Folding and insertion of transmembrane helices at the ER

In eukaryotic cells, the endoplasmic reticulum (ER) is the entry point for newly synthesized proteins that are subsequently distributed to organelles of the endomembrane system. Some of these proteins are completely translocated into the lumen of the ER while others integrate stretches of amino acids into the greasy 30 Å wide interior of the ER membrane bilayer. It is generally accepted that to exist in this non-aqueous environment the majority of membrane integrated amino acids are primarily non-polar/hydrophobic and adopt an α-helical conformation. These stretches are typically around 20 amino acids long and are known as transmembrane (TM) helices. In this review, we will consider how transmembrane helices achieve membrane integration. We will address questions such as: Where do the stretches of amino acids fold into a helical conformation? What is/are the route/routes that these stretches take from synthesis at the ribosome to integration through the ER translocon? How do these stretches 'know' to integrate and in which orientation? How do marginally hydrophobic stretches of amino acids integrate and survive as transmembrane helices

New Inheritance Models That Facilitate Source Code Reuse in Object-oriented Programming

Code reusability is a primary objective in the development of software systems. The object-oriented programming methodology is one of the areas that facilitate the development of software systems by allowing and promoting code reuse and modular designs. Object-oriented programming languages (OOPLs) provide different facilities to attain efficient reuse and reliable extension of existing software components. Inheritance is an important language feature that is conducive to reusability and extensibility. Various OOPLs provide different inheritance models based on different interpretations of the inheritance notion. Therefore, OOPLs have different characteristics derived from their respective inheritance models. This dissertation is concerned with solutions for three major problems that limit the utilization of inheritance for code reusability. The range of object -oriented applications and thus the usage of object-oriented programming in general is also discussed. The three major problems are: 1) the relationship between inheritance and other related issues such as encapsulation, access techniques, visibility of inheritance, and subtyping; 2) the hierarchical structure imposed by inheritance among classes; and 3) the accessibility of previous versions of the modified methods defmed in classes located at higher levels of the inheritance structure than the parent classes. 1be proposed solutions for these problems are presented as new inheritance models that facilitate code reuse and relax the restrictions imposed on inheritance models by languages. A survey and taxonomy of the conventional inheritance models, and a comparison and analysis of some of the common OOPLs are also presented in the dissertation.Computer Scienc

FROM MUSIC INFORMATION RETRIEVAL (MIR) TO INFORMATION RETRIEVAL FOR MUSIC (IRM)

This thesis reviews and discusses certain techniques from the domain of (Music) Information Retrieval, in particular some general data mining algorithms. It also describes their specific adaptations for use as building blocks in the CACE4 software application. The use of Augmented Transition Networks (ATN) from the field of (Music) Information Retrieval is, to a certain extent, adequate as long as one keeps the underlying tonal constraints and rules as a guide to understanding the structure one is looking for. However since a large proportion of algorithmic music, including music composed by the author, is atonal, tonal constraints and rules are of little use. Analysis methods from Hierarchical Clustering Techniques (HCT) such as k-means and Expectation-Maximisation (EM) facilitate other approaches and are better suited for finding (clustered) structures in large data sets. ART2 Neural Networks (Adaptive Resonance Theory) for example, can be used for analysing and categorising these data sets. Statistical tools such as histogram analysis, mean, variance as well as correlation calculations can provide information about connections between members in a data set. Altogether this provides a diverse palette of usable data analysis methods and strategies for creating algorithmic atonal music. Now acting as (software) strategy tools, their use is determined by the quality of their output within a musical context, as demonstrated when developed and programmed into the Computer Assisted Composition Environment: CACE4. Music Information Retrieval techniques are therefore inverted: their specific techniques and associated methods of Information Retrieval and general data mining are used to access the organisation and constraints of abstract (non-specific musical) data in order to use and transform it in a musical composition

Unanswered Questions in the Electroweak Theory

This article is devoted to the status of the electroweak theory on the eve of experimentation at CERN's Large Hadron Collider. A compact summary of the logic and structure of the electroweak theory precedes an examination of what experimental tests have established so far. The outstanding unconfirmed prediction of the electroweak theory is the existence of the Higgs boson, a weakly interacting spin-zero particle that is the agent of electroweak symmetry breaking, the giver of mass to the weak gauge bosons, the quarks, and the leptons. General arguments imply that the Higgs boson or other new physics is required on the TeV energy scale. Indirect constraints from global analyses of electroweak measurements suggest that the mass of the standard-model Higgs boson is less than 200 GeV. Once its mass is assumed, the properties of the Higgs boson follow from the electroweak theory, and these inform the search for the Higgs boson. Alternative mechanisms for electroweak symmetry breaking are reviewed, and the importance of electroweak symmetry breaking is illuminated by considering a world without a specific mechanism to hide the electroweak symmetry. For all its triumphs, the electroweak theory has many shortcomings. . . .Comment: 31 pages, 20 figures; prepared for Annual Review of Nuclear and Particle Science (minor changes

Designing Scalable Networks for Future Large Datacenters

Modern datacenters require a network with high cross-section bandwidth, fine-grained security, support for virtualization, and simple management that can scale to hundreds of thousands of hosts at low cost. This thesis first presents the firmware for Rain Man, a novel datacenter network architecture that meets these requirements, and then performs a general scalability study of the design space. The firmware for Rain Man, a scalable Software-Defined Networking architecture, employs novel algorithms and uses previously unused forwarding hardware. This allows Rain Man to scale at high performance to networks of forty thousand hosts on arbitrary network topologies. In the general scalability study of the design space of SDN architectures, this thesis identifies three different architectural dimensions common among the networks: source versus hop-by-hop routing, the granularity at which flows are routed, and arbitrary versus restrictive routing and finds that a source-routed, host-pair granularity network with arbitrary routes is the most scalable

Meson and baryon spectrum for QCD with two light dynamical quarks

We present results of meson and baryon spectroscopy using the Chirally Improved Dirac operator on lattices of size 16**3 x 32 with two mass-degenerate light sea quarks. Three ensembles with pion masses of 322(5), 470(4) and 525(7) MeV and lattice spacings close to 0.15 fm are investigated. Results on ground and excited states for several channels are given, including spin two mesons and hadrons with strange valence quarks. The analysis of the states is done with the variational method, including two kinds of Gaussian sources and derivative sources. We obtain several ground states fairly precisely and find radial excitations in various channels. Excited baryon results seem to suffer from finite size effects, in particular at small pion masses. We discuss the possible appearance of scattering states in various channels, considering masses and eigenvectors. Partially quenched results in the scalar channel suggest the presence of a 2-particle state, however, in most channels we cannot identify them. Where available, we compare our results to results of quenched simulations using the same action.Comment: 27 pages, 29 figures, 11 table

Suporte de parallel scan em OpenMP

Orientadores: Guido Costa Souza de Araújo, Marcio Machado PereiraDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: Prefix Scan (ou simplesmente scan) é um operador que computa todas as somas parciais de um vetor. A operação scan retorna um vetor onde cada elemento é a soma de todos os elementos precedentes até a posição correspondente. Scan é uma operação fundamental para muitos problemas relevantes, tais como: algoritmos de ordenação, análise léxica, comparação de cadeias de caracteres, filtragem de imagens, dentre outros. Embora exis- tam bibliotecas que fornecem versões paralelizadas de scan em CUDA e OpenCL, não existe uma implementação paralela do operador scan em OpenMP. Este trabalho propõe uma nova clausula que permite o uso automático do scan paralelo. Ao usar a cláusula pro- posta, um programador pode reduzir consideravelmente a complexidade dos algoritmos, permitindo que ele concentre a atenção no problema, e não em aprender novos modelos de programação paralela ou linguagens de programação. Scan foi projetado em ACLang (www.aclang.org), um framework de código aberto baseado no compilador LLVM/Clang, que recentemente implementou o OpenMP 4.X Accelerator Programming Model . AClang converte regiões do programa de OpenMP 4.X para OpenCL. Experimentos com um con- junto de algoritmos baseados em Scan foram executados nas GPUs da NVIDIA, Intel e ARM, e mostraram que o desempenho da clausula proposta é equivalente ao alcan- çado pela biblioteca de OpenCL, mas com a vantagem de uma menor complexidade para escrever o códigoAbstract: Prefix Scan (or simply scan) is an operator that computes all the partial sums of a vec- tor. A scan operation results in a vector where each element is the sum of the preceding elements in the original vector up to the corresponding position. Scan is a key opera- tion in many relevant problems like sorting, lexical analysis, string comparison, image filtering among others. Although there are libraries that provide hand-parallelized im- plementations of the scan in CUDA and OpenCL, no automatic parallelization solution exists for this operator in OpenMP. This work proposes a new clause to OpenMP which enables the automatic synthesis of the parallel scan. By using the proposed clause a programmer can considerably reduce the complexity of designing scan based algorithms, thus allowing he/she to focus the attention on the problem and not on learning new paral- lel programming models or languages. Scan was designed in AClang (www.aclang.org), an open-source LLVM/Clang compiler framework that implements the recently released OpenMP 4.X Accelerator Programming Model. AClang automatically converts OpenMP 4.X annotated program regions to OpenCL. Experiments running a set of typical scan based algorithms on NVIDIA, Intel, and ARM GPUs reveal that the performance of the proposed OpenMP clause is equivalent to that achieved when using OpenCL library calls, with the advantage of a simpler programming complexityMestradoCiência da ComputaçãoMestre em Ciência da ComputaçãoCAPE