A topological algorithm for identification of structural domains of proteins

Background: Identification of the structural domains of proteins is important for our understanding of the organizational principles and mechanisms of protein folding, and for insights into protein function and evolution. Algorithmic methods of dissecting protein of known structure into domains developed so far are based on an examination of multiple geometrical, physical and topological features. Successful as many of these approaches are, they employ a lot of heuristics, and it is not clear whether they illuminate any deep underlying principles of protein domain organization. Other well-performing domain dissection methods rely on comparative sequence analysis. These methods are applicable to sequences with known and unknown structure alike, and their success highlights a fundamental principle of protein modularity, but this does not directly improve our understanding of protein spatial structure.

Adaptive Code Allocation for Interference Management on the Downlink of DS-CDMA Systems

A new technique based on adaptive code-to-user allocation for interference management on the downlink of BPSK based TDD DS-CDMA systems is presented. The principle of the proposed technique is to exploit the dependency of multiple access interference on the instantaneous symbol values of the active users. The objective is to adaptively allocate the available spreading sequences to users on a symbol-by-symbol basis to optimize the decision variables at the downlink receivers. The presented simulations show an overall system BER performance improvement of more than an order of a magnitude with the proposed technique while the adaptation overhead is kept less than 10% of the available bandwidth.

Assessing the daily consistency of bladder filling using an ultrasonic Bladderscan device in men receiving radical conformal radiotherapy for prostate cancer

Consistency in target organ and organ at risk position from planning to treatment is an important basic principle of radiotherapy. This study evaluates the effectiveness of bladder-filling instructions in achieving a consistent and reproducible bladder volume at the time of planning CT and daily during the course of radical radiotherapy for prostate cancer. It also assessed the rate of bladder filling before and at the end of radiotherapy.

Multiculturalism, freedom of religion, equality, and the British constitution: The JFS case considered

In the JFS case, the Supreme Court of the United Kingdom held that the admissions policy of a Jewish faith school constituted unlawful racial discrimination because it used the Orthodox Jewish interpretation of who is Jewish as a criterion for determining admission to the school. A detailed discussion of the case is located in the context of two broader debates in Britain, which are characterized as constitutional in character or, at least, as possessing constitutional properties. The first is the debate concerning the treatment of minority groups, multiculturalism, and the changing perceptions in public policy of the role of race and religion in national life. It is suggested that this debate has become imbued with strong elements of what has been termed “post-multiculturalism”. The second debate is broader still, and pertains to shifting approaches to “constitutionalism” in Britain. It is suggested that, with the arrival of the European Convention on Human Rights and EU law, the U.K. has seen a shift from a pragmatic approach to constitutional thinking, in which legislative compromise played a key part, to the recognition of certain quasi-constitutional principles, allowing the judiciary greatly to expand its role in protecting individual rights while requiring the judges, at the same time, to articulate a principled basis for doing so. In both these debates, the principle of equality plays an important role. The JFS case is an important illustration of some of the implications of these developments.

Measuring the blame of each formula for inconsistent prioritized knowledge bases.

It is increasingly recognized that identifying the degree of blame or responsibility of each formula for inconsistency of a knowledge base (i.e. a set of formulas) is useful for making rational decisions to resolve inconsistency in that knowledge base. Most current techniques for measuring the blame of each formula with regard to an inconsistent knowledge base focus on classical knowledge bases only. Proposals for measuring the blames of formulas with regard to an inconsistent prioritized knowledge base have not yet been given much consideration. However, the notion of priority is important in inconsistency-tolerant reasoning. This article investigates this issue and presents a family of measurements for the degree of blame of each formula in an inconsistent prioritized knowledge base by using the minimal inconsistent subsets of that knowledge base. First of all, we present a set of intuitive postulates as general criteria to characterize rational measurements for the blames of formulas of an inconsistent prioritized knowledge base. Then we present a family of measurements for the blame of each formula in an inconsistent prioritized knowledge base under the guidance of the principle of proportionality, one of the intuitive postulates. We also demonstrate that each of these measurements possesses the properties that it ought to have. Finally, we use a simple but explanatory example in requirements engineering to illustrate the application of these measurements. Compared to the related works, the postulates presented in this article consider the special characteristics of minimal inconsistent subsets as well as the priority levels of formulas. This makes them more appropriate to characterizing the inconsistency measures defined from minimal inconsistent subsets for prioritized knowledge bases as well as classical knowledge bases. Correspondingly, the measures guided by these postulates can intuitively capture the inconsistency for prioritized knowledge bases.

Performance and characteristics of platinum, palladium/rhodium and palladium automotive catalysts when subjected to ethanol, acetaldehyde and a synthetic E85 exhaust gas mixture

The performance optimisation of automotive catalysts has been the focus of a great deal of research for many years as the automotive industry has endeavored to reduce the emission of toxic and pollutant gases generated from internal combustion engines. Just as the emissions from diesel and gasoline combustion vary so do the emissions from combustion of alternative fuels such as ethanol; the variation is in both quantity and chemical composition. In particular, when ethanol is contained in the fuel, ethanol and acetaldehyde are present in the exhaust gas stream and these are two compounds which the catalytic converter has not traditionally been designed to manage. The aim of the study outlined in this paper was to assess the performance of various catalyst formulations when subjected to a representative ethanol exhaust gas mixture. Three automotive catalytic converter formulations were tested including a fully Pt sample, a PdRh three-way catalyst sample and a fully Pd sample. Initially the samples were tested using single component hydrocarbon light-off tests followed by a set of tests with carbon monoxide included as an inlet gas to observe its effect on each individual hydrocarbon oxidation. Finally, each formulation was tested using a full E85 exhaust gas mixture. The study was carried out using a synthetic gas reactor along with FTIR and FID exhaust gas analysers. All formulations showed selectivity toward acetaldehyde formation from ethanol dehydrogenation which resulted in negative acetaldehyde conversion across each of the samples during the mixture tests. The fully Pt sample was the most detrimentally affected by the introduction of carbon monoxide into the gas feed. The Pd and PdRh samples exhibited a tendency toward acetaldehyde decomposition resulting in methane and carbon monoxide formation. The Pt sample did not form methane but did form ethylene as a result of ethanol dehydration.

A novel dual-fluorescence strategy for functionally validating microRNA targets in 3-prime untranslated regions: regulation of the inward rectifier potassium channel Kir2.1 by miR-212.

Gene targeting by microRNAs is important in health and disease. We developed a functional assay for identifying microRNA targets and applied it to the K+ channel Kir2.1 (KCNJ2) which is dysregulated in cardiac and vascular disorders. The 3'UTR was inserted downstream of the mCherry red fluorescent protein coding sequence in a mammalian expression plasmid. MicroRNA sequences were inserted into the pSM30 expression vector which provides enhanced green fluorescent protein as an indicator of microRNA expression. HEK293 cells were co-transfected with the mCherry-3'UTR plasmid and a pSM30-based plasmid with a microRNA insert. The principle of the assay is that functional targeting of the 3'UTR by the microRNA results in a decrease in the red/green fluorescence intensity ratio as determined by automated image analysis. The method was validated with miR-1, a known downregulator of Kir2.1 expression, and was used to investigate targeting of the Kir2.1 3'UTR by miR-212. Red/green ratio was lower in miR-212-expressing cells compared to non-targeting controls, an effect that was attenuated by mutating the predicted target site. MiR-212 also reduced inward rectifier current and Kir2.1 protein in HeLa cells. This novel assay has several advantages over traditional luciferase-based assays including larger sample size, amenability to time course studies and adaptability to high-throughput screening.

The Literature of Early Modern Childhoods

The texts adapted for, printed for and marketed to children and youths in the 16th and 17th centuries, the books read by boys and girls in this period, and writings by Renaissance children constitute the literature of early modern childhoods. Yet traditional histories of children’s literature, posing narrow definitions of this genre, have largely overlooked this period. In the past decade, fresh work by early modern scholars attending to the diverse elements of the literature of early modern childhoods has flourished. This essay evaluates the absence of early modern children’s literature from early studies and considers the ways in which this recent work in Renaissance studies has vitally transformed the field through its exploration of alternative definitions of childhood and children’s literature. This work is at an early stage but it has placed the interconnections between early modern childhoods and children’s literature at the centre of both Renaissance studies and childhood studies and has established key topics for future research.

Radiochromic film imaging spectroscopy of laser-accelerated proton beams

This article reports on an experimental method to fully reconstruct laser-accelerated proton beam parameters called radiochromic film imaging spectroscopy (RIS). RIS allows for the characterization of proton beams concerning real and virtual source size, envelope- and microdivergence, normalized transverse emittance, phase space, and proton spectrum. This technique requires particular targets and a high resolution proton detector. Therefore thin gold foils with a microgrooved rear side were manufactured and characterized. Calibrated GafChromic radiochromic film (RCF) types MD-55, HS, and HD-810 in stack configuration were used as spatial and energy resolved film detectors. The principle of the RCF imaging spectroscopy was demonstrated at four different laser systems. This can be a method to characterize a laser system with respect to its proton-acceleration capability. In addition, an algorithm to calculate the spatial and energy resolved proton distribution has been developed and tested to get a better idea of laser-accelerated proton beams and their energy deposition with respect to further applications.

A test of the extended intergroup contact hypothesis: The mediating role of intergroup anxiety, perceived ingroup and outgroup norms, and inclusion of the outgroup in the self

S. C. Wright, A. Aron, T. McLaughlin-Volpe, and S. A. Ropp (1997) proposed that the benefits associated with cross-group friendship might also stem from vicarious experiences of friendship. Extended contact was proposed to reduce prejudice by reducing intergroup anxiety, by generating perceptions of positive ingroup and outgroup norms regarding the other group, and through inclusion of the outgroup in the self. This article documents the first test of Wright et al.'s model, which used structural equation modeling among two independent samples in the context of South Asian-White relations in the United Kingdom. Supporting the model, all four variables mediated the relationship between extended contact and outgroup attitude, controlling for the effect of direct contact. A number of alternative models were ruled out, indicating that the four mediators operate concurrently rather than predicting one another.

Toxicity of diclofenac to Gyps vultures

Three endemic vulture species Gyps bengalensis, Gyps indicus and Gyps tenuirostris are critically endangered following dramatic declines in South Asia resulting from exposure to diclofenac, a veterinary drug present in the livestock carcasses that they scavenge. Diclofenac is widely used globally and could present a risk to Gyps species from other regions. In this study, we test the toxicity of diclofenac to a Eurasian (Gyps fulvus) and an African (Gyps africanus) species, neither of which is threatened. A dose of 0.8 mg kg(-1) of diclofenac was highly toxic to both species, indicating that they are at least as sensitive to diclofenac as G. bengalensis, for which we estimate an LD50 of 0.1-0.2 mg kg(-1). We suggest that diclofenac is likely to be toxic to all eight Gyps species, and that G. africanus, which is phylogenetically close to G. bengalensis, would be a suitable surrogate for the safety testing of alternative drugs to diclofenac.

Waterpower: Politics and the Geography of Water Provision

Access to potable water is frequently said to be the defining world crisis of the twenty-first century. The argument is usually framed in terms of either direct environmental constraints or various totalistic views of how the political determines outcomes. There is little or no scope for the agency of practical politics. Both physical and human geographers tend to be dismissive of the possibilities of democratic politics ever resolving crises such as those of the geography of water provision, in part because of views of scientific expertise that devalue popular participation in decisions about technical matters such as water quality and distribution. Such dismissal also has much to do with a more generalized denigration of politics. Politics (the art of political deliberation, negotiation, and compromise) needs defending against its critics and many of its practitioners. Showing how politics is at work around the world in managing water problems and identifying the challenges that water problems pose for politics provides a retort to those who can only envisage inevitable destruction or a totalistic political panacea as the outcomes of the crisis of the century.

The Challenge of Consociation in Northern Ireland

This article assesses the role played by the principle of consociational government in promoting Northern Ireland's peace agreement. It reviews the central concept of consociation as it has evolved in recent comparative studies of the politics of divided societies. It describes the stages by which this concept moved to the centre of the political agenda in Northern Ireland, resting on contributions by policy-makers, academics, journalists and others. It reviews the difficult history of efforts to translate this principle into practice, contrasting the failed attempt to promote this formula in 1973 with the much more successful experiment in 1998. Using the classical literature on consociation, an effort is made to explain the difference between these outcomes, a difference with implications for Northern Ireland's future stability.

Identifying research priorities on infections in older adults:Proceedings of an interdisciplinary workshop

Background: Infections pose a substantial burden to the health of older adults. In this report, we describe the proceedings of a workshop to formulate and prioritize research questions about infections in older adults using an interdisciplinary approach. Methods: Researchers from four sectors (basic science, clinical sciences, health services and epidemiology/determinants of health) and representatives from various Canadian local, provincial, and federal stakeholder groups were invited to a two-day workshop. Five multi-disciplinary groups and stakeholders from each of three healthcare settings (long term, acute care and community) discussed research priorities for each of the settings. Five to ten research questions were identified for each setting. Results: The research questions proposed ranged from risk factors and outcomes for different infections to the effect of nutrition on infection and the role of alternative and complementary medicine in treating infections. Health service issues included barriers to immunization, prolongation of hospital length of stay by infection, use of care paths for managing infections, and decision-making in determining the site of care for individuals with infections. Clinical questions included risk factor assessment for infection, the effectiveness of preventative strategies, and technology evaluation. Epidemiologic issues included the challenge of achieving a better understanding of respiratory infections in the community and determining the prevalence of colonization with multi-resistant bacteria. Conclusions: The questions are of direct relevance to researchers in a wide variety of fields. Bringing together a multi-disciplinary group of researchers to frame and prioritize research questions about aging is feasible, participants valued the opinions of people working in other areas.

Analysis of Biological Interactions and Recognitions by Surface Plasmon Resonance

This chapter contains sections titled:

•Introduction to Surface Plasmon Resonance Technology

•Working Principle of SPR

•Sensor Surface Chemistry and Its Fabrications

•Important Factors Impacting on the Performance of SPR-Based Analyses of Biological Interactions on the Nonbiological Transducer Surface

•Localized SPR of Inorganic Nanoparticles for Analyses of Biological Interaction

•References