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.

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.

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.

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.

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

A Hamiltonian approach to simulation of acoustic systems involving nonlinear interactions

Nonlinear interactions take place in most systems that arise in music acoustics, usually as a result of player-instrument coupling. Several time-stepping methods exist for the numerical simulation of such systems. These methods generally involve the discretization of the Newtonian description of the system. However, it is not always possible to prove the stability of the resulting algorithms, especially when dealing with systems where the underlying force is a non-analytic function of the phase space variables. On the other hand, if the discretization is carried out on the Hamiltonian description of the system, it is possible to prove the stability of the derived numerical schemes. This Hamiltonian approach is applied to a series of test models of single or multiple nonlinear collisions and the energetic properties of the derived schemes are discussed. After establishing that the schemes respect the principle of conservation of energy, a nonlinear single-reed model is formulated and coupled to a digital bore, in order to synthesize clarinet-like sounds.

Selective High Impedance Surface Active Region Loading of Archimedean Spiral Antenna

We show that a significant increase in the gain and front-to-back ratio is obtained when different high impedance surface (HIS) sections are placed below the active regions of an Archimedean spiral antenna. The principle of operation is demonstrated at 3, 6, and 9 GHz for an antenna design that employs a ground plane composed of two dissimilar HISs. The unit cells of the HISs are collocated and resonant at the same frequency as the 3- and 6-GHz active regions of the wideband spiral. It is shown that the former HIS must also be designed to resonate at 9 GHz to avoid the generation of a boresight null that occurs because the structure is physically large enough to support higher-order modes. The improvement that is obtained at each of the three frequencies investigated is shown by comparing the predicted and measured radiation patterns for the free space and HIS-backed antenna.

Clarifying the acquis humanitaire: a transnational legal perspective on the internalization of humanitarian norms

Although the international obligations and institutional frameworks for disaster response are not yet settled, as evidenced by the International Law Commission’s work on the protection of persons in the event of disasters and the on-going promotion of disaster laws by the Red Cross Movement; the diverse source and nature of such initiatives suggests that the international community is engaged in a process of norm creation, elaboration and interpretation reflecting a desire for legal clarity in humanitarian operations. Situated within the framework of transnational law, this paper argues that an acquis humanitaire, based on the principle of humanity, encapsulates the evolving body of law and practice specifically relating to the protection of persons in times of humanitarian crisis in both armed conflicts and natural or human-made disasters. Reflecting the non-traditional, non-statist, dynamic and normative basis of transnational legal process, as elaborated by Harold Koh, the constant flow of ideas and principles between the national, regional and international spheres provides an analytical framework for the on-going transnational dialogues on the social, political and legal internalization of humanitarian norms. Drawing on the internalization of humanitarian norms within the United Kingdom, this paper concludes that as the international community examines the codification of a universal legal framework for the protection of persons in the event of disasters it is necessary to understand the transnational process of interpretation and internalization of humanitarian norms, and how this may vary across different regions and countries.

Sovereignty, Article 4(2) TEU and the Respect of National Identities: Swinging the Balance of Power in Favour of the Member States?

The question of whether and to what extent sovereignty has been transferred to the European Union (EU) from its Member States remains a central debate within the EU and is interlinked with issues such as Kompetenz-Kompetenz, direct effect and primacy. Central to any claim to sovereignty is the principle of primacy, which requires that Member States uphold EU law over national law where there is a conflict. However, limitations to primacy can traditionally be found in national jurisprudence and the Maastricht Treaty introduced a possible EU limitation with the requirement that the EU respect national identities of Member States. The Lisbon Treaty provided only minimal further support to the principle of primacy whilst simultaneously developing the provision on national identities, now found within Article 4(2) TEU. There are indications from the literature, national constitutional courts and the Court of Justice of the EU that the provision is gathering strength as a legal tool and is likely to have a wider scope than the text might indicate. In its new role, Article 4(2) TEU bolsters the Member States’ claim to sovereignty and the possibility to uphold aspects crucial to them in conflict with EU law and the principle of primacy. Consequently, it is central to the relationship between the constitutional courts of the Member States and the CJEU, and where the final elements of control remain in ‘hard cases’. However, it does so as part of EU law, thereby facilitating the evasion of direct fundamental conflicts and reflecting the concept of constitutional pluralism.

An Ambiguity Aversion Framework of Security Game under Ambiguities

Security is a critical concern around the world. Since resources for security are always limited, lots of interest have arisen in using game theory to handle security resource allocation problems. However, most of the existing work does not address adequately how a defender chooses his optimal strategy in a game with absent, inaccurate, uncertain, and even ambiguous strategy profiles' payoffs. To address this issue, we propose a general framework of security games under ambiguities based on Dempster-Shafer theory and the ambiguity aversion principle of minimax regret. Then, we reveal some properties of this framework. Also, we present two methods to reduce the influence of complete ignorance. Our investigation shows that this new framework is better in handling security resource allocation problems under ambiguities.

Equality, justice and feasibility: an ethical analysis of the WBGU’s budget approach

According to the Budget Approach proposed by the German Advisory Council on Global Change (WBGU), allocating CO2 emission rights to countries on an equal per-capita basis would provide an ethically justified response to global climate change. In this paper, we will highlight four normative issues which beset the WBGU’s Budget Approach: (1) the approach’s core principle of distributive justice, the principle of equality, and its associated policy of emissions egalitarianism are much more complex than it initially appears; (2) the “official” rationale for determining the size of the budget should be modified in order to avoid implausible normative assumptions about the imposition of permissible intergenerational risks; (3) the approach heavily relies on trade-offs between justice and feasibility which should be stated more explicitly; and (4) part of the approach’s ethical appeal depends on policy instruments which are “detachable” from the approach’s core principle of distributive justice.