The impact of genotyping error on haplotype reconstruction and frequency estimation

The choice of genotyping families vs unrelated individuals is a critical factor in any large-scale linkage disequilibrium (LD) study. The use of unrelated individuals for such studies is promising, but in contrast to family designs, unrelated samples do not facilitate detection of genotyping errors, which have been shown to be of great importance for LD and linkage studies and may be even more important in genotyping collaborations across laboratories. Here we employ some of the most commonly-used analysis methods to examine the relative accuracy of haplotype estimation using families vs unrelateds in the presence of genotyping error. The results suggest that even slight amounts of genotyping error can significantly decrease haplotype frequency and reconstruction accuracy, that the ability to detect such errors in large families is essential when the number/complexity of haplotypes is high (low LD/common alleles). In contrast, in situations of low haplotype complexity (high LD and/or many rare alleles) unrelated individuals offer such a high degree of accuracy that there is little reason for less efficient family designs. Moreover, parent-child trios, which comprise the most popular family design and the most efficient in terms of the number of founder chromosomes per genotype but which contain little information for error detection, offer little or no gain over unrelated samples in nearly all cases, and thus do not seem a useful sampling compromise between unrelated individuals and large families. The implications of these results are discussed in the context of large-scale LD mapping projects such as the proposed genome-wide haplotype map.

Spoilage patterns of skim and whole milks

The reason for the reported difference in spoilage behaviour of skim and whole pasteurised milks was investigated The rates of growth of psychrotrophic bacteria were not significantly different in the two milks and the bacterial types. till pseudomonad, present at spoilage were also similar. However. when representative spoilage organisms were cultured into freshly pasteurised skim and whole milks, skim milks exhibited predominantly bitter flavours while whole milk showed mostly sour flavours. The different spoilage, behaviours can be largely explained by greater proteolysis in skim milk than in whole milk. caused by, higher production of protease and greater susceptibility of the protein to protease attack. In addition, lipolysis in whole milk, caused by the substantial quantities of lipase produced by spoilage pseudomonads in this milk. also contributes to the different flavours produced during cold storage of these milk types.

Habitat-predator association and avoidance in rainbowfish (Melanotaenia spp.)

The ability to recall the location of a predator and later avoid it was tested in nine populations of rainbowfish (Melanotaenia spp.), representing three species from a variety of environments. Following the introduction of a model predator into a particular microhabitat, the model was removed, the arena rotated and the distribution of the fish recorded again. In this manner it could be determined what cues the fish relied on in order to recall the previous location of the predator model. Fish from all populations but one (Dirran Creek) were capable of avoiding the predator by remembering either the location and/or the microhabitat in which the predator was recently observed. Reliance on different types of visual cues appears to vary between populations but the reason for this variation remains elusive. Of the ecological variables tested (flow variability, predator density and habitat complexity), only the level of predation appeared to be correlated with the orientation technique employed by each population. There was no effect of species identity, which suggests that the habitat that each population occupies plays a strong role in the development of both predator avoidance responses and the cues used to track predators in the wild.

Yablo's paradox and referring to infinite objects

The blame for the semantic and set-theoretic paradoxes is often placed on self-reference and circularity. Some years ago, Yablo [1985; 1993] challenged this diagnosis, by producing a paradox that's liar-like but does not seem to involve circularity. But is Yablo's paradox really non-circular? In a recent paper, Beall [2001] has suggested that there are no means available to refer to Yablo's paradox without invoking descriptions, and since Priest [1997] has shown that any such description is circular, Beall concludes that Yablo's paradox itself is circular. In this paper, we argue that Beall's conclusion is unwarranted, given that (1) descriptions are not the only way to refer to Yablo's paradox, and (ii) we have no reason to believe that because the description involves self-reference, the denotation of the description is also circular. As a result, for all that's been said so far, we have no reason to believe that Yablo's paradox is circular.

Narrating the guillotine: Punishment technology as myth and symbol

The work of Michel Foucault sees modern penal technology its ann expression of power that operates through and is motivated by a dry instrumental reason. This article draws upon Durkheim and Bakhtin to advance a radically alternative approach. It is suggested that such technology is invested with sacred and profane symbolism and is understood via emotionally charged, dramatically compelling narrative frames. Tensions between official and unauthorized discourses can be understood through a center/periphery model of culture. In an extended case study of the guillotine, it is shown dial the apparatus was initially legitimated as an expression of a sacred revolutionary code. Such a discourse was subsequently destabilized by popular medical debates that raised the specter of pain after decapitation. While inconclusive, these new motifs mobilized Gothic and grotesque themes that confronted the rationalist aesthetics of the guillotine. A situation of Bakhtinian hetoroglossia eventuated. Uncertainty, the uncanny and fable entered a discursive field of increasing complexity.

The European Union and the Member States: two different perceptions of border

Abstract In this article we analyze two different perceptions of border inside Europe. On the one hand, we have the perception idealized by the European Union as an international organization, which believes that states benefit more from cooperation and dilution of borders in a common space than from keeping its borders as a symbol of its sovereignty. On the other hand, we have the European member states, taken individually, with particular interests and goals that, given the threat of illegal immigration, which is currently felt in the large-scale Europe, adopt a realistic perception of the border, and look at each territory as a space that needs protection from external threats. Following this argument, we reason that the current construction of walls in several European countries reflects the rebirth of a realistic perception of the border, and this is one more challenge for Europe regarding its unity and solidarity. Is this the end of the Schengen Agreement? What is going to happen to the European project if each state unilaterally adopts a strategy to deal with illegal immigration and refugees that are coming to Europe? Can immigration lead to a retrocession of the EU idealist significance of border?

Mortality problems in Brazil and in Germany: past-present-future. Learning from each other?

This article was written by a Swiss-German historical demographer after having visited different Brazilian Universities in 1984 as a guest-professor. It aims at promoting a real dialog between developed and developing countries, commencing the discussion with the question: Can we learn from each other? An affirmative answer is given, but not in the superficial manner in which the discussion partners simply want to give each other some "good advice" or in which the one declares his country's own development to be the solely valid standard. Three points are emphasized: 1. Using infant mortality in S. Paulo from 1908 to 1983 as an example, it is shown that Brazil has at its disposal excellent, highly varied research literature that is unjustifiably unknown to us (in Europe) for the most part. Brazil by no means needs our tutoring lessons as regards the causal relationships; rather, we could learn two things from Brazil about this. For one, it becomes clear that our almost exclusively medical-biological view is inappropriate for passing a judgment on the present-day problems in Brazil and that any conclusions so derived are thus only transferable to a limited extent. For another, we need to reinterpret the history of infant mortality in our own countries up to the past few decades in a much more encompassing "Brazilian" sense. 2. A fruitful dialog can only take place if both partners frankly present their problems. For this reason, the article refers with much emprasis to our present problems in dealing with death and dying - problems arising near the end of the demographic and epidemiologic transitions: the superanuation of the population, chronic-incurable illnesses as the main causes of death, the manifold dependencies of more and more elderly and really old people at the end of a long life. Brazil seems to be catching up to us in this and will be confronted with these problems sooner or later. A far-sighted discussion already at this time seems thus to be useful. 3. The article, however, does not want to conclude with the rather depressing state of affairs of problems alternatingly superseding each other. Despite the caution which definitely has a place when prognoses are being made on the basis of extrapolations from historical findings, the foreseeable development especially of the epidemiologic transition in the direction of a rectangular survival curve does nevertheless provide good reason for being rather optimistic towards the future: first in regards to the development in our own countries, but then - assuming that the present similar tendencies of development are stuck to - also in regard to Brazil.

Risk assessment in occupational exposure to formaldehyde: differences between anatomy and pathology laboratories and formaldehyde-resins production

Formaldehyde (CH2O), the most simple and reactive of all aldehydes, is colorless, and readily polymerizing gas at normal temperature. The most extensive use is in production of resins and has an important application as a disinfectant and preservative, reason why relevant workplace exposure may also occur in pathology and anatomy laboratories and in mortuaries. A study was carried out in Portugal, in a formaldehyde production resins factory and in 10 pathology and anatomy laboratories. It was applied a risk assessment methodology based on Queensland University proposal that permitted to perform risk assessment for each activity developed in a work station. This methodology was applied in 83 different activities developed in the laboratories and in 18 activities of the factory. Also, Micronucleus Test was performed in lymphocytes from 30 factory workers and 50 laboratories workers.

Moodle and multiple-choice tests

Multiple-Choice items are used in many different kinds of tests in several areas of knowledge. They can be considered an interesting tool to the self-assessing or as an alternative or complementary instrument to the traditional methods for assessing knowledge. The objectivity and accuracy of the multiple-choice tests is an important reason to think about. They are especially useful when the number of students to evaluate is too large. Moodle (Modular Object-Oriented Dynamic Learning Environment) is an Open Source course management system centered around learners' needs and designed to support collaborative approaches to teaching and learning. Moodle offers to the users a rich interface, context-specific help buttons, and a wide variety of tools such as discussion forums, wikis, chat, surveys, quizzes, glossaries, journals, grade books and more, that allow them to learn and collaborate in a truly interactive space. Come together the interactivity of the Moodle platform and the objectivity of this kind of tests one can easily build manifold random tests. The proposal of this paper is to relate our journey in the construction of these tests and share our experience in the use of the Moodle platform to create, take advantage and improve the multiple-choices tests in the Mathematic area.

Biochemical and structural characterization of β-lactamases tem-180 and tem-201

With the constant development of new antibiotics, selective pressure is a force to reckon when investigating antibiotic resistance. Although advantageous for medical treatments, it leads to increasing resistance. It is essential to use more potent and toxic antibiotics. Enzymes capable of hydrolyzing antibiotics are among the most common ways of resistance and TEM variants have been detected in several resistant isolates. Due to the rapid evolution of these variants, complex phenotypes have emerged and the need to understand their biological activity becomes crucial. To investigate the biochemical properties of TEM-180 and TEM-201 several computational methodologies have been used, allowing the comprehension of their structure and catalytic activity, which translates into their biological phenotype. In this work we intent to characterize the interface between these proteins and the several antibiotics used as ligands. We performed explicit solvent molecular dynamics (MD) simulations of these complexes and studied a variety of structural and energetic features. The interfacial residues show a distinct behavior when in complex with different antibiotics. Nevertheless, it was possible to identify some common Hot Spots among several complexes – Lys73, Tyr105 and Glu166. The structural changes that occur during the Molecular Dynamic (MD) simulation lead to the conclusion that these variants have an inherent capacity of adapting to the various antibiotics. This capability might be the reason why they can hydrolyze antibiotics that have not been described until now to be degraded by TEM variants. The results obtained with computational and experimental methodologies for the complex with Imipenem have shown that in order to this type of enzymes be able to acylate the antibiotics, they need to be capable to protect the ligand from water molecules.

Smart offices and intelligent decision rooms

Nowadays computing technology research is focused on the development of Smart Environments. Following that line of thought several Smart Rooms projects were developed and their appliances are very diversified. The appliances include projects in the context of workplace or everyday living, entertainment, play and education. These appliances envisage to acquire and apply knowledge about the environment state in order to reason about it so as to define a desired state for its inhabitants and perform adaptation adaptation to these desires and therefore improving their involvement and satisfaction with that environment.

Evaluation of IMRT and VMAT techniques with and without flattening filter using pareto optimal fronts

Mestrado em Radiações Aplicadas às Tecnologias da Saúde.

Side information creation for efficient Wyner-Ziv video coding: Classifying and reviewing

Video coding technologies have played a major role in the explosion of large market digital video applications and services. In this context, the very popular MPEG-x and H-26x video coding standards adopted a predictive coding paradigm, where complex encoders exploit the data redundancy and irrelevancy to 'control' much simpler decoders. This codec paradigm fits well applications and services such as digital television and video storage where the decoder complexity is critical, but does not match well the requirements of emerging applications such as visual sensor networks where the encoder complexity is more critical. The Slepian Wolf and Wyner-Ziv theorems brought the possibility to develop the so-called Wyner-Ziv video codecs, following a different coding paradigm where it is the task of the decoder, and not anymore of the encoder, to (fully or partly) exploit the video redundancy. Theoretically, Wyner-Ziv video coding does not incur in any compression performance penalty regarding the more traditional predictive coding paradigm (at least for certain conditions). In the context of Wyner-Ziv video codecs, the so-called side information, which is a decoder estimate of the original frame to code, plays a critical role in the overall compression performance. For this reason, much research effort has been invested in the past decade to develop increasingly more efficient side information creation methods. This paper has the main objective to review and evaluate the available side information methods after proposing a classification taxonomy to guide this review, allowing to achieve more solid conclusions and better identify the next relevant research challenges. After classifying the side information creation methods into four classes, notably guess, try, hint and learn, the review of the most important techniques in each class and the evaluation of some of them leads to the important conclusion that the side information creation methods provide better rate-distortion (RD) performance depending on the amount of temporal correlation in each video sequence. It became also clear that the best available Wyner-Ziv video coding solutions are almost systematically based on the learn approach. The best solutions are already able to systematically outperform the H.264/AVC Intra, and also the H.264/AVC zero-motion standard solutions for specific types of content. (C) 2013 Elsevier B.V. All rights reserved.

Mathematical education and interdisciplinarity : promoting public awareness of mathematics in the Azores

Mathematical literacy in Portugal is very unsatisfactory in what concerns international standards. Even more disturbingly, the Azores archipelago ranks as one of the worst regions of Portugal in this respect. We reason that the popularisation of Mathematics through interactive exhibitions and activities can contribute actively to disseminate mathematical knowledge, increase awareness of the importance of Mathematics in today’s world and change its negative perception by the majority of the citizens. Although a significant investment has been undertaken by the local regional government in creating several science centres for the popularisation of Science, there is no centre for the popularisation of Mathematics. We present our first steps towards bringing Mathematics to unconventional settings by means of hands-on activities. We describe in some detail three activities. One activity has to do with applying trigonometry to measure distances in Astronomy, which can also be applied to Earth objects. Another activity concerns the presence of numerical patterns in the Azorean flora. The third activity explores geometrical patterns in the Azorean cultural heritage. It is our understanding that the implementation of these and other easy-to-follow and challenging activities will contribute to the awareness of the importance and beauty of Mathematics.

Social gender stereotypes and their implications in Hindi

This essay looks at the subtle ways in which gender identities are constructed and reinforced in India through social norms of language use. Language itself becomes a medium for perpetuating gender stereotypes, forcing its speakers to confirm to socially defined gender roles. Using examples from a classroom discussion about a film, this essay will highlight the underlying rigid male-female stereotypes in Indian society with their more obvious expressions in language. For the urban woman in India globalisation meant increased economic equality and exposure to changed lifestyles. On an individual level it also meant redefining gender relations and changing the hierarchy in man-woman relationships. With the economic independence there is a heightened sense of liberation in all spheres of social life, a confidence to fuzz the rigid boundaries of gender roles. With the new films and media celebrating this liberated woman, who is ready to assert her sexual needs, who is ready to explode those long held notions of morality, one would expect that the changes are not just superficial. But as it soon became obvious in the course of a classroom discussion about relationships and stereotypes related to age, the surface changes can not become part of the common vocabulary, for the obvious reason that there is still a vast gap between the screen image of this new woman and the ground reality. Social considerations define the limits of this assertiveness of women, whereas men are happy to be liberal within the larger frame of social sanctions. The educated urban woman in India speaks in favour of change and the educated urban male supports her, but one just needs to scratch the surface to see the time tested formulae of gender roles firmly in place. The way the urban woman happily balances this emerging promise of independence with her gendered social identity, makes it necessary to rethink some aspects of looking at gender in a gradually changing, traditional society like India.