Jet:progress in performance and understanding

In 1990 JET operated with a number of technical improvements which led to advances in performance and permitted the carrying out of experiments specifically aimed at improving physics understanding of selected topics relevant to the "NEXT STEP". The new facilities include beryllium antenna screens, a prototype lower hybrid current drive system, and modification of the NI system to enable the injection of He-3 and He-4. Continued investigation of the hot-ion H-mode produced a value of n(D)(0)tau-E(T)(i)(0) = 9 x 10(20)m-3s keV, which is near conditions required for Q(DT) = 1, while a new peaked density profile H-mode was developed with only slightly lower performance. Progress towards steady state operation has been made by achieving ELMy H-modes under certain operating conditions, while maintaining good tau-E values. Experimental simulation of He ash transport indicates effective removal of alpha-particles from the plasma core for both L and H mode plasmas. Detailed analyses of particle and energy transport have helped establish a firmer link between particle and energy transport, and have suggested a connection between reduced energy transport and reversed shear. Numerical and analytic studies of divertor physics carried out for the pumped divertor phase of JET have helped clarify the key parameters governing impurity retention, and an intensive model validation effort has begun. Experimental simulation of alpha-particle effects with beta-fast up to 8% have shown that the slowing down processes are classical, and have given no evidence of deleterious collective effects.

Studies on the nutritional value of cassava (Manihot utillisima) peels as energy source in the diet of Oreochromis niloticus fry fed in indoor glass aquaria

This study, though, has as its core objective cost reduction in aquaculture nutrition was equally designed to investigate the value of the peels of cassava (Manihot utillisima) as energy source in the diet of Oreochromis niloticus fry. Three levels of cassava peels diet and a control (100% yellow maize in the carbohydrate mixture) was prepared and tested on O. niloticus fry for ten (10) weeks. The fry with mean weight of 0.32g were grouped fifteen (15) in each of the glass aquaria measuring 60x30x30cm with a maximum capacity of 52 litres of water. The fry were fed twice daily at 10% biomass. Weekly, the fry were weighed to determine the weight increment or otherwise and the quality of feed adjusted accordingly. Water quality parameters like temperature, pH and dissolved oxygen (D.0) were monitored and found to be at desirable level. DT 3 (97 % cassava peels and 3% yellow maize) in the carbohydrate mixture gave the best growth performance. The fry fed, this diet gained mean weight of 1.18g for the period of the experiment. However, the poorest performance in terms of growth was from fry fed the control diet (100%yellow maize in the carbohydrate mixture) fry fed this diet gained mean weight of 0.80 for the duration of the experiment. Analysis of the various growth indices like SGR, PER, FCR and NPU shows that DT3 was the overall best diet with an SGR value of2.40 and FCR of 43.83. However, DT 1 (70% cassava peels and 30% yellow maize) gave the poorest SGR of 1.61 and FCR of 67.58. The difference in weight gain among the fry fed the three levels of cassava peels diet and the control was not statically significant (P>0.05)

Functional genomic studies of the structure and regulation of eukaryotic transcriptomes

The main focus of this thesis is the use of high-throughput sequencing technologies in functional genomics (in particular in the form of ChIP-seq, chromatin immunoprecipitation coupled with sequencing, and RNA-seq) and the study of the structure and regulation of transcriptomes. Some parts of it are of a more methodological nature while others describe the application of these functional genomic tools to address various biological problems. A significant part of the research presented here was conducted as part of the ENCODE (ENCyclopedia Of DNA Elements) Project.

The first part of the thesis focuses on the structure and diversity of the human transcriptome. Chapter 1 contains an analysis of the diversity of the human polyadenylated transcriptome based on RNA-seq data generated for the ENCODE Project. Chapter 2 presents a simulation-based examination of the performance of some of the most popular computational tools used to assemble and quantify transcriptomes. Chapter 3 includes a study of variation in gene expression, alternative splicing and allelic expression bias on the single-cell level and on a genome-wide scale in human lymphoblastoid cells; it also brings forward a number of critical to the practice of single-cell RNA-seq measurements methodological considerations.

The second part presents several studies applying functional genomic tools to the study of the regulatory biology of organellar genomes, primarily in mammals but also in plants. Chapter 5 contains an analysis of the occupancy of the human mitochondrial genome by TFAM, an important structural and regulatory protein in mitochondria, using ChIP-seq. In Chapter 6, the mitochondrial DNA occupancy of the TFB2M transcriptional regulator, the MTERF termination factor, and the mitochondrial RNA and DNA polymerases is characterized. Chapter 7 consists of an investigation into the curious phenomenon of the physical association of nuclear transcription factors with mitochondrial DNA, based on the diverse collections of transcription factor ChIP-seq datasets generated by the ENCODE, mouseENCODE and modENCODE consortia. In Chapter 8 this line of research is further extended to existing publicly available ChIP-seq datasets in plants and their mitochondrial and plastid genomes.

The third part is dedicated to the analytical and experimental practice of ChIP-seq. As part of the ENCODE Project, a set of metrics for assessing the quality of ChIP-seq experiments was developed, and the results of this activity are presented in Chapter 9. These metrics were later used to carry out a global analysis of ChIP-seq quality in the published literature (Chapter 10). In Chapter 11, the development and initial application of an automated robotic ChIP-seq (in which these metrics also played a major role) is presented.

The fourth part presents the results of some additional projects the author has been involved in, including the study of the role of the Piwi protein in the transcriptional regulation of transposon expression in Drosophila (Chapter 12), and the use of single-cell RNA-seq to characterize the heterogeneity of gene expression during cellular reprogramming (Chapter 13).

The last part of the thesis provides a review of the results of the ENCODE Project and the interpretation of the complexity of the biochemical activity exhibited by mammalian genomes that they have revealed (Chapters 15 and 16), an overview of the expected in the near future technical developments and their impact on the field of functional genomics (Chapter 14), and a discussion of some so far insufficiently explored research areas, the future study of which will, in the opinion of the author, provide deep insights into many fundamental but not yet completely answered questions about the transcriptional biology of eukaryotes and its regulation.

Quantum Mechanics Studies of Fuel Cell Catalysts and Proton Conducting Ceramics with Validation by Experiment

We carried out quantum mechanics (QM) studies aimed at improving the performance of hydrogen fuel cells. This led to predictions of improved materials, some of which were subsequently validated with experiments by our collaborators.

In part I, the challenge was to find a replacement for the Pt cathode that would lead to improved performance for the Oxygen Reduction Reaction (ORR) while remaining stable under operational conditions and decreasing cost. Our design strategy was to find an alloy with composition Pt3M that would lead to surface segregation such that the top layer would be pure Pt, with the second and subsequent layers richer in M. Under operating conditions we expect the surface to have significant O and/or OH chemisorbed on the surface, and hence we searched for M that would remain segregated under these conditions. Using QM we examined surface segregation for 28 Pt₃M alloys, where M is a transition metal. We found that only Pt₃Os and Pt₃Ir showed significant surface segregation when O and OH are chemisorbed on the catalyst surfaces. This result indicates that Pt₃Os and Pt3Ir favor formation of a Pt-skin surface layer structure that would resist the acidic electrolyte corrosion during fuel cell operation environments. We chose to focus on Os because the phase diagram for Pt-Ir indicated that Pt-Ir could not form a homogeneous alloy at lower temperature. To determine the performance for ORR, we used QM to examine all intermediates, reaction pathways, and reaction barriers involved in the processes for which protons from the anode reactions react with O₂ to form H₂O. These QM calculations used our Poisson-Boltzmann implicit solvation model include the effects of the solvent (water with dielectric constant 78 with pH 7 at 298K). We found that the rate determination step (RDS) was the O_ad hydration reaction (O_ad + H₂O_ad -> OH_ad + OH_ad) in both cases, but that the barrier for pure Pt of 0.50 eV is reduced to 0.48 eV for Pt₃Os, which at 80 degrees C would increase the rate by 218%. We collaborated with the Pu-Wei Wu’s group to carry out experiments, where we found that the dealloying process-treated Pt2Os catalyst showed two-fold higher activity at 25 degrees C than pure Pt and that the alloy had 272% improved stability, validating our theoretical predictions.

We also carried out similar QM studies followed by experimental validation for the Os/Pt core-shell catalyst fabricated by the underpotential deposition (UPD) method. The QM results indicated that the RDS for ORR is a compromise between the OOH formation step (0.37 eV for Pt, 0.23 eV for Pt_2ML/Os core-shell) and H₂O formation steps (0.32 eV for Pt, 0.22 eV for Pt_2ML/Os core-shell). We found that Pt_2ML/Os has the highest activity (compared to pure Pt and to the Pt₃Os alloy) because the 0.37 eV barrier decreases to 0.23 eV. To understand what aspects of the core shell structure lead to this improved performance, we considered the effect on ORR of compressing the alloy slab to the dimensions of pure Pt. However this had little effect, with the same RDS barrier 0.37 eV. This shows that the ligand effect (the electronic structure modification resulting from the Os substrate) plays a more important role than the strain effect, and is responsible for the improved activity of the core- shell catalyst. Experimental materials characterization proves the core-shell feature of our catalyst. The electrochemical experiment for Pt_2ML/Os/C showed 3.5 to 5 times better ORR activity at 0.9V (vs. NHE) in 0.1M HClO₄ solution at 25 degrees C as compared to those of commercially available Pt/C. The excellent correlation between experimental half potential and the OH binding energies and RDS barriers validate the feasibility of predicting catalyst activity using QM calculation and a simple Langmuir–Hinshelwood model.

In part II, we used QM calculations to study methane stream reforming on a Ni-alloy catalyst surfaces for solid oxide fuel cell (SOFC) application. SOFC has wide fuel adaptability but the coking and sulfur poisoning will reduce its stability. Experimental results suggested that the Ni4Fe alloy improves both its activity and stability compared to pure Ni. To understand the atomistic origin of this, we carried out QM calculations on surface segregation and found that the most stable configuration for Ni₄Fe has a Fe atom distribution of (0%, 50%, 25%, 25%, 0%) starting at the bottom layer. We calculated that the binding of C atoms on the Ni4Fe surface is 142.9 Kcal/mol, which is about 10 Kcal/mol weaker compared to the pure Ni surface. This weaker C binding energy is expected to make coke formation less favorable, explaining why Ni₄Fe has better coking resistance. This result confirms the experimental observation. The reaction energy barriers for CHx decomposition and C binding on various alloy surface, Ni₄X (X=Fe, Co, Mn, and Mo), showed Ni₄Fe, Ni₄Co, and Fe₄Mn all have better coking resistance than pure Ni, but that only Ni₄Fe and Fe₄Mn have (slightly) improved activity compared to pure Ni.

In part III, we used QM to examine the proton transport in doped perovskite-ceramics. Here we used a 2x2x2 supercell of perovskite with composition Ba₈X₇M₁(OH)₁O₂₃ where X=Ce or Zr and M=Y, Gd, or Dy. Thus in each case a 4⁺ X is replace by a 3⁺ M plus a proton on one O. Here we predicted the barriers for proton diffusion allowing both includes intra-octahedron and inter-octahedra proton transfer. Without any restriction, we only observed the inter-octahedra proton transfer with similar energy barrier as previous computational work but 0.2 eV higher than experimental result for Y doped zirconate. For one restriction in our calculations is that the O_donor-O_acceptor atoms were kept at fixed distances, we found that the barrier difference between cerates/zirconates with various dopants are only 0.02~0.03 eV. To fully address performance one would need to examine proton transfer at grain boundaries, which will require larger scale ReaxFF reactive dynamics for systems with millions of atoms. The QM calculations used here will be used to train the ReaxFF force field.

Estudo de eventos amparado em métricas contábeis: detectando performance operacional anormal em firmas brasileiras

O estudo de eventos amparado em métricas contábeis pode ser considerado como aquele que investiga se os retornos anormais no mercado acionário possuem uma contrapartida no lado real, ou seja, se a performance operacional da firma sofreu modificação decorrente de um determinado evento econômico. O presente estudo tem como foco as escolhas que um pesquisador deve fazer na hora da modelagem de um estudo de evento amparado em métricas contábeis, tais como: que medida de performance utilizar, que modelo de expectativa de performance operacional servirá como benchmark, e que teste estatístico poderia detectar com mais eficiência as anormalidades. Um exemplo de estudo que testa empiricamente, nos EUA, o efeito das escolhas acima nas especificações e poder dos testes estatísticos é o de Barber e Lyon (1996). O presente trabalho pretende testar empiricamente os modelos, analisados por esses autores, nas empresas brasileiras. Para tal, foram extraídas da base de dados da Economática todas as empresas listadas na Bolsa de Valores de São Paulo BOVESPA, com dados contábeis disponíveis para os anos de 2004 a 2010, sendo que foram objeto de análise os anos de 2005 a 2010. Obtiveram-se dados para 605 empresas, e uma média de 1606 observações por métrica contábil. Foram testadas 6 medidas contábeis de performance operacional e 13 modelos de expectativa de desempenho. Para atingir o objetivo, a pesquisa foi dividida em três fases. Fase I Elaboração dos Modelos de Expectativa e formação dos Grupos de Controle; Fase II Teste do Poder explicativo dos Modelos de Expectativa; Fase III Testes para Detectar Performance Operacional Anormal. Para o caso brasileiro, pode-se dizer que a melhor medida para detectar performances operacionais anormais é o ROA2 (Ebitda/Ativo Total), já que foi a que apresentou mais modelos que atenderam a todos os testes estabelecidos, em todas as fases da pesquisa. Quanto ao benchmark, o melhor apontado pelos resultados foi o filtro indústria, classificação Economática. O modelo de desempenho defasado da firma, também apresentou resultados satisfatórios. Por fim, o teste estatístico mais apropriado para detectar performances operacionais anormais é o de Wilcoxon.

Temporal Changes in a Tropical Nekton Assemblage and Performance of a Prawn Selective Gear

The temporal variation of components of a moderately diverse (H=1.46) tropical estuarine fish assemblage (long. 146°30'E, lat. 8°45'S) was directed by salinities that had been determined by local oceanographic and probably topographic conditions. For this assemblage, two types of intrayear component profiles are predicted. Pooled data (1988-91) reveal a large component of regular/resident species (43%) in an assemblage which has been under a narrow temperature regime «5T). These results facilitate a discussion on the relevance and usefulness of three hypotheses often cited in studies concerning species diversity and component characteristics of the subtropical/tropical coastal nonreef fish assemblages. Manifestations of the assemblage are reflected in catch composition and weights of 39 trials conducted for a selective prawning gear whose performance in bycatch reduction, mainly for finfishes, is judged by an index, E, we have previously proposed. This gear is capable of harvesting the prawn while conserving the demersal fish. Behavioral responses to netting of the prawns and the finfishes, especially the nearshore surface schoolers such as leiognathids, are discussed from several points of view. An adaptation in terms of group selection for leiognathids of their locking mechanism of median fin spines has been interpreted. For the purpose of bycatch reduction or E enhancement, suggestions for improvements in net design and trawl configuration by considering the behavioral features of fish are made. Our original formula of E is modified for general use. Bycatch problems in the regional prawn fisheries and their possible impacts on fishery planning and development in Papua New Guinea as a developing country are discussed. The gear tested may offer enormous ecological and economic benefits. The gear is multipurpose, extremely simple, and can also be used as a biological sampler.

Performance: o desenrolar do drama em um grupo de Capoeira Angola

Este trabalho é um estudo de caso cujo objeto consiste em um grupo de capoeira angola que passava por um momento de transição. A partir do rompimento entre os dois principais líderes do grupo sem mestre, investigou-se as tensões existentes reveladoras de diferentes pontos de vista sobre a capoeira e a atuação do mesmo em suas redes de relacionamento. Estas diferenças são significativas uma vez que estão relacionadas com as transformações em torno das concepções sobre esta atividade e também se inserem no contexto de transformações em curso na cidade do Rio de Janeiro. Concebendo-se a capoeira angola como um estilo de vida, as diversas maneiras de pensá-la também geram diferentes maneiras de atuar na sociedade. A metodologia consiste na pesquisa qualitativa com observação participante. Escolheu-se a abordagem pela performance por se acreditar que os valores são comunicados também por meio das diferenças de movimentação. Ao final da pesquisa, concluiu-se que o grupo investigado passava por um momento de transição, que considero como uma passagem apoiada nas considerações de Victor Turner, já em vias de transição para a fase seguinte a partir da indicação do treinel que ficou responsável de se juntar a um grupo já estabelecido.

A contribuição da epidemiologia aos estudos de avaliação da performance clínica através de um evento traçador: o caso das prescrições médicas às crianças com infecção respiratória aguda.

Esta dissertação discute os possíveis delineamentos epidemiológicos e estratégias de análise de dados capazes de apreender as funções de ocorrência de interesse nos estudos de fatores de risco para a prescrição médica inadequada as crianças com infecção respirat6ria aguda, atendidas na rede ambulatorial. Para tal, os principais marcos teóricos que devem nortear a construção de um desenho de estudo epidemiológico são apresentados, assim como as diferentes etapas que devem ser consideradas quando se esta planejando um processo de analise estatística de dados em estudos epidemiológicos. A partir da elaboração de um modelo teórico-conceitual que represente as relações entre os diversos fatores que parecem estar envolvidos com a prescrição e o consumo de medicamentos, diferentes estratégias de pesquisa e pianos de analise são discutidos, alertando-se para os principais problemas a serem evitados quando se busca um estudo com validade e precisão entre satisfatórias.

Wadge Bank trawl fishery studies. Pt. 1. The effect of the 1928 to 1935 commercial trawling on the demersal stock

The demersal fish stock of Wadge Bank is one of the important fish resources for both Sri Lanka and India. Sivalingam and Medcof (1957) have given an account of its history, general features and relative productivity. According to records the total fishing effort on the bank had been fluctuating and very recently the number of boats operating on the bank has suddenly increased, and there is a possibility that still more will begin operating on the bank in the near future (Mendis, 1965). The increased fishing effort with the possibility of still further increase calls for proper management practices by those concerned, in order to obtain the maximum sustained yield from the demersal stock. For this purpose a detailed study of the past performance of the fishery is essential. With this in view all records of commercial operations up to 1960 are being analysed by the present author and are to be published in a series. This is the first paper in the series and gives a detailed analysis of the first commercial trawling operations from 1928 to 1935. Since there had been a major break of about 10 years between this and the present fishery this data is being analysed separately.

Performance of single mode laser components using 2D photonic lattice reflectors

This paper will report studies of the placement of 2D photonic gratings on either side of the ridge in a Fabry Perot laser device in order to cause single mode emission. Using this approach, side mode suppression ratios of up to 30 dB are achieved, the emission remaining single mode even under 10 Gb/s large signal modulation. It is found that the use of the grating not only causes spectrally dependent reflection but in addition can lead to transverse mode fluctuations. The action of the grating has been studied not just in terms of its edge emission where conversion of the transverse modes is achieved, but also through measurement of the vertical emission from the structure where strong filtering action is observed.

Growth performance, recovery rate and fish yield of GIFT strain at various water depths under rice-fish culture systems

Effect of water depth on recovery rate, growth performance and fish yield of GIFT in the rice-fish production systems was studies in experimental plots of 123 m2 with a pond refuge of I meter deep which covered 10% of the total land area. Mortality rate of fish was very low ranging from 0.81-1.63%. However, at harvest, recovery rate ranged from 76.69-82.93% with the highest recovery at 11-15 em of water depth. Significantly the highest absolute growth (99.97) and specific growth rate (2.42%) were found at 21-25 cm water depth. The same treatment also produced significantly higher fish yield (909.76 kg/ha) although statistically similar to the fish yield (862.60 kg/ha) obtained at ll-15 em of water depth. Results also suggested that higher water depth can produce bigger fish but no significant effects of water depth was found on fish yield in the treatments 11-15 cm and 21-25 cm water depths of this experiment.

Studies on isolation of salmonella from sea foods 1. Comparison of enrichment and selective media for recovery of salmonellae from fish

Three enrichment broths and six plating media were compared for efficiency of detection Salmonella in the presence of numbers of Coliforms (10super(5)/ml) and proteus (10super(3)/ml) from artificially inoculated fish samples. Recovery experiments Salmonella anatum, S. typhimurium and S. enteritidis indicated that the two enrichment broths Dulcitol Selinite (DSE) and Selinite Cystine (SC) were equally efficient. Further, the viability of Salmonella, inoculated into fish muscle and kept at 4°C for 48 hours, was found to be not affected by the low temperature storage. Selective plating media like Xylose Lysine Deoxycholate agar (XLD), Brilliant Green Sulphadiazine agar (BGS) and Brilliant Green agar (BG) were found to be superior in performance to Salmonella-Shigella agar: (SS) and Bismuth Sui phite agar (BiS).

Studies on arsenical creosote as a wood preservative for marine structures. Part 2. Observation on leaching, corrosion and resistance to borer attack

A detailed study on arsenical creosote with reference to leaching, corrosion and anti-borer properties was carried out. Results showed that aging had very little effect on the preservative which suggested better fixation of the preservative into the wood. Corrosion of mild steel, galvanised iron, aluminium-magnesium alloy (M57S) and copper panels in the preservative was found to be negligible. Normal creosote and low temperature creosote of Regional Research Laboratory, Hyderabad, both fortified with arsenic trioxide resisted borer damage on wooden panels for a period of over five months in the port of Cochin. The performance of low temperature creosote fortified with arsenic was found to be equally satisfactory when compared to normal creosote fortified in the same manner. A loading of 208.6 Kgs/ml³ for Haldu (Adina cordifolia) and 138 Kgs/m³ for Mango (Mangifera indica) in the case of normal creosote and 177 Kgs/m³ for Mango the case of RRL creosote were found to be sufficient for treating the wood.

Shore seines for reservoirs - Part 1 - Design and performance

Based on the studies to introduce active gears in reservoirs, a prototype shore seine was designed and tested, the details of which are presented in this communication. The results revealed that the operation of this gear could effectively control the proliferation of under-exploited species.

Predicting the performance of an office under climate change: A study of metrics, sensitivity and zonal resolution

Climate change is expected to have significant impact on the future thermal performance of buildings. Building simulation and sensitivity analysis can be employed to predict these impacts, guiding interventions to adapt buildings to future conditions. This article explores the use of simulation to study the impact of climate change on a theoretical office building in the UK, employing a probabilistic approach. The work studies (1) appropriate performance metrics and underlying modelling assumptions, (2) sensitivity of computational results to identify key design parameters and (3) the impact of zonal resolution. The conclusions highlight the importance of assumptions in the field of electricity conversion factors, proper management of internal heat gains, and the need to use an appropriately detailed zonal resolution. © 2010 Elsevier B.V. All rights reserved.