A homogeneous DNA hybridization system by using a new luminescence terbium chelate

Homogeneous DNA hybridization assay based on the luminescence resonance energy transfer (LRET) from a new luminescence terbium chelate, N,N,N-1,N-1-[2,6-bis(3'-aminomethyl-1'-pyrazolyl)-4-phenylpyridine]tetrakis(acetic acid) (BPTA)-Tb3+ (lambda(ex) = 325 nm and lambda(em) = 545 nm) to an organic dye, Cy3 (A,. = 548 nm and A,. = 565 nm), has been developed. In the system, two DNA probes whose sequences are complementary to the two different consecutive sequences of a target DNA are used; one of the probes is labeled with the Tb3+ chelate at the T-end, and the other is with Cy3 at the 5'-end. Labeling of the Tb3+ chelate is accomplished via the linkage of a biotin-labeled DNA probe with the Tb3+ chelate-labeled streptavidin. Strong sensitized emission of Cy3 was observed upon excitation of the Tb3+ chelate at 325 run, when the two probe DNAs were hybridized with the target DNA. The sensitivity of the assay was very high compared with those of the previous homogeneous-format assays using the conventional organic dyes; the detection limit of the present assay is about 30 pM of the target DNA strand.

A Parallelizing Compiler Based on Partial Evaluation

We constructed a parallelizing compiler that utilizes partial evaluation to achieve efficient parallel object code from very high-level data independent source programs. On several important scientific applications, the compiler attains parallel performance equivalent to or better than the best observed results from the manual restructuring of code. This is the first attempt to capitalize on partial evaluation's ability to expose low-level parallelism. New static scheduling techniques are used to utilize the fine-grained parallelism of the computations. The compiler maps the computation graph resulting from partial evaluation onto the Supercomputer Toolkit, an eight VLIW processor parallel computer.

NAVPRO 3.0: tutorial de instalação e utilização.

Este documento apresenta os procedimentos para instalação e utilização do sistema NAVPRO 3.0, desenvolvido para o processamento automático e geração de produtos de imagens do sensor Advanced Very High Resolution Radiometer (AVHRR) a bordo dos satélites da National Oceanic Atmospheric Administration (NOAA). O sistema NAVPRO foi criado pela Embrapa Informática Agropecuária em parceria com a Universidade Estadual de Campinas (Unicamp), que contou com o repasse do pacote computacional NAV (NAVigation), desenvolvido pelo Colorado Center for Astrodynamics Research (CCAR), da Universidade do Colorado, Boulder, EUA. O diferencial do sistema é seu método de georreferenciamento automático e preciso, capaz de gerar imagens com deslocamentos máximos de 1 pixel, valor aceito em aplicações envolvendo dados de baixa resolução espacial.

NAVPRO: um sistema para processamento e geração de produtos de imagens AVHRR-NOAA.

Nos últimos anos, as imagens de sensores remotos orbitais têm sido uma fonte importante de informação para estudos geográficos, agrometeorológicos e ambientais em nível regional, por oferecerem a necessária repetitividade temporal da superfície terrestre. Um sensor particularmente importante é o Advanced Very High Resolution Radiometer (AVHRR), a bordo da série de satélites da National Oceanic and Atmospheric Administration (NOAA).

NAVLivre 1.0: Procedimentos de instalação e utilização.

Este documento apresenta os procedimentos para instalação e utilização do sistema NAVLivre 1.0, um software de código livre desenvolvido para o processamento automático de imagens do sensor Advanced Very High Resolution Radiometer (AVHRR) a bordo dos satélites da National Oceanic Atmospheric Administration (NOAA). O NAVLivre é uma derivação do sistema NAVPRO, criado pela Embrapa Informática Agropecuária em parceria com a Universidade Estadual de Campinas (Unicamp), que contou com o repasse do pacote computacional NAV (NAVigation), desenvolvido pelo Colorado Center for Astrodynamics Research (CCAR), da Universidade do Colorado, Boulder, EUA. O diferencial do NAVLivre é a ausência dos módulos desenvolvidos em Interactive Data Language (IDL), presentes no NAVPRO, e dependentes de softwares proprietários. O NAVLivre é um pacote totalmente livre, que realiza de forma automática as principais etapas do processamento das imagens NOAA, como a correção radiométrica, o georreferenciamento preciso e a geração da imagem final em formato GeoTIFF, compatível com os principais pacotes de processamento de imagens. O NAVLivre é executado em plataforma Linux e foi implementado em script c-shell e linguagem C. Seu uso é indicado aos usuários avançados de imagens NOAA, que demandam o processamento em lote de grandes volumes de dados. As rotinas e scripts aqui descritos são de domínio público, podendo ser alterados conforme necessidade do usuário.

Precisão posicional dos focos de queimadas no Estado de Mato Grosso.

Para estimar a precisão posicional dos pontos de queimadas, fornecidos pelo Inpe e identificados com auxilio das imagens National Oceanic and Atmospheric Administration (NOAA) e o Advanced Very High Resolution Radiometer (AVHRR), foram utilizados diferentes conjuntos de dados de queimadas, obtidos pela internet diretamente do site de queimadas do Inpe (INPE, 2007), imagens do satélite Landsat, composição colorida das bandas R5, G4 e B3, com data de aquisição situada até 30 dias posteriores à ocorrência dos focos de calor. O período máximo de defasagem entre a ocorrência e identificação dos pontos de calor pelo Inpe e a data de aquisição das imagens de satélite, de 30 dias, foi estabelecido com o objetivo de assegurar que as evidências da ocorrência das queimadas identificadas não fossem significativamente alteradas pela ação dos ventos ou das chuvas que transportam, lixiviam ou lavam as cinzas que são depositadas sobre o solo após a ocorrência de uma queimada.

Salicylate accumulation inhibits growth at chilling temperature in Arabidopsis

Ian M. Scott, Shannon M. Clarke, Jacqueline E. Wood and Luis A.J. Mur (2004). Salicylate accumulation inhibits growth at chilling temperature in Arabidopsis. Plant Physiology, 135(2), 1040-1049. RAE2008

Abandono e absentismo escolar no concelho de Ponta Delgada

Dissertação apresentada à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Mestre em Ciências da Educação: Educação Especial, área de especialização em Domínio Emocional e da Personalidade

Household Health and Cocoa Production: A Baseline Survey of Smallholder Farming Households in Western Region, Ghana

Background Chronic illness and premature mortality from malaria, water-borne diseases, and respiratory illnesses have long been known to diminish the welfare of individuals and households in developing countries. Previous research has also shown that chronic diseases among farming populations suppress labor productivity and agricultural output. As the illness and death toll from HIV/AIDS continues to climb in most of sub-Saharan Africa, concern has arisen that the loss of household labor it causes will reduce crop yields, impoverish farming households, intensify malnutrition, and suppress growth in the agricultural sector. If chronic morbidity and premature mortality among individuals in farming households have substantial impacts on household production, and if a large number of households are affected, it is possible that an increase in morbidity and mortality from HIV/AIDS or other diseases could affect national aggregate output and exports. If, on the other hand, the impact at the household farm level is modest, or if relatively few households are affected, there is likely to be little effect on aggregate production across an entire country. Which of these outcomes is more likely in West Africa is unknown. Little rigorous, quantitative research has been published on the impacts of AIDS on smallholder farm production, particularly in West Africa. The handful of studies that have been conducted have looked mainly at small populations in areas of very high HIV prevalence in southern and eastern Africa. Conclusions about how HIV/AIDS, and other causes of chronic morbidity and mortality, are affecting agriculture across the continent cannot be drawn from these studies. In view of the importance of agriculture, and particularly smallholder agriculture, in the economies of most African countries and the scarcity of resources for health interventions, it is valuable to identify, describe, and quantify the impact of chronic morbidity and mortality on smallholder production of important crops in West Africa. One such crop is cocoa. In Ghana, cocoa is a crop of national importance that is produced almost exclusively by smallholder households. In 2003, Ghana was the world’s second-largest producer of cocoa. Cocoa accounted for a quarter of Ghana’s export revenues that year and generated 15 percent of employment. The success and growth of the cocoa industry is thus vital to the country’s overall social and economic development. Study Objectives and Methods In February and March 2005, the Center for International Health and Development of Boston University (CIHD) and the Department of Agricultural Economics and Agribusiness (DAEA) of the University of Ghana, with financial support from the Africa Bureau of the U.S. Agency for International Development and from Mars, Inc., which is a major purchaser of West African cocoa, conducted a survey of a random sample of cocoa farming households in the Western Region of Ghana. The survey documented the extent of chronic morbidity and mortality in cocoa growing households in the Western Region of Ghana, the country’s largest cocoa growing region, and analyzed the impact of morbidity and mortality on cocoa production. It aimed to answer three specific research questions. (1) What is the baseline status of the study population in terms of household size and composition, acute and chronic morbidity, recent mortality, and cocoa production? (2) What is the relationship between household size and cocoa production, and how can this relationship be used to understand the impact of adult mortality and chronic morbidity on the production of cocoa at the household level? The study population was the approximately 42,000 cocoa farming households in the southern part of Ghana’s Western Region. A random sample of households was selected from a roster of eligible households developed from existing administrative information. Under the supervision of the University of Ghana field team, enumerators were graduate students of the Department of Agricultural Economics and Agribusiness or employees of the Cocoa Services Division. A total of 632 eligible farmers participated in the survey. Of these, 610 provided complete responses to all questions needed to complete the multivariate statistical analysis reported here.

Efficiently and Fairly Allocating Bandwidth at a Highly Congested Link

We consider the problem of efficiently and fairly allocating bandwidth at a highly congested link to a diverse set of flows, including TCP flows with various Round Trip Times (RTT), non-TCP-friendly flows such as Constant-Bit-Rate (CBR) applications using UDP, misbehaving, or malicious flows. Though simple, a FIFO queue management is vulnerable. Fair Queueing (FQ) can guarantee max-min fairness but fails at efficiency. RED-PD exploits the history of RED's actions in preferentially dropping packets from higher-rate flows. Thus, RED-PD attempts to achieve fairness at low cost. By relying on RED's actions, RED-PD turns out not to be effective in dealing with non-adaptive flows in settings with a highly heterogeneous mix of flows. In this paper, we propose a new approach we call RED-NB (RED with No Bias). RED-NB does not rely on RED's actions. Rather it explicitly maintains its own history for the few high-rate flows. RED-NB then adaptively adjusts flow dropping probabilities to achieve max-min fairness. In addition, RED-NB helps RED itself at very high loads by tuning RED's dropping behavior to the flow characteristics (restricted in this paper to RTTs) to eliminate its bias against long-RTT TCP flows while still taking advantage of RED's features at low loads. Through extensive simulations, we confirm the fairness of RED-NB and show that it outperforms RED, RED-PD, and CHOKe in all scenarios.

GreedyDual-Join: Locality-Aware Buffer Management for Approximate Join Processing Over Data Streams

We investigate adaptive buffer management techniques for approximate evaluation of sliding window joins over multiple data streams. In many applications, data stream processing systems have limited memory or have to deal with very high speed data streams. In both cases, computing the exact results of joins between these streams may not be feasible, mainly because the buffers used to compute the joins contain much smaller number of tuples than the tuples contained in the sliding windows. Therefore, a stream buffer management policy is needed in that case. We show that the buffer replacement policy is an important determinant of the quality of the produced results. To that end, we propose GreedyDual-Join (GDJ) an adaptive and locality-aware buffering technique for managing these buffers. GDJ exploits the temporal correlations (at both long and short time scales), which we found to be prevalent in many real data streams. We note that our algorithm is readily applicable to multiple data streams and multiple joins and requires almost no additional system resources. We report results of an experimental study using both synthetic and real-world data sets. Our results demonstrate the superiority and flexibility of our approach when contrasted to other recently proposed techniques.

To Queue or Not to Queue: When Queueing is Better Than Timesharing in a Distributed System

We examine the question of whether to employ the first-come-first-served (FCFS) discipline or the processor-sharing (PS) discipline at the hosts in a distributed server system. We are interested in the case in which service times are drawn from a heavy-tailed distribution, and so have very high variability. Traditional wisdom when task sizes are highly variable would prefer the PS discipline, because it allows small tasks to avoid being delayed behind large tasks in a queue. However, we show that system performance can actually be significantly better under FCFS queueing, if each task is assigned to a host based on the task's size. By task assignment, we mean an algorithm that inspects incoming tasks and assigns them to hosts for service. The particular task assignment policy we propose is called SITA-E: Size Interval Task Assignment with Equal Load. Surprisingly, under SITA-E, FCFS queueing typically outperforms the PS discipline by a factor of about two, as measured by mean waiting time and mean slowdown (waiting time of task divided by its service time). We compare the FCFS/SITA-E policy to the processor-sharing case analytically; in addition we compare it to a number of other policies in simulation. We show that the benefits of SITA-E are present even in small-scale distributed systems (four or more hosts). Furthermore, SITA-E is a static policy that does not incorporate feedback knowledge of the state of the hosts, which allows for a simple and scalable implementation.

Accelerating Internet Streaming Media Delivery Using Network-Aware Partial Caching

Internet streaming applications are adversely affected by network conditions such as high packet loss rates and long delays. This paper aims at mitigating such effects by leveraging the availability of client-side caching proxies. We present a novel caching architecture (and associated cache management algorithms) that turn edge caches into accelerators of streaming media delivery. A salient feature of our caching algorithms is that they allow partial caching of streaming media objects and joint delivery of content from caches and origin servers. The caching algorithms we propose are both network-aware and stream-aware; they take into account the popularity of streaming media objects, their bit-rate requirements, and the available bandwidth between clients and servers. Using realistic models of Internet bandwidth (derived from proxy cache logs and measured over real Internet paths), we have conducted extensive simulations to evaluate the performance of various cache management alternatives. Our experiments demonstrate that network-aware caching algorithms can significantly reduce service delay and improve overall stream quality. Also, our experiments show that partial caching is particularly effective when bandwidth variability is not very high.

Synthesis and reactivity of alpha-thio-beta-chloroacrylamides and alpha-thio-beta-chloroenones

Development of novel synthetic methodology for selective transformation of organic compounds is a central element underpinning organic synthesis with control of chemo-, regio- and stereoselectivity a very high priority. Reactions which can be conducted under mild reaction conditions and, ideally in an environmentally attractive manner, are particularly advantageous. The principal objective of this thesis was to explore the synthesis, reactivity and synthetic utility of a series of α,β-thio-β-chloroenones. The stereochemical features of these transformations and the potential of this novel series of compounds in the synthesis of bioactive compounds were of particular interest. In exploring the reactivity of these compounds, the key transformations included nucleophilic additions and Stille cross-coupling at the β-carbon. Chapter 1 reviews the literature relevant to the research conducted, and focuses in particular on the synthesis of β-chloroenones and related unsaturated carbonyl compounds. The synthesis of chalcone compounds from various precursors is also discussed, with particular emphasis on the use of palladium cross-coupling reactions in the preparation of these compounds. The biological activity of chalcones is also summarised in this chapter. The second chapter delineates the stereoselective synthesis of the novel α-thio-β-chloroenones from the corresponding α-thioketones in a multistep reaction cascade initiated by a NCS-mediated chlorination. A range of both alkyl and aryl β-chloroenones were prepared in this work and the oxidation of these compounds to the corresponding sulfoxides and sulfones is also outlined. The electrophilicity of the β-carbon of the enones was examined in nucleophilic addition/substitution reactions with successful access to a variety of synthetically useful novel adducts including acetals and enaminoketones. Investigation of the synthetic potential of the Stille cross-coupling reaction with the novel α-thio-β-chloroenones was explored and provided an efficient route for the synthesis of a novel series of chalcones. Most importantly this new methodology provided a new and synthetically powerful approach for carbon-carbon bond formation at the β-carbon under mild neutral conditions. A preliminary investigation into the use of these β-chloroenones as dienophiles in Diels-Alder cycloaddition reactions is also discussed in this chapter. Chapter 2 also reports the nucleophilic addition of N, O, S and C nucleophiles to previously described β-chloroacrylamides and their corresponding sulfoxide derivatives. This work builds on previous research carried out in this programme and the reactivity of these β-chloroacrylamides at the sulfide and sulfoxide level is compared. Comparison of the reactivity of the β-chloroacrylamides, in nucleophilic substitution and Stille-coupling, with that of the novel β-chloroenones is of interest. Finally, the biological activity of both the β-chloroenones and the β-chloroacrylamides in terms of cytotoxicity is summarised in Chapter 2. The final chapter, Chapter 3, details the full experimental procedures, including spectroscopic and analytical data for the compounds prepared during this research.

Bridge-vehicle interaction for structural health monitoring: potentials, applications, and limitations

Structural Health Monitoring (SHM) is an integral part of infrastructure maintenance and management systems due to socio-economic, safety and security reasons. The behaviour of a structure under vibration depends on structure characteristics. The change of structure characteristics may suggest the change in system behaviour due to the presence of damage(s) within. Therefore the consistent, output signal guided, and system dependable markers would be convenient tool for the online monitoring, the maintenance, rehabilitation strategies, and optimized decision making policies as required by the engineers, owners, managers, and the users from both safety and serviceability aspects. SHM has a very significant advantage over traditional investigations where tangible and intangible costs of a very high degree are often incurred due to the disruption of service. Additionally, SHM through bridge-vehicle interaction opens up opportunities for continuous tracking of the condition of the structure. Research in this area is still in initial stage and is extremely promising. This PhD focuses on using bridge-vehicle interaction response for SHM of damaged or deteriorating bridges to monitor or assess them under operating conditions. In the present study, a number of damage detection markers have been investigated and proposed in order to identify the existence, location, and the extent of an open crack in the structure. The theoretical and experimental investigation has been conducted on Single Degree of Freedom linear system, simply supported beams. The novel Delay Vector Variance (DVV) methodology has been employed for characterization of structural behaviour by time-domain response analysis. Also, the analysis of responses of actual bridges using DVV method has been for the first time employed for this kind of investigation.