The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags

Whereas genome sequencing defines the genetic potential of an organism, transcript sequencing defines the utilization of this potential and links the genome with most areas of biology. To exploit the information within the human genome in the fight against cancer, we have deposited some two million expressed sequence tags (ESTs) from human tumors and their corresponding normal tissues in the public databases. The data currently define approximate to23,500 genes, of which only approximate to1,250 are still represented only by ESTs. Examination of the EST coverage of known cancer-related (CR) genes reveals that <1% do not have corresponding ESTs, indicating that the representation of genes associated with commonly studied tumors is high. The careful recording of the origin of all ESTs we have produced has enabled detailed definition of where the genes they represent are expressed in the human body. More than 100,000 ESTs are available for seven tissues, indicating a surprising variability of gene usage that has led to the discovery of a significant number of genes with restricted expression, and that may thus be therapeutically useful. The ESTs also reveal novel nonsynonymous germline variants (although the one-pass nature of the data necessitates careful validation) and many alternatively spliced transcripts. Although widely exploited by the scientific community, vindicating our totally open source policy, the EST data generated still provide extensive information that remains to be systematically explored, and that may further facilitate progress toward both the understanding and treatment of human cancers.

An alternative modal representation of a symmetrical nontransposed three-phase transmission line

The objective of this letter is to propose an alternative modal representation of a nontransposed three-phase transmission line with a vertical symmetry plane by using two transformation matrices. Initially, Clarke's matrix is used to separate the line into components a, 0, and zero. Because a and zero components are not exact modes, they can be considered as being a two-phase line that will be decomposed in its exact modes by using a 2 x 2 modal transformation matrix. This letter will describe the characteristics of the two-phase line before mentioned. This modal representation is applied to decouple a nontransposed three-phase transmission line with a vertical symmetry plane whose nominal voltage is 440 kV.

Modal representation of three-phase lines applying two transformation matrices: Evaluation of its eigenvectors

The objective of this paper is to show an alternative representation in time domain of a non-transposed three-phase transmission line decomposed in its exact modes by using two transformation matrices. The first matrix is Clarke's matrix that is real, frequency independent, easily represented in computational transient programs (EMTP) and separates the line into Quasi-modes alpha, beta and zero. After that, Quasi-modes a and zero are decomposed into their exact modes by using a modal transformation matrix whose elements can be synthesized in time domain through standard curve-fitting techniques. The main advantage of this alternative representation is to reduce the processing time because a frequency dependent modal transformation matrix of a three-phase line has nine elements to be represented in time domain while a modal transformation matrix of a two-phase line has only four elements. This paper shows modal decomposition process and eigenvectors of a nontransposed three-phase line with a vertical symmetry plane whose nominal voltage is 440 kV and line length is 500 km.

A procedure to estimate parameters of a line segment taking into account its representation through pi circuits: Theoretical development

The objective of this paper is to show an alternative methodology to estimate per unit length parameters of a line segment of a transmission line. With this methodology the line segment parameters can be obtained starting from the phase currents and -voltages in receiving and sending end of the line segment. If the line segment is represented as being one or more pi circuits whose frequency dependent parameters are considered lumped, its impedance and admittance can be easily expressed as functions of the currents and voltages at the sending and receiving end. Because we are supposing that voltages and currents at the sending and receiving end of the tine segment (in frequency domain) are known, it is possible to obtains its impedance and admittance and consequently its per unit length longitudinal and transversal parameters. The procedure will be applied to estimate the longitudinal and transversal parameters of a small segment of a single-phase line that is already built.

Analyses of the modifications in the pi circuits for inclusion of frequency influence in transmission line representation

In this article, it is represented by state variables phase a transmission line which parameters are considered frequency independently and frequency dependent. It is analyzed what is the reasonable number of pi circuits and the number of blocks composed by parallel resistor and inductor in parallel for reduction of numerical oscillations. It is simulated the numerical routine with and without the effect of frequency in the longitudinal parameters. Initially, it is used state variables and pi circuits representing the transmission line composing a linear system which is solved by numerical routines based on the trapezoidal rule. The effect of frequency on the line is synthesized by resistors and inductors in parallel and this representation is analyzed in details. It is described transmission lines and the frequency influence in these lines through the state variables.

A stochastic shift model for economically designed charts constrained by the process stage configuration

An economic model including the labor resource and the process stage configuration is proposed to design g charts allowing for all the design parameters to be varied in an adaptive way. A random shift size is considered during the economic design selection. The results obtained for a benchmark of 64 process stage scenarios show that the activities configuration and some process operating parameters influence the selection of the best control chart strategy: to model the random shift size, its exact distribution can be approximately fitted by a discrete distribution obtained from a relatively small sample of historical data. However, an accurate estimation of the inspection costs associated to the SPC activities is far from being achieved. An illustrative example shows the implementation of the proposed economic model in a real industrial case. (C) 2011 Elsevier B.V. All rights reserved.

Knowledge Representation and Orthophemism: A Reflection Aiming to a Concept

Characteristics of speech, especially figures of speech, are used by specific communities or domains, and, in this way, reflect their identities through their choice of vocabulary. This topic should be an object of study in the context of knowledge representation once it deals with different contexts of production of documents. This study aims to explore the dimensions of the concepts of euphemism, dysphemism, and orthophemism, focusing on the latter with the goal of extracting a concept which can be included in discussions about subject analysis and indexing. Euphemism is used as an alternative to a non-preferred expression or as an alternative to an offensive attribution-to avoid potential offense taken by the listener or by other persons, for instance, pass away. Dysphemism, on the other hand, is used by speakers to talk about people and things that frustrate and annoy them-their choice of language indicates disapproval and the topic is therefore denigrated, humiliated, or degraded, for instance, kick the bucket. While euphemism tries to make something sound better, dysphemism tries to make something sound worse. Orthophemism (Allan and Burridge 2006) is also used as an alternative to expressions, but it is a preferred, formal, and direct language of expression when representing an object or a situation, for instance, die. This paper suggests that the comprehension and use of such concepts could support the following issues: possible contributions from linguistics and terminology to subject analysis as demonstrated by Talamo et al. (1992); decrease of polysemy and ambiguity of terms used to represent certain topics of documents; and construction and evaluation of indexing languages. The concept of orthophemism can also serves to support associative relationships in the context of subject analysis, indexing, and even information retrieval related to more specific requests.

A GEOGRAPHICAL REPRESENTATION IN Coats of arms of LATIN AMERICA

This article seeks to reflect on geographic representation in the coats of arms of countries in Latin America, showing how the physical, aspects of the landscape, the elements of the economy and the republican symbols were used by local elites to compose an imaginary nation in the nineteenth century. This process of "naturalization of territory" was used as an important feature in the national discourse, because this time, in most cases, the Latin American nations were composed of multi-ethnic states, with strong differences of class and a large illiterate population plus a very tenuous territory from the point of view of national integration. Thus, the elements related to geographic image through the use of coats of arms, conveyed strong messages to citizens, showing how these heraldic symbols can become an important source of research to unravel the process of building the imaginary nation.

Stochastic field processes in the mathematical modelling of damped transmission line vibrations

Wind-excited vibrations in the frequency range of 10 to 50 Hz due to vortex shedding often cause fatigue failures in the cables of overhead transmission lines. Damping devices, such as the Stockbridge dampers, have been in use for a long time for supressing these vibrations. The dampers are conveniently modelled by means of their driving point impedance, measured in the lab over the frequency range under consideration. The cables can be modelled as strings with additional small bending stiffness. The main problem in modelling the vibrations does however lay in the aerodynamic forces, which usually are approximated by the forces acting on a rigid cylinder in planar flow. In the present paper, the wind forces are represented by stochastic processes with arbitrary crosscorrelation in space; the case of a Kármán vortex street on a rigid cylinder in planar flow is contained as a limit case in this approach. The authors believe that this new view of the problem may yield useful results, particularly also concerning the reliability of the lines and the probability of fatigue damages. © 1987.

Squeezed states phase space representation and semiclassical approximations in many-body systems

We derive an alternative semiclassical approach (to the Wigner-Kirkwood method) for many-body systems using a mapping scheme based on the squeezed states phase space representation. The new expansion is applied to the usual harmonic oscillator case and the differences with the Wigner-Kirkwood results are discussed. © 1990.

Entropy, information and doubly stochastic transformations

I analyze two inequalities on entropy and information, one due to von Neumann and a recent one to Schiffer, and show that the relevant quantities in these inequalities are related by special doubly stochastic matrices (DSM). I then use generalization of the first inequality to prove algebraically a generalization of Schiffer's inequality to arbitrary DSM. I also give a second interpretation to the latter inequality, determine its domain of applicability, and illustrate it by using Zeeman splitting. This example shows that symmetric (degenerate) systems have less entropy than the corresponding split systems, if compared at the same average energy. This seemingly counter-intuitive result is explained thermodynamically. © 1991.

Extended Hierarchical Censored Production Rules (EHCPRs) system: An approach toward generalized knowledge representation

One common problem in all basic techniques of knowledge representation is the handling of the trade-off between precision of inferences and resource constraints, such as time and memory. Michalski and Winston (1986) suggested the Censored Production Rule (CPR) as an underlying representation and computational mechanism to enable logic based systems to exhibit variable precision in which certainty varies while specificity stays constant. As an extension of CPR, the Hierarchical Censored Production Rules (HCPRs) system of knowledge representation, proposed by Bharadwaj & Jain (1992), exhibits both variable certainty as well as variable specificity and offers mechanisms for handling the trade-off between the two. An HCPR has the form: Decision If(preconditions) Unless(censor) Generality(general_information) Specificity(specific_information). As an attempt towards evolving a generalized knowledge representation, an Extended Hierarchical Censored Production Rules (EHCPRs) system is suggested in this paper. With the inclusion of new operators, an Extended Hierarchical Censored Production Rule (EHCPR) takes the general form: Concept If (Preconditions) Unless (Exceptions) Generality (General-Concept) Specificity (Specific Concepts) Has_part (default: structural-parts) Has_property (default:characteristic-properties) Has_instance (instances). How semantic networks and frames are represented in terms of an EHCPRs is shown. Multiple inheritance, inheritance with and without cancellation, recognition with partial match, and a few default logic problems are shown to be tackled efficiently in the proposed system.

The gradually truncated Lévy flight: Stochastic process for complex systems

Power-law distributions, i.e. Levy flights have been observed in various economical, biological, and physical systems in high-frequency regime. These distributions can be successfully explained via gradually truncated Levy flight (GTLF). In general, these systems converge to a Gaussian distribution in the low-frequency regime. In the present work, we develop a model for the physical basis for the cut-off length in GTLF and its variation with respect to the time interval between successive observations. We observe that GTLF automatically approach a Gaussian distribution in the low-frequency regime. We applied the present method to analyze time series in some physical and financial systems. The agreement between the experimental results and theoretical curves is excellent. The present method can be applied to analyze time series in a variety of fields, which in turn provide a basis for the development of further microscopic models for the system. © 2000 Elsevier Science B.V. All rights reserved.

Economic viability and selection of irrigation systems using simulation and stochastic dominance

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)