Epidemic store for massive scale systems

The MAP-i doctoral program of the Universities of Minho, Aveiro and Porto

The synthesis of novel 5-aminoimidazoles derivatives with anticancer activity

[Excerpt] The imidazole nucleus is present in a significant number of biomolecules and the inclusion of this moiety in organic scaffolds is considered an important synthetic strategy in drug discovery.[1] 5-Aminoimidazoles are interesting building blocks in medicinal chemistry since they are key components in many bioactive molecules and their derivatives showed a wide pharmacological potential as anticancer drugs.[1] The hydrazones constitute an important class of biological active drug molecules due to their wide range of pharmacological properties that include antitumoral activities.[2] Amidrazone derivatives could be considered very promising in the perspective of new drug discovery, because they are very effective as building blocks to obtain various heterocycles.[2,3] The α-hydrazononitriles are a special case of compounds belonging to the family of hydrazones that is less common in the literature, but has a great interest due to their pharmacological applications.[4] (...)

In search of mathematical primitives for deriving universal projective hash families

We provide some guidelines for deriving new projective hash families of cryptographic interest. Our main building blocks are so called group action systems; we explore what properties of this mathematical primitives may lead to the construction of cryptographically useful projective hash families. We point out different directions towards new constructions, deviating from known proposals arising from Cramer and Shoup's seminal work.

SwissSidechain: a molecular and structural database of non-natural sidechains.

Amino acids form the building blocks of all proteins. Naturally occurring amino acids are restricted to a few tens of sidechains, even when considering post-translational modifications and rare amino acids such as selenocysteine and pyrrolysine. However, the potential chemical diversity of amino acid sidechains is nearly infinite. Exploiting this diversity by using non-natural sidechains to expand the building blocks of proteins and peptides has recently found widespread applications in biochemistry, protein engineering and drug design. Despite these applications, there is currently no unified online bioinformatics resource for non-natural sidechains. With the SwissSidechain database (http://www.swisssidechain.ch), we offer a central and curated platform about non-natural sidechains for researchers in biochemistry, medicinal chemistry, protein engineering and molecular modeling. SwissSidechain provides biophysical, structural and molecular data for hundreds of commercially available non-natural amino acid sidechains, both in l- and d-configurations. The database can be easily browsed by sidechain names, families or physico-chemical properties. We also provide plugins to seamlessly insert non-natural sidechains into peptides and proteins using molecular visualization software, as well as topologies and parameters compatible with molecular mechanics software.

Sound Texture Modelling

In the PhD thesis “Sound Texture Modeling” we deal with statistical modelling or textural sounds like water, wind, rain, etc. For synthesis and classification. Our initial model is based on a wavelet tree signal decomposition and the modeling of the resulting sequence by means of a parametric probabilistic model, that can be situated within the family of models trainable via expectation maximization (hidden Markov tree model ). Our model is able to capture key characteristics of the source textures (water, rain, fire, applause, crowd chatter ), and faithfully reproduces some of the sound classes. In terms of a more general taxonomy of natural events proposed by Graver, we worked on models for natural event classification and segmentation. While the event labels comprise physical interactions between materials that do not have textural propierties in their enterity, those segmentation models can help in identifying textural portions of an audio recording useful for analysis and resynthesis. Following our work on concatenative synthesis of musical instruments, we have developed a pattern-based synthesis system, that allows to sonically explore a database of units by means of their representation in a perceptual feature space. Concatenative syntyhesis with “molecules” built from sparse atomic representations also allows capture low-level correlations in perceptual audio features, while facilitating the manipulation of textural sounds based on their physical and perceptual properties. We have approached the problem of sound texture modelling for synthesis from different directions, namely a low-level signal-theoretic point of view through a wavelet transform, and a more high-level point of view driven by perceptual audio features in the concatenative synthesis setting. The developed framework provides unified approach to the high-quality resynthesis of natural texture sounds. Our research is embedded within the Metaverse 1 European project (2008-2011), where our models are contributting as low level building blocks within a semi-automated soundscape generation system.

Design of Novel Frequency Generation Circuit with Application to Ultra-Wideband Distributed Oscillators

Given the urgence of a new paradigm in wireless digital trasmission which should allow for higher bit rate, lower latency and tigher delay constaints, it has been proposed to investigate the fundamental building blocks that at the circuital/device level, will boost the change towards a more efficient network architecture, with high capacity, higher bandwidth and a more satisfactory end user experience. At the core of each transciever, there are inherently analog devices capable of providing the carrier signal, the oscillators. It is strongly believed that many limitations in today's communication protocols, could be relieved by permitting high carrier frequency radio transmission, and having some degree of reconfigurability. This led us to studying distributed oscillator architectures which work in the microwave range and possess wideband tuning capability. As microvave oscillators are essentially nonlinear devices, a full nonlinear analyis, synthesis, and optimization had to be considered for their implementation. Consequently, all the most used nonlinear numerical techniques in commercial EDA software had been reviewed. An application of all the aforementioned techniques has been shown, considering a systems of three coupled oscillator ("triple push" oscillator) in which the stability of the various oscillating modes has been studied. Provided that a certain phase distribution is maintained among the oscillating elements, this topology permits a rise in the output power of the third harmonic; nevertheless due to circuit simmetry, "unwanted" oscillating modes coexist with the intenteded one. Starting with the necessary background on distributed amplification and distributed oscillator theory, the design of a four stage reverse mode distributed voltage controlled oscillator (DVCO) using lumped elments has been presented. All the design steps have been reported and for the first time a method for an optimized design with reduced variations in the output power has been presented. Ongoing work is devoted to model a wideband DVCO and to implement a frequency divider.

Structuring OER Using Learning Trajectories

The Wikiwijs program in the Netherlands is experimenting in structuring a repository with digital learning materials by labelling these materials with the learning goals and subjects handled by it. This makes it possible to create an interdependent arrangement of learning materials as building blocks for a curriculum. Such arrangements are called learning trajectories. A datamodel is presented in which the entities involved and their relationships are depicted. A first implementation of this is realized and published in September 2010.

On AUV control architecture

This paper surveys control architectures proposed in the literature and describes a control architecture that is being developed for a semi-autonomous underwater vehicle for intervention missions (SAUVIM) at the University of Hawaii. Conceived as hybrid, this architecture has been organized in three layers: planning, control and execution. The mission is planned with a sequence of subgoals. Each subgoal has a related task supervisor responsible for arranging a set of pre-programmed task modules in order to achieve the subgoal. Task modules are the key concept of the architecture. They are the main building blocks and can be dynamically re-arranged by the task supervisor. In our architecture, deliberation takes place at the planning layer while reaction is dealt through the parallel execution of the task modules. Hence, the system presents both a hierarchical and an heterarchical decomposition, being able to show a predictable response while keeping rapid reactivity to the dynamic environment

Algorithmic aspects of bio-inspired string operations

We present building blocks for algorithms for the efficient reduction of square factor, i.e. direct repetitions in strings. So the basic problem is this: given a string, compute all strings that can be obtained by reducing factors of the form zz to z. Two types of algorithms are treated: an offline algorithm is one that can compute a data structure on the given string in advance before the actual search for the square begins; in contrast, online algorithms receive all input only at the time when a request is made. For offline algorithms we treat the following problem: Let u and w be two strings such that w is obtained from u by reducing a square factor zz to only z. If we further are given the suffix table of u, how can we derive the suffix table for w without computing it from scratch? As the suffix table plays a key role in online algorithms for the detection of squares in a string, this derivation can make the iterated reduction of squares more efficient. On the other hand, we also show how a suffix array, used for the offline detection of squares, can be adapted to the new string resulting from the deletion of a square. Because the deletion is a very local change, this adaption is more eficient than the computation of the new suffix array from scratch.

Gondwana-derived microcontinents - The constituents of the Variscan and Alpine collisional orogens

The European Variscan and Alpine mountain chains are collisional orogens, and are built up of pre-Variscan ``building blocks'' which, in most. cases, originated at the Gondwana margin. Such pre-Variscan elements were part of a pre-Ordovician archipelago-like continental ribbon in the former eastern prolongation of Avalonia, and their present-day distribution resulted from juxtaposition through Variscan and/or Alpine tectonic evolution. The well-known nomenclatures applied to these mountain chains are the mirror of Variscan resp. Alpine organization. It is the aim of this paper to present a terminology taking into account their pre-Variscan evolution at the Gondwana margin. They may contain relics of volcanic islands with pieces of Cadomian crust, relics of volcanic arc settings, and accretionary wedges, which were separated from Gondwana by initial stages of Rheic ocean. opening. After a short-lived Ordovician orogenic event and amalgamation of these elements at the Gondwanan margin, the still continuing Gondwana-directed subduction triggered the formation of Ordovician Al-rich granitoids and; the latest Ordovician opening of Palaeo-Tethys. An example from the Alps (External Massifs) illustrates the gradual reworking of Gondwana-derived, pre-Variscan. elements during the Variscan and Alpine/ Tertiary orogenic cycles. (C) 2003 Elsevier Science B.V. All rights reserved.

Avoiding transcription factor competition at promoter level increases the chances of obtaining oscillations

Background: The ultimate goal of synthetic biology is the conception and construction of genetic circuits that are reliable with respect to their designed function (e.g. oscillators, switches). This task remains still to be attained due to the inherent synergy of the biological building blocks and to an insufficient feedback between experiments and mathematical models. Nevertheless, the progress in these directions has been substantial. Results: It has been emphasized in the literature that the architecture of a genetic oscillator must include positive (activating) and negative (inhibiting) genetic interactions in order to yield robust oscillations. Our results point out that the oscillatory capacity is not only affected by the interaction polarity but by how it is implemented at promoter level. For a chosen oscillator architecture, we show by means of numerical simulations that the existence or lack of competition between activator and inhibitor at promoter level affects the probability of producing oscillations and also leaves characteristic fingerprints on the associated period/amplitude features. Conclusions: In comparison with non-competitive binding at promoters, competition drastically reduces the region of the parameters space characterized by oscillatory solutions. Moreover, while competition leads to pulse-like oscillations with long-tail distribution in period and amplitude for various parameters or noisy conditions, the non-competitive scenario shows a characteristic frequency and confined amplitude values. Our study also situates the competition mechanism in the context of existing genetic oscillators, with emphasis on the Atkinson oscillator.

Synthesis and Biological Evaluation of S-Neofucopeptides as E- and P-Selectin Inhibitors.

The synthesis of /-L-fucosylated cysteamine, 3-thiopropionic acid, and 3-thioacetic acid derivatives as building blocks for the preparation of S-neofucopeptides is shown. These compounds were used in the synthesis of new thiofucosides derivatives (8, 9, 9, 10, 22, 22, 24, 26) that show affinity towards E- and P-selectins. They constitute a new series of hydrolytically stable and low-molecular-weight mimetics of the natural SLex tetrasaccharide.

Mining and exploiting domain-specific corpora in the PANACEA platform

The objective of the PANACEA ICT-2007.2.2 EU project is to build a platform that automates the stages involved in the acquisition,production, updating and maintenance of the large language resources required by, among others, MT systems. The development of a Corpus Acquisition Component (CAC) for extracting monolingual and bilingual data from the web is one of the most innovative building blocks of PANACEA. The CAC, which is the first stage in the PANACEA pipeline for building Language Resources, adopts an efficient and distributed methodology to crawl for web documents with rich textual content in specific languages and predefined domains. The CAC includes modules that can acquire parallel data from sites with in-domain content available in more than one language. In order to extrinsically evaluate the CAC methodology, we have conducted several experiments that used crawled parallel corpora for the identification and extraction of parallel sentences using sentence alignment. The corpora were then successfully used for domain adaptation of Machine Translation Systems.

Rebuild Iowa Office Quarterly Performance Report 3rd Quarter, April 2009

As the anniversaries of 2008 tornado’s and floods approach, the Rebuild Iowa Office vision of a safer, stronger and smarter Iowa is coming into sharper focus. While much more remains to be done, hundreds of displaced Iowans and businesses are on the road to recovery and the building blocks for communities coming together. While recovery is a marathon and not a sprint, the work done so far couldn’t have been accomplished without an extensive recovery planning effort and an unprecedented level of cooperation among local, state and federal governments, private citizens, businesses and non-profit organizations, there is a rebirth and recovery underway in Iowa.

Modular support for developing mobile ad hoc applications

Abstract This PhD thesis addresses the issue of alleviating the burden of developing ad hoc applications. Such applications have the particularity of running on mobile devices, communicating in a peer-to-peer manner and implement some proximity-based semantics. A typical example of such application can be a radar application where users see their avatar as well as the avatars of their friends on a map on their mobile phone. Such application become increasingly popular with the advent of the latest generation of mobile smart phones with their impressive computational power, their peer-to-peer communication capabilities and their location detection technology. Unfortunately, the existing programming support for such applications is limited, hence the need to address this issue in order to alleviate their development burden. This thesis specifically tackles this problem by providing several tools for application development support. First, it provides the location-based publish/subscribe service (LPSS), a communication abstraction, which elegantly captures recurrent communication issues and thus allows to dramatically reduce the code complexity. LPSS is implemented in a modular manner in order to be able to target two different network architectures. One pragmatic implementation is aimed at mainstream infrastructure-based mobile networks, where mobile devices can communicate through fixed antennas. The other fully decentralized implementation targets emerging mobile ad hoc networks (MANETs), where no fixed infrastructure is available and communication can only occur in a peer-to-peer fashion. For each of these architectures, various implementation strategies tailored for different application scenarios that can be parametrized at deployment time. Second, this thesis provides two location-based message diffusion protocols, namely 6Shot broadcast and 6Shot multicast, specifically aimed at MANETs and fine tuned to be used as building blocks for LPSS. Finally this thesis proposes Phomo, a phone motion testing tool that allows to test proximity semantics of ad hoc applications without having to move around with mobile devices. These different developing support tools have been packaged in a coherent middleware framework called Pervaho.