Parallel dynamic graph-partitioning for unstructured meshes

A parallel method for the dynamic partitioning of unstructured meshes is described. The method introduces a new iterative optimisation technique known as relative gain optimisation which both balances the workload and attempts to minimise the interprocessor communications overhead. Experiments on a series of adaptively refined meshes indicate that the algorithm provides partitions of an equivalent or higher quality to static partitioners (which do not reuse the existing partition) and much more rapidly. Perhaps more importantly, the algorithm results in only a small fraction of the amount of data migration compared to the static partitioners.

Dynamic multi-partitioning for parallel finite element applications

The central product of the DRAMA (Dynamic Re-Allocation of Meshes for parallel Finite Element Applications) project is a library comprising a variety of tools for dynamic re-partitioning of unstructured Finite Element (FE) applications. The input to the DRAMA library is the computational mesh, and corresponding costs, partitioned into sub-domains. The core library functions then perform a parallel computation of a mesh re-allocation that will re-balance the costs based on the DRAMA cost model. We discuss the basic features of this cost model, which allows a general approach to load identification, modelling and imbalance minimisation. Results from crash simulations are presented which show the necessity for multi-phase/multi-constraint partitioning components.

Parallel ruptures: Jews of Bessarabia and Transnistria between Romanian nationalism and Soviet communism, 1918-1940

“Parallel Ruptures: Jews of Bessarabia and Transnistria between Romanian Nationalism and Soviet Communism, 1918-1940,” explores the political and social debates that took place in Jewish communities in Romanian-held Bessarabia and the Moldovan Autonomous Soviet Socialist Republic during the interwar era. Both had been part of the Russian Pale of Settlement until its dissolution in 1917; they were then divided by the Romanian Army’s occupation of Bessarabia in 1918 with the establishment of a well-guarded border along the Dniester River between two newly-formed states, Greater Romania and the Soviet Union. At its core, the project focuses in comparative context on the traumatic and multi-faceted confrontation with these two modernizing states: exclusion, discrimination and growing violence in Bessarabia; destruction of religious tradition, agricultural resettlement, and socialist re-education and assimilation in Soviet Transnistria. It examines also the similarities in both states’ striving to create model subjects usable by the homeland, as well as commonalities within Jewish responses on both sides of the border. Contacts between Jews on either side of the border remained significant after 1918 despite the efforts of both states to curb them, thereby necessitating a transnational view in order to examine Jewish political and social life in borderland regions. The desire among Jewish secular leaders to mold their co-religionists into modern Jews reached across state borders and ideological divides and sought to manipulate respective governments to establish these goals, however unsuccessful in the final analysis. Finally, strained relations between Jews in peripheral borderlands with those at national/imperial cores, Moscow and Bucharest, sheds light on the complex circumstances surrounding the inclusion versus exclusion debates at the heart of all interwar European states and the complicated negotiations that took place within all minority communities that responded to state policies.

Aplicación web basado en el programa de reaprovisionamiento continuo utilizando la tecnología de códigos QR para mejorar los procesos de distribución, en una empresa comercializadora de vehículos

Tesis de pregrado

Design and implementation of a floating point unit for rigel, a massively parallel accelerator

Scientific applications rely heavily on floating point data types. Floating point operations are complex and require complicated hardware that is both area and power intensive. The emergence of massively parallel architectures like Rigel creates new challenges and poses new questions with respect to floating point support. The massively parallel aspect of Rigel places great emphasis on area efficient, low power designs. At the same time, Rigel is a general purpose accelerator and must provide high performance for a wide class of applications. This thesis presents an analysis of various floating point unit (FPU) components with respect to Rigel, and attempts to present a candidate design of an FPU that balances performance, area, and power and is suitable for massively parallel architectures like Rigel.

Macrophage adaptation leads to parallel evolution of genetically diverseEscherichia colismall-colony variants with increased fitness in vivo and antibiotic collateral sensitivity

Small-colony variants (SCVs) are commonly observed in evolution experiments and clinical isolates, being associated with antibiotic resistance and persistent infections. We recently observed the repeated emergence of Escherichia coli SCVs during adaptation to the interaction with macrophages. To identify the genetic targets underlying the emergence of this clinically relevant morphotype, we performed whole-genome sequencing of independently evolved SCV clones. We uncovered novel mutational targets, not previously associated with SCVs (e.g. cydA, pepP) and observed widespread functional parallelism. All SCV clones had mutations in genes related to the electron-transport chain. As SCVs emerged during adaptation to macrophages, and often show increased antibiotic resistance, we measured SCV fitness inside macrophages and measured their antibiotic resistance profiles. SCVs had a fitness advantage inside macrophages and showed increased aminoglycoside resistance in vitro, but had collateral sensitivity to other antibiotics (e.g. tetracycline). Importantly, we observed similar results in vivo. SCVs had a fitness advantage upon colonization of the mouse gut, which could be tuned by antibiotic treatment: kanamycin (aminoglycoside) increased SCV fitness, but tetracycline strongly reduced it. Our results highlight the power of using experimental evolution as the basis for identifying the causes and consequences of adaptation during host-microbe interactions.

Novo roteiro para a Arte Nova em Aveiro e Ílhavo: proposta de uma aplicação mobile

A presente investigação tem como objeto de estudo a Arte Nova nas cidades de Aveiro e Ílhavo, traduzindo-se posteriormente na criação de uma aplicação mobile de um roteiro diferenciador referente ao património Arte Nova localizado nas duas cidades. Existe em Aveiro, uma tomada de consciência notória relativa ao património que se enquadra no espírito e nas características do estilo Arte Nova. Isso em muito se deve à originalidade e diversidade de interpretações que a caracterizam localmente. No entanto, apesar dos melhoramentos efetuados na comunicação deste património, especialmente depois da reabilitação do edifício Mário Belmonte Pessoa e da sua transformação em Museu Arte Nova, o roteiro atual não contempla todos os artefactos do estilo existentes na cidade e exclui aqueles que se encontram fora do centro urbano da cidade de Aveiro. Em Ílhavo a realidade é completamente díspar da encontrada na cidade vizinha, Aveiro, não existindo grande decoro pelo tratamento da informação referente ao estilo Arte Nova, apenas algumas referencias breves em guias culturais e um roteiro limitado no site da Câmara Municipal de Ílhavo. Paralelamente a isto, a região de Aveiro tornou-se numa das regiões com o espólio mais significativo do país. Dada à sua importância cultural e local, o roteiro diferenciador que propomos nesta investigação irá intervir de forma a melhorar o que já existe, passando pelo aprofundamento de conhecimentos sobre o tema, catalogação, cruzamento e agrupamento de toda a informação dos artefactos que se encontrem dispersos pelas duas cidades, de forma a tornar mais fácil a procura e o acesso à informação. Numa primeira fase, a investigação irá focar-se nos conteúdos afetos a cada um dos artefactos, sendo estes metodologicamente trabalhados através do método triangular de Francisco Providência, a interpretação autoral (autoria) que se traduz na evolução dos edifícios (tecnologia) e a relevância da sua história (programa) para o património nacional. Posteriormente, os conteúdos anteriormente referidos serão adaptados a uma aplicação mobile que facilitará o acesso à informação previamente selecionada referente a cada artefacto, apresentando uma breve história sobre as manifestações da Arte Nova nas cidades de Aveiro e Ílhavo. Esta aplicação mobile permitirá perceber a evolução dos edifícios desde a sua construção até à atualidade, ao nível de recuperação estrutural ou da falta de reabilitação e recuperação dos mesmos. Contribuirá para conhecer se os edifícios mantiveram (ou não) as suas características originais relativas ao desenho e tecnologia, para tal fará valerse de tecnologias como Realidade Aumentada, assim como os princípios de elaboração e leitura de QR codes, para facilitar o acesso, localização e compreensão dessa mesma informação, permitindo ainda que o seu utilizador embarque numa viagem no tempo e experiencie o roteiro de uma forma diferente. Paralelamente, pretende-se que este roteiro funcione como um roteiro único do património Arte Nova nas duas cidades, com o intuito de se expandir a outras cidades e se tornar num roteiro único do património Arte Nova na região de Aveiro. A diversidade do património Arte Nova nesta região assenta no cunho pessoal e social que os proprietários atribuíram aos seus artefactos, assim como na formação e a capacidade artística fortemente influenciada pela técnica pessoal, temperamento e sensibilidade dos seus autores, fazendo destes artefactos autênticas obras de arte, que merecem o seu estudo. Constatou-se, ao nível dos resultados que o protótipo da aplicação mobile, se adequaram ao que foi anunciado, a nível investigativo, e por isso, interessou a este estudo confirmar a demonstração do que foi enunciado. No entanto, concluiu-se que o respetivo protótipo necessita de ser ‘afinado’ em estudos futuros. Independentemente, das fragilidades encontradas, considera-se que este protótipo de aplicação mobile poderá servir como meio de excelência para a integração de conteúdos que vão mais além do que a visualização dos artefactos. Assim, contribui-se para o adensamento e acesso ao conhecimento sobre a história da Arte Nova em Portugal.

A parallel numerical solver using hierarchically tiled arrays

Solving linear systems is an important problem for scientific computing. Exploiting parallelism is essential for solving complex systems, and this traditionally involves writing parallel algorithms on top of a library such as MPI. The SPIKE family of algorithms is one well-known example of a parallel solver for linear systems. The Hierarchically Tiled Array data type extends traditional data-parallel array operations with explicit tiling and allows programmers to directly manipulate tiles. The tiles of the HTA data type map naturally to the block nature of many numeric computations, including the SPIKE family of algorithms. The higher level of abstraction of the HTA enables the same program to be portable across different platforms. Current implementations target both shared-memory and distributed-memory models. In this thesis we present a proof-of-concept for portable linear solvers. We implement two algorithms from the SPIKE family using the HTA library. We show that our implementations of SPIKE exploit the abstractions provided by the HTA to produce a compact, clean code that can run on both shared-memory and distributed-memory models without modification. We discuss how we map the algorithms to HTA programs as well as examine their performance. We compare the performance of our HTA codes to comparable codes written in MPI as well as current state-of-the-art linear algebra routines.

Mobiili oppimateriaali ja QR-koodit käsityön opetuksessa ja konekohtaisessa perehdytyksessä

Tämän tutkimuksen tarkoituksena on selvittää, miten Turun yliopiston Rauman yksikön opiskelijat kokevat QR- koodien avulla esitettävien perehdytysvideoiden hyödyntävän aineenhallintaansa ja työturvallisuustaitoja työstökoneiden kanssa työskenneltäessä. Lisäksi tutkitaan, kokiko jokin tietty opiskelijaryhmä videoiden parantavan aineenhallintaansa työstökoneiden käytössä paremmin. Tutkimuksen teoriaosassa käsitellään käsityötä oppiaineena, oppimisympäristöä, verkko-opetusta sekä työturvallisuutta. Teoriaosan lopussa käydään läpi taidon opettamisen perinteisiä teorioita. Teoriaosan perusteella on muodostettu kyselylomake, joka perustuu verkko-oppimateriaalin laatukriteereihin. Laatukriteerit ovat vaikuttaneet perehdytysvideoiden tekemiseen sekä QR-koodien sijoitteluun. Tutkimuksessa tehtiin kysely Turun yliopiston opettajankoulutuslaitoksen Rauman yksikön opiskelijoille. Kysely oli täytettävissä Webropol -sivustolla. Linkki kyselyyn oli sijoitettuna työstökoneiden läheisyyteen, samasta paperista löytyi myös linkki perehdytysvideoon. Linkit aukesivat mobiililaitteen QR-koodeja lukevan sovelluksen avulla. Tutkimus on strategialtaan kvantitatiivinen Survey-tutkimus. Kyselyyn vastasi 39 opiskelijaa ja kyselystä saatu aineisto analysoitiin SPSS ohjelmalla. Tutkimustulokset saatiin vertailemalla keskeisiä tunnuslukuja sekä korrelaatiotestejä ja varianssianalyysejä hyödyntämällä. Tutkimuksen tulosten perusteella perehdytysvideot hyödyttävät tehokkaiten opiskelijoita, joiden aikaisemmat taidot ovat heikot. Aikaisempien taitojen ja perehdytysvideosta saadun hyödyn välillä huomattiin selkeä korrelaatio. Perehdytysvideoiden saavutettavuudella ja käytettävyydellä ei nähty keskinäistä korrelaatiota. Tulosten perusteella huomattiin, että luokanopettajaopiskelijat arvioivat omat taitonsa työstökoneiden käytössä heikommaksi, jolloin he myös hyötyivät perehdytysvideoista enemmän.

Parallel Cyclostationarity-Exploiting Algorithm for Energy-Efficient Spectrum Sensing

The evolution of wireless communication systems leads to Dynamic Spectrum Allocation for Cognitive Radio, which requires reliable spectrum sensing techniques. Among the spectrum sensing methods proposed in the literature, those that exploit cyclostationary characteristics of radio signals are particularly suitable for communication environments with low signal-to-noise ratios, or with non-stationary noise. However, such methods have high computational complexity that directly raises the power consumption of devices which often have very stringent low-power requirements. We propose a strategy for cyclostationary spectrum sensing with reduced energy consumption. This strategy is based on the principle that p processors working at slower frequencies consume less power than a single processor for the same execution time. We devise a strict relation between the energy savings and common parallel system metrics. The results of simulations show that our strategy promises very significant savings in actual devices.

The RGBarrier assay: the parallel study of gene regulatory element performance at defined chromosomal locations

Vertebrate genomes are organised into a variety of nuclear environments and chromatin states that have profound effects on the regulation of gene transcription. This variation presents a major challenge to the expression of transgenes for experimental research, genetic therapies and the production of biopharmaceuticals. The majority of transgenes succumb to transcriptional silencing by their chromosomal environment when they are randomly integrated into the genome, a phenomenon known as chromosomal position effect (CPE). It is not always feasible to target transgene integration to transcriptionally permissive “safe harbour” loci that favour transgene expression, so there remains an unmet need to identify gene regulatory elements that can be added to transgenes which protect them against CPE. Dominant regulatory elements (DREs) with chromatin barrier (or boundary) activity have been shown to protect transgenes from CPE. The HS4 element from the chicken beta-globin locus and the A2UCOE element from a human housekeeping gene locus have been shown to function as DRE barriers in a wide variety of cell types and species. Despite rapid advances in the profiling of transcription factor binding, chromatin states and chromosomal looping interactions, progress towards functionally validating the many candidate barrier elements in vertebrates has been very slow. This is largely due to the lack of a tractable and efficient assay for chromatin barrier activity. In this study, I have developed the RGBarrier assay system to test the chromatin barrier activity of candidate DREs at pre-defined isogenic loci in human cells. The RGBarrier assay consists in a Flp-based RMCE reaction for the integration of an expression construct, carrying candidate DREs, in a pre-characterised chromosomal location. The RGBarrier system involves the tracking of red, green and blue fluorescent proteins by flow cytometry to monitor on-target versus off-target integration and transgene expression. The analysis of the reporter (GFP) expression for several weeks gives a measure of the protective ability of each candidate elements from chromosomal silencing. This assay can be scaled up to test tens of new putative barrier elements in the same chromosomal context in parallel. The defined chromosomal contexts of the RGBarrier assays will allow for detailed mechanistic studies of chromosomal silencing and DRE barrier element action. Understanding these mechanisms will be of paramount importance for the design of specific solutions for overcoming chromosomal silencing in specific transgenic applications.

Easy PRAM-based High-performance Parallel Programming with ICE

A poster of this paper will be presented at the 25th International Conference on Parallel Architecture and Compilation Technology (PACT ’16), September 11-15, 2016, Haifa, Israel.

Invertibility characterization of Wiener-Hopf plus Hankel operators on variable exponent Lebesgue spaces via even asymmetric factorization

We obtain invertibility and Fredholm criteria for the Wiener-Hopf plus Hankel operators acting between variable exponent Lebesgue spaces on the real line. Such characterizations are obtained via the so-called even asymmetric factorization which is applied to the Fourier symbols of the operators under study.

Improving drug discovery using a neural networks based parallel scoring function

Virtual Screening (VS) methods can considerably aid clinical research, predicting how ligands interact with drug targets. Most VS methods suppose a unique binding site for the target, but it has been demonstrated that diverse ligands interact with unrelated parts of the target and many VS methods do not take into account this relevant fact. This problem is circumvented by a novel VS methodology named BINDSURF that scans the whole protein surface to find new hotspots, where ligands might potentially interact with, and which is implemented in massively parallel Graphics Processing Units, allowing fast processing of large ligand databases. BINDSURF can thus be used in drug discovery, drug design, drug repurposing and therefore helps considerably in clinical research. However, the accuracy of most VS methods is constrained by limitations in the scoring function that describes biomolecular interactions, and even nowadays these uncertainties are not completely understood. In order to solve this problem, we propose a novel approach where neural networks are trained with databases of known active (drugs) and inactive compounds, and later used to improve VS predictions.