Characteristics of biochemical markers and quality parameters using whole wheat flours in Korean wheat cultivars and lines

Tese de doutoramento em Ciências e Tecnologias da Informação, apresentada ao Departamento de Engenharia Informática da Faculdade de Ciências e Tecnologia da Universidade de CoimbraO espectro rádio tem vindo a ser regulado de um modo estático. Ou seja, este encontra-se essencialmente dividido em bandas de frequência licenciadas, com utilização restringida a um número limitado de utilizadores autorizados, e em algumas bandas de frequência não licenciadas para utilização livre. Devido à falta de flexibilidade resultante desta abordagem, partes significativas do espectro rádio encontram-se subutilizadas. Em simultâneo, outras bandas de frequência estão a ficar cada vez mais saturadas, nomeadamente as não licenciadas em áreas densamente povoadas. O Rádio Cognitivo é um paradigma recente cujo objetivo é melhorar o nível de eficiência na utilização do espectro rádio. Os seus princípios gerais consistem em permitir que dispositivos sem fios não licenciados (os denominados Utilizadores Secundários) possam aceder às bandas de frequência licenciadas desde que estes não interferiram de forma prejudicial com os utilizadores licenciados (os denominados Utilizadores Primários). A abordagem preponderante na área de Rádio Cognitivo consiste em ter utilizadores secundários com capacidade para, de um modo dinâmico, detetar e aceder a oportunidades espectrais, ou seja, bandas de frequência que não estão a ser acedidas pelos respetivos utilizadores primários num determinado momento numa determinada localização. Neste contexto, os utilizadores secundários devem ser capazes de analisar o espectro rádio com precisão e, de preferência, possuírem mecanismos de aprendizagem baseados em observação local e experiência passada. Apesar da área de Rádio Cognitivo ter implicações na totalidade das camadas das pilhas protocolares de comunicação, os seus problemas fundamentais localizam-se nos níveis físico (PHY) e de controlo de acesso ao meio (MAC). Em particular, os protocolos de controlo de acesso ao meio desempenham um papel fundamental no âmbito de operações de controlo de acesso ao espectro rádio e de suporte à cooperação entre utilizadores secundários. Os utilizadores primários, quanto a eles, devem manter-se abstraídos das operações de Rádio Cognitivo e, em consequência, não estarem sujeitos a qualquer tipo de alteração em cenários de Rádio Cognitivo. Esta tese apresenta cinco contribuições, essencialmente relacionadas com o nível do controlo de acesso ao meio, com o objetivo de incrementar os níveis de proteção dos utilizadores primários e de desempenho dos utilizadores secundários em redes de Rádio Cognitivo distribuídas, especialmente quando os utilizadores secundários não têm antecipadamente acesso a qualquer tipo de informação, tal como a localização de utilizadores primários. Neste tipo de cenário, não existe qualquer entidade central responsável por recolher e processar dados de origem diversa ou tomar decisões de acesso ao espectro rádio. Ou seja, as soluções propostas adequam-se a utilizadores secundários que operam de um modo autónomo e cooperativo. Estes tomam as suas decisões baseando-se, essencialmente, em observações locais, em eventuais resultados de aprendizagem e em dados trocados entre si. A primeira contribuição desta tese consiste numa descrição da área de Rádio Cognitivo através de um estado da arte detalhado. A segunda contribuição resulta na definição de um protocolo de controlo de acesso ao meio apoiado num mecanismo inovador, designado COSBET (Cooperative Sense-Before-Transmit), que oferece um nível superior de proteção dos utilizadores primários em cenários de Rádio Cognitivo distribuídos sujeitos ao problema do utilizador primário oculto. Este tipo de anomalia ocorre quando um utilizador secundário é incapaz de detetar as atividades de um determinado utilizador primário apesar de poder provocar interferências na respetiva área de abrangência. Tal como já foi referido, na área de Rádio Cognitivo, é considerado desejável os utilizadores secundários terem capacidades de aprendizagem baseadas em observação local e experiência passada. No entanto, em cenários distribuídos, o problema do utilizador primário oculto afeta negativamente a qualidade dos resultados de aprendizagem obtidos e, em consequência, o nível efetivamente alcançado em termos de proteção dos utilizadores primários. Sendo assim, esta tese também analisa esta questão e propõe uma solução destinada a tratá-la, estando esta terceira contribuição baseada num conceito chave designado FIBASC (Filtering Based on Suspicious Channels). A troca de informação de controlo em redes de Rádio Cognitivo distribuídas é frequentemente suportada por um canal partilhado e acessível à globalidade dos utilizadores secundários. Este é o designado canal de controlo comum (CCC), sendo igualmente esta a abordagem seguida pelo protocolo COSBET-MAC proposto. No entanto, os CCC estão sujeitos a problemas de saturação. A ocorrência deste tipo de problema impede os utilizadores secundários de tirarem pleno proveito das potencialidades oferecidas pelo Rádio Cognitivo, acabando por limitar os níveis de desempenho de comunicação alcançáveis. Sendo assim, nesta tese também analisamos esta questão e propomos uma solução destinada a abordá-la, correspondendo esta à nossa quarta contribuição. A solução proposta, designada CORHYS (Cognitive Radio Hybrid Signalling), baseia-se num esquema de sinalização híbrido que recorre simultaneamente a um CCC e aos canais de dados que vão sendo alocados de forma dinâmica. A quinta e última contribuição desta tese consiste na definição de uma estratégia adicional, igualmente localizada no nível do controlo de acesso ao meio, destinada a melhorar o desempenho dos utilizadores secundários em cenários de Rádio Cognitivo distribuídos em que se recorre a um CCC. Fazem parte das suas linhas orientadoras a otimização da reutilização espacial do espectro rádio e a redução do tráfego de controlo gerado entre utilizadores secundários. As soluções de Rádio Cognitivo propostas no âmbito desta tese foram avaliadas em ambiente de simulação, sendo esta uma prática comum, nomeadamente devido a limitações de tempo e de outros tipos de recursos. Para o efeito, recorreu-se ao OMNET++ (Objective Modular Network Testbed in C++), um simulador baseado em eventos discretos e de código aberto. A totalidade das contribuições da presente tese podem ser aplicadas em conjunto. A integração destas deu origem a uma solução única e otimizada de controlo de acesso ao meio destinada a cenários de Rádio Cognitivo distribuídos. Esta aborda as duas principais preocupações existentes em cenários de Rádio Cognitivo: proteger os utilizadores primários de qualquer tipo de interferência prejudicial; e melhorar o desempenho de comunicação dos utilizadores secundários. Tanto quanto sabemos, as várias soluções propostas e o nível de completude que a utilização conjunta destas permite não são oferecidos por qualquer outra proposta de controlo de acesso ao meio existente para cenários de Rádio Cognitivo distribuídos. As contribuições desta tese também apontam direções que podem ser seguidas no âmbito de outros protocolos de controlo de acesso ao meio, especialmente aqueles que se destinam a redes de Rádio Cognitivo distribuídas.The radio spectrum has been statically regulated, i.e., essentially partitioned into licensed frequency bands, which are accessed exclusively by authorized users, and unlicensed frequency bands that can be freely accessed. Due to this inflexible policy, large portions of the entire radio spectrum remain unused independently of time and location in the world, while some frequency bands suffer from increasing levels of saturation, particularly the unlicensed ones in densely populated areas. Cognitive Radio (CR) is a recent paradigm that aims at improving efficiency regarding spectrum utilization. Its principles consist in allowing unlicensed wireless devices (i.e., secondary users) to access licensed frequency bands provided that the respective incumbent users (i.e., primary users) do not suffer any harmful interference. The most preponderant CR approach consists in having a secondary user (SU) dynamically locating and accessing spectrum opportunities, i.e., frequency bands that are not being accessed by any primary user (PU) at a given time and location. Consequently, sensing the spectrum and learning through local observation and past experience, which enables proactive spectrum decision, are key CR issues. Despite CR has implications in all the layers of the communication protocol stack, its fundamentals are mainly related to the physical (PHY) and medium access control (MAC) levels. In fact, CR MAC protocols are at the heart of spectrum access control and cooperation between SUs. PUs are expected to be unware of CR operations and, consequently, should not suffer any modification under CR scenarios. This thesis provides five contributions, essentially related to the MAC level, with the aim of improving the protection of PUs and the communication performance of SUs in cooperative distributed CR networks, particularly when there is no access to any a priori known information, such as the locations of primary transmitters. In this type of scenario, there are no central entities that collect and fuse data, or take spectrum decisions. That is, the proposed solutions fit into totally autonomous and cooperating SUs, i.e., SUs that take their own decisions based on local observation, on learning outcomes if any is available, and on data they exchange with each other. The first contribution of this thesis consists in a description of the CR area through an indepth state of the art. The second contribution lies in the definition of a CR MAC protocol that follows a novel approach, named Cooperative Sense-Before-Transmit (COSBET), which provides a higher protection of PUs in distributed CR scenarios that suffer from the hidden PU problem. This issue occurs when a SU cannot sense the activities of a given PU despite it can cause harmful interference to its coverage area. As already mentioned, CR considers that the SUs might have learning capabilities based on local observation and past experience. However, in distributed scenarios, the hidden PU problem affects the accuracy of learning and, therefore, the effectiveness of PU protection. For that reason, in this thesis we also discuss this issue and propose a novel solution that addresses it. This solution is based on a key concept named FIBASC (Filtering Based on Suspicious Channels). Utilizing a common control channel (CCC), i.e., a channel that is available to all the SUs in a CR network, for signalling purposes is a frequent practice concerning existing distributed CR MAC solutions. It is also the solution adopted by COSBET-MAC. However, a CCC is susceptible to saturation and can, therefore, become a performance bottleneck that inhibits the SUs from taking full advantage of CR potentialities. Consequently, the fourth contribution of this thesis consists in analysing this issue and addressing it through a novel solution, which we named CORHYS (Cognitive Radio Hybrid Signalling). CORHYS is based on a hybrid signalling approach that performs signalling over the CCC and over the allocated data channels simultaneously. The fifth and last contribution of this thesis consists in a MAC-level strategy that aims at further improving the performance of SUs in distributed CR scenarios that are based on a CCC. The key guidelines for this strategy are optimizing the spatial reuse of the radio spectrum and reducing control traffic. The CR solutions that resulted from this thesis were evaluated through simulation, which is a common practice, particularly due to time and other resource restrictions. For this purpose, we used OMNET++ (Objective Modular Network Testbed in C++), an open source discrete event simulator. The contributions of this thesis can be applied jointly and were successfully integrated with each other, which resulted in an optimized CR MAC solution that addresses the two main concerns in distributed CR scenarios: protecting the PUs from harmful interference; and improving the communication performance of the SUs. To the best of our knowledge, the proposed solutions and the level of completeness that they jointly achieve are not found in any other existing distributed CR MAC proposal. We also note that they define directions that can be followed by other CR MAC protocols, particularly those that target distributed CR networks

Cross-Talk and Information Transfer in Mammalian and Bacterial Signaling

In mammalian and bacterial cells simple phosphorylation circuits play an important role in signaling. Bacteria have hundreds of two-component signaling systems that involve phosphotransfer between a receptor and a response regulator. In mammalian cells a similar pathway is the TGF-beta pathway, where extracellular TGF-beta ligands activate cell surface receptors that phosphorylate Smad proteins, which in turn activate many genes. In TGF-beta signaling the multiplicity of ligands begs the question as to whether cells can distinguish signals coming from different ligands, but transduced through a small set of Smads. Here we use information theory with stochastic simulations of networks to address this question. We find that when signals are transduced through only one Smad, the cell cannot distinguish between different levels of the external ligands. Increasing the number of Smads from one to two significantly improves information transmission as well as the ability to discriminate between ligands. Surprisingly, both total information transmitted and the capacity to discriminate between ligands are quite insensitive to high levels of cross-talk between the two Smads. Robustness against cross-talk requires that the average amplitude of the signals are large. We find that smaller systems, as exemplified by some two-component systems in bacteria, are significantly much less robust against cross-talk. For such system sizes phosphotransfer is also less robust against cross-talk than phosphorylation. This suggests that mammalian signal transduction can tolerate a high amount of cross-talk without degrading information content. This may have played a role in the evolution of new functionalities from small mutations in signaling pathways, allowed for the development of cross-regulation and led to increased overall robustness due to redundancy in signaling pathways. On the other hand the lack of cross-regulation observed in many bacterial two-component systems may partly be due to the loss of information content due to cross-talk

Phylodynamics of HIV-1 Subtype B among the Men-Having-Sex-with-Men (MSM) Population in Hong Kong

The men-having-sex-with-men (MSM) population has become one of the major risk groups for HIV-1 infection in the Asia Pacific countries. Hong Kong is located in the centre of Asia and the transmission history of HIV-1 subtype B transmission among MSM remained unclear. The aim of this study was to investigate the transmission dynamics of HIV-1 subtype B virus in the Hong Kong MSM population. Samples of 125 HIV-1 subtype B infected MSM patients were recruited in this study. Through this study, the subtype B epidemic in the Hong Kong MSM population was identified spreading mainly among local Chinese who caught infection locally. On the other hand, HIV-1 subtype B infected Caucasian MSM caught infection mainly outside Hong Kong. The Bayesian phylogenetic analysis also indicated that 3 separate subtype B epidemics with divergence dates in the 1990s had occurred. The first and latest epidemics were comparatively small-scaled; spreading among the local Chinese MSM while sauna-visiting was found to be the major sex partner sourcing reservoir for the first subtype B epidemic. However, the second epidemic was spread in a large-scale among local Chinese MSM with a number of them having sourced their sex partners through the internet. The epidemic virus was estimated to have a divergence date in 1987 and the infected population in Hong Kong had a logistic growth throughout the past 20 years. Our study elucidated the evolutionary and demographic history of HIV-1 subtype B virus in Hong Kong MSM population. The understanding of transmission and growth model of the subtype B epidemic provides more information on the HIV-1 transmission among MSM population in other Asia Pacific high-income countries

Jet energy measurement with the ATLAS detector in proton-proton collisions at root s=7 TeV

The jet energy scale and its systematic uncertainty are determined for jets measured with the ATLAS detector at the LHC in proton-proton collision data at a centre-of-mass energy of √s = 7TeV corresponding to an integrated luminosity of 38 pb-1. Jets are reconstructed with the anti-kt algorithm with distance parameters R=0. 4 or R=0. 6. Jet energy and angle corrections are determined from Monte Carlo simulations to calibrate jets with transverse momenta pT≥20 GeV and pseudorapidities {pipe}η{pipe}<4. 5. The jet energy systematic uncertainty is estimated using the single isolated hadron response measured in situ and in test-beams, exploiting the transverse momentum balance between central and forward jets in events with dijet topologies and studying systematic variations in Monte Carlo simulations. The jet energy uncertainty is less than 2. 5 % in the central calorimeter region ({pipe}η{pipe}<0. 8) for jets with 60≤pT<800 GeV, and is maximally 14 % for pT<30 GeV in the most forward region 3. 2≤{pipe}η{pipe}<4. 5. The jet energy is validated for jet transverse momenta up to 1 TeV to the level of a few percent using several in situ techniques by comparing a well-known reference such as the recoiling photon pT, the sum of the transverse momenta of tracks associated to the jet, or a system of low-pT jets recoiling against a high-pT jet. More sophisticated jet calibration schemes are presented based on calorimeter cell energy density weighting or hadronic properties of jets, aiming for an improved jet energy resolution and a reduced flavour dependence of the jet response. The systematic uncertainty of the jet energy determined from a combination of in situ techniques is consistent with the one derived from single hadron response measurements over a wide kinematic range. The nominal corrections and uncertainties are derived for isolated jets in an inclusive sample of high-pT jets. Special cases such as event topologies with close-by jets, or selections of samples with an enhanced content of jets originating from light quarks, heavy quarks or gluons are also discussed and the corresponding uncertainties are determined. © 2013 CERN for the benefit of the ATLAS collaboration

Measurement of the inclusive and dijet cross-sections of b-jets in pp collisions at sqrt(s) = 7 TeV with the ATLAS detector

The inclusive and dijet production cross-sections have been measured for jets containing b-hadrons (b-jets) in proton-proton collisions at a centre-of-mass energy of sqrt(s) = 7 TeV, using the ATLAS detector at the LHC. The measurements use data corresponding to an integrated luminosity of 34 pb^-1. The b-jets are identified using either a lifetime-based method, where secondary decay vertices of b-hadrons in jets are reconstructed using information from the tracking detectors, or a muon-based method where the presence of a muon is used to identify semileptonic decays of b-hadrons inside jets. The inclusive b-jet cross-section is measured as a function of transverse momentum in the range 20 < pT < 400 GeV and rapidity in the range |y| < 2.1. The bbbar-dijet cross-section is measured as a function of the dijet invariant mass in the range 110 < m_jj < 760 GeV, the azimuthal angle difference between the two jets and the angular variable chi in two dijet mass regions. The results are compared with next-to-leading-order QCD predictions. Good agreement is observed between the measured cross-sections and the predictions obtained using POWHEG + Pythia. MC@NLO + Herwig shows good agreement with the measured bbbar-dijet cross-section. However, it does not reproduce the measured inclusive cross-section well, particularly for central b-jets with large transverse momenta.Comment: 10 pages plus author list (21 pages total), 8 figures, 1 table, final version published in European Physical Journal

Haplotype Analysis Improved Evidence for Candidate Genes for Intramuscular Fat Percentage from a Genome Wide Association Study of Cattle

In genome wide association studies (GWAS), haplotype analyses of SNP data are neglected in favour of single point analysis of associations. In a recent GWAS, we found that none of the known candidate genes for intramuscular fat (IMF) had been identified. In this study, data from the GWAS for these candidate genes were re-analysed as haplotypes. First, we confirmed that the methodology would find evidence for association between haplotypes in candidate genes of the calpain-calpastatin complex and musculus longissimus lumborum peak force (LLPF), because these genes had been confirmed through single point analysis in the GWAS. Then, for intramuscular fat percent (IMF), we found significant partial haplotype substitution effects for the genes ADIPOQ and CXCR4, as well as suggestive associations to the genes CEBPA, FASN, and CAPN1. Haplotypes for these genes explained 80% more of the phenotypic variance compared to the best single SNP. For some genes the analyses suggested that there was more than one causative mutation in some genes, or confirmed that some causative mutations are limited to particular subgroups of a species. Fitting the SNPs and their interactions simultaneously explained a similar amount of the phenotypic variance compared to haplotype analyses. Haplotype analysis is a neglected part of the suite of tools used to analyse GWAS data, would be a useful method to extract more information from these data sets, and may contribute to reducing the missing heritability problem

Meta-Analysis of the Immunogenicity and Tolerability of Pandemic Influenza A 2009 (H1N1) Vaccines

Background: Although the 2009 (H1N1) influenza pandemic officially ended in August 2010, the virus will probably circulate in future years. Several types of H1N1 vaccines have been tested including various dosages and adjuvants, and meta-analysis is needed to identify the best formulation. Methods: We searched MEDLINE, EMBASE, and nine clinical trial registries to April 2011, in any language for randomized clinical trials (RCTs) on healthy children, adolescents, adults and the elderly. Primary outcome was the seroconversion rate according to hemagglutinination-inhibition (HI); secondary outcomes were adverse events. For the primary outcome, we used head-to-head meta-analysis and multiple-treatments meta-analysis. Results: Eighteen RCTs could be included in all primary analyses, for a total of 76 arms (16,725 subjects). After 2 doses, all 2009 H1N1 split/subunit inactivated vaccines were highly immunogenic and overcome CPMP seroconversion criteria. After 1 dose only, all split/subunit vaccines induced a satisfactory immunogenicity (> = 70%) in adults and adolescents, while only some formulations showed acceptable results for children and elderly (non-adjuvanted at high-doses and oil-in-water adjuvanted vaccines). Vaccines with oil-in-water adjuvants were more immunogenic than both nonadjuvanted and aluminum-adjuvanted vaccines at equal doses and their immunogenicity at doses < = 6 μg (even with as little as 1.875 μg of hemagglutinin antigen) was not significantly lower than that achieved after higher doses. Finally, the rate of serious vaccine-related adverse events was low for all 2009 H1N1 vaccines (3 cases, resolved in 10 days, out of 22826 vaccinated subjects). However, mild to moderate adverse reactions were more (and very) frequent for oil-in-water adjuvanted vaccines. Conclusions: Several one-dose formulations might be valid for future vaccines, but 2 doses may be needed for children, especially if a low-dose non-adjuvanted vaccine is used. Given that 15 RCTs were sponsored by vaccine manufacturers, future trials sponsored by non-industry agencies and comparing vaccines using different types of adjuvants are needed

The effects of Δ9-tetrahydrocannabinol on the dopamine system

Δ(9)-tetrahydrocannabinol (THC), the main psychoactive ingredient in cannabis, is a pressing concern to global mental health. Patterns of use are changing drastically due to legalisation, availability of synthetic analogues (‘spice’), cannavaping and aggrandizements in the purported therapeutic effects of cannabis. Many of THC’s reinforcing effects are mediated by the dopamine system. Due to complex cannabinoid-dopamine interactions there is conflicting evidence from human and animal research fields. Acute THC causes increased dopamine release and neuron activity, whilst long-term use is associated with blunting of the dopamine system. Future research must examine the long-term and developmental dopaminergic effects of the drug