Significance analysis of microarrays applied to the ionizing radiation response

Microarrays can measure the expression of thousands of genes to identify changes in expression between different biological states. Methods are needed to determine the significance of these changes while accounting for the enormous number of genes. We describe a method, Significance Analysis of Microarrays (SAM), that assigns a score to each gene on the basis of change in gene expression relative to the standard deviation of repeated measurements. For genes with scores greater than an adjustable threshold, SAM uses permutations of the repeated measurements to estimate the percentage of genes identified by chance, the false discovery rate (FDR). When the transcriptional response of human cells to ionizing radiation was measured by microarrays, SAM identified 34 genes that changed at least 1.5-fold with an estimated FDR of 12%, compared with FDRs of 60 and 84% by using conventional methods of analysis. Of the 34 genes, 19 were involved in cell cycle regulation and 3 in apoptosis. Surprisingly, four nucleotide excision repair genes were induced, suggesting that this repair pathway for UV-damaged DNA might play a previously unrecognized role in repairing DNA damaged by ionizing radiation.

Random circular permutation of genes and expressed polypeptide chains: application of the method to the catalytic chains of aspartate transcarbamoylase.

Recent studies on proteins whose N and C termini are in close proximity have demonstrated that folding of polypeptide chains and assembly of oligomers can be accomplished with circularly permuted chains. As yet no methodical study has been conducted to determine how extensively new termini can be introduced and where such termini cannot be tolerated. We have devised a procedure to generate random circular permutations of the catalytic chains of Escherichia coli aspartate transcarbamoylase (ATCase; EC 2.1.3.2) and to select clones that produce active or stable holoenzyme containing permuted chains. A tandem gene construct was made, based on the desired linkage between amino acid residues in the C- and N-terminal regions of the polypeptide chain, and this DNA was treated with a suitable restriction enzyme to yield a fragment containing the rearranged coding sequence for the chain. Circularization achieved with DNA ligase, followed by linearization at random with DNase I, and incorporation of the linearized, repaired, blunt-ended, rearranged genes into a suitable plasmid permitted the expression of randomly permuted polypeptide chains. The plasmid with appropriate stop codons also contained pyrI, the gene encoding the regulatory chain of ATCase. Colonies expressing detectable amounts of ATCase-like molecules containing permuted catalytic chains were identified by an immunoblot technique or by their ability to grow in the absence of pyrimidines in the growth medium. Sequencing of positive clones revealed a variety of novel circular permutations. Some had N and C termini within helices of the wild-type enzyme as well as deletions and insertions. Permutations were concentrated in the C-terminal domain and only few were detected in the N-terminal domain. The technique, which is adaptable generally to proteins whose N and C termini are near each other, can be of value in relating in vivo folding of nascent, growing polypeptide chains to in vitro renaturation of complete chains and determining the role of protein sequence in folding kinetics.

Inovação e indústria da moda: um modelo de inovação em estilos e tendências.

Este trabalho tem como intuito propor um modelo de inovação para a indústria da moda feminina. O modelo visa compreender o comportamento de estilos e tendências determinados e difundidos pelas empresas. A construção deste modelo é justificada pela contribuição que um estudo sobre inovação pode proporcionar à indústria da moda, a qual enfrenta baixos padrões de competitividade no mercado externo e interno. Além disso, embora existam muitos artigos sobre o assunto, poucos foram os modelos de inovação para a indústria da moda encontrados por esta pesquisa. Uma avaliação destes modelos indicou que existe espaço para a proposta de um modelo que aborde o comportamento de estilos e tendências ao longo do tempo. A estrutura de composição do modelo é sustentada por três pilares conceituais: teoria econômica neoschumpeteriana, modelos de inovação e modelos de inovação para a indústria da moda. A característica central do modelo é avaliar se existem estilos que permanecem em moda de maneira contínua ou descontínua. Como existe similaridade conceitual entre os estilos, no que se refere à identidade de gênero (androginia e feminilidade), foi efetuada uma aglutinação de alguns estilos dentro desta denominação. Nem todos os estilos se encaixaram nesta classificação. Então, estes estilos foram denominados como neutros. Como a pesquisa tem abordagem fenomenológica, qualitativa e longitudinal, foi adotada a metodologia hipotética dedutiva para a construção do modelo. Para verificação da validade das hipóteses foi usada uma análise exploratória dos dados por meio de estatística descritiva e decomposição da estrutura de variabilidade através de uma análise de componentes principais (PCA). Ambas as análises forneceram evidências a respeito das hipóteses em questão, as quais também foram testadas através de um teste binomial e de uma análise de variância multivariada por meio de permutações. Os resultados comprovaram que existem estilos que permanecem em moda de maneira contínua e que existem períodos de polarização das aglutinações de estilo.

Reinterpreting Coatlicue : the Sculptural Narrative of Defeat at the Shrine of Huitzilopochtli

"Images of the decapitated, dismembered female warrior Coyolxauhqui, a main character in the Mexica mythology of Huitzilopochtli, figured prominently in Imperial Mexica sculptural campaigns at the Templo Mayor. However, monoliths of a terrifying, dismembered female from the shrine have traditionally been identified as Huitzilopochtli’s nurturing mother Coatlicue, or permutations of goddesses. Such studies do not adequately address why these sculptures depict mutilated beings whose characteristics are antithetical to Coatlicue’s appropriate female behavior depicted in myths and images"

A study of data manipulation algorithms in magnetic bubble memories /

Thesis--Illinois.

Choice and chance with 1000 exercises,

Mode of access: Internet.

Lehrbegriff der syntactik, oder combinationslehre.

"Literatur der Syntactik": p. [529]-541.

Choice and chance, with 1000 exercises.

Mode of access: Internet.

Sammlung combinatorisch-analytischer abhandlungen /

Mode of access: Internet.

Formal group laws and hypergraph colorings

Thesis (Ph.D.)--University of Washington, 2016-06

Structure and folding of potato type II proteinase inhibitors: Circular permutation and intramolecular domain swapping

Potato type II serine proteinase inhibitors are proteins that consist of multiple sequence repeats, and exhibit a multidomain structure. The structural domains are circular permutations of the repeat sequence.. as a result or intramolecular domain swapping. Structural studies give indications for the origins of this folding behaviour, and the evolution of the inhibitor family.

Continuous-variable quantum-state sharing via quantum disentanglement

Quantum-state sharing is a protocol where perfect reconstruction of quantum states is achieved with incomplete or partial information in a multipartite quantum network. Quantum-state sharing allows for secure communication in a quantum network where partial information is lost or acquired by malicious parties. This protocol utilizes entanglement for the secret-state distribution and a class of quantum disentangling protocols for the state reconstruction. We demonstrate a quantum-state sharing protocol in which a tripartite entangled state is used to encode and distribute a secret state to three players. Any two of these players can collaborate to reconstruct the secret state, while individual players obtain no information. We investigate a number of quantum disentangling processes and experimentally demonstrate quantum-state reconstruction using two of these protocols. We experimentally measure a fidelity, averaged over all reconstruction permutations, of F=0.73 +/- 0.02. A result achievable only by using quantum resources.

Dynamic response: Real-time adaptation for music emotion

Music plays an enormous role in today's computer games; it serves to elicit emotion, generate interest and convey important information. Traditional gaming music is fixed at the event level, where tracks loop until a state change is triggered. This behaviour however does not reflect musically the in-game state between these events. We propose a dynamic music environment, where music tracks adjust in real-time to the emotion of the in-game state. We are looking to improve the affective response to symbolic music through the modification of structural and performative characteristics through the application of rule-based techniques. In this paper we undertake a multidiscipline approach, and present a series of primary music-emotion structural rules for implementation. The validity of these rules was tested in small study involving eleven participants, each listening to six permutations from two musical works. Preliminary results indicate that the environment was generally successful in influencing the emotion of the musical works for three of the intended four directions (happier, sadder & content/dreamier). Our secondary aim of establishing that the use of music-emotion rules, sourced predominantly from Western classical music, could be applied with comparable results to modern computer gaming music was also largely successfully.

Recovery of multiple amplitude levels from a DQPSK NRZ signal using a single Mach-Zehnder Interferometer

In this research the recovery of a DQPSK signal will be demonstrated using a single Mach-Zehnder Interferometer (MZI). By changing the phase delay in one of the arms it will be shown that different delays will produce different output levels. It will also be shown that with a certain level of phase shift the DQPSK signal can be converted into four different equally spaced optical power levels. With each decoded level representing one of the four possible bit permutations. By using this additional phase shift in one of the arms the number of MZIs required for decoding can be reduced from two to one.

An Effective Exact Algorithm for One Particular Case of the Travelling-Salesman Problem

The article presents the exact algorithm for solving one case of the job-scheduling problem for the case when the source matrix is ordered by rows.