Amino acid pairing preferences in parallel beta-sheets in proteins

Statistical approaches have been applied to examine amino acid pairing preferences within parallel beta-sheets. The main chain hydrogen bonding pattern in parallel beta-sheets means that, for each residue pair, only one of the residues is involved in main chain hydrogen bonding with the strand containing the partner residue. We call this the hydrogen bonded (HB) residue and the partner residue the non-hydrogen bonded (nHB) residue, and differentiate between the favourability of a pair and that of its reverse pair, e.g. Asn(HB)-Thr(nHB) versus Thr(HB)-Asn(nHB). Significantly (p <= 0.000001) favoured pairings were rationalised using stereochemical arguments. For instance, Asn(HB)-Thr(nHB) and Arg(HB)-Thr(nHB) were favoured pairs, where the residues adopted favoured chi(1) rotamer positions that allowed side-chain interactions to occur. In contrast, Thr(HB)-Asn(nHB) and Thr(HB)-Arg(nHB) were not significantly favoured, and could only form side-chain interactions if the residues involved adopted less favourable chi(1) conformations. The favourability of hydrophobic pairs e.g. Ile(HB)-Ile(nHB), Val(HB)-Val(nHB) and Leu(HB)-Ile(nHB) was explained by the residues adopting their most preferred chi(1) and chi(2) conformations, which enabled them to form nested arrangements. Cysteine-cysteine pairs are significantly favoured, although these do not form intrasheet disulphide bridges. Interactions between positively and negatively charged residues were asymmetrically preferred: those with the negatively charged residue at the HB position were more favoured. This trend was accounted for by the presence of general electrostatic interactions, which, based on analysis of distances between charged atoms, were likely to be stronger when the negatively charged residue is the HB partner. The Arg(HB)-Asp(nHB) interaction was an exception to this trend and its favourability was rationalised by the formation of specific side-chain interactions. This research provides rules that could be applied to protein structure prediction, comparative modelling and protein engineering and design. The methods used to analyse the pairing preferences are automated and detailed results are available (http:// www.rubic.rdg.ac.uk/betapairprefsparallel/). (c) 2005 Elsevier Ltd. All rights reserved.

Genetic evidence of frequent long-distance recruitment in a vertebrate-dispersed tree

The importance of dispersal for the maintenance of biodiversity, while long-recognized, has remained unresolved. We used molecular markers to measure effective dispersal in a natural population of the vertebrate-dispersed Neotropical tree, Simarouba amara (Simaroubaceae) by comparing the distances between maternal parents and their offspring and comparing gene movement via seed and pollen in the 50 ha plot of the Barro Colorado Island forest, Central Panama. In all cases (parent-pair, mother-offspring, father-offspring, sib-sib) distances between related pairs were significantly greater than distances to nearest possible neighbours within each category. Long-distance seedling establishment was frequent: 74% of assigned seedlings established > 100 m from the maternal parent [mean = 392 +/- 234.6 m (SD), range = 9.3-1000.5 m] and pollen-mediated gene flow was comparable to that of seed [mean = 345.0 +/- 157.7 m (SD), range 57.6-739.7 m]. For S. amara we found approximately a 10-fold difference between distances estimated by inverse modelling and mean seedling recruitment distances (39 m vs. 392 m). Our findings have important implications for future studies in forest demography and regeneration, with most seedlings establishing at distances far exceeding those demonstrated by negative density-dependent effects.

The adsorption geometry of sulphur on Ir{100}: a quantitative LEED study

A quantitative low energy electron diffraction (LEED) analysis has been performed for the p(2 x 2)-S and c(2 x 2)-S surface structures formed by exposing the (1 x 1) phase of Ir{100} to H2S at 750 K. S is found to adsorb on the fourfold hollow sites in both structures leading to Pendry R-factor values of 0.17 for the p(2 x 2)-S and 0.16 for the c(2 x 2)-S structures. The distances between S and the nearest and next-nearest Ir atoms were found to be similar in both structures: 2.36 +/- 0.01 angstrom and 3.33 +/- 0.01 angstrom, respectively. The buckling in the second substrate layer is consistent with other structural studies for S adsorption on fcc{100} transition metal surfaces: 0.09 angstrom for p(2 x 2)-S and 0.02 angstrom for c(2 x 2)-S structures. The (1 x 5) reconstruction, which is the most stable phase for clean Ir{100}, is completely lifted and a c(2 x 2)-S overlayer is formed after exposure to H,S at 300 K followed by annealing to 520 K. CO temperature-programmed desorption (TPD) experiments indicate that the major factor in the poisoning of Ir by S is site blocking. (c) 2005 Elsevier B.V. All rights reserved.

Receding and disparity cues aid relaxation of accommodation

Purpose. Accommodation can mask hyperopia and reduce the accuracy of non-cycloplegic refraction. It is, therefore, important to minimize accommodation to obtain a measure of hyperopia as accurate as possible. To characterize the parameters required to measure the maximally hyperopic error using photorefraction, we used different target types and distances to determine which target was most likely to maximally relax accommodation and thus more accurately detect hyperopia in an individual. Methods. A PlusoptiX SO4 infra-red photorefractor was mounted in a remote haploscope which presented the targets. All participants were tested with targets at four fixation distances between 0.3 and 2 m containing all combinations of blur, disparity, and proximity/looming cues. Thirty-eight infants (6 to 44 weeks) were studied longitudinally, and 104 children [4 to 15 years (mean 6.4)] and 85 adults, with a range of refractive errors and binocular vision status, were tested once. Cycloplegic refraction data were available for a sub-set of 59 participants spread across the age range. Results. The maximally hyperopic refraction (MHR) found at any time in the session was most frequently found when fixating the most distant targets and those containing disparity and dynamic proximity/looming cues. Presence or absence of blur was less significant, and targets in which only single cues to depth were present were also less likely to produce MHR. MHR correlated closely with cycloplegic refraction (r = 0.93, mean difference 0.07 D, p = n.s., 95% confidence interval +/-<0.25 D) after correction by a calibration factor. Conclusions. Maximum relaxation of accommodation occurred for binocular targets receding into the distance. Proximal and disparity cues aid relaxation of accommodation to a greater extent than blur, and thus non-cycloplegic refraction targets should incorporate these cues. This is especially important in screening contexts with a brief opportunity to test for significant hyperopia. MHR in our laboratory was found to be a reliable estimation of cycloplegic refraction. (Optom Vis Sci 2009;86:1276-1286)

The role of spectral- and temporal-envelope room-acoustic cues in auditory selective attention

Listeners can attend to one of several simultaneous messages by tracking one speaker’s voice characteristics. Using differences in the location of sounds in a room, we ask how well cues arising from spatial position compete with these characteristics. Listeners decided which of two simultaneous target words belonged in an attended “context” phrase when it was played simultaneously with a different “distracter” context. Talker difference was in competition with position difference, so the response indicates which cue‐type the listener was tracking. Spatial position was found to override talker difference in dichotic conditions when the talkers are similar (male). The salience of cues associated with differences in sounds, bearings decreased with distance between listener and sources. These cues are more effective binaurally. However, there appear to be other cues that increase in salience with distance between sounds. This increase is more prominent in diotic conditions, indicating that these cues are largely monaural. Distances between spectra calculated using a gammatone filterbank (with ERB‐spaced CFs) of the room’s impulse responses at different locations were computed, and comparison with listeners’ responses suggested some slight monaural loudness cues, but also monaural “timbre” cues arising from the temporal‐ and spectral‐envelope differences in the speech from different locations.

Decreased accommodation during decompensation of distance exotropia

Objective. Disparity cues can be a major drive to accommodation via the CA/C (convergence accommodation to convergence) linkage but, on decompensation of exotropia, disparity cues are extinguished by suppression, so this drive is lost. This study investigated accommodation and vergence responses to disparity, blur and proximal cues in a group of distance exotropes aged between 4-11 years both during decompensation and when exotropic. Methods. 19 participants with distance exotropia were tested using a PlusoptiXSO4 photorefractor set in a remote haploscopic device which assessed simultaneous vergence and accommodation to a range of targets incorporating different combinations of blur, disparity and proximal cues at four fixation distances between 2m and 33cm. Responses on decompensation were compared to those from the same children when their deviation was controlled. Results. Manifest exotropia was more common in the more impoverished cue conditions. When decompensated for near, mean accommodation gain for the all-cue (naturalistic) target reduced significantly (p<0.0001), with resultant mean under-accommodation of 2.33D at 33cm. The profile of near cues usage changed after decompensation, with blur and proximity driving residual responses, but these remaining cues did not compensate for loss of accommodation caused by the removal of disparity. Conclusions. Accommodation often reduces on decompensation of distance exotropia as the drive from convergence is extinguished, providing a further reason to try to prevent decompensation for near.

Evidence that convergence rather than accommodation controls intermittent distance exotropia

Purpose. This study considered whether vergence drives accommodation or accommodation drives vergence during the control of distance exotropia for near fixation. High accommodative convergence to accommodation (AC/A) ratios are often used to explain this control, but the role of convergence to drive accommodation (the CA/C relationship) is rarely considered. Atypical CA/C characteristics could equally, or better, explain common clinical findings. Methods. 19 distance exotropes, aged 4-11 years, were compared while controlling their deviation with 27 non-exotropic controls aged 5-9 years. Simultaneous vergence and accommodation responses were measured to a range of targets incorporating different combinations of blur, disparity and looming cues at four fixation distances between 2m and 33cm. Stimulus and response AC/A and CA/C ratios were calculated. Results. Accommodation responses for near targets (p=0.017) response gains (p=0.026) were greater in the exotropes than the controls. Despite higher clinical stimulus AC/A ratios, the distance exotropes showed lower laboratory response AC/A ratios (p=0.02), but significantly higher CA/C ratios (p=0.02). All the exotropes, whether the angle changed most with lenses (“controlled by accommodation”) or on occlusion (“controlled by fusion”), used binocular disparity not blur as their main cue to target distance. Conclusions. Increased vergence demand to control intermittent distance exotropia for near also drives significantly more accommodation. Minus lens therapy is more likely to act by correcting over-accommodation driven by controlling convergence, rather than by inducing blur-driven vergence. The use of convergence as a major drive to accommodation explains many clinical characteristics of distance exotropia, including apparently high near stimulus AC/A ratios.

TNF-alpha mediated transport of NF-kappaB to the nucleus is independent of the cytoskeleton-based transport system in non-neuronal cells

In unstimulated cells, proteins of the nuclear factor kappaB (NF-kappaB) transcription factor family are sequestered in the cytoplasm through interactions with IkappaB inhibitor proteins. Tumor necrosis factor alpha (TNF-alpha) activates the degradation of IkappaB-alpha and the nuclear import of cytoplasmic NF-kappaB. Nuclear localization of numerous cellular proteins is mediated by the ability of the cytoskeleton, usually microtubules, to direct their perinuclear accumulation. In a former study we have shown that activated NF-kappaB rapidly moves from distal processes in neurons towards the nucleus. The fast transport rate suggests the involvement of motor proteins in the transport of NF-kappaB. Here we address the question how NF-kappaB arrives at the nuclear membrane before import in non-neuronal cells, i.e., by diffusion alone or with the help of active transport mechanisms. Using confocal microscopy imaging and analysis of nuclear protein extracts, we show that NF-kappaB movement through the cytoplasm to the nucleus is independent of the cytoskeleton, in the three cell lines investigated here. Additionally we demonstrate that NF-kappaB p65 is not associated with the dynein/dynactin molecular motor complex. We propose that cells utilize two distinct mechanisms of NF-kappaB transport: (1) signaling via diffusion over short distances in non-neuronal cells and (2) transport via motor proteins that move along the cytoskeleton in neuronal processes where the distances between sites of NF-kappaB activation and nucleus can be vast.

An algorithm for automatic checking of exercises in a dynamic geometry system: iGeom

One of the key issues in e-learning environments is the possibility of creating and evaluating exercises. However, the lack of tools supporting the authoring and automatic checking of exercises for specifics topics (e.g., geometry) drastically reduces advantages in the use of e-learning environments on a larger scale, as usually happens in Brazil. This paper describes an algorithm, and a tool based on it, designed for the authoring and automatic checking of geometry exercises. The algorithm dynamically compares the distances between the geometric objects of the student`s solution and the template`s solution, provided by the author of the exercise. Each solution is a geometric construction which is considered a function receiving geometric objects (input) and returning other geometric objects (output). Thus, for a given problem, if we know one function (construction) that solves the problem, we can compare it to any other function to check whether they are equivalent or not. Two functions are equivalent if, and only if, they have the same output when the same input is applied. If the student`s solution is equivalent to the template`s solution, then we consider the student`s solution as a correct solution. Our software utility provides both authoring and checking tools to work directly on the Internet, together with learning management systems. These tools are implemented using the dynamic geometry software, iGeom, which has been used in a geometry course since 2004 and has a successful track record in the classroom. Empowered with these new features, iGeom simplifies teachers` tasks, solves non-trivial problems in student solutions and helps to increase student motivation by providing feedback in real time. (c) 2008 Elsevier Ltd. All rights reserved.

Gas-filled, flat plate solar collectors

This work treats the thermal and mechanical performances of gas-filled, flat plate solar collectors in order to achieve a better performance than that of air filled collectors. The gases examined are argon, krypton and xenon which all have lower thermal conductivity than air. The absorber is formed as a tray connected to the glass. The pressure of the gas inside is near to the ambient and since the gas volume will vary as the temperature changes, there are potential risks for fatigue in the material. One heat transfer model and one mechanical model were built. The mechanical model gave stresses and information on the movements. The factors of safety were calculated from the stresses, and the movements were used as input for the heat transfer model where the thermal performance was calculated. It is shown that gas-filled, flat plate solar collectors can be designed to achieve good thermal performance at a competitive cost. The best yield is achieved with a xenon gas filling together with a normal thick absorber, where normal thick means a 0.25 mm copper absorber. However, a great deal of energy is needed to produce the xenon gas, and if this aspect is taken into account, the krypton filling is better. Good thermal performance can also be achieved using less material; a collector with a 0.1 mm thick copper absorber and the third best gas, which is argon, still gives a better operating performance than a common, commercially produced, air filled collector with a 0.25 mm absorber. When manufacturing gas-filled flat plate solar collectors, one way of decreasing the total material costs significantly, is by changing absorber material from copper to aluminium. Best yield per monetary outlay is given by a thin (0.3 mm) alu-minium absorber with an argon filling. A high factor of safety is achieved with thin absorbers, large absorber areas, rectangular constructions with long tubes and short distances between glass and absorber. The latter will also give a thin layer of gas which gives good thermal performance. The only doubtii ful construction is an argon filled collector with a normal thick (> 0.50 mm) aluminium absorber. In general, an assessment of the stresses for the proposed construction together with appropriate tests are recommended before manufacturing, since it is hard to predict the factor of safety; if one part is reinforced, some other parts can experience more stress and the factor of safety actually drops.

Transformação genética em cevada por bombardeamento de partículas

A presente Tese de Doutorado objetivou: (1) definir um método eficiente de transformação genética, por bombardeamento de partículas, para a obtenção de plantas transgênicas de cultivares brasileiras de cevada e (2) identificar gene(s) codificante(s) de quitinase(s) potencialmente capaz(es) de conferir resistência ao fungo patogênico de cevada Bipolaris sorokiniana. Culturas de calos obtidos a partir de escutelos imaturos das cultivares Brasileiras de cevada MN-599 e MN-698 (Cia. de Bebidas das Américas, AMBEV) foram bombardeadas com partículas de tungstênio e avaliadas quanto à expressão do gene repórter gusA através de ensaios histoquímicos de GUS e quanto ao efeito dos bombardeamentos na indução estruturas embriogênicas e regeneração de plantas. As condições de biobalística analisadas incluíram a região promotora regulando a expressão de gusA, tipo e pressão de gás hélio de dois aparelhos de bombardeamento, distância de migração das partículas, número de tiros e a realização de pré e pós-tratamento osmótico dos tecidos-alvo. No presente trabalho foram obtidos um número bastante alto de pontos azuis por calo, a indução de calos embriogênicos e embriões somáticos em uma freqüência de até 58,3% e a regeneração de 60 plantas, sendo 43 de calos bombardeados. As melhores condições observadas foram o promotor e primeiro íntron do gene Adh de milho (plasmídeo pNGI), o aparelho de bombardeamento “ Particle Inflow Gun” (PIG) utilizando-se a distância de migração de partículas de 14,8 cm, dois tiros disparados por placa e a realização de tratamento osmótico dos explantes com 0,2 M de manitol e 0,2 M de sorbitol 4-5 horas antes e 17-19 horas depois dos bombardeamentos. Das 43 plantas obtidas de calos bombardeadas, 3 apresentaram atividade de GUS na base das suas folhas. A utilização de primers sintéticos definidos a partir de genes de quitinases descritos na literatura em PCRs resultou na amplificação de dois fragmentos de aproximadamente 700 e 500 pb a partir de DNA total das cvs. MN-599 e MN-698 de cevada e um fragmento, com aproximadamente 500 pb, a partir do DNA total do isolado A4c de Trichoderma sp. Estes fragmentos foram purificados dos géis de agarose e diretamente seqüenciados de forma manual e automática. Os fragmentos de 700 e 500 pb amplificados do genoma da cultivar MN-599 foram identificados como genes de quitinases de cevada e o fragmento de 500 pb do isolado A4c de Trichoderma sp. não apresentou homologia com seqüências conhecidas de quitinases depositadas no EMBL/GenBank. A utilização de novos pares de primers, representando seqüências conservadas de quitinases do fungo Metarhizium anisopliae, resultou na amplificação de 3 fragmentos a partir do DNA total do isolado A4b de Trichoderma sp., que estão sendo purificados para realização de seqüenciamento.

A localização da indústria de transformação brasileira nas últimas três décadas

O propósito dessa dissertação é avaliar, numa perspectiva geográfica, os setores industriais no Brasil nas últimas três décadas. Numa primeira instância, o objetivo é verificar o nível de especialização e concentração dos estados brasileiros em termos industriais, utilizando-se os índices de Krugman e Gini, respectivamente. Com os resultados desses dois índices, os estados brasileiros são separados em quatro grupos, segundo o método de grupamento de médias K. Através de um produto interno usual entre o vetor da distribuição da produção industrial dos setores nos estados e vetores de algumas características desses setores (chamado de Viés das Características da Indústria - VCI), verifica-se em que tipos de indústrias os estados estão se especializando e/ou concentrando. Uma análise multivariada de componentes principais é feita com os VCI’s, na qual esses componentes principais são usados para verificar a similaridade dos estados. Sob outra perspectiva, busca-se investigar o nível de concentração geográfico dos setores industriais brasileiros. Para tanto, utilizaram-se o índice Gini e o índice de Venables. Nesse último, a distância entre os estados não é negligenciada para mensuração da concentração. Os setores industriais são separados em três grupos pelo método de grupamento de médias K, no qual as variáveis utilizadas são os componentes principais das características das indústrias. Utilizando outro produto interno, o Viés da Característica dos Estados (VCE), observa-se em que tipo de estados os setores industriais estão se concentrando ou não. Para visualizar como essas duas perspectivas, ou seja, como as características dos estados e das indústrias influenciam a localização dos setores industriais no território brasileiro, um modelo econométrico de dados cruzados de Midelfart-Knarvik e outros (2000) é estabelecido para o caso brasileiro. Neste modelo econométrico, é possível investigar como a interação das características das indústrias e dos estados podem determinar onde a indústria se localiza. Os principais resultados mostram que os fortes investimentos em infraestrutura na década de 70 e a abertura comercial na década de 90 foram marcantes para localização da indústria brasileira.

Impacto da divulgação das notas no Enem na concorrência entre escolas

A partir 2006, o INEP (Instituto Nacional de Estudos e Pesquisa) passou a divulgar anualmente as notas das escolas no Exame Nacional do Ensino Médio (Enem). Tal divulgação já faz parte do calendário das escolas, professores, jornais e revistas que cobrem o setor educacional e até de pais de alunos. Este estudo visa analisar o impacto da divulgação dessas notas na competição entre as instituições de ensino médio e, mais especificamente, avaliar o efeito da nota média das escolas concorrentes na nota de uma dada escola, em relação aos anos anteriores à divulgação. A concorrência será analisada do ponto de vista espacial, de modo que, o peso atribuído à nota de uma instituição na estimação da nota de outra escola é inversamente proporcional à distâncias entre as mesmas. Essa análise empírica de instituições públicas e privadas foi realizada por meio da estimação em mínimos quadrados, utilizando-se variáveis de controle relacionadas às instituições e ao perfil socioeconômico dos alunos. Para tanto, foram utilizadas as bases de microdados do Censo Escolar e do Enem no período de 2004 à 2011. Os resultados indicam a existência de competição entre as escolas, com aumento no grupo de escolas públicas no período posterior à divulgação.

Estudo paramétrico da injeção de vapor em reservatórios delgados

Exploration of heavy oil reservoirs is increasing every year in worldwide, because the discovery of light oil reservoirs is becoming increasingly rare. This fact has stimulated the research with the purpose of becoming viable, technically and economically, the exploration of such oil reserves. In Brazil, in special in the Northeast region, there is a large amount of heavy oil reservoir, where the recovery by the so called secondary methods Water injection or gas injection is inefficient or even impracticable in some reservoirs with high viscosity oils (heavy oils). In this scenario, steam injection appears as an interesting alternative for recover of these kinds of oil reservoirs. Its main mechanism consists of oil viscosity reduction through steam injection, increasing reservoir temperature. This work presents a parametric simulation study of some operational and reservoir variables that had influence on oil recovery in thin reservoirs typically found in Brazilian Northeast Basins, that use the steam injection as improved oil recovery method. To carry out simulations, it was used the commercial software STARS (Steam, Thermal, and Advanced Processes Reservoir Simulator) from CMG (Computer Modeling Group) version 2007.11. Reservoirs variables studied were horizontal permeability, vertical and horizontal permeability ratio, water zone and pay zone thickness ratio, pay zone thickness and thermal conductivity of the rock. Whereas, operational parameters studied were distance between wells and steam injection rate. Results showed that reservoir variables that had more influence on oil recovery were horizontal permeability and water zone and pay zone thickness ratio. In relation to operational variables, results showed that short distances between wells and low steam injection rates improved oil recovery

Influência da areia argilosa na recuperação de petróleo por injeção de vapor

Continuous steam injection is one of heavy oil thermal recovery methods used in the Brazilian Northeast because of high occurrence of heavy oil reservoir. In this process, the oil into the reservoir is heated while reduces, substantially, its viscosity and improves the production. This work analyzed how the shaly sand layers influenced in the recovery. The studied models were synthetics, but the used reservoir data can be extrapolated to real situations of Potiguar Basin. The modeling was executed using the STARS - Steam Thermal and Advanced Process Reservoir Simulator - whose version was 2007.10. STARS is a tool of CMG Computer Modeling Group. The study was conducted in two stages, the first we analyzed the influence of reservoir parameters in the thermal process, so some of these were studied, including: horizontal permeability of the reservoir and the layer of shaly sand, ratio of horizontal permeability to vertical permeability, the influence of capillary pressure layer of shaly sand and as the location and dimensions of this heterogeneity can affect the productivity of oil. Among the parameters studied the horizontal permeability of the reservoir showed the most significant influence on the process followed by diversity. In the second stage three models were selected and studied some operational parameters such as injection rate, distance between wells, production time and completion intervals. Among the operating parameters studied the low rate and intermediate distances between wells showed the best recoveries