Determining the Contribution of Epidermal Cell Shape to Petal Wettability Using Isogenic Antirrhinum Lines

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PocketMatch: A new algorithm to compare binding sites in protein structures

Background: Recognizing similarities and deriving relationships among protein molecules is a fundamental
requirement in present-day biology. Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. In some cases similarities obscure at these levels could be present merely in the substructures at their binding sites. Inferring functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. One of
the main reasons for this is the limitation in the choice of appropriate analytical tools that can compare binding sites with high sensitivity. To benefit from the enormous amount of structural data that is being rapidly accumulated, it is essential to have high throughput tools that enable large scale binding site comparison.

Results: Here we present a new algorithm PocketMatch for comparison of binding sites in a frame invariant
manner. Each binding site is represented by 90 lists of sorted distances capturing shape and chemical nature of the site. The sorted arrays are then aligned using an incremental alignment method and scored to obtain PMScores for pairs of sites. A comprehensive sensitivity analysis and an extensive validation of the algorithm have been carried out. Perturbation studies where the geometry of a given site was retained but the residue types were changed randomly, indicated that chance similarities were virtually non-existent. Our analysis also demonstrates that shape information alone is insufficient to discriminate between diverse binding sites, unless
combined with chemical nature of amino acids.

Conclusions: A new algorithm has been developed to compare binding sites in accurate, efficient and
high-throughput manner. Though the representation used is conceptually simplistic, we demonstrate that along
with the new alignment strategy used, it is sufficient to enable binding comparison with high sensitivity. Novel methodology has also been presented for validating the algorithm for accuracy and sensitivity with respect to geometry and chemical nature of the site. The method is also fast and takes about 1/250th second for one comparison on a single processor. A parallel version on BlueGene has also been implemented

A genetic algorithm based determination of the ground and excited ( 1 L b ) state structure and the orientation of the transition dipole moment of benzimidazolew

The structure of benzimidazole has been determined in the electronic ground and excited states using rotationally resolved electronic spectroscopy. The rovibronic spectra of four isotopomers and subsequently the structure of benzimidazole have been automatically assigned and fitted using a genetic algorithm based fitting strategy. The lifetimes of the deuterated isotopomers have been shown to depend on the position of deuteration. The angle of the transition dipole moment with the inertial a-axis could be determined to be À301. Structures and transition dipole moment orientation have been calculated at various levels of theory and were compared to the experimental results

Avaliação de Programas de Controle de Infecção relacionada a Assistência à Saúde de Hospitais

RESUMO Objetivo Avaliar os Programas de Controle de Infecção em hospitais do Paraná, considerando como hipótese desempenho geral mínimo de 75%. Método Estudo transversal de avaliação processual, por meio de instrumento previamente validado, composto por quatro indicadores que avaliam a estrutura técnico-operacional (PCET), as diretrizes operacionais (PCDO), o sistema de vigilância epidemiológica (PCVE) e as atividades de controle e prevenção (PCCP). O estudo foi realizado de 2013 a 2014 em 50 hospitais por amostra de acesso. Resultados A conformidade geral obtida foi 71,0% (23,88dp), sendo indicador PCET 79,4% (18,9dp); PCVE 76,0% (30,5dp); PCDO 65,5% (26,9dp); e PCCP 63,2%/ (39,5dp). Houve significância estatística para melhor desempenho dos PCIRAS a realização de auditorias internas (p=0,0099), certificação de qualidade (p=0,01949), enfermeiro exclusivo (p<0,0001), profissionais médicos contratados ou concursados (p=0,0005), maior carga horária de dedicação exclusiva dos médicos, 4 horas (p=0,001), maior tempo de experiência de médicos (p=0,0028) e enfermeiros (p=0,0094). Conclusão A conformidade geral desses programas não alcançou a hipótese inicialmente formulada, devido aos indicadores PCDO e PCCP. Desse modo, é possível considerar que os programas apresentavam adequação mínima para sua operacionalização e para realizar a vigilância epidemiológica de IRAS, mas estavam prejudicados quanto à insuficiência quantitativa e qualitativa de diretrizes operacionais (PCDO) e de ações para o controle e prevenção dessas infecções (PCCP)

X-Ray Spectroscopy of Stars

(abridged) Non-degenerate stars of essentially all spectral classes are soft X-ray sources. Low-mass stars on the cooler part of the main sequence and their pre-main sequence predecessors define the dominant stellar population in the galaxy by number. Their X-ray spectra are reminiscent, in the broadest sense, of X-ray spectra from the solar corona. X-ray emission from cool stars is indeed ascribed to magnetically trapped hot gas analogous to the solar coronal plasma. Coronal structure, its thermal stratification and geometric extent can be interpreted based on various spectral diagnostics. New features have been identified in pre-main sequence stars; some of these may be related to accretion shocks on the stellar surface, fluorescence on circumstellar disks due to X-ray irradiation, or shock heating in stellar outflows. Massive, hot stars clearly dominate the interaction with the galactic interstellar medium: they are the main sources of ionizing radiation, mechanical energy and chemical enrichment in galaxies. High-energy emission permits to probe some of the most important processes at work in these stars, and put constraints on their most peculiar feature: the stellar wind. Here, we review recent advances in our understanding of cool and hot stars through the study of X-ray spectra, in particular high-resolution spectra now available from XMM-Newton and Chandra. We address issues related to coronal structure, flares, the composition of coronal plasma, X-ray production in accretion streams and outflows, X-rays from single OB-type stars, massive binaries, magnetic hot objects and evolved WR stars.Comment: accepted for Astron. Astrophys. Rev., 98 journal pages, 30 figures (partly multiple); some corrections made after proof stag

Explaining counterterrorism in the UK: Normal politics, securitized politics or performativity of the neoliberal state?

This paper seeks to explore the politics of counter terrorism in the UK. It argues that for a number of reasons, counter terrorism policy has been separated off from other policy areas and seen as securitised, exceptional or just different. The paper argues that such a separation from “normal” politics is problematic, both conceptually and empirically. It argues that much can be gained by considering counter terrorism policy through the lenses, concepts and debates which feature in other areas of British politics. The paper then examines two such lenses/debates – depoliticisation and neoliberalism. An argument is developed that counter terrorism policy is not, in the main, depoliticised, but rather overt, politicised and visible. This prominence, it is argued, is due to the ways in which neoliberalism has reduced many of the traditional roles of the state. Drawing on the work of Wacquant and Hall, the paper argues that in the absence of such traditional roles, counter terrorism offers the state an opportunity to perform its own “stateness”, to visibly display its sovereign power in a context of ever more (self-imposed) diminished powers

Lambda and Antilambda polarization from deep inelastic muon scattering

We report results of the first measurements of Lambda and Antilambda polarization produced in deep inelastic polarized muon scattering on the nucleon. The results are consistent with an expected trend towards positive polarization with increasing x_F. The polarizations of Lambda and Antilambda appear to have opposite signs. A large negative polarization for Lambda at low positive x_F is observed and is not explained by existing models.A possible interpretation is presented.Comment: 9 pages, 2 figure

Old World Monkeys Compare to Apes in the Primate Cognition Test Battery

Understanding the evolution of intelligence rests on comparative analyses of brain sizes as well as the assessment of cognitive skills of different species in relation to potential selective pressures such as environmental conditions and social organization. Because of the strong interest in human cognition, much previous work has focused on the comparison of the cognitive skills of human toddlers to those of our closest living relatives, i.e. apes. Such analyses revealed that apes and children have relatively similar competencies in the physical domain, while human children excel in the socio-cognitive domain; in particular in terms of attention sharing, cooperation, and mental state attribution. To develop a full understanding of the evolutionary dynamics of primate intelligence, however, comparative data for monkeys are needed. We tested 18 Old World monkeys (long-tailed macaques and olive baboons) in the so-called Primate Cognition Test Battery (PCTB) (Herrmann et al. 2007, Science). Surprisingly, our tests revealed largely comparable results between Old World monkeys and the Great apes. Single comparisons showed that chimpanzees performed only better than the macaques in experiments on spatial understanding and tool use, but in none of the socio-cognitive tasks. These results question the clear-cut relationship between cognitive performance and brain size and – prima facie – support the view of an accelerated evolution of social intelligence in humans. One limitation, however, is that the initial experiments were devised to tap into human specific skills in the first place, thus potentially underestimating both true nonhuman primate competencies as well as species differences

The genomes of two key bumblebee species with primitive eusocial organization

Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation

Virus Infection Suppresses Nicotiana benthamiana Adaptive Phenotypic Plasticity

Competition and parasitism are two important selective forces that shape life-histories, migration rates and population dynamics. Recently, it has been shown in various pathosystems that parasites can modify intraspecific competition, thus generating an indirect cost of parasitism. Here, we investigated if this phenomenon was present in a plant-potyvirus system using two viruses of different virulence (Tobacco etch virus and Turnip mosaic virus). Moreover, we asked if parasitism interacted with the shade avoidance syndrome, the plant-specific phenotypic plasticity in response to intraspecific competition. Our results indicate that the modification of intraspecific competition by parasitism is not present in the Nicotiana benthamiana – potyvirus system and suggests that this phenomenon is not universal but depends on the peculiarities of each pathosystem. However, whereas the healthy N. benthamiana presented a clear shade avoidance syndrome, this phenotypic plasticity totally disappeared when the plants were infected with TEV and TuMV, very likely resulting in a fitness loss and being another form of indirect cost of parasitism. This result suggests that the suppression or the alteration of adaptive phenotypic plasticity might be a component of virulence that is often overlooked