Stay-green wheat for Australia's changing; dry environment

Tese de doutoramento em Ciências e Tecnologias da Informação, apresentada ao Departamento de Engenharia Informática da Faculdade de Ciências e Tecnologia da Universidade de CoimbraThis doctoral thesis investigates user provided networks. Such networks have become important research subjects in the field of informatics engineering due to the recent popularity of smart phones. User provided networks are independent from traditional Internet service providers. Communication and information exchange between users occurs opportunistically, i.e., when the smart phones are close enough to exchange information. Most user provided networks are based on the radio standard IEEE 802.11, popularly known as 'wi-fi'. However, some networks are based on other low range radio standards, such as Bluetooth and IEEE 802.15.4. User provided networks are important to the society in general when the traditional Internet service providers become unavailable. For example, this may occur in terrorist attacks, earthquakes, or even cyber attacks. In these emergency situations, when users have a greater interest in common, an efficient system for non-presencial information exchange is necessary. Such networks are also interesting in a social context, when users must be incentivized to share their resources (storage capacity, wireless connectivity and battery) to enable the exchange of information. This doctoral thesis addresses both situations: i) networks whose users have a common interest and ii) networks whose users need to be encouraged to share resources. Among the various contributions of this doctoral thesis are the Delay Tolerant Reinforcement-Based routing solution and the Messages on oFfer incentive mechanism. The first is a routing solution for users-provided networks when the users have a prior interest in common. The second is an incentive mechanism to encourage users to exchange information. Both solutions showed excellent results in the simulation environment.Esta tese de doutoramento investiga as redes providas pelos usuários. Com a popularização do telemóvel esperto (smart phone) tais redes se tornaram objeto de pesquisa na área de engenharia informática. Uma característica básica das redes providas pelo usuário é a sua independência em relação aos provedores de serviço tradicionais. A comunicação e troca de informação entre usuários ocorre de forma oportuna, isto é, quando os telemóveis estão próximos o suficiente para se comunicarem. A maioria das redes providas por usuários é baseada no padrão de rádio IEEE 802.11, popularmente conhecido como 'wi-fi'. No entanto, algumas redes se baseiam em outros padrões de baixo alcance, por exemplo Bluetooth e IEEE 802.15.4. As redes providas por usuários são importantes para a sociedade no advento dos provedores de serviço tradicionais ficarem indisponíveis. Por exemplo, isso pode ocorrer em ataques terroristas, terremotos, ou mesmo em ataques virtuais. Nessas situações de emergência, quando os usuários têm um interesse maior em comum, é necessário um sistema de troca de mensagens não presencial eficiente. Tais redes também são importantes em um contexto social, quando os usuários precisam ser incentivados a compartilhar os seus recursos (capacidade de armazenamento, conectividade sem-fio e bateria) para que ocorra troca de informação. Essa tese de doutoramento aborda ambas as situações: i) redes cujos usuários têm um interesse em comum e ii) redes cujos usuários precisam ser incentivados a compartilhar recursos. Dentro das diversas contribuições que esta tese de doutoramento apresenta estão a solução de roteamento Delay Tolerant Reinforcement-Based e o mecanismo de incentivo Messages on oFfer. A primeira é uma solução de encaminhamento para redes providas por usuários que tenham um interesse em comum prévio. A segunda é um mecanismo de incentivo para estimular que os usuários troquem informação quando não houver o interesse em comum. Ambas as soluções apresentaram excelentes resultados no ambiente de simulação desenvolvido nesta tese.FCT - PTDC/EEA-TEL/103637/200

Determination of the characteristic directions of lossless linear optical elements

We show that the problem of finding the primary and secondary characteristic directions of a linear lossless optical element can be reformulated in terms of an eigenvalue problem related to the unimodular factor of the transfer matrix of the optical device. This formulation makes any actual computation of the characteristic directions amenable to pre-implemented numerical routines, thereby facilitating the decomposition of the transfer matrix into equivalent linear retarders and rotators according to the related Poincare equivalence theorem. The method is expected to be useful whenever the inverse problem of reconstruction of the internal state of a transparent medium from optical data obtained by tomographical methods is an issue.Comment: Replaced with extended version as published in JM

Mitochondrial fission facilitates the selective mitophagy of protein aggregates

Within the mitochondrial matrix, protein aggregation activates the mitochondrial unfolded protein response and PINK1–Parkin-mediated mitophagy to mitigate proteotoxicity. We explore how autophagy eliminates protein aggregates from within mitochondria and the role of mitochondrial fission in mitophagy. We show that PINK1 recruits Parkin onto mitochondrial subdomains after actinonin-induced mitochondrial proteotoxicity and that PINK1 recruits Parkin proximal to focal misfolded aggregates of the mitochondrial-localized mutant ornithine transcarbamylase (ΔOTC). Parkin colocalizes on polarized mitochondria harboring misfolded proteins in foci with ubiquitin, optineurin, and LC3. Although inhibiting Drp1-mediated mitochondrial fission suppresses the segregation of mitochondrial subdomains containing ΔOTC, it does not decrease the rate of ΔOTC clearance. Instead, loss of Drp1 enhances the recruitment of Parkin to fused mitochondrial networks and the rate of mitophagy as well as decreases the selectivity for ΔOTC during mitophagy. These results are consistent with a new model that, instead of promoting mitophagy, fission protects healthy mitochondrial domains from elimination by unchecked PINK1–Parkin activity

From a Conceptual Model to a Knowledge Graph for Genomic Datasets

Data access at genomic repositories is problematic, as data is described by heterogeneous and hardly comparable metadata. We previously introduced a unified conceptual schema, collected metadata in a single repository and provided classical search methods upon them. We here propose a new paradigm to support semantic search of integrated genomic metadata, based on the Genomic Knowledge Graph, a semantic graph of genomic terms and concepts, which combines the original information provided by each source with curated terminological content from specialized ontologies. Commercial knowledge-assisted search is designed for transparently supporting keyword-based search without explaining inferences; in biology, inference understanding is instead critical. For this reason, we propose a graph-based visual search for data exploration; some expert users can navigate the semantic graph along the conceptual schema, enriched with simple forms of homonyms and term hierarchies, thus understanding the semantic reasoning behind query results

Negative and positive selection of antigen-specific cytotoxic T lymphocytes affected by the α3 domain of MHC I molecules

THE α1 and α2 domains of major histocompatibility complex (MHC) class I molecules function in the binding and presentation of foreign peptides to the T-cell antigen receptor and control both negative and positive selection of the T-cell repertoire. Although the α3 domain of class I is not involved in peptide binding, it does interact with the T-cell accessory molecule, CDS. CDS is important in the selection of T cells as anti-CDS antibody injected into perinatal mice interfers with this process. We previously used a hybrid class I molecule with the α1/α2 domains from L^d and the α3 domain from Q7^b and showed that this molecule binds an L^d-restricted peptide but does not interact with CD8-dependent cytotoxic T lymphocytes. Expression of this molecule in transgenic mice fails to negatively select a subpopulation of anti-L^d cytotoxic T lymphocytes. In addition, positive selection of virus-specific L^d-restricted cytotoxic T lymphocytes does not occur. We conclude that besides the α1/α2 domains of class I, the α3 domain plays an important part in both positive and negative selection of antigen-specific cells

Steam reforming on transition-metal carbides from density-functional theory

A screening study of the steam reforming reaction (CH_4 + H_2O -> CO + 3H_2) on early transition-metal carbides (TMC's) is performed by means of density-functional theory calculations. The set of considered surfaces includes the alpha-Mo_2C(100) surfaces, the low-index (111) and (100) surfaces of TiC, VC, and delta-MoC, and the oxygenated alpha-Mo_2C(100) and TMC(111) surfaces. It is found that carbides provide a wide spectrum of reactivities towards the steam reforming reaction, from too reactive via suitable to too inert. The reactivity is discussed in terms of the electronic structure of the clean surfaces. Two surfaces, the delta-MoC(100) and the oxygen passivated alpha-Mo_2C(100) surfaces, are identified as promising steam reforming catalysts. These findings suggest that carbides provide a playground for reactivity tuning, comparable to the one for pure metals.Comment: 6 pages, 4 figure

Development and Validation of a Composite Programmatic Assessment Tool for HIV Therapy

Background We developed and validated a new and simple metric, the Programmatic Compliance Score (PCS), based on the IAS-USA antiretroviral therapy management guidelines for HIV-infected adults, as a predictor of all-cause mortality, at a program-wide level. We hypothesized that non-compliance would be associated with the highest probability of mortality. Methods and Findings 3543 antiretroviral-naive HIV-infected patients aged ≥19 years who initiated antiretroviral therapy between January 1, 2000 and August 31, 2009 in British Columbia (BC), Canada, were followed until August 31, 2010. The PCS is composed by six non-performance indicators based on the IAS-USA guidelines: (1) having <3 CD4 count tests in the first year after starting antiretroviral therapy; (2) having <3 plasma viral load tests in the first year after starting antiretroviral therapy; (3) not having drug resistance testing done prior to starting antiretroviral therapy; (4) starting on a non-recommended antiretroviral therapy regimen; (5) starting therapy with CD4 <200 cells/mm3; and (6) not achieving viral suppression within 6 months since antiretroviral therapy initiation. The sum of these six indicators was used to develop the PCS score - higher score indicates poorer performance. The main outcome was all-cause mortality. Each PCS component was independently associated with mortality. In the mortality analysis, the odds ratio (OR) for PCS ≥4 versus 0 was 22.37 (95% CI 10.46–47.84). Conclusions PCS was strongly associated with all-cause mortality. These results lend independent validation to the IAS-USA treatment guidelines for HIV-infected adults. Further efforts are warranted to enhance the PCS as a means to further improve clinical outcomes. These should be specifically evaluated and targeted at healthcare providers and patients

Ancient Migratory Events in the Middle East: New Clues from the Y-Chromosome Variation of Modern Iranians

Knowledge of high resolution Y-chromosome haplogroup diversification within Iran provides important geographic context regarding the spread and compartmentalization of male lineages in the Middle East and southwestern Asia. At present, the Iranian population is characterized by an extraordinary mix of different ethnic groups speaking a variety of Indo-Iranian, Semitic and Turkic languages. Despite these features, only few studies have investigated the multiethnic components of the Iranian gene pool. In this survey 938 Iranian male DNAs belonging to 15 ethnic groups from 14 Iranian provinces were analyzed for 84 Y-chromosome biallelic markers and 10 STRs. The results show an autochthonous but non-homogeneous ancient background mainly composed by J2a sub-clades with different external contributions. The phylogeography of the main haplogroups allowed identifying post-glacial and Neolithic expansions toward western Eurasia but also recent movements towards the Iranian region from western Eurasia (R1b-L23), Central Asia (Q-M25), Asia Minor (J2a-M92) and southern Mesopotamia (J1-Page08). In spite of the presence of important geographic barriers (Zagros and Alborz mountain ranges, and the Dasht-e Kavir and Dash-e Lut deserts) which may have limited gene flow, AMOVA analysis revealed that language, in addition to geography, has played an important role in shaping the nowadays Iranian gene pool. Overall, this study provides a portrait of the Y-chromosomal variation in Iran, useful for depicting a more comprehensive history of the peoples of this area as well as for reconstructing ancient migration routes. In addition, our results evidence the important role of the Iranian plateau as source and recipient of gene flow between culturally and genetically distinct population