Identification of cancer/testis-antigen genes by massively parallel signature sequencing.

Massively parallel signature sequencing (MPSS) generates millions of short sequence tags corresponding to transcripts from a single RNA preparation. Most MPSS tags can be unambiguously assigned to genes, thereby generating a comprehensive expression profile of the tissue of origin. From the comparison of MPSS data from 32 normal human tissues, we identified 1,056 genes that are predominantly expressed in the testis. Further evaluation by using MPSS tags from cancer cell lines and EST data from a wide variety of tumors identified 202 of these genes as candidates for encoding cancer/testis (CT) antigens. Of these genes, the expression in normal tissues was assessed by RT-PCR in a subset of 166 intron-containing genes, and those with confirmed testis-predominant expression were further evaluated for their expression in 21 cancer cell lines. Thus, 20 CT or CT-like genes were identified, with several exhibiting expression in five or more of the cancer cell lines examined. One of these genes is a member of a CT gene family that we designated as CT45. The CT45 family comprises six highly similar (>98% cDNA identity) genes that are clustered in tandem within a 125-kb region on Xq26.3. CT45 was found to be frequently expressed in both cancer cell lines and lung cancer specimens. Thus, MPSS analysis has resulted in a significant extension of our knowledge of CT antigens, leading to the discovery of a distinctive X-linked CT-antigen gene family.

C4 Photosynthesis evolved in grasses via parallel adaptive genetic changes.

Phenotypic convergence is a widespread and well-recognized evolutionary phenomenon. However, the responsible molecular mechanisms remain often unknown mainly because the genes involved are not identified. A well-known example of physiological convergence is the C4 photosynthetic pathway, which evolved independently more than 45 times [1]. Here, we address the question of the molecular bases of the C4 convergent phenotypes in grasses (Poaceae) by reconstructing the evolutionary history of genes encoding a C4 key enzyme, the phosphoenolpyruvate carboxylase (PEPC). PEPC genes belong to a multigene family encoding distinct isoforms of which only one is involved in C4 photosynthesis [2]. By using phylogenetic analyses, we showed that grass C4 PEPCs appeared at least eight times independently from the same non-C4 PEPC. Twenty-one amino acids evolved under positive selection and converged to similar or identical amino acids in most of the grass C4 PEPC lineages. This is the first record of such a high level of molecular convergent evolution, illustrating the repeatability of evolution. These amino acids were responsible for a strong phylogenetic bias grouping all C4 PEPCs together. The C4-specific amino acids detected must be essential for C4 PEPC enzymatic characteristics, and their identification opens new avenues for the engineering of the C4 pathway in crops.

Corpus Oral Dialectal (COD). Presentació

Aquest document conté el text Presentació, una introducció al CD del Corpus Oral Dialectal (COD). El COD és un component del Corpus de Català Contemporani de la Universitat de Barcelona (CCCUB), un arxiu de corpus de llengua catalana oral contemporània que ha estat confegit pel grup de recerca Grup d'Estudi de la Variació (GEV) amb la finalitat de contribuir a l'estudi de la variació dialectal, social i funcional en la llengua catalana. Una selecció de materials del CCCUB ha estat dipositada al RECERCAT (Dipòsit de la Recerca de Catalunya, www.recercat.net), i també és accessible a través del web del CCCUB: http://www.ub.edu/cccub.

Corpus Oral Dialectal (COD). Presentation_English

Aquest document conté el text Presentation_English, una introducció en anglès al CD del Corpus Oral Dialectal (COD). El COD és un component del Corpus de Català Contemporani de la Universitat de Barcelona (CCCUB), un arxiu de corpus de llengua catalana oral contemporània que ha estat confegit pel grup de recerca Grup d'Estudi de la Variació (GEV) amb la finalitat de contribuir a l'estudi de la variació dialectal, social i funcional en la llengua catalana. Aquest i altres materials del CCCUB són accessibles directament al Dipòsit UB o a través del web del CCCUB (http://www.ub.edu/cccub).

Corpus Oral Dialectal (COD). Presentation_English

Aquest document conté el text Presentation_English, una introducció en anglès al CD del Corpus Oral Dialectal (COD). El COD és un component del Corpus de Català Contemporani de la Universitat de Barcelona (CCCUB), un arxiu de corpus de llengua catalana oral contemporània que ha estat confegit pel grup de recerca Grup d'Estudi de la Variació (GEV) amb la finalitat de contribuir a l'estudi de la variació dialectal, social i funcional en la llengua catalana. Aquest i altres materials del CCCUB són accessibles directament al Dipòsit UB o a través del web del CCCUB (http://www.ub.edu/cccub).

Corpus Oral Dialectal (COD). Presentation_English

Aquest document conté el text Presentation_English, una introducció en anglès al CD del Corpus Oral Dialectal (COD). El COD és un component del Corpus de Català Contemporani de la Universitat de Barcelona (CCCUB), un arxiu de corpus de llengua catalana oral contemporània que ha estat confegit pel grup de recerca Grup d'Estudi de la Variació (GEV) amb la finalitat de contribuir a l'estudi de la variació dialectal, social i funcional en la llengua catalana. Aquest i altres materials del CCCUB són accessibles directament al Dipòsit UB o a través del web del CCCUB (http://www.ub.edu/cccub).

Corpus Oral Dialectal (COD). Presentació

Aquest document conté el text Presentació, una introducció al CD del Corpus Oral Dialectal (COD). El COD és un component del Corpus de Català Contemporani de la Universitat de Barcelona (CCCUB), un arxiu de corpus de llengua catalana oral contemporània que ha estat confegit pel grup de recerca Grup d'Estudi de la Variació (GEV) amb la finalitat de contribuir a l'estudi de la variació dialectal, social i funcional en la llengua catalana. Una selecció de materials del CCCUB ha estat dipositada al RECERCAT (Dipòsit de la Recerca de Catalunya, www.recercat.net), i també és accessible a través del web del CCCUB: http://www.ub.edu/cccub.

Corpus Oral Dialectal (COD). Presentation_English

Aquest document conté el text Presentation_English, una introducció en anglès al CD del Corpus Oral Dialectal (COD). El COD és un component del Corpus de Català Contemporani de la Universitat de Barcelona (CCCUB), un arxiu de corpus de llengua catalana oral contemporània que ha estat confegit pel grup de recerca Grup d'Estudi de la Variació (GEV) amb la finalitat de contribuir a l'estudi de la variació dialectal, social i funcional en la llengua catalana. Aquest i altres materials del CCCUB són accessibles directament al Dipòsit UB o a través del web del CCCUB (http://www.ub.edu/cccub).

Corpus Oral Dialectal (COD). Caràtula

Aquest document conté la imatge de la caràtula del CD "COD. Corpus Oral Dialectal". El COD és un component del Corpus de Català Contemporani de la Universitat de Barcelona (CCCUB), un arxiu de corpus de llengua catalana oral contemporània que ha estat confegit pel grup de recerca Grup d'Estudi de la Variació (GEV) amb la finalitat de contribuir a l'estudi de la variació dialectal, social i funcional en la llengua catalana. Aquest i altres materials del CCCUB són accessibles directament al Dipòsit Digital de la UB (http://diposit.ub.edu) o a través del web del CCCUB (http://www.ub.edu/cccub).

Corpus Oral Dialectal (COD). Presentation_English

Aquest document conté el text Presentation_English, una introducció en anglès al CD del Corpus Oral Dialectal (COD). El COD és un component del Corpus de Català Contemporani de la Universitat de Barcelona (CCCUB), un arxiu de corpus de llengua catalana oral contemporània que ha estat confegit pel grup de recerca Grup d'Estudi de la Variació (GEV) amb la finalitat de contribuir a l'estudi de la variació dialectal, social i funcional en la llengua catalana. Aquest i altres materials del CCCUB són accessibles directament al Dipòsit UB o a través del web del CCCUB (http://www.ub.edu/cccub).

Corpus Oral Dialectal (COD). Presentation_English

Aquest document conté el text Presentation_English, una introducció en anglès al CD del Corpus Oral Dialectal (COD). El COD és un component del Corpus de Català Contemporani de la Universitat de Barcelona (CCCUB), un arxiu de corpus de llengua catalana oral contemporània que ha estat confegit pel grup de recerca Grup d'Estudi de la Variació (GEV) amb la finalitat de contribuir a l'estudi de la variació dialectal, social i funcional en la llengua catalana. Aquest i altres materials del CCCUB són accessibles directament al Dipòsit UB o a través del web del CCCUB (http://www.ub.edu/cccub).

Data-parallel computation in parallel and distributed environments

The past few decades have seen a considerable increase in the number of parallel and distributed systems. With the development of more complex applications, the need for more powerful systems has emerged and various parallel and distributed environments have been designed and implemented. Each of the environments, including hardware and software, has unique strengths and weaknesses. There is no single parallel environment that can be identified as the best environment for all applications with respect to hardware and software properties. The main goal of this thesis is to provide a novel way of performing data-parallel computation in parallel and distributed environments by utilizing the best characteristics of difference aspects of parallel computing. For the purpose of this thesis, three aspects of parallel computing were identified and studied. First, three parallel environments (shared memory, distributed memory, and a network of workstations) are evaluated to quantify theirsuitability for different parallel applications. Due to the parallel and distributed nature of the environments, networks connecting the processors in these environments were investigated with respect to their performance characteristics. Second, scheduling algorithms are studied in order to make them more efficient and effective. A concept of application-specific information scheduling is introduced. The application- specific information is data about the workload extractedfrom an application, which is provided to a scheduling algorithm. Three scheduling algorithms are enhanced to utilize the application-specific information to further refine their scheduling properties. A more accurate description of the workload is especially important in cases where the workunits are heterogeneous and the parallel environment is heterogeneous and/or non-dedicated. The results obtained show that the additional information regarding the workload has a positive impact on the performance of applications. Third, a programming paradigm for networks of symmetric multiprocessor (SMP) workstations is introduced. The MPIT programming paradigm incorporates the Message Passing Interface (MPI) with threads to provide a methodology to write parallel applications that efficiently utilize the available resources and minimize the overhead. The MPIT allows for communication and computation to overlap by deploying a dedicated thread for communication. Furthermore, the programming paradigm implements an application-specific scheduling algorithm. The scheduling algorithm is executed by the communication thread. Thus, the scheduling does not affect the execution of the parallel application. Performance results achieved from the MPIT show that considerable improvements over conventional MPI applications are achieved.

Introducing massively parallel computers into operational weather forecasting

Numerical weather prediction and climate simulation have been among the computationally most demanding applications of high performance computing eversince they were started in the 1950's. Since the 1980's, the most powerful computers have featured an ever larger number of processors. By the early 2000's, this number is often several thousand. An operational weather model must use all these processors in a highly coordinated fashion. The critical resource in running such models is not computation, but the amount of necessary communication between the processors. The communication capacity of parallel computers often fallsfar short of their computational power. The articles in this thesis cover fourteen years of research into how to harness thousands of processors on a single weather forecast or climate simulation, so that the application can benefit as much as possible from the power of parallel high performance computers. The resultsattained in these articles have already been widely applied, so that currently most of the organizations that carry out global weather forecasting or climate simulation anywhere in the world use methods introduced in them. Some further studies extend parallelization opportunities into other parts of the weather forecasting environment, in particular to data assimilation of satellite observations.