Development of new approaches for the synthesis and decoding of one-bead one-compound cyclic peptide libraries

La plupart des processus cellulaires et biologiques reposent, à un certain niveau, sur des interactions protéine-protéine (IPP). Leur manipulation avec des composés chimiques démontre un grand potentiel pour la découverte de nouveaux médicaments. Malgré la demande toujours croissante en molécules capables d’interrompre sélectivement des IPP, le développement d’inhibiteurs d’IPP est fortement limité par la grande taille de la surface d’interaction. En considérant la nature de cette surface, la capacité à mimer des structures secondaires de protéines est très importante pour lier une protéine et inhiber une IPP. Avec leurs grandes capacités peptidomimétiques et leurs propriétés pharmacologiques intéressan-tes, les peptides cycliques sont des prototypes moléculaires de choix pour découvrir des ligands de protéines et développer de nouveaux inhibiteurs d’IPP. Afin d’exploiter pleinement la grande diversité accessible avec les peptides cycliques, l’approche combinatoire «one-bead-one-compound» (OBOC) est l’approche la plus accessible et puissante. Cependant, l’utilisation des peptides cycliques dans les chimiothèques OBOC est limitée par les difficultés à séquencer les composés actifs après le criblage. Sans amine libre en N-terminal, la dégradation d’Edman et la spectrométrie de masse en tandem (MS/MS) ne peuvent pas être utilisées. À cet égard, nous avons développé de nouvelles approches par ouverture de cycle pour préparer et décoder des chimiothèques OBOC de peptides cycliques. Notre stratégie était d’introduire un résidu sensible dans le macrocycle et comme ancrage pour permettre la linéarisation des peptides et leur largage des billes pour le séquençage par MS/MS. Tout d’abord, des résidus sensibles aux nucléophiles, aux ultraviolets ou au bromure de cyanogène ont été introduits dans un peptide cyclique et leurs rendements de clivage évalués. Ensuite, les résidus les plus prometteurs ont été utilisés dans la conception et le développement d’approches en tandem ouverture de cycle / clivage pour le décodage de chimiothèques OBOC de peptides cycliques. Dans la première approche, une méthionine a été introduite dans le macrocycle comme ancrage pour simultanément permettre l’ouverture du cycle et le clivage des billes par traitement au bromure de cyanogène. Dans la seconde approche, un résidu photosensible a été utilisé dans le macrocycle comme ancrage pour permettre l’ouverture du cycle et le clivage suite à une irradiation aux ultraviolets. Le peptide linéaire généré par ces approches peut alors être efficacement séquencé par MS/MS. Enfin, une chimiothèque OBOC a été préparée et criblée la protéine HIV-1 Nef pour identifier des ligands sélectifs. Le développement de ces méthodologies permttra l’utilisation de composés macrocycliques dans les chimiothèques OBOC et constitue une contribution importante en chimie médicinale pour la découverte de ligands de protéines et le développement d’inhibiteurs d’IPP.

The modified Max-Log-MAP turbo decoding algorithm by extrinsic information scaling for wireless applications

The iterative nature of turbo-decoding algorithms increases their complexity compare to conventional FEC decoding algorithms. Two iterative decoding algorithms, Soft-Output-Viterbi Algorithm (SOVA) and Maximum A posteriori Probability (MAP) Algorithm require complex decoding operations over several iteration cycles. So, for real-time implementation of turbo codes, reducing the decoder complexity while preserving bit-error-rate (BER) performance is an important design consideration. In this chapter, a modification to the Max-Log-MAP algorithm is presented. This modification is to scale the extrinsic information exchange between the constituent decoders. The remainder of this chapter is organized as follows: An overview of the turbo encoding and decoding processes, the MAP algorithm and its simplified versions the Log-MAP and Max-Log-MAP algorithms are presented in section 1. The extrinsic information scaling is introduced, simulation results are presented, and the performance of different methods to choose the best scaling factor is discussed in Section 2. Section 3 discusses trends and applications of turbo coding from the perspective of wireless applications.

Parallel decoding of turbo codes using multi-point trellis termination and collision-free interleavers

The UMTS turbo encoder is composed of parallel concatenation of two Recursive Systematic Convolutional (RSC) encoders which start and end at a known state. This trellis termination directly affects the performance of turbo codes. This paper presents performance analysis of multi-point trellis termination of turbo codes which is to terminate RSC encoders at more than one point of the current frame while keeping the interleaver length the same. For long interleaver lengths, this approach provides dividing a data frame into sub-frames which can be treated as independent blocks. A novel decoding architecture using multi-point trellis termination and collision-free interleavers is presented. Collision-free interleavers are used to solve memory collision problems encountered by parallel decoding of turbo codes. The proposed parallel decoding architecture reduces the decoding delay caused by the iterative nature and forward-backward metric computations of turbo decoding algorithms. Our simulations verified that this turbo encoding and decoding scheme shows Bit Error Rate (BER) performance very close to that of the UMTS turbo coding while providing almost %50 time saving for the 2-point termination and %80 time saving for the 5-point termination.

Increasing the speed of parallel decoding of turbo codes

Turbo codes experience a significant decoding delay because of the iterative nature of the decoding algorithms, the high number of metric computations and the complexity added by the (de)interleaver. The extrinsic information is exchanged sequentially between two Soft-Input Soft-Output (SISO) decoders. Instead of this sequential process, a received frame can be divided into smaller windows to be processed in parallel. In this paper, a novel parallel processing methodology is proposed based on the previous parallel decoding techniques. A novel Contention-Free (CF) interleaver is proposed as part of the decoding architecture which allows using extrinsic Log-Likelihood Ratios (LLRs) immediately as a-priori LLRs to start the second half of the iterative turbo decoding. The simulation case studies performed in this paper show that our parallel decoding method can provide %80 time saving compared to the standard decoding and %30 time saving compared to the previous parallel decoding methods at the expense of 0.3 dB Bit Error Rate (BER) performance degradation.

Self-similarity principle: the reduced description of randomness

A new general fitting method based on the Self-Similar (SS) organization of random sequences is presented. The proposed analytical function helps to fit the response of many complex systems when their recorded data form a self-similar curve. The verified SS principle opens new possibilities for the fitting of economical, meteorological and other complex data when the mathematical model is absent but the reduced description in terms of some universal set of the fitting parameters is necessary. This fitting function is verified on economical (price of a commodity versus time) and weather (the Earth’s mean temperature surface data versus time) and for these nontrivial cases it becomes possible to receive a very good fit of initial data set. The general conditions of application of this fitting method describing the response of many complex systems and the forecast possibilities are discussed.

Climate Change, Neutrality and the Harm Principle

This paper aims at evaluating the compatibility of coercive climate policies with liberal neutrality. More precisely, it focuses on the doctrine of state neutrality as associated with the "harm principle". It argues that given the difficulty of attributing causal responsibilities for climate harms to individuals, the harm principle doesn't work in this case, at least if one endorses a liberal atomistic ontology. Furthermore, the definition of what constitutes climate harms implies making moral assumptions, which makes it impossible to justify climate policies in a neutral way. Finally, the paper shows another consequence of applying neutrality to the case of climate change, that is the risk of a shift from political forms of decision-making to technocracy. Focusing too much on liberty of choice may (paradoxically) be to the detriment of political freedom. The paper concludes that climate change is an intrinsically moral issue and that it should be the occasion of a political debate about our current values and lifestyles. It should not be reduced to a mere question of carbon metric.

Tourism and the precautionary principle : a survey of academic and government stakeholders

The purpose of this exploratory investigation was to provide a more precise understanding and basis from which to assess the potential role of the precautionary principle in tourism. The precautionary principle, analogous to the ideal of sustainable development, is a future-focused planning and regulatory mechanism that emphasizes pro-action and recognizes the limitations of contemporary scientific methods. A total of 100 respondents (80 tourism academics, 20 regional government tourism officials) from Canada, United States, United Kingdom, Australia and New Zealand completed the webbased survey between May and June 2003. Respondents reported their understanding of the precautionary principle, rated stakeholder involvement and education strategies, assessed potential barriers in implementation, and appraised steps of a proposed fi-amework for implementation. Due to low sub sample numbers, measures of central tendency were primarily used to compare groups, while inferential statistics were applied when warranted. Results indicated that most respondents (79%) felt the principle could be a guiding principle for tourism, while local and regional government entities were reported to have the most power in the implementation process. Findings suggested close links between the precautionary principle and sustainability, as concern for future generations was the most critical element of the principle for tourism. Overall, tourism academics were more supportive of the precautionary principle in tourism than were regional government tourism officials. Only minor variation was found in responses among regional groups across all variables. This study established basic ground for understanding the precautionary principle in tourism and has been effective in formulating more precise questions for future research.

Decoding algorithms using side-effect machines

Bioinformatics applies computers to problems in molecular biology. Previous research has not addressed edit metric decoders. Decoders for quaternary edit metric codes are finding use in bioinformatics problems with applications to DNA. By using side effect machines we hope to be able to provide efficient decoding algorithms for this open problem. Two ideas for decoding algorithms are presented and examined. Both decoders use Side Effect Machines(SEMs) which are generalizations of finite state automata. Single Classifier Machines(SCMs) use a single side effect machine to classify all words within a code. Locking Side Effect Machines(LSEMs) use multiple side effect machines to create a tree structure of subclassification. The goal is to examine these techniques and provide new decoders for existing codes. Presented are ideas for best practices for the creation of these two types of new edit metric decoders.

Can Mixed Martial Arts be Ethically Defended?: Autonomy, Paternalism and the Harm Principle

Abstract Mixed Martial Arts (MMA) and the Ultimate Fighting Championship (UFC) founded in 1993 have been under scrutiny for the past two decades. Unlike boxing, the ethical status of MMA and whether it is morally defensible have rarely been analyzed in the academic literature. I argue that MMA requires such an analysis because it is inherently violent. The purpose of this study was to examine elite-level MMA by referring to the ethical concepts of autonomy, paternalism and the Harm Principle. Findings from interviews with MMA athletes as well as my personal experience of MMA were presented to establish a deeper understanding of the sport and what it means to train and compete in a sport defined as violent. The conceptual analysis and findings of MMA athletes' experiences in this investigation resulted in the conclusion that MMA is ethically defensible. Additional findings, implications and recommendations for further research were also discussed.

Online Anonymity and the Kantian Publicity Principle: Can the Internet Solve the Paradox of Tyranny?

Immanuel Kant’s publicity maxim states that other-regarding actions are wrong if their maxim is not compatible with their being made public. This has the effect of forbidding dissent or rebellion against tyranny, since rebels cannot make their intentions and plans public. However, new internet technologies offer public speech from behind the “shield” of anonymity, allowing dissent to be public but preventing reprisals from tyrants. This thesis examines not only this possibility, but the value of internet-based discursive spaces for politics, their viability as a mode for political communication, and their implications for Classical and Enlightenment approaches to politics and intellectual virtue. Anonymous internet communications favour logos-based reasoning and discourse, which, in the liberal-democratic tradition, is preferable to phronesis and its attendant elitism and chauvinism. These technologies can open new vistas for liberal-democratic politics.

Multiple Public Goods and Lexicographic Preferences Replacement Principle.

We study the problem of locating two public goods for a group of agents with single-peaked preferences over an interval. An alternative specifies a location for each public good. In Miyagawa (1998), each agent consumes only his most preferred public good without rivalry. We extend preferences lexicographically and characterize the class of single-peaked preference rules by Pareto-optimality and replacement-domination. This result is considerably different from the corresponding characterization by Miyagawa (2001a).

Driedger's 'Modern Principle' at the Supreme Court of Canada: Interpretation, Justification, Legitimization

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Impoverishment of The Law by The Law: A Critique of The Attorney General's Vision of The Rule of Law and The Federal Principle

This brief article is devoted to a critique of the arguments put forward by the Attorney General of Canada in connection with the Reference concerning certain questions relating to the secession of Quebec (hereinafter, "the Reference"). This critique will not be presented from a plainly positivist standpoint. On the contrary, I will be examining in particular (1) how the approach taken by the Attorney General impoverished the legal concepts of the rule of law anf federalism, both of which were, however, central to her submission; and, in a more general way, (2) how the excessively detailed analysis of constitutional texts contributes to the impoverishment of the symbolic function of the law, however essential that dimension may be to its legitimacy. My criticism will take into account the reasons for judgement delivered recently by the Supreme Court in the Reference.

Implementing the Precautionary Principle through Stakeholder Engagement for Product and Service Development

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