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Search Results: 1 - 10 of 117299 matches for " Diana O Perkins "
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Gene processing control loops suggested by sequencing, splicing, and RNA folding
Clark D Jeffries, Diana O Perkins, Xiaojun Guan
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-602
Abstract: Deep sequencing technology has enabled discovery of a novel 16-nt RNA sequence in total RNA from human brain that we propose is derived from RNU1, an RNA component of spliceosome assembly. Bioinformatic alignments compel inquiring whether the novel 16-nt sequence or its precursor have a regulatory function as well as determining aspects of how processing intersects with the miRNA biogenesis pathway. Specifically, our preliminary in silico investigations reveal the sequence could regulate splicing factor Arg/Ser rich 1 (SFRS1), a gene coding an essential protein component of the spliceosome. All 16-base source sequences in the UCSC Human Genome Browser are within the 14 instances of RNU1 genes listed in wgEncodeGencodeAutoV3. Furthermore, 10 of the 14 instances of the sequence are also within a common 28-nt hairpin-forming subsequence of RNU1.An abundant 16-nt RNA sequence is sourced from a spliceosomal RNA, lies in a stem of a predicted RNA hairpin, and includes reverse complements of subsequences of the 3'UTR of a gene coding for a spliceosome protein. Thus RNU1 could function both as a component of spliceosome assembly and as inhibitor of production of the essential, spliceosome protein coded by SFRS1. Beyond this example, a general procedure is needed for systematic discovery of multiple alignments of sequencing, splicing, and RNA folding data.The numerous, very dissimilar types of bioinformatic data conspire to make integration a central problem for efficient and effective application of biological findings. Integration of data of three particular types is the goal of this paper. Gene splicing is the focus, held up as an example of how sequencing, splicing, and RNA folding data types might be used to guide research that could illuminate major mechanisms of cell biology such control of levels of ribonucleoprotein species.Function and dysfunction of gene splicing impact embryogenesis, cell motility and viability, cell cycle arrest, and many other mechanisms of met
Discovering collectively informative descriptors from high-throughput experiments
Clark D Jeffries, William O Ward, Diana O Perkins, Fred A Wright
BMC Bioinformatics , 2009, DOI: 10.1186/1471-2105-10-431
Abstract: This paper describes a novel algorithm called BLANKET for symmetric analysis of two experiments that assess informativeness of descriptors. The experiments are required to be related only in that their descriptor sets intersect substantially and their definitions of case and control are consistent. From resulting lists of n descriptors ranked by informativeness, BLANKET determines shortlists of descriptors from each experiment, generally of different lengths p and q. For any pair of shortlists, four numbers are evident: the number of descriptors appearing in both shortlists, in exactly one shortlist, or in neither shortlist. From the associated contingency table, BLANKET computes Right Fisher Exact Test (RFET) values used as scores over a plane of possible pairs of shortlist lengths [1,2]. BLANKET then chooses a pair or pairs with RFET score less than a threshold; the threshold depends upon n and shortlist length limits and represents a quality of intersection achieved by less than 5% of random lists.Researchers seek within a universe of descriptors some minimal subset that collectively and efficiently predicts experimental outcomes. Ideally, any smaller subset should be insufficient for reliable prediction and any larger subset should have little additional accuracy. As a method, BLANKET is easy to conceptualize and presents only moderate computational complexity. Many existing databases could be mined using BLANKET to suggest optimal sets of predictive descriptors.In contemporary high-throughput experiments, very many descriptor values can be measured, leading to the issue of correction for multiple testing to minimize false positives at the cost of a high number of false negatives. Reconciliation entails compromises that are to some extent arbitrary. A deterministic method is needed for selecting a minimal, distinguished set of descriptors that collectively provide effective, efficient prediction. Researchers can subsequently investigate members of such a subset
microRNA expression in the prefrontal cortex of individuals with schizophrenia and schizoaffective disorder
Diana O Perkins, Clark D Jeffries, L Fredrik Jarskog, J Michael Thomson, Keith Woods, Martin A Newman, Joel S Parker, Jianping Jin, Scott M Hammond
Genome Biology , 2007, DOI: 10.1186/gb-2007-8-2-r27
Abstract: We hypothesized that schizophrenia might be associated with altered miRNA profiles. To investigate this possibility we compared the expression of 264 human miRNAs from postmortem prefrontal cortex tissue of individuals with schizophrenia (n = 13) or schizoaffective disorder (n = 2) to tissue of 21 psychiatrically unaffected individuals using a custom miRNA microarray. Allowing a 5% false discovery rate, we found that 16 miRNAs were differentially expressed in prefrontal cortex of patient subjects, with 15 expressed at lower levels (fold change 0.63 to 0.89) and 1 at a higher level (fold change 1.77) than in the psychiatrically unaffected comparison subjects. The expression levels of 12 selected miRNAs were also determined by quantitative RT-PCR in our lab. For the eight miRNAs distinguished by being expressed at lower microarray levels in schizophrenia samples versus comparison samples, seven were also expressed at lower levels with quantitative RT-PCR.This study is the first to find altered miRNA profiles in postmortem prefrontal cortex from schizophrenia patients.Schizophrenia is a common neuropsychiatric disorder affecting one percent of the general population. The personal, familial, and societal costs of the disease are enormous, with chronic symptoms that result in marked functional disability. In fact, approximately three percent of all person-years lived with disability are due to schizophrenia [1].It is clear that schizophrenia has a strong genetic component, although its genetic basis remains unknown [2]. Consistent with a disease mechanism that involves post-transcriptional dysregulation of gene expression, postmortem studies find altered levels of mRNA and proteins rather than a specific abnormal protein [3]. Postmortem studies also find differences between schizophrenia and unaffected comparison subjects in the relationship of such mRNAs and cognate proteins [4,5].microRNAs (miRNAs) are a class of noncoding RNAs (ncRNAs) that in animals regulate gene ex
Magnetic excitations in vanadium spinels
N. B. Perkins,O. Sikora
Physics , 2007, DOI: 10.1103/PhysRevB.76.214434
Abstract: We study magnetic excitations in vanadium spinel oxides AV$_2$O$_4$ (A=Zn, Mg, Cd) using two models: first one is a superexchange model for vanadium S=1 spins, second one includes in addition spin-orbit coupling, and crystal anisotropy. We show that the experimentally observed magnetic ordering can be obtained in both models, however the orbital ordering is different with and without spin-orbit coupling and crystal anisotropy. We demonstrate that this difference strongly affects the spin-wave excitation spectrum above the magnetically ordered state, and argue that the neutron measurement of such dispersion is a way to distinguish between the two possible orbital orderings in AV$_2$O$_4$.
Birthday Inequalities, Repulsion, and Hard Spheres
Will Perkins
Mathematics , 2015,
Abstract: We study a birthday inequality in random geometric graphs: the probability of the empty graph is upper bounded by the product of the probabilities that each edge is absent. We show the birthday inequality holds at low densities, but does not hold in general. We give three different applications of the birthday inequality in statistical physics and combinatorics: we prove lower bounds on the free energy of the hard sphere model and upper bounds on the number of independent sets and matchings of a given size in d-regular graphs. The birthday inequality is implied by a repulsion inequality: the expected volume of the union of spheres of radius r around n randomly placed centers increases if we condition on the event that the centers are at pairwise distance greater than r. Surprisingly we show that the repulsion inequality is not true in general, and in particular that it fails in 24-dimensional Euclidean space: conditioning on the pairwise repulsion of centers of 24-dimensional spheres can decrease the expected volume of their union.
Random k-SAT and the Power of Two Choices
Will Perkins
Computer Science , 2012,
Abstract: We study an Achlioptas-process version of the random k-SAT process: a bounded number of k-clauses are drawn uniformly at random at each step, and exactly one added to the growing formula according to a particular rule. We prove the existence of a rule that shifts the satisfiability threshold. This extends a well-studied area of probabilistic combinatorics (Achlioptas processes) to random CSP's. In particular, while a rule to delay the 2-SAT threshold was known previously, this is the first proof of a rule to shift the threshold of k-SAT for k >= 3. We then propose a gap decision problem based upon this semi-random model. The aim of the problem is to investigate the hardness of the random k-SAT decision problem, as opposed to the problem of finding an assignment or certificate of unsatisfiability. Finally, we discuss connections to the study of Achlioptas random graph processes.
La Autoridad en el caso de una Alianza: Preguntas desde la gestión
Londo?o C,Diana;
Pensamiento & Gestión , 2008,
Abstract: authority as a type of power is the characteristic selected by weber ([1922]1997) for describing the business enterprise. the new institutional economics (nie) has recognized authority as the explanation for the existence of the firms because it permits lowering coordination costs if compared with those of the market. today, cooperation agreements or alliances are common and some new institutional economists have considered the costs of structuring the contracts that make them pos- sible but they have left authority behind and with it, the coordination of activities in those alliances where no new firm is constituted. this subject is the one that is considered, and the analysis of one case is the source for the different questions asked. in the case studied, two parallel authority structures leave areas in which authority becomes diffuse and coordination debilitates.
La Autoridad en el caso de una Alianza: Preguntas desde la gestión
Diana Londo?o C
Pensamiento & Gestión , 2008,
Abstract: La Autoridad como un tipo de poder es la característica seleccionada por Weber ([1922]1997) para describir la empresa capitalista y ésta ha sido reconocida por la economía neoinstitucional como explicación para la existencia de las firmas dada su capacidad para la disminución de costos de coordinación si se compara con los del mercado. Hoy son frecuentes los acuerdos de cooperación, y si bien se ha indagado sobre los costos de estructurar el contrato que los propician, se ha obviado el tema de la autoridad como base de la coordinación, la cual se queda sin sustento en esos tipos de acuerdos en los que no se crea una nueva empresa. Al rededor del tema se plantean preguntas apoyadas en el caso de una alianza en la que dos estructuras paralelas dejan espacios en los cuales la autoridad se desdibuja y se debilita la coordinación. Authority as a type of power is the characteristic selected by Weber ([1922]1997) for describing the business enterprise. The New Institutional Economics (NIE) has recognized authority as the explanation for the existence of the firms because it permits lowering coordination costs if compared with those of the market. Today, cooperation agreements or alliances are common and some New Institutional Economists have considered the costs of structuring the contracts that make them pos- sible but they have left authority behind and with it, the coordination of activities in those alliances where no new firm is constituted. This subject is the one that is considered, and the analysis of one case is the source for the different questions asked. In the case studied, two parallel authority structures leave areas in which authority becomes diffuse and coordination debilitates.
La biodiversidad en la ecorregión de los Llanos de Venezuela y las prioridades para su conservación
Diana Ruiz Brice?o
Ecosistemas , 2004,
Abstract:
Los cambios en el control de mando en las firmas según la teoría de agencia: una hipótesis para explicar el surgimiento del Sindicato Antioque o Los cambios en el control de mando en las firmas según la teoría de agencia: una hipótesis para explicar el surgimiento del Sindicato Antioque o
Diana Londo?o Correa
AD-minister , 2005,
Abstract: En este artículo se sintetizan los planteamientos de la teoría de agencia y se hace énfasis enla vertiente positivista de esta teoría, la cual muestra fortalezas para explicar el surgimientodel Sindicato Antioque o, hoy llamado Grupo Empresarial Antioque o (GEA), uno de losgrandes grupos económicos colombianos. En este trabajo se muestra cómo los intereses delos administradores de las empresas y de un grupo de los accionistas guiaron las actividadesque dieron como resultado el entrecruce de acciones entre empresas a partir del cual se hancoordinado las operaciones de un conjunto de sociedades con sede en Medellín. Este documentoes un subproducto de la investigación “Caracterización del centro corporativo del SindicatoAntioque o” realizada en el marco de la Maestría en Ciencias de la Administración de laUniversidad EAFIT. This paper reviews the main aspects of the agency theory, and emphasizes on the positivist line, which shows strengths in explaining the birth of the Sindicato Antioque o or the Grupo Empresarial Antioque o (GEA), recognized as one of the largest Colombian economic groups. The main conclusion is that the managers’ interests as well as those of a group of shareholders where the ones pursued, and that in the process, cross ownership between the companies were established. This article is a result of the research “Characterization of the Sindicato Antioque os′s Head Quarters”.
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