26 results on '"Steve Szabo"'
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2. Abelian right McCoy rings and related notions
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Sergio Lopez-Permouth, Steve Szabo, and Henry Chimal-Dzul
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Computational Theory and Mathematics ,General Mathematics ,Statistics, Probability and Uncertainty - Published
- 2022
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3. Minimal rings related to generalized quaternion rings
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Jose Maria GRAU, Antonio M. OLLER-MARCEN, and Steve SZABO
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Algebra and Number Theory - Abstract
The family of rings of the form \frac{\mathbb{Z}_{4}\left \langle x,y \right \rangle}{\left \langle x^2-a,y^2-b,yx-xy-2(c+dx+ey+fxy) \right \rangle} is investigated which contains the generalized Hamilton quaternions over $\Z_4$. These rings are local rings of order 256. This family has 256 rings contained in 88 distinct isomorphism classes. Of the 88 non-isomorphic rings, 10 are minimal reversible nonsymmetric rings and 21 are minimal abelian reflexive nonsemicommutative rings. Few such examples have been identified in the literature thus far. The computational methods used to identify the isomorphism classes are also highlighted. Finally, some generalized Hamilton quaternion rings over $\Z_{p^s}$ are characterized.
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- 2023
4. Pain Intensity and Pain Interference in Male and Female Iraq/Afghanistan-era Veterans
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Jennifer C. Naylor, H. Ryan Wagner, Cynthia Johnston, Eric E. Elbogen, Mira Brancu, Christine E. Marx, Jennifer L. Strauss, Jean C. Beckham, Patrick S. Calhoun, Eric Dedert, John A. Fairbank, Jason D. Kilts, Nathan A. Kimbrel, Angela Kirby, Scott D. Moore, Larry A. Tupler, Robin Hurley, Scott D. McDonald, Katherine H. Taber, Rajendra Morey, Jared Rowland, Cindy Swinkels, Steve Szabo, Elizabeth Van Voorhees, Ruth Yoash-Gantz, John D. Curry, Michelle L. Kelley, Erin Kurtz, and Megan Shepherd-Banigan
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Adult ,Male ,medicine.medical_specialty ,Health (social science) ,Functional impairment ,Pain ,Pain Interference ,03 medical and health sciences ,Sex Factors ,0302 clinical medicine ,Quality of life ,030202 anesthesiology ,Sex factors ,Maternity and Midwifery ,medicine ,Humans ,Sex Distribution ,Iraq War, 2003-2011 ,Acute pain ,Veterans ,Afghan Campaign 2001 ,business.industry ,Afghanistan ,Public Health, Environmental and Occupational Health ,Chronic pain ,Obstetrics and Gynecology ,medicine.disease ,United States ,humanities ,Intensity (physics) ,Iraq ,Quality of Life ,Physical therapy ,Pain psychology ,Female ,business ,030217 neurology & neurosurgery - Abstract
Background Chronic pain conditions are common among both male and female Iraq/Afghanistan-era veterans and can have substantial negative impacts on quality of life and function. Although in general women tend to report higher levels of pain intensity than men, findings remain mixed on whether gender differences in pain exist in Iraq/Afghanistan-era veterans. Additionally, the relationships between functional impairment, pain intensity, and gender remain unknown. Methods This project examined gender differences in pain intensity and pain interference in 875 male and female Iraq/Afghanistan-era veterans. Nonparametric Wilcoxon rank-tests examined gender differences in pain scores. Multivariable generalized linear regression modeling was used to evaluate the magnitude of pain intensity and interference across levels of chronicity and gender, and to evaluate the role of chronicity in gender effects in measures of pain and function. Results Pain intensity and interference scores were significantly greater among both male and female veterans reporting chronic pain relative to acute pain. Women veterans endorsed higher levels of pain intensity and pain interference compared with men. Results derived from multivariable analyses implicated pain intensity as a factor underlying gender differences in functional impairment among chronic pain sufferers, indicating that gender differences in functional measures were eliminated after controlling statistically for pain intensity. Conclusions Results demonstrate that the effects of functional impairment are impacted by pain intensity, and not by gender.
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- 2019
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5. Some minimal rings related to 2-primal rings
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Steve Szabo
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Pure mathematics ,Algebra and Number Theory ,Mathematics::Commutative Algebra ,Rings and Algebras (math.RA) ,Taxonomy (general) ,010102 general mathematics ,FOS: Mathematics ,Mathematics - Rings and Algebras ,010103 numerical & computational mathematics ,0101 mathematics ,01 natural sciences ,Commutative property ,Mathematics - Abstract
In a paper on the taxonomy of 2-primal rings, examples of various types of rings that are related to commutativity such as reduced, symmetric, duo, reversible and PS~I were given in order to show that the ring class inclusions were strict. Many of the rings given in the examples were infinite. In this paper, where possible, examples of minimal finite rings of the various types are given. Along with the rings in the previous taxonomy, NI, abelian and reflexive rings are also included.
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- 2019
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6. Correction to: Abelian right McCoy rings and related notions
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Sergio Lopez-Permouth, Steve Szabo, and Henry Chimal-Dzul
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Computational Theory and Mathematics ,General Mathematics ,Statistics, Probability and Uncertainty - Published
- 2022
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7. Minimal Reflexive Nonsemicommutative Rings
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Steve Szabo and Henry Chimal-Dzul
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Pure mathematics ,Ring (mathematics) ,Algebra and Number Theory ,Mathematics::Commutative Algebra ,Applied Mathematics ,010102 general mathematics ,Order (ring theory) ,0102 computer and information sciences ,Mathematics - Rings and Algebras ,01 natural sciences ,Rings and Algebras (math.RA) ,010201 computation theory & mathematics ,Reflexivity ,Taxonomy (general) ,FOS: Mathematics ,0101 mathematics ,Mathematics - Abstract
It has recently been shown that a minimal reversible nonsymmetric ring has order 256 answering a question originally posed in a paper on a taxonomy of 2-primal rings. In a different work, questions on minimal rings having to do with this taxonomy were also answered. In this work it is shown that a minimal abelian reflexive nonsemicommutative ring also has order 256, a related question left open in these previous works. It is also shown here that [Formula: see text] is such a minimal ring. This is a consequence of the main result of the paper which is that a finite abelian reflexive ring of order [Formula: see text] for some prime [Formula: see text] and [Formula: see text] is reversible.
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- 2020
8. On Codes Over Frobenius Rings: Generating Characters, Macwilliams Identities And Generator Matrices
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Esengül Saltürk, Steven T. Dougherty, and Steve Szabo
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Pure mathematics ,Ring (mathematics) ,Algebra and Number Theory ,Mathematics::Commutative Algebra ,Applied Mathematics ,Order (ring theory) ,020206 networking & telecommunications ,0102 computer and information sciences ,02 engineering and technology ,01 natural sciences ,Character (mathematics) ,010201 computation theory & mathematics ,Theory of computation ,0202 electrical engineering, electronic engineering, information engineering ,Generator matrix ,Focus (optics) ,Commutative property ,Mathematics - Abstract
Codes over commutative Frobenius rings are studied with a focus on local Frobenius rings of order 16 for illustration. The main purpose of this work is to present a method for constructing a generating character for any commutative Frobenius ring. Given such a character, the MacWilliams identities for the complete and symmetrized weight enumerators can be easily found. As examples, generating characters for all commutative local Frobenius rings of order 16 are given. In addition, a canonical generator matrix for codes over local non-chain rings is discussed. The purpose is to show that when working over local non-chain rings, a canonical generator matrix exists but is less than useful which emphases the difficulties in working over such rings.
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- 2019
9. The monochromatic column problem with a prime number of colors
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Steve Szabo and Loran Crowell
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Sequence ,Coprime integers ,General Mathematics ,Prime number ,ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION ,MathematicsofComputing_GENERAL ,Chinese remainder theorem ,11A07 ,Column (database) ,monochromatic column problem ,Combinatorics ,multiple sequence alignment problem ,Matrix (mathematics) ,Monochromatic color ,05A15 ,Mathematics - Abstract
Let [math] be a sequence of [math] pairwise coprime positive integers, [math] , and [math] be a sequence of [math] different colors. Let [math] be an [math] matrix of colors in which row [math] consists of blocks of [math] consecutive entries of the same color with colors 0 through [math] repeated cyclically. The monochromatic column problem is to determine the number of columns of [math] in which every entry is the same color. The solution for a prime number of colors is provided.
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- 2019
10. On a class of repeated-root monomial-like abelian codes
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Steve Szabo, Ferruh Özbudak, Edgar Martínez-Moro, and Hakan Ozadam
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Discrete mathematics ,Monomial ,Class (set theory) ,Algebra and Number Theory ,Weight-retaining property ,lcsh:Mathematics ,Root (chord) ,Hamming distance ,lcsh:QA1-939 ,Combinatorics ,Group code ,Product (mathematics) ,Repeated-root Cyclic code ,Discrete Mathematics and Combinatorics ,Abelian code ,Abelian group ,Mathematics ,Variable (mathematics) - Abstract
In this paper we study polycyclic codes of length $p^{s_1} \times \cdots \times p^{s_n}$\ over $\F_{p^a}$\ generated by a single monomial. These codes form a special class of abelian codes. We show that these codes arise from the product of certain single variable codes and we determine their minimum Hamming distance. Finally we extend the results of Massey et. al. in \cite{MASSEY_1973} on the weight retaining property of monomials in one variable to the weight retaining property of monomials in several variables.
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- 2015
11. Convolutional codes with additional algebraic structure
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S. R. López-Permouth and Steve Szabo
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Discrete mathematics ,Block code ,Finite group ,Ring (mathematics) ,Algebra and Number Theory ,Group (mathematics) ,Reed–Solomon error correction ,Convolutional code ,Polynomial ring ,Linear code ,Mathematics - Abstract
Convolutional codes have appeared in the literature endowed with sufficient additional algebraic structure to be considered as (left) ideals of a (code-ambient) automorphism-twisted polynomial ring with coefficients in a (word-ambient) semisimple finite group ring. In this paper we extend the present scope of the theory by considering a code-ambient twisted polynomial ring having, in addition to an automorphism σ , the action of a σ -derivation δ . In addition, we develop the basic theory without any specific restrictions for the semisimple finite word-ambient ring. This second element therefore extends even the original notions of both cyclic and group convolutional codes considered thus far in the literature. Among other results, in this paper we develop a matrix-based approach to the study of our extended notion of group convolutional codes (and therefore of cyclic convolutional codes as well), inspired by the use of circulant matrices by Gluesing-Luerssen and Schmale, and then use it to extend to this level the results on the existence of dual codes that were originally established by those authors for cyclic codes (in the narrower sense without a σ -derivation). Various examples illustrate the potential value of extending the search for good convolutional codes in this direction.
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- 2013
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12. Properties of dual codes defined by nondegenerate forms
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Steve Szabo and Jay A. Wood
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Discrete mathematics ,Block code ,Algebra and Number Theory ,Sesquilinear form ,lcsh:Mathematics ,Bilinear form ,lcsh:QA1-939 ,Linear code ,Dual code ,Cardinality ,Discrete Mathematics and Combinatorics ,Hamming weight ,Dual pair ,Mathematics - Abstract
Dual codes are defined with respect to non-degenerate sesquilinear or bilinear forms over a finite Frobenius ring. These dual codes have the properties one expects from a dual code: they satisfy a double-dual property, they have cardinality complementary to that of the primal code, and they satisfy the MacWilliams identities for the Hamming weight.
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- 2017
13. Minimal Reversible Nonsymmetric Rings
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Steve Szabo
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Ring (mathematics) ,Algebra and Number Theory ,Mathematics::Commutative Algebra ,010102 general mathematics ,Quaternion group ,Mathematics - Rings and Algebras ,01 natural sciences ,Combinatorics ,Rings and Algebras (math.RA) ,0103 physical sciences ,FOS: Mathematics ,Cardinality (SQL statements) ,010307 mathematical physics ,0101 mathematics ,Algebra over a field ,2-group ,Mathematics - Abstract
Marks showed that F 2 Q 8 , the F 2 group algebra over the quaternion group, is a reversible nonsymmetric ring, then questioned whether or not this ring is minimal with respect to cardinality. In this work, it is shown that the cardinality of a minimal reversible nonsymmetric ring is indeed 256. Furthermore, it is shown that although F 2 Q 8 is a duo ring, there are also examples of minimal reversible nonsymmetric rings which are nonduo.
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- 2017
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14. Duality Preserving Gray Maps for Codes over Rings
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Steve Szabo, Felix Ulmer, Eastern Kentucky University, Institut de Recherche Mathématique de Rennes ( IRMAR ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST-École normale supérieure - Rennes ( ENS Rennes ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National des Sciences Appliquées ( INSA ) -Université de Rennes 2 ( UR2 ), Université de Rennes ( UNIV-RENNES ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Recherche Mathématique de Rennes (IRMAR), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO Agrocampus Ouest, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
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FOS: Computer and information sciences ,Pure mathematics ,Finite ring ,Trace (linear algebra) ,Computer Science - Information Theory ,Duality (optimization) ,0102 computer and information sciences ,02 engineering and technology ,01 natural sciences ,[ INFO.INFO-IT ] Computer Science [cs]/Information Theory [cs.IT] ,FOS: Mathematics ,0202 electrical engineering, electronic engineering, information engineering ,codes over rings ,Computer Science::General Literature ,Self-dual codes ,Mathematics ,Algebra and Number Theory ,symmetric basis ,Information Theory (cs.IT) ,Applied Mathematics ,Astrophysics::Instrumentation and Methods for Astrophysics ,Computer Science::Computation and Language (Computational Linguistics and Natural Language and Speech Processing) ,020206 networking & telecommunications ,Mathematics - Rings and Algebras ,94B05, 94B60 ,16. Peace & justice ,Subring ,Rings and Algebras (math.RA) ,010201 computation theory & mathematics ,[INFO.INFO-IT]Computer Science [cs]/Information Theory [cs.IT] ,codes over non commutative rings ,Gray (horse) ,trace orthogonal basis - Abstract
article number 1750161; International audience; Given a finite ring $A$ which is a free left module over a subring $R$ of $A$, two types of $R$-bases are defined which in turn are used to define duality preserving maps from codes over $A$ to codes over $R$. The first type, pseudo-self-dual bases, are a generalization of trace orthogonal bases for fields. The second are called symmetric bases. Both types are illustrated with skew cyclic codes which are codes that are $A$-submodules of the skew polynomial ring $A[X;\theta]/\langle X^n-1\rangle$ (the classical cyclic codes are the case when $\theta=id$). When $A$ is commutative, there exists criteria for a skew cyclic code over $A$ to be self-dual. With this criteria and a duality preserving map, many self-dual codes over the subring $R$ can easily be found. In this fashion, numerous examples are given, some of which are not chain or serial rings.
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- 2017
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15. Polycyclic codes over Galois rings with applications to repeated-root constacyclic codes
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Steve Szabo, Ferruh Özbudak, Sergio R. López-Permouth, and Hakan Ozadam
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FOS: Computer and information sciences ,Computer Science - Information Theory ,Polynomial ring ,Structure (category theory) ,Root (chord) ,0102 computer and information sciences ,02 engineering and technology ,01 natural sciences ,Theoretical Computer Science ,Combinatorics ,Gröbner basis ,FOS: Mathematics ,0202 electrical engineering, electronic engineering, information engineering ,Engineering(all) ,Mathematics ,Ring (mathematics) ,Algebra and Number Theory ,Mathematics::Commutative Algebra ,Information Theory (cs.IT) ,Applied Mathematics ,General Engineering ,Galois rings ,020206 networking & telecommunications ,Hamming distance ,Mathematics - Rings and Algebras ,Rings and Algebras (math.RA) ,010201 computation theory & mathematics ,Quotient ring - Abstract
Cyclic, negacyclic and constacyclic codes are part of a larger class of codes called polycyclic codes; namely, those codes which can be viewed as ideals of a factor ring of a polynomial ring. The structure of the ambient ring of polycyclic codes over GR(p^a,m) and generating sets for its ideals are considered. Along with some structure details of the ambient ring, the existance of a certain type of generating set for an ideal is proven., arXiv admin note: text overlap with arXiv:0906.4008
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- 2013
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16. Dual generalizations of the concept of cyclicity of codes
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Benigno R. Parra-Avila, Sergio R. López-Permouth, and Steve Szabo
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Pure mathematics ,Algebra and Number Theory ,Computer Networks and Communications ,If and only if ,Applied Mathematics ,Duality (mathematics) ,Discrete Mathematics and Combinatorics ,Microbiology ,Algorithm ,Astrophysics::Galaxy Astrophysics ,Mathematics ,Dual (category theory) - Abstract
In this paper we focus on two generalizations of the notion of cyclicity of codes: polycyclic codes and sequential codes. We establish a duality between these two generalizations and also show connections between them and other well-known generalizations of cyclicity such as the notions of negacyclicity and constacyclicity. In particular, it is shown that a code $C$ is sequential and polycyclic if and only if $C$ and its dual C⊥ are both sequential if and only if $C$ and its dual C⊥ are both polycyclic. Furthermore, any one of these equivalent statements characterizes the family of constacyclic codes.
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- 2009
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17. On the Hamming weight of repeated root cyclic and negacyclic codes over Galois rings
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Steve Szabo and Sergio R. López-Permouth
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Ring (mathematics) ,Algebra and Number Theory ,Mathematics::Commutative Algebra ,Computer Networks and Communications ,Applied Mathematics ,Local ring ,Root (chord) ,Galois rings ,Hamming distance ,Microbiology ,Ambient space ,Combinatorics ,Simple (abstract algebra) ,Discrete Mathematics and Combinatorics ,Hamming weight ,Mathematics - Abstract
Repeated root Cyclic and Negacyclic codes over Galois rings have been studied much less than their simple root counterparts. This situation is beginning to change. For example, repeated root codes of length ps, where $p$ is the characteristic of the alphabet ring, have been studied under some additional hypotheses. In each one of those cases, the ambient space for the codes has turned out to be a chain ring. In this paper, all remaining cases of cyclic and negacyclic codes of length ps over a Galois ring alphabet are considered. In these cases the ambient space is a local ring with simple socle but not a chain ring. Nonetheless, by reducing the problem to one dealing with uniserial subambients, a method for computing the Hamming distance of these codes is provided.
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- 2009
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18. The Monochromatic Column problem
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Steve Szabo and Ashish K. Srivastava
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Discrete mathematics ,Sequence ,Coprime integers ,Monochromatic Column ,Column (database) ,Chinese Remainder Theorem ,Theoretical Computer Science ,Combinatorics ,Matrix (mathematics) ,Integer ,Discrete Mathematics and Combinatorics ,Monochromatic color ,Chinese remainder theorem ,M-matrix ,Mathematics - Abstract
Let p"1, p"2,..., p"n be a sequence of n pairwise coprime positive integers, and let P=p"1p"2...p"n. Let 0,1,...,m-1 be a sequence of m different colors. Let A be an nxmP matrix of colors in which row i consists of blocks of p"i consecutive entries of the same color, with colors 0 through m-1 repeated cyclically. The Monochromatic Column problem is to determine the number of columns of A in which every entry is the same color. The solution for m=3 colors is presented and proved.
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- 2008
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19. The Genomic Landscapes of Human Breast and Colorectal Cancers
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Laura D. Wood, D. Williams Parsons, Siân Jones, Jimmy Lin, Tobias Sjöblom, Rebecca J. Leary, Dong Shen, Simina M. Boca, Thomas Barber, Janine Ptak, Natalie Silliman, Steve Szabo, Zoltan Dezso, Vadim Ustyanksky, Tatiana Nikolskaya, Yuri Nikolsky, Rachel Karchin, Paul A. Wilson, Joshua S. Kaminker, Zemin Zhang, Randal Croshaw, Joseph Willis, Dawn Dawson, Michail Shipitsin, James K. V. Willson, Saraswati Sukumar, Kornelia Polyak, Ben Ho Park, Charit L. Pethiyagoda, P. V. Krishna Pant, Dennis G. Ballinger, Andrew B. Sparks, James Hartigan, Douglas R. Smith, Erick Suh, Nickolas Papadopoulos, Phillip Buckhaults, Sanford D. Markowitz, Giovanni Parmigiani, Kenneth W. Kinzler, Victor E. Velculescu, and Bert Vogelstein
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Sequence analysis ,Breast Neoplasms ,Biology ,medicine.disease_cause ,Genome ,Cell Line ,Mice ,Breast cancer ,Databases, Genetic ,medicine ,Animals ,Humans ,Gene ,Genetics ,Mutation ,Multidisciplinary ,Genome, Human ,Chromosome Mapping ,Computational Biology ,Cancer ,DNA, Neoplasm ,Sequence Analysis, DNA ,medicine.disease ,Neoplasm Proteins ,Cancer Genome Project ,Colorectal Neoplasms ,Carcinogenesis ,Metabolic Networks and Pathways ,Genes, Neoplasm - Abstract
Human cancer is caused by the accumulation of mutations in oncogenes and tumor suppressor genes. To catalog the genetic changes that occur during tumorigenesis, we isolated DNA from 11 breast and 11 colorectal tumors and determined the sequences of the genes in the Reference Sequence database in these samples. Based on analysis of exons representing 20,857 transcripts from 18,191 genes, we conclude that the genomic landscapes of breast and colorectal cancers are composed of a handful of commonly mutated gene “mountains” and a much larger number of gene “hills” that are mutated at low frequency. We describe statistical and bioinformatic tools that may help identify mutations with a role in tumorigenesis. These results have implications for understanding the nature and heterogeneity of human cancers and for using personal genomics for tumor diagnosis and therapy.
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- 2007
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20. The Consensus Coding Sequences of Human Breast and Colorectal Cancers
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Tobias Sjöblom, Siân Jones, Laura D. Wood, D. Williams Parsons, Jimmy Lin, Thomas D. Barber, Diana Mandelker, Rebecca J. Leary, Janine Ptak, Natalie Silliman, Steve Szabo, Phillip Buckhaults, Christopher Farrell, Paul Meeh, Sanford D. Markowitz, Joseph Willis, Dawn Dawson, James K. V. Willson, Adi F. Gazdar, James Hartigan, Leo Wu, Changsheng Liu, Giovanni Parmigiani, Ben Ho Park, Kurtis E. Bachman, Nickolas Papadopoulos, Bert Vogelstein, Kenneth W. Kinzler, and Victor E. Velculescu
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Male ,Colorectal cancer ,Sequence analysis ,Breast Neoplasms ,Biology ,Polymerase Chain Reaction ,Genome ,Breast cancer ,Cell Line, Tumor ,Consensus Sequence ,medicine ,Consensus sequence ,Humans ,Neoplasm ,Gene ,Multidisciplinary ,Genome, Human ,Computational Biology ,Sequence Analysis, DNA ,medicine.disease ,Amino Acid Substitution ,Mutation ,Immunology ,Cancer research ,Female ,Human genome ,Colorectal Neoplasms ,Databases, Nucleic Acid ,Genes, Neoplasm - Abstract
The elucidation of the human genome sequence has made it possible to identify genetic alterations in cancers in unprecedented detail. To begin a systematic analysis of such alterations, we determined the sequence of well-annotated human protein-coding genes in two common tumor types. Analysis of 13,023 genes in 11 breast and 11 colorectal cancers revealed that individual tumors accumulate an average of ∼90 mutant genes but that only a subset of these contribute to the neoplastic process. Using stringent criteria to delineate this subset, we identified 189 genes (average of 11 per tumor) that were mutated at significant frequency. The vast majority of these genes were not known to be genetically altered in tumors and are predicted to affect a wide range of cellular functions, including transcription, adhesion, and invasion. These data define the genetic landscape of two human cancer types, provide new targets for diagnostic and therapeutic intervention, and open fertile avenues for basic research in tumor biology.
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- 2006
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21. Mutational Analysis of the Tyrosine Phosphatome in Colorectal Cancers
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Giovanni Parmigiani, Bert Vogelstein, Natalie Silliman, Victor E. Velculescu, Zhenghe Wang, Greg Riggins, Michiel S. van der Heijden, Steven M. Powell, Steve Szabo, D. Williams Parsons, Hai Yan, Dong Shen, Jason Sager, Brock A. Peters, Sanford D. Markowitz, Tian Li Wang, Janine Ptak, Alberto Bardelli, James K V Willson, and Kenneth W. Kinzler
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DNA Mutational Analysis ,Mutation, Missense ,Protein Tyrosine Phosphatase, Non-Receptor Type 13 ,Nerve Tissue Proteins ,Protein tyrosine phosphatase ,Biology ,PTPRF ,Transfection ,Receptor tyrosine kinase ,chemistry.chemical_compound ,Catalytic Domain ,Humans ,Genes, Tumor Suppressor ,Phosphorylation ,Frameshift Mutation ,PTPRT ,Multidisciplinary ,Receptor-Like Protein Tyrosine Phosphatases, Class 5 ,Protein Tyrosine Phosphatase, Non-Receptor Type 3 ,Computational Biology ,Tyrosine phosphorylation ,Exons ,Molecular biology ,Markov Chains ,PTPN11 ,Kinetics ,Receptor-Like Protein Tyrosine Phosphatases ,chemistry ,Codon, Nonsense ,Mutation ,Cancer research ,biology.protein ,Tyrosine ,Protein Tyrosine Phosphatases ,Colorectal Neoplasms ,Cell Division ,Signal Transduction - Abstract
Tyrosine phosphorylation, regulated by protein tyrosine phosphatases (PTPs) and kinases (PTKs), is important in signaling pathways underlying tumorigenesis. A mutational analysis of the tyrosine phosphatase gene superfamily in human cancers identified 83 somatic mutations in six PTPs ( PTPRF, PTPRG, PTPRT, PTPN3, PTPN13, PTPN14 ), affecting 26% of colorectal cancers and a smaller fraction of lung, breast, and gastric cancers. Fifteen mutations were nonsense, frameshift, or splice-site alterations predicted to result in truncated proteins lacking phosphatase activity. Five missense mutations in the most commonly altered PTP ( PTPRT ) were biochemically examined and found to reduce phosphatase activity. Expression of wild-type but not a mutant PTPRT in human cancer cells inhibited cell growth. These observations suggest that the mutated tyrosine phosphatases are tumor suppressor genes, regulating cellular pathways that may be amenable to therapeutic intervention.
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- 2004
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22. On a class of repeated-root monomial-like abelian codes
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Edgar Martinez-Moro, Hakan Ozadam, Ferruh Ozbudak, Steve Szabo and Edgar Martinez-Moro, Hakan Ozadam, Ferruh Ozbudak, Steve Szabo
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In this paper we study polycyclic codes of length $p^{s_1} \times \cdots \times p^{s_n}$\ over $\F_{p^a}$\ generated by a single monomial. These codes form a special class of abelian codes. We show that these codes arise from the product of certain single variable codes and we determine their minimum Hamming distance. Finally we extend the results of Massey et. al. on the weight retaining property of monomials in one variable to the weight retaining property of monomials in several variables.
- Published
- 2015
23. Detection and quantification of mutations in the plasma of patients with colorectal tumors
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Kerstin David, Devin Dressman, Hartmut Juhl, Steven N. Goodman, Dong Shen, Luis A. Diaz, Steve Szabo, Frank Diehl, Meng Li, Kenneth W. Kinzler, Bert Vogelstein, and Yiping He
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Adult ,Male ,Genes, APC ,Tumor suppressor gene ,Adenomatous polyposis coli ,Colorectal cancer ,Mutant ,medicine.disease_cause ,Sensitivity and Specificity ,chemistry.chemical_compound ,medicine ,Humans ,Aged ,Aged, 80 and over ,Mutation ,Multidisciplinary ,biology ,Cancer ,DNA, Neoplasm ,Middle Aged ,Biological Sciences ,medicine.disease ,Circulating Cell-Free DNA ,chemistry ,Immunology ,biology.protein ,Cancer research ,Female ,Colorectal Neoplasms ,DNA - Abstract
The early detection of cancers through analysis of circulating DNA could have a substantial impact on morbidity and mortality. To achieve this goal, it is essential to determine the number of mutant molecules present in the circulation of cancer patients and to develop methods that are sufficiently sensitive to detect these mutations. Using a modified version of a recently developed assay for this purpose, we found that patients with advanced colorectal cancers consistently contained mutant adenomatous polyposis coli ( APC ) DNA molecules in their plasma. The median number of APC DNA fragments in such patients was 47,800 per ml of plasma, of which 8% were mutant. Mutant APC molecules were also detected in >60% of patients with early, presumably curable colorectal cancers, at levels ranging from 0.01% to 1.7% of the total APC molecules. These results have implications for the mechanisms through which tumor DNA is released into the circulation and for diagnostic tests based on this phenomenon.
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- 2005
24. Three classes of genes mutated in colorectal cancers with chromosomal instability
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Dong Shen, Natalie Silliman, Victor E. Velculescu, Roger E. Karess, Michael L. Goldberg, D. Williams Parsons, Sanford D. Markowitz, Janine Ptak, Bert Vogelstein, Tian Li Wang, Steve Szabo, Christoph Lengauer, Mark M. Awad, Giovanni Traverso, Jordan M. Cummins, Kenneth W. Kinzler, James K V Willson, Zhenghe Wang, Prasad V. Jallepalli, and Daniel P. Cahill
- Subjects
Cancer Research ,Somatic cell ,Saccharomyces cerevisiae ,Cell Cycle Proteins ,Biology ,medicine.disease_cause ,Chromosome segregation ,Chromosome instability ,Chromosomal Instability ,medicine ,Animals ,Humans ,Gene ,Sequence (medicine) ,Genetics ,Polycomb Repressive Complex 1 ,Mutation ,MRE11 Homologue Protein ,Chromosome ,biology.organism_classification ,DNA-Binding Proteins ,Drosophila melanogaster ,Oncology ,Female ,Colorectal Neoplasms - Abstract
Although most colorectal cancers are chromosomally unstable, the basis for this instability has not been defined. To determine whether genes shown to cause chromosomal instability in model systems were mutated in colorectal cancers, we identified their human homologues and determined their sequence in a panel of colorectal cancers. We found 19 somatic mutations in five genes representing three distinct instability pathways. Seven mutations were found in MRE11, whose product is involved in double-strand break repair. Four mutations were found among hZw10, hZwilch/FLJ10036, and hRod/KNTC, whose products bind to one another in a complex that localizes to kinetochores and controls chromosome segregation. Eight mutations were found in Ding, a previously uncharacterized gene with sequence similarity to the Saccharomyces cerevisiae Pds1, whose product is essential for proper chromosome disjunction. This analysis buttresses the evidence that chromosomal instability has a genetic basis and provides clues to the mechanistic basis of instability in cancers.
- Published
- 2004
25. Mutational analysis of the tyrosine kinome in colorectal cancers
- Author
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Natalie Silliman, James K V Willson, Saurabh Saha, Bert Vogelstein, Sanford D. Markowitz, Alberto Bardelli, Kenneth W. Kinzler, Victor E. Velculescu, Steve Szabo, D. Williams Parsons, Janine Ptak, and Giovanni Parmigiani
- Subjects
DNA Mutational Analysis ,Molecular Sequence Data ,Motility ,Biology ,Polymerase Chain Reaction ,Transcription (biology) ,Fusion Proteins, gag-onc ,Humans ,Receptor, trkB ,Kinome ,Receptor, trkC ,Amino Acid Sequence ,Tyrosine ,Multidisciplinary ,Receptor, EphA3 ,Computational Biology ,Exons ,Sequence Analysis, DNA ,Protein-Tyrosine Kinases ,Vascular Endothelial Growth Factor Receptor-2 ,Protein Structure, Tertiary ,Apoptosis ,Guanylate Cyclase ,Immunology ,Mutation ,Cancer research ,Signal transduction ,Colorectal Neoplasms ,Tyrosine kinase - Abstract
Tyrosine kinases (TKs) are central regulators of signaling pathways that control differentiation, transcription, cell cycle progression, apoptosis, motility, and invasion ( [1][1] ). Although a few TK genes have been shown to be mutationally altered in specific human cancers ( [1][1] ), it is not
- Published
- 2003
26. Mutations in a signalling pathway
- Author
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Christoph Lengauer, D. Williams Parsons, Alberto Bardelli, Natalie Silliman, Laura DeLong, Janine Ptak, Victor E. Velculescu, James K V Willson, Sanford D. Markowitz, Jordan M. Cummins, Tian Li Wang, Kenneth W. Kinzler, Bert Vogelstein, Yardena Samuels, and Steve Szabo
- Subjects
Cell signaling ,Multidisciplinary ,Kinase ,Colorectal cancer ,Cancer ,Biology ,Bioinformatics ,medicine.disease ,Hedgehog signaling pathway ,DNA Mutational Analysis ,medicine ,Cancer research ,Signal transduction ,Gene - Abstract
Protein kinases are enzymes that are important for controlling cellular growth and invasion, and their malfunction is implicated in the development of some tumours. We analysed human colorectal cancers for genetic mutations in 340 serine/threonine kinases and found mutations in eight genes, including in three members of the phosphatidylinositol-3-OH kinase (PI(3)K) pathway. The discovery of this mutational activation of a key cell-signalling pathway may provide new targets for therapeutic intervention.
- Published
- 2005
- Full Text
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