jack superpolynomials: physical and combinatorial definitions
International Nuclear Information System (INIS)
Desrosiers, P.; Mathieu, P.; Lapointe, L.
2004-01-01
Jack superpolynomials are eigenfunctions of the supersymmetric extension of the quantum trigonometric Calogero-Moser-Sutherland Hamiltonian. They are orthogonal with respect to the scalar product, dubbed physical, that is naturally induced by this quantum-mechanical problem. But Jack superpolynomials can also be defined more combinatorially, starting from the multiplicative bases of symmetric superpolynomials, enforcing orthogonality with respect to a one-parameter deformation of the combinatorial scalar product. Both constructions turn out to be equivalent. (author)
Superlubricity of Graphite Induced by Multiple Transferred Graphene Nanoflakes.
Li, Jinjin; Gao, Tianyang; Luo, Jianbin
2018-03-01
2D or 3D layered materials, such as graphene, graphite, and molybdenum disulfide, usually exhibit superlubricity properties when sliding occurs between the incommensurate interface lattices. This study reports the superlubricity between graphite and silica under ambient conditions, induced by the formation of multiple transferred graphene nanoflakes on the asperities of silica surfaces after the initial frictional sliding. The friction coefficient can be reduced to as low as 0.0003 with excellent robustness and is independent of the surface roughness, sliding velocities, and rotation angles. The superlubricity mechanism can be attributed to the extremely weak interaction and easy sliding between the transferred graphene nanoflakes and graphite in their incommensurate contact. This finding has important implications for developing approaches to achieve superlubricity of layered materials at the nanoscale by tribointeractions.
Combinatorial commutative algebra
Miller, Ezra
2005-01-01
Offers an introduction to combinatorial commutative algebra, focusing on combinatorial techniques for multigraded polynomial rings, semigroup algebras, and determined rings. The chapters in this work cover topics ranging from homological invariants of monomial ideals and their polyhedral resolutions, to tools for studying algebraic varieties.
Dynamic combinatorial chemistry
Otto, Sijbren; Furlan, Ricardo L.E.; Sanders, Jeremy K.M.
2002-01-01
A combinatorial library that responds to its target by increasing the concentration of strong binders at the expense of weak binders sounds ideal. Dynamic combinatorial chemistry has the potential to achieve exactly this. In this review, we will highlight the unique features that distinguish dynamic
Multiple ovulation and embryo transfer (MOET in camels: An overview
Directory of Open Access Journals (Sweden)
Binoy S. Vettical
2016-04-01
Full Text Available Unlike in other domestic animal species like cattle, reproductive biotechnologies like Artificial Insemination (AI and Embryo Transfer (ET are not well developed and thus are not being used as routine breeding procedures in camels. One of the important objectives of this manuscript is to focus on analyzing the present status of Multiple Ovulation and Embryo Transfer (MOET in camels and its future perspectives. Camels are induced ovulators, thus require hormonal treatment to induce ovulation and control the follicular cycles, which is the main reason why protocols used in other domestic animal species cannot be directly used in this species. The review suggests that the best method for super stimulation of ovaries in camels is use of a combination of Equine Chorionic Gonadotropin (eCG and Follicle Stimulating Hormone (FSH at any stage after elimination of dominant follicle if any or at the early stage of the follicular wave and ovulation of the developed multiple follicles can be achieved by mating donors. The review highlights that a better pregnancy rate is achieved with recipients who ovulate 24 h after the donor.
Integer and combinatorial optimization
Nemhauser, George L
1999-01-01
Rave reviews for INTEGER AND COMBINATORIAL OPTIMIZATION ""This book provides an excellent introduction and survey of traditional fields of combinatorial optimization . . . It is indeed one of the best and most complete texts on combinatorial optimization . . . available. [And] with more than 700 entries, [it] has quite an exhaustive reference list.""-Optima ""A unifying approach to optimization problems is to formulate them like linear programming problems, while restricting some or all of the variables to the integers. This book is an encyclopedic resource for such f
Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi.
Ropars, Jeanne; Rodríguez de la Vega, Ricardo C; López-Villavicencio, Manuela; Gouzy, Jérôme; Sallet, Erika; Dumas, Émilie; Lacoste, Sandrine; Debuchy, Robert; Dupont, Joëlle; Branca, Antoine; Giraud, Tatiana
2015-10-05
Domestication is an excellent model for studies of adaptation because it involves recent and strong selection on a few, identified traits [1-5]. Few studies have focused on the domestication of fungi, with notable exceptions [6-11], despite their importance to bioindustry [12] and to a general understanding of adaptation in eukaryotes [5]. Penicillium fungi are ubiquitous molds among which two distantly related species have been independently selected for cheese making-P. roqueforti for blue cheeses like Roquefort and P. camemberti for soft cheeses like Camembert. The selected traits include morphology, aromatic profile, lipolytic and proteolytic activities, and ability to grow at low temperatures, in a matrix containing bacterial and fungal competitors [13-15]. By comparing the genomes of ten Penicillium species, we show that adaptation to cheese was associated with multiple recent horizontal transfers of large genomic regions carrying crucial metabolic genes. We identified seven horizontally transferred regions (HTRs) spanning more than 10 kb each, flanked by specific transposable elements, and displaying nearly 100% identity between distant Penicillium species. Two HTRs carried genes with functions involved in the utilization of cheese nutrients or competition and were found nearly identical in multiple strains and species of cheese-associated Penicillium fungi, indicating recent selective sweeps; they were experimentally associated with faster growth and greater competitiveness on cheese and contained genes highly expressed in the early stage of cheese maturation. These findings have industrial and food safety implications and improve our understanding of the processes of adaptation to rapid environmental changes. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.
DEFF Research Database (Denmark)
Larsen, Jesper Abildgaard; Wisniewski, Rafal; Grunnet, Jacob Deleuran
2008-01-01
indicates for a given face the future simplex. In the suggested definition we allow nondeterminacy in form of splitting and merging of solution trajectories. The combinatorial vector field gives rise to combinatorial counterparts of most concepts from dynamical systems, such as duals to vector fields, flow......, flow lines, fixed points and Lyapunov functions. Finally it will be shown how this theory extends to switched dynamical systems and an algorithmic overview of how to do supervisory control will be shown towards the end....
Dendrimer-based dynamic combinatorial libraries
Chang, T.; Meijer, E.W.
2005-01-01
The aim of this project is to create water-sol. dynamic combinatorial libraries based upon dendrimer-guest complexes. The guest mols. are designed to bind to dendrimers using multiple secondary interactions, such as electrostatics and hydrogen bonding. We have been able to incorporate various guest
Combinatorial Aspects of the Generalized Euler's Totient
Directory of Open Access Journals (Sweden)
Nittiya Pabhapote
2010-01-01
Full Text Available A generalized Euler's totient is defined as a Dirichlet convolution of a power function and a product of the Souriau-Hsu-Möbius function with a completely multiplicative function. Two combinatorial aspects of the generalized Euler's totient, namely, its connections to other totients and its relations with counting formulae, are investigated.
Controlling energy transfer between multiple dopants within a single nanoparticle
DiMaio, Jeffrey R.; Sabatier, Clément; Kokuoz, Baris; Ballato, John
2008-01-01
Complex core-shell architectures are implemented within LaF3 nanoparticles to allow for a tailored degree of energy transfer (ET) between different rare earth dopants. By constraining specific dopants to individual shells, their relative distance to one another can be carefully controlled. Core-shell LaF3 nanoparticles doped with Tb3+ and Eu3+ and consisting of up to four layers were synthesized with an outer diameter of ≈10 nm. It is found that by varying the thicknesses of an undoped layer between a Tb3+-doped layer and a Eu3+-doped layer, the degree of ET can be engineered to allow for zero, partial, or total ET from a donor ion to an acceptor ion. More specifically, the ratio of the intensities of the 541-nm Tb3+ and 590 nm Eu3+ peaks was tailored from core-shell configuration that restricts ET is used. Beyond simply controlling ET, which can be limiting when designing materials for optical applications, this approach can be used to obtain truly engineered spectral features from nanoparticles and composites made from them. Further, it allows for a single excitation source to yield multiple discrete emissions from numerous lanthanide dopants that heretofore would have been quenched in a more conventional active optical material. PMID:18250307
Introduction to combinatorial designs
Wallis, WD
2007-01-01
Combinatorial theory is one of the fastest growing areas of modern mathematics. Focusing on a major part of this subject, Introduction to Combinatorial Designs, Second Edition provides a solid foundation in the classical areas of design theory as well as in more contemporary designs based on applications in a variety of fields. After an overview of basic concepts, the text introduces balanced designs and finite geometries. The author then delves into balanced incomplete block designs, covering difference methods, residual and derived designs, and resolvability. Following a chapter on the e
Infinitary Combinatory Reduction Systems
DEFF Research Database (Denmark)
Ketema, Jeroen; Simonsen, Jakob Grue
2011-01-01
We define infinitary Combinatory Reduction Systems (iCRSs), thus providing the first notion of infinitary higher-order rewriting. The systems defined are sufficiently general that ordinary infinitary term rewriting and infinitary ¿-calculus are special cases. Furthermore,we generalise a number...
Manipulating Combinatorial Structures.
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…
Introduction to combinatorial geometry
International Nuclear Information System (INIS)
Gabriel, T.A.; Emmett, M.B.
1985-01-01
The combinatorial geometry package as used in many three-dimensional multimedia Monte Carlo radiation transport codes, such as HETC, MORSE, and EGS, is becoming the preferred way to describe simple and complicated systems. Just about any system can be modeled using the package with relatively few input statements. This can be contrasted against the older style geometry packages in which the required input statements could be large even for relatively simple systems. However, with advancements come some difficulties. The users of combinatorial geometry must be able to visualize more, and, in some instances, all of the system at a time. Errors can be introduced into the modeling which, though slight, and at times hard to detect, can have devastating effects on the calculated results. As with all modeling packages, the best way to learn the combinatorial geometry is to use it, first on a simple system then on more complicated systems. The basic technique for the description of the geometry consists of defining the location and shape of the various zones in terms of the intersections and unions of geometric bodies. The geometric bodies which are generally included in most combinatorial geometry packages are: (1) box, (2) right parallelepiped, (3) sphere, (4) right circular cylinder, (5) right elliptic cylinder, (6) ellipsoid, (7) truncated right cone, (8) right angle wedge, and (9) arbitrary polyhedron. The data necessary to describe each of these bodies are given. As can be easily noted, there are some subsets included for simplicity
Problems with multiple use of transfer buffer in protein electrophoretic transfer.
Dorri, Yaser; Kurien, Biji T; Scofield, R Hal
2010-04-01
Two-dimensional gel electrophoresis (2DE) and SDS-PAGE are the two most useful methods in protein separation. Proteins separated by 2DE or SDS-PAGE are usually transferred to membranes using a variety of methods, such as electrophoretic transfer, heat-mediated transfer, or nonelectrophoretic transfer, for specific protein detection and/or analysis. In a recent study, Pettegrew et al. claim to reuse transfer buffer containing methanol for at least five times for transferring proteins from SDS-PAGE to polyvinylidene difluoride. They add 150-200 ml fresh transfer solution each time for extended use as a result of loss of transfer buffer. Finally, they test efficiency of each protein transfer by chemiluminescence detection. Here, we comment on this report, as we believe this method is not accurate and useful for protein analysis, and it can cause background binding as well as inaccurate protein analysis.
Intergenic and intragenic conjugal transfer of multiple antibiotic ...
African Journals Online (AJOL)
Conjugation process was conducted to determine the means of transferring ... In this study, it was surprisingly observed that tetracycline resistant gene was ... among pathogenic bacteria, particularly since antibiotics are indiscriminately used in ...
Maximization of Tsallis entropy in the combinatorial formulation
International Nuclear Information System (INIS)
Suyari, Hiroki
2010-01-01
This paper presents the mathematical reformulation for maximization of Tsallis entropy S q in the combinatorial sense. More concretely, we generalize the original derivation of Maxwell-Boltzmann distribution law to Tsallis statistics by means of the corresponding generalized multinomial coefficient. Our results reveal that maximization of S 2-q under the usual expectation or S q under q-average using the escort expectation are naturally derived from the combinatorial formulations for Tsallis statistics with respective combinatorial dualities, that is, one for additive duality and the other for multiplicative duality.
cDREM: inferring dynamic combinatorial gene regulation.
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.
Energy Technology Data Exchange (ETDEWEB)
Randrup, J.
1979-07-01
This lecture discusses a theory for the transport of mass, charge, linear, and angular momentum and energy in damped nuclear collisions, as induced by multiple transfer of individual nucleons. 11 references.
Sidoli, Simone; Schwämmle, Veit; Ruminowicz, Chrystian; Hansen, Thomas A; Wu, Xudong; Helin, Kristian; Jensen, Ole N
2014-10-01
We present an integrated middle-down proteomics platform for sensitive mapping and quantification of coexisting PTMs in large polypeptides (5-7 kDa). We combined an RP trap column with subsequent weak cation exchange-hydrophilic interaction LC interfaced directly to high mass accuracy ESI MS/MS using electron transfer dissociation. This enabled automated and efficient separation and sequencing of hypermodified histone N-terminal tails for unambiguous localization of combinatorial PTMs. We present Histone Coder and IsoScale software to extract, filter, and analyze MS/MS data, including quantification of cofragmenting isobaric polypeptide species. We characterized histone tails derived from murine embryonic stem cells knockout in suppressor of zeste12 (Suz12(-/-) ) and quantified 256 combinatorial histone marks in histones H3, H4, and H2A. Furthermore, a total of 713 different combinatorial histone marks were identified in purified histone H3. We measured a seven-fold reduction of H3K27me2/me3 (where me2 and me3 are dimethylation and trimethylation, respectively) in Suz12(-) (/) (-) cells and detected significant changes of the relative abundance of 16 other single PTMs of histone H3 and other combinatorial marks. We conclude that the inactivation of Suz12 is associated with changes in the abundance of not only H3K27 methylation but also multiple other PTMs in histone H3 tails. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Multiple flow patterns and heat transfer in confined jet impingement
International Nuclear Information System (INIS)
Li Xianchang; Gaddis, J. Leo; Wang Ting
2005-01-01
The flow field of a 2-D laminar confined impinging slot jet is investigated. Numerical results indicate that there exist two different solutions in some range of geometric and flow parameters. The two steady flow patterns are obtained under identical boundary conditions but only with different initial flow fields. Two different exit boundary conditions are investigated with two commercial software packages to eliminate artificial or computational effects. The different flow patterns are observed to significantly affect the heat transfer. A flow visualization experiment is carried out to verify the computational results and both flow patterns are observed. The bifurcation mechanism is interpreted and discussed
Pregnancy and Multiple Births rate after Transferring 2 or 3 Embryos
Directory of Open Access Journals (Sweden)
F Mostajeran
2006-05-01
Full Text Available Background: In vitro fertilization (IVF is a progressing common reproduction method and if the number of transferred embryo increases, the pregnancy rate and multiple pregnancies will increase which may lead to higher medical costs and human suffering. We compared pregnancy and multiple pregnancies rate after two or three transferred embryo via IVF. Methods: From April 2003 to June 2004, 301 referred infertile women to Isfahan infertility center underwent IVF with transferring two or three good quality embryos. Results: From 298 patients, 2 and 3 embryos were transferred in 155 patients and in 143 patients, respectively. Pregnancy rate was 19.4% versus 24.5% in 2 and 3 embryos transferred patients, respectively. Twin gestations were found in 5(3.2% of 2 embryos transferred patients and in 11(7.7% of 3 embryos transferred patients. Discussion: Transferring two or three embryos with good quality increase the rate of twin gestations in young women, without significant improve in the chance of singleton conception. Key words: In Vitro Fertilization, Multiple gestations, Embryo transfer
Directory of Open Access Journals (Sweden)
Igor V. Protasov
2013-09-01
$\\Delta(A=\\{g\\in G:|gA\\cap A|=\\infty\\}$. The mapping $\\Delta:\\mathcal{P}_G\\rightarrow\\mathcal{P}_G$, $A\\mapsto\\Delta(A$, is called a combinatorial derivation and can be considered as an analogue of the topological derivation $d:\\mathcal{P}_X\\rightarrow\\mathcal{P}_X$, $A\\mapsto A^d$, where $X$ is a topological space and $A^d$ is the set of all limit points of $A$. Content: elementary properties, thin and almost thin subsets, partitions, inverse construction and $\\Delta$-trajectories, $\\Delta$ and $d$.
Dynamic Combinatorial Chemistry
DEFF Research Database (Denmark)
Lisbjerg, Micke
This thesis is divided into seven chapters, which can all be read individually. The first chapter, however, contains a general introduction to the chemistry used in the remaining six chapters, and it is therefore recommended to read chapter one before reading the other chapters. Chapter 1...... is a general introductory chapter for the whole thesis. The history and concepts of dynamic combinatorial chemistry are described, as are some of the new and intriguing results recently obtained. Finally, the properties of a broad range of hexameric macrocycles are described in detail. Chapter 2 gives...
Implications of magma transfer between multiple reservoirs on eruption cycling.
Elsworth, Derek; Mattioli, Glen; Taron, Joshua; Voight, Barry; Herd, Richard
2008-10-10
Volcanic eruptions are episodic despite being supplied by melt at a nearly constant rate. We used histories of magma efflux and surface deformation to geodetically image magma transfer within the deep crustal plumbing of the Soufrière Hills volcano on Montserrat, West Indies. For three cycles of effusion followed by discrete pauses, supply of the system from the deep crust and mantle was continuous. During periods of reinitiated high surface efflux, magma rose quickly and synchronously from a deflating mid-crustal reservoir (at about 12 kilometers) augmented from depth. During repose, the lower reservoir refilled from the deep supply, with only minor discharge transiting the upper chamber to surface. These observations are consistent with a model involving the continuous supply of magma from the deep crust and mantle into a voluminous and compliant mid-crustal reservoir, episodically valved below a shallow reservoir (at about 6 kilometers).
Conventional MRI and magnetisation transfer imaging of tumour-like multiple sclerosis in a child
International Nuclear Information System (INIS)
Metafratzi, Z.; Argyropoulou, M.I.; Efremidis, S.C.; Tzoufi, M.; Papadopoulou, Z.
2002-01-01
Tumefactive multiple sclerosis is a rare entity in children. Differential diagnosis includes other mass lesions such as neoplasm and abscess. A case of tumefactive multiple sclerosis in a child is presented. The open-ring pattern of enhancement on conventional MRI and magnetisation transfer imaging was important for the initial diagnosis and the evaluation of the course of the disease. (orig.)
Boltzmann Oracle for Combinatorial Systems
Pivoteau , Carine; Salvy , Bruno; Soria , Michèle
2008-01-01
International audience; Boltzmann random generation applies to well-deﬁned systems of recursive combinatorial equations. It relies on oracles giving values of the enumeration generating series inside their disk of convergence. We show that the combinatorial systems translate into numerical iteration schemes that provide such oracles. In particular, we give a fast oracle based on Newton iteration.
Quantum fields and processes a combinatorial approach
Gough, John
2018-01-01
Wick ordering of creation and annihilation operators is of fundamental importance for computing averages and correlations in quantum field theory and, by extension, in the Hudson-Parthasarathy theory of quantum stochastic processes, quantum mechanics, stochastic processes, and probability. This book develops the unified combinatorial framework behind these examples, starting with the simplest mathematically, and working up to the Fock space setting for quantum fields. Emphasizing ideas from combinatorics such as the role of lattice of partitions for multiple stochastic integrals by Wallstrom-Rota and combinatorial species by Joyal, it presents insights coming from quantum probability. It also introduces a 'field calculus' which acts as a succinct alternative to standard Feynman diagrams and formulates quantum field theory (cumulant moments, Dyson-Schwinger equation, tree expansions, 1-particle irreducibility) in this language. Featuring many worked examples, the book is aimed at mathematical physicists, quant...
Quantum fields and processes a combinatorial approach
Gough, John
2018-01-01
Wick ordering of creation and annihilation operators is of fundamental importance for computing averages and correlations in quantum field theory and, by extension, in the Hudson–Parthasarathy theory of quantum stochastic processes, quantum mechanics, stochastic processes, and probability. This book develops the unified combinatorial framework behind these examples, starting with the simplest mathematically, and working up to the Fock space setting for quantum fields. Emphasizing ideas from combinatorics such as the role of lattice of partitions for multiple stochastic integrals by Wallstrom–Rota and combinatorial species by Joyal, it presents insights coming from quantum probability. It also introduces a 'field calculus' which acts as a succinct alternative to standard Feynman diagrams and formulates quantum field theory (cumulant moments, Dyson–Schwinger equation, tree expansions, 1-particle irreducibility) in this language. Featuring many worked examples, the book is aimed at mathematical physicists,...
Mitjana, Margarida
2018-01-01
This book contains the notes of the lectures delivered at an Advanced Course on Combinatorial Matrix Theory held at Centre de Recerca Matemàtica (CRM) in Barcelona. These notes correspond to five series of lectures. The first series is dedicated to the study of several matrix classes defined combinatorially, and was delivered by Richard A. Brualdi. The second one, given by Pauline van den Driessche, is concerned with the study of spectral properties of matrices with a given sign pattern. Dragan Stevanović delivered the third one, devoted to describing the spectral radius of a graph as a tool to provide bounds of parameters related with properties of a graph. The fourth lecture was delivered by Stephen Kirkland and is dedicated to the applications of the Group Inverse of the Laplacian matrix. The last one, given by Ángeles Carmona, focuses on boundary value problems on finite networks with special in-depth on the M-matrix inverse problem.
Cryptographic Combinatorial Securities Exchanges
Thorpe, Christopher; Parkes, David C.
We present a useful new mechanism that facilitates the atomic exchange of many large baskets of securities in a combinatorial exchange. Cryptography prevents information about the securities in the baskets from being exploited, enhancing trust. Our exchange offers institutions who wish to trade large positions a new alternative to existing methods of block trading: they can reduce transaction costs by taking advantage of other institutions’ available liquidity, while third party liquidity providers guarantee execution—preserving their desired portfolio composition at all times. In our exchange, institutions submit encrypted orders which are crossed, leaving a “remainder”. The exchange proves facts about the portfolio risk of this remainder to third party liquidity providers without revealing the securities in the remainder, the knowledge of which could also be exploited. The third parties learn either (depending on the setting) the portfolio risk parameters of the remainder itself, or how their own portfolio risk would change if they were to incorporate the remainder into a portfolio they submit. In one setting, these third parties submit bids on the commission, and the winner supplies necessary liquidity for the entire exchange to clear. This guaranteed clearing, coupled with external price discovery from the primary markets for the securities, sidesteps difficult combinatorial optimization problems. This latter method of proving how taking on the remainder would change risk parameters of one’s own portfolio, without revealing the remainder’s contents or its own risk parameters, is a useful protocol of independent interest.
Combinatorial optimization games
Energy Technology Data Exchange (ETDEWEB)
Deng, X. [York Univ., North York, Ontario (Canada); Ibaraki, Toshihide; Nagamochi, Hiroshi [Kyoto Univ. (Japan)
1997-06-01
We introduce a general integer programming formulation for a class of combinatorial optimization games, which immediately allows us to improve the algorithmic result for finding amputations in the core (an important solution concept in cooperative game theory) of the network flow game on simple networks by Kalai and Zemel. An interesting result is a general theorem that the core for this class of games is nonempty if and only if a related linear program has an integer optimal solution. We study the properties for this mathematical condition to hold for several interesting problems, and apply them to resolve algorithmic and complexity issues for their cores along the line as put forward in: decide whether the core is empty; if the core is empty, find an imputation in the core; given an imputation x, test whether x is in the core. We also explore the properties of totally balanced games in this succinct formulation of cooperative games.
DEFF Research Database (Denmark)
Larsen, Peter Gorm; Lausdahl, Kenneth; Battle, Nick
2010-01-01
by forgotten preconditions as well as broken invariants and post-conditions. Trace definitions are defined as regular expressions describing possible sequences of operation calls, and are conceptually similar to UML sequence diagrams. In this paper we present a tool enabling test automation based on VDM traces......Abstract—Combinatorial testing in VDM involves the automatic generation and execution of a large collection of test cases derived from templates provided in the form of trace definitions added to a VDM specification. The main value of this is the rapid detection of run-time errors caused......, and explain how it is possible to reduce large collections of test cases in different ways. Its use is illustrated with a small case study....
Jensen, Erik C.; Stockton, Amanda M.; Chiesl, Thomas N.; Kim, Jungkyu; Bera, Abhisek; Mathies, Richard A.
2013-01-01
A digitally programmable microfluidic Automaton consisting of a 2-dimensional array of pneumatically actuated microvalves is programmed to perform new multiscale mixing and sample processing operations. Large (µL-scale) volume processing operations are enabled by precise metering of multiple reagents within individual nL-scale valves followed by serial repetitive transfer to programmed locations in the array. A novel process exploiting new combining valve concepts is developed for continuous rapid and complete mixing of reagents in less than 800 ms. Mixing, transfer, storage, and rinsing operations are implemented combinatorially to achieve complex assay automation protocols. The practical utility of this technology is demonstrated by performing automated serial dilution for quantitative analysis as well as the first demonstration of on-chip fluorescent derivatization of biomarker targets (carboxylic acids) for microchip capillary electrophoresis on the Mars Organic Analyzer. A language is developed to describe how unit operations are combined to form a microfluidic program. Finally, this technology is used to develop a novel microfluidic 6-sample processor for combinatorial mixing of large sets (>26 unique combinations) of reagents. The digitally programmable microfluidic Automaton is a versatile programmable sample processor for a wide range of process volumes, for multiple samples, and for different types of analyses. PMID:23172232
On an extension of a combinatorial identity
Indian Academy of Sciences (India)
to an infinite family of 4-way combinatorial identities. In some particular cases we get even 5-way combinatorial identities which give us four new combinatorial versions of. Göllnitz–Gordon identities. Keywords. n-Color partitions; lattice paths; Frobenius partitions; Göllnitz–Gordon identities; combinatorial interpretations. 1.
Combinatorial Nano-Bio Interfaces.
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 designs constructions and analysis
Stinson, Douglas R
2004-01-01
Created to teach students many of the most important techniques used for constructing combinatorial designs, this is an ideal textbook for advanced undergraduate and graduate courses in combinatorial design theory. The text features clear explanations of basic designs, such as Steiner and Kirkman triple systems, mutual orthogonal Latin squares, finite projective and affine planes, and Steiner quadruple systems. In these settings, the student will master various construction techniques, both classic and modern, and will be well-prepared to construct a vast array of combinatorial designs. Design theory offers a progressive approach to the subject, with carefully ordered results. It begins with simple constructions that gradually increase in complexity. Each design has a construction that contains new ideas or that reinforces and builds upon similar ideas previously introduced. A new text/reference covering all apsects of modern combinatorial design theory. Graduates and professionals in computer science, applie...
Combinatorial Mathematics: Research into Practice
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.
Combinatorial methods with computer applications
Gross, Jonathan L
2007-01-01
Combinatorial Methods with Computer Applications provides in-depth coverage of recurrences, generating functions, partitions, and permutations, along with some of the most interesting graph and network topics, design constructions, and finite geometries. Requiring only a foundation in discrete mathematics, it can serve as the textbook in a combinatorial methods course or in a combined graph theory and combinatorics course.After an introduction to combinatorics, the book explores six systematic approaches within a comprehensive framework: sequences, solving recurrences, evaluating summation exp
Number systems and combinatorial problems
Yordzhev, Krasimir
2014-01-01
The present work has been designed for students in secondary school and their teachers in mathematics. We will show how with the help of our knowledge of number systems we can solve problems from other fields of mathematics for example in combinatorial analysis and most of all when proving some combinatorial identities. To demonstrate discussed in this article method we have chosen several suitable mathematical tasks.
Relativity in Combinatorial Gravitational Fields
Directory of Open Access Journals (Sweden)
Mao Linfan
2010-04-01
Full Text Available A combinatorial spacetime $(mathscr{C}_G| uboverline{t}$ is a smoothly combinatorial manifold $mathscr{C}$ underlying a graph $G$ evolving on a time vector $overline{t}$. As we known, Einstein's general relativity is suitable for use only in one spacetime. What is its disguise in a combinatorial spacetime? Applying combinatorial Riemannian geometry enables us to present a combinatorial spacetime model for the Universe and suggest a generalized Einstein gravitational equation in such model. Forfinding its solutions, a generalized relativity principle, called projective principle is proposed, i.e., a physics law ina combinatorial spacetime is invariant under a projection on its a subspace and then a spherically symmetric multi-solutions ofgeneralized Einstein gravitational equations in vacuum or charged body are found. We also consider the geometrical structure in such solutions with physical formations, and conclude that an ultimate theory for the Universe maybe established if all such spacetimes in ${f R}^3$. Otherwise, our theory is only an approximate theory and endless forever.
Directory of Open Access Journals (Sweden)
Narayanamoorthi R.
2018-01-01
Full Text Available Simultaneous power transfer to multiple receiver (Rx system is one of the key advantages of wireless power transfer (WPT system using magnetic resonance. However, determining the optimal condition to uniformly transfer the power to a selected Rx at high efficiency is the challenging task under the dynamic environment. The cross-coupling and frequency splitting are the dominant issues present in the multiple Rx dynamic WPT system. The existing analysis is performed by considering any one issue present in the system; on the other hand, the cross coupling and frequency splitting issues are interrelated in dynamic Rx’s, which requires a comprehensive design strategy by considering both the problems. This paper proposes an optimal design of multiple Rx WPT system, which can eliminate cross coupling, frequency splitting issues and increase the power transfer efficiency (PTE of selected Rx. The cross-coupling rejection, uniform power transfer is performed by adding an additional relay coil and independent resonance frequency tuning with capacitive compensation to each Rx unit. The frequency splitting phenomena are eliminated using non-identical transmitter (Tx and Rx coil structure which can maintain the coupling between the coil under the critical coupling limit. The mathematical analysis of the compensation capacitance calculation and optimal Tx coil size identification is performed for the four Rx WPT system. Finite element analysis and experimental investigation are carried out for the proposed design in static and dynamic conditions.
Transfer functions of double- and multiple-cavity Fabry-Perot filters driven by Lorentzian sources.
Marti, J; Capmany, J
1996-12-20
We derive expressions for the transfer functions of double- and multiple-cavity Fabry-Perot filters driven by laser sources with Lorentzian spectrum. These are of interest because of their applications in sensing and channel filtering in optical frequency-division multiplexing networks.
Fisher, Wayne W.; Greer, Brian D.; Fuhrman, Ashley M.; Querim, Angie C.
2015-01-01
Multiple schedules with signaled periods of reinforcement and extinction have been used to thin reinforcement schedules during functional communication training (FCT) to make the intervention more practical for parents and teachers. We evaluated whether these signals would also facilitate rapid transfer of treatment effects across settings and…
Multiple recent horizontal transfers of a large genomic region in cheese making fungi.
Cheeseman, Kevin; Ropars, Jeanne; Renault, Pierre; Dupont, Joëlle; Gouzy, Jérôme; Branca, Antoine; Abraham, Anne-Laure; Ceppi, Maurizio; Conseiller, Emmanuel; Debuchy, Robert; Malagnac, Fabienne; Goarin, Anne; Silar, Philippe; Lacoste, Sandrine; Sallet, Erika; Bensimon, Aaron; Giraud, Tatiana; Brygoo, Yves
2014-01-01
While the extent and impact of horizontal transfers in prokaryotes are widely acknowledged, their importance to the eukaryotic kingdom is unclear and thought by many to be anecdotal. Here we report multiple recent transfers of a huge genomic island between Penicillium spp. found in the food environment. Sequencing of the two leading filamentous fungi used in cheese making, P. roqueforti and P. camemberti, and comparison with the penicillin producer P. rubens reveals a 575 kb long genomic island in P. roqueforti--called Wallaby--present as identical fragments at non-homologous loci in P. camemberti and P. rubens. Wallaby is detected in Penicillium collections exclusively in strains from food environments. Wallaby encompasses about 250 predicted genes, some of which are probably involved in competition with microorganisms. The occurrence of multiple recent eukaryotic transfers in the food environment provides strong evidence for the importance of this understudied and probably underestimated phenomenon in eukaryotes.
Directory of Open Access Journals (Sweden)
Uma M Sundhararaj
2017-01-01
Full Text Available Background: Historically, to achieve higher pregnancy rates, multiple embryos were transferred after an in-vitro fertilisation (IVF. However, this practice is being reassessed, because it leads to multiple pregnancies that is known to cause adverse maternal and fetal outcomes. Aim: To compare the pregnancy outcomes in fresh IVF or intracytoplasmic sperm injection (ICSI cycles among women undergoing elective single blastocyst transfer (eSBT vs. those undergoing double blastocyst transfer (DBT. Settings and Design: It is a retrospective data analysis of 582 patients undergoing fresh IVF/ICSI cycles performed from January 2012 to June 2015. Materials and Methods: Patients, who underwent IVF/ICSI and developed more than one blastocyst, were included in the study. Donor cycles were excluded from the study. All the embryos were cultured to blastocyst stage in sequential media followed by transfer of two blastocysts (DBT or eSBT and cryopreservation of the remaining. Statistical Analysis: Statistical analysis was performed using chi square test. Results: Out of 582 patients, in 149 patients one blastocyst was transferred and in 433 patients two blastocysts were transferred. There was no statistical difference in the biochemical pregnancy rate, clinical pregnancy rate and live birth rate in both the groups. Statistics demonstrated a significant drop in miscarriage rate in eSBT group. There was no incidence of twins in eSBT group, whereas twin birth rate per clinical pregnancy was 29.02% in DBT group. Conclusion: Single blastocyst transfer is an effective method to reduce the risk of multiple births without compromising the pregnancy outcomes. Given the promising potential of vitrification; the remaining blastocyst can be cryopreserved.
Fisher, Wayne W; Greer, Brian D; Fuhrman, Ashley M; Querim, Angie C
2015-12-01
Multiple schedules with signaled periods of reinforcement and extinction have been used to thin reinforcement schedules during functional communication training (FCT) to make the intervention more practical for parents and teachers. We evaluated whether these signals would also facilitate rapid transfer of treatment effects across settings and therapists. With 2 children, we conducted FCT in the context of mixed (baseline) and multiple (treatment) schedules introduced across settings or therapists using a multiple baseline design. Results indicated that when the multiple schedules were introduced, the functional communication response came under rapid discriminative control, and problem behavior remained at near-zero rates. We extended these findings with another individual by using a more traditional baseline in which problem behavior produced reinforcement. Results replicated those of the previous participants and showed rapid reductions in problem behavior when multiple schedules were implemented across settings. © Society for the Experimental Analysis of Behavior.
A combinatorial approximation algorithm for CDMA downlink rate allocation
Boucherie, Richardus J.; Bumb, A.F.; Endrayanto, A.I.; Woeginger, Gerhard; Raghavan, S.; Anandalingam, G.
2006-01-01
This paper presents a combinatorial algorithm for downlink rate allocation in Code Division Multiple Access (CDMA) mobile networks. By discretizing the coverage area into small segments, the transmit power requirements are characterized via a matrix representation that separates user and system
A combinatorial approximation algorithm for CDMA downlink rate allocation
Boucherie, Richardus J.; Bumb, A.F.; Endrayanto, A.I.; Woeginger, Gerhard
2004-01-01
This paper presents a combinatorial algorithm for downlink rate allocation in Code Division Multiple Access (CDMA) mobile networks. By discretizing the coverage area into small segments, the transmit power requirements are characterized via a matrix representation that separates user and system
A computational procedure for finding multiple solutions of convective heat transfer equations
International Nuclear Information System (INIS)
Mishra, S; DebRoy, T
2005-01-01
In recent years numerical solutions of the convective heat transfer equations have provided significant insight into the complex materials processing operations. However, these computational methods suffer from two major shortcomings. First, these procedures are designed to calculate temperature fields and cooling rates as output and the unidirectional structure of these solutions preclude specification of these variables as input even when their desired values are known. Second, and more important, these procedures cannot determine multiple pathways or multiple sets of input variables to achieve a particular output from the convective heat transfer equations. Here we propose a new method that overcomes the aforementioned shortcomings of the commonly used solutions of the convective heat transfer equations. The procedure combines the conventional numerical solution methods with a real number based genetic algorithm (GA) to achieve bi-directionality, i.e. the ability to calculate the required input variables to achieve a specific output such as temperature field or cooling rate. More important, the ability of the GA to find a population of solutions enables this procedure to search for and find multiple sets of input variables, all of which can lead to the desired specific output. The proposed computational procedure has been applied to convective heat transfer in a liquid layer locally heated on its free surface by an electric arc, where various sets of input variables are computed to achieve a specific fusion zone geometry defined by an equilibrium temperature. Good agreement is achieved between the model predictions and the independent experimental results, indicating significant promise for the application of this procedure in finding multiple solutions of convective heat transfer equations
Combinatorial synthesis of natural products
DEFF Research Database (Denmark)
Nielsen, John
2002-01-01
Combinatorial syntheses allow production of compound libraries in an expeditious and organized manner immediately applicable for high-throughput screening. Natural products possess a pedigree to justify quality and appreciation in drug discovery and development. Currently, we are seeing a rapid...... increase in application of natural products in combinatorial chemistry and vice versa. The therapeutic areas of infectious disease and oncology still dominate but many new areas are emerging. Several complex natural products have now been synthesised by solid-phase methods and have created the foundation...... for preparation of combinatorial libraries. In other examples, natural products or intermediates have served as building blocks or scaffolds in the synthesis of complex natural products, bioactive analogues or designed hybrid molecules. Finally, structural motifs from the biologically active parent molecule have...
Combinatorial optimization theory and algorithms
Korte, Bernhard
2018-01-01
This comprehensive textbook on combinatorial optimization places special emphasis on theoretical results and algorithms with provably good performance, in contrast to heuristics. It is based on numerous courses on combinatorial optimization and specialized topics, mostly at graduate level. This book reviews the fundamentals, covers the classical topics (paths, flows, matching, matroids, NP-completeness, approximation algorithms) in detail, and proceeds to advanced and recent topics, some of which have not appeared in a textbook before. Throughout, it contains complete but concise proofs, and also provides numerous exercises and references. This sixth edition has again been updated, revised, and significantly extended. Among other additions, there are new sections on shallow-light trees, submodular function maximization, smoothed analysis of the knapsack problem, the (ln 4+ɛ)-approximation for Steiner trees, and the VPN theorem. Thus, this book continues to represent the state of the art of combinatorial opti...
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.
Directory of Open Access Journals (Sweden)
Hans-Werner Schmidt
2013-04-01
Full Text Available 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.
Lexicographic goal programming and assessment tools for a combinatorial production problem.
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...
Effect of the Implicit Combinatorial Model on Combinatorial Reasoning in Secondary School Pupils.
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…
In vitro transfer of multiple resistance observed in vivo during a Salmonella london epidemic.
Lantos, J; Marjai, E
1980-01-01
Between 1976 and 1978, waves of Salmonella london infections conveyed by raw meat and meat products were observed. The strains isolated during the epidemic were first susceptible then developed multiple antibiotic resistance. The identical antibiotic resistance patterns of the strain and their more frequent occurrence in hospital environments indicated plasmid-mediated resistance. R-plasmid transfer, minimum inhibition concentration and resistance elimination were studied in representative strains. The resistant S. london strain and transconjugants of Escherichia coli rendered resistant were compared. The results proved that multiple resistance was plasmid-mediated.
Energy Technology Data Exchange (ETDEWEB)
Hellgartner, Stefanie Christine
2015-11-13
In this work, the N=40 subshell closure is investigated with two complementary methods using a radioactive {sup 72}Zn ISOLDE beam: One- and two-neutron transfer reactions and multiple Coulomb excitation. In the one-neutron transfer reaction, two new levels of {sup 73}Zn were discovered. The two-neutron transfer channel allowed to study the differential cross section of the ground state and the 2{sup +}{sub 1} state of {sup 74}Zn. In the Coulomb excitation experiment, the measured B(E2) values and quadrupole moments of {sup 72}Zn showed that the yrast states 0{sup +}{sub 1}, 2{sup +}{sub 1} and 4{sup +}{sub 1} are moderately collective. Contrary, the 0{sup +}{sub 2} state has a different structure, since it features a stronger closed N=40 configuration compared to the ground state.
Combinatorial optimization networks and matroids
Lawler, Eugene
2011-01-01
Perceptively written text examines optimization problems that can be formulated in terms of networks and algebraic structures called matroids. Chapters cover shortest paths, network flows, bipartite matching, nonbipartite matching, matroids and the greedy algorithm, matroid intersections, and the matroid parity problems. A suitable text or reference for courses in combinatorial computing and concrete computational complexity in departments of computer science and mathematics.
Algorithms in combinatorial design theory
Colbourn, CJ
1985-01-01
The scope of the volume includes all algorithmic and computational aspects of research on combinatorial designs. Algorithmic aspects include generation, isomorphism and analysis techniques - both heuristic methods used in practice, and the computational complexity of these operations. The scope within design theory includes all aspects of block designs, Latin squares and their variants, pairwise balanced designs and projective planes and related geometries.
Computational Complexity of Combinatorial Surfaces
Vegter, Gert; Yap, Chee K.
1990-01-01
We investigate the computational problems associated with combinatorial surfaces. Specifically, we present an algorithm (based on the Brahana-Dehn-Heegaard approach) for transforming the polygonal schema of a closed triangulated surface into its canonical form in O(n log n) time, where n is the
Combinatorial synthesis of ceramic materials
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.
Combinatorial auctions for electronic business
Indian Academy of Sciences (India)
R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22
(6) Information feedback: An auction protocol may be a direct mechanism or an .... transparency of allocation decisions arise in resolving these ties. .... bidding, however more recently, combinatorial bids are allowed [50] making ...... Also, truth revelation and other game theoretic considerations are not taken into account.
Combinatorial Proofs and Algebraic Proofs
Indian Academy of Sciences (India)
Permanent link: https://www.ias.ac.in/article/fulltext/reso/018/07/0630-0645. Keywords. Combinatorial proof; algebraic proof; binomial identity; recurrence relation; composition; Fibonacci number; Fibonacci identity; Pascal triangle. Author Affiliations. Shailesh A Shirali1. Sahyadri School Tiwai Hill, Rajgurunagar Pune 410 ...
Recent advances in combinatorial biosynthesis for drug discovery
Directory of Open Access Journals (Sweden)
Sun H
2015-02-01
Full Text Available Huihua Sun,1,* Zihe Liu,1,* Huimin Zhao,1,2 Ee Lui Ang1 1Metabolic Engineering Research Laboratory, Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research, Singapore; 2Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA *These authors contributed equally to this work Abstract: Because of extraordinary structural diversity and broad biological activities, natural products have played a significant role in drug discovery. These therapeutically important secondary metabolites are assembled and modified by dedicated biosynthetic pathways in their host living organisms. Traditionally, chemists have attempted to synthesize natural product analogs that are important sources of new drugs. However, the extraordinary structural complexity of natural products sometimes makes it challenging for traditional chemical synthesis, which usually involves multiple steps, harsh conditions, toxic organic solvents, and byproduct wastes. In contrast, combinatorial biosynthesis exploits substrate promiscuity and employs engineered enzymes and pathways to produce novel “unnatural” natural products, substantially expanding the structural diversity of natural products with potential pharmaceutical value. Thus, combinatorial biosynthesis provides an environmentally friendly way to produce natural product analogs. Efficient expression of the combinatorial biosynthetic pathway in genetically tractable heterologous hosts can increase the titer of the compound, eventually resulting in less expensive drugs. In this review, we will discuss three major strategies for combinatorial biosynthesis: 1 precursor-directed biosynthesis; 2 enzyme-level modification, which includes swapping of the entire domains, modules and subunits, site-specific mutagenesis, and directed evolution; 3 pathway-level recombination. Recent examples of combinatorial biosynthesis employing these
Obfuscation Framework Based on Functionally Equivalent Combinatorial Logic Families
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 Speculations and the Combinatorial Conjecture for Mathematics
Mao, Linfan
2006-01-01
Combinatorics is a powerful tool for dealing with relations among objectives mushroomed in the past century. However, an more important work for mathematician is to apply combinatorics to other mathematics and other sciences not merely to find combinatorial behavior for objectives. Recently, such research works appeared on journals for mathematics and theoretical physics on cosmos. The main purpose of this paper is to survey these thinking and ideas for mathematics and cosmological physics, s...
Katul, Gabriel; Liu, Heping
2017-02-01
A large corpus of field and laboratory experiments support the finding that the water side transfer velocity kL of sparingly soluble gases near air-water interfaces scales as kL˜(νɛ)1/4, where ν is the kinematic water viscosity and ɛ is the mean turbulent kinetic energy dissipation rate. Originally predicted from surface renewal theory, this scaling appears to hold for marine and coastal systems and across many environmental conditions. It is shown that multiple approaches to representing the effects of turbulence on kL lead to this expression when the Kolmogorov microscale is assumed to be the most efficient transporting eddy near the interface. The approaches considered range from simplified surface renewal schemes with distinct models for renewal durations, scaling and dimensional considerations, and a new structure function approach derived using analogies between scalar and momentum transfer. The work offers a new perspective as to why the aforementioned 1/4 scaling is robust.
Multiple scattering of polarized light: comparison of Maxwell theory and radiative transfer theory.
Voit, Florian; Hohmann, Ansgar; Schäfer, Jan; Kienle, Alwin
2012-04-01
For many research areas in biomedical optics, information about scattering of polarized light in turbid media is of increasing importance. Scattering simulations within this field are mainly performed on the basis of radiative transfer theory. In this study a polarization sensitive Monte Carlo solution of radiative transfer theory is compared to exact Maxwell solutions for all elements of the scattering Müller matrix. Different scatterer volume concentrations are modeled as a multitude of monodisperse nonabsorbing spheres randomly positioned in a cubic simulation volume which is irradiated with monochromatic incident light. For all Müller matrix elements effects due to dependent scattering and multiple scattering are analysed. The results are in overall good agreement between the two methods with deviations related to dependent scattering being prominent for high volume concentrations and high scattering angles.
MicroRNA Transfer Between Bone Marrow Adipose and Multiple Myeloma Cells.
Soley, Luna; Falank, Carolyne; Reagan, Michaela R
2017-06-01
Multiple myeloma remains an incurable disease, largely due to the tumor-supportive role of the bone marrow microenvironment. Bone marrow adipose tissue (BMAT) is one component of the fertile microenvironment which is believed to contribute to myeloma progression and drug resistance, as well as participate in a vicious cycle of osteolysis and tumor growth. MicroRNAs (miRNAs) have recently emerged as instrumental regulators of cellular processes that enable the development and dissemination of cancer. This review highlights the intersection between two emerging research fields and pursues the scientific and clinical implications of miRNA transfer between BMAT and myeloma cells. This review provides a concise and provocative summary of the evidence to support exosome-mediated transfer of tumor-supportive miRNAs. The work may prompt researchers to better elucidate the mechanisms by which this novel means of genetic communication between tumor cells and their environment could someday yield targeted therapeutics.
Combinatorial algebra syntax and semantics
Sapir, Mark V
2014-01-01
Combinatorial Algebra: Syntax and Semantics provides a comprehensive account of many areas of combinatorial algebra. It contains self-contained proofs of more than 20 fundamental results, both classical and modern. This includes Golod–Shafarevich and Olshanskii's solutions of Burnside problems, Shirshov's solution of Kurosh's problem for PI rings, Belov's solution of Specht's problem for varieties of rings, Grigorchuk's solution of Milnor's problem, Bass–Guivarc'h theorem about the growth of nilpotent groups, Kleiman's solution of Hanna Neumann's problem for varieties of groups, Adian's solution of von Neumann-Day's problem, Trahtman's solution of the road coloring problem of Adler, Goodwyn and Weiss. The book emphasize several ``universal" tools, such as trees, subshifts, uniformly recurrent words, diagrams and automata. With over 350 exercises at various levels of difficulty and with hints for the more difficult problems, this book can be used as a textbook, and aims to reach a wide and diversified...
Combinatorial aspects of covering arrays
Directory of Open Access Journals (Sweden)
Charles J. Colbourn
2004-11-01
Full Text Available Covering arrays generalize orthogonal arrays by requiring that t -tuples be covered, but not requiring that the appearance of t -tuples be balanced.Their uses in screening experiments has found application in software testing, hardware testing, and a variety of fields in which interactions among factors are to be identified. Here a combinatorial view of covering arrays is adopted, encompassing basic bounds, direct constructions, recursive constructions, algorithmic methods, and applications.
Study on oxygen transfer by solid jet aerator with multiple openings
Directory of Open Access Journals (Sweden)
B.K. Shukla
2018-04-01
Full Text Available In the current study, two different sets of solid jet aerators having area of openings equal to 594.96 mm2 and 246.30 mm2 with rectangular nozzles having rounded ends were studied. Each set consisted of aerators having one, two, four and eight openings. The oxygenation performance of every model was studied for five different discharges of 1.11 l/s, 2.10 l/s, 2.96 l/s, 3.83 l/s and 4.69 l/s were studied. At low discharges, the aerator having lesser number of openings demonstrated more oxygen-transfer efficiency whereas at higher discharges, the aerator having more number of openings yielded more oxygenation-efficiency. Maximum value of oxygen-transfer efficiency of 21.53 kg-O2/kW-hr was obtained for the discharge of 1.11 l/s for single nozzle aerator; however the maximum oxygen-transfer factor of 2.0 × 10−2 s−1 was obtained at discharge of 4.69 l/s for aerator having eight numbers of openings having area of 594.96 mm2. On the other hand, maximum oxygen transfer efficiency of 10.93 kg-O2/kW-hr was demonstrated by aerator with single opening at a discharge of 1.11 l/s and maximum oxygen transfer factor of 7.83 × 10−3 s−1 was obtained from aerator with eight openings at a discharge of 4.69 l/s corresponding to set of aerators with area of openings equal to 246.30 mm2. Multiple non-linear regression modelling was applied to predict oxygen transfer of the aerators for different combinations of input parameters. At the end, the models were compared with conventional methods of aeration and were found to be competitive with traditional devices. Keywords: Plunging jet, Jet aerator, Oxygen transfer, Aeration, Dissolved oxygen
Directory of Open Access Journals (Sweden)
Hyung-Jun Kim
2018-01-01
Full Text Available Extreme rainfall causes surface runoff to flow towards lowlands and subterranean facilities, such as subway stations and buildings with underground spaces in densely packed urban areas. These facilities and areas are therefore vulnerable to catastrophic submergence. However, flood modeling of underground space has not yet been adequately studied because there are difficulties in reproducing the associated multiple horizontal layers connected with staircases or elevators. This study proposes a convenient approach to simulate underground inundation when two layers are connected. The main facet of this approach is to compute the flow flux passing through staircases in an upper layer and to transfer the equivalent quantity to a lower layer. This is defined as the ‘adaptive transfer method’. This method overcomes the limitations of 2D modeling by introducing layers connecting concepts to prevent large variations in mesh sizes caused by complicated underlying obstacles or local details. Consequently, this study aims to contribute to the numerical analysis of flow in inundated underground spaces with multiple floors.
Park, Seongjun; Grewe, Felix; Zhu, Andan; Ruhlman, Tracey A; Sabir, Jamal; Mower, Jeffrey P; Jansen, Robert K
2015-10-01
The exchange of genetic material between cellular organelles through intracellular gene transfer (IGT) or between species by horizontal gene transfer (HGT) has played an important role in plant mitochondrial genome evolution. The mitochondrial genomes of Geraniaceae display a number of unusual phenomena including highly accelerated rates of synonymous substitutions, extensive gene loss and reduction in RNA editing. Mitochondrial DNA sequences assembled for 17 species of Geranium revealed substantial reduction in gene and intron content relative to the ancestor of the Geranium lineage. Comparative analyses of nuclear transcriptome data suggest that a number of these sequences have been functionally relocated to the nucleus via IGT. Evidence for rampant HGT was detected in several Geranium species containing foreign organellar DNA from diverse eudicots, including many transfers from parasitic plants. One lineage has experienced multiple, independent HGT episodes, many of which occurred within the past 5.5 Myr. Both duplicative and recapture HGT were documented in Geranium lineages. The mitochondrial genome of Geranium brycei contains at least four independent HGT tracts that are absent in its nearest relative. Furthermore, G. brycei mitochondria carry two copies of the cox1 gene that differ in intron content, providing insight into contrasting hypotheses on cox1 intron evolution. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.
International Nuclear Information System (INIS)
Ma, L.X.; Tan, J.Y.; Zhao, J.M.; Wang, F.Q.; Wang, C.A.
2017-01-01
The radiative transfer equation (RTE) has been widely used to deal with multiple scattering of light by sparsely and randomly distributed discrete particles. However, for densely packed particles, the RTE becomes questionable due to strong dependent scattering effects. This paper examines the accuracy of RTE by comparing with the exact electromagnetic theory. For an imaginary spherical volume filled with randomly distributed, densely packed spheres, the RTE is solved by the Monte Carlo method combined with the Percus–Yevick hard model to consider the dependent scattering effect, while the electromagnetic calculation is based on the multi-sphere superposition T-matrix method. The Mueller matrix elements of the system with different size parameters and volume fractions of spheres are obtained using both methods. The results verify that the RTE fails to deal with the systems with a high-volume fraction due to the dependent scattering effects. Apart from the effects of forward interference scattering and coherent backscattering, the Percus–Yevick hard sphere model shows good accuracy in accounting for the far-field interference effects for medium or smaller size parameters (up to 6.964 in this study). For densely packed discrete spheres with large size parameters (equals 13.928 in this study), the improvement of dependent scattering correction tends to deteriorate. The observations indicate that caution must be taken when using RTE in dealing with the radiative transfer in dense discrete random media even though the dependent scattering correction is applied. - Highlights: • The Muller matrix of randomly distributed, densely packed spheres are investigated. • The effects of multiple scattering and dependent scattering are analyzed. • The accuracy of radiative transfer theory for densely packed spheres is discussed. • Dependent scattering correction takes effect at medium size parameter or smaller. • Performance of dependent scattering correction
The construction of combinatorial manifolds with prescribed sets of links of vertices
International Nuclear Information System (INIS)
Gaifullin, A A
2008-01-01
To every oriented closed combinatorial manifold we assign the set (with repetitions) of isomorphism classes of links of its vertices. The resulting transformation L is the main object of study in this paper. We pose an inversion problem for 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 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 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 ξ of a space X, this construction enables us to find explicitly a combinatorial manifold M and a map φ:M→X such that φ * [M]=r[ξ] for some positive integer r. The construction is based on resolving singularities of ξ. 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
A binary plasmid system for shuffling combinatorial antibody libraries.
Collet, T A; Roben, P; O'Kennedy, R; Barbas, C F; Burton, D R; Lerner, R A
1992-01-01
We have used a binary system of replicon-compatible plasmids to test the potential for promiscuous recombination of heavy and light chains within sets of human Fab fragments isolated from combinatorial antibody libraries. Antibody molecules showed a surprising amount of promiscuity in that a particular heavy chain could recombine with multiple light chains with retention of binding to a protein antigen. The degree to which a given heavy chain productively paired with any light chain to bind a...
The energy transport in a vegetated (corn) surface layer is examined by solving the vector radiative transfer equation using a numerical iterative approach. This approach allows a higher order that includes the multiple scattering effects. Multiple scattering effects are important when the optical t...
Paths and partitions: Combinatorial descriptions of the parafermionic states
Mathieu, Pierre
2009-09-01
The Zk parafermionic conformal field theories, despite the relative complexity of their modes algebra, offer the simplest context for the study of the bases of states and their different combinatorial representations. Three bases are known. The classic one is given by strings of the fundamental parafermionic operators whose sequences of modes are in correspondence with restricted partitions with parts at distance k -1 differing at least by 2. Another basis is expressed in terms of the ordered modes of the k -1 different parafermionic fields, which are in correspondence with the so-called multiple partitions. Both types of partitions have a natural (Bressoud) path representation. Finally, a third basis, formulated in terms of different paths, is inherited from the solution of the restricted solid-on-solid model of Andrews-Baxter-Forrester. The aim of this work is to review, in a unified and pedagogical exposition, these four different combinatorial representations of the states of the Zk parafermionic models. The first part of this article presents the different paths and partitions and their bijective relations; it is purely combinatorial, self-contained, and elementary; it can be read independently of the conformal-field-theory applications. The second part links this combinatorial analysis with the bases of states of the Zk parafermionic theories. With the prototypical example of the parafermionic models worked out in detail, this analysis contributes to fix some foundations for the combinatorial study of more complicated theories. Indeed, as we briefly indicate in ending, generalized versions of both the Bressoud and the Andrews-Baxter-Forrester paths emerge naturally in the description of the minimal models.
Non-unique factorizations algebraic, combinatorial and analytic theory
Geroldinger, Alfred
2006-01-01
From its origins in algebraic number theory, the theory of non-unique factorizations has emerged as an independent branch of algebra and number theory. Focused efforts over the past few decades have wrought a great number and variety of results. However, these remain dispersed throughout the vast literature. For the first time, Non-Unique Factorizations: Algebraic, Combinatorial, and Analytic Theory offers a look at the present state of the theory in a single, unified resource.Taking a broad look at the algebraic, combinatorial, and analytic fundamentals, this book derives factorization results and applies them in concrete arithmetical situations using appropriate transfer principles. It begins with a basic introduction that can be understood with knowledge of standard basic algebra. The authors then move to the algebraic theory of monoids, arithmetic theory of monoids, the structure of sets of lengths, additive group theory, arithmetical invariants, and the arithmetic of Krull monoids. They also provide a s...
DEFF Research Database (Denmark)
Dalby, Arne Brejning
1994-01-01
A flow graph relating voltages and the forward and reflected propagation modes (¿ TEM) on multiple coupled transmission lines in an inhomogeneous dielectric medium is presented. This flow graph directy gives the different transfer functions, including S-parameters, in matrix form needed to calcul......A flow graph relating voltages and the forward and reflected propagation modes (¿ TEM) on multiple coupled transmission lines in an inhomogeneous dielectric medium is presented. This flow graph directy gives the different transfer functions, including S-parameters, in matrix form needed...
Dynamic combinatorial libraries : new opportunities in systems chemistry
Hunt, Rosemary A. R.; Otto, Sijbren; Hunt, Rosemary A.R.
2011-01-01
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
The Yoccoz Combinatorial Analytic Invariant
DEFF Research Database (Denmark)
Petersen, Carsten Lunde; Roesch, Pascale
2008-01-01
In this paper we develop a combinatorial analytic encoding of the Mandelbrot set M. The encoding is implicit in Yoccoz' proof of local connectivity of M at any Yoccoz parameter, i.e. any at most finitely renormalizable parameter for which all periodic orbits are repelling. Using this encoding we ...... to reprove that the dyadic veins of M are arcs and that more generally any two Yoccoz parameters are joined by a unique ruled (in the sense of Douady-Hubbard) arc in M....
Probabilistic methods in combinatorial analysis
Sachkov, Vladimir N
2014-01-01
This 1997 work explores the role of probabilistic methods for solving combinatorial problems. These methods not only provide the means of efficiently using such notions as characteristic and generating functions, the moment method and so on but also let us use the powerful technique of limit theorems. The basic objects under investigation are nonnegative matrices, partitions and mappings of finite sets, with special emphasis on permutations and graphs, and equivalence classes specified on sequences of finite length consisting of elements of partially ordered sets; these specify the probabilist
Log-balanced combinatorial sequences
Directory of Open Access Journals (Sweden)
Tomislav Došlic
2005-01-01
Full Text Available We consider log-convex sequences that satisfy an additional constraint imposed on their rate of growth. We call such sequences log-balanced. It is shown that all such sequences satisfy a pair of double inequalities. Sufficient conditions for log-balancedness are given for the case when the sequence satisfies a two- (or more- term linear recurrence. It is shown that many combinatorially interesting sequences belong to this class, and, as a consequence, that the above-mentioned double inequalities are valid for all of them.
Indirect Optimization of Three-Dimensional Multiple-Impulse Moon-to-Earth Transfers
Shen, Hong-Xin; Casalino, Lorenzo
2014-11-01
This paper illustrates an indirect method to optimize multiple-impulse trajectories from circular lunar orbit to Earth. Optimization is performed in the circular restricted three-body problem, and the necessary optimality conditions are found through optimal control theory. In order to overcome the difficulty of initial adjoints estimation, a homotopic approach, which is based on an auxiliary optimization problem with known solution, is developed; this approach proves to be robust and efficient. Examples are presented for a range of lunar orbit orientations to assess the impact on velocity impulse requirements. Optimization results for trajectories with different number of impulses are also compared. The developed procedure can support fast and accurate evaluation of the transfer costs for Moon-to-Earth trajectories both in nominal conditions and for contingency plans.
Monjas, Leticia; Swier, Lotteke J Y M; Setyawati, Inda; Slotboom, Dirk Jan; Hirsch, Anna Katharina Herta
2017-01-01
We applied dynamic combinatorial chemistry (DCC) to identify ligands of ThiT, the S-component of the energy-coupling factor (ECF) transporter for thiamine in Lactococcus lactis. We used a pre-equilibrated dynamic combinatorial library (DCL) and saturation-transfer difference (STD) NMR spectroscopy
Combinatorial optimization on a Boltzmann machine
Korst, J.H.M.; Aarts, E.H.L.
1989-01-01
We discuss the problem of solving (approximately) combinatorial optimization problems on a Boltzmann machine. It is shown for a number of combinatorial optimization problems how they can be mapped directly onto a Boltzmann machine by choosing appropriate connection patterns and connection strengths.
Combinatorial Interpretation of General Eulerian Numbers
Tingyao Xiong; Jonathan I. Hall; Hung-Ping Tsao
2014-01-01
Since 1950s, mathematicians have successfully interpreted the traditional Eulerian numbers and $q-$Eulerian numbers combinatorially. In this paper, the authors give a combinatorial interpretation to the general Eulerian numbers defined on general arithmetic progressions { a, a+d, a+2d,...}.
Fourier analysis in combinatorial number theory
International Nuclear Information System (INIS)
Shkredov, Il'ya D
2010-01-01
In this survey applications of harmonic analysis to combinatorial number theory are considered. Discussion topics include classical problems of additive combinatorics, colouring problems, higher-order Fourier analysis, theorems about sets of large trigonometric sums, results on estimates for trigonometric sums over subgroups, and the connection between combinatorial and analytic number theory. Bibliography: 162 titles.
Fourier analysis in combinatorial number theory
Energy Technology Data Exchange (ETDEWEB)
Shkredov, Il' ya D [M. V. Lomonosov Moscow State University, Moscow (Russian Federation)
2010-09-16
In this survey applications of harmonic analysis to combinatorial number theory are considered. Discussion topics include classical problems of additive combinatorics, colouring problems, higher-order Fourier analysis, theorems about sets of large trigonometric sums, results on estimates for trigonometric sums over subgroups, and the connection between combinatorial and analytic number theory. Bibliography: 162 titles.
Toward Chemical Implementation of Encoded Combinatorial Libraries
DEFF Research Database (Denmark)
Nielsen, John; Janda, Kim D.
1994-01-01
The recent application of "combinatorial libraries" to supplement existing drug screening processes might simplify and accelerate the search for new lead compounds or drugs. Recently, a scheme for encoded combinatorial chemistry was put forward to surmount a number of the limitations possessed...
Electron pumping of the ground state of 21Ne. Transfers and multiple diffusion processes
International Nuclear Information System (INIS)
Stoeckel, F.; Lombardi, M.
1978-01-01
The electron-pumping process of the ground state of 21 Ne has been studied. It is demonstrated how in a neon cell at a pressure of 10 -4 to 10 -2 torr, a high frequency discharge can create a nuclear spin alignment in the fundamental level (I=3/2) when the excited levels are themselves aligned. The nuclear alignment is observed by monitoring the change of the linear polarization of several optical transitions during the magnetic resonance of the fundamental level. Various transfers of the alignments are investigated and a detailed study of the influence of the multiple diffusion is carried out. The multiple diffusion produces a depolarization and a relaxation of the nuclear spin. A theoretical calculation has been made for a two-level system with a J=1 radiative level and a J=0 ground state. Experimentally a relaxation time of the nuclear alignment varying from 37 ms to 240 ms is observed when the neon pressure decreases from 10 -2 to 10 -4 torr [fr
Seven-Tesla Magnetization Transfer Imaging to Detect Multiple Sclerosis White Matter Lesions.
Chou, I-Jun; Lim, Su-Yin; Tanasescu, Radu; Al-Radaideh, Ali; Mougin, Olivier E; Tench, Christopher R; Whitehouse, William P; Gowland, Penny A; Constantinescu, Cris S
2018-03-01
Fluid-attenuated inversion recovery (FLAIR) imaging at 3 Tesla (T) field strength is the most sensitive modality for detecting white matter lesions in multiple sclerosis. While 7T FLAIR is effective in detecting cortical lesions, it has not been fully optimized for visualization of white matter lesions and thus has not been used for delineating lesions in quantitative magnetic resonance imaging (MRI) studies of the normal appearing white matter in multiple sclerosis. Therefore, we aimed to evaluate the sensitivity of 7T magnetization-transfer-weighted (MT w ) images in the detection of white matter lesions compared with 3T-FLAIR. Fifteen patients with clinically isolated syndrome, 6 with multiple sclerosis, and 10 healthy participants were scanned with 7T 3-dimensional (D) MT w and 3T-2D-FLAIR sequences on the same day. White matter lesions visible on either sequence were delineated. Of 662 lesions identified on 3T-2D-FLAIR images, 652 were detected on 7T-3D-MT w images (sensitivity, 98%; 95% confidence interval, 97% to 99%). The Spearman correlation coefficient between lesion loads estimated by the two sequences was .910. The intrarater and interrater reliability for 7T-3D-MT w images was good with an intraclass correlation coefficient (ICC) of 98.4% and 81.8%, which is similar to that for 3T-2D-FLAIR images (ICC 96.1% and 96.7%). Seven-Tesla MT w sequences detected most of the white matter lesions identified by FLAIR at 3T. This suggests that 7T-MT w imaging is a robust alternative for detecting demyelinating lesions in addition to 3T-FLAIR. Future studies need to compare the roles of optimized 7T-FLAIR and of 7T-MT w imaging. © 2017 The Authors. Journal of Neuroimaging published by Wiley Periodicals, Inc. on behalf of American Society of Neuroimaging.
Kurien, Biji T; Scofield, R Hal
2009-01-01
Protein blotting is an invaluable technique in immunology to detect and characterize proteins of low abundance. Proteins resolved on sodium dodecyl sulfate (SDS) polyacrylamide gels are normally transferred electrophoretically to adsorbent membranes such as nitrocellulose or polyvinylidene diflouride membranes. Here, we describe the nonelectrophroretic transfer of the Ro 60 (or SSA) autoantigen, 220- and 240-kD spectrin antigens, and prestained molecular weight standards from SDS polyacrylamide gels to obtain up to 12 immunoblots from a single gel and multiple sera.
Directory of Open Access Journals (Sweden)
David A. Rudko
2016-01-01
Full Text Available The purpose of our study was to evaluate the utility of measurements of cortical surface magnetization transfer ratio (csMTR on the inner, mid and outer cortical boundaries as clinically accessible biomarkers of cortical gray matter pathology in multiple sclerosis (MS. Twenty-five MS patients and 12 matched controls were recruited from the MS Clinic of the Montreal Neurological Institute. Anatomical and magnetization transfer ratio (MTR images were acquired using 3 Tesla MRI at baseline and two-year time-points. MTR maps were smoothed along meshes representing the inner, mid and outer neocortical boundaries. To evaluate csMTR reductions suggestive of sub-pial demyelination in MS patients, a mixed model analysis was carried out at both the individual vertex level and in anatomically parcellated brain regions. Our results demonstrate that focal areas of csMTR reduction are most prevalent along the outer cortical surface in the superior temporal and posterior cingulate cortices, as well as in the cuneus and precentral gyrus. Additionally, age regression analysis identified that reductions of csMTR in MS patients increase with age but appear to hit a plateau in the outer caudal anterior cingulate, as well as in the precentral and postcentral cortex. After correction for the naturally occurring gradient in cortical MTR, the difference in csMTR between the inner and outer cortex in focal areas in the brains of MS patients correlated with clinical disability. Overall, our findings support multi-surface analysis of csMTR as a sensitive marker of cortical sub-pial abnormality indicative of demyelination in MS patients.
Standardization of milk mid-infrared spectrometers for the transfer and use of multiple models.
Grelet, C; Pierna, J A Fernández; Dardenne, P; Soyeurt, H; Vanlierde, A; Colinet, F; Bastin, C; Gengler, N; Baeten, V; Dehareng, F
2017-10-01
An increasing number of models are being developed to provide information from milk Fourier transform mid-infrared (FT-MIR) spectra on fine milk composition, technological properties of milk, or even cows' physiological status. In this context, and to take advantage of these existing models, the purpose of this work was to evaluate whether a spectral standardization method can enable the use of multiple equations within a network of different FT-MIR spectrometers. The piecewise direct standardization method was used, matching "slave" instruments to a common reference, the "master." The effect of standardization on network reproducibility was assessed on 66 instruments from 3 different brands by comparing the spectral variability of the slaves and the master with and without standardization. With standardization, the global Mahalanobis distance from the slave spectra to the master spectra was reduced on average from 2,655.9 to 14.3, representing a significant reduction of noninformative spectral variability. The transfer of models from instrument to instrument was tested using 3 FT-MIR models predicting (1) the quantity of daily methane emitted by dairy cows, (2) the concentration of polyunsaturated fatty acids in milk, and (3) the fresh cheese yield. The differences, in terms of root mean squared error, between master predictions and slave predictions were reduced after standardization on average from 103 to 17 g/d, from 0.0315 to 0.0045 g/100 mL of milk, and from 2.55 to 0.49 g of curd/100 g of milk, respectively. For all the models, standard deviations of predictions among all the instruments were also reduced by 5.11 times for methane, 5.01 times for polyunsaturated fatty acids, and 7.05 times for fresh cheese yield, showing an improvement of prediction reproducibility within the network. Regarding the results obtained, spectral standardization allows the transfer and use of multiple models on all instruments as well as the improvement of spectral and prediction
Energy Technology Data Exchange (ETDEWEB)
Silver, N.C. [NMR Research Unit and Department of Clinical Neurology, Institute of Neurology, Queen Square, London WC1N 3BG (United Kingdom); Barker, G.J. [NMR Research Unit and Department of Clinical Neurology, Institute of Neurology, Queen Square, London WC1N 3BG (United Kingdom); Losseff, N.A. [NMR Research Unit and Department of Clinical Neurology, Institute of Neurology, Queen Square, London WC1N 3BG (United Kingdom); Gawne-Cain, M.L. [NMR Research Unit and Department of Clinical Neurology, Institute of Neurology, Queen Square, London WC1N 3BG (United Kingdom); MacManus, D.G. [NMR Research Unit and Department of Clinical Neurology, Institute of Neurology, Queen Square, London WC1N 3BG (United Kingdom); Thompson, A.J. [NMR Research Unit and Department of Clinical Neurology, Institute of Neurology, Queen Square, London WC1N 3BG (United Kingdom); Miller, D.H. [NMR Research Unit and Department of Clinical Neurology, Institute of Neurology, Queen Square, London WC1N 3BG (United Kingdom)
1997-06-01
MRI readily detects the lesions of multiple sclerosis (MS) in the brain and spinal cord. Conventional MRI sequences do not, however, permit distinction between the various pathological characteristics (oedema, demyelination, axonal loss and gliosis) of lesions in MS. Magnetisation transfer (MT) imaging may be more specific in distinguishing the pathologies responsible for disability in MS, namely demyelination and axonal loss, and therefore may have a potential role in monitoring treatment. We have applied MT imaging to the cervical spinal cord to see if it is feasible to measure MT ratios (MTR) in this region where pathological changes may result in considerable disability. We studied 12 patients with MS and 12 age- and sex-matched normal controls using a sagittal T2-weighted fast spin-echo sequence with and without an MT pulse. The median value for cervical cord mean MTR measurement in normal controls was 19.30 % units (interquartile range 19.05-19.55), whereas values were significantly lower in MS patients (median = 17.95 % units, interquartile range 17.25-19.00, P = 0.0004). There was a low intrarater variability for repeated mean MTR measurements. We conclude that it is possible to measure MTR in the cervical spinal cord, that a significant reduction occurs in patients with MS, and that there may be a role for this measure in future MS treatment trials. (orig.). With 2 figs., 1 tab.
International Nuclear Information System (INIS)
Silver, N.C.; Barker, G.J.; Losseff, N.A.; Gawne-Cain, M.L.; MacManus, D.G.; Thompson, A.J.; Miller, D.H.
1997-01-01
MRI readily detects the lesions of multiple sclerosis (MS) in the brain and spinal cord. Conventional MRI sequences do not, however, permit distinction between the various pathological characteristics (oedema, demyelination, axonal loss and gliosis) of lesions in MS. Magnetisation transfer (MT) imaging may be more specific in distinguishing the pathologies responsible for disability in MS, namely demyelination and axonal loss, and therefore may have a potential role in monitoring treatment. We have applied MT imaging to the cervical spinal cord to see if it is feasible to measure MT ratios (MTR) in this region where pathological changes may result in considerable disability. We studied 12 patients with MS and 12 age- and sex-matched normal controls using a sagittal T2-weighted fast spin-echo sequence with and without an MT pulse. The median value for cervical cord mean MTR measurement in normal controls was 19.30 % units (interquartile range 19.05-19.55), whereas values were significantly lower in MS patients (median = 17.95 % units, interquartile range 17.25-19.00, P 0.0004). There was a low intrarater variability for repeated mean MTR measurements. We conclude that it is possible to measure MTR in the cervical spinal cord, that a significant reduction occurs in patients with MS, and that there may be a role for this measure in future MS treatment trials. (orig.). With 2 figs., 1 tab
A MULTIPLE SCATTERING POLARIZED RADIATIVE TRANSFER MODEL: APPLICATION TO HD 189733b
Energy Technology Data Exchange (ETDEWEB)
Kopparla, Pushkar; Yung, Yuk L. [Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA (United States); Natraj, Vijay; Swain, Mark R. [Jet Propulsion Laboratory (NASA-JPL), Pasadena, CA (United States); Zhang, Xi [Lunar and Planetary Laboratory, University of Arizona, Tucson, AZ (United States); Wiktorowicz, Sloane J., E-mail: pkk@gps.caltech.edu [Department of Astronomy and Astrophysics, University of California, Santa Cruz, CA (United States)
2016-01-20
We present a multiple scattering vector radiative transfer model that produces disk integrated, full phase polarized light curves for reflected light from an exoplanetary atmosphere. We validate our model against results from published analytical and computational models and discuss a small number of cases relevant to the existing and possible near-future observations of the exoplanet HD 189733b. HD 189733b is arguably the most well observed exoplanet to date and the only exoplanet to be observed in polarized light, yet it is debated if the planet’s atmosphere is cloudy or clear. We model reflected light from clear atmospheres with Rayleigh scattering, and cloudy or hazy atmospheres with Mie and fractal aggregate particles. We show that clear and cloudy atmospheres have large differences in polarized light as compared to simple flux measurements, though existing observations are insufficient to make this distinction. Futhermore, we show that atmospheres that are spatially inhomogeneous, such as being partially covered by clouds or hazes, exhibit larger contrasts in polarized light when compared to clear atmospheres. This effect can potentially be used to identify patchy clouds in exoplanets. Given a set of full phase polarimetric measurements, this model can constrain the geometric albedo, properties of scattering particles in the atmosphere, and the longitude of the ascending node of the orbit. The model is used to interpret new polarimetric observations of HD 189733b in a companion paper.
Gamma-ray multiplicity measurements and angular momentum transfer in deeply inelastic collisions
International Nuclear Information System (INIS)
Perrin, N.; Peter, J.
1977-01-01
In DIC, the part of the initial orbital angular momentum l which is transferred into internal angular momenta Δl of the fragments depends on the degree of cohesion of the composite system. The (few) measured gamma-rays multiplicities are compared to those observed for similar compound nuclei and for fission fragments. Δl increases with the kinetic energy relaxation. For medium-mass systems, the cohesion varies continuously from the rolling to the sticking situation when the decay time of the composite system increases. The rigid body situation is obtained for a small part of the relaxed events. For heavy systems, rigid rotation seems to be much more common, which will allow to extract information on the deflection function. The time needed to reach the rigid situation is intermediate between those of kinetic energy relaxation and mass asymmetry relaxation. An additional angular momentum can be added in the fragments, due to a bending mode at the scission-point, like in fission. That can explain the observed low anisotropy of the gamma-rays angular distribution
DEFF Research Database (Denmark)
Palmgren, Michael; Engström, Karin; Hallström, Björn M.
2017-01-01
the evolutionary origin of AS3MT and assessed the ability of different genotypes to produce methylated arsenic metabolites. Phylogenetic analysis suggests that multiple, independent horizontal gene transfers between different bacteria, and from bacteria to eukaryotes, increased tolerance to environmental arsenic...
Mesaros, S.; Rocca, M.A.; Sormani, M.P.; Valsasina, P.; Markowitz, C.; De Stefano, N.; Montalban, X.; Barkhof, F.; Ranjeva, J.P.; Sailer, M.; Kappos, L.; Comi, G.; Filippi, M.
2010-01-01
This study was performed to assess the temporal evolution of damage within lesions and the normal-appearing white matter, measured using frequent magnetization transfer (MT) MRI, in relapsing-remitting multiple sclerosis (RRMS). The relationship of MT ratio (MTR) changes with measures of lesion
Thielen, L.; Hanjalić, K.; Jonker, H.; Manceau, R.
2005-01-01
We present numerical computations of flow and heat transfer in multiple jets impinging normally on a flat heated surface, obtained with a new second-moment turbulence closure combined with an elliptic blending model of non-viscous wall blocking effect. This model provides the mean velocity and
DEFF Research Database (Denmark)
Wahlgren, Bjarne; Aarkrog, Vibe
Bogen er den første samlede indføring i transfer på dansk. Transfer kan anvendes som praksis-filosofikum. Den giver en systematisk indsigt til den studerende, der spørger: Hvordan kan teoretisk viden bruges til at reflektere over handlinger i situationer, der passer til min fremtidige arbejdsplads?...
Tumor-targeting peptides from combinatorial libraries*
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
Combinatorial Micro-Macro Dynamical Systems
Diaz, Rafael; Villamarin, Sergio
2015-01-01
The second law of thermodynamics states that the entropy of an isolated system is almost always increasing. We propose combinatorial formalizations of the second law and explore their conditions of possibilities.
Cubical version of combinatorial differential forms
DEFF Research Database (Denmark)
Kock, Anders
2010-01-01
The theory of combinatorial differential forms is usually presented in simplicial terms. We present here a cubical version; it depends on the possibility of forming affine combinations of mutual neighbour points in a manifold, in the context of synthetic differential geometry.......The theory of combinatorial differential forms is usually presented in simplicial terms. We present here a cubical version; it depends on the possibility of forming affine combinations of mutual neighbour points in a manifold, in the context of synthetic differential geometry....
Conferences on Combinatorial and Additive Number Theory
2014-01-01
This proceedings volume is based on papers presented at the Workshops on Combinatorial and Additive Number Theory (CANT), which were held at the Graduate Center of the City University of New York in 2011 and 2012. The goal of the workshops is to survey recent progress in combinatorial number theory and related parts of mathematics. The workshop attracts researchers and students who discuss the state-of-the-art, open problems, and future challenges in number theory.
Roberts, Sa; McGowan, L; Hirst, Wm; Brison, Dr; Vail, A; Lieberman, Ba
2010-07-01
In vitro fertilisation (IVF) treatments involve an egg retrieval process, fertilisation and culture of the resultant embryos in the laboratory, and the transfer of embryos back to the mother over one or more transfer cycles. The first transfer is usually of fresh embryos and the remainder may be cryopreserved for future frozen cycles. Most commonly in UK practice two embryos are transferred (double embryo transfer, DET). IVF techniques have led to an increase in the number of multiple births, carrying an increased risk of maternal and infant morbidity. The UK Human Fertilisation and Embryology Authority (HFEA) has adopted a multiple birth minimisation strategy. One way of achieving this would be by increased use of single embryo transfer (SET). To collate cohort data from treatment centres and the HFEA; to develop predictive models for live birth and twinning probabilities from fresh and frozen embryo transfers and predict outcomes from treatment scenarios; to understand patients' perspectives and use the modelling results to investigate the acceptability of twin reduction policies. A multidisciplinary approach was adopted, combining statistical modelling with qualitative exploration of patients' perspectives: interviews were conducted with 27 couples at various stages of IVF treatment at both UK NHS and private clinics; datasets were collated of over 90,000 patients from the HFEA registry and nearly 9000 patients from five clinics, both over the period 2000-5; models were developed to determine live birth and twin outcomes and predict the outcomes of policies for selecting patients for SET or DET in the fresh cycle following egg retrieval and fertilisation, and the predictions were used in simulations of treatments; two focus groups were convened, one NHS and one web based on a patient organisation's website, to present the results of the statistical analyses and explore potential treatment policies. The statistical analysis revealed no characteristics that
International Nuclear Information System (INIS)
Papanikolaou, Nickolas; Papadaki, Eufrosini; Karampekios, Spyros; Maris, Thomas; Prassopoulos, Panos; Gourtsoyiannis, Nicholas; Spilioti, Martha
2004-01-01
The aim of the current study was to perform T2 relaxation time measurements in multiple sclerosis (MS) patients and correlate them with magnetization transfer ratio (MTR) measurements, in order to investigate in more detail the various histopathological changes that occur in lesions and normal-appearing white matter (NAWM). A total number of 291 measurements of MTR and T2 relaxation times were performed in 13 MS patients and 10 age-matched healthy volunteers. Measurements concerned MS plaques (105), NAWM (80), and ''dirty'' white matter (DWM; 30), evenly divided between the MS patients, and normal white matter (NWM; 76) in the healthy volunteers. Biexponential T2 relaxation-time analysis was performed, and also possible linearity between MTR and mean T2 relaxation times was evaluated using linear regression analysis in all subgroups. Biexponential relaxation was more pronounced in ''black-hole'' lesions (16.6%) and homogeneous enhancing plaques (10%), whereas DWM, NAWM, and mildly hypointense lesions presented biexponential behavior with a lower frequency(6.6, 5, and 3.1%, respectively). Non-enhancing isointense lesions and normal white matter did not reveal any biexponentional behavior. Linear regression analysis between monoexponential T2 relaxation time and MTR measurements demonstrated excellent correlation for DWM(r=-0.78, p<0.0001), very good correlation for black-hole lesions(r=-0.71, p=0.002), good correlation for isointense lesions(r=-0.60, p=0.005), moderate correlation for mildly hypointense lesions(r=-0.34, p=0.007), and non-significant correlation for homogeneous enhancing plaques, NAWM, and NWM. Biexponential T2 relaxation-time behavior is seen in only very few lesions (mainly on plaques with high degree of demyelination and axonal loss). A strong correlation between MTR and monoexponential T2 values was found in regions where either inflammation or demyelination predominates; however, when both pathological conditions coexist, this linear
Quantification of blood-to-brain transfer rate in multiple sclerosis
Taheri, Saeid; Rosenberg, Gary A.; Ford, Corey
2016-01-01
Blood–brain barrier (BBB) disruption visualized in lesions by MRI is a major biomarker of disease activity in multiple sclerosis (MS). However, in MS, destruction occurs to a variable extent in lesions as well as in gray matter (GM) and in the normal appearing white matter (NAWM). A method to quantify the BBB disruption in lesions as well as in non-lesion areas would be useful for assessment of MS progression and treatments. The objective of this study was to quantify the BBB transfer rate (Ki) in WM lesions, in the NAWM, and in the full-brain of MS patients. Thirteen MS patients with active lesions and 10 healthy controls with age and gender matching were recruited for full-brain and WM Ki studies. Dynamic contrast-enhanced MRI (DCEMRI) scans were conducted using T1 mapping with partial inversion recovery (TAPIR), a fast T1 mapping technique, following administration of a quarter-dose of the contrast agent Gadolinium-DTPA (Gd-DTPA). The Patlak modeling technique was used to derive a voxel-based map of Ki. In all patients contrast-enhanced lesions, quantified by Ki maps, were observed. Compared with controls, patients with MS exhibited an increase in mean Ki of the full-brain (P-value<0.05) but no significant difference in mean Ki of NAWM. The identified increase in full-brain Ki of MS patients suggests a global vascular involvement associated with MS disease. The lack of observed significant decrease in Ki in NAWM suggests lower involvement of WM vasculature than full-brain vasculature in MS. Ki maps constructed from time series data acquired by DCEMRI provide additional information about BBB that could be used for evaluation of vascular involvement in MS and monitoring treatment effectiveness. PMID:25877634
Multiple Scattering Principal Component-based Radiative Transfer Model (PCRTM) from Far IR to UV-Vis
Liu, X.; Wu, W.; Yang, Q.
2017-12-01
Modern satellite hyperspectral satellite remote sensors such as AIRS, CrIS, IASI, CLARREO all require accurate and fast radiative transfer models that can deal with multiple scattering of clouds and aerosols to explore the information contents. However, performing full radiative transfer calculations using multiple stream methods such as discrete ordinate (DISORT), doubling and adding (AD), successive order of scattering order of scattering (SOS) are very time consuming. We have developed a principal component-based radiative transfer model (PCRTM) to reduce the computational burden by orders of magnitudes while maintain high accuracy. By exploring spectral correlations, the PCRTM reduce the number of radiative transfer calculations in frequency domain. It further uses a hybrid stream method to decrease the number of calls to the computational expensive multiple scattering calculations with high stream numbers. Other fast parameterizations have been used in the infrared spectral region reduce the computational time to milliseconds for an AIRS forward simulation (2378 spectral channels). The PCRTM has been development to cover spectral range from far IR to UV-Vis. The PCRTM model have been be used for satellite data inversions, proxy data generation, inter-satellite calibrations, spectral fingerprinting, and climate OSSE. We will show examples of applying the PCRTM to single field of view cloudy retrievals of atmospheric temperature, moisture, traces gases, clouds, and surface parameters. We will also show how the PCRTM are used for the NASA CLARREO project.
Transfer buffer containing methanol can be reused multiple times in protein electrotransfer.
Pettegrew, Colin J; Jayini, Renuka; Islam, M Rafiq
2009-04-01
We investigated the feasibility of repeated use of transfer buffer containing methanol in electrotransfer of proteins from sodium dodecyl sulfate-polyacrylamide gels to polyvinylidene difluoride (PVDF) membrane using a prestained protein marker of broad molecular sizes. Transfer of the antitumor protein p53 in HEK293T cell extracts, using fresh and used transfer buffer, followed by detection with anti-p53 antibody was also performed to test detectability in immunoblot. Results from these experiments indicate that the transfer buffer can be reused at least five times and maintain a similar extent of protein transfer to PVDF membrane. Repeated use of the transfer buffer containing methanol will significantly reduce the volume of hazardous waste generated and its disposal cost as well as its adverse effect on environment.
Janssen, Alisha; Boster, Aaron; Lee, HyunKyu; Patterson, Beth; Prakash, Ruchika Shaurya
2015-01-01
Multiple sclerosis (MS) is a neurodegenerative disease of the central nervous system that results in diffuse nerve damage and associated physical and cognitive impairments. Of the few comprehensive rehabilitation options that exist for populations with lower baseline cognitive functioning, those that have been successful at eliciting broad cognitive improvements have focused on a multimodal training approach, emphasizing complex cognitive processing that utilizes multiple domains simultaneously. The current study sought to determine the feasibility of an 8-week, hybrid-variable priority training (HVT) program, with a secondary aim to assess the success of this training paradigm at eliciting broad cognitive transfer effects. Capitalizing on the multimodal training modalities offered by the Space Fortress platform, we compared the HVT strategy-based intervention with a waitlist control group, to primarily assess skill acquisition and secondarily determine presence of cognitive transfer. Twenty-eight participants met inclusionary criteria for the study and were randomized to either training or waitlist control groups. To assess broad transfer effects, a battery of neuropsychological tests was administered pre- and post-intervention. The results indicated an overall improvement in skill acquisition and evidence for the feasibility of the intervention, but a lack of broad transfer to tasks of cognitive functioning. Participants in the training group, however, did show improvements on a measure of spatial short-term memory. The current investigation provided support for the feasibility of a multimodal training approach, using the HVT strategy, within the MS population, but lacked broad transfer to multiple domains of cognitive functioning. Future improvements to obtain greater cognitive transfer efficacy would include a larger sample size, a longer course of training to evoke greater game score improvement, the inclusion of only cognitively impaired individuals, and
International Nuclear Information System (INIS)
Capony, V.
1996-01-01
This thesis presents the works performed for the experiment NA50 at CERN, in he framework of the development of its multiplicity detector. The two first chapters describe the physical aims of the experiment and the apparatus used. The remaining part of this document shows the data readout device, developed for the multiplicity detector. Built on a T8 transputer network, this system is able to treat 8 Mbytes of data at each SPS accelerator cycle. It integrates an on-line event-builder. A filtering algorithm estimates the validity of the information and allows the flagging of all the data. The last function of this transputers network is to transfer data from the detector to the data acquisition system. Our system is able to control a data rate transfer of 35 Gbytes per day. (author)
Takashima, Ryoichi; Takiguchi, Tetsuya; Ariki, Yasuo
2013-02-01
This paper presents a method for discriminating the location of the sound source (talker) using only a single microphone. In a previous work, the single-channel approach for discriminating the location of the sound source was discussed, where the acoustic transfer function from a user's position is estimated by using a hidden Markov model of clean speech in the cepstral domain. In this paper, each cepstral dimension of the acoustic transfer function is newly weighted, in order to obtain the cepstral dimensions having information that is useful for classifying the user's position. Then, this paper proposes a feature-weighting method for the cepstral parameter using multiple kernel learning, defining the base kernels for each cepstral dimension of the acoustic transfer function. The user's position is trained and classified by support vector machine. The effectiveness of this method has been confirmed by sound source (talker) localization experiments performed in different room environments.
Lovell, Heather
2016-01-01
This paper draws on Kingdon’s Multiple Streams Approach (MSA) to consider international flows of policy, not just domestic. It is argued that using the MSA in conjunction with international policy transfer and mobility theories allows for a fuller explanation of the development of smart electricity metering policy in Australia. The MSA is based originally on empirical research within a single country - the USA - in the late 1970s, and all three of the ‘streams’ identified as important to poli...
Voit, Florian; Schäfer, Jan; Kienle, Alwin
2009-09-01
We present a methodology to compare results of classical radiative transfer theory against exact solutions of Maxwell theory for a high number of spheres. We calculated light propagation in a cubic scattering region (20 x 20 x 20 microm(3)) consisting of different concentrations of polystyrene spheres in water (diameter 2 microm) by an analytical solution of Maxwell theory and by a numerical solution of radiative transfer theory. The relative deviation of differential as well as total scattering cross sections obtained by both approaches was evaluated for each sphere concentration. For the considered case, we found that deviations due to radiative transfer theory remain small, even for concentrations up to ca. 20 vol. %.
African Journals Online (AJOL)
This paper reports on further studies on long range energy transfer between curcumine as donor and another thiazine dye, thionine, which is closely related to methylene blue as energy harvester (Figure 1). Since thionine is known to have a higher quantum yield of singlet oxygen sensitization than methylene blue [8], it is ...
Combinatorial stresses kill pathogenic Candida species
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
Bo Göransson; Rasigan Maharajh; Ulrich Schmoch
2009-01-01
The third mission encompasses all activities of universities beyond their first and second missions, education and research. An analysis of various countries with different economic, political and geographic features reveals an increased demand for such activities in particular with regard to technology transfer, but also as to the support of the civil society in more general terms. Therefore the universities have to find a new balance between education, research and transfer/extension. Howev...
Peters, Sanne; Clarebout, Geraldine; van Nuland, Marc; Aertgeerts, Bert; Roex, Ann
2018-01-01
Phenomenon: Transfer of learning between classroom and workplace appears to be difficult. Various conceptions about learning in either the classroom or the workplace exist among stakeholders, yet little is known about their conceptions of the transfer of learning between both settings. This study explored stakeholders' conceptions about transfer of learning between classroom-based learning and workplace practice. Homogeneous focus groups with students, medical teachers, and workplace supervisors were conducted using a constructivist grounded theory approach. The 54 participants' conceptions mainly related to their beliefs about who was responsible for (a) preparing for transfer of learning, (b) being at the workplace and connecting back to classroom-based learning, and (c) reflecting on transfer of learning and continuing the process. A continuum was recognized between those who held medical teachers/workplace supervisors responsible and those who held students responsible. Insights: There appears to be a variety of conceptions about who is responsible for enabling the transfer process. These conceptions may influence learning and instructional activities. Hence, it may be necessary to make these beliefs explicit in order to better align stakeholders' conceptions. To this end, the conceptual framework created in this study may be a useful tool.
Park, Marcelo; Costa, Eduardo Leite Vieira; Maciel, Alexandre Toledo; Silva, Débora Prudêncio E; Friedrich, Natalia; Barbosa, Edzangela Vasconcelos Santos; Hirota, Adriana Sayuri; Schettino, Guilherme; Azevedo, Luciano Cesar Pontes
2013-01-01
Extracorporeal membrane oxygenation (ECMO) has gained renewed interest in the treatment of respiratory failure since the advent of the modern polymethylpentene membranes. Limited information exists, however, on the performance of these membranes in terms of gas transfers during multiple organ failure (MOF). We investigated determinants of oxygen and carbon dioxide transfer as well as biochemical alterations after the circulation of blood through the circuit in a pig model under ECMO support before and after induction of MOF. A predefined sequence of blood and sweep flows was tested before and after the induction of MOF with fecal peritonitis and saline lavage lung injury. In the multivariate analysis, oxygen transfer had a positive association with blood flow (slope = 66, Pmembrane PaCO(2) (slope = -0.96, P = 0.001) and SatO(2) (slope = -1.7, Ptransfer had a positive association with blood flow (slope = 17, Pmembrane PaCO(2) (slope = 1.2, Ptransfers were significantly determined by blood flow. Oxygen transfer was modulated by the pre-membrane SatO(2) and CO(2), while carbon dioxide transfer was affected by the gas flow, pre-membrane CO(2) and hemoglobin.
Local formulae for combinatorial Pontryagin classes
International Nuclear Information System (INIS)
Gaifullin, Alexander A
2004-01-01
Let p(|K|) be the characteristic class of a combinatorial manifold K given by a polynomial p in the rational Pontryagin classes of K. We prove that for any polynomial p there is a function taking each combinatorial manifold K to a cycle z p (K) in its rational simplicial chains such that: 1) the Poincare dual of z p (K) represents the cohomology class p(|K|); 2) the coefficient of each simplex Δ in the cycle z p (K) is determined solely by the combinatorial type of linkΔ. We explicitly describe all such functions for the first Pontryagin class. We obtain estimates for the denominators of the coefficients of the simplices in the cycles z p (K)
Accessing Specific Peptide Recognition by Combinatorial Chemistry
DEFF Research Database (Denmark)
Li, Ming
Molecular recognition is at the basis of all processes for life, and plays a central role in many biological processes, such as protein folding, the structural organization of cells and organelles, signal transduction, and the immune response. Hence, my PhD project is entitled “Accessing Specific...... Peptide Recognition by Combinatorial Chemistry”. Molecular recognition is a specific interaction between two or more molecules through noncovalent bonding, such as hydrogen bonding, metal coordination, van der Waals forces, π−π, hydrophobic, or electrostatic interactions. The association involves kinetic....... Combinatorial chemistry was invented in 1980s based on observation of functional aspects of the adaptive immune system. It was employed for drug development and optimization in conjunction with high-throughput synthesis and screening. (chapter 2) Combinatorial chemistry is able to rapidly produce many thousands...
A quark interpretation of the combinatorial hierarchy
International Nuclear Information System (INIS)
Enqvist, Kari.
1979-01-01
We propose a physical interpretation of the second level of the combinatorial hierarchy in terms of three quarks, three antiquarks and the vacuum. This interpretation allows us to introduce a new quantum number, which measures electromagnetic mass splitting of the quarks. We extend our argument by analogue to baryons, and find some SU(3) and some new mass formulas for baryons. The generalization of our approach to other hierarchy levels is discussed. We present also an empirical mass formula for baryons, which seems to be loosely connected with the combinatorial hierarchy. (author)
Combinatorial designs a tribute to Haim Hanani
Hartman, A
1989-01-01
Haim Hanani pioneered the techniques for constructing designs and the theory of pairwise balanced designs, leading directly to Wilson''s Existence Theorem. He also led the way in the study of resolvable designs, covering and packing problems, latin squares, 3-designs and other combinatorial configurations.The Hanani volume is a collection of research and survey papers at the forefront of research in combinatorial design theory, including Professor Hanani''s own latest work on Balanced Incomplete Block Designs. Other areas covered include Steiner systems, finite geometries, quasigroups, and t-designs.
Zhou, Qiao; Du, Can; Yang, Li; Zhao, Meiyu; Dai, Yumei; Song, Peng
2017-06-22
The single and dual cooperated proton transfer dynamic process in the excited state of 1,5-dihydroxyanthraquinone (1,5-DHAQ) was theoretically investigated, taking solvent effects (ethanol) into account. The absorption and fluorescence spectra were simulated, and dual fluorescence exhibited, which is consistent with previous experiments. Analysis of the calculated IR and Raman vibration spectra reveals that the intramolecular hydrogen bonding interactions (O 20 -H 21 ···O 24 and O 22 -H 23 ···O 25 ) are strengthened following the excited proton transfer process. Finally, by constructing the potential energy surfaces of the ground state, first excited singlet state, and triplet state, the mechanism of the intramolecular proton transfer of 1,5-DHAQ can be revealed.
Dynamic combinatorial chemistry with diselenides and disulfides in water
DEFF Research Database (Denmark)
Rasmussen, Brian; Sørensen, Anne; Gotfredsen, Henrik
2014-01-01
Diselenide exchange is introduced as a reversible reaction in dynamic combinatorial chemistry in water. At neutral pH, diselenides are found to mix with disulfides and form dynamic combinatorial libraries of diselenides, disulfides, and selenenylsulfides. This journal is......Diselenide exchange is introduced as a reversible reaction in dynamic combinatorial chemistry in water. At neutral pH, diselenides are found to mix with disulfides and form dynamic combinatorial libraries of diselenides, disulfides, and selenenylsulfides. This journal is...
A New Approach for Proving or Generating Combinatorial Identities
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…
Asessing for Structural Understanding in Childrens' Combinatorial Problem Solving.
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…
Steenhuis, H.J.; de Bruijn, E.J.
2005-01-01
International technology transfer occurs frequently in international operations, for example in cases of foreign direct investment where companies set-up existing manufacturing lines in new locations. It also occurs in situations of international outsourcing where a new supplier receives product
Combinatorial biosynthesis of medicinal plant secondary metabolites
Julsing, Mattijs K.; Koulman, Albert; Woerdenbag, Herman J.; Quax, Wim J.; Kayser, Oliver
2006-01-01
Combinatorial biosynthesis is a new tool in the generation of novel natural products and for the production of rare and expensive natural products. The basic concept is combining metabolic pathways in different organisms on a genetic level. As a consequence heterologous organisms provide precursors
Infinitary Combinatory Reduction Systems: Normalising Reduction Strategies
Ketema, J.; Simonsen, Jakob Grue
2010-01-01
We study normalising reduction strategies for infinitary Combinatory Reduction Systems (iCRSs). We prove that all fair, outermost-fair, and needed-fair strategies are normalising for orthogonal, fully-extended iCRSs. These facts properly generalise a number of results on normalising strategies in
PIPERIDINE OLIGOMERS AND COMBINATORIAL LIBRARIES THEREOF
DEFF Research Database (Denmark)
1999-01-01
The present invention relates to piperidine oligomers, methods for the preparation of piperidine oligomers and compound libraries thereof, and the use of piperidine oligomers as drug substances. The present invention also relates to the use of combinatorial libraries of piperidine oligomers...... in libraries (arrays) of compounds especially suitable for screening purposes....
Gian-Carlos Rota and Combinatorial Math.
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
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…
Torus actions, combinatorial topology, and homological algebra
International Nuclear Information System (INIS)
Bukhshtaber, V M; Panov, T E
2000-01-01
This paper is a survey of new results and open problems connected with fundamental combinatorial concepts, including polytopes, simplicial complexes, cubical complexes, and arrangements of subspaces. Attention is concentrated on simplicial and cubical subdivisions of manifolds, and especially on spheres. Important constructions are described that enable one to study these combinatorial objects by using commutative and homological algebra. The proposed approach to combinatorial problems is based on the theory of moment-angle complexes recently developed by the authors. The crucial construction assigns to each simplicial complex K with m vertices a T m -space Z K with special bigraded cellular decomposition. In the framework of this theory, well-known non-singular toric varieties arise as orbit spaces of maximally free actions of subtori on moment-angle complexes corresponding to simplicial spheres. It is shown that diverse invariants of simplicial complexes and related combinatorial-geometric objects can be expressed in terms of bigraded cohomology rings of the corresponding moment-angle complexes. Finally, it is shown that the new relationships between combinatorics, geometry, and topology lead to solutions of some well-known topological problems
Quantum Resonance Approach to Combinatorial Optimization
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.
Logging to Facilitate Combinatorial System Testing
Kruse, P.M.; Prasetya, I.S.W.B.; Hage, J; Elyasov, Alexander
2014-01-01
Testing a web application is typically very complicated. Imposing simple coverage criteria such as function or line coverage is often not sufficient to uncover bugs due to incorrect components integration. Combinatorial testing can enforce a stronger criterion, while still allowing the
Czech Academy of Sciences Publication Activity Database
Mahelka, Václav; Krak, Karol; Kopecký, David; Fehrer, Judith; Šafář, Jan; Bartoš, Jan; Hobza, Roman; Blavet, Nicolas; Blattner, F.R.
2017-01-01
Roč. 114, č. 7 (2017), s. 1726-1731 ISSN 0027-8424 R&D Projects: GA MŠk(CZ) LO1204; GA ČR GA13-04454S Institutional support: RVO:67985939 ; RVO:61389030 Keywords : Triticeae * Panicoideae * horizantal genen transfer Subject RIV: EF - Botanics; EF - Botanics (UEB-Q) OBOR OECD: Plant sciences, botany; Plant sciences, botany (UEB-Q) Impact factor: 9.661, year: 2016
Criticism of EFSA's scientific opinion on combinatorial effects of 'stacked' GM plants.
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 binary plasmid system for shuffling combinatorial antibody libraries.
Collet, T A; Roben, P; O'Kennedy, R; Barbas, C F; Burton, D R; Lerner, R A
1992-11-01
We have used a binary system of replicon-compatible plasmids to test the potential for promiscuous recombination of heavy and light chains within sets of human Fab fragments isolated from combinatorial antibody libraries. Antibody molecules showed a surprising amount of promiscuity in that a particular heavy chain could recombine with multiple light chains with retention of binding to a protein antigen. The degree to which a given heavy chain productively paired with any light chain to bind antigen varied from 43% to 100% and depended strongly on the heavy-chain sequence. Such productive crosses resulted in a set of Fab fragments of similar apparent binding constants, which seemed to differ mainly in the amount of active Fab fragment produced in the bacterial cell. The dominance of the heavy chain in the antibody-antigen interaction was further explored in a set of directed crosses, in which heavy and light chains derived from antigen-specific clones were crossed with nonrelated heavy and light chains. In these crosses, an Fab fragment retained antigen binding only if it contained a heavy chain from an antigen-specific clone. In no case did the light chain confer detectable affinity when paired with indifferent heavy chains. The surprising promiscuity of heavy chains has ramifications for the evaluation of the diversity of combinatorial libraries made against protein antigens and should allow the combination of one such promiscuous heavy chain with an engineered light chain to form an Fab fragment carrying synthetic cofactors to assist in antibody catalysis.
Dack, Charlotte; Reed, Phil; McHugh, Louise
2010-11-01
The aim of the four present experiments was to explore how different schedules of reinforcement influence schedule-induced behavior, their impact on evaluative ratings given to conditioned stimuli associated with each schedule through evaluative conditioning, and the transfer of these evaluations through derived stimulus networks. Experiment 1 compared two contrasting response reinforcement rules (variable ratio [VR], variable interval [VI]). Experiment 2 varied the response to reinforcement rule between two schedules but equated the outcome to response rate (differential reinforcement of high rate [DRH] vs. VR). Experiment 3 compared molar and molecular aspects of contingencies of reinforcement (tandem VIVR vs. tandem VRVI). Finally, Experiment 4 employed schedules that induced low rates of responding to determine whether, under these circumstances, responses were more sensitive to the molecular aspects of a schedule (differential reinforcement of low rate [DRL] vs. VI). The findings suggest that the transfer of evaluative functions is determined mainly by differences in response rate between the schedules and the molar aspects of the schedules. However, when neither schedule was based on a strong response reinforcement rule, the transfer of evaluative judgments came under the control of the molecular aspects of the schedule.
Combinatorial structures to modeling simple games and applications
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.
DEFF Research Database (Denmark)
Sidoli, Simone; Schwämmle, Veit; Ruminowicz, Chrystian
2014-01-01
chromatography (WCX-HILIC) interfaced directly to high mass accuracy ESI MS/MS using electron transfer dissociation (ETD). This enabled automated and efficient separation and sequencing of hypermodified histone N-terminal tails for unambiguous localization of combinatorial PTMs. We present Histone Coder and Iso...
International Nuclear Information System (INIS)
Iyer, S.V.; Vafai, K.
1999-01-01
The study of natural convection flow and heat transfer within a cylindrical annulus has received considerable attention because of its numerous applications, such as in nuclear reactor design, electronic component cooling, thermal storage systems, energy conservation, energy storage, and energy transmission. Here, the effects of multiple geometric perturbations on the inner and outer cylinders of an annulus with impermeable end walls are investigated in this work. A three-dimensional study was done using a numerical scheme based on a Galerkin method of finite element formulation. The nature of the buoyancy-induced flow field has been analyzed in detail. The flow fields for the cases considered were found to be qualitatively similar, and the introduction of each additional perturbation altered the flow field in a regular and recurring manner. The introduction of each perturbation on the outer cylinder causes clockwise and counterclock-wise rotating patterns on either side of the perturbation in the upper circumferential regions of the annulus. The motion of the fluid entrained by these circulatory patterns constitutes the key features of the flow pattern observed in the annulus. It is observed that the presence of multiple perturbations on the inner and outer cylinders substantially increases the overall heat transfer rate as compared to the regular annulus without any perturbation. Key qualitative and quantitative effects of the introduction of perturbations on both the inner and outer cylinders of the annulus are discussed
IVF policy and global/local politics: the making of multiple-embryo transfer regulation in Taiwan.
Wu, Chia-Ling
2012-08-01
This paper analyzes the regulatory trajectory of multiple-embryo transfer in in-vitro fertilization (IVF) in Taiwan. Taking a latecomer to policy-making as the case, it argues the importance of conceptualizing the global/local dynamics in policy-making for assisted reproductive technology (ART). The conceptual framework is built upon recent literature on standardization, science policy, and global assemblage. I propose three interrelated features that reveal the "global in the local": (1) the power relationships among stakeholders, (2) the selected global form that involved actors drew upon, and (3) the re-contextualized assemblage made of local networks. Data included archives, interviews, and participant observation. In different historical periods the specific stakeholders selected different preferred global forms for Taiwan, such as Britain's code of ethics in the 1990s, the American guideline in the early 2000s, and the European trend in the mid-2000s. The global is heterogeneous. The failure to transfer the British regulation, the revision of the American guideline by adding one more embryo than it specified, and the gap between the cited European trend and the "no more than four" in Taiwan's 2007 Human Reproduction Law all show that the local network further transforms the selected global form, confining it to rhetoric only or tailoring it to local needs. Overall, Taiwanese practitioners successfully maintained their medical autonomy to build a 'flexible standardization'. Multiple pregnancy remains the most common health risk of IVF in Taiwan. Copyright © 2012 Elsevier Ltd. All rights reserved.
K-shell-hole production, multiple-hole production, charge transfer, and antisymmetry
International Nuclear Information System (INIS)
Reading, J.F.; Ford, A.L.
1980-01-01
In calculating K-shell-hole production when an ion collides with an atom, account must be taken of the fact that processes involving electrons other than the K-shell electron can occur. For example, after making a K-shell hole an L-shell electron may be knocked into it, or an L-shell vacancy may be produced and the K-shell electron promoted to that vacancy in the ''Fermi sea'' of the target-atom orbitals. In 1973 a theorem was proved by one of the present authors demonstrating that all these multielectron processes cancel in an independent-particle model for the target atom. In this paper it is shown that the same thing occurs for hole production by charge transfer to the ion. The authors demonstrate that multihole production does not obey this simple rule and that the probability for multihole production is not the product of independent single-electron probabilities. The correct expressions that should be used for these processes are given, together with new results for charge-transfer processes accompanied by hole production
Gems of combinatorial optimization and graph algorithms
Skutella, Martin; Stiller, Sebastian; Wagner, Dorothea
2015-01-01
Are you looking for new lectures for your course on algorithms, combinatorial optimization, or algorithmic game theory? Maybe you need a convenient source of relevant, current topics for a graduate student or advanced undergraduate student seminar? Or perhaps you just want an enjoyable look at some beautiful mathematical and algorithmic results, ideas, proofs, concepts, and techniques in discrete mathematics and theoretical computer science? Gems of Combinatorial Optimization and Graph Algorithms is a handpicked collection of up-to-date articles, carefully prepared by a select group of international experts, who have contributed some of their most mathematically or algorithmically elegant ideas. Topics include longest tours and Steiner trees in geometric spaces, cartograms, resource buying games, congestion games, selfish routing, revenue equivalence and shortest paths, scheduling, linear structures in graphs, contraction hierarchies, budgeted matching problems, and motifs in networks. This ...
Three Syntactic Theories for Combinatory Graph Reduction
DEFF Research Database (Denmark)
Danvy, Olivier; Zerny, Ian
2011-01-01
in a third syntactic theory. The structure of the store-based abstract machine corresponding to this third syntactic theory oincides with that of Turner's original reduction machine. The three syntactic theories presented here The three syntactic heories presented here therefore have the following......We present a purely syntactic theory of graph reduction for the canonical combinators S, K, and I, where graph vertices are represented with evaluation contexts and let expressions. We express this syntactic theory as a reduction semantics, which we refocus into the first storeless abstract machine...... for combinatory graph reduction, which we refunctionalize into the first storeless natural semantics for combinatory graph reduction.We then factor out the introduction of let expressions to denote as many graph vertices as possible upfront instead of on demand, resulting in a second syntactic theory, this one...
Three Syntactic Theories for Combinatory Graph Reduction
DEFF Research Database (Denmark)
Danvy, Olivier; Zerny, Ian
2013-01-01
, as a store-based reduction semantics of combinatory term graphs. We then refocus this store-based reduction semantics into a store-based abstract machine. The architecture of this store-based abstract machine coincides with that of Turner's original reduction machine. The three syntactic theories presented......We present a purely syntactic theory of graph reduction for the canonical combinators S, K, and I, where graph vertices are represented with evaluation contexts and let expressions. We express this rst syntactic theory as a storeless reduction semantics of combinatory terms. We then factor out...... the introduction of let expressions to denote as many graph vertices as possible upfront instead of on demand . The factored terms can be interpreted as term graphs in the sense of Barendregt et al. We express this second syntactic theory, which we prove equivalent to the rst, as a storeless reduction semantics...
DNA-Encoded Dynamic Combinatorial Chemical Libraries.
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.
Exploiting Quantum Resonance to Solve Combinatorial Problems
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.
Systematic identification of combinatorial drivers and targets in cancer cell lines.
Directory of Open Access Journals (Sweden)
Adel Tabchy
Full Text Available 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.
Systematic identification of combinatorial drivers and targets in cancer cell lines.
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.
International Nuclear Information System (INIS)
Schenck, Peter K.; Bassim, Nabil D.; Otani, Makoto; Oguchi, Hiroyuki; Green, Martin L.
2007-01-01
The goal of the design of pulsed laser deposition (PLD) combinatorial library films is to optimize the compositional coverage of the films while maintaining a uniform thickness. The deposition pattern of excimer laser PLD films can be modeled with a bimodal cos n distribution. Deposited films were characterized using a spectroscopic reflectometer (250-1000 nm) to map the thickness of both single composition calibration films and combinatorial library films. These distribution functions were used to simulate the composition and thickness of multiple target combinatorial library films. The simulations were correlated with electron-probe microanalysis wavelength-dispersive spectroscopy (EPMA-WDS) composition maps. The composition and thickness of the library films can be fine-tuned by adjusting the laser spot size, fluence, background gas pressure, target geometry and other processing parameters which affect the deposition pattern. Results from compositionally graded combinatorial library films of the ternary system Al 2 O 3 -HfO 2 -Y 2 O 3 are discussed
Combinatorial Cis-regulation in Saccharomyces Species
Directory of Open Access Journals (Sweden)
Aaron T. Spivak
2016-03-01
Full Text Available Transcriptional control of gene expression requires interactions between the cis-regulatory elements (CREs controlling gene promoters. We developed a sensitive computational method to identify CRE combinations with conserved spacing that does not require genome alignments. When applied to seven sensu stricto and sensu lato Saccharomyces species, 80% of the predicted interactions displayed some evidence of combinatorial transcriptional behavior in several existing datasets including: (1 chromatin immunoprecipitation data for colocalization of transcription factors, (2 gene expression data for coexpression of predicted regulatory targets, and (3 gene ontology databases for common pathway membership of predicted regulatory targets. We tested several predicted CRE interactions with chromatin immunoprecipitation experiments in a wild-type strain and strains in which a predicted cofactor was deleted. Our experiments confirmed that transcription factor (TF occupancy at the promoters of the CRE combination target genes depends on the predicted cofactor while occupancy of other promoters is independent of the predicted cofactor. Our method has the additional advantage of identifying regulatory differences between species. By analyzing the S. cerevisiae and S. bayanus genomes, we identified differences in combinatorial cis-regulation between the species and showed that the predicted changes in gene regulation explain several of the species-specific differences seen in gene expression datasets. In some instances, the same CRE combinations appear to regulate genes involved in distinct biological processes in the two different species. The results of this research demonstrate that (1 combinatorial cis-regulation can be inferred by multi-genome analysis and (2 combinatorial cis-regulation can explain differences in gene expression between species.
The Combinatorial Trace Method in Action
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…
Semidefinite Relaxation-Based Optimization of Multiple-Input Wireless Power Transfer Systems
Lang, Hans-Dieter; Sarris, Costas D.
2017-11-01
An optimization procedure for multi-transmitter (MISO) wireless power transfer (WPT) systems based on tight semidefinite relaxation (SDR) is presented. This method ensures physical realizability of MISO WPT systems designed via convex optimization -- a robust, semi-analytical and intuitive route to optimizing such systems. To that end, the nonconvex constraints requiring that power is fed into rather than drawn from the system via all transmitter ports are incorporated in a convex semidefinite relaxation, which is efficiently and reliably solvable by dedicated algorithms. A test of the solution then confirms that this modified problem is equivalent (tight relaxation) to the original (nonconvex) one and that the true global optimum has been found. This is a clear advantage over global optimization methods (e.g. genetic algorithms), where convergence to the true global optimum cannot be ensured or tested. Discussions of numerical results yielded by both the closed-form expressions and the refined technique illustrate the importance and practicability of the new method. It, is shown that this technique offers a rigorous optimization framework for a broad range of current and emerging WPT applications.
Christin, Pascal-Antoine; Wallace, Mark J; Clayton, Harmony; Edwards, Erika J; Furbank, Robert T; Hattersley, Paul W; Sage, Rowan F; Macfarlane, Terry D; Ludwig, Martha
2012-10-01
The Neurachninae is the only grass lineage known to contain C(3), C(4), and C(3)-C(4) intermediate species, and as such has been suggested as a model system for studies of photosynthetic pathway evolution in the Poaceae; however, a lack of a robust phylogenetic framework has hindered this possibility. In this study, plastid and nuclear markers were used to reconstruct evolutionary relationships among Neurachninae species. In addition, photosynthetic types were determined with carbon isotope ratios, and genome sizes with flow cytometry. A high frequency of autopolyploidy was found in the Neurachninae, including in Neurachne munroi F.Muell. and Paraneurachne muelleri S.T.Blake, which independently evolved C(4) photosynthesis. Phylogenetic analyses also showed that following their separate C(4) origins, these two taxa exchanged a gene encoding the C(4) form of phosphoenolpyruvate carboxylase. The C(3)-C(4) intermediate Neurachne minor S.T.Blake is phylogenetically distinct from the two C(4) lineages, indicating that intermediacy in this species evolved separately from transitional stages preceding C(4) origins. The Neurachninae shows a substantial capacity to evolve new photosynthetic pathways repeatedly. Enablers of these transitions might include anatomical pre-conditions in the C(3) ancestor, and frequent autopolyploidization. Transfer of key C(4) genetic elements between independently evolved C(4) taxa may have also facilitated a rapid adaptation of photosynthesis in these grasses that had to survive in the harsh climate appearing during the late Pliocene in Australia.
Soil to plant transfer of radionuclides: predicting the fate of multiple radioisotopes in plants
International Nuclear Information System (INIS)
Willey, Neil J.
2014-01-01
Predicting soil-to-plant transfer of radionuclides is restricted by the range of species for which concentration ratios (CRs) have been measured. Here the radioecological utility of meta-analyses of phylogenetic effects on alkali earth metals will be explored for applications such as ‘gap-filling’ of CRs, the identification of sentinel biomonitor plants and the selection of taxa for phytoremediation of radionuclide contaminated soils. REML modelling of extensive CR/concentration datasets shows that the concentrations in plants of Ca, Mg and Sr are significantly influenced by phylogeny. Phylogenetic effects of these elements are shown here to be similar. Ratios of Ca/Mg and Ca/Sr are known to be quite stable in plants so, assuming that Sr/Ra ratios are stable, phylogenetic effects and estimated mean CRs are used to predict Ra CRs for groups of plants with few measured data. Overall, there are well quantified plant variables that could contribute significantly to improving predictions of the fate radioisotopes in the soil-plant system
International Nuclear Information System (INIS)
Lee, J.H.; Andrews, R.W.; Chambre, P.L.
1996-01-01
A robust engineered barrier system (EBS) is employed in the current design concept for the potential high-level nuclear waste repository at Yucca Mountain, Nevada, US. The primary component of the EBS is a multi-barrier waste package container. Simplifying the geometry of the cylindrical waste package container and the underlying invert into the equivalent spherical configuration, mathematical models are developed for steady-state and transient diffusive releases from the failed waste container with multiple perforations (or pit penetrations) at the boundary of the invert. Using the models the steady-state and transient diffusive release behaviors form the failed waste container are studied. The analyses show that the number of perforations, the size of perforation, the container wall thickness, the geometry of the waste container and invert, and the adsorption of radionuclide in the invert are the important parameters that control the diffusive release rate. It is emphasized that the failed (or perforated) waste package container can still perform as a potentially important barrier (or diffusion barrier) to radionuclide release
Liu, Ding; Huang, Weichao; Zhang, Ni
2017-07-01
A two-dimensional axisymmetric swirling model based on the lattice Boltzmann method (LBM) in a pseudo Cartesian coordinate system is posited to simulate Czochralski (Cz) crystal growth in this paper. Specifically, the multiple-relaxation-time LBM (MRT-LBM) combined with the finite difference method (FDM) is used to analyze the melt convection and heat transfer in the process of Cz crystal growth. An incompressible axisymmetric swirling MRT-LB D2Q9 model is applied to solve for the axial and radial velocities by inserting thermal buoyancy and rotational inertial force into the two-dimensional lattice Boltzmann equation. In addition, the melt temperature and the azimuthal velocity are solved by MRT-LB D2Q5 models, and the crystal temperature is solved by FDM. The comparison results of stream functions values of different methods demonstrate that our hybrid model can be used to simulate the fluid-thermal coupling in the axisymmetric swirling model correctly and effectively. Furthermore, numerical simulations of melt convection and heat transfer are conducted under the conditions of high Grashof (Gr) numbers, within the range of 105 ˜ 107, and different high Reynolds (Re) numbers. The experimental results show our hybrid model can obtain the exact solution of complex crystal-growth models and analyze the fluid-thermal coupling effectively under the combined action of natural convection and forced convection.
International Nuclear Information System (INIS)
Rovira, A.; Alonso, J.; Cucurella, G.; Nos, C.; Tintore, M.; Pedraza, S.; Rio, J.; Montalban, X.
1997-01-01
To demonstrate the changes in the magnetization transfer ratio (MTR) of different demyelinating plaques, correlating them with the baseline values in T1-weighted contrast-enhanced magnetic resonance (MR) sequences in order to relate them more closely to the underlying disease. The study was based on 33 demyelinating plaques obtained from six patients clinically diagnosed as having remitting-recurring multiple sclerosis (MS). All the patients underwent two MR studies at a 3 to 5-month interval, including contrast-enhanced T1 and T2- weighted sequences and magnetization transfer images. The latter were used to calculate the MTR for each of the demyelinating plaques included in the study. The statistical analysis of the results obtained revealed statistically significant between initial MTR values and those of subsequent T1-weighted sequences. The MTR demonstrate significant differences between plaques according to contrast-enhanced T1-weigh tes sequences, probably indicating variable degrees of edema, demyelination and tissue destruction. These differences should be taken into account to enable the use of T1-weighted sequences to quantify the lesion load in MS patients. (Author) 35 refs
MIFT: GIFT Combinatorial Geometry Input to VCS Code
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
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).
Sills, Eric Scott; Yang, Zhihong; Walsh, David J; Salem, Shala A
2012-09-01
The unacceptable multiple gestation rate currently associated with in vitro fertilization (IVF) would be substantially alleviated if the routine practice of transferring more than one embryo were reconsidered. While transferring a single embryo is an effective method to reduce the clinical problem of multiple gestation, rigid adherence to this approach has been criticized for negatively impacting clinical pregnancy success in IVF. In general, single embryo transfer is viewed cautiously by IVF patients although greater acceptance would result from a more effective embryo selection method. Selection of one embryo for fresh transfer on the basis of chromosomal normalcy should achieve the dual objective of maintaining satisfactory clinical pregnancy rates and minimizing the multiple gestation problem, because embryo aneuploidy is a major contributing factor in implantation failure and miscarriage in IVF. The initial techniques for preimplantation genetic screening unfortunately lacked sufficient sensitivity and did not yield the expected results in IVF. However, newer molecular genetic methods could be incorporated with standard IVF to bring the goal of single embryo transfer within reach. Aiming to make multiple embryo transfers obsolete and unnecessary, and recognizing that array comparative genomic hybridization (aCGH) will typically require an additional 12 h of laboratory time to complete, we propose adopting aCGH for mainstream use in clinical IVF practice. As aCGH technology continues to develop and becomes increasingly available at lower cost, it may soon be considered unusual for IVF laboratories to select a single embryo for fresh transfer without regard to its chromosomal competency. In this report, we provide a rationale supporting aCGH as the preferred methodology to provide a comprehensive genetic assessment of the single embryo before fresh transfer in IVF. The logistics and cost of integrating aCGH with IVF to enable fresh embryo transfer are also
Use of combinatorial chemistry to speed drug discovery.
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.
Advanced Aqueous Phase Catalyst Development using Combinatorial Methods, Phase II
National Aeronautics and Space Administration — Combinatorial methods are proposed to develop advanced Aqueous Oxidation Catalysts (AOCs) with the capability to mineralize organic contaminants present in effluents...
Effects of Suboptimal Bidding in Combinatorial Auctions
Schneider, Stefan; Shabalin, Pasha; Bichler, Martin
Though the VCG auction assumes a central place in the mechanism design literature, there are a number of reasons for favoring iterative combinatorial auction designs. Several promising ascending auction formats have been developed throughout the past few years based on primal-dual and subgradient algorithms and linear programming theory. Prices are interpreted as a feasible dual solution and the provisional allocation is interpreted as a feasible primal solution. iBundle( 3) (Parkes and Ungar 2000), dVSV (de Vries et al. 2007) and the Ascending Proxy auction (Ausubel and Milgrom 2002) result in VCG payoffs when the coalitional value function satisfies the buyer submodularity condition and bidders bid straightforward, which is an expost Nash equilibrium in that case. iBEA and CreditDebit auctions (Mishra and Parkes 2007) do not even require the buyer submodularity condition and achieve the same properties for general valuations. In many situations, however, one cannot assume bidders to bid straightforward and it is not clear from the theory how these non-linear personalized price auctions (NLPPAs) perform in this case. Robustness of auctions with respect to different bidding behavior is therefore a critical issue for any application. We have conducted a large number of computational experiments to analyze the performance of NLPPA designs with respect to different bidding strategies and different valuation models. We compare the results of NLPPAs to those of the VCG auction and those of iterative combinatorial auctions with approximate linear prices, such as ALPS (Bichler et al. 2009) and the Combinatorial Clock auction (Porter et al. 2003).
Recursive deconvolution of combinatorial chemical libraries.
Erb, E; Janda, K D; Brenner, S
1994-01-01
A recursive strategy that solves for the active members of a chemical library is presented. A pentapeptide library with an alphabet of Gly, Leu, Phe, and Tyr (1024 members) was constructed on a solid support by the method of split synthesis. One member of this library (NH2-Tyr-Gly-Gly-Phe-Leu) is a native binder to a beta-endorphin antibody. A variation of the split synthesis approach is used to build the combinatorial library. In four vials, a member of the library's alphabet is coupled to a...
Dynamical System Approaches to Combinatorial Optimization
DEFF Research Database (Denmark)
Starke, Jens
2013-01-01
of large times as an asymptotically stable point of the dynamics. The obtained solutions are often not globally optimal but good approximations of it. Dynamical system and neural network approaches are appropriate methods for distributed and parallel processing. Because of the parallelization......Several dynamical system approaches to combinatorial optimization problems are described and compared. These include dynamical systems derived from penalty methods; the approach of Hopfield and Tank; self-organizing maps, that is, Kohonen networks; coupled selection equations; and hybrid methods...... thereof can be used as models for many industrial problems like manufacturing planning and optimization of flexible manufacturing systems. This is illustrated for an example in distributed robotic systems....
Quantum resonance for simulating combinatorial problems
International Nuclear Information System (INIS)
Zak, Michail; Fijany, Amir
2005-01-01
Quantum computing by simulations is based upon similarity between mathematical formalism of a quantum phenomenon and phenomena to be analyzed. In this Letter, the mathematical formalism of quantum resonance combined with tensor product decomposability of unitary evolutions is mapped onto a class of NP-complete combinatorial problems. It has been demonstrated that nature has polynomial resources for solving NP-complete problems and that will help to develop a new strategy for artificial intelligence, as well as to re-evaluate the role of natural selection in biological evolution
Automatic generation of combinatorial test data
Zhang, Jian; Ma, Feifei
2014-01-01
This book reviews the state-of-the-art in combinatorial testing, with particular emphasis on the automatic generation of test data. It describes the most commonly used approaches in this area - including algebraic construction, greedy methods, evolutionary computation, constraint solving and optimization - and explains major algorithms with examples. In addition, the book lists a number of test generation tools, as well as benchmarks and applications. Addressing a multidisciplinary topic, it will be of particular interest to researchers and professionals in the areas of software testing, combi
Method and apparatus for combinatorial chemistry
Foote, Robert S [Oak Ridge, TN
2012-06-05
A method and apparatus are provided for performing light-directed reactions in spatially addressable channels within a plurality of channels. One aspect of the invention employs photoactivatable reagents in solutions disposed into spatially addressable flow streams to control the parallel synthesis of molecules immobilized within the channels. The reagents may be photoactivated within a subset of channels at the site of immobilized substrate molecules or at a light-addressable site upstream from the substrate molecules. The method and apparatus of the invention find particularly utility in the synthesis of biopolymer arrays, e.g., oligonucleotides, peptides and carbohydrates, and in the combinatorial synthesis of small molecule arrays for drug discovery.
On Definitions and Existence of Combinatorial Entropy of 2d Fields
DEFF Research Database (Denmark)
Forchhammer, Søren Otto; Shtarkov, Yuri; Justesen, Jørn
1998-01-01
Different definitions of combinatorial entropy is presented and conditions for their existence examined.......Different definitions of combinatorial entropy is presented and conditions for their existence examined....
Combinatorial Quantum Field Theory and Gluing Formula for Determinants
Reshetikhin, N.; Vertman, B.
2015-01-01
We define the combinatorial Dirichlet-to-Neumann operator and establish a gluing formula for determinants of discrete Laplacians using a combinatorial Gaussian quantum field theory. In case of a diagonal inner product on cochains we provide an explicit local expression for the discrete
Combinatorial Libraries of Bis-Heterocyclic Compounds with Skeletal Diversity
Soural, Miroslav; Bouillon, Isabelle; Krchňák, Viktor
2009-01-01
Combinatorial solid-phase synthesis of bis-heterocyclic compounds, characterized by the presence of two heterocyclic cores connected by a spacer of variable length/structure, provided structurally heterogeneous libraries with skeletal diversity. Both heterocyclic rings were assembled on resin in a combinatorial fashion. PMID:18811208
Combinatorial Libraries of Bis-Heterocyclic Compounds with Skeletal Diversity
Soural, Miroslav; Bouillon, Isabelle; Krchňák, Viktor
2008-01-01
Combinatorial solid-phase synthesis of bis-heterocyclic compounds, characterized by the presence of two heterocyclic cores connected by a spacer of variable length/structure, provided structurally heterogeneous libraries with skeletal diversity. Both heterocyclic rings were assembled on resin in a combinatorial fashion.
Combinatorial identities for tenth order mock theta functions
Indian Academy of Sciences (India)
44
which lead us to one 4-way and one 3-way combinatorial identity. ... mock theta functions, partition identities and different combinatorial parameters, see for ... 3. Example 1.1. There are twelve (n + 1)–color partitions of 2: 21, 21 + 01, 11 + 11, ...
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
Exact model reduction of combinatorial reaction networks
Directory of Open Access Journals (Sweden)
Fey Dirk
2008-08-01
Full Text Available Abstract Background Receptors and scaffold proteins usually possess a high number of distinct binding domains inducing the formation of large multiprotein signaling complexes. Due to combinatorial reasons the number of distinguishable species grows exponentially with the number of binding domains and can easily reach several millions. Even by including only a limited number of components and binding domains the resulting models are very large and hardly manageable. A novel model reduction technique allows the significant reduction and modularization of these models. Results We introduce methods that extend and complete the already introduced approach. For instance, we provide techniques to handle the formation of multi-scaffold complexes as well as receptor dimerization. Furthermore, we discuss a new modeling approach that allows the direct generation of exactly reduced model structures. The developed methods are used to reduce a model of EGF and insulin receptor crosstalk comprising 5,182 ordinary differential equations (ODEs to a model with 87 ODEs. Conclusion The methods, presented in this contribution, significantly enhance the available methods to exactly reduce models of combinatorial reaction networks.
International Nuclear Information System (INIS)
Schwerdtfeger, Christine A.; Soudackov, Alexander V.; Hammes-Schiffer, Sharon
2014-01-01
The development of efficient theoretical methods for describing electron transfer (ET) reactions in condensed phases is important for a variety of chemical and biological applications. Previously, dynamical dielectric continuum theory was used to derive Langevin equations for a single collective solvent coordinate describing ET in a polar solvent. In this theory, the parameters are directly related to the physical properties of the system and can be determined from experimental data or explicit molecular dynamics simulations. Herein, we combine these Langevin equations with surface hopping nonadiabatic dynamics methods to calculate the rate constants for thermal ET reactions in polar solvents for a wide range of electronic couplings and reaction free energies. Comparison of explicit and implicit solvent calculations illustrates that the mapping from explicit to implicit solvent models is valid even for solvents exhibiting complex relaxation behavior with multiple relaxation time scales and a short-time inertial response. The rate constants calculated for implicit solvent models with a single solvent relaxation time scale corresponding to water, acetonitrile, and methanol agree well with analytical theories in the Golden rule and solvent-controlled regimes, as well as in the intermediate regime. The implicit solvent models with two relaxation time scales are in qualitative agreement with the analytical theories but quantitatively overestimate the rate constants compared to these theories. Analysis of these simulations elucidates the importance of multiple relaxation time scales and the inertial component of the solvent response, as well as potential shortcomings of the analytical theories based on single time scale solvent relaxation models. This implicit solvent approach will enable the simulation of a wide range of ET reactions via the stochastic dynamics of a single collective solvent coordinate with parameters that are relevant to experimentally accessible
Heterogenous phase as a mean in combinatorial chemistry
International Nuclear Information System (INIS)
Abdel-Hamid, S.G.
2007-01-01
Combinatorial chemistry is a rapid and inexpensive technique for the synthesis of hundreds of thousands of organic compounds of potential medicinal activity. In the past few decades a large number of combinatorial libraries have been constructed, and significantly supplement the chemical diversity of the traditional collections of the potentially active medicinal compounds. Solid phase synthesis was used to enrich the combinatorial chemistry libraries, through the use of solid supports (resins) and their modified forms. Most of the new libraries of compounds appeared recently, were synthesized by the use of solid-phase. Solid-phase combinatorial chemistry (SPCC) is now considered as an outstanding branch in pharmaceutical chemistry research and used extensively as a tool for drug discovery within the context of high-throughput chemical synthesis. The best pure libraries synthesized by the use of solid phase combinatorial chemistry (SPCC) may well be those of intermediate complexity that are free of artifact-causing nuisance compounds. (author)
Combinatorial Models for Assembly and Decomposition of Products
Directory of Open Access Journals (Sweden)
A. N. Bojko
2015-01-01
Full Text Available The paper discusses the most popular combinatorial models that are used for the synthesis of design solutions at the stage of the assembly process flow preparation. It shows that while assembling the product the relations of parts can be represented as a structure of preferences, which is formed on the basis of objective design restrictions put in at the stage of the product design. This structure is a binary preference relation pre-order. Its symmetrical part is equivalence and describes the entry of parts into the assembly unit. The asymmetric part is a partial order. It specifies part- ordering time in in the course of the assembly process. The structure of preferences is a minimal description of the restrictions and constraints in the assembly process. It can serve as a source for generating multiple assembly sequences of a product and its components, which are allowed by design. This multiplicity increases the likelihood of rational choice under uncertainty, unpredictable changes in the properties of technological or industrial systems.Incomplete dominance relation gives grounds for further examination and better understanding of the project situation. Operation field of the study is limited to a set of disparate elements of the partial order. Different strategies for processing the disparate elements may be offered, e.g. selection of the most informative pairs, comparison of which foremost linearizes the original partial order.
D- production by multiple charge-transfer collisions in metal-vapor targets. [1 to 50 keV D/sup +/
Energy Technology Data Exchange (ETDEWEB)
Schlachter, A.S.
1977-09-01
A beam of D/sup -/ions can be produced by multiple charge-transfer collisions of a D/sup +/ beam in a thick metal-vapor target. Cross sections and equilibrium charge-state fractions are presented and discussed.
Kosgey, I.S.; Kahi, A.K.; Arendonk, van J.A.M.
2005-01-01
The potential benefits of closed adult nucleus multiple ovulation and embryo transfer (MOET) and conventional progeny testing (CNS) schemes, and the logistics of their integration into large-scale continuous production of crossbred cattle were studied by deterministic simulation. The latter was
A Combinatorial Kin Discrimination System in Bacillus subtilis.
Lyons, Nicholas A; Kraigher, Barbara; Stefanic, Polonca; Mandic-Mulec, Ines; Kolter, Roberto
2016-03-21
Multicellularity inherently involves a number of cooperative behaviors that are potentially susceptible to exploitation but can be protected by mechanisms such as kin discrimination. Discrimination of kin from non-kin has been observed in swarms of the bacterium Bacillus subtilis, but the underlying molecular mechanism has been unknown. We used genetic, transcriptomic, and bioinformatic analyses to uncover kin recognition factors in this organism. Our results identified many molecules involved in cell-surface modification and antimicrobial production and response. These genes varied significantly in expression level and mutation phenotype among B. subtilis strains, suggesting interstrain variation in the exact kin discrimination mechanism used. Genome analyses revealed a substantial diversity of antimicrobial genes present in unique combinations in different strains, with many likely acquired by horizontal gene transfer. The dynamic combinatorial effect derived from this plethora of kin discrimination genes creates a tight relatedness cutoff for cooperation that has likely led to rapid diversification within the species. Our data suggest that genes likely originally selected for competitive purposes also generate preferential interactions among kin, thus stabilizing multicellular lifestyles. Copyright © 2016 Elsevier Ltd. All rights reserved.
Combinatorial chemoenzymatic synthesis and high-throughput screening of sialosides.
Chokhawala, Harshal A; Huang, Shengshu; Lau, Kam; Yu, Hai; Cheng, Jiansong; Thon, Vireak; Hurtado-Ziola, Nancy; Guerrero, Juan A; Varki, Ajit; Chen, Xi
2008-09-19
Although the vital roles of structures containing sialic acid in biomolecular recognition are well documented, limited information is available on how sialic acid structural modifications, sialyl linkages, and the underlying glycan structures affect the binding or the activity of sialic acid-recognizing proteins and related downstream biological processes. A novel combinatorial chemoenzymatic method has been developed for the highly efficient synthesis of biotinylated sialosides containing different sialic acid structures and different underlying glycans in 96-well plates from biotinylated sialyltransferase acceptors and sialic acid precursors. By transferring the reaction mixtures to NeutrAvidin-coated plates and assaying for the yields of enzymatic reactions using lectins recognizing sialyltransferase acceptors but not the sialylated products, the biotinylated sialoside products can be directly used, without purification, for high-throughput screening to quickly identify the ligand specificity of sialic acid-binding proteins. For a proof-of-principle experiment, 72 biotinylated alpha2,6-linked sialosides were synthesized in 96-well plates from 4 biotinylated sialyltransferase acceptors and 18 sialic acid precursors using a one-pot three-enzyme system. High-throughput screening assays performed in NeutrAvidin-coated microtiter plates show that whereas Sambucus nigra Lectin binds to alpha2,6-linked sialosides with high promiscuity, human Siglec-2 (CD22) is highly selective for a number of sialic acid structures and the underlying glycans in its sialoside ligands.
Binary Cockroach Swarm Optimization for Combinatorial Optimization Problem
Directory of Open Access Journals (Sweden)
Ibidun Christiana Obagbuwa
2016-09-01
Full Text Available The Cockroach Swarm Optimization (CSO algorithm is inspired by cockroach social behavior. It is a simple and efficient meta-heuristic algorithm and has been applied to solve global optimization problems successfully. The original CSO algorithm and its variants operate mainly in continuous search space and cannot solve binary-coded optimization problems directly. Many optimization problems have their decision variables in binary. Binary Cockroach Swarm Optimization (BCSO is proposed in this paper to tackle such problems and was evaluated on the popular Traveling Salesman Problem (TSP, which is considered to be an NP-hard Combinatorial Optimization Problem (COP. A transfer function was employed to map a continuous search space CSO to binary search space. The performance of the proposed algorithm was tested firstly on benchmark functions through simulation studies and compared with the performance of existing binary particle swarm optimization and continuous space versions of CSO. The proposed BCSO was adapted to TSP and applied to a set of benchmark instances of symmetric TSP from the TSP library. The results of the proposed Binary Cockroach Swarm Optimization (BCSO algorithm on TSP were compared to other meta-heuristic algorithms.
Bifurcation-based approach reveals synergism and optimal combinatorial perturbation.
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.
Characterizing the combinatorial beam angle selection problem
Bangert, Mark; Ziegenhein, Peter; Oelfke, Uwe
2012-10-01
The beam angle selection (BAS) problem in intensity-modulated radiation therapy is often interpreted as a combinatorial optimization problem, i.e. finding the best combination of η beams in a discrete set of candidate beams. It is well established that the combinatorial BAS problem may be solved efficiently with metaheuristics such as simulated annealing or genetic algorithms. However, the underlying parameters of the optimization process, such as the inclusion of non-coplanar candidate beams, the angular resolution in the space of candidate beams, and the number of evaluated beam ensembles as well as the relative performance of different metaheuristics have not yet been systematically investigated. We study these open questions in a meta-analysis of four strategies for combinatorial optimization in order to provide a reference for future research related to the BAS problem in intensity-modulated radiation therapy treatment planning. We introduce a high-performance inverse planning engine for BAS. It performs a full fluence optimization for ≈3600 treatment plans per hour while handling up to 50 GB of dose influence data (≈1400 candidate beams). For three head and neck patients, we compare the relative performance of a genetic, a cross-entropy, a simulated annealing and a naive iterative algorithm. The selection of ensembles with 5, 7, 9 and 11 beams considering either only coplanar or all feasible candidate beams is studied for an angular resolution of 5°, 10°, 15° and 20° in the space of candidate beams. The impact of different convergence criteria is investigated in comparison to a fixed termination after the evaluation of 10 000 beam ensembles. In total, our simulations comprise a full fluence optimization for about 3000 000 treatment plans. All four combinatorial BAS strategies yield significant improvements of the objective function value and of the corresponding dose distributions compared to standard beam configurations with equi
Combinatorial nanomedicines for colon cancer therapy.
Anitha, A; Maya, S; Sivaram, Amal J; Mony, U; Jayakumar, R
2016-01-01
Colon cancer is one of the major causes of cancer deaths worldwide. Even after surgical resection and aggressive chemotherapy, 50% of colorectal carcinoma patients develop recurrent disease. Thus, the rationale of developing new therapeutic approaches to improve the current chemotherapeutic regimen would be highly recommended. There are reports on the effectiveness of combination chemotherapy in colon cancer and it has been practiced in clinics for long time. These approaches are associated with toxic side effects. Later, the drug delivery research had shown the potential of nanoencapsulation techniques and active targeting as an effective method to improve the effectiveness of chemotherapy with less toxicity. This current focus article provides a brief analysis of the ongoing research in the colon cancer area using the combinatorial nanomedicines and its outcome. © 2015 Wiley Periodicals, Inc.
Identification and Interrogation of Combinatorial Histone Modifications
Directory of Open Access Journals (Sweden)
Kelly R Karch
2013-12-01
Full Text Available Histone proteins are dynamically modified to mediate a variety of cellular processes including gene transcription, DNA damage repair, and apoptosis. Regulation of these processes occurs through the recruitment of non-histone proteins to chromatin by specific combinations of histone post-translational modifications (PTMs. Mass spectrometry has emerged as an essential tool to discover and quantify histone PTMs both within and between samples in an unbiased manner. Developments in mass spectrometry that allow for characterization of large histone peptides or intact protein has made it possible to determine which modifications occur simultaneously on a single histone polypeptide. A variety of techniques from biochemistry, biophysics, and chemical biology have been employed to determine the biological relevance of discovered combinatorial codes. This review first describes advancements in the field of mass spectrometry that have facilitated histone PTM analysis and then covers notable approaches to probe the biological relevance of these modifications in their nucleosomal context.
Characterizing the combinatorial beam angle selection problem
International Nuclear Information System (INIS)
Bangert, Mark; Ziegenhein, Peter; Oelfke, Uwe
2012-01-01
The beam angle selection (BAS) problem in intensity-modulated radiation therapy is often interpreted as a combinatorial optimization problem, i.e. finding the best combination of η beams in a discrete set of candidate beams. It is well established that the combinatorial BAS problem may be solved efficiently with metaheuristics such as simulated annealing or genetic algorithms. However, the underlying parameters of the optimization process, such as the inclusion of non-coplanar candidate beams, the angular resolution in the space of candidate beams, and the number of evaluated beam ensembles as well as the relative performance of different metaheuristics have not yet been systematically investigated. We study these open questions in a meta-analysis of four strategies for combinatorial optimization in order to provide a reference for future research related to the BAS problem in intensity-modulated radiation therapy treatment planning. We introduce a high-performance inverse planning engine for BAS. It performs a full fluence optimization for ≈3600 treatment plans per hour while handling up to 50 GB of dose influence data (≈1400 candidate beams). For three head and neck patients, we compare the relative performance of a genetic, a cross-entropy, a simulated annealing and a naive iterative algorithm. The selection of ensembles with 5, 7, 9 and 11 beams considering either only coplanar or all feasible candidate beams is studied for an angular resolution of 5°, 10°, 15° and 20° in the space of candidate beams. The impact of different convergence criteria is investigated in comparison to a fixed termination after the evaluation of 10 000 beam ensembles. In total, our simulations comprise a full fluence optimization for about 3000 000 treatment plans. All four combinatorial BAS strategies yield significant improvements of the objective function value and of the corresponding dose distributions compared to standard beam configurations with equi
Combinatorial nuclear level-density model
International Nuclear Information System (INIS)
Uhrenholt, H.; Åberg, S.; Dobrowolski, A.; Døssing, Th.; Ichikawa, T.; Möller, P.
2013-01-01
A microscopic nuclear level-density model is presented. The model is a completely combinatorial (micro-canonical) model based on the folded-Yukawa single-particle potential and includes explicit treatment of pairing, rotational and vibrational states. The microscopic character of all states enables extraction of level-distribution functions with respect to pairing gaps, parity and angular momentum. The results of the model are compared to available experimental data: level spacings at neutron separation energy, data on total level-density functions from the Oslo method, cumulative level densities from low-lying discrete states, and data on parity ratios. Spherical and deformed nuclei follow basically different coupling schemes, and we focus on deformed nuclei
DEFF Research Database (Denmark)
Nielsen, Søren Bo
2014-01-01
Against a background of rather mixed evidence about transfer pricing practices in multinational enterprises (MNEs) and varying attitudes on the part of tax authorities, this paper explores how multiple aims in transfer pricing can be pursued across four different transfer pricing regimes. A MNE h...
On the Cut-off Point for Combinatorial Group Testing
DEFF Research Database (Denmark)
Fischer, Paul; Klasner, N.; Wegener, I.
1999-01-01
is answered by 1 if Q contains at least one essential object and by 0 otherwise. In the statistical setting the objects are essential, independently of each other, with a given probability p combinatorial setting the number k ... group testing is equal to p* = 12(3 - 5), i.e., the strategy of testing each object individually minimizes the average number of queries iff p >= p* or n = 1. In the combinatorial setting the worst case number of queries is of interest. It has been conjectured that the cut-off point of combinatorial...
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.
Directory of Open Access Journals (Sweden)
Arindam Deb
Full Text Available Combinations of cis-regulatory elements (CREs present at the promoters facilitate the binding of several transcription factors (TFs, thereby altering the consequent gene expressions. Due to the eminent complexity of the regulatory mechanism, the combinatorics of CRE-mediated transcriptional regulation has been elusive. In this work, we have developed a new methodology that quantifies the co-occurrence tendencies of CREs present in a set of promoter sequences; these co-occurrence scores are filtered in three consecutive steps to test their statistical significance; and the significantly co-occurring CRE pairs are presented as networks. These networks of co-occurring CREs are further transformed to derive higher order of regulatory combinatorics. We have further applied this methodology on the differentially up-regulated gene-sets of rice tissues under fungal (Magnaporthe infected conditions to demonstrate how it helps to understand the CRE-mediated combinatorial gene regulation. Our analysis includes a wide spectrum of biologically important results. The CRE pairs having a strong tendency to co-occur often exhibit very similar joint distribution patterns at the promoters of rice. We couple the network approach with experimental results of plant gene regulation and defense mechanisms and find evidences of auto and cross regulation among TF families, cross-talk among multiple hormone signaling pathways, similarities and dissimilarities in regulatory combinatorics between different tissues, etc. Our analyses have pointed a highly distributed nature of the combinatorial gene regulation facilitating an efficient alteration in response to fungal attack. All together, our proposed methodology could be an important approach in understanding the combinatorial gene regulation. It can be further applied to unravel the tissue and/or condition specific combinatorial gene regulation in other eukaryotic systems with the availability of annotated genomic
Garcia, F; Arruda-Neto, J D; Manso, M V; Helene, O M; Vanin, V R; Rodriguez, O; Mesa, J; Likhachev, V P; Filho, J W; Deppman, A; Perez, G; Guzman, F; de Camargo, S P
1999-10-01
A new and simple statistical procedure (STATFLUX) for the calculation of transfer coefficients of radionuclide transport to animals and plants is proposed. The method is based on the general multiple-compartment model, which uses a system of linear equations involving geometrical volume considerations. By using experimentally available curves of radionuclide concentrations versus time, for each animal compartment (organs), flow parameters were estimated by employing a least-squares procedure, whose consistency is tested. Some numerical results are presented in order to compare the STATFLUX transfer coefficients with those from other works and experimental data.
International Nuclear Information System (INIS)
Garcia, F.; Manso, M.V.; Rodriguez, O.; Mesa, J.; Arruda-Neto, J.D.T.; Helene, O.M.; Vanin, V.R.; Likhachev, V.P.; Pereira Filho, J.W.; Deppman, A.; Perez, G.; Guzman, F.; Camargo, S.P. de
1999-01-01
A new and simple statistical procedure (STATFLUX) for the calculation of transfer coefficients of radionuclide transport to animals and plants is proposed. The method is based on the general multiple-compartment model, which uses a system of linear equations involving geometrical volume considerations. By using experimentally available curves of radionuclide concentrations versus time, for each animal compartment (organs), flow parameters were estimated by employing a least-squares procedure, whose consistency is tested. Some numerical results are presented in order to compare the STATFLUX transfer coefficients with those from other works and experimental data. (author)
Individualized Pixel Synthesis and Characterization of Combinatorial Materials Chips
Directory of Open Access Journals (Sweden)
Xiao-Dong Xiang
2015-06-01
Full Text Available Conventionally, an experimentally determined phase diagram requires studies of phase formation at a range of temperatures for each composition, which takes years of effort from multiple research groups. Combinatorial materials chip technology, featuring high-throughput synthesis and characterization, is able to determine the phase diagram of an entire composition spread of a binary or ternary system at a single temperature on one materials library, which, though significantly increasing efficiency, still requires many libraries processed at a series of temperatures in order to complete a phase diagram. In this paper, we propose a “one-chip method” to construct a complete phase diagram by individually synthesizing each pixel step by step with a progressive pulse of energy to heat at different temperatures while monitoring the phase evolution on the pixel in situ in real time. Repeating this process pixel by pixel throughout the whole chip allows the entire binary or ternary phase diagram to be mapped on one chip in a single experiment. The feasibility of this methodology is demonstrated in a study of a Ge-Sb-Te ternary alloy system, on which the amorphous-crystalline phase boundary is determined.
Directed combinatorial mutagenesis of Escherichia coli for complex phenotype engineering
Energy Technology Data Exchange (ETDEWEB)
Liu, Rongming; Liang, Liya; Garst, Andrew D.; Choudhury, Alaksh; Nogué, Violeta Sànchez i.; Beckham, Gregg T.; Gill, Ryan T.
2018-05-01
Strain engineering for industrial production requires a targeted improvement of multiple complex traits, which range from pathway flux to tolerance to mixed sugar utilization. Here, we report the use of an iterative CRISPR EnAbled Trackable genome Engineering (iCREATE) method to engineer rapid glucose and xylose co-consumption and tolerance to hydrolysate inhibitors in E. coli. Deep mutagenesis libraries were rationally designed, constructed, and screened to target ~40,000 mutations across 30 genes. These libraries included global and high-level regulators that regulate global gene expression, transcription factors that play important roles in genome-level transcription, enzymes that function in the sugar transport system, NAD(P)H metabolism, and the aldehyde reduction system. Specific mutants that conferred increased growth in mixed sugars and hydrolysate tolerance conditions were isolated, confirmed, and evaluated for changes in genome-wide expression levels. We tested the strain with positive combinatorial mutations for 3-hydroxypropionic acid (3HP) production under high furfural and high acetate hydrolysate fermentation, which demonstrated a 7- and 8-fold increase in 3HP productivity relative to the parent strain, respectively.
Implementation of a combinatorial cleavage and deprotection scheme
DEFF Research Database (Denmark)
Nielsen, John; Rasmussen, Palle H.
1996-01-01
Phthalhydrazide libraries are synthesized in solution from substituted hydrazines and phthalimides in several different library formats including single compounds, indexed sub-libraries and a full library. When carried out during solid-phase synthesis, this combinatorial cleavage and deprotection...
ON 3-WAY COMBINATORIAL IDENTITIES A. K. AGARWAL MEGHA ...
Indian Academy of Sciences (India)
36
∗Corresponding author: Department of Basic and Applied Sciences, University College of Engineering,. Punjabi ... In this paper we provide combinatorial meanings to two generalized basic ... 2010 Mathematics Subject Classification. 05A15 ...
Analysis and design of algorithms for combinatorial problems
Ausiello, G
1985-01-01
Combinatorial problems have been from the very beginning part of the history of mathematics. By the Sixties, the main classes of combinatorial problems had been defined. During that decade, a great number of research contributions in graph theory had been produced, which laid the foundations for most of the research in graph optimization in the following years. During the Seventies, a large number of special purpose models were developed. The impressive growth of this field since has been strongly determined by the demand of applications and influenced by the technological increases in computing power and the availability of data and software. The availability of such basic tools has led to the feasibility of the exact or well approximate solution of large scale realistic combinatorial optimization problems and has created a number of new combinatorial problems.
Olefin Metathesis in Peptidomimetics, Dynamic Combinatorial Chemistry, and Molecular Imprinting
National Research Council Canada - National Science Library
Low, Tammy K
2006-01-01
.... Our research goals consisted of employing olefin metathesis in the synthesis of peptidomimetics, and studying the feasibility of this method in dynamic combinatorial chemistry and molecular imprinting of nerve agents...
Dynamic combinatorial libraries: from exploring molecular recognition to systems chemistry.
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.
Novel Combinatorial Chemistry-Derived Inhibitors of Oncogenic Phosphatases
National Research Council Canada - National Science Library
Lazo, John
1999-01-01
Our overall goal of this US Army Breast Cancer Grant entitled "Novel Combinatorial Chemistry-Derived Inhibitors of Oncogenic Phosphatases" is to identity and develop novel therapeutic agents for human breast cancer...
The Combinatorial Rigidity Conjecture is False for Cubic Polynomials
DEFF Research Database (Denmark)
Henriksen, Christian
2003-01-01
We show that there exist two cubic polynomials with connected Julia sets which are combinatorially equivalent but not topologically conjugate on their Julia sets. This disproves a conjecture by McMullen from 1995.......We show that there exist two cubic polynomials with connected Julia sets which are combinatorially equivalent but not topologically conjugate on their Julia sets. This disproves a conjecture by McMullen from 1995....
Distributing the computation in combinatorial optimization experiments over the cloud
Mario Brcic; Nikica Hlupic; Nenad Katanic
2017-01-01
Combinatorial optimization is an area of great importance since many of the real-world problems have discrete parameters which are part of the objective function to be optimized. Development of combinatorial optimization algorithms is guided by the empirical study of the candidate ideas and their performance over a wide range of settings or scenarios to infer general conclusions. Number of scenarios can be overwhelming, especially when modeling uncertainty in some of the problem’s parameters....
Enabling high performance computational science through combinatorial algorithms
International Nuclear Information System (INIS)
Boman, Erik G; Bozdag, Doruk; Catalyurek, Umit V; Devine, Karen D; Gebremedhin, Assefaw H; Hovland, Paul D; Pothen, Alex; Strout, Michelle Mills
2007-01-01
The Combinatorial Scientific Computing and Petascale Simulations (CSCAPES) Institute is developing algorithms and software for combinatorial problems that play an enabling role in scientific and engineering computations. Discrete algorithms will be increasingly critical for achieving high performance for irregular problems on petascale architectures. This paper describes recent contributions by researchers at the CSCAPES Institute in the areas of load balancing, parallel graph coloring, performance improvement, and parallel automatic differentiation
On the combinatorial foundations of Regge-calculus
International Nuclear Information System (INIS)
Budach, L.
1989-01-01
Lipschitz-Killing curvatures of piecewise flat spaces are combinatorial analogues of Lipschitz-Killing curvatures of Riemannian manifolds. In the following paper rigorous combinatorial representations and proofs of all basic results for Lipschitz-Killing curvatures not using analytic arguments are given. The principal tools for an elementary representation of Regge calculus can be developed by means of basic properties of dihedral angles. (author)
Immune-Stimulating Combinatorial Therapy for Prostate Cancer
2016-10-01
Overlap: None 20 90061946 (Drake) Title: Epigenetic Drugs and Immuno Therapy for Prostate Cancer (EDIT-PC) Effort: 1.2 calendar months (10% effort...AWARD NUMBER: W81XWH-15-1-0667 TITLE: Immune-Stimulating Combinatorial Therapy for Prostate Cancer PRINCIPAL INVESTIGATOR: Robert Ivkov...Stimulating Combinatorial Therapy for Prostate Cancer 5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-15-1-0667 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S
Enabling high performance computational science through combinatorial algorithms
Energy Technology Data Exchange (ETDEWEB)
Boman, Erik G [Discrete Algorithms and Math Department, Sandia National Laboratories (United States); Bozdag, Doruk [Biomedical Informatics, and Electrical and Computer Engineering, Ohio State University (United States); Catalyurek, Umit V [Biomedical Informatics, and Electrical and Computer Engineering, Ohio State University (United States); Devine, Karen D [Discrete Algorithms and Math Department, Sandia National Laboratories (United States); Gebremedhin, Assefaw H [Computer Science and Center for Computational Science, Old Dominion University (United States); Hovland, Paul D [Mathematics and Computer Science Division, Argonne National Laboratory (United States); Pothen, Alex [Computer Science and Center for Computational Science, Old Dominion University (United States); Strout, Michelle Mills [Computer Science, Colorado State University (United States)
2007-07-15
The Combinatorial Scientific Computing and Petascale Simulations (CSCAPES) Institute is developing algorithms and software for combinatorial problems that play an enabling role in scientific and engineering computations. Discrete algorithms will be increasingly critical for achieving high performance for irregular problems on petascale architectures. This paper describes recent contributions by researchers at the CSCAPES Institute in the areas of load balancing, parallel graph coloring, performance improvement, and parallel automatic differentiation.
Combinatorial Dyson-Schwinger equations and inductive data types
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.
Intrinsic information carriers in combinatorial dynamical systems
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
Intrinsic information carriers in combinatorial dynamical systems.
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
Stuart, Jessica F.
The primary focus of this work has been to develop high-energy capacity batteries capable of undergoing multiple electron charge transfer redox reactions to address the growing demand for improved electrical energy storage systems that can be applied to a range of applications. As the levels of carbon dioxide (CO2) increase in the Earth's atmosphere, the effects on climate change become increasingly apparent. According to the Energy Information Administration (EIA), the U.S. electric power sector is responsible for the release of 2,039 million metric tons of CO2 annually, equating to 39% of total U.S. energy-related CO2 emissions. Both nationally and abroad, there are numerous issues associated with the generation and use of electricity aside from the overwhelming dependence on fossil fuels and the subsequent carbon emissions, including reliability of the grid and the utilization of renewable energies. Renewable energy makes up a relatively small portion of total energy contributions worldwide, accounting for only 13% of the 3,955 billion kilowatt-hours of electricity produced each year, as reported by the EIA. As the demand to reduce our dependence on fossils fuels and transition to renewable energy sources increases, cost effective large-scale electrical energy storage must be established for renewable energy to become a sustainable option for the future. A high capacity energy storage system capable of leveling the intermittent nature of energy sources such as solar, wind, and water into the electric grid and provide electricity at times of high demand will facilitate this transition. In 2008, the Licht Group presented the highest volumetric energy capacity battery, the vanadium diboride (VB2) air battery, exceedingly proficient in transferring eleven electrons per molecule. This body of work focuses on new developments to this early battery such as fundamentally understanding the net discharge mechanism of the system, evaluation of the properties and
A combinatorial approach to angiosperm pollen morphology.
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).
Exact combinatorial approach to finite coagulating systems
Fronczak, Agata; Chmiel, Anna; Fronczak, Piotr
2018-02-01
This paper outlines an exact combinatorial approach to finite coagulating systems. In this approach, cluster sizes and time are discrete and the binary aggregation alone governs the time evolution of the systems. By considering the growth histories of all possible clusters, an exact expression is derived for the probability of a coagulating system with an arbitrary kernel being found in a given cluster configuration when monodisperse initial conditions are applied. Then this probability is used to calculate the time-dependent distribution for the number of clusters of a given size, the average number of such clusters, and that average's standard deviation. The correctness of our general expressions is proved based on the (analytical and numerical) results obtained for systems with the constant kernel. In addition, the results obtained are compared with the results arising from the solutions to the mean-field Smoluchowski coagulation equation, indicating its weak points. The paper closes with a brief discussion on the extensibility to other systems of the approach presented herein, emphasizing the issue of arbitrary initial conditions.
Scalable Combinatorial Tools for Health Disparities Research
Directory of Open Access Journals (Sweden)
Michael A. Langston
2014-10-01
Full Text Available Despite staggering investments made in unraveling the human genome, current estimates suggest that as much as 90% of the variance in cancer and chronic diseases can be attributed to factors outside an individual’s genetic endowment, particularly to environmental exposures experienced across his or her life course. New analytical approaches are clearly required as investigators turn to complicated systems theory and ecological, place-based and life-history perspectives in order to understand more clearly the relationships between social determinants, environmental exposures and health disparities. While traditional data analysis techniques remain foundational to health disparities research, they are easily overwhelmed by the ever-increasing size and heterogeneity of available data needed to illuminate latent gene x environment interactions. This has prompted the adaptation and application of scalable combinatorial methods, many from genome science research, to the study of population health. Most of these powerful tools are algorithmically sophisticated, highly automated and mathematically abstract. Their utility motivates the main theme of this paper, which is to describe real applications of innovative transdisciplinary models and analyses in an effort to help move the research community closer toward identifying the causal mechanisms and associated environmental contexts underlying health disparities. The public health exposome is used as a contemporary focus for addressing the complex nature of this subject.
Combinatorial effects of odorants on mouse behavior
Saraiva, Luis R.; Kondoh, Kunio; Ye, Xiaolan; Yoon, Kyoung-hye; Hernandez, Marcus; Buck, Linda B.
2016-01-01
The mechanisms by which odors induce instinctive behaviors are largely unknown. Odor detection in the mouse nose is mediated by >1, 000 different odorant receptors (ORs) and trace amine-associated receptors (TAARs). Odor perceptions are encoded combinatorially by ORs and can be altered by slight changes in the combination of activated receptors. However, the stereotyped nature of instinctive odor responses suggests the involvement of specific receptors and genetically programmed neural circuits relatively immune to extraneous odor stimuli and receptor inputs. Here, we report that, contrary to expectation, innate odor-induced behaviors can be context-dependent. First, different ligands for a given TAAR can vary in behavioral effect. Second, when combined, some attractive and aversive odorants neutralize one another’s behavioral effects. Both a TAAR ligand and a common odorant block aversion to a predator odor, indicating that this ability is not unique to TAARs and can extend to an aversive response of potential importance to survival. In vitro testing of single receptors with binary odorant mixtures indicates that behavioral blocking can occur without receptor antagonism in the nose. Moreover, genetic ablation of a single receptor prevents its cognate ligand from blocking predator odor aversion, indicating that the blocking requires sensory input from the receptor. Together, these findings indicate that innate odor-induced behaviors can depend on context, that signals from a single receptor can block innate odor aversion, and that instinctive behavioral responses to odors can be modulated by interactions in the brain among signals derived from different receptors. PMID:27208093
Ding, Xu; Han, Jianghong; Shi, Lei
2015-01-01
In this paper, the optimal working schemes for wireless sensor networks with multiple base stations and wireless energy transfer devices are proposed. The wireless energy transfer devices also work as data gatherers while charging sensor nodes. The wireless sensor network is firstly divided into sub networks according to the concept of Voronoi diagram. Then, the entire energy replenishing procedure is split into the pre-normal and normal energy replenishing stages. With the objective of maximizing the sojourn time ratio of the wireless energy transfer device, a continuous time optimization problem for the normal energy replenishing cycle is formed according to constraints with which sensor nodes and wireless energy transfer devices should comply. Later on, the continuous time optimization problem is reshaped into a discrete multi-phased optimization problem, which yields the identical optimality. After linearizing it, we obtain a linear programming problem that can be solved efficiently. The working strategies of both sensor nodes and wireless energy transfer devices in the pre-normal replenishing stage are also discussed in this paper. The intensive simulations exhibit the dynamic and cyclic working schemes for the entire energy replenishing procedure. Additionally, a way of eliminating “bottleneck” sensor nodes is also developed in this paper. PMID:25785305
Ding, Xu; Han, Jianghong; Shi, Lei
2015-03-16
In this paper, the optimal working schemes for wireless sensor networks with multiple base stations and wireless energy transfer devices are proposed. The wireless energy transfer devices also work as data gatherers while charging sensor nodes. The wireless sensor network is firstly divided into sub networks according to the concept of Voronoi diagram. Then, the entire energy replenishing procedure is split into the pre-normal and normal energy replenishing stages. With the objective of maximizing the sojourn time ratio of the wireless energy transfer device, a continuous time optimization problem for the normal energy replenishing cycle is formed according to constraints with which sensor nodes and wireless energy transfer devices should comply. Later on, the continuous time optimization problem is reshaped into a discrete multi-phased optimization problem, which yields the identical optimality. After linearizing it, we obtain a linear programming problem that can be solved efficiently. The working strategies of both sensor nodes and wireless energy transfer devices in the pre-normal replenishing stage are also discussed in this paper. The intensive simulations exhibit the dynamic and cyclic working schemes for the entire energy replenishing procedure. Additionally, a way of eliminating "bottleneck" sensor nodes is also developed in this paper.
Solid-Phase Synthesis of Small Molecule Libraries using Double Combinatorial Chemistry
DEFF Research Database (Denmark)
Nielsen, John; Jensen, Flemming R.
1997-01-01
The first synthesis of a combinatorial library using double combinatorial chemistry is presented. Coupling of unprotected Fmoc-tyrosine to the solid support was followed by Mitsunobu O-alkylation. Introduction of a diacid linker yields a system in which the double combinatorial step can be demons......The first synthesis of a combinatorial library using double combinatorial chemistry is presented. Coupling of unprotected Fmoc-tyrosine to the solid support was followed by Mitsunobu O-alkylation. Introduction of a diacid linker yields a system in which the double combinatorial step can...
Directory of Open Access Journals (Sweden)
Béla-Gergely RÁCZ
2016-12-01
Full Text Available This study investigates how the absorptive capacity could be increased to improve internal and external knowledge transfer in subsidiaries of multinational companies. We look at the way in which the literature on absorptive capacity has evolved, and how it links the internal and external knowledge transfer. Based on 3 case studies conducted at Romanian subsidiaries of multinational companies, we find some patterns, which could explain how the successful knowledge flows should be managed within the multinational company and outside of it, in the supply chain network.
Physical interpretation of the combinatorial hierarchy
International Nuclear Information System (INIS)
Bastin, T.; Noyes, H.P.
1978-01-01
The combinatorial hierarchy model for base particle processes is compared and contrasted with the Ur-theory as developed at the Tutzing Conferences. It agrees with Ur-theory about a finite basis, the ''fixed past--uncertain future'' aspects of physics, and the necessity of dropping Bohr's requirement of reduction to the haptic language of commonsense and classical physics. However, it retains a constructive, hierarchial approach with can yield only an approximate and discrete ''space time'', and introduces the observation metaphysic at the start. Concrete interpretation of the four levels of the hierarchy (with cardinals 3, 7, 127, 2 127 -1 approx. =10 38 ) associates the three levels which map up and down with three absolute conservation laws (charge, baryon number, lepton number) and the spin dichotomy. The first level represents +, -, and +- unit charge. The second has the quantum nubmers of a baryon--antibaryon pair and associated charged meson (e.g., n anti n, p anti n, p anti p, n anti p, π + , π 0 , π - ). The third level associates this pair, now including four spin states as well as four charge states, with a neutral lepton--antilepton pair (e anti e or ν anti ν) in four spin states (total, 64 states): three charged spinless, three charged spin-1, and neutral spin-1 mesons (15 states), and a neutral vector boson associated with the leptons; this gives 3 + 15 + 3 x 15 = 63 possible boson states, so a total correct count of 63 + 64 = 127 states. Something like SU 2 X SU 3 and other indications of quark quantum numbers can occur as substructures at the fourth (unstable) level. A slight extension gives the usual static approximation to the building energy of the hydrogen atom, α 2 m/sub e/c 2 . Cosmological implications of the theory are in accord with current experience. A beginning in the physical interpretation of a theory which could eventually encompass all branches of physics was made. 3 figures, 6 tables
Combinatorial explosion in model gene networks
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
Morphological Constraints on Cerebellar Granule Cell Combinatorial Diversity.
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
The priming of basic combinatory responses in MEG.
Blanco-Elorrieta, Esti; Ferreira, Victor S; Del Prato, Paul; Pylkkänen, Liina
2018-01-01
Priming has been a powerful tool for the study of human memory and especially the memory representations relevant for language. However, although it is well established that lexical access can be primed, we do not know exactly what types of computations can be primed above the word level. This work took a neurobiological approach and assessed the ways in which the complex representation of a minimal combinatory phrase, such as red boat, can be primed, as evidenced by the spatiotemporal profiles of magnetoencephalography (MEG) signals. Specifically, we built upon recent progress on the neural signatures of phrasal composition and tested whether the brain activities implicated for the basic combination of two words could be primed. In two experiments, MEG was recorded during a picture naming task where the prime trials were designed to replicate previously reported combinatory effects and the target trials to test whether those combinatory effects could be primed. The manipulation of the primes was successful in eliciting larger activity for adjective-noun combinations than single nouns in left anterior temporal and ventromedial prefrontal cortices, replicating prior MEG studies on parallel contrasts. Priming of similarly timed activity was observed during target trials in anterior temporal cortex, but only when the prime and target shared an adjective. No priming in temporal cortex was observed for single word repetition and two control tasks showed that the priming effect was not elicited if the prime pictures were simply viewed but not named. In sum, this work provides evidence that very basic combinatory operations can be primed, with the necessity for some lexical overlap between prime and target suggesting combinatory conceptual, as opposed to syntactic processing. Both our combinatory and priming effects were early, onsetting between 100 and 150ms after picture onset and thus are likely to reflect the very earliest planning stages of a combinatory message
Energy Technology Data Exchange (ETDEWEB)
Fang, Chin [SLAC National Accelerator Lab., Menlo Park, CA (United States); Corttrell, R. A. [SLAC National Accelerator Lab., Menlo Park, CA (United States)
2015-05-06
This Technical Note provides an overview of high-performance parallel Big Data transfers with and without encryption for data in-transit over multiple network channels. It shows that with the parallel approach, it is feasible to carry out high-performance parallel "encrypted" Big Data transfers without serious impact to throughput. But other impacts, e.g. the energy-consumption part should be investigated. It also explains our rationales of using a statistics-based approach for gaining understanding from test results and for improving the system. The presentation is of high-level nature. Nevertheless, at the end we will pose some questions and identify potentially fruitful directions for future work.
Directory of Open Access Journals (Sweden)
Yoichiro Ito
Full Text Available Combinatorial screening used together with a broad library of gene expression cassettes is expected to produce a powerful tool for the optimization of the simultaneous expression of multiple enzymes. Recently, we proposed a highly tunable protein expression system that utilized multiple genome-integrated target genes to fine-tune enzyme expression in yeast cells. This tunable system included a library of expression cassettes each composed of three gene-expression control elements that in different combinations produced a wide range of protein expression levels. In this study, four gene expression cassettes with graded protein expression levels were applied to the expression of three cellulases: cellobiohydrolase 1, cellobiohydrolase 2, and endoglucanase 2. After combinatorial screening for transgenic yeasts simultaneously secreting these three cellulases, we obtained strains with higher cellulase expressions than a strain harboring three cellulase-expression constructs within one high-performance gene expression cassette. These results show that our method will be of broad use throughout the field of metabolic engineering.
Ito, Yoichiro; Yamanishi, Mamoru; Ikeuchi, Akinori; Imamura, Chie; Matsuyama, Takashi
2015-01-01
Combinatorial screening used together with a broad library of gene expression cassettes is expected to produce a powerful tool for the optimization of the simultaneous expression of multiple enzymes. Recently, we proposed a highly tunable protein expression system that utilized multiple genome-integrated target genes to fine-tune enzyme expression in yeast cells. This tunable system included a library of expression cassettes each composed of three gene-expression control elements that in different combinations produced a wide range of protein expression levels. In this study, four gene expression cassettes with graded protein expression levels were applied to the expression of three cellulases: cellobiohydrolase 1, cellobiohydrolase 2, and endoglucanase 2. After combinatorial screening for transgenic yeasts simultaneously secreting these three cellulases, we obtained strains with higher cellulase expressions than a strain harboring three cellulase-expression constructs within one high-performance gene expression cassette. These results show that our method will be of broad use throughout the field of metabolic engineering. PMID:26692026
Summation on the basis of combinatorial representation of equal powers
Directory of Open Access Journals (Sweden)
Alexander I. Nikonov
2016-03-01
Full Text Available In the paper the conclusion of combinatorial expressions for the sums of members of several sequences is considered. Conclusion is made on the basis of combinatorial representation of the sum of the weighted equal powers. The weighted members of a geometrical progression, the simple arithmetic-geometrical and combined progressions are subject to summation. One of principal places in the given conclusion occupies representation of members of each of the specified progressions in the form of matrix elements. The row of this matrix is formed with use of a gang of equal powers with the set weight factor. Besides, in work formulas of combinatorial identities with participation of free components of the sums of equal powers, and also separate power-member of sequence of equal powers or a geometrical progression are presented. All presented formulas have the general basis-components of the sums of equal powers.
Combinatorial vector fields and the valley structure of fitness landscapes.
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.
International Nuclear Information System (INIS)
Sun Hechao; Godoy-Ruiz, Raquel; Tugarinov, Vitali
2012-01-01
Relaxation violated coherence transfer NMR spectroscopy (Tugarinov et al. in J Am Chem Soc 129:1743–1750, 2007) is an established experimental tool for quantitative estimation of the amplitudes of side-chain motions in methyl-protonated, highly deuterated proteins. Relaxation violated coherence transfer experiments monitor the build-up of methyl proton multiple-quantum coherences that can be created in magnetically equivalent spin-systems as long as their transverse magnetization components relax with substantially different rates. The rate of this build-up is a reporter of the methyl-bearing side-chain mobility. Although the build-up of multiple-quantum 1 H coherences is monitored in these experiments, the decay of the methyl signal during relaxation delays occurs when methyl proton magnetization is in a single-quantum state. We describe a relaxation violated coherence transfer approach where the relaxation of multiple-quantum 1 H– 13 C methyl coherences during the relaxation delay period is quantified. The NMR experiment and the associated fitting procedure that models the time-dependence of the signal build-up, are applicable to the characterization of side-chain order in [ 13 CH 3 ]-methyl-labeled, highly deuterated protein systems up to ∼100 kDa in molecular weight. The feasibility of extracting reliable measures of side-chain order is experimentally verified on methyl-protonated, perdeuterated samples of an 8.5-kDa ubiquitin at 10°C and an 82-kDa Malate Synthase G at 37°C.
Unravelling radiative energy transfer in solid-state lighting
Melikov, Rustamzhon; Press, Daniel Aaron; Ganesh Kumar, Baskaran; Sadeghi, Sadra; Nizamoglu, Sedat
2018-01-01
Today, a wide variety of organic and inorganic luminescent materials (e.g., phosphors, quantum dots, etc.) are being used for lighting and new materials (e.g., graphene, perovskite, etc.) are currently under investigation. However, the understanding of radiative energy transfer is limited, even though it is critical to understand and improve the performance levels of solid-state lighting devices. In this study, we derived a matrix approach that includes absorption, reabsorption, inter-absorption and their iterative and combinatorial interactions for one and multiple types of fluorophores, which is simplified to an analytical matrix. This mathematical approach gives results that agree well with the measured spectral and efficiency characteristics of color-conversion light-emitting diodes. Moreover, it also provides a deep physical insight by uncovering the entire radiative interactions and their contribution to the output optical spectrum. The model is universal and applicable for all kinds of fluorophores.
Stamnes, Knut; Tsay, S.-CHEE; Jayaweera, Kolf; Wiscombe, Warren
1988-01-01
The transfer of monochromatic radiation in a scattering, absorbing, and emitting plane-parallel medium with a specified bidirectional reflectivity at the lower boundary is considered. The equations and boundary conditions are summarized. The numerical implementation of the theory is discussed with attention given to the reliable and efficient computation of eigenvalues and eigenvectors. Ways of avoiding fatal overflows and ill-conditioning in the matrix inversion needed to determine the integration constants are also presented.
Combinatorial methods for advanced materials research and development
Energy Technology Data Exchange (ETDEWEB)
Cremer, R.; Dondorf, S.; Hauck, M.; Horbach, D.; Kaiser, M.; Krysta, S.; Kyrylov, O.; Muenstermann, E.; Philipps, M.; Reichert, K.; Strauch, G. [Rheinisch-Westfaelische Technische Hochschule Aachen (Germany). Lehrstuhl fuer Theoretische Huettenkunde
2001-10-01
The applicability of combinatorial methods in developing advanced materials is illustrated presenting four examples for the deposition and characterization of one- and two-dimensionally laterally graded coatings, which were deposited by means of (reactive) magnetron sputtering and plasma-enhanced chemical vapor deposition. To emphasize the advantages of combinatorial approaches, metastable hard coatings like (Ti,Al)N and (Ti,Al,Hf)N respectively, as well as Ge-Sb-Te based films for rewritable optical data storage were investigated with respect to the relations between structure, composition, and the desired materials properties. (orig.)
Combinatorial algebraic geometry selected papers from the 2016 apprenticeship program
Sturmfels, Bernd
2017-01-01
This volume consolidates selected articles from the 2016 Apprenticeship Program at the Fields Institute, part of the larger program on Combinatorial Algebraic Geometry that ran from July through December of 2016. Written primarily by junior mathematicians, the articles cover a range of topics in combinatorial algebraic geometry including curves, surfaces, Grassmannians, convexity, abelian varieties, and moduli spaces. This book bridges the gap between graduate courses and cutting-edge research by connecting historical sources, computation, explicit examples, and new results.
Combinatorial reasoning an introduction to the art of counting
DeTemple, Duane
2014-01-01
Written by well-known scholars in the field, this book introduces combinatorics alongside modern techniques, showcases the interdisciplinary aspects of the topic, and illustrates how to problem solve with a multitude of exercises throughout. The authors' approach is very reader-friendly and avoids the ""scholarly tone"" found in many books on this topic. Combinatorial Reasoning: An Introduction to the Art of Counting: Focuses on enumeration and combinatorial thinking as a way to develop a variety of effective approaches to solving counting problemsIncludes brief summaries of basic concepts f
Mitigation of Control Channel Jamming via Combinatorial Key Distribution
Falahati, Abolfazl; Azarafrooz, Mahdi
The problem of countering control channel jamming against internal adversaries in wireless ad hoc networks is addressed. Using combinatorial key distribution, a new method to secure the control channel access is introduced. This method, utilizes the established keys in the key establishment phase to hide the location of control channels without the need for a secure BS. This is in obtained by combination of a collision free one-way function and a combinatorial key establishment method. The proposed scheme can be considered as a special case of the ALOHA random access schemes which uses the common established keys as its seeds to generate the pattern of transmission.
Polyhedral and semidefinite programming methods in combinatorial optimization
Tunçel, Levent
2010-01-01
Since the early 1960s, polyhedral methods have played a central role in both the theory and practice of combinatorial optimization. Since the early 1990s, a new technique, semidefinite programming, has been increasingly applied to some combinatorial optimization problems. The semidefinite programming problem is the problem of optimizing a linear function of matrix variables, subject to finitely many linear inequalities and the positive semidefiniteness condition on some of the matrix variables. On certain problems, such as maximum cut, maximum satisfiability, maximum stable set and geometric r
Some results from the combinatorial approach to quantum logic
International Nuclear Information System (INIS)
Greechie, R.J.
1976-01-01
The combinatorial approach to quantum logic focuses on certain interconnections between graphs, combinatorial designs, and convex sets as applied to a quantum logic. This article is concerned only with orthomodular lattices and associated structures. A class of complete atomic irreducible semimodular orthomodular lattices is derived which may not be represented as linear subspaces of a vector space over a division ring. Each of these lattices is a proposition system of dimension three. These proposition systems form orthocomplemented non-Desarguesian projective geometries. (B.R.H.)
Markov's theorem and algorithmically non-recognizable combinatorial manifolds
International Nuclear Information System (INIS)
Shtan'ko, M A
2004-01-01
We prove the theorem of Markov on the existence of an algorithmically non-recognizable combinatorial n-dimensional manifold for every n≥4. We construct for the first time a concrete manifold which is algorithmically non-recognizable. A strengthened form of Markov's theorem is proved using the combinatorial methods of regular neighbourhoods and handle theory. The proofs coincide for all n≥4. We use Borisov's group with insoluble word problem. It has two generators and twelve relations. The use of this group forms the base for proving the strengthened form of Markov's theorem
On some interconnections between combinatorial optimization and extremal graph theory
Directory of Open Access Journals (Sweden)
Cvetković Dragoš M.
2004-01-01
Full Text Available The uniting feature of combinatorial optimization and extremal graph theory is that in both areas one should find extrema of a function defined in most cases on a finite set. While in combinatorial optimization the point is in developing efficient algorithms and heuristics for solving specified types of problems, the extremal graph theory deals with finding bounds for various graph invariants under some constraints and with constructing extremal graphs. We analyze by examples some interconnections and interactions of the two theories and propose some conclusions.
Binomial Rings: Axiomatisation, Transfer and Classification
Xantcha, Qimh Richey
2011-01-01
Hall's binomial rings, rings with binomial coefficients, are given an axiomatisation and proved identical to the numerical rings studied by Ekedahl. The Binomial Transfer Principle is established, enabling combinatorial proofs of algebraical identities. The finitely generated binomial rings are completely classified. An application to modules over binomial rings is given.
Fast Combinatorial Algorithm for the Solution of Linearly Constrained Least Squares Problems
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.
Affinity-based screening of combinatorial libraries using automated, serial-column chromatography
Energy Technology Data Exchange (ETDEWEB)
Evans, D.M.; Williams, K.P.; McGuinness, B. [PerSeptive Biosystems, Framingham, MA (United States)] [and others
1996-04-01
The authors have developed an automated serial chromatographic technique for screening a library of compounds based upon their relative affinity for a target molecule. A {open_quotes}target{close_quotes} column containing the immobilized target molecule is set in tandem with a reversed-phase column. A combinatorial peptide library is injected onto the target column. The target-bound peptides are eluted from the first column and transferred automatically to the reversed-phase column. The target-specific peptide peaks from the reversed-phase column are identified and sequenced. Using a monoclonal antibody (3E-7) against {beta}-endorphin as a target, we selected a single peptide with sequence YGGFL from approximately 5800 peptides present in a combinatorial library. We demonstrated the applicability of the technology towards selection of peptides with predetermined affinity for bacterial lipopolysaccharide (LPS, endotoxin). We expect that this technology will have broad applications for high throughput screening of chemical libraries or natural product extracts. 21 refs., 4 figs.
Theory of site-specific interactions of the combinatorial transcription factors with DNA
International Nuclear Information System (INIS)
Murugan, R
2010-01-01
We derive a functional relationship between the mean first passage time associated with the concurrent binding of multiple transcription factors (TFs) at their respective combinatorial cis-regulatory module sites (CRMs) and the number n of TFs involved in the regulation of the initiation of transcription of a gene of interest. Our results suggest that the overall search time τ s that is required by the n TFs to locate their CRMs which are all located on the same DNA chain scales with n as τ s ∼n α where α ∼ (2/5). When the jump size k that is associated with the dynamics of all the n TFs along DNA is higher than that of the critical jump size k c that scales with the size of DNA N as k c ∼ N 2/3 , we observe a similar power law scaling relationship and also the exponent α. When k c , α shows a strong dependence on both n and k. Apparently there is a critical number of combinatorial TFs n c ∼ 20 that is required to efficiently regulate the initiation of transcription of a given gene below which (2/5) 1. These results seem to be independent of the initial distances between the TFs and their corresponding CRMs and also suggest that the maximum number of TFs involved in a given combinatorial regulation of the initiation of transcription of a gene of interest seems to be restricted by the degree of condensation of the genomic DNA. The optimum number m opt of roadblock protein molecules per genome at which the search time associated with these n TFs to locate their binding sites is a minimum seems to scale as m opt ∼Ln α/2 where L is the sliding length of TFs whose maximum value seems to be such that L ≤ 10 4 bps for the E. coli bacterial genome.
Solid-Phase Synthesis of Small Molecule Libraries using Double Combinatorial Chemistry
DEFF Research Database (Denmark)
Nielsen, John; Jensen, Flemming R.
1997-01-01
The first synthesis of a combinatorial library using double combinatorial chemistry is presented. Coupling of unprotected Fmoc-tyrosine to the solid support was followed by Mitsunobu O-alkylation. Introduction of a diacid linker yields a system in which the double combinatorial step can be demons...
Energy Technology Data Exchange (ETDEWEB)
Bellmann-Strobl, J.; Paul, F.; Aktas, O.; Zipp, F. [Charite - University Medicine Berlin and Max Delbrueck Center for Molecular Medicine, Cecilie Vogt Clinic for Neurology, Berlin (Germany); Stiepani, H.; Bohner, G.; Klingebiel, R. [Charite - University Medicine Berlin, Department of Neuroradiology, Berlin (Germany); Wuerfel, J. [Charite - University Medicine Berlin and Max Delbrueck Center for Molecular Medicine, Cecilie Vogt Clinic for Neurology, Berlin (Germany); University Schleswig-Holstein, Institute of Neuroradiology, Campus Luebeck, Kiel (Germany); Warmuth, C. [Charite - University Medicine Berlin, Department of Radiology, Berlin (Germany); Wandinger, K.P. [Charite - University Medicine Berlin, Department of Neurology, Berlin (Germany)
2009-08-15
The purpose of this study was to correlate magnetic resonance imaging (MRI)-based lesion load assessment with clinical disability in early relapsing remitting multiple sclerosis (RRMS). Seventeen untreated patients (ten women, seven men; mean age 33.0{+-}7.9 years) with the initial diagnosis of RRMS were included for cross-sectional as well as longitudinal (24 months) clinical and MRI-based assessment in comparison with age-matched healthy controls. Conventional MR sequences, MR spectroscopy (MRS) and magnetisation transfer imaging (MTI) were performed at 1.5 T. Lesion number and volume, MRS and MTI measurements for lesions and normal appearing white matter (NAWM) were correlated to clinical scores [Expanded Disability Status Scale (EDSS), Multiple Sclerosis Functional Composite (MSFC)] for monitoring disease course after treatment initiation (interferon {beta}-1a). MTI and MRS detected changes [magnetisation transfer ratio (MTR), N-acetylaspartate (NAA)/creatine ratio] in NAWM over time. EDSS and lesional MTR increases correlated throughout the disease course. Average MTR of NAWM raised during the study (p<0.05) and correlated to the MSFC score (r=0.476, p<0.001). At study termination, NAA/creatine ratio of NAWM correlated to the MSFC score (p<0.05). MTI and MRS were useful for initial disease assessment in NAWM. MTI and MRS correlated with clinical scores, indicating potential for monitoring the disease course and gaining new insights into treatment-related effects. (orig.)
International Nuclear Information System (INIS)
Bellmann-Strobl, J.; Paul, F.; Aktas, O.; Zipp, F.; Stiepani, H.; Bohner, G.; Klingebiel, R.; Wuerfel, J.; Warmuth, C.; Wandinger, K.P.
2009-01-01
The purpose of this study was to correlate magnetic resonance imaging (MRI)-based lesion load assessment with clinical disability in early relapsing remitting multiple sclerosis (RRMS). Seventeen untreated patients (ten women, seven men; mean age 33.0±7.9 years) with the initial diagnosis of RRMS were included for cross-sectional as well as longitudinal (24 months) clinical and MRI-based assessment in comparison with age-matched healthy controls. Conventional MR sequences, MR spectroscopy (MRS) and magnetisation transfer imaging (MTI) were performed at 1.5 T. Lesion number and volume, MRS and MTI measurements for lesions and normal appearing white matter (NAWM) were correlated to clinical scores [Expanded Disability Status Scale (EDSS), Multiple Sclerosis Functional Composite (MSFC)] for monitoring disease course after treatment initiation (interferon β-1a). MTI and MRS detected changes [magnetisation transfer ratio (MTR), N-acetylaspartate (NAA)/creatine ratio] in NAWM over time. EDSS and lesional MTR increases correlated throughout the disease course. Average MTR of NAWM raised during the study (p<0.05) and correlated to the MSFC score (r=0.476, p<0.001). At study termination, NAA/creatine ratio of NAWM correlated to the MSFC score (p<0.05). MTI and MRS were useful for initial disease assessment in NAWM. MTI and MRS correlated with clinical scores, indicating potential for monitoring the disease course and gaining new insights into treatment-related effects. (orig.)
Energy Technology Data Exchange (ETDEWEB)
Gavra, M.M.; Gouliamos, A.D.; Vlahos, L.J. [Department of Radiology, ' ' Aretaieion' ' Hospital,University of Athens Medical School, Athens (Greece); Voumvourakis, C.; Sfagos, C. [Department of Neurology, ' ' Eginiteion' ' Hospital, University of Athens Medical School, Athens (Greece)
2004-03-01
Our purpose was to evaluate the role of magnetization transfer and image subtraction in detecting more enhancing lesions in brain MR imaging of patients with multiple sclerosis (MS). Thirty-one MS patients underwent MR imaging of the brain with T1-weighted spin echo sequences without and with magnetization transfer (MT) using a 1.5 T imager. Both sequences were acquired before and after intravenous injection of a paramagnetic contrast agent. Subtraction images in T1-weighted sequences were obtained by subtracting the pre-contrast images from the post-contrast ones. A significant difference was found between the numbers of enhanced areas in post-gadolinium T1-weighted images without and with MT (p=0.020). The post-gadolinium T1-weighted images with MT allowed the detection of an increased (13) number of enhancing lesions compared with post-gadolinium T1-weighted images without MT. A significant difference was also found between the numbers of enhanced areas in post-gadolinium T1-weighted images without MT and subtraction images without MT (p=0.020). The subtraction images without MT allowed the detection of an increased (10) number of enhancing lesions compared with post-gadolinium T1-weighted images without MT. Magnetization transfer contrast and subtraction techniques appear to be the simplest and least time-consuming applications to improve the conspicuity and detection of contrast-enhancing lesions in patients with MS. (orig.)
International Nuclear Information System (INIS)
Gavra, M.M.; Gouliamos, A.D.; Vlahos, L.J.; Voumvourakis, C.; Sfagos, C.
2004-01-01
Our purpose was to evaluate the role of magnetization transfer and image subtraction in detecting more enhancing lesions in brain MR imaging of patients with multiple sclerosis (MS). Thirty-one MS patients underwent MR imaging of the brain with T1-weighted spin echo sequences without and with magnetization transfer (MT) using a 1.5 T imager. Both sequences were acquired before and after intravenous injection of a paramagnetic contrast agent. Subtraction images in T1-weighted sequences were obtained by subtracting the pre-contrast images from the post-contrast ones. A significant difference was found between the numbers of enhanced areas in post-gadolinium T1-weighted images without and with MT (p=0.020). The post-gadolinium T1-weighted images with MT allowed the detection of an increased (13) number of enhancing lesions compared with post-gadolinium T1-weighted images without MT. A significant difference was also found between the numbers of enhanced areas in post-gadolinium T1-weighted images without MT and subtraction images without MT (p=0.020). The subtraction images without MT allowed the detection of an increased (10) number of enhancing lesions compared with post-gadolinium T1-weighted images without MT. Magnetization transfer contrast and subtraction techniques appear to be the simplest and least time-consuming applications to improve the conspicuity and detection of contrast-enhancing lesions in patients with MS. (orig.)
Novel modeling of combinatorial miRNA targeting identifies SNP with potential role in bone density.
Directory of Open Access Journals (Sweden)
Claudia Coronnello
Full Text Available MicroRNAs (miRNAs are post-transcriptional regulators that bind to their target mRNAs through base complementarity. Predicting miRNA targets is a challenging task and various studies showed that existing algorithms suffer from high number of false predictions and low to moderate overlap in their predictions. Until recently, very few algorithms considered the dynamic nature of the interactions, including the effect of less specific interactions, the miRNA expression level, and the effect of combinatorial miRNA binding. Addressing these issues can result in a more accurate miRNA:mRNA modeling with many applications, including efficient miRNA-related SNP evaluation. We present a novel thermodynamic model based on the Fermi-Dirac equation that incorporates miRNA expression in the prediction of target occupancy and we show that it improves the performance of two popular single miRNA target finders. Modeling combinatorial miRNA targeting is a natural extension of this model. Two other algorithms show improved prediction efficiency when combinatorial binding models were considered. ComiR (Combinatorial miRNA targeting, a novel algorithm we developed, incorporates the improved predictions of the four target finders into a single probabilistic score using ensemble learning. Combining target scores of multiple miRNAs using ComiR improves predictions over the naïve method for target combination. ComiR scoring scheme can be used for identification of SNPs affecting miRNA binding. As proof of principle, ComiR identified rs17737058 as disruptive to the miR-488-5p:NCOA1 interaction, which we confirmed in vitro. We also found rs17737058 to be significantly associated with decreased bone mineral density (BMD in two independent cohorts indicating that the miR-488-5p/NCOA1 regulatory axis is likely critical in maintaining BMD in women. With increasing availability of comprehensive high-throughput datasets from patients ComiR is expected to become an essential
Isocyanide based multi component reactions in combinatorial chemistry.
Dömling, A.
1998-01-01
Although usually regarded as a recent development, the combinatorial approach to the synthesis of libraries of new drug candidates was first described as early as 1961 using the isocyanide-based one-pot multicomponent Ugi reaction. Isocyanide-based multi component reactions (MCR's) markedly differ
Dynamic Combinatorial Chemistry with Diselenides, Disulfides, Imines and Metal Coordination
DEFF Research Database (Denmark)
Sørensen, Anne
combinatorial chemistry, namely the reversible diselenide exchange reaction. The first part of the thesis describes the development of a thermally induced OAr → SeAr migration reaction. Here, it was proven possible to rearrange a variety of substituted O-aryl selenocarbamates into the corresponding Se...
Dynamic combinatorial chemistry at the phospholipid bilayer interface
Mansfeld, Friederike M.; Au-Yeung, Ho Yu; Sanders, Jeremy K.M.; Otto, Sijbren
2010-01-01
Background: Molecular recognition at the environment provided by the phospholipid bilayer interface plays an important role in biology and is subject of intense investigation. Dynamic combinatorial chemistry is a powerful approach for exploring molecular recognition, but has thus far not been
Confluence of an extension of combinatory logic by Boolean constants
DEFF Research Database (Denmark)
Czajka, Łukasz
2017-01-01
We show confluence of a conditional term rewriting system CL-pc1, which is an extension of Combinatory Logic by Boolean constants. This solves problem 15 from the RTA list of open problems. The proof has been fully formalized in the Coq proof assistant....
Combinatorial Solid-Phase Synthesis of Balanol Analogues
DEFF Research Database (Denmark)
Nielsen, John; Lyngsø, Lars Ole
1996-01-01
The natural product balanol has served as a template for the design and synthesis of a combinatorial library using solid-phase chemistry. Using a retrosynthetic analysis, the structural analogues have been assembled from three relatively accessible building blocks. The solid-phase chemistry inclu...
Combinatorial algorithms enabling computational science: tales from the front
International Nuclear Information System (INIS)
Bhowmick, Sanjukta; Boman, Erik G; Devine, Karen; Gebremedhin, Assefaw; Hendrickson, Bruce; Hovland, Paul; Munson, Todd; Pothen, Alex
2006-01-01
Combinatorial algorithms have long played a crucial enabling role in scientific and engineering computations. The importance of discrete algorithms continues to grow with the demands of new applications and advanced architectures. This paper surveys some recent developments in this rapidly changing and highly interdisciplinary field
Combinatorial structures and processing in neural blackboard architectures
van der Velde, Frank; van der Velde, Frank; de Kamps, Marc; Besold, Tarek R.; d'Avila Garcez, Artur; Marcus, Gary F.; Miikkulainen, Risto
2015-01-01
We discuss and illustrate Neural Blackboard Architectures (NBAs) as the basis for variable binding and combinatorial processing the brain. We focus on the NBA for sentence structure. NBAs are based on the notion that conceptual representations are in situ, hence cannot be copied or transported.
Combinatorial chemistry approach to development of molecular plastic solar cells
Godovsky, Dmitri; Inganäs, Olle; Brabec, Christoph J.; Sariciftci, N. Serdar; Hummelen, Jan C.; Janssen, Rene A.J.; Prato, M.; Maggini, M.; Segura, Jose; Martin, Nazario
1999-01-01
We used a combinatorial chemistry approach to develop the molecular plastic solar cells based on soluble fullerene derivatives or solubilized TCNQ molecules in combination with conjugated polymers. Profiles, formed by the diffusion of low molecular weight component in the spin-cast polymer host were
Angelin, Marcus; Larsson, Rikard; Vongvilai, Pornrapee; Ramstrom, Olof
2010-01-01
In this laboratory experiment, college students are introduced to dynamic combinatorial chemistry (DCC) and apply it to determine the substrate selectivity of acetylcholinesterase (AChE). Initially, the students construct a chemical library of dynamically interchanging thioesters and thiols. Then, AChE is added and allowed to select and hydrolyze…
Dynamic combinatorial libraries based on hydrogen-bonde molecular boxes
Kerckhoffs, J.M.C.A.; Mateos timoneda, Miguel; Reinhoudt, David; Crego Calama, Mercedes
2007-01-01
This article describes two different types of dynamic combinatorial libraries of host and guest molecules. The first part of this article describes the encapsulation of alizarin trimer 2 a3 by dynamic mixtures of up to twenty different self-assembled molecular receptors together with the
Anti-termite efficacy of Capparis decidua and its combinatorial ...
African Journals Online (AJOL)
Michael Horsfall
ABSTRACT: Capparis deciduas and its combinatorial mixtures were evaluated to observe the anti-termite efficacy against Indian white termite Odontotermes obesus. These have shown very high termiticidal activity and wood protection in the soil. It is proved by very low LD50 values i.e. 0.0218mg/g and 0.021mg/g obtained ...
Combinatorial algorithms enabling computational science: tales from the front
Energy Technology Data Exchange (ETDEWEB)
Bhowmick, Sanjukta [Mathematics and Computer Science Division, Argonne National Laboratory (United States); Boman, Erik G [Discrete Algorithms and Math Department, Sandia National Laboratories (United States); Devine, Karen [Discrete Algorithms and Math Department, Sandia National Laboratories (United States); Gebremedhin, Assefaw [Computer Science Department, Old Dominion University (United States); Hendrickson, Bruce [Discrete Algorithms and Math Department, Sandia National Laboratories (United States); Hovland, Paul [Mathematics and Computer Science Division, Argonne National Laboratory (United States); Munson, Todd [Mathematics and Computer Science Division, Argonne National Laboratory (United States); Pothen, Alex [Computer Science Department, Old Dominion University (United States)
2006-09-15
Combinatorial algorithms have long played a crucial enabling role in scientific and engineering computations. The importance of discrete algorithms continues to grow with the demands of new applications and advanced architectures. This paper surveys some recent developments in this rapidly changing and highly interdisciplinary field.
Some Combinatorial Interpretations and Applications of Fuss-Catalan Numbers
Lin, Chin-Hung
2011-01-01
Fuss-Catalan number is a family of generalized Catalan numbers. We begin by two definitions of Fuss-Catalan numbers and some basic properties. And we give some combinatorial interpretations different from original Catalan numbers. Finally we generalize the Jonah's theorem as its applications.
A Combinatorial Proof of a Result on Generalized Lucas Polynomials
Directory of Open Access Journals (Sweden)
Laugier Alexandre
2016-09-01
Full Text Available We give a combinatorial proof of an elementary property of generalized Lucas polynomials, inspired by [1]. These polynomials in s and t are defined by the recurrence relation 〈n〉 = s〈n-1〉+t〈n-2〉 for n ≥ 2. The initial values are 〈0〉 = 2; 〈1〉= s, respectively.
Some experience of shielding calculations by combinatorial method
International Nuclear Information System (INIS)
Korobejnikov, V.V.; Oussanov, V.I.
1996-01-01
Some aspects of the compound systems shielding calculations by a combinatorial approach are discussed. The effectiveness of such an approach is based on the fundamental characteristic of a compound system: if some element of the system have in itself mathematical or physical properties favorable for calculation, these properties may be used in a combinatorial approach and are lost when the system is being calculated in the whole by a direct approach. The combinatorial technique applied is well known. A compound system are being splitting for two or more auxiliary subsystems (so that calculation each of them is a more simple problem than calculation of the original problem (or at last is a soluble problem if original one is not). Calculation of every subsystem are carried out by suitable method and code, the coupling being made through boundary conditions or boundary source. The special consideration in the paper is given to a fast reactor shielding combinatorial analysis and to the testing of the results received. (author)
A combinatorial enumeration problem of RNA secondary structures
African Journals Online (AJOL)
use
2011-12-21
Dec 21, 2011 ... interesting combinatorial questions (Chen et al., 2005;. Liu, 2006; Schmitt and Waterman 1994; Stein and. Waterman 1978). The research on the enumeration of. RNA secondary structures becomes one of the hot topics in Computational Molecular Biology. An RNA molecule is described by its sequences of.
Directory of Open Access Journals (Sweden)
Takishita Kiyotaka
2012-02-01
Full Text Available Abstract Sterols are key components of eukaryotic cellular membranes that are synthesized by multi-enzyme pathways that require molecular oxygen. Because prokaryotes fundamentally lack sterols, it is unclear how the vast diversity of bacterivorous eukaryotes that inhabit hypoxic environments obtain, or synthesize, sterols. Here we show that tetrahymanol, a triterpenoid that does not require molecular oxygen for its biosynthesis, likely functions as a surrogate of sterol in eukaryotes inhabiting oxygen-poor environments. Genes encoding the tetrahymanol synthesizing enzyme squalene-tetrahymanol cyclase were found from several phylogenetically diverged eukaryotes that live in oxygen-poor environments and appear to have been laterally transferred among such eukaryotes. Reviewers This article was reviewed by Eric Bapteste and Eugene Koonin.
Latimer, Luke N; Dueber, John E
2017-06-01
A common challenge in metabolic engineering is rapidly identifying rate-controlling enzymes in heterologous pathways for subsequent production improvement. We demonstrate a workflow to address this challenge and apply it to improving xylose utilization in Saccharomyces cerevisiae. For eight reactions required for conversion of xylose to ethanol, we screened enzymes for functional expression in S. cerevisiae, followed by a combinatorial expression analysis to achieve pathway flux balancing and identification of limiting enzymatic activities. In the next round of strain engineering, we increased the copy number of these limiting enzymes and again tested the eight-enzyme combinatorial expression library in this new background. This workflow yielded a strain that has a ∼70% increase in biomass yield and ∼240% increase in xylose utilization. Finally, we chromosomally integrated the expression library. This library enriched for strains with multiple integrations of the pathway, which likely were the result of tandem integrations mediated by promoter homology. Biotechnol. Bioeng. 2017;114: 1301-1309. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Boehm, Markus; Wu, Tong-Ying; Claussen, Holger; Lemmen, Christian
2008-04-24
Large collections of combinatorial libraries are an integral element in today's pharmaceutical industry. It is of great interest to perform similarity searches against all virtual compounds that are synthetically accessible by any such library. Here we describe the successful application of a new software tool CoLibri on 358 combinatorial libraries based on validated reaction protocols to create a single chemistry space containing over 10 (12) possible products. Similarity searching with FTrees-FS allows the systematic exploration of this space without the need to enumerate all product structures. The search result is a set of virtual hits which are synthetically accessible by one or more of the existing reaction protocols. Grouping these virtual hits by their synthetic protocols allows the rapid design and synthesis of multiple follow-up libraries. Such library ideas support hit-to-lead design efforts for tasks like follow-up from high-throughput screening hits or scaffold hopping from one hit to another attractive series.
Potyrailo, Radislav A.; Chisholm, Bret J.; Olson, Daniel R.; Brennan, Michael J.; Molaison, Chris A.
2002-02-01
Design, validation, and implementation of an optical spectroscopic system for high-throughput analysis of combinatorially developed protective organic coatings are reported. Our approach replaces labor-intensive coating evaluation steps with an automated system that rapidly analyzes 8x6 arrays of coating elements that are deposited on a plastic substrate. Each coating element of the library is 10 mm in diameter and 2 to 5 micrometers thick. Performance of coatings is evaluated with respect to their resistance to wear abrasion because this parameter is one of the primary considerations in end-use applications. Upon testing, the organic coatings undergo changes that are impossible to quantitatively predict using existing knowledge. Coatings are abraded using industry-accepted abrasion test methods at single-or multiple-abrasion conditions, followed by high- throughput analysis of abrasion-induced light scatter. The developed automated system is optimized for the analysis of diffusively scattered light that corresponds to 0 to 30% haze. System precision of 0.1 to 2.5% relative standard deviation provides capability for the reliable ranking of coatings performance. While the system was implemented for high-throughput screening of combinatorially developed organic protective coatings for automotive applications, it can be applied to a variety of other applications where materials ranking can be achieved using optical spectroscopic tools.
IκBα mediates prostate cancer cell death induced by combinatorial targeting of the androgen receptor
International Nuclear Information System (INIS)
Carter, Sarah Louise; Centenera, Margaret Mary; Tilley, Wayne Desmond; Selth, Luke Ashton; Butler, Lisa Maree
2016-01-01
Combining different clinical agents to target multiple pathways in prostate cancer cells, including androgen receptor (AR) signaling, is potentially an effective strategy to improve outcomes for men with metastatic disease. We have previously demonstrated that sub-effective concentrations of an AR antagonist, bicalutamide, and the histone deacetylase inhibitor, vorinostat, act synergistically when combined to cause death of AR-dependent prostate cancer cells. In this study, expression profiling of human prostate cancer cells treated with bicalutamide or vorinostat, alone or in combination, was employed to determine the molecular mechanisms underlying this synergistic action. Cell viability assays and quantitative real time PCR were used to validate identified candidate genes. A substantial proportion of the genes modulated by the combination of bicalutamide and vorinostat were androgen regulated. Independent pathway analysis identified further pathways and genes, most notably NFKBIA (encoding IκBα, an inhibitor of NF-κB and p53 signaling), as targets of this combinatorial treatment. Depletion of IκBα by siRNA knockdown enhanced apoptosis of prostate cancer cells, while ectopic overexpression of IκBα markedly suppressed cell death induced by the combination of bicalutamide and vorinostat. These findings implicate IκBα as a key mediator of the apoptotic action of this combinatorial AR targeting strategy and a promising new therapeutic target for prostate cancer. The online version of this article (doi:10.1186/s12885-016-2188-2) contains supplementary material, which is available to authorized users
Directory of Open Access Journals (Sweden)
Angelika eHilbeck
2015-11-01
Full Text Available Stacked GM crops expressing up to six Cry toxins from Bacillus thuringiensis are today replacing the formerly grown single- transgene GM crop varieties. Stacking of multiple Cry toxins not only increase the environmental load of toxins but also raise the question on how possible interactions of the toxins can be assessed for risk assessment, which is mandatory for GM crops. However, no operational guidelines for a testing strategy or testing procedures exist. From the developers point of view, little data testing for combinatorial effects of Cry toxins is necessary as the range of affected organisms is focused on pest species and no evidence is claimed to exists pointing to combinatorial effects on nontarget organisms. We have examined this rationale critically using information reported in the scientific literature. To do so we address the hypothesis of narrow specificity of Cry toxins subdivided into three underlying different conceptual conditions i 'efficacy' in target pests as indicator for 'narrow specificity', ii lack of reported adverse effects of Cry toxins on nontarget organisms, and iii proposed modes of action of Cry toxins (or the lack thereof as mechanisms underlying the reported activity/efficacy/specificity of Cry toxins. Complementary to this information we evaluate reports about outcomes of combinatorial effect testing of Cry toxins in the scientific literature and relate those findings to the practice of the environmental risk assessment of Bt-corps in general and of stacked Bt-events in particular.
Jiménez-Moreno, Ester; Gómez, Ana M; Bastida, Agatha; Corzana, Francisco; Jiménez-Oses, Gonzalo; Jiménez-Barbero, Jesús; Asensio, Juan Luis
2015-03-27
Electrostatic and charge-transfer contributions to CH-π complexes can be modulated by attaching electron-withdrawing substituents to the carbon atom. While clearly stabilizing in the gas phase, the outcome of this chemical modification in water is more difficult to predict. Herein we provide a definitive and quantitative answer to this question employing a simple strategy based on dynamic combinatorial chemistry. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Pichlmaier, Markus; Winter, Rainer F; Zabel, Manfred; Zális, Stanislav
2009-04-08
Ruthenium and osmium complexes 2a,b and 3a,b featuring the N-4,6-dioxo-5,5-dibutyl- or the N-4,6-dioxo-5,5-di-(2-propenyl)-1,4,5,6-tetrahydropyrimidin-2-yl-N'(4-ethenylphenyl)-urea ligand dimerize by a self-complementary quadruply hydrogen-bonding donor/donor/acceptor/acceptor (DDAA) motif. We provide evidence that the dimeric structures are maintained in nonpolar solvents and in 0.1 M NBu(4)PF(6)/CH(2)Cl(2) supporting electrolyte solution. All complexes are reversibly oxidized in two consecutive two-electron oxidations (DeltaE(1/2) approximately = 500 mV) without any discernible potential splitting for the oxidation of the individual hydrogen-bridged redox active moieties. IR and UV/vis/NIR spectroelectrochemistry show a one-step conversion of the neutral to the dication without any discernible features of an intermediate monooxidized radical cation. Oxidation-induced IR changes of the NH and CO groups that are involved in hydrogen bonding are restricted to the styryl-bonded urea NH function. IR band assignments are aided by quantum chemical calculations. Our experimental findings clearly show that, at least in the present systems, the ureapyrimidinedione (Upy) DDAA hydrogen-bonding motif does not support electron transfer. The apparent reason is that neither of the hydrogen-bonding functionalities contributes to the occupied frontier levels. This results in nearly degenerate pairs of MOs representing the in-phase and out-of-phase combinations of the individual monomeric building blocks.
Energy Technology Data Exchange (ETDEWEB)
Rovira, A; Alonso, J; Cucurella, G; Nos, C; Tintore, M; Pedraza, S; Rio, J; Montalban, X [Hospital General i Universitari Vall d` Hebron. Barcelona (Spain)
1998-12-31
To demonstrate the changes in the magnetization transfer ratio (MTR) of different demyelinating plaques, correlating them with the baseline values in T1-weighted contrast-enhanced magnetic resonance (MR) sequences in order to relate them more closely to the underlying disease. The study was based on 33 demyelinating plaques obtained from six patients clinically diagnosed as having remitting-recurring multiple sclerosis (MS). All the patients underwent two MR studies at a 3 to 5-month interval, including contrast-enhanced T1 and T2- weighted sequences and magnetization transfer images. The latter were used to calculate the MTR for each of the demyelinating plaques included in the study. The statistical analysis of the results obtained revealed statistically significant between initial MTR values and those of subsequent T1-weighted sequences. The MTR demonstrate significant differences between plaques according to contrast-enhanced T1-weigh tes sequences, probably indicating variable degrees of edema, demyelination and tissue destruction. These differences should be taken into account to enable the use of T1-weighted sequences to quantify the lesion load in MS patients. (Author) 35 refs.
Mallik, Shahrukh; Muhlert, Nils; Samson, Rebecca S; Sethi, Varun; Wheeler-Kingshott, Claudia A M; Miller, David H; Chard, Declan T
2015-04-01
In multiple sclerosis (MS), demyelination and neuro-axonal loss occur in the brain grey matter (GM). We used magnetic resonance imaging (MRI) measures of GM magnetisation transfer ratio (MTR) and volume to assess the regional localisation of reduced MTR (reflecting demyelination) and atrophy (reflecting neuro-axonal loss) in relapsing-remitting MS (RRMS), secondary progressive MS (SPMS) and primary progressive MS (PPMS). A total of 98 people with MS (51 RRMS, 28 SPMS, 19 PPMS) and 29 controls had T1-weighted volumetric and magnetisation transfer scans. SPM8 was used to undertake voxel-based analysis (VBA) of GM tissue volumes and MTR. MS subgroups were compared with controls, adjusting for age and gender. A voxel-by-voxel basis correlation analysis between MTR and volume within each subject group was performed, using biological parametric mapping. MTR reduction was more extensive than atrophy. RRMS and SPMS patients showed proportionately more atrophy in the deep GM. SPMS and PPMS patients showed proportionately greater cortical MTR reduction. RRMS patients demonstrated the most correlation of MTR reduction and atrophy in deep GM. In SPMS and PPMS patients, there was less extensive correlation. These results suggest that in the deep GM of RRMS patients, demyelination and neuro-axonal loss may be linked, while in SPMS and PPMS patients, neuro-axonal loss and demyelination may occur mostly independently. © The Author(s), 2014.
Yaldizli, Özgür; Pardini, Matteo; Sethi, Varun; Muhlert, Nils; Liu, Zheng; Tozer, Daniel J; Samson, Rebecca S; Wheeler-Kingshott, Claudia Am; Yousry, Tarek A; Miller, David H; Chard, Declan T
2016-02-01
In multiple sclerosis (MS), diffusion tensor and magnetisation transfer imaging are both abnormal in lesional and extra-lesional cortical grey matter, but differences between clinical subtypes and associations with clinical outcomes have only been partly assessed. To compare mean diffusivity, fractional anisotropy and magnetisation transfer ratio (MTR) in cortical grey matter lesions (detected using phase-sensitive inversion recovery (PSIR) imaging) and extra-lesional cortical grey matter, and assess associations with disability in relapse-onset MS. Seventy-two people with MS (46 relapsing-remitting (RR), 26 secondary progressive (SP)) and 36 healthy controls were included in this study. MTR, mean diffusivity and fractional anisotropy were measured in lesional and extra-lesional cortical grey matter. Mean fractional anisotropy was higher and MTR lower in lesional compared with extra-lesional cortical grey matter. In extra-lesional cortical grey matter mean fractional anisotropy and MTR were lower, and mean diffusivity was higher in the MS group compared with controls. Mean MTR was lower and mean diffusivity was higher in lesional and extra-lesional cortical grey matter in SPMS when compared with RRMS. These differences were independent of disease duration. In multivariate analyses, MTR in extra-lesional more so than lesional cortical grey matter was associated with disability. Magnetic resonance abnormalities in lesional and extra-lesional cortical grey matter are greater in SPMS than RRMS. Changes in extra-lesional compared with lesional cortical grey matter are more consistently associated with disability. © The Author(s), 2015.
Directory of Open Access Journals (Sweden)
M Taki
2017-05-01
Full Text Available Introduction Controlling greenhouse microclimate not only influences the growth of plants, but also is critical in the spread of diseases inside the greenhouse. The microclimate parameters were inside air, greenhouse roof and soil temperature, relative humidity and solar radiation intensity. Predicting the microclimate conditions inside a greenhouse and enabling the use of automatic control systems are the two main objectives of greenhouse climate model. The microclimate inside a greenhouse can be predicted by conducting experiments or by using simulation. Static and dynamic models are used for this purpose as a function of the metrological conditions and the parameters of the greenhouse components. Some works were done in past to 2015 year to simulation and predict the inside variables in different greenhouse structures. Usually simulation has a lot of problems to predict the inside climate of greenhouse and the error of simulation is higher in literature. The main objective of this paper is comparison between heat transfer and regression models to evaluate them to predict inside air and roof temperature in a semi-solar greenhouse in Tabriz University. Materials and Methods In this study, a semi-solar greenhouse was designed and constructed at the North-West of Iran in Azerbaijan Province (geographical location of 38°10′ N and 46°18′ E with elevation of 1364 m above the sea level. In this research, shape and orientation of the greenhouse, selected between some greenhouses common shapes and according to receive maximum solar radiation whole the year. Also internal thermal screen and cement north wall was used to store and prevent of heat lost during the cold period of year. So we called this structure, ‘semi-solar’ greenhouse. It was covered with glass (4 mm thickness. It occupies a surface of approximately 15.36 m2 and 26.4 m3. The orientation of this greenhouse was East–West and perpendicular to the direction of the wind prevailing
The Combinatorial Multi-Mode Resource Constrained Multi-Project Scheduling Problem
Directory of Open Access Journals (Sweden)
Denis Pinha
2016-11-01
Full Text Available This paper presents the formulation and solution of the Combinatorial Multi-Mode Resource Constrained Multi-Project Scheduling Problem. The focus of the proposed method is not on finding a single optimal solution, instead on presenting multiple feasible solutions, with cost and duration information to the project manager. The motivation for developing such an approach is due in part to practical situations where the definition of optimal changes on a regular basis. The proposed approach empowers the project manager to determine what is optimal, on a given day, under the current constraints, such as, change of priorities, lack of skilled worker. The proposed method utilizes a simulation approach to determine feasible solutions, under the current constraints. Resources can be non-consumable, consumable, or doubly constrained. The paper also presents a real-life case study dealing with scheduling of ship repair activities.
Programme for test generation for combinatorial and sequential systems
International Nuclear Information System (INIS)
Tran Huy Hoan
1973-01-01
This research thesis reports the computer-assisted search for tests aimed at failure detection in combinatorial and sequential logic circuits. As he wants to deal with complex circuits with many modules such as those met in large scale integrated circuits (LSI), the author used propagation paths. He reports the development of a method which is valid for combinatorial systems and for several sequential circuits comprising elementary logic modules and JK and RS flip-flops. This method is developed on an IBM 360/91 computer in PL/1 language. The used memory space is limited and adjustable with respect to circuit dimension. Computing time is short when compared to that needed by other programmes. The solution is practical and efficient for failure test and localisation
Bioinspired computation in combinatorial optimization: algorithms and their computational complexity
DEFF Research Database (Denmark)
Neumann, Frank; Witt, Carsten
2012-01-01
Bioinspired computation methods, such as evolutionary algorithms and ant colony optimization, are being applied successfully to complex engineering and combinatorial optimization problems, and it is very important that we understand the computational complexity of these algorithms. This tutorials...... problems. Classical single objective optimization is examined first. They then investigate the computational complexity of bioinspired computation applied to multiobjective variants of the considered combinatorial optimization problems, and in particular they show how multiobjective optimization can help...... to speed up bioinspired computation for single-objective optimization problems. The tutorial is based on a book written by the authors with the same title. Further information about the book can be found at www.bioinspiredcomputation.com....
An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man
Ravasi, Timothy; Suzuki, Harukazu; Cannistraci, Carlo; Katayama, Shintaro; Bajic, Vladimir B.; Tan, Kai; Akalin, Altuna; Schmeier, Sebastian; Kanamori-Katayama, Mutsumi; Bertin, Nicolas; Carninci, Piero; Daub, Carsten O.; Forrest, Alistair R.R.; Gough, Julian; Grimmond, Sean; Han, Jung-Hoon; Hashimoto, Takehiro; Hide, Winston; Hofmann, Oliver; Kamburov, Atanas; Kaur, Mandeep; Kawaji, Hideya; Kubosaki, Atsutaka; Lassmann, Timo; van Nimwegen, Erik; MacPherson, Cameron Ross; Ogawa, Chihiro; Radovanovic, Aleksandar; Schwartz, Ariel; Teasdale, Rohan D.; Tegné r, Jesper; Lenhard, Boris; Teichmann, Sarah A.; Arakawa, Takahiro; Ninomiya, Noriko; Murakami, Kayoko; Tagami, Michihira; Fukuda, Shiro; Imamura, Kengo; Kai, Chikatoshi; Ishihara, Ryoko; Kitazume, Yayoi; Kawai, Jun; Hume, David A.; Ideker, Trey; Hayashizaki, Yoshihide
2010-01-01
Combinatorial interactions among transcription factors are critical to directing tissue-specific gene expression. To build a global atlas of these combinations, we have screened for physical interactions among the majority of human and mouse DNA-binding transcription factors (TFs). The complete networks contain 762 human and 877 mouse interactions. Analysis of the networks reveals that highly connected TFs are broadly expressed across tissues, and that roughly half of the measured interactions are conserved between mouse and human. The data highlight the importance of TF combinations for determining cell fate, and they lead to the identification of a SMAD3/FLI1 complex expressed during development of immunity. The availability of large TF combinatorial networks in both human and mouse will provide many opportunities to study gene regulation, tissue differentiation, and mammalian evolution.
CUNY Graduate Center Workshops on Combinatorial and Additive Number Theory
2017-01-01
Based on talks from the 2015 and 2016 Combinatorial and Additive Number Theory (CANT) workshops at the City University of New York, these proceedings offer 19 peer-reviewed and edited papers on current topics in number theory. Held every year since 2003, the workshop series surveys state-of-the-art open problems in combinatorial and additive number theory and related parts of mathematics. Sumsets, partitions, convex polytopes and discrete geometry, Ramsey theory, primality testing, and cryptography are among the topics featured in this volume. Each contribution is dedicated to a specific topic that reflects the latest results by experts in the field. Researchers and graduate students interested in the current progress in number theory will find this selection of articles relevant and compelling. .
Combinatorial geometry domain decomposition strategies for Monte Carlo simulations
Energy Technology Data Exchange (ETDEWEB)
Li, G.; Zhang, B.; Deng, L.; Mo, Z.; Liu, Z.; Shangguan, D.; Ma, Y.; Li, S.; Hu, Z. [Institute of Applied Physics and Computational Mathematics, Beijing, 100094 (China)
2013-07-01
Analysis and modeling of nuclear reactors can lead to memory overload for a single core processor when it comes to refined modeling. A method to solve this problem is called 'domain decomposition'. In the current work, domain decomposition algorithms for a combinatorial geometry Monte Carlo transport code are developed on the JCOGIN (J Combinatorial Geometry Monte Carlo transport INfrastructure). Tree-based decomposition and asynchronous communication of particle information between domains are described in the paper. Combination of domain decomposition and domain replication (particle parallelism) is demonstrated and compared with that of MERCURY code. A full-core reactor model is simulated to verify the domain decomposition algorithms using the Monte Carlo particle transport code JMCT (J Monte Carlo Transport Code), which has being developed on the JCOGIN infrastructure. Besides, influences of the domain decomposition algorithms to tally variances are discussed. (authors)
Combinatorial geometry domain decomposition strategies for Monte Carlo simulations
International Nuclear Information System (INIS)
Li, G.; Zhang, B.; Deng, L.; Mo, Z.; Liu, Z.; Shangguan, D.; Ma, Y.; Li, S.; Hu, Z.
2013-01-01
Analysis and modeling of nuclear reactors can lead to memory overload for a single core processor when it comes to refined modeling. A method to solve this problem is called 'domain decomposition'. In the current work, domain decomposition algorithms for a combinatorial geometry Monte Carlo transport code are developed on the JCOGIN (J Combinatorial Geometry Monte Carlo transport INfrastructure). Tree-based decomposition and asynchronous communication of particle information between domains are described in the paper. Combination of domain decomposition and domain replication (particle parallelism) is demonstrated and compared with that of MERCURY code. A full-core reactor model is simulated to verify the domain decomposition algorithms using the Monte Carlo particle transport code JMCT (J Monte Carlo Transport Code), which has being developed on the JCOGIN infrastructure. Besides, influences of the domain decomposition algorithms to tally variances are discussed. (authors)
Laguerre-type derivatives: Dobinski relations and combinatorial identities
International Nuclear Information System (INIS)
Penson, K. A.; Blasiak, P.; Horzela, A.; Duchamp, G. H. E.; Solomon, A. I.
2009-01-01
We consider properties of the operators D(r,M)=a r (a † a) M (which we call generalized Laguerre-type derivatives), with r=1,2,..., M=0,1,..., where a and a † are boson annihilation and creation operators, respectively, satisfying [a,a † ]=1. We obtain explicit formulas for the normally ordered form of arbitrary Taylor-expandable functions of D(r,M) with the help of an operator relation that generalizes the Dobinski formula. Coherent state expectation values of certain operator functions of D(r,M) turn out to be generating functions of combinatorial numbers. In many cases the corresponding combinatorial structures can be explicitly identified.
An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man
Ravasi, Timothy
2010-03-01
Combinatorial interactions among transcription factors are critical to directing tissue-specific gene expression. To build a global atlas of these combinations, we have screened for physical interactions among the majority of human and mouse DNA-binding transcription factors (TFs). The complete networks contain 762 human and 877 mouse interactions. Analysis of the networks reveals that highly connected TFs are broadly expressed across tissues, and that roughly half of the measured interactions are conserved between mouse and human. The data highlight the importance of TF combinations for determining cell fate, and they lead to the identification of a SMAD3/FLI1 complex expressed during development of immunity. The availability of large TF combinatorial networks in both human and mouse will provide many opportunities to study gene regulation, tissue differentiation, and mammalian evolution.
Combinatorial Optimization in Project Selection Using Genetic Algorithm
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.
Combinatorial nuclear level density by a Monte Carlo method
International Nuclear Information System (INIS)
Cerf, N.
1994-01-01
We present a new combinatorial method for the calculation of the nuclear level density. It is based on a Monte Carlo technique, in order to avoid a direct counting procedure which is generally impracticable for high-A nuclei. The Monte Carlo simulation, making use of the Metropolis sampling scheme, allows a computationally fast estimate of the level density for many fermion systems in large shell model spaces. We emphasize the advantages of this Monte Carlo approach, particularly concerning the prediction of the spin and parity distributions of the excited states,and compare our results with those derived from a traditional combinatorial or a statistical method. Such a Monte Carlo technique seems very promising to determine accurate level densities in a large energy range for nuclear reaction calculations
Combinatorial drug screening identifies Ewing sarcoma-specific sensitivities
Radic-Sarikas, Branka; Tsafou, Kalliopi P.; Emdal, Kristina B.; Papamarkou, Theodore; Huber, Kilian V.M.; Mutz, Cornelia; Toretsky, Jeffrey A.; Bennett, Keiryn L.; Olsen, Jesper V.; Brunak, Søren; Kovar, Heinrich; Superti-Furga, Giulio
2017-01-01
Improvements in survival for Ewing sarcoma pediatric and adolescent patients have been modest over the past 20 years. Combinations of anticancer agents endure as an option to overcome resistance to single treatments caused by compensatory pathways. Moreover, combinations are thought to lessen any associated adverse side effects through reduced dosing, which is particularly important in childhood tumors. Using a parallel phenotypic combinatorial screening approach of cells derived from three p...
Rapid mapping of protein functional epitopes by combinatorial alanine scanning
Weiss, GA; Watanabe, CK; Zhong, A; Goddard, A; Sidhu, SS
2000-01-01
A combinatorial alanine-scanning strategy was used to determine simultaneously the functional contributions of 19 side chains buried at the interface between human growth hormone and the extracellular domain of its receptor. A phage-displayed protein library was constructed in which the 19 side chains were preferentially allowed to vary only as the wild type or alanine. The library pool was subjected to binding selections to isolate functional clones, and DNA sequencing was used to determine ...
Combinatorial Models for Assembly and Decomposition of Products
A. N. Bojko
2015-01-01
The paper discusses the most popular combinatorial models that are used for the synthesis of design solutions at the stage of the assembly process flow preparation. It shows that while assembling the product the relations of parts can be represented as a structure of preferences, which is formed on the basis of objective design restrictions put in at the stage of the product design. This structure is a binary preference relation pre-order. Its symmetrical part is equivalence and describes the...
From combinatorial optimization to real algebraic geometry and back
Directory of Open Access Journals (Sweden)
Janez Povh
2014-12-01
Full Text Available In this paper, we explain the relations between combinatorial optimization and real algebraic geometry with a special focus to the quadratic assignment problem. We demonstrate how to write a quadratic optimization problem over discrete feasible set as a linear optimization problem over the cone of completely positive matrices. The latter formulation enables a hierarchy of approximations which rely on results from polynomial optimization, a sub-eld of real algebraic geometry.
Distributing the computation in combinatorial optimization experiments over the cloud
Directory of Open Access Journals (Sweden)
Mario Brcic
2017-12-01
Full Text Available Combinatorial optimization is an area of great importance since many of the real-world problems have discrete parameters which are part of the objective function to be optimized. Development of combinatorial optimization algorithms is guided by the empirical study of the candidate ideas and their performance over a wide range of settings or scenarios to infer general conclusions. Number of scenarios can be overwhelming, especially when modeling uncertainty in some of the problem’s parameters. Since the process is also iterative and many ideas and hypotheses may be tested, execution time of each experiment has an important role in the efficiency and successfulness. Structure of such experiments allows for significant execution time improvement by distributing the computation. We focus on the cloud computing as a cost-efficient solution in these circumstances. In this paper we present a system for validating and comparing stochastic combinatorial optimization algorithms. The system also deals with selection of the optimal settings for computational nodes and number of nodes in terms of performance-cost tradeoff. We present applications of the system on a new class of project scheduling problem. We show that we can optimize the selection over cloud service providers as one of the settings and, according to the model, it resulted in a substantial cost-savings while meeting the deadline.
View discovery in OLAP databases through statistical combinatorial optimization
Energy Technology Data Exchange (ETDEWEB)
Hengartner, Nick W [Los Alamos National Laboratory; Burke, John [PNNL; Critchlow, Terence [PNNL; Joslyn, Cliff [PNNL; Hogan, Emilie [PNNL
2009-01-01
OnLine Analytical Processing (OLAP) is a relational database technology providing users with rapid access to summary, aggregated views of a single large database, and is widely recognized for knowledge representation and discovery in high-dimensional relational databases. OLAP technologies provide intuitive and graphical access to the massively complex set of possible summary views available in large relational (SQL) structured data repositories. The capability of OLAP database software systems to handle data complexity comes at a high price for analysts, presenting them a combinatorially vast space of views of a relational database. We respond to the need to deploy technologies sufficient to allow users to guide themselves to areas of local structure by casting the space of 'views' of an OLAP database as a combinatorial object of all projections and subsets, and 'view discovery' as an search process over that lattice. We equip the view lattice with statistical information theoretical measures sufficient to support a combinatorial optimization process. We outline 'hop-chaining' as a particular view discovery algorithm over this object, wherein users are guided across a permutation of the dimensions by searching for successive two-dimensional views, pushing seen dimensions into an increasingly large background filter in a 'spiraling' search process. We illustrate this work in the context of data cubes recording summary statistics for radiation portal monitors at US ports.
A combinatorial perspective of the protein inference problem.
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.
View Discovery in OLAP Databases through Statistical Combinatorial Optimization
Energy Technology Data Exchange (ETDEWEB)
Joslyn, Cliff A.; Burke, Edward J.; Critchlow, Terence J.
2009-05-01
The capability of OLAP database software systems to handle data complexity comes at a high price for analysts, presenting them a combinatorially vast space of views of a relational database. We respond to the need to deploy technologies sufficient to allow users to guide themselves to areas of local structure by casting the space of ``views'' of an OLAP database as a combinatorial object of all projections and subsets, and ``view discovery'' as an search process over that lattice. We equip the view lattice with statistical information theoretical measures sufficient to support a combinatorial optimization process. We outline ``hop-chaining'' as a particular view discovery algorithm over this object, wherein users are guided across a permutation of the dimensions by searching for successive two-dimensional views, pushing seen dimensions into an increasingly large background filter in a ``spiraling'' search process. We illustrate this work in the context of data cubes recording summary statistics for radiation portal monitors at US ports.
Combinatorial constructions in ergodic theory and dynamics
Katok, Anatole
2003-01-01
Ergodic theory studies measure-preserving transformations of measure spaces. These objects are intrinsically infinite and the notion of an individual point or an orbit makes no sense. Still there is a variety of situations when a measure-preserving transformation (and its asymptotic behavior) can be well described as a limit of certain finite objects (periodic processes). In the first part of this book this idea is developed systematically, genericity of approximation in various categories is explored, and numerous applications are presented, including spectral multiplicity and properties of the maximal spectral type. The second part of the book contains a treatment of various constructions of cohomological nature with an emphasis on obtaining interesting asymptotic behavior from approximate pictures at different time scales. The book presents a view of ergodic theory not found in other expository sources and is suitable for graduate students familiar with measure theory and basic functional analysis.
International Nuclear Information System (INIS)
Martin, Brian; Colorado School of Mines, Golden, CO; Samimi, Peyman; Colorado School of Mines, Golden, CO; Collins, Peter
2017-01-01
A novel method to systematically vary temperature and thus study the resulting microstructure of a material is presented. This new method has the potential to be used in a combinatorial fashion, allowing the rapid study of thermal holds on microstructures to be conducted. This is demonstrated on a beta titanium alloy, where the thermal history has a strong effect on microstructure. It is informed by simulation and executed using the resistive heating capabilities of a Gleeble 3800 thermomechanical simulator. Spatially varying isothermal holds of 4 h were affected, where the temperature range of the multiple isothermal holds varied by ~175 °C.
Set Partitions and the Multiplication Principle
Lockwood, Elise; Caughman, John S., IV
2016-01-01
To further understand student thinking in the context of combinatorial enumeration, we examine student work on a problem involving set partitions. In this context, we note some key features of the multiplication principle that were often not attended to by students. We also share a productive way of thinking that emerged for several students who…
van Heesch, M M J; van Asselt, A D I; Evers, J L H; van der Hoeven, M A H B M; Dumoulin, J C M; van Beijsterveldt, C E M; Bonsel, G J; Dykgraaf, R H M; van Goudoever, J B; Koopman-Esseboom, C; Nelen, W L D M; Steiner, K; Tamminga, P; Tonch, N; Torrance, H L; Dirksen, C D
2016-11-01
What is the cost-effectiveness of elective single embryo transfer (eSET) versus double embryo transfer (DET) strategies from a societal perspective, when applying a time horizon of 1, 5 and 18 years? From a short-term perspective (1 year) it is cost-effective to replace DET with single embryo transfer; however when intermediate- (5 years) and long-term (18 years) costs and consequences are incorporated, DET becomes the most cost-effective strategy, given a ceiling ratio of €20 000 per quality-adjusted life years (QALY) gained. According to previous cost-effectiveness research into embryo transfer strategies, DET is considered cost-effective if society is willing to pay around €20 000 for an extra live birth. However, interpretation of those studies is complicated, as those studies fail to incorporate long-term costs and outcomes and used live birth as a measure of effectiveness instead of QALYs. With this outcome, both multiple and singletons were valued as one live birth, whereas costs of all children of a multiple were incorporated. A Markov model (cycle length: 1 year; time horizon: 1, 5 and 18 years) was developed comparing a maximum of: (i) three cycles of eSET in all patients; (ii) four cycles of eSET in all patients; (iii) five cycles of eSET in all patients; (iv) three cycles of standard treatment policy (STP), i.e. eSET in women costs were estimated for all comparators. Input parameters were derived from a retrospective cohort study, in which hospital resource data were collected (n=580) and a parental questionnaire was sent out (431 respondents). Probabilistic sensitivity analysis (5000 iterations) was performed. With a time horizon of 18 years, DETx3 is most effective (0.54 live births, 10.2 LYs and 9.8 QALYs) and expensive (€37 871) per couple starting IVF. Three cycles of eSET are least effective (0.43 live births, 7.1 LYs and 6.8 QALYs) and expensive (€25 563). We assumed that society is willing to pay €20 000 per QALY gained. With a time
Directory of Open Access Journals (Sweden)
Jonathan Göke
2011-12-01
Full Text Available Transcription factors are proteins that regulate gene expression by binding to cis-regulatory sequences such as promoters and enhancers. In embryonic stem (ES cells, binding of the transcription factors OCT4, SOX2 and NANOG is essential to maintain the capacity of the cells to differentiate into any cell type of the developing embryo. It is known that transcription factors interact to regulate gene expression. In this study we show that combinatorial binding is strongly associated with co-localization of the transcriptional co-activator Mediator, H3K27ac and increased expression of nearby genes in embryonic stem cells. We observe that the same loci bound by Oct4, Nanog and Sox2 in ES cells frequently drive expression in early embryonic development. Comparison of mouse and human ES cells shows that less than 5% of individual binding events for OCT4, SOX2 and NANOG are shared between species. In contrast, about 15% of combinatorial binding events and even between 53% and 63% of combinatorial binding events at enhancers active in early development are conserved. Our analysis suggests that the combination of OCT4, SOX2 and NANOG binding is critical for transcription in ES cells and likely plays an important role for embryogenesis by binding at conserved early developmental enhancers. Our data suggests that the fast evolutionary rewiring of regulatory networks mainly affects individual binding events, whereas "gene regulatory hotspots" which are bound by multiple factors and active in multiple tissues throughout early development are under stronger evolutionary constraints.
International Nuclear Information System (INIS)
Ito, Yuki; Jung, Changho; Luo, Yi; Koyama, Michihisa; Endou, Akira; Kubo, Momoji; Imamura, Akira; Miyamoto, Akira
2006-01-01
Recently, we have developed a new tight-binding quantum chemical molecular dynamics program 'Colors' for combinatorial computational chemistry approach. This methodology is based on our original tight-binding approximation and realized over 5000 times acceleration compared to the conventional first-principles molecular dynamics method. In the present study, we applied our new program to the simulations on various realistic large-scale models of the automotive three-way catalysts, ultrafine Pt particle/CeO 2 (111) support. Significant electron transfer from the Pt particle to the CeO 2 (111) surface was observed and it was found to strongly depend on the size of the Pt particle. Furthermore, our simulation results suggest that the reduction of the Ce atom due to the electron transfer from the Pt particle to the CeO 2 surface is a main reason for the strong interaction of the Pt particle and CeO 2 (111) support
Energy Technology Data Exchange (ETDEWEB)
Zhang, X.D. [School of Material Science and Engineering, Central South University, Changsha, Hunan, 410083 (China); Liu, L.B., E-mail: lbliu.csu@gmail.com [School of Material Science and Engineering, Central South University, Changsha, Hunan, 410083 (China); State Key Laboratory for Powder Metallurgy, Changsha, Hunan, 410083 (China); Zhao, J.-C. [State Key Laboratory for Powder Metallurgy, Changsha, Hunan, 410083 (China); Department of Materials Science and Engineering, The Ohio State University, 2041 College Road, Columbus, OH 43210 (United States); Wang, J.L.; Zheng, F.; Jin, Z.P. [School of Material Science and Engineering, Central South University, Changsha, Hunan, 410083 (China)
2014-06-01
A high-efficiency combinatorial approach has been applied to rapidly build the database of composition-dependent elastic modulus and hardness of the Ti–Ta and Ti–Zr–Ta systems. A diffusion multiple of the Ti–Zr–Ta system was manufactured, then annealed at 1173 K for 1800 h, and water quenched to room temperature. Extensive interdiffusion among Ti, Zr and Ta has taken place. Combining nanoindentation and electron probe micro-analysis (EPMA), the elastic modulus, hardness as well as composition across the diffusion multiple were determined. The composition/elastic modulus/hardness relationship of the Ti–Ta and Ti–Zr–Ta alloys has been obtained. It was found that the elastic modulus and hardness depend strongly on the Ta and Zr content. The result can be used to accelerate the discovery/development of bio-titanium alloys for different components in implant prosthesis. - Highlights: • High-efficiency diffusion multiple of Ti–Zr–Ta was manufactured. • Composition-dependent elastic modulus and hardness of the Ti–Ta and Ti–Zr–Ta systems have been obtained effectively, • The methodology and the information can be used to accelerate the discovery/development of bio-titanium alloys.
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/. © The Author(s) 2015. Published by Oxford University Press.
Combinatorial effects of arginine and fluoride on oral bacteria.
Zheng, X; Cheng, X; Wang, L; Qiu, W; Wang, S; Zhou, Y; Li, M; Li, Y; Cheng, L; Li, J; Zhou, X; Xu, X
2015-02-01
Dental caries is closely associated with the microbial disequilibrium between acidogenic/aciduric pathogens and alkali-generating commensal residents within the dental plaque. Fluoride is a widely used anticaries agent, which promotes tooth hard-tissue remineralization and suppresses bacterial activities. Recent clinical trials have shown that oral hygiene products containing both fluoride and arginine possess a greater anticaries effect compared with those containing fluoride alone, indicating synergy between fluoride and arginine in caries management. Here, we hypothesize that arginine may augment the ecological benefit of fluoride by enriching alkali-generating bacteria in the plaque biofilm and thus synergizes with fluoride in controlling dental caries. Specifically, we assessed the combinatory effects of NaF/arginine on planktonic and biofilm cultures of Streptococcus mutans, Streptococcus sanguinis, and Porphyromonas gingivalis with checkerboard microdilution assays. The optimal NaF/arginine combinations were selected, and their combinatory effects on microbial composition were further examined in single-, dual-, and 3-species biofilm using bacterial species-specific fluorescence in situ hybridization and quantitative polymerase chain reaction. We found that arginine synergized with fluoride in suppressing acidogenic S. mutans in both planktonic and biofilm cultures. In addition, the NaF/arginine combination synergistically reduced S. mutans but enriched S. sanguinis within the multispecies biofilms. More importantly, the optimal combination of NaF/arginine maintained a "streptococcal pressure" against the potential growth of oral anaerobe P. gingivalis within the alkalized biofilm. Taken together, we conclude that the combinatory application of fluoride and arginine has a potential synergistic effect in maintaining a healthy oral microbial equilibrium and thus represents a promising ecological approach to caries management. © International & American
Estimating meme fitness in adaptive memetic algorithms for combinatorial problems.
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
Combinatorial interpretations of binomial coefficient analogues related to Lucas sequences
Sagan, Bruce; Savage, Carla
2009-01-01
Let s and t be variables. Define polynomials {n} in s, t by {0}=0, {1}=1, and {n}=s{n-1}+t{n-2} for n >= 2. If s, t are integers then the corresponding sequence of integers is called a Lucas sequence. Define an analogue of the binomial coefficients by C{n,k}={n}!/({k}!{n-k}!) where {n}!={1}{2}...{n}. It is easy to see that C{n,k} is a polynomial in s and t. The purpose of this note is to give two combinatorial interpretations for this polynomial in terms of statistics on integer partitions in...
First steps in combinatorial optimization on graphons: matchings
Czech Academy of Sciences Publication Activity Database
Doležal, Martin; Hladký, J.; Hu, P.; Piguet, Diana
2017-01-01
Roč. 61, August (2017), s. 359-365 ISSN 1571-0653 R&D Projects: GA ČR GA16-07378S; GA ČR GJ16-07822Y EU Projects: European Commission(XE) 628974 - PAECIDM Institutional support: RVO:67985840 ; RVO:67985807 Keywords : graphon * graph limits * matching * combinatorial optimization Subject RIV: BA - General Mathematics ; BA - General Mathematics (UIVT-O) OBOR OECD: Pure mathematics ; Pure mathematics (UIVT-O) http://www.sciencedirect.com/science/article/pii/S1571065317301452
Combinatorial synthesis of oxazol-thiazole bis-heterocyclic compounds.
Murru, Siva; Nefzi, Adel
2014-01-13
A combinatorial library of novel oxazol-thiazole bis-heterocycles was synthesized in good to excellent overall yields with high purity using a solution and solid-phase parallel synthesis approach. Oxazole amino acids, prepared from serine methyl ester and amino acids via coupling and cyclodehydration, were treated with Fmoc-NCS and α-haloketones for the parallel synthesis of diverse bis-heterocycles. Fmoc-isothiocyanate is used as a traceless reagent for thiazole formation. Oxazole diversity can be achieved by using variety of amino acids, whereas thiazole diversity is produced with various haloketones.
Advances in bio-inspired computing for combinatorial optimization problems
Pintea, Camelia-Mihaela
2013-01-01
Advances in Bio-inspired Combinatorial Optimization Problems' illustrates several recent bio-inspired efficient algorithms for solving NP-hard problems.Theoretical bio-inspired concepts and models, in particular for agents, ants and virtual robots are described. Large-scale optimization problems, for example: the Generalized Traveling Salesman Problem and the Railway Traveling Salesman Problem, are solved and their results are discussed.Some of the main concepts and models described in this book are: inner rule to guide ant search - a recent model in ant optimization, heterogeneous sensitive a
Proceedings of the 8th Nordic Combinatorial Conference
DEFF Research Database (Denmark)
Geil, Olav; Andersen, Lars Døvling
The Nordic Combinatorial Conferences were initiated in 1981 by mathematicians from Stavanger. Held approximately every three years since then, the conferences have been able to sustain the interest from combinatorialists all over the Nordic countries. In 2004 the 8th conference is held in Aalborg......, Denmark. We are pleased that so many people have chosen to attend, and that lectures were offered from more participants than we had originally reserved time for. We asked two mathematicians to give special lectures and are happy that both accepted immediately. Andries Brouwer from the Technical...
Combinatorial interpretation of Haldane-Wu fractional exclusion statistics.
Aringazin, A K; Mazhitov, M I
2002-08-01
Assuming that the maximal allowed number of identical particles in a state is an integer parameter, q, we derive the statistical weight and analyze the associated equation that defines the statistical distribution. The derived distribution covers Fermi-Dirac and Bose-Einstein ones in the particular cases q=1 and q--> infinity (n(i)/q-->1), respectively. We show that the derived statistical weight provides a natural combinatorial interpretation of Haldane-Wu fractional exclusion statistics, and present exact solutions of the distribution equation.
What Diagrams Argue in Late Imperial Chinese Combinatorial Texts.
Bréard, Andrea
2015-01-01
Attitudes towards diagrammatic reasoning and visualization in mathematics were seldom spelled out in texts from pre-modern China, although illustrations figure prominently in mathematical literature since the eleventh century. Taking the sums of finite series and their combinatorial interpretation as a case study, this article investigates the epistemological function of illustrations from the eleventh to the nineteenth century that encode either the mathematical objects themselves or represent their related algorithms. It particularly focuses on the two illustrations given in Wang Lai's (1768-1813) Mathematical Principles of Sequential Combinations, arguing that they reflect a specific mode of nineteenth-century mathematical argumentative practice and served as a heuristic model for later authors.
Design of diversity and focused combinatorial libraries in drug discovery.
Young, S Stanley; Ge, Nanxiang
2004-05-01
Using well-characterized chemical reactions and readily available monomers, chemists are able to create sets of compounds, termed libraries, which are useful in drug discovery processes. The design of combinatorial chemical libraries can be complex and there has been much information recently published offering suggestions on how the design process can be carried out. This review focuses on literature with the goal of organizing current thinking. At this point in time, it is clear that benchmarking of current suggested methods is required as opposed to further new methods.
First steps in combinatorial optimization on graphons: matchings
Czech Academy of Sciences Publication Activity Database
Doležal, Martin; Hladký, J.; Hu, P.; Piguet, Diana
2017-01-01
Roč. 61, August (2017), s. 359-365 ISSN 1571-0653 R&D Projects: GA ČR GA16-07378S; GA ČR GJ16-07822Y EU Projects: European Commission(XE) 628974 - PAECIDM Institutional support: RVO:67985840 ; RVO:67985807 Keywords : graphon * graph limits * matching * combinatorial optimization Subject RIV: BA - General Mathematics; BA - General Mathematics (UIVT-O) OBOR OECD: Pure mathematics; Pure mathematics (UIVT-O) http://www.sciencedirect.com/science/article/pii/S1571065317301452
Orbit Clustering Based on Transfer Cost
Gustafson, Eric D.; Arrieta-Camacho, Juan J.; Petropoulos, Anastassios E.
2013-01-01
We propose using cluster analysis to perform quick screening for combinatorial global optimization problems. The key missing component currently preventing cluster analysis from use in this context is the lack of a useable metric function that defines the cost to transfer between two orbits. We study several proposed metrics and clustering algorithms, including k-means and the expectation maximization algorithm. We also show that proven heuristic methods such as the Q-law can be modified to work with cluster analysis.
Enumeration of Combinatorial Classes of Single Variable Complex Polynomial Vector Fields
DEFF Research Database (Denmark)
Dias, Kealey
A vector field in the space of degree d monic, centered single variable complex polynomial vector fields has a combinatorial structure which can be fully described by a combinatorial data set consisting of an equivalence relation and a marked subset on the integers mod 2d-2, satisfying certain...
Combinatorial enzyme technology for the conversion of agricultural fibers to functional properties
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...
Validation of an Instrument and Testing Protocol for Measuring the Combinatorial Analysis Schema.
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)
International Nuclear Information System (INIS)
Azmy, Y. Y.
2004-01-01
An approach is developed for solving the neutron diffusion equation on combinatorial geometry computational cells, that is computational cells composed by combinatorial operations involving simple-shaped component cells. The only constraint on the component cells from which the combinatorial cells are assembled is that they possess a legitimate discretization of the underlying diffusion equation. We use the Finite Difference (FD) approximation of the x, y-geometry diffusion equation in this work. Performing the same combinatorial operations involved in composing the combinatorial cell on these discrete-variable equations yields equations that employ new discrete variables defined only on the combinatorial cell's volume and faces. The only approximation involved in this process, beyond the truncation error committed in discretizing the diffusion equation over each component cell, is a consistent-order Legendre series expansion. Preliminary results for simple configurations establish the accuracy of the solution to the combinatorial geometry solution compared to straight FD as the system dimensions decrease. Furthermore numerical results validate the consistent Legendre-series expansion order by illustrating the second order accuracy of the combinatorial geometry solution, the same as standard FD. Nevertheless the magnitude of the error for the new approach is larger than FD's since it incorporates the additional truncated series approximation. (authors)
An Investigation into Post-Secondary Students' Understanding of Combinatorial Questions
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…
ON range searching in the group model and combinatorial discrepancy
DEFF Research Database (Denmark)
Larsen, Kasper Green
2014-01-01
In this paper we establish an intimate connection between dynamic range searching in the group model and combinatorial discrepancy. Our result states that, for a broad class of range searching data structures (including all known upper bounds), it must hold that $t_u t_q=\\Omega(\\mbox{disc}^2......)$, where $t_u$ is the worst case update time, $t_q$ is the worst case query time, and disc is the combinatorial discrepancy of the range searching problem in question. This relation immediately implies a whole range of exceptionally high and near-tight lower bounds for all of the basic range searching...... problems. We list a few of them in the following: (1) For $d$-dimensional halfspace range searching, we get a lower bound of $t_u t_q=\\Omega(n^{1-1/d})$. This comes within an lg lg $n$ factor of the best known upper bound. (2) For orthogonal range searching, we get a lower bound of $t_u t...
Combinatorial therapy discovery using mixed integer linear programming.
Pang, Kaifang; Wan, Ying-Wooi; Choi, William T; Donehower, Lawrence A; Sun, Jingchun; Pant, Dhruv; Liu, Zhandong
2014-05-15
Combinatorial therapies play increasingly important roles in combating complex diseases. Owing to the huge cost associated with experimental methods in identifying optimal drug combinations, computational approaches can provide a guide to limit the search space and reduce cost. However, few computational approaches have been developed for this purpose, and thus there is a great need of new algorithms for drug combination prediction. Here we proposed to formulate the optimal combinatorial therapy problem into two complementary mathematical algorithms, Balanced Target Set Cover (BTSC) and Minimum Off-Target Set Cover (MOTSC). Given a disease gene set, BTSC seeks a balanced solution that maximizes the coverage on the disease genes and minimizes the off-target hits at the same time. MOTSC seeks a full coverage on the disease gene set while minimizing the off-target set. Through simulation, both BTSC and MOTSC demonstrated a much faster running time over exhaustive search with the same accuracy. When applied to real disease gene sets, our algorithms not only identified known drug combinations, but also predicted novel drug combinations that are worth further testing. In addition, we developed a web-based tool to allow users to iteratively search for optimal drug combinations given a user-defined gene set. Our tool is freely available for noncommercial use at http://www.drug.liuzlab.org/. zhandong.liu@bcm.edu Supplementary data are available at Bioinformatics online.
Causal gene identification using combinatorial V-structure search.
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.
A combinatorial approach to diffeomorphism invariant quantum gauge theories
International Nuclear Information System (INIS)
Zapata, J.A.
1997-01-01
Quantum gauge theory in the connection representation uses functions of holonomies as configuration observables. Physical observables (gauge and diffeomorphism invariant) are represented in the Hilbert space of physical states; physical states are gauge and diffeomorphism invariant distributions on the space of functions of the holonomies of the edges of a certain family of graphs. Then a family of graphs embedded in the space manifold (satisfying certain properties) induces a representation of the algebra of physical observables. We construct a quantum model from the set of piecewise linear graphs on a piecewise linear manifold, and another manifestly combinatorial model from graphs defined on a sequence of increasingly refined simplicial complexes. Even though the two models are different at the kinematical level, they provide unitarily equivalent representations of the algebra of physical observables in separable Hilbert spaces of physical states (their s-knot basis is countable). Hence, the combinatorial framework is compatible with the usual interpretation of quantum field theory. copyright 1997 American Institute of Physics
A combinatorial approach to the design of vaccines.
Martínez, Luis; Milanič, Martin; Legarreta, Leire; Medvedev, Paul; Malaina, Iker; de la Fuente, Ildefonso M
2015-05-01
We present two new problems of combinatorial optimization and discuss their applications to the computational design of vaccines. In the shortest λ-superstring problem, given a family S1,...,S(k) of strings over a finite alphabet, a set Τ of "target" strings over that alphabet, and an integer λ, the task is to find a string of minimum length containing, for each i, at least λ target strings as substrings of S(i). In the shortest λ-cover superstring problem, given a collection X1,...,X(n) of finite sets of strings over a finite alphabet and an integer λ, the task is to find a string of minimum length containing, for each i, at least λ elements of X(i) as substrings. The two problems are polynomially equivalent, and the shortest λ-cover superstring problem is a common generalization of two well known combinatorial optimization problems, the shortest common superstring problem and the set cover problem. We present two approaches to obtain exact or approximate solutions to the shortest λ-superstring and λ-cover superstring problems: one based on integer programming, and a hill-climbing algorithm. An application is given to the computational design of vaccines and the algorithms are applied to experimental data taken from patients infected by H5N1 and HIV-1.
Device for preparing combinatorial libraries in powder metallurgy.
Yang, Shoufeng; Evans, Julian R G
2004-01-01
This paper describes a powder-metering, -mixing, and -dispensing mechanism that can be used as a method for producing large numbers of samples for metallurgical evaluation or electrical or mechanical testing from multicomponent metal and cermet powder systems. It is designed to make use of the same commercial powders that are used in powder metallurgy and, therefore, to produce samples that are faithful to the microstructure of finished products. The particle assemblies produced by the device could be consolidated by die pressing, isostatic pressing, laser sintering, or direct melting. The powder metering valve provides both on/off and flow rate control of dry powders in open capillaries using acoustic vibration. The valve is simple and involves no relative movement, avoiding seizure with fine powders. An orchestra of such valves can be arranged on a building platform to prepare multicomponent combinatorial libraries. As with many combinatorial devices, identification and evaluation of sources of mixing error as a function of sample size is mandatory. Such an analysis is presented.
Dissection of combinatorial control by the Met4 transcriptional complex.
Lee, Traci A; Jorgensen, Paul; Bognar, Andrew L; Peyraud, Caroline; Thomas, Dominique; Tyers, Mike
2010-02-01
Met4 is the transcriptional activator of the sulfur metabolic network in Saccharomyces cerevisiae. Lacking DNA-binding ability, Met4 must interact with proteins called Met4 cofactors to target promoters for transcription. Two types of DNA-binding cofactors (Cbf1 and Met31/Met32) recruit Met4 to promoters and one cofactor (Met28) stabilizes the DNA-bound Met4 complexes. To dissect this combinatorial system, we systematically deleted each category of cofactor(s) and analyzed Met4-activated transcription on a genome-wide scale. We defined a core regulon for Met4, consisting of 45 target genes. Deletion of both Met31 and Met32 eliminated activation of the core regulon, whereas loss of Met28 or Cbf1 interfered with only a subset of targets that map to distinct sectors of the sulfur metabolic network. These transcriptional dependencies roughly correlated with the presence of Cbf1 promoter motifs. Quantitative analysis of in vivo promoter binding properties indicated varying levels of cooperativity and interdependency exists between members of this combinatorial system. Cbf1 was the only cofactor to remain fully bound to target promoters under all conditions, whereas other factors exhibited different degrees of regulated binding in a promoter-specific fashion. Taken together, Met4 cofactors use a variety of mechanisms to allow differential transcription of target genes in response to various cues.
Simultaneous Disulfide and Boronic Acid Ester Exchange in Dynamic Combinatorial Libraries
Directory of Open Access Journals (Sweden)
Sanna L. Diemer
2015-09-01
Full Text Available Dynamic combinatorial chemistry has emerged as a promising tool for the discovery of complex receptors in supramolecular chemistry. At the heart of dynamic combinatorial chemistry are the reversible reactions that enable the exchange of building blocks between library members in dynamic combinatorial libraries (DCLs ensuring thermodynamic control over the system. If more than one reversible reaction operates in a single dynamic combinatorial library, the complexity of the system increases dramatically, and so does its possible applications. One can imagine two reversible reactions that operate simultaneously or two reversible reactions that operate independently. Both these scenarios have advantages and disadvantages. In this contribution, we show how disulfide exchange and boronic ester transesterification can function simultaneous in dynamic combinatorial libraries under appropriate conditions. We describe the detailed studies necessary to establish suitable reaction conditions and highlight the analytical techniques appropriate to study this type of system.
International Nuclear Information System (INIS)
Anon.
1977-01-01
Illustrated by the example of the FRG's nuclear energy exports, it is shown that the nuclear technology transfer leads to new dimensions of intergovernmental relations, which hold within themselves on account of multiple state-to-state, scientific, industrial and - last but not least - personal contacts the chance of far-reaching friendships between countries and people. If the chance is taken, this can also be seen as an important contribution towards maintaining the peace. (orig.) [de
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.
Development of Combinatorial Methods for Alloy Design and Optimization
International Nuclear Information System (INIS)
Pharr, George M.; George, Easo P.; Santella, Michael L
2005-01-01
The primary goal of this research was to develop a comprehensive methodology for designing and optimizing metallic alloys by combinatorial principles. Because conventional techniques for alloy preparation are unavoidably restrictive in the range of alloy composition that can be examined, combinatorial methods promise to significantly reduce the time, energy, and expense needed for alloy design. Combinatorial methods can be developed not only to optimize existing alloys, but to explore and develop new ones as well. The scientific approach involved fabricating an alloy specimen with a continuous distribution of binary and ternary alloy compositions across its surface--an ''alloy library''--and then using spatially resolved probing techniques to characterize its structure, composition, and relevant properties. The three specific objectives of the project were: (1) to devise means by which simple test specimens with a library of alloy compositions spanning the range interest can be produced; (2) to assess how well the properties of the combinatorial specimen reproduce those of the conventionally processed alloys; and (3) to devise screening tools which can be used to rapidly assess the important properties of the alloys. As proof of principle, the methodology was applied to the Fe-Ni-Cr ternary alloy system that constitutes many commercially important materials such as stainless steels and the H-series and C-series heat and corrosion resistant casting alloys. Three different techniques were developed for making alloy libraries: (1) vapor deposition of discrete thin films on an appropriate substrate and then alloying them together by solid-state diffusion; (2) co-deposition of the alloying elements from three separate magnetron sputtering sources onto an inert substrate; and (3) localized melting of thin films with a focused electron-beam welding system. Each of the techniques was found to have its own advantages and disadvantages. A new and very powerful technique for
van Heesch, M. M. J.; van Asselt, A. D. I.; Evers, J. L. H.; van der Hoeven, M. A. H. B. M.; Dumoulin, J. C. M.; van Beijsterveldt, C. E. M.; Bonsel, G. J.; Dykgraaf, R. H. M.; van Goudoever, J. B.; Koopman-Esseboom, C.; Nelen, W. L. D. M.; Steiner, K.; Tamminga, P.; Tonch, N.; Torrance, H. L.; Dirksen, C. D.
2016-01-01
STUDY QUESTION: What is the cost-effectiveness of elective single embryo transfer (eSET) versus double embryo transfer (DET) strategies from a societal perspective, when applying a time horizon of 1, 5 and 18 years? SUMMARY ANSWER: From a short-term perspective (1 year) it is cost-effective to
Combinatorial Drug Screening Identifies Ewing Sarcoma-specific Sensitivities
DEFF Research Database (Denmark)
Radic-Sarikas, Branka; Tsafou, Kalliopi P; Emdal, Kristina B.
2017-01-01
Improvements in survival for Ewing sarcoma pediatric and adolescent patients have been modest over the past 20 years. Combinations of anticancer agents endure as an option to overcome resistance to single treatments caused by compensatory pathways. Moreover, combinations are thought to lessen any...... associated adverse side effects through reduced dosing, which is particularly important in childhood tumors. Using a parallel phenotypic combinatorial screening approach of cells derived from three pediatric tumor types, we identified Ewing sarcoma-specific interactions of a diverse set of targeted agents...... including approved drugs. We were able to retrieve highly synergistic drug combinations specific for Ewing sarcoma and identified signaling processes important for Ewing sarcoma cell proliferation determined by EWS-FLI1 We generated a molecular target profile of PKC412, a multikinase inhibitor with strong...
Combinatorial study of zinc tin oxide thin-film transistors
McDowell, M. G.; Sanderson, R. J.; Hill, I. G.
2008-01-01
Groups of thin-film transistors using a zinc tin oxide semiconductor layer have been fabricated via a combinatorial rf sputtering technique. The ZnO :SnO2 ratio of the film varies as a function of position on the sample, from pure ZnO to SnO2, allowing for a study of zinc tin oxide transistor performance as a function of channel stoichiometry. The devices were found to have mobilities ranging from 2to12cm2/Vs, with two peaks in mobility in devices at ZnO fractions of 0.80±0.03 and 0.25±0.05, and on/off ratios as high as 107. Transistors composed predominantly of SnO2 were found to exhibit light sensitivity which affected both the on/off ratios and threshold voltages of these devices.
A Simple Combinatorial Codon Mutagenesis Method for Targeted Protein Engineering.
Belsare, Ketaki D; Andorfer, Mary C; Cardenas, Frida S; Chael, Julia R; Park, Hyun June; Lewis, Jared C
2017-03-17
Directed evolution is a powerful tool for optimizing enzymes, and mutagenesis methods that improve enzyme library quality can significantly expedite the evolution process. Here, we report a simple method for targeted combinatorial codon mutagenesis (CCM). To demonstrate the utility of this method for protein engineering, CCM libraries were constructed for cytochrome P450 BM3 , pfu prolyl oligopeptidase, and the flavin-dependent halogenase RebH; 10-26 sites were targeted for codon mutagenesis in each of these enzymes, and libraries with a tunable average of 1-7 codon mutations per gene were generated. Each of these libraries provided improved enzymes for their respective transformations, which highlights the generality, simplicity, and tunability of CCM for targeted protein engineering.
Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort.
Jeschek, Markus; Gerngross, Daniel; Panke, Sven
2016-03-31
Rational flux design in metabolic engineering approaches remains difficult since important pathway information is frequently not available. Therefore empirical methods are applied that randomly change absolute and relative pathway enzyme levels and subsequently screen for variants with improved performance. However, screening is often limited on the analytical side, generating a strong incentive to construct small but smart libraries. Here we introduce RedLibs (Reduced Libraries), an algorithm that allows for the rational design of smart combinatorial libraries for pathway optimization thereby minimizing the use of experimental resources. We demonstrate the utility of RedLibs for the design of ribosome-binding site libraries by in silico and in vivo screening with fluorescent proteins and perform a simple two-step optimization of the product selectivity in the branched multistep pathway for violacein biosynthesis, indicating a general applicability for the algorithm and the proposed heuristics. We expect that RedLibs will substantially simplify the refactoring of synthetic metabolic pathways.
Discovery of DNA repair inhibitors by combinatorial library profiling
Moeller, Benjamin J.; Sidman, Richard L.; Pasqualini, Renata; Arap, Wadih
2011-01-01
Small molecule inhibitors of DNA repair are emerging as potent and selective anti-cancer therapies, but the sheer magnitude of the protein networks involved in DNA repair processes poses obstacles to discovery of effective candidate drugs. To address this challenge, we used a subtractive combinatorial selection approach to identify a panel of peptide ligands that bind DNA repair complexes. Supporting the concept that these ligands have therapeutic potential, we show that one selected peptide specifically binds and non-competitively inactivates DNA-PKcs, a protein kinase critical in double-strand DNA break repair. In doing so, this ligand sensitizes BRCA-deficient tumor cells to genotoxic therapy. Our findings establish a platform for large-scale parallel screening for ligand-directed DNA repair inhibitors, with immediate applicability to cancer therapy. PMID:21343400
A Robust Parallel Algorithm for Combinatorial Compressed Sensing
Mendoza-Smith, Rodrigo; Tanner, Jared W.; Wechsung, Florian
2018-04-01
In previous work two of the authors have shown that a vector $x \\in \\mathbb{R}^n$ with at most $k Parallel-$\\ell_0$ decoding algorithm, where $\\mathrm{nnz}(A)$ denotes the number of nonzero entries in $A \\in \\mathbb{R}^{m \\times n}$. In this paper we present the Robust-$\\ell_0$ decoding algorithm, which robustifies Parallel-$\\ell_0$ when the sketch $Ax$ is corrupted by additive noise. This robustness is achieved by approximating the asymptotic posterior distribution of values in the sketch given its corrupted measurements. We provide analytic expressions that approximate these posteriors under the assumptions that the nonzero entries in the signal and the noise are drawn from continuous distributions. Numerical experiments presented show that Robust-$\\ell_0$ is superior to existing greedy and combinatorial compressed sensing algorithms in the presence of small to moderate signal-to-noise ratios in the setting of Gaussian signals and Gaussian additive noise.
The Complement of Binary Klein Quadric as a Combinatorial Grassmannian
Directory of Open Access Journals (Sweden)
Metod Saniga
2015-06-01
Full Text Available Given a hyperbolic quadric of PG(5, 2, there are 28 points off this quadric and 56 lines skew to it. It is shown that the (286; 563-configuration formed by these points and lines is isomorphic to the combinatorial Grassmannian of type G2(8. It is also pointed out that a set of seven points of G2(8 whose labels share a mark corresponds to a Conwell heptad of PG(5, 2. Gradual removal of Conwell heptads from the (286; 563-configuration yields a nested sequence of binomial configurations identical with part of that found to be associated with Cayley-Dickson algebras (arXiv:1405.6888.
Statistical physics of hard combinatorial optimization: Vertex cover problem
Zhao, Jin-Hua; Zhou, Hai-Jun
2014-07-01
Typical-case computation complexity is a research topic at the boundary of computer science, applied mathematics, and statistical physics. In the last twenty years, the replica-symmetry-breaking mean field theory of spin glasses and the associated message-passing algorithms have greatly deepened our understanding of typical-case computation complexity. In this paper, we use the vertex cover problem, a basic nondeterministic-polynomial (NP)-complete combinatorial optimization problem of wide application, as an example to introduce the statistical physical methods and algorithms. We do not go into the technical details but emphasize mainly the intuitive physical meanings of the message-passing equations. A nonfamiliar reader shall be able to understand to a large extent the physics behind the mean field approaches and to adjust the mean field methods in solving other optimization problems.
Fabrication and characterization of thin-film phosphor combinatorial libraries
Mordkovich, V. Z.; Jin, Zhengwu; Yamada, Y.; Fukumura, T.; Kawasaki, M.; Koinuma, H.
2002-05-01
The laser molecular beam epitaxy method was employed to fabricate thin-film combinatorial libraries of ZnO-based phosphors on different substrates. Fabrication of both pixel libraries, on the example of Fe-doped ZnO, and spread libraries, on the example of Eu-doped ZnO, has been demonstrated. Screening of the Fe-doped ZnO libraries led to the discovery of weak green cathodoluminescence with the maximum efficiency at the Fe content of 0.58 mol %. Screening of the Eu-doped ZnO libraries led to the discovery of unusual reddish-violet cathodoluminescence which is observed in a broad range of Eu concentration. No photoluminescence was registered in either system.
Combinatorial and geometric aspects of Feynman graphs and Feynman integrals
Energy Technology Data Exchange (ETDEWEB)
Bergbauer, Christoph
2009-06-11
The integrals associated to Feynman graphs must have been a source of frustration for particle physicists ever since. Indeed there is a delicate difference between being able to draw a Feynman graph and being able to compute the associated Feynman integral. Although perturbation theory has brought enormous breakthroughs, many physicists turned to more abstract developments in quantum field theory, looked for other ways to produce perturbational results, or left the field entirely. Nonetheless there is a significant number of physicists, computational and theoretical, who pursue the quest for concepts and algorithms to compute and understand those integrals to higher and higher orders. Their motivation is to help test the validity of the underlying physical theory. For a mathematician, Feynman graphs and their integrals provide a rich subject in their own right, independent of their computability. It was only recently though that the work of Bloch, Esnault and Kreimer has brought a growing interest of mathematicians from various disciplines to the subject. In fact it opened up a completely new direction of research: a motivic interpretation of Feynman graphs that unites their combinatorial, geometric and arithmetic aspects. This idea had been in the air for a while, based on computational results of Broadhurst and Kreimer, and on a theorem of Belkale and Brosnan related to a conjecture of Kontsevich about the generality of the underlying motives. A prerequisite for the motivic approach is a profound understanding of renormalization that was established less recently in a modern language by Connes and Kreimer. This dissertation studies the renormalization of Feynman graphs in position space using an adapted resolution of singularities, and makes two other contributions of mostly combinatorial nature to the subject. I hope this may serve as a reference for somebody who feels comfortable with the traditional position space literature and looks for a transition to the
Combinatorial and geometric aspects of Feynman graphs and Feynman integrals
International Nuclear Information System (INIS)
Bergbauer, Christoph
2009-01-01
The integrals associated to Feynman graphs must have been a source of frustration for particle physicists ever since. Indeed there is a delicate difference between being able to draw a Feynman graph and being able to compute the associated Feynman integral. Although perturbation theory has brought enormous breakthroughs, many physicists turned to more abstract developments in quantum field theory, looked for other ways to produce perturbational results, or left the field entirely. Nonetheless there is a significant number of physicists, computational and theoretical, who pursue the quest for concepts and algorithms to compute and understand those integrals to higher and higher orders. Their motivation is to help test the validity of the underlying physical theory. For a mathematician, Feynman graphs and their integrals provide a rich subject in their own right, independent of their computability. It was only recently though that the work of Bloch, Esnault and Kreimer has brought a growing interest of mathematicians from various disciplines to the subject. In fact it opened up a completely new direction of research: a motivic interpretation of Feynman graphs that unites their combinatorial, geometric and arithmetic aspects. This idea had been in the air for a while, based on computational results of Broadhurst and Kreimer, and on a theorem of Belkale and Brosnan related to a conjecture of Kontsevich about the generality of the underlying motives. A prerequisite for the motivic approach is a profound understanding of renormalization that was established less recently in a modern language by Connes and Kreimer. This dissertation studies the renormalization of Feynman graphs in position space using an adapted resolution of singularities, and makes two other contributions of mostly combinatorial nature to the subject. I hope this may serve as a reference for somebody who feels comfortable with the traditional position space literature and looks for a transition to the
Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space
Lonardi, Stefano; Duma, Denisa; Alpert, Matthew; Cordero, Francesca; Beccuti, Marco; Bhat, Prasanna R.; Wu, Yonghui; Ciardo, Gianfranco; Alsaihati, Burair; Ma, Yaqin; Wanamaker, Steve; Resnik, Josh; Bozdag, Serdar; Luo, Ming-Cheng; Close, Timothy J.
2013-01-01
For the vast majority of species – including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution) so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding. PMID:23592960
Combinatorial pooling enables selective sequencing of the barley gene space.
Directory of Open Access Journals (Sweden)
Stefano Lonardi
2013-04-01
Full Text Available For the vast majority of species - including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding.
Combinatorial pooling enables selective sequencing of the barley gene space.
Lonardi, Stefano; Duma, Denisa; Alpert, Matthew; Cordero, Francesca; Beccuti, Marco; Bhat, Prasanna R; Wu, Yonghui; Ciardo, Gianfranco; Alsaihati, Burair; Ma, Yaqin; Wanamaker, Steve; Resnik, Josh; Bozdag, Serdar; Luo, Ming-Cheng; Close, Timothy J
2013-04-01
For the vast majority of species - including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution) so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding.
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.
Energy Technology Data Exchange (ETDEWEB)
Fang, Chin [SLAC National Accelerator Lab., Menlo Park, CA (United States)
2015-02-07
This Technical Note describes how the Zettar team came up with a data transfer cluster design that convincingly proved the feasibility of using high-density servers for high-performance Big Data transfers. It then outlines the tests, operations, and observations that address a potential over-heating concern regarding the use of Non-Volatile Memory Host Controller Interface Specification (NVMHCI aka NVM Express or NVMe) Gen 3 PCIe SSD cards in high-density servers. Finally, it points out the possibility of developing a new generation of high-performance Science DMZ data transfer system for the data-intensive research community and commercial enterprises.
DEFF Research Database (Denmark)
Tong, Glenn; Nielsen, John
1996-01-01
The actinomycin antibiotics bind to nucleic acids via both intercalation and hydrogen bonding. We found this 'double-action attack' mechanism very attractive in our search for a novel class of nucleic acid binders. A highly convergent, solid-phase synthetic strategy has been developed for a class...... with the requirements for combinatorial synthesis and furthermore, the final segment condensation allows, for the first time, double-combinatorial chemistry to be performed where two combinatorial libraries can be reacted with each other. Copyright (C) 1996 Elsevier Science Ltd....
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
Reddy, S G; Cochran, B J; Worth, L L; Knutson, V P; Haddox, M K
1994-04-01
A high-resolution isoelectric focusing vertical slab gel method which can resolve proteins which differ by a single charge was developed and this method was applied to the study of the multiple isoelectric forms of ornithine decarboxylase. Separation of proteins at this high level of resolution was achieved by increasing the ampholyte concentration in the gels to 6%. Various lots of ampholytes, from the same or different commercial sources, differed significantly in their protein binding capacity. Ampholytes bound to proteins interfered both with the electrophoretic transfer of proteins from the gel to immunoblotting membranes and with the ability of antibodies to interact with proteins on the immunoblotting membranes. Increasing the amount of protein loaded into a gel lane also decreased the efficiency of the electrophoretic transfer and immunodetection. To overcome these problems, both gel washing and gel electrophoretic transfer protocols for disrupting the ampholyte-protein binding and enabling a quantitative electrophoretic transfer of proteins were developed. Two gel washing procedures, with either thiocyanate or borate buffers, and a two-step electrophoretic transfer method are described. The choice of which method to use to optimally disrupt the ampholyte-protein binding was found to vary with each lot of ampholytes employed.
Brödel, Andreas K; Jaramillo, Alfonso; Isalan, Mark
2017-09-01
Directed evolution is a powerful tool to improve the characteristics of biomolecules. Here we present a protocol for the intracellular evolution of proteins with distinct differences and advantages in comparison with established techniques. These include the ability to select for a particular function from a library of protein variants inside cells, minimizing undesired coevolution and propagation of nonfunctional library members, as well as allowing positive and negative selection logics using basally active promoters. A typical evolution experiment comprises the following stages: (i) preparation of a combinatorial M13 phagemid (PM) library expressing variants of the gene of interest (GOI) and preparation of the Escherichia coli host cells; (ii) multiple rounds of an intracellular selection process toward a desired activity; and (iii) the characterization of the evolved target proteins. The system has been developed for the selection of new orthogonal transcription factors (TFs) but is capable of evolving any gene-or gene circuit function-that can be linked to conditional M13 phage replication. Here we demonstrate our approach using as an example the directed evolution of the bacteriophage λ cI TF against two synthetic bidirectional promoters. The evolved TF variants enable simultaneous activation and repression against their engineered promoters and do not cross-react with the wild-type promoter, thus ensuring orthogonality. This protocol requires no special equipment, allowing synthetic biologists and general users to evolve improved biomolecules within ∼7 weeks.
Combinatorial Algorithms for Portfolio Optimization Problems - Case of Risk Moderate Investor
Juarna, A.
2017-03-01
Portfolio optimization problem is a problem of finding optimal combination of n stocks from N ≥ n available stocks that gives maximal aggregate return and minimal aggregate risk. In this paper given N = 43 from the IDX (Indonesia Stock Exchange) group of the 45 most-traded stocks, known as the LQ45, with p = 24 data of monthly returns for each stock, spanned over interval 2013-2014. This problem actually is a combinatorial one where its algorithm is constructed based on two considerations: risk moderate type of investor and maximum allowed correlation coefficient between every two eligible stocks. The main outputs resulted from implementation of the algorithms is a multiple curve of three portfolio’s attributes, e.g. the size, the ratio of return to risk, and the percentage of negative correlation coefficient for every two chosen stocks, as function of maximum allowed correlation coefficient between each two stocks. The output curve shows that the portfolio contains three stocks with ratio of return to risk at 14.57 if the maximum allowed correlation coefficient between every two eligible stocks is negative and contains 19 stocks with maximum allowed correlation coefficient 0.17 to get maximum ratio of return to risk at 25.48.
Extensions of Dynamic Programming: Decision Trees, Combinatorial Optimization, and Data Mining
Hussain, Shahid
2016-01-01
This thesis is devoted to the development of extensions of dynamic programming to the study of decision trees. The considered extensions allow us to make multi-stage optimization of decision trees relative to a sequence of cost functions, to count the number of optimal trees, and to study relationships: cost vs cost and cost vs uncertainty for decision trees by construction of the set of Pareto-optimal points for the corresponding bi-criteria optimization problem. The applications include study of totally optimal (simultaneously optimal relative to a number of cost functions) decision trees for Boolean functions, improvement of bounds on complexity of decision trees for diagnosis of circuits, study of time and memory trade-off for corner point detection, study of decision rules derived from decision trees, creation of new procedure (multi-pruning) for construction of classifiers, and comparison of heuristics for decision tree construction. Part of these extensions (multi-stage optimization) was generalized to well-known combinatorial optimization problems: matrix chain multiplication, binary search trees, global sequence alignment, and optimal paths in directed graphs.
Combinatorial development of antibacterial Zr-Cu-Al-Ag thin film metallic glasses.
Liu, Yanhui; Padmanabhan, Jagannath; Cheung, Bettina; Liu, Jingbei; Chen, Zheng; Scanley, B Ellen; Wesolowski, Donna; Pressley, Mariyah; Broadbridge, Christine C; Altman, Sidney; Schwarz, Udo D; Kyriakides, Themis R; Schroers, Jan
2016-05-27
Metallic alloys are normally composed of multiple constituent elements in order to achieve integration of a plurality of properties required in technological applications. However, conventional alloy development paradigm, by sequential trial-and-error approach, requires completely unrelated strategies to optimize compositions out of a vast phase space, making alloy development time consuming and labor intensive. Here, we challenge the conventional paradigm by proposing a combinatorial strategy that enables parallel screening of a multitude of alloys. Utilizing a typical metallic glass forming alloy system Zr-Cu-Al-Ag as an example, we demonstrate how glass formation and antibacterial activity, two unrelated properties, can be simultaneously characterized and the optimal composition can be efficiently identified. We found that in the Zr-Cu-Al-Ag alloy system fully glassy phase can be obtained in a wide compositional range by co-sputtering, and antibacterial activity is strongly dependent on alloy compositions. Our results indicate that antibacterial activity is sensitive to Cu and Ag while essentially remains unchanged within a wide range of Zr and Al. The proposed strategy not only facilitates development of high-performing alloys, but also provides a tool to unveil the composition dependence of properties in a highly parallel fashion, which helps the development of new materials by design.
Yosipof, Abraham; Nahum, Oren E; Anderson, Assaf Y; Barad, Hannah-Noa; Zaban, Arie; Senderowitz, Hanoch
2015-06-01
Growth in energy demands, coupled with the need for clean energy, are likely to make solar cells an important part of future energy resources. In particular, cells entirely made of metal oxides (MOs) have the potential to provide clean and affordable energy if their power conversion efficiencies are improved. Such improvements require the development of new MOs which could benefit from combining combinatorial material sciences for producing solar cells libraries with data mining tools to direct synthesis efforts. In this work we developed a data mining workflow and applied it to the analysis of two recently reported solar cell libraries based on Titanium and Copper oxides. Our results demonstrate that QSAR models with good prediction statistics for multiple solar cells properties could be developed and that these models highlight important factors affecting these properties in accord with experimental findings. The resulting models are therefore suitable for designing better solar cells. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Extensions of Dynamic Programming: Decision Trees, Combinatorial Optimization, and Data Mining
Hussain, Shahid
2016-07-10
This thesis is devoted to the development of extensions of dynamic programming to the study of decision trees. The considered extensions allow us to make multi-stage optimization of decision trees relative to a sequence of cost functions, to count the number of optimal trees, and to study relationships: cost vs cost and cost vs uncertainty for decision trees by construction of the set of Pareto-optimal points for the corresponding bi-criteria optimization problem. The applications include study of totally optimal (simultaneously optimal relative to a number of cost functions) decision trees for Boolean functions, improvement of bounds on complexity of decision trees for diagnosis of circuits, study of time and memory trade-off for corner point detection, study of decision rules derived from decision trees, creation of new procedure (multi-pruning) for construction of classifiers, and comparison of heuristics for decision tree construction. Part of these extensions (multi-stage optimization) was generalized to well-known combinatorial optimization problems: matrix chain multiplication, binary search trees, global sequence alignment, and optimal paths in directed graphs.
KENO-IV/CG, the combinatorial geometry version of the KENO Monte Carlo criticality safety program
International Nuclear Information System (INIS)
West, J.T.; Petrie, L.M.; Fraley, S.K.
1979-09-01
KENO-IV/CG was developed to merge the simple geometry input description utilized by combinatorial geometry with the repeating lattice feature of the original KENO geometry package. The result is a criticality code with the ability to model a complex system of repeating rectangular lattices inside a complicated three-dimensional geometry system. Furthermore, combinatorial geometry was modified to differentiate between combinatorial zones describing a particular KENO BOX to be repeated in a KENO array and those combinatorial zones describing geometry external to an array. This allows the user to maintain a simple coordinate system without any geometric conflict due to spatial overlap. Several difficult criticality design problems have been solved with the new geometry package in KENO-IV/CG, thus illustrating the power of the code to model difficult geometries with a minimum of effort
Combinatorial thin film materials science: From alloy discovery and optimization to alloy design
Energy Technology Data Exchange (ETDEWEB)
Gebhardt, Thomas, E-mail: gebhardt@mch.rwth-aachen.de; Music, Denis; Takahashi, Tetsuya; Schneider, Jochen M.
2012-06-30
This paper provides an overview of modern alloy development, from discovery and optimization towards alloy design, based on combinatorial thin film materials science. The combinatorial approach, combining combinatorial materials synthesis of thin film composition-spreads with high-throughput property characterization has proven to be a powerful tool to delineate composition-structure-property relationships, and hence to efficiently identify composition windows with enhanced properties. Furthermore, and most importantly for alloy design, theoretical models and hypotheses can be critically appraised. Examples for alloy discovery, optimization, and alloy design of functional as well as structural materials are presented. Using Fe-Mn based alloys as an example, we show that the combination of modern electronic-structure calculations with the highly efficient combinatorial thin film composition-spread method constitutes an effective tool for knowledge-based alloy design.
Capability of focused Ar ion beam sputtering for combinatorial synthesis of metal films
International Nuclear Information System (INIS)
Nagata, T.; Haemori, M.; Chikyow, T.
2009-01-01
The authors examined the use of focused Ar ion beam sputtering (FAIS) for combinatorial synthesis. A Langmuir probe revealed that the electron temperature and density for FAIS of metal film deposition was lower than that of other major combinatorial thin film growth techniques such as pulsed laser deposition. Combining FAIS with the combinatorial method allowed the compositional fraction of the Pt-Ru binary alloy to be systematically controlled. Pt-Ru alloy metal film grew epitaxially on ZnO substrates, and crystal structures changed from the Pt phase (cubic structure) to the Ru phase (hexagonal structure) in the Pt-Ru alloy phase diagram. The alloy film has a smooth surface, with the Ru phase, in particular, showing a clear step-and-terrace structure. The combination of FAIS and the combinatorial method has major potential for the fabrication of high quality composition-spread metal film.
Capability of focused Ar ion beam sputtering for combinatorial synthesis of metal films
Energy Technology Data Exchange (ETDEWEB)
Nagata, T.; Haemori, M.; Chikyow, T. [Advanced Electric Materials Center, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044 (Japan)
2009-05-15
The authors examined the use of focused Ar ion beam sputtering (FAIS) for combinatorial synthesis. A Langmuir probe revealed that the electron temperature and density for FAIS of metal film deposition was lower than that of other major combinatorial thin film growth techniques such as pulsed laser deposition. Combining FAIS with the combinatorial method allowed the compositional fraction of the Pt-Ru binary alloy to be systematically controlled. Pt-Ru alloy metal film grew epitaxially on ZnO substrates, and crystal structures changed from the Pt phase (cubic structure) to the Ru phase (hexagonal structure) in the Pt-Ru alloy phase diagram. The alloy film has a smooth surface, with the Ru phase, in particular, showing a clear step-and-terrace structure. The combination of FAIS and the combinatorial method has major potential for the fabrication of high quality composition-spread metal film.
Combinatorial computational chemistry approach to the design of metal catalysts for deNOx
International Nuclear Information System (INIS)
Endou, Akira; Jung, Changho; Kusagaya, Tomonori; Kubo, Momoji; Selvam, Parasuraman; Miyamoto, Akira
2004-01-01
Combinatorial chemistry is an efficient technique for the synthesis and screening of a large number of compounds. Recently, we introduced the combinatorial approach to computational chemistry for catalyst design and proposed a new method called ''combinatorial computational chemistry''. In the present study, we have applied this combinatorial computational chemistry approach to the design of precious metal catalysts for deNO x . As the first step of the screening of the metal catalysts, we studied Rh, Pd, Ag, Ir, Pt, and Au clusters regarding the adsorption properties towards NO molecule. It was demonstrated that the energetically most stable adsorption state of NO on Ir model cluster, which was irrespective of both the shape and number of atoms including the model clusters
Solidified self-nanoemulsifying formulation for oral delivery of combinatorial therapeutic regimen
DEFF Research Database (Denmark)
Jain, Amit K; Thanki, Kaushik; Jain, Sanyog
2014-01-01
PURPOSE: The present work reports rationalized development and characterization of solidified self-nanoemulsifying drug delivery system for oral delivery of combinatorial (tamoxifen and quercetin) therapeutic regimen. METHODS: Suitable oil for the preparation of liquid SNEDDS was selected based...
Directory of Open Access Journals (Sweden)
Jean-Louis Dornstetter
2002-12-01
Full Text Available This paper is devoted to the presentation of a combinatorial approach, based on the theory of symmetric functions, for analyzing the performance of a family of demodulation methods used in mobile telecommunications.
INdAM conference "CoMeTA 2013 - Combinatorial Methods in Topology and Algebra"
Delucchi, Emanuele; Moci, Luca
2015-01-01
Combinatorics plays a prominent role in contemporary mathematics, due to the vibrant development it has experienced in the last two decades and its many interactions with other subjects. This book arises from the INdAM conference "CoMeTA 2013 - Combinatorial Methods in Topology and Algebra,'' which was held in Cortona in September 2013. The event brought together emerging and leading researchers at the crossroads of Combinatorics, Topology and Algebra, with a particular focus on new trends in subjects such as: hyperplane arrangements; discrete geometry and combinatorial topology; polytope theory and triangulations of manifolds; combinatorial algebraic geometry and commutative algebra; algebraic combinatorics; and combinatorial representation theory. The book is divided into two parts. The first expands on the topics discussed at the conference by providing additional background and explanations, while the second presents original contributions on new trends in the topics addressed by the conference.
Jean-Louis Dornstetter; Daniel Krob; Jean-Yves Thibon; Ekaterina A. Vassilieva
2002-01-01
This paper is devoted to the presentation of a combinatorial approach, based on the theory of symmetric functions, for analyzing the performance of a family of demodulation methods used in mobile telecommunications.
Combinatorial thin film materials science: From alloy discovery and optimization to alloy design
International Nuclear Information System (INIS)
Gebhardt, Thomas; Music, Denis; Takahashi, Tetsuya; Schneider, Jochen M.
2012-01-01
This paper provides an overview of modern alloy development, from discovery and optimization towards alloy design, based on combinatorial thin film materials science. The combinatorial approach, combining combinatorial materials synthesis of thin film composition-spreads with high-throughput property characterization has proven to be a powerful tool to delineate composition–structure–property relationships, and hence to efficiently identify composition windows with enhanced properties. Furthermore, and most importantly for alloy design, theoretical models and hypotheses can be critically appraised. Examples for alloy discovery, optimization, and alloy design of functional as well as structural materials are presented. Using Fe-Mn based alloys as an example, we show that the combination of modern electronic-structure calculations with the highly efficient combinatorial thin film composition-spread method constitutes an effective tool for knowledge-based alloy design.
Correction of measured multiplicity distributions by the simulated annealing method
International Nuclear Information System (INIS)
Hafidouni, M.
1993-01-01
Simulated annealing is a method used to solve combinatorial optimization problems. It is used here for the correction of the observed multiplicity distribution from S-Pb collisions at 200 GeV/c per nucleon. (author) 11 refs., 2 figs
Hartmann, Alexander K
2005-01-01
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
Mongelli, Pietro
2011-01-01
The Jacobi-Stirling numbers and the Legendre-Stirling numbers of the first and second kind were first introduced in [6], [7]. In this paper we note that Jacobi-Stirling numbers and Legendre-Stirling numbers are specializations of elementary and complete symmetric functions. We then study combinatorial interpretations of this specialization and obtain new combinatorial interpretations of the Jacobi-Stirling and Legendre-Stirling numbers.
Shi, Jian-Wen; Ma, Dandan; Zou, Yajun; Fan, Zhaoyang; Shi, Jinwen; Cheng, Linhao; Ji, Xin; Niu, Chunming
2018-03-01
The design of efficient and stable photocatalyst plays a critical role in the photocatalytic hydrogen evolution from water splitting. Herein, we develop a novel ZnS/CdS/ZnO ternary heterostructure by the in-situ sulfuration of CdS/ZnO, which includes four contact interfaces: CdS-ZnS interface, ZnS-ZnO interface, CdS-ZnO interface and ZnS-CdS-ZnO ternary interface, forming three charge carrier-transfer modes (type-I, type-II and direct Z-scheme) through five carrier-transfer pathways. As a result, the separation and transfer of photoexcited electron-hole pairs are promoted significantly, resulting in a high hydrogen evolution rate of 44.70 mmol h-1 g-1, which is 2, 3.7 and 8 times higher than those of binary heterostructures, CdS/ZnO, CdS/ZnS and ZnS/ZnO, respectively, and 26.5, 280 and 298 times higher than those of single CdS, ZnO and ZnS, respectively. As a counterpart ternary heterostructure, CdS/ZnS/ZnO contains only two interfaces: CdS-ZnS interface and ZnS-ZnO interface, which form two charge carrier-transfer modes (type-I and type-II) through two carrier-transfer pathways, leading to its much lower hydrogen evolution rate (27.25 mmol h-1 g-1) than ZnS/CdS/ZnO ternary heterostructure. This work is relevant for understanding the charge-transfer pathways between multi-interfaces in multicomponent heterojunctions.
Combinatorial and off-shell effects in new physics cascades
Energy Technology Data Exchange (ETDEWEB)
Wiesler, Daniel
2012-12-15
Up to now, the Standard Model of elementary particle physics is in very good agreement with most data. However, it has various shortcomings which motivate the presence of new physics at the TeV scale. The first major step following a potential discovery of new particles at the Large Hadron Collider (LHC) is the determination of their intrinsic properties, foremost masses and spins. Event topologies of new physics signals with a conserved parity motivated by precision data and the dark matter paradigm require for sophisticated measurement procedures, which have been developed in recent years. These techniques often rely on simplifying assumptions, albeit they need not necessarily be fulfilled. In this thesis we investigate the impact of combinatorial and off-shell effects on new physics cascades in three different contexts. A detailed understanding of these effects is essential for the topic of model parameter determination of new physics signatures at the LHC. First, we study the non-resonant contributions of a broad gluino on mass and spin measurements as a prime example for the importance of off-shell effects. A phenomenological scan over the gluino's width-to-mass ratio yields a severe smearing of invariant mass distributions and as a consequence thereof drastically shifted endpoint positions. Spin determinations, on the other hand, are barely affected and a model discrimination of the two prime candidates SUSY and UED is not at risk. In the second part, we assess the feasibility of the gluino dijet endpoint measurement in three fully inclusive scenarios at the LHC to investigate the impact of combinatorial and SUSY backgrounds on its precise determination. We develop a method to disentangle two major signal contributions and extract their associated edges with good accuracy. For this we use existent kinematic variables and propose new ones to overcome the former's deficiencies. The last part governs the issue of so-called 'fake combinatorics
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.
DEFF Research Database (Denmark)
Zhang, Xuping; Sørensen, Rasmus; RahbekIversen, Mathias
2018-01-01
, and then is linearized based on the acceleration-based state vector. The transfer matrices for each type of components/elements are developed, and used to establish the system equations of a flexible robot manipulator by concatenating the state vector from the base to the end-effector. With this strategy, the size...... manipulators, and only involves calculating and transferring component/element dynamic equations that have small size. The numerical simulations and experimental testing of flexible-link manipulators are conducted to validate the proposed methodologies....
Multichannel transfer function with dimensionality reduction
Kim, Han Suk; Schulze, Jü rgen P.; Cone, Angela C.; Sosinsky, Gina E.; Martone, Maryann E.
2010-01-01
. Our new method provides a framework to combine multiple approaches and pushes the boundary of gradient-based transfer functions to multiple channels, while still keeping the dimensionality of transfer functions to a manageable level, i.e., a maximum
TRANSFERENCE BEFORE TRANSFERENCE.
Bonaminio, Vincenzo
2017-10-01
This paper is predominantly a clinical presentation that describes the transmigration of one patient's transference to another, with the analyst functioning as a sort of transponder. It involves an apparently accidental episode in which there was an unconscious intersection between two patients. The author's aim is to show how transference from one case may affect transference in another, a phenomenon the author calls transference before transference. The author believes that this idea may serve as a tool for understanding the unconscious work that takes place in the clinical situation. In a clinical example, the analyst finds himself caught up in an enactment involving two patients in which he becomes the medium of what happens in session. © 2017 The Psychoanalytic Quarterly, Inc.
Photoelectrochemical Hydrogen Production Using New Combinatorial Chemistry Derived Materials
Energy Technology Data Exchange (ETDEWEB)
Jaramillo, Thomas F.; Baeck, Sung-Hyeon; Kleiman-Shwarsctein, Alan; Stucky, Galen D. (PI); McFarland, Eric W. (PI)
2004-10-25
Solar photoelectrochemical water-splitting has long been viewed as one of the “holy grails” of chemistry because of its potential impact as a clean, renewable method of fuel production. Several known photocatalytic semiconductors can be used; however, the fundamental mechanisms of the process remain poorly understood and no known material has the required properties for cost effective hydrogen production. In order to investigate morphological and compositional variations in metal oxides as they relate to opto-electrochemical properties, we have employed a combinatorial methodology using automated, high-throughput, electrochemical synthesis and screening together with conventional solid-state methods. This report discusses a number of novel, high-throughput instruments developed during this project for the expeditious discovery of improved materials for photoelectrochemical hydrogen production. Also described within this report are results from a variety of materials (primarily tungsten oxide, zinc oxide, molybdenum oxide, copper oxide and titanium dioxide) whose properties were modified and improved by either layering, inter-mixing, or doping with one or more transition metals. Furthermore, the morphologies of certain materials were also modified through the use of structure directing agents (SDA) during synthesis to create mesostructures (features 2-50 nm) that increased surface area and improved rates of hydrogen production.
Geometric differential evolution for combinatorial and programs spaces.
Moraglio, A; Togelius, J; Silva, S
2013-01-01
Geometric differential evolution (GDE) is a recently introduced formal generalization of traditional differential evolution (DE) that can be used to derive specific differential evolution algorithms for both continuous and combinatorial spaces retaining the same geometric interpretation of the dynamics of the DE search across representations. In this article, we first review the theory behind the GDE algorithm, then, we use this framework to formally derive specific GDE for search spaces associated with binary strings, permutations, vectors of permutations and genetic programs. The resulting algorithms are representation-specific differential evolution algorithms searching the target spaces by acting directly on their underlying representations. We present experimental results for each of the new algorithms on a number of well-known problems comprising NK-landscapes, TSP, and Sudoku, for binary strings, permutations, and vectors of permutations. We also present results for the regression, artificial ant, parity, and multiplexer problems within the genetic programming domain. Experiments show that overall the new DE algorithms are competitive with well-tuned standard search algorithms.
Combinatorial Drug Screening Identifies Ewing Sarcoma-specific Sensitivities.
Radic-Sarikas, Branka; Tsafou, Kalliopi P; Emdal, Kristina B; Papamarkou, Theodore; Huber, Kilian V M; Mutz, Cornelia; Toretsky, Jeffrey A; Bennett, Keiryn L; Olsen, Jesper V; Brunak, Søren; Kovar, Heinrich; Superti-Furga, Giulio
2017-01-01
Improvements in survival for Ewing sarcoma pediatric and adolescent patients have been modest over the past 20 years. Combinations of anticancer agents endure as an option to overcome resistance to single treatments caused by compensatory pathways. Moreover, combinations are thought to lessen any associated adverse side effects through reduced dosing, which is particularly important in childhood tumors. Using a parallel phenotypic combinatorial screening approach of cells derived from three pediatric tumor types, we identified Ewing sarcoma-specific interactions of a diverse set of targeted agents including approved drugs. We were able to retrieve highly synergistic drug combinations specific for Ewing sarcoma and identified signaling processes important for Ewing sarcoma cell proliferation determined by EWS-FLI1 We generated a molecular target profile of PKC412, a multikinase inhibitor with strong synergistic propensity in Ewing sarcoma, revealing its targets in critical Ewing sarcoma signaling routes. Using a multilevel experimental approach including quantitative phosphoproteomics, we analyzed the molecular rationale behind the disease-specific synergistic effect of simultaneous application of PKC412 and IGF1R inhibitors. The mechanism of the drug synergy between these inhibitors is different from the sum of the mechanisms of the single agents. The combination effectively inhibited pathway crosstalk and averted feedback loop repression, in EWS-FLI1-dependent manner. Mol Cancer Ther; 16(1); 88-101. ©2016 AACR. ©2016 American Association for Cancer Research.
Combinatorial approaches to evaluate nanodiamond uptake and induced cellular fate
Eldawud, Reem; Reitzig, Manuela; Opitz, Jörg; Rojansakul, Yon; Jiang, Wenjuan; Nangia, Shikha; Zoica Dinu, Cerasela
2016-02-01
Nanodiamonds (NDs) are an emerging class of engineered nanomaterials that hold great promise for the next generation of bionanotechnological products to be used for drug and gene delivery, or for bio-imaging and biosensing. Previous studies have shown that upon their cellular uptake, NDs exhibit high biocompatibility in various in vitro and in vivo set-ups. Herein we hypothesized that the increased NDs biocompatibility is a result of minimum membrane perturbations and their reduced ability to induce disruption or damage during cellular translocation. Using multi-scale combinatorial approaches that simulate ND-membrane interactions, we correlated NDs real-time cellular uptake and kinetics with the ND-induced membrane fluctuations to derive energy requirements for the uptake to occur. Our discrete and real-time analyses showed that the majority of NDs internalization occurs within 2 h of cellular exposure, however, with no effects on cellular viability, proliferation or cellular behavior. Furthermore, our simulation analyses using coarse-grained models identified key changes in the energy profile, membrane deformation and recovery time, all functions of the average ND or ND-based agglomerate size. Understanding the mechanisms responsible for ND-cell membrane interactions could possibly advance their implementation in various biomedical applications.
Combinatorial approaches to evaluate nanodiamond uptake and induced cellular fate
Eldawud, Reem; Reitzig, Manuela; Opitz, Jörg; Rojansakul, Yon; Jiang, Wenjuan; Nangia, Shikha; Dinu, Cerasela Zoica
2016-01-01
Nanodiamonds (NDs) are an emerging class of engineered nanomaterials that hold great promise for the next generation of bionanotechnological products to be used for drug and gene delivery, or for bio-imaging and biosensing. Previous studies have shown that upon their cellular uptake, NDs exhibit high biocompatibility in various in vitro and in vivo set-ups. Herein we hypothesized that the increased NDs biocompatibility is a result of minimum membrane perturbations and their reduced ability to induce disruption or damage during cellular translocation. Using multi-scale combinatorial approaches that simulate ND-membrane interactions, we correlated NDs real-time cellular uptake and kinetics with the ND-induced membrane fluctuations to derive energy requirements for the uptake to occur. Our discrete and real-time analyses showed that the majority of NDs internalization occurs within 2 h of cellular exposure, however, with no effects on cellular viability, proliferation or cellular behavior. Furthermore, our simulation analyses using coarse-grained models identified key changes in the energy profile, membrane deformation and recovery time, all functions of the average ND or ND-based agglomerate size. Understanding the mechanisms responsible for ND-cell membrane interactions could possibly advance their implementation in various biomedical applications. PMID:26820775
Quantum particle swarm approaches applied to combinatorial problems
Energy Technology Data Exchange (ETDEWEB)
Nicolau, Andressa dos S.; Schirru, Roberto; Lima, Alan M.M. de, E-mail: andressa@lmp.ufrj.br [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Programa de Engenharia Nuclear
2017-07-01
Quantum Particle Swarm Optimization (QPSO) is a global convergence algorithm that combines the classical PSO philosophy and quantum mechanics to improve performance of PSO. Different from PSO it only has the 'measurement' of the position equation for all particles. The process of 'measurement' in quantum mechanics, obey classic laws while the particle itself follows the quantum rules. QPSO works like PSO in search ability but has fewer parameters control. In order to improve the QPSO performance, some strategies have been proposed in the literature. Weighted QPSO (WQPSO) is a version of QPSO, where weight parameter is insert in the calculation of the balance between the global and local searching of the algorithm. It has been shown to perform well in finding the optimal solutions for many optimization problems. In this article random confinement was introduced in WQPSO. The WQPSO with random confinement was tested in two combinatorial problems. First, we execute the model on Travelling Salesman Problem (TSP) to find the parameters' values resulting in good solutions in general. Finally, the model was tested on Nuclear Reactor Reload Problem, and the performance was compared with QPSO standard. (author)
Combinatorial Approaches for the Identification of Brain Drug Delivery Targets
Stutz, Charles C.; Zhang, Xiaobin; Shusta, Eric V.
2018-01-01
The blood-brain barrier (BBB) represents a large obstacle for the treatment of central nervous system diseases. Targeting endogenous nutrient transporters that transcytose the BBB is one promising approach to selectively and noninvasively deliver a drug payload to the brain. The main limitations of the currently employed transcytosing receptors are their ubiquitous expression in the peripheral vasculature and the inherent low levels of transcytosis mediated by such systems. In this review, approaches designed to increase the repertoire of transcytosing receptors which can be targeted for the purpose of drug delivery are discussed. In particular, combinatorial protein libraries can be screened on BBB cells in vitro or in vivo to isolate targeting peptides or antibodies that can trigger transcytosis. Once these targeting reagents are discovered, the cognate BBB transcytosis system can be identified using techniques such as expression cloning or immunoprecipitation coupled with mass spectrometry. Continued technological advances in BBB genomics and proteomics, membrane protein manipulation, and in vitro BBB technology promise to further advance the capability to identify and optimize peptides and antibodies capable of mediating drug transport across the BBB. PMID:23789958
Combinatorial set theory with a gentle introduction to forcing
Halbeisen, Lorenz J
2017-01-01
This book, now in a thoroughly revised second edition, provides a comprehensive and accessible introduction to modern set theory. Following an overview of basic notions in combinatorics and first-order logic, the author outlines the main topics of classical set theory in the second part, including Ramsey theory and the axiom of choice. The revised edition contains new permutation models and recent results in set theory without the axiom of choice. The third part explains the sophisticated technique of forcing in great detail, now including a separate chapter on Suslin’s problem. The technique is used to show that certain statements are neither provable nor disprovable from the axioms of set theory. In the final part, some topics of classical set theory are revisited and further developed in light of forcing, with new chapters on Sacks Forcing and Shelah’s astonishing construction of a model with finitely many Ramsey ultrafilters. Written for graduate students in axiomatic set theory, Combinatorial Set Th...
Combinatorial MAPLE gradient thin film assemblies signalling to human osteoblasts
International Nuclear Information System (INIS)
Axente, Emanuel; Sima, Felix; Elena Sima, Livia; Serban, Natalia; Ristoscu, Carmen; Mihailescu, Ion N; Erginer, Merve; Toksoy Oner, Ebru; Eroglu, Mehmet S; Petrescu, Stefana M
2014-01-01
There is increased interest in smart bioactive materials to control tissue regeneration for the engineering of cell instructive scaffolds. We introduced combinatorial matrix-assisted pulsed laser evaporation (C-MAPLE) as a new method for the fabrication of organic thin films with a compositional gradient. Synchronized C-MAPLE of levan and oxidized levan was employed to assemble a two-compound biopolymer film structure. The gradient of the film composition was validated by fluorescence microscopy. In this study, we investigated the cell response induced by the compositional gradient using imaging of early osteoblast attachment and analysis of signalling phosphoprotein expression. Cells attached along the gradient in direct proportion to oxidized levan concentration. During this process distinct areas of the binary gradient have been shown to modulate the osteoblasts’ extracellular signal-regulated kinase signalling with different propensity. The proposed fabrication method results in the preparation of a new bioactive material, which could control the cell signalling response. This approach can be extended to screen new bioactive interfaces for tissue regeneration. (papers)
Combinatorial neural codes from a mathematical coding theory perspective.
Curto, Carina; Itskov, Vladimir; Morrison, Katherine; Roth, Zachary; Walker, Judy L
2013-07-01
Shannon's seminal 1948 work gave rise to two distinct areas of research: information theory and mathematical coding theory. While information theory has had a strong influence on theoretical neuroscience, ideas from mathematical coding theory have received considerably less attention. Here we take a new look at combinatorial neural codes from a mathematical coding theory perspective, examining the error correction capabilities of familiar receptive field codes (RF codes). We find, perhaps surprisingly, that the high levels of redundancy present in these codes do not support accurate error correction, although the error-correcting performance of receptive field codes catches up to that of random comparison codes when a small tolerance to error is introduced. However, receptive field codes are good at reflecting distances between represented stimuli, while the random comparison codes are not. We suggest that a compromise in error-correcting capability may be a necessary price to pay for a neural code whose structure serves not only error correction, but must also reflect relationships between stimuli.
On Some Algebraic and Combinatorial Properties of Dunkl Elements
Kirillov, Anatol N.
2013-06-01
We introduce and study a certain class of nonhomogeneous quadratic algebras together with the special set of mutually commuting elements inside of each, the so-called Dunkl elements. We describe relations among the Dunkl elements. This result is a further generalization of similar results obtained in [S. Fomin and A. N. Kirillov, Quadratic algebras, Dunkl elements and Schubert calculus, in Advances in Geometry (eds. J.-S. Brylinski, V. Nistor, B. Tsygan and P. Xu), Progress in Math. Vol. 172 (Birkhäuser Boston, Boston, 1995), pp. 147-182, A. Postnikov, On a quantum version of Pieri's formula, in Advances in Geometry (eds. J.-S. Brylinski, R. Brylinski, V. Nistor, B. Tsygan and P. Xu), Progress in Math. Vol. 172 (Birkhäuser Boston, 1995), pp. 371-383 and A. N. Kirillov and T. Maenor, A Note on Quantum K-Theory of Flag Varieties, preprint]. As an application we describe explicitly the set of relations among the Gaudin elements in the group ring of the symmetric group, cf. [E. Mukhin, V. Tarasov and A. Varchenko, Bethe Subalgebras of the Group Algebra of the Symmetric Group, preprint arXiv:1004.4248]. Also we describe a few combinatorial properties of some special elements in the associative quasi-classical Yang-Baxter algebra in a connection with the values of the β-Grothendieck polynomials for some special permutations, and on the other hand, with the Ehrhart polynomial of the Chan-Robbins polytope.
Quantum particle swarm approaches applied to combinatorial problems
International Nuclear Information System (INIS)
Nicolau, Andressa dos S.; Schirru, Roberto; Lima, Alan M.M. de
2017-01-01
Quantum Particle Swarm Optimization (QPSO) is a global convergence algorithm that combines the classical PSO philosophy and quantum mechanics to improve performance of PSO. Different from PSO it only has the 'measurement' of the position equation for all particles. The process of 'measurement' in quantum mechanics, obey classic laws while the particle itself follows the quantum rules. QPSO works like PSO in search ability but has fewer parameters control. In order to improve the QPSO performance, some strategies have been proposed in the literature. Weighted QPSO (WQPSO) is a version of QPSO, where weight parameter is insert in the calculation of the balance between the global and local searching of the algorithm. It has been shown to perform well in finding the optimal solutions for many optimization problems. In this article random confinement was introduced in WQPSO. The WQPSO with random confinement was tested in two combinatorial problems. First, we execute the model on Travelling Salesman Problem (TSP) to find the parameters' values resulting in good solutions in general. Finally, the model was tested on Nuclear Reactor Reload Problem, and the performance was compared with QPSO standard. (author)
Peptide mimic for influenza vaccination using nonnatural combinatorial chemistry
Miles, John J.; Tan, Mai Ping; Dolton, Garry; Galloway, Sarah A.E.; Laugel, Bruno; Makinde, Julia; Matthews, Katherine K.; Watkins, Thomas S.; Wong, Yide; Clark, Richard J.; Pentier, Johanne M.; Attaf, Meriem; Lissina, Anya; Ager, Ann; Gallimore, Awen; Gras, Stephanie; Rossjohn, Jamie; Burrows, Scott R.; Cole, David K.; Price, David A.
2018-01-01
Polypeptide vaccines effectively activate human T cells but suffer from poor biological stability, which confines both transport logistics and in vivo therapeutic activity. Synthetic biology has the potential to address these limitations through the generation of highly stable antigenic “mimics” using subunits that do not exist in the natural world. We developed a platform based on D–amino acid combinatorial chemistry and used this platform to reverse engineer a fully artificial CD8+ T cell agonist that mirrored the immunogenicity profile of a native epitope blueprint from influenza virus. This nonnatural peptide was highly stable in human serum and gastric acid, reflecting an intrinsic resistance to physical and enzymatic degradation. In vitro, the synthetic agonist stimulated and expanded an archetypal repertoire of polyfunctional human influenza virus–specific CD8+ T cells. In vivo, specific responses were elicited in naive humanized mice by subcutaneous vaccination, conferring protection from subsequent lethal influenza challenge. Moreover, the synthetic agonist was immunogenic after oral administration. This proof-of-concept study highlights the power of synthetic biology to expand the horizons of vaccine design and therapeutic delivery. PMID:29528337
Combinatorial approaches to evaluate nanodiamond uptake and induced cellular fate
International Nuclear Information System (INIS)
Eldawud, Reem; Dinu, Cerasela Zoica; Reitzig, Manuela; Opitz, Jörg; Rojansakul, Yon; Jiang, Wenjuan; Nangia, Shikha
2016-01-01
Nanodiamonds (NDs) are an emerging class of engineered nanomaterials that hold great promise for the next generation of bionanotechnological products to be used for drug and gene delivery, or for bio-imaging and biosensing. Previous studies have shown that upon their cellular uptake, NDs exhibit high biocompatibility in various in vitro and in vivo set-ups. Herein we hypothesized that the increased NDs biocompatibility is a result of minimum membrane perturbations and their reduced ability to induce disruption or damage during cellular translocation. Using multi-scale combinatorial approaches that simulate ND-membrane interactions, we correlated NDs real-time cellular uptake and kinetics with the ND-induced membrane fluctuations to derive energy requirements for the uptake to occur. Our discrete and real-time analyses showed that the majority of NDs internalization occurs within 2 h of cellular exposure, however, with no effects on cellular viability, proliferation or cellular behavior. Furthermore, our simulation analyses using coarse-grained models identified key changes in the energy profile, membrane deformation and recovery time, all functions of the average ND or ND-based agglomerate size. Understanding the mechanisms responsible for ND-cell membrane interactions could possibly advance their implementation in various biomedical applications. (paper)
Combinatorial quantization of the Hamiltonian Chern-Simons theory
International Nuclear Information System (INIS)
Alekseev, A.Yu.; Grosse, H.; Schomerus, V.
1996-01-01
This paper further develops the combinatorial approach to quantization of the Hamiltonian Chern Simons theory. Using the theory of quantum Wilson lines, we show how the Verlinde algebra appears within the context of quantum group gauge theory. This allows to discuss flatness of quantum connections so that we can give a mathematically rigorous definition of the algebra of observables A CS of the Chern Simons model. It is a *-algebra of ''functions on the quantum moduli space of flat connections'' and comes equipped with a positive functional ω (''integration''). We prove that this data does not depend on the particular choices which have been made in the construction. The algebra A CS provides a deformation quantization of the algebra of functions on the moduli space along the natural Poisson bracket induced by the Chern Simons action. We evaluate a volume of the quantized moduli space and prove that it coincides with the Verlinde number. This answer is also interpreted as a partition partition function of the lattice Yang-Mills theory corresponding to a quantum gauge group. (orig.). With 1 fig
Automated Implanter Endstation for Combinatorial Materials Science with Ion Beams
International Nuclear Information System (INIS)
Grosshans, I.; Karl, H.; Stritzker, B.
2003-01-01
The discovery, understanding and optimization of new complex functional materials requires combinatorial synthesis techniques and fast screening instrumentation for the measurement of the samples. In this contribution the synthesis of buried II-VI compound semiconductor nanocrystals by ion-implantation in SiO2 on silicon will be presented. For that we constructed a computer controlled implanter target end station, in which a 4-inch wafer can be implanted with a lateral pattern of distinct dose, composition or energy combinations. The chemical reaction of the constituents is initiated either during the implantation process or ex-situ by a rapid thermal process, where a reactive atmosphere can be applied. The resulting optical photoluminescence properties of the individual fields of the pattern can then be screened in rapid succession in an optical cryostat into which the whole wafer is mounted and cooled down. In this way, complex interdependences of the physical parameters can be studied on a single wafer and the technically relevant properties optimized
Combinatorial approaches to evaluate nanodiamond uptake and induced cellular fate.
Eldawud, Reem; Reitzig, Manuela; Opitz, Jörg; Rojansakul, Yon; Jiang, Wenjuan; Nangia, Shikha; Dinu, Cerasela Zoica
2016-02-26
Nanodiamonds (NDs) are an emerging class of engineered nanomaterials that hold great promise for the next generation of bionanotechnological products to be used for drug and gene delivery, or for bio-imaging and biosensing. Previous studies have shown that upon their cellular uptake, NDs exhibit high biocompatibility in various in vitro and in vivo set-ups. Herein we hypothesized that the increased NDs biocompatibility is a result of minimum membrane perturbations and their reduced ability to induce disruption or damage during cellular translocation. Using multi-scale combinatorial approaches that simulate ND-membrane interactions, we correlated NDs real-time cellular uptake and kinetics with the ND-induced membrane fluctuations to derive energy requirements for the uptake to occur. Our discrete and real-time analyses showed that the majority of NDs internalization occurs within 2 h of cellular exposure, however, with no effects on cellular viability, proliferation or cellular behavior. Furthermore, our simulation analyses using coarse-grained models identified key changes in the energy profile, membrane deformation and recovery time, all functions of the average ND or ND-based agglomerate size. Understanding the mechanisms responsible for ND-cell membrane interactions could possibly advance their implementation in various biomedical applications.
DEFF Research Database (Denmark)
Lennen, Rebecca; Herrgard, Markus
2014-01-01
High-cell-density fermentation for industrial production of chemicals can impose numerous stresses on cells due to high substrate, product, and by-product concentrations; high osmolarity; reactive oxygen species; and elevated temperatures. There is a need to develop platform strains of industrial...
Combining multiple ChIP-seq peak detection systems using combinatorial fusion.
Schweikert, Christina; Brown, Stuart; Tang, Zuojian; Smith, Phillip R; Hsu, D Frank
2012-01-01
Due to the recent rapid development in ChIP-seq technologies, which uses high-throughput next-generation DNA sequencing to identify the targets of Chromatin Immunoprecipitation, there is an increasing amount of sequencing data being generated that provides us with greater opportunity to analyze genome-wide protein-DNA interactions. In particular, we are interested in evaluating and enhancing computational and statistical techniques for locating protein binding sites. Many peak detection systems have been developed; in this study, we utilize the following six: CisGenome, MACS, PeakSeq, QuEST, SISSRs, and TRLocator. We define two methods to merge and rescore the regions of two peak detection systems and analyze the performance based on average precision and coverage of transcription start sites. The results indicate that ChIP-seq peak detection can be improved by fusion using score or rank combination. Our method of combination and fusion analysis would provide a means for generic assessment of available technologies and systems and assist researchers in choosing an appropriate system (or fusion method) for analyzing ChIP-seq data. This analysis offers an alternate approach for increasing true positive rates, while decreasing false positive rates and hence improving the ChIP-seq peak identification process.
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
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.
Oriented matroids—combinatorial structures underlying loop quantum gravity
Brunnemann, Johannes; Rideout, David
2010-10-01
We analyze combinatorial structures which play a central role in determining spectral properties of the volume operator (Ashtekar A and Lewandowski J 1998 Adv. Theor. Math. Phys. 1 388) in loop quantum gravity (LQG). These structures encode geometrical information of the embedding of arbitrary valence vertices of a graph in three-dimensional Riemannian space and can be represented by sign strings containing relative orientations of embedded edges. We demonstrate that these signature factors are a special representation of the general mathematical concept of an oriented matroid (Ziegler G M 1998 Electron. J. Comb.; Björner A et al 1999 Oriented Matroids (Cambridge: Cambridge University Press)). Moreover, we show that oriented matroids can also be used to describe the topology (connectedness) of directed graphs. Hence, the mathematical methods developed for oriented matroids can be applied to the difficult combinatorics of embedded graphs underlying the construction of LQG. As a first application we revisit the analysis of Brunnemann and Rideout (2008 Class. Quantum Grav. 25 065001 and 065002), and find that enumeration of all possible sign configurations used there is equivalent to enumerating all realizable oriented matroids of rank 3 (Ziegler G M 1998 Electron. J. Comb.; Björner A et al 1999 Oriented Matroids (Cambridge: Cambridge University Press)), and thus can be greatly simplified. We find that for 7-valent vertices having no coplanar triples of edge tangents, the smallest non-zero eigenvalue of the volume spectrum does not grow as one increases the maximum spin jmax at the vertex, for any orientation of the edge tangents. This indicates that, in contrast to the area operator, considering large jmax does not necessarily imply large volume eigenvalues. In addition we give an outlook to possible starting points for rewriting the combinatorics of LQG in terms of oriented matroids.
Development of a large peptoid-DOTA combinatorial library.
Singh, Jaspal; Lopes, Daniel; Gomika Udugamasooriya, D
2016-09-01
Conventional one-bead one-compound (OBOC) library synthesis is typically used to identify molecules with therapeutic value. The design and synthesis of OBOC libraries that contain molecules with imaging or even potentially therapeutic and diagnostic capacities (e.g. theranostic agents) has been overlooked. The development of a therapeutically active molecule with a built-in imaging component for a certain target is a daunting task, and structure-based rational design might not be the best approach. We hypothesize to develop a combinatorial library with potentially therapeutic and imaging components fused together in each molecule. Such molecules in the library can be used to screen, identify, and validate as direct theranostic candidates against targets of interest. As the first step in achieving that aim, we developed an on-bead library of 153,600 Peptoid-DOTA compounds in which the peptoids are the target-recognizing and potentially therapeutic components and the DOTA is the imaging component. We attached the DOTA scaffold to TentaGel beads using one of the four arms of DOTA, and we built a diversified 6-mer peptoid library on the remaining three arms. We evaluated both the synthesis and the mass spectrometric sequencing capacities of the test compounds and of the final library. The compounds displayed unique ionization patterns including direct breakages of the DOTA scaffold into two units, allowing clear decoding of the sequences. Our approach provides a facile synthesis method for the complete on-bead development of large peptidomimetic-DOTA libraries for screening against biological targets for the identification of potential theranostic agents in the future. © 2016 The Authors. Biopolymers Published by Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 673-684, 2016. © 2016 The Authors. Biopolymers Published by Wiley Periodicals, Inc.
DEFF Research Database (Denmark)
Guo, Meng; Bo Elmedyb, Thomas; Jensen, Søren Holdt
2011-01-01
In this work, we analyze a general multiple-microphone and single-loudspeaker audio processing system, where a multichannel adaptive system is used to cancel the effect of acoustic feedback/echo, and a beamformer processes the feedback/echo canceled signals. We introduce and derive an accurate...
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.
Prabhu, Varun V; Talekar, Mala K; Lulla, Amriti R; Kline, C Leah B; Zhou, Lanlan; Hall, Junior; Van den Heuvel, A Pieter J; Dicker, David T; Babar, Jawad; Grupp, Stephan A; Garnett, Mathew J; McDermott, Ultan; Benes, Cyril H; Pu, Jeffrey J; Claxton, David F; Khan, Nadia; Oster, Wolfgang; Allen, Joshua E; El-Deiry, Wafik S
2018-01-01
ONC201, founding member of the imipridone class of small molecules, is currently being evaluated in advancer cancer clinical trials. We explored single agent and combinatorial efficacy of ONC201 in preclinical models of hematological malignancies. ONC201 demonstrated (GI50 1-8 µM) dose- and time-dependent efficacy in acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), chronic myelogenous leukemia (CML), chronic lymphocytic leukemia (CLL), diffuse large B-cell lymphoma (DLBCL), mantle cell lymphoma (MCL), Burkitt's lymphoma, anaplastic large cell lymphoma (ALCL), cutaneous T-cell lymphoma (CTCL), Hodgkin's lymphoma (nodular sclerosis) and multiple myeloma (MM) cell lines including cells resistant to standard of care (dexamethasone in MM) and primary samples. ONC201 induced caspase-dependent apoptosis that involved activation of the integrated stress response (ATF4/CHOP) pathway, inhibition of Akt phosphorylation, Foxo3a activation, downregulation of cyclin D1, IAP and Bcl-2 family members. ONC201 synergistically reduced cell viability in combination with cytarabine and 5-azacytidine in AML cells. ONC201 combined with cytarabine in a Burkitt's lymphoma xenograft model induced tumor growth inhibition that was superior to either agent alone. ONC201 synergistically combined with bortezomib in MM, MCL and ALCL cells and with ixazomib or dexamethasone in MM cells. ONC201 combined with bortezomib in a Burkitt's lymphoma xenograft model reduced tumor cell density and improved CHOP induction compared to either agent alone. These results serve as a rationale for ONC201 single-agent trials in relapsed/refractory acute leukemia, non-Hodgkin's lymphoma, MM and combination trial with dexamethasone in MM, provide pharmacodynamic biomarkers and identify further synergistic combinatorial regimens that can be explored in the clinic.
Einstein, Thomas H.
1961-01-01
Equations were derived representing heat transfer and pressure drop for a gas flowing in the passages of a heater composed of a series of parallel flat plates. The plates generated heat which was transferred to the flowing gas by convection. The relatively high temperature level of this system necessitated the consideration of heat transfer between the plates by radiation. The equations were solved on an IBM 704 computer, and results were obtained for hydrogen as the working fluid for a series of cases with a gas inlet temperature of 200 R, an exit temperature of 5000 0 R, and exit Mach numbers ranging from 0.2 to O.8. The length of the heater composed of the plates ranged from 2 to 4 feet, and the spacing between the plates was varied from 0.003 to 0.01 foot. Most of the results were for a five- plate heater, but results are also given for nine plates to show the effect of increasing the number of plates. The heat generation was assumed to be identical for each plate but was varied along the length of the plates. The axial variation of power used to obtain the results presented is the so-called "2/3-cosine variation." The boundaries surrounding the set of plates, and parallel to it, were assumed adiabatic, so that all the power generated in the plates went into heating the gas. The results are presented in plots of maximum plate and maximum adiabatic wall temperatures as functions of parameters proportional to f(L/D), for the case of both laminar and turbulent flow. Here f is the Fanning friction factor and (L/D) is the length to equivalent diameter ratio of the passages in the heater. The pressure drop through the heater is presented as a function of these same parameters, the exit Mach number, and the pressure at the exit of the heater.
Combinatorial chemistry on solid support in the search for central nervous system agents.
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.
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.
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.
Constrained Combinatorial Libraries of Gp2 Proteins Enhance Discovery of PD-L1 Binders.
Kruziki, Max A; Sarma, Vidur; Hackel, Benjamin J
2018-06-05
Engineered protein ligands are used for molecular therapy, diagnostics, and industrial biotechnology. The Gp2 domain is a 45-amino acid scaffold that has been evolved for specific, high-affinity binding to multiple targets by diversification of two solvent-exposed loops. Inspired by sitewise enrichment of select amino acids, including cysteine pairs, in earlier Gp2 discovery campaigns, we hypothesized that the breadth and efficiency of de novo Gp2 discovery will be aided by sitewise amino acid constraint within combinatorial library design. We systematically constructed eight libraries and comparatively evaluated their efficacy for binder discovery via yeast display against a panel of targets. Conservation of a cysteine pair at the termini of the first diversified paratope loop increased binder discovery 16-fold ( p libraries with conserved cysteine pairs, within the second loop or an interloop pair, did not aid discovery thereby indicating site-specific impact. Via a yeast display protease resistance assay, Gp2 variants from the loop one cysteine pair library were 3.3 ± 2.1-fold ( p = 0.005) more stable than nonconstrained variants. Sitewise constraint of noncysteine residues-guided by previously evolved binders, natural Gp2 homology, computed stability, and structural analysis-did not aid discovery. A panel of binders to programmed death ligand 1 (PD-L1), a key target in cancer immunotherapy, were discovered from the loop 1 cysteine constraint library. Affinity maturation via loop walking resulted in strong, specific cellular PD-L1 affinity ( K d = 6-9 nM).
DEFF Research Database (Denmark)
Zhang, Xuping; Sørensen, Rasmus; RahbekIversen, Mathias
2018-01-01
This paper presents a novel and computationally efficient modeling method for the dynamics of flexible-link robot manipulators. In this method, a robot manipulator is decomposed into components/elements. The component/element dynamics is established using Newton–Euler equations, and then is linea......This paper presents a novel and computationally efficient modeling method for the dynamics of flexible-link robot manipulators. In this method, a robot manipulator is decomposed into components/elements. The component/element dynamics is established using Newton–Euler equations......, and then is linearized based on the acceleration-based state vector. The transfer matrices for each type of components/elements are developed, and used to establish the system equations of a flexible robot manipulator by concatenating the state vector from the base to the end-effector. With this strategy, the size...... manipulators, and only involves calculating and transferring component/element dynamic equations that have small size. The numerical simulations and experimental testing of flexible-link manipulators are conducted to validate the proposed methodologies....
Combinatorial Clustering Algorithm of Quantum-Behaved Particle Swarm Optimization and Cloud Model
Directory of Open Access Journals (Sweden)
Mi-Yuan Shan
2013-01-01
Full Text Available We propose a combinatorial clustering algorithm of cloud model and quantum-behaved particle swarm optimization (COCQPSO to solve the stochastic problem. The algorithm employs a novel probability model as well as a permutation-based local search method. We are setting the parameters of COCQPSO based on the design of experiment. In the comprehensive computational study, we scrutinize the performance of COCQPSO on a set of widely used benchmark instances. By benchmarking combinatorial clustering algorithm with state-of-the-art algorithms, we can show that its performance compares very favorably. The fuzzy combinatorial optimization algorithm of cloud model and quantum-behaved particle swarm optimization (FCOCQPSO in vague sets (IVSs is more expressive than the other fuzzy sets. Finally, numerical examples show the clustering effectiveness of COCQPSO and FCOCQPSO clustering algorithms which are extremely remarkable.
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.
Steponavičius, Raimundas; Thennadil, Suresh N
2011-03-15
The effectiveness of a scatter correction approach based on decoupling absorption and scattering effects through the use of the radiative transfer theory to invert a suitable set of measurements is studied by considering a model multicomponent suspension. The method was used in conjunction with partial least-squares regression to build calibration models for estimating the concentration of two types of analytes: an absorbing (nonscattering) species and a particulate (absorbing and scattering) species. The performances of the models built by this approach were compared with those obtained by applying empirical scatter correction approaches to diffuse reflectance, diffuse transmittance, and collimated transmittance measurements. It was found that the method provided appreciable improvement in model performance for the prediction of both types of analytes. The study indicates that, as long as the bulk absorption spectra are accurately extracted, no further empirical preprocessing to remove light scattering effects is required.
Counting in Lattices: Combinatorial Problems from Statistical Mechanics.
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
International Nuclear Information System (INIS)
Burns, T.J.
1992-01-01
A graphical-based code system is being developed at ORNL to manipulate combinatorial geometries for radiation transport and shielding applications. The current version (basically a combinatorial geometry debugger) consists of two parts: a FORTRAN-based ''view'' generator and a Microsoft Windows application for displaying the geometry. Options and features of both modules are discussed. Examples illustrating the various options available are presented. The potential for utilizing the images produced using the debugger as a visualization tool for the output of the radiation transport codes is discussed as is the future direction of the development
Directory of Open Access Journals (Sweden)
Iman Yousefi
2015-01-01
Full Text Available This paper presents parameter estimation of Permanent Magnet Synchronous Motor (PMSM using a combinatorial algorithm. Nonlinear fourth-order space state model of PMSM is selected. This model is rewritten to the linear regression form without linearization. Noise is imposed to the system in order to provide a real condition, and then combinatorial Orthogonal Projection Algorithm and Recursive Least Squares (OPA&RLS method is applied in the linear regression form to the system. Results of this method are compared to the Orthogonal Projection Algorithm (OPA and Recursive Least Squares (RLS methods to validate the feasibility of the proposed method. Simulation results validate the efficacy of the proposed algorithm.
International Nuclear Information System (INIS)
Fujimoto, K.; Takahashi, H.; Ito, S.; Inoue, S.; Watanabe, M.
2006-01-01
As a tool to facilitate future material explorations, our group has developed a new combinatorial system for the high-throughput preparation of compounds made up of more than three components. The system works in two steps: the atomization of a liquid by a high electric field followed by deposition to a grounded substrate. The combinatorial system based on this method has plural syringe pumps. The each starting materials are fed through the syringe pumps into a manifold, thoroughly mixed as they pass through the manifold, and atomized from the tip of a stainless steel nozzle onto a grounded substrate
Sentence processing in an artificial language: Learning and using combinatorial constraints.
Amato, Michael S; MacDonald, Maryellen C
2010-07-01
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' sensitivity to nonadjacent combinatorial constraints, without explicit awareness of the probabilities embedded in the language. These results show that even newly-learned constraints have an identifiable effect on online sentence processing. The rapidity of learning in this paradigm relative to others has implications for theories of implicit learning and its role in language acquisition. 2010 Elsevier B.V. All rights reserved.
Solutions manual to accompany Combinatorial reasoning an introduction to the art of counting
DeTemple, Duane
2014-01-01
This is a solutions manual to accompany Combinatorial Reasoning: An Introduction to the Art of CountingWritten by well-known scholars in the field, Combinatorial Reasoning: An Introduction to the Art of Counting introduces combinatorics alongside modern techniques, showcases the interdisciplinary aspects of the topic, and illustrates how to problem solve with a multitude of exercises throughout. The authors'' approach is very reader-friendly and avoids the ""scholarly tone"" found in many books on this topic.
Skeletal Diversity in Combinatorial Fashion: A New Format for the Castagnoli-Cushman Reaction.
Lepikhina, Anastasia; Dar'in, Dmitry; Bakulina, Olga; Chupakhin, Evgeny; Krasavin, Mikhail
2017-11-13
A new format for the Castagnoli-Cushman reaction of structurally diverse dicarboxylic acids, amines, and aldehydes in the presence of acetic anhydride as dehydrating agent is described. The reaction is distinctly amenable to parallel format: the combinatorial array of 180 reactions delivered 157 products of >85% purity without chromatographic purification (of this number, 143 compounds had >94% purity). The new method offers a convenient preparation of the skeletally and peripherally diverse, lead- and druglike γ- and δ-lactam carboxylic acids with high diastereoselectivity in combinatorial fashion.
Functional completeness of the mixed λ-calculus and combinatory logic
DEFF Research Database (Denmark)
Nielson, Hanne Riis; Nielson, Flemming
1990-01-01
Functional completeness of the combinatory logic means that every lambda-expression may be translated into an equivalent combinator expression and this is the theoretical basis for the implementation of functional languages on combinator-based abstract machines. To obtain efficient implementations...... it is important to distinguish between early and late binding times, i.e. to distinguish between compile-time and run-time computations. The authors therefore introduce a two-level version of the lambda-calculus where this distinction is made in an explicit way. Turning to the combinatory logic they generate...
Doerr, Timothy P.; Alves, Gelio; Yu, Yi-Kuo
2005-08-01
Typical combinatorial optimizations are NP-hard; however, for a particular class of cost functions the corresponding combinatorial optimizations can be solved in polynomial time using the transfer matrix technique or, equivalently, the dynamic programming approach. This suggests a way to efficiently find approximate solutions-find a transformation that makes the cost function as similar as possible to that of the solvable class. After keeping many high-ranking solutions using the approximate cost function, one may then re-assess these solutions with the full cost function to find the best approximate solution. Under this approach, it is important to be able to assess the quality of the solutions obtained, e.g., by finding the true ranking of the kth best approximate solution when all possible solutions are considered exhaustively. To tackle this statistical issue, we provide a systematic method starting with a scaling function generated from the finite number of high-ranking solutions followed by a convergent iterative mapping. This method, useful in a variant of the directed paths in random media problem proposed here, can also provide a statistical significance assessment for one of the most important proteomic tasks-peptide sequencing using tandem mass spectrometry data. For directed paths in random media, the scaling function depends on the particular realization of randomness; in the mass spectrometry case, the scaling function is spectrum-specific.
Ngongang Ndjawa, Guy Olivier; Graham, Kenneth; Mollinger, Sonya; Wu, Di M.; Hanifi, David; Prasanna, Rohit; Rose, Bradley Daniel; Dey, Sukumar; Yu, Liyang; Bredas, Jean-Luc; McGehee, Michael D.; Salleo, Alberto; Amassian, Aram
2017-01-01
In organic solar cells (OSCs), the energy of the charge-transfer (CT) complexes at the donor-acceptor interface, E , determines the maximum open-circuit voltage (V ). The coexistence of phases with different degrees of order in the donor or the acceptor, as in blends of semi-crystalline donors and fullerenes in bulk heterojunction layers, influences the distribution of CT states and the V enormously. Yet, the question of how structural heterogeneities alter CT states and the V is seldom addressed systematically. In this work, we combine experimental measurements of vacuum-deposited rubrene/C bilayer OSCs, with varying microstructure and texture, with density functional theory calculations to determine how relative molecular orientations and extents of structural order influence E and V . We find that varying the microstructure of rubrene gives rise to CT bands with varying energies. The CT band that originates from crystalline rubrene lies up to ≈0.4 eV lower in energy compared to the one that arises from amorphous rubrene. These low-lying CT states contribute strongly to V losses and result mainly from hole delocalization in aggregated rubrene. This work points to the importance of realizing interfacial structural control that prevents the formation of low E configurations and maximizes V .
Coffey, Lee; Owens, Erica; Tambling, Karen; O'Neill, David; O'Connor, Laura; O'Reilly, Catherine
2010-11-01
Nitriles are widespread in the environment as a result of biological and industrial activity. Nitrile hydratases catalyse the hydration of nitriles to the corresponding amide and are often associated with amidases, which catalyze the conversion of amides to the corresponding acids. Nitrile hydratases have potential as biocatalysts in bioremediation and biotransformation applications, and several successful examples demonstrate the advantages. In this work a real-time PCR assay was designed for the detection of Fe-type nitrile hydratase genes from environmental isolates purified from nitrile-enriched soils and seaweeds. Specific PCR primers were also designed for amplification and sequencing of the genes. Identical or highly homologous nitrile hydratase genes were detected from isolates of numerous genera from geographically diverse sites, as were numerous novel genes. The genes were also detected from isolates of genera not previously reported to harbour nitrile hydratases. The results provide further evidence that many bacteria have acquired the genes via horizontal gene transfer. The real-time PCR assay should prove useful in searching for nitrile hydratases that could have novel substrate specificities and therefore potential in industrial applications.
International Nuclear Information System (INIS)
Diaz, M. Elena; Cerro, Ramon L.
2005-01-01
The effects of pH and counterions on the type of deposition of Langmuir-Blodgett (LB) arachidic acid films onto hydrophobic glass slides is revisited. Unusually large differences in contact angles and transfer ratios (TR) were observed for subphase containing 10 -4 M of zinc sulfate and 2.10 -4 M of cadmium chloride, respectively, for a wide range of pH. Variations in TR occur at the same pH for different subphase cations and at different pH for the same divalent cations. These large variations in dynamic contact angles and TR as a function of pH point to the crucial role of electrical double layer forces in LB deposition phenomena. Transitions from Y- to X-type deposition are reported for pH larger or smaller than the pK A of the fatty acid-subphase salt system. Experimental results are compared with data reported in literature showing Z- to Y-transitions at pH close to the pK A of docosanoic acid monolayers
Ngongang Ndjawa, Guy Olivier
2017-01-16
In organic solar cells (OSCs), the energy of the charge-transfer (CT) complexes at the donor-acceptor interface, E , determines the maximum open-circuit voltage (V ). The coexistence of phases with different degrees of order in the donor or the acceptor, as in blends of semi-crystalline donors and fullerenes in bulk heterojunction layers, influences the distribution of CT states and the V enormously. Yet, the question of how structural heterogeneities alter CT states and the V is seldom addressed systematically. In this work, we combine experimental measurements of vacuum-deposited rubrene/C bilayer OSCs, with varying microstructure and texture, with density functional theory calculations to determine how relative molecular orientations and extents of structural order influence E and V . We find that varying the microstructure of rubrene gives rise to CT bands with varying energies. The CT band that originates from crystalline rubrene lies up to ≈0.4 eV lower in energy compared to the one that arises from amorphous rubrene. These low-lying CT states contribute strongly to V losses and result mainly from hole delocalization in aggregated rubrene. This work points to the importance of realizing interfacial structural control that prevents the formation of low E configurations and maximizes V .
Development of combinatorial bacteria for metal and radionuclide bioremediation
International Nuclear Information System (INIS)
A. C. Matin
2006-01-01
The grant concerned chromate [Cr(VI)] bioremediation and it was our aim from the outset to construct individual bacterial strains capable of improved bioremediation of multiple pollutants and to identify the enzymes suited to this end. Bacteria with superior capacity to remediate multiple pollutants can be an asset for the cleanup of DOE sites as they contain mixed waste. I describe below the progress made during the period of the current grant, providing appropriate context
Development of combinatorial bacteria for metal and radionuclide bioremediation
Energy Technology Data Exchange (ETDEWEB)
A. C. Matin, Ph. D.
2006-06-15
The grant concerned chromate [Cr(VI)] bioremediation and it was our aim from the outset to construct individual bacterial strains capable of improved bioremediation of multiple pollutants and to identify the enzymes suited to this end. Bacteria with superior capacity to remediate multiple pollutants can be an asset for the cleanup of DOE sites as they contain mixed waste. I describe below the progress made during the period of the current grant, providing appropriate context.
A combinatorial approach to the development of a creep resistant beta titanium alloy
Peterson, Benjamin H.
Timetal 21S has been selected as a baseline for the development of a new high temperature beta titanium alloy. A combinatorial approach employing directed laser deposition of elemental powders has been used to produce a number of test coupons with controlled variations of composition. In addition to the variation of the baseline elements (Ti, Mo, Nb, Al and Si), the alloys contain varying amounts of neutral elements (Zr and Sn), beta-stabilizers (W) and dispersoid formers (B, C and Ge). Subsequently, the creep properties, represented by their minimum creep rates, have been assessed using an Instron Electrothermal Mechanical Tester (ETMT). The microstructures of the test coupons have been characterized using a range of techniques and have been quantified using rigorous stereological techniques to populate databases and subsequently train and test Bayesian Neural Network models for the prediction of creep properties. Additionally, advanced characterization techniques and computation tools have been employed to aid in the identification of the creep rate-limiting microstructural features. For example, SEM and TEM studies show a critical dependence of the size of alpha-denuded beta regions on the creep properties in these beta-Ti alloys. The most important microstructural features (volume fraction alpha, alpha lath thickness and beta mean free path) and alloying additions (Sn and Ge) have been identified and are discussed. The ETMT, used to investigate creep properties in the work, has also been characterized and compared with traditional tensile and creep testing methods. Computational models incorporating heat transfer and electrostatics were used to investigate the temperature profiles that result from the interaction of joule heating, conductive cooling and radiative cooling in subscale Ti-6Al-4V samples at five current densities in the ETMT. The tensile properties, including YS, UTS, E and total elongation, of sub-scale specimens have been evaluated over a range
Czech Academy of Sciences Publication Activity Database
Rech, C.; Rosencrantz, R. R.; Křenek, Karel; Pelantová, Helena; Bojarová, Pavla; Roemer, Ch. E.; Hanisch, F.-G.; Křen, Vladimír; Elling, L.
2011-01-01
Roč. 353, č. 13 (2011), s. 2492-2500 ISSN 1615-4150 R&D Projects: GA MŠk OC09045 Institutional research plan: CEZ:AV0Z50200510 Keywords : combinatorial chemistry * biocatalysis * carbohydrates Subject RIV: CC - Organic Chemistry Impact factor: 6.048, year: 2011
Sentence Processing in an Artificial Language: Learning and Using Combinatorial Constraints
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'…
van der Laan, G.; Talman, A.J.J.; Yang, Z.F.
2007-01-01
Tucker's well-known combinatorial lemma states that for any given symmetric triangulation of the n-dimensional unit cube and for any integer labeling that assigns to each vertex of the triangulation a label from the set f§1;§2; ¢ ¢ ¢ ;§ng with the property that antipodal vertices on the boundary of
Efficient Discovery of Nonlinear Dependencies in a Combinatorial Catalyst Data Set
Czech Academy of Sciences Publication Activity Database
Cawse, J.N.; Baerns, M.; Holeňa, Martin
2004-01-01
Roč. 44, č. 3 (2004), s. 143-146 ISSN 0095-2338 Source of funding: V - iné verejné zdroje Keywords : combinatorial catalysis * genetic algorithms * nonlinear dependency * data analysis * high-order interactions Subject RIV: IN - Informatics, Computer Science Impact factor: 2.810, year: 2004
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...
Complexity and Tractability Islands for Combinatorial Auctions on Discrete Intervals with Gaps
Döcker, J.; Dorn, B.; Endriss, U.; Krüger, D.; Kaminka, G.A.; Fox, M.; Bouquet, P.; Hüllermeyer, E.; Dignum, V.; Dignum, F.; van Harmelen, F.
2016-01-01
Combinatorial auctions are mechanisms for allocating bundles of goods to agents who each have preferences over these goods. Finding an economically efficient allocation, the so-called winner determination problem, is computationally intractable in the general case, which is why it is important to
A combinatorial framework to quantify peak/pit asymmetries in complex dynamics
Hasson, Uri; Iacovacci, Jacopo; Davis, Ben; Flanagan, Ryan; Tagliazucchi, E.; Laufs, Helmut; Lacasa, Lucas
2018-01-01
We explore a combinatorial framework which efficiently quantifies the asymmetries between minima and maxima in local fluctuations of time series. We first showcase its performance by applying it to a battery of synthetic cases. We find rigorous results on some canonical dynamical models (stochastic
Roberts, Sarah L.; Furlan, Ricardo L.E.; Otto, Sijbren; Sanders, Jeremy K.M.
2003-01-01
Three building blocks of general structure (MeO)2CH–aromatic linker–Pro–amino acid–NHNH2 have been prepared and tested in acid-catalysed dynamic combinatorial libraries. Exposure of these libraries to LiI and NaI led to the amplification of three macrocyclic pseudopeptide receptors. The receptors
DEFF Research Database (Denmark)
Bundgaard, Peer
2006-01-01
beyond the scope of the clause. To this end it exposes two major principles of semantic combination that are active through all levels of linguistic composition: viz. frame-schematic structure and narrative structure. These principles are considered as being components of a semantic combinatorial system...
A new evolutionary algorithm with LQV learning for combinatorial problems optimization
International Nuclear Information System (INIS)
Machado, Marcelo Dornellas; Schirru, Roberto
2000-01-01
Genetic algorithms are biologically motivated adaptive systems which have been used, with good results, for combinatorial problems optimization. In this work, a new learning mode, to be used by the population-based incremental learning algorithm, has the aim to build a new evolutionary algorithm to be used in optimization of numerical problems and combinatorial problems. This new learning mode uses a variable learning rate during the optimization process, constituting a process known as proportional reward. The development of this new algorithm aims its application in the optimization of reload problem of PWR nuclear reactors, in order to increase the useful life of the nuclear fuel. For the test, two classes of problems are used: numerical problems and combinatorial problems. Due to the fact that the reload problem is a combinatorial problem, the major interest relies on the last class. The results achieved with the tests indicate the applicability of the new learning mode, showing its potential as a developing tool in the solution of reload problem. (author)
Editorial: Cologne/Twente workshop on graphs and combinatorial optimization CTW 2007
Faigle, U.; Hurink, Johann L.
2010-01-01
The 6th Cologne-Twente Workshop on Graphs and Combinatorial Optimization (CTW 2007) was held at the University of Twente, The Netherlands, 29-31 May, 2007. The CTW started as a series of biennial meetings at the Universities of Cologne in Germany and Twente in the Netherlands. Ever increasing
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…
A combinatorial proof of Postnikov's identity and a generalized enumeration of labeled trees
Seo, Seunghyun
2004-01-01
In this paper, we give a simple combinatorial explanation of a formula of A. Postnikov relating bicolored rooted trees to bicolored binary trees. We also present generalized formulas for the number of labeled k-ary trees, rooted labeled trees, and labeled plane trees.
A model-based combinatorial optimisation approach for energy-efficient processing of microalgae
Slegers, P.M.; Koetzier, B.J.; Fasaei, F.; Wijffels, R.H.; Straten, van G.; Boxtel, van A.J.B.
2014-01-01
The analyses of algae biorefinery performance are commonly based on fixed performance data for each processing step. In this work, we demonstrate a model-based combinatorial approach to derive the design-specific upstream energy consumption and biodiesel yield in the production of biodiesel from
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
Random vs. Combinatorial Methods for Discrete Event Simulation of a Grid Computer Network
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.
Comprehensive human transcription factor binding site map for combinatory binding motifs discovery.
Directory of Open Access Journals (Sweden)
Arnoldo J Müller-Molina
Full Text Available 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.
Energy Technology Data Exchange (ETDEWEB)
NONE
2000-03-01
Efforts to develop a task oriented multiple transfer robot system which will promptly and flexibly respond to changes in the task of transfer are reported. In the development of a positioning module, a dead-reckoning system (gyro, wheel encoder, etc.) is incorporated into a laser-aided positioning system for improvement in precision, and the result is tested and evaluated. In the development of a platoon transfer and cooperative transfer module, the method of pursuing the tracks of the preceding vehicle is improved for higher precision, and the resultant transfer module is tested and evaluated. A transfer management module is tested and evaluated in a transfer control simulation in which a communication system and a transfer robot are integrated. In the development of environmental state recognition and obstacle avoidance technologies, a real-time visual system is completed in which a wide-angle camera detects color-marked objects and a stereographic camera measures the range, and is subjected to performance evaluation. Studies are also made about an environmental state recognition module, the control of obstacle avoiding run, and the behavior of avoidance. A transfer mode and cooperative transfer in which plural standard robots are combined is also studied. (NEDO)
Axen, G. J.; Luther, A. L.; Selverstone, J.; Mozley, P.
2011-12-01
Unique layered cataclasites (LCs) occur locally along footwall splays, S of the ~N-dipping, top-E WSDF. They are well exposed in a NW-plunging antiform that folds the LCs and their upper and lower bounding faults. Layers range from very fine-grained granular shear zones 1-2 mm thick and cm's to m's long, to medium- to coarse-grained isotropic granular cataclasite with floating clasts up to 4-5 cm diameter in layers up to ~30 cm thick and 3 to >10 m long. The top, N-flank contact is ~5 m structurally below the main WSDF. Maximum thickness of the LCs is ~5 m on the S flank of the antiform, where the upper 10-50 cm of LCs are composed of relatively planar layers that are subparallel to the upper fault, which locally displays ultracataclasite. Deeper layers are folded into open to isoclinal folds and are faulted. Most shear-sense indicators show N-side-to-E or -SE slip, and include: (1) aligned biotite flakes and mm-scale shear bands that locally define a weak foliation dipping ~ESE, (2) sharp to granular shears, many of which merge up or down into fine-grained layers and, in the base of the overlying granodiorite, (3) primary reidel shears and (4) folded pegmatite dikes. Biotite is unaltered and feldspars are weakly to strongly altered to clays and zeolites. Zeolites also grew in pores between clasts. XRF analyses suggest minimal chemical alteration. The upper fault is sharp and relatively planar, carries granular to foliated cataclasitic granodiorite that grades up over ~2-4 m into punky, microcracked but plutonic-textured rock with much of the feldspar alteration seen in LC clasts. Some upper-plate reidels bend into parallelism with the top fault and bound newly formed LC layers. The basal fault truncates contorted layers and lacks evidence of layers being added there. We infer that the deeper, contorted layers are older and that the LC package grew upward by transfer of cataclasized slices from the overlying granodiorite while folding was ongoing. Particle
Kahraman, Korhan; Berker, Bulent; Atabekoglu, Cem Somer; Sonmezer, Murat; Cetinkaya, Esra; Aytac, Rusen; Satiroglu, Hakan
2009-06-01
To compare the efficacy of microdose GnRH agonist (GnRH-a) flare-up and multiple dose GnRH antagonist protocols in patients who have a poor response to a long luteal GnRH-a protocol. Prospective, randomized, clinical study. University hospital. Forty-two poor responder patients undergoing intracytoplasmic sperm injection (ICSI)-embryo transfer cycle. Twenty-one patients received microdose leuprolide acetate (LA) (50 microg twice daily) starting on the second day of withdrawal bleeding. The other 21 patients received 0.25 mg of cetrorelix daily when the leading follicle reached 14 mm in diameter. Serum E(2) levels, number of growing follicles and mature oocytes, embryo quality, dose of gonadotropin used, cancellation, fertilization, implantation rate and pregnancy rate (PR). The mean serum E(2) concentration on the day of hCG administration was significantly higher in the microdose GnRH-a group than in the GnRH antagonist group (1,904 vs. 1,362 pg/mL). The clinical PRs per started cycle of microdose GnRH-a and GnRH antagonist groups were 14.2% and 9.5%, respectively. There were no statistically significant differences in the other ovulation induction characteristics, fertilization and implantation rates. Microdose GnRH-a flare-up protocol and multiple dose GnRH antagonist protocol seem to have similar efficacy in improving treatment outcomes of poor responder patients.
Shi, Z; Ma, X H; Qin, C; Jia, J; Jiang, Y Y; Tan, C Y; Chen, Y Z
2012-02-01
Selective multi-target serotonin reuptake inhibitors enhance antidepressant efficacy. Their discovery can be facilitated by multiple methods, including in silico ones. In this study, we developed and tested an in silico method, combinatorial support vector machines (COMBI-SVMs), for virtual screening (VS) multi-target serotonin reuptake inhibitors of seven target pairs (serotonin transporter paired with noradrenaline transporter, H(3) receptor, 5-HT(1A) receptor, 5-HT(1B) receptor, 5-HT(2C) receptor, melanocortin 4 receptor and neurokinin 1 receptor respectively) from large compound libraries. COMBI-SVMs trained with 917-1951 individual target inhibitors correctly identified 22-83.3% (majority >31.1%) of the 6-216 dual inhibitors collected from literature as independent testing sets. COMBI-SVMs showed moderate to good target selectivity in misclassifying as dual inhibitors 2.2-29.8% (majority virtual hits correlate with the reported effects of their predicted targets. COMBI-SVM is potentially useful for searching selective multi-target agents without explicit knowledge of these agents. Copyright © 2011 Elsevier Inc. All rights reserved.
Yu, Xue; Chen, Wei-Neng; Gu, Tianlong; Zhang, Huaxiang; Yuan, Huaqiang; Kwong, Sam; Zhang, Jun
2017-08-07
This paper studies a specific class of multiobjective combinatorial optimization problems (MOCOPs), namely the permutation-based MOCOPs. Many commonly seen MOCOPs, e.g., multiobjective traveling salesman problem (MOTSP), multiobjective project scheduling problem (MOPSP), belong to this problem class and they can be very different. However, as the permutation-based MOCOPs share the inherent similarity that the structure of their search space is usually in the shape of a permutation tree, this paper proposes a generic multiobjective set-based particle swarm optimization methodology based on decomposition, termed MS-PSO/D. In order to coordinate with the property of permutation-based MOCOPs, MS-PSO/D utilizes an element-based representation and a constructive approach. Through this, feasible solutions under constraints can be generated step by step following the permutation-tree-shaped structure. And problem-related heuristic information is introduced in the constructive approach for efficiency. In order to address the multiobjective optimization issues, the decomposition strategy is employed, in which the problem is converted into multiple single-objective subproblems according to a set of weight vectors. Besides, a flexible mechanism for diversity control is provided in MS-PSO/D. Extensive experiments have been conducted to study MS-PSO/D on two permutation-based MOCOPs, namely the MOTSP and the MOPSP. Experimental results validate that the proposed methodology is promising.
Indian Academy of Sciences (India)
First page Back Continue Last page Overview Graphics. Heat transfer. Heat conduction in solid slab. Convective heat transfer. Non-linear temperature. variation due to flow. HEAT FLUX AT SURFACE. conduction/diffusion.
International Nuclear Information System (INIS)
Saad, M.A.
1985-01-01
Heat transfer takes place between material systems as a result of a temperature difference. The transmission process involves energy conversions governed by the first and second laws of thermodynamics. The heat transfer proceeds from a high-temperature region to a low-temperature region, and because of the finite thermal potential, there is an increase in entropy. Thermodynamics, however, is concerned with equilibrium states, which includes thermal equilibrium, irrespective of the time necessary to attain these equilibrium states. But heat transfer is a result of thermal nonequilibrium conditions, therefore, the laws of thermodynamics alone cannot describe completely the heat transfer process. In practice, most engineering problems are concerned with the rate of heat transfer rather than the quantity of heat being transferred. Resort then is directed to the particular laws governing the transfer of heat. There are three distinct modes of heat transfer: conduction, convection, and radiation. Although these modes are discussed separately, all three types may occur simultaneously
Lewis, Jared C.; Mantovani, Simone M.; Fu, Yu; Snow, Christopher D.; Komor, Russell S.; Wong , Chi-Huey; Arnold, Frances H.
2010-01-01
Made for each other: Combinatorial alanine substitution of active site residues in a thermostable cytochrome P450BM3 variant was used to generate an enzyme that is active with large substrates. Selective hydroxylation of methoxymethylated
Besenius, Pol; Cormack, Peter A.G.; Liu, Jingyuan; Otto, Sijbren; Sanders, Jeremy K.M.; Sherrington, David C.
2008-01-01
The thermodynamically controlled synthesis and isolation of macrocyclic receptors from dynamic combinatorial libraries has been achieved in a single step using a polymer-supported template. The templates were cinchona alkaloids which show interesting enantio- and diastereoselective molecular
Combinatorial regulation of tissue specification by GATA and FOG factors
Chlon, Timothy M.; Crispino, John D.
2012-01-01
The development of complex organisms requires the formation of diverse cell types from common stem and progenitor cells. GATA family transcriptional regulators and their dedicated co-factors, termed Friend of GATA (FOG) proteins, control cell fate and differentiation in multiple tissue types from Drosophila to man. FOGs can both facilitate and antagonize GATA factor transcriptional regulation depending on the factor, cell, and even the specific gene target. In this review, we highlight recent studies that have elucidated mechanisms by which FOGs regulate GATA factor function and discuss how these factors use these diverse modes of gene regulation to control cell lineage specification throughout metazoans. PMID:23048181
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.
ACRE: Absolute concentration robustness exploration in module-based combinatorial networks
Kuwahara, Hiroyuki; Umarov, Ramzan; Almasri, Islam; Gao, Xin
2017-01-01
To engineer cells for industrial-scale application, a deep understanding of how to design molecular control mechanisms to tightly maintain functional stability under various fluctuations is crucial. Absolute concentration robustness (ACR) is a category of robustness in reaction network models in which the steady-state concentration of a molecular species is guaranteed to be invariant even with perturbations in the other molecular species in the network. Here, we introduce a software tool, absolute concentration robustness explorer (ACRE), which efficiently explores combinatorial biochemical networks for the ACR property. ACRE has a user-friendly interface, and it can facilitate efficient analysis of key structural features that guarantee the presence and the absence of the ACR property from combinatorial networks. Such analysis is expected to be useful in synthetic biology as it can increase our understanding of how to design molecular mechanisms to tightly control the concentration of molecular species. ACRE is freely available at https://github.com/ramzan1990/ACRE.
Combinatorial identities for Stirling numbers the unpublished notes of H. W. Gould
Quaintance, Jocelyn
2016-01-01
This book is a unique work which provides an in-depth exploration into the mathematical expertise, philosophy, and knowledge of H W Gould. It is written in a style that is accessible to the reader with basic mathematical knowledge, and yet contains material that will be of interest to the specialist in enumerative combinatorics. This book begins with exposition on the combinatorial and algebraic techniques that Professor Gould uses for proving binomial identities. These techniques are then applied to develop formulas which relate Stirling numbers of the second kind to Stirling numbers of the first kind. Professor Gould's techniques also provide connections between both types of Stirling numbers and Bernoulli numbers. Professor Gould believes his research success comes from his intuition on how to discover combinatorial identities.This book will appeal to a wide audience and may be used either as lecture notes for a beginning graduate level combinatorics class, or as a research supplement for the specialist in...
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
Discovery of Cationic Polymers for Non-viral Gene Delivery using Combinatorial Approaches
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
Two is better than one; toward a rational design of combinatorial therapy.
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.
COGEDIF - automatic TORT and DORT input generation from MORSE combinatorial geometry models
International Nuclear Information System (INIS)
Castelli, R.A.; Barnett, D.A.
1992-01-01
COGEDIF is an interactive utility which was developed to automate the preparation of two and three dimensional geometrical inputs for the ORNL-TORT and DORT discrete ordinates programs from complex three dimensional models described using the MORSE combinatorial geometry input description. The program creates either continuous or disjoint mesh input based upon the intersections of user defined meshing planes and the MORSE body definitions. The composition overlay of the combinatorial geometry is used to create the composition mapping of the discretized geometry based upon the composition found at the centroid of each of the mesh cells. This program simplifies the process of using discrete orthogonal mesh cells to represent non-orthogonal geometries in large models which require mesh sizes of the order of a million cells or more. The program was specifically written to take advantage of the new TORT disjoint mesh option which was developed at ORNL
Geometric Generalisation of Surrogate Model-Based Optimisation to Combinatorial and Program Spaces
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Yong-Hyuk Kim
2014-01-01
Full Text Available Surrogate models (SMs can profitably be employed, often in conjunction with evolutionary algorithms, in optimisation in which it is expensive to test candidate solutions. The spatial intuition behind SMs makes them naturally suited to continuous problems, and the only combinatorial problems that have been previously addressed are those with solutions that can be encoded as integer vectors. We show how radial basis functions can provide a generalised SM for combinatorial problems which have a geometric solution representation, through the conversion of that representation to a different metric space. This approach allows an SM to be cast in a natural way for the problem at hand, without ad hoc adaptation to a specific representation. We test this adaptation process on problems involving binary strings, permutations, and tree-based genetic programs.
Development of automatic combinatorial system for synthesis of nanoparticles using microreactors
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Watanabe, Kosuke; Maeda, Hideaki [Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-koen, Kasuga, Fukuoka, 816-8580 (Japan); Orimoto, Yuuichi; Yamashita, Kenichi; Uehara, Masato; Nakamura, Hiroyuki [Measurement Solution Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 807-1, Shuku, Tosu, Saga, 841-0052 (Japan); Furuya, Takeshi, E-mail: maeda-h@aist.go.jp [Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8565 (Japan)
2011-10-29
In this study, automatic system for combinatorial synthesis of nanoparticles (NPs) was developed and optimization of reaction parameter for NPs synthesis was performed. Microreactor was employed for kinetic control constantly. Programmable equipments were employed for additional speed up and used a microreactor. Six reaction condition parameters were systematically combined to produce CdSe synthesis condition sets. Reaction conditions of 3404 experimental sets were synthesized and characterized in 1 month. As a result of some multivariate analyses using the numerous and complicated data, we found as follows: 1) neural network is an effective method to analyze data from combinatorial synthesis, 2) weighting evaluation method was effective to find the condition for balanced NP properties.