Information profiles for DNA pattern discovery

Finite-context modeling is a powerful tool for compressing and hence for representing DNA sequences. We describe an algorithm to detect genomic regularities, within a blind discovery strategy. The algorithm uses information profiles built using suitable combinations of finite-context models. We used the genome of the fission yeast Schizosaccharomyces pombe strain 972 h- for illustration, unveilling locations of low information content, which are usually associated with DNA regions of potential biological interest.Comment: Full version of DCC 2014 paper "Information profiles for DNA pattern discovery

Quasi-Topological Quantum Field Theories and Z2Z_2 Lattice Gauge Theories

We consider a two parameter family of $Z_2$ gauge theories on a lattice discretization $T(M)$ of a 3-manifold $M$ and its relation to topological field theories. Familiar models such as the spin-gauge model are curves on a parameter space $\Gamma$. We show that there is a region $\Gamma_0$ of $\Gamma$ where the partition function and the expectation value of the Wilson loop for a curve $\gamma$ can be exactly computed. Depending on the point of $\Gamma_0$, the model behaves as topological or quasi-topological. The partition function is, up to a scaling factor, a topological number of $M$. The Wilson loop on the other hand, does not depend on the topology of $\gamma$. However, for a subset of $\Gamma_0$, depends on the size of $\gamma$ and follows a discrete version of an area law. At the zero temperature limit, the spin-gauge model approaches the topological and the quasi-topological regions depending on the sign of the coupling constant.Comment: 19 pages, 13 figure

Fluorescence and diffuse reflectance spectroscopy for early cancer detection using a new strategy towards the development of a miniaturized system

This paper describes the design of a miniature, cost-effective spectroscopy system for assessing tissue biochemical and morphological information using a few wavelengths. This instrument will integrate thin-film optical filters and silicon photodiodes, avoiding the use of a spectrograph and optical fibers. The components in the set-up design are described. The feasibility of using only 16 wavelengths to accurately extract tissue properties is confirmed on physical tissue models. Also, the suitable spectral performance of several optical filters for the selection of these wavelengths is demonstrated. The small size of this device will enable implementation in an endoscopic capsule.This research was supported by the Portuguese Foundation of Science and Technology and the MIT|Portugal Program (SFRH/BD/38978/2007

Fragility functions for tall URM buildings around early 20th century in Lisbon. Part 1: Methodology and application at building level

The article proposes a procedure for the derivation of fragility functions for unreinforced masonry buildings considering the in-plane and out-of-plane response. Different approaches are considered for the generation of the corresponding fragility functions and for the evaluation of the propagation of uncertainties. The contributions for the dispersion of the fragility functions account for the variability in the definition of the capacity, the aleatory uncertainty in the definition of the seismic demand and the aleatory uncertainty in the definition of the modified/floor response spectrum, when the local mechanisms are located in the upper level of the building. In the end, the individual fragility curves are properly combined in order to define a single fragility curve for the class of buildings. As a case study, the procedure is applied to the assessment of one of the most vulnerable unreinforced masonry buildings constructed in the early 20th century in Lisbon, considering a typical prototype building with five storeys high. Results for a seismic event, as defined in the earthquake-resistant code for Lisbon, indicate that the typical building has about 50% probability of having heavy damage and about 30% probability of collapse.The first author would like to acknowledge the financial support of Fundação para a Ciência e a Tecnologia (FCT, Ministério da Educação e Ciência, Portugal) through the scholarship PD/BD/106076/2015 through the FCT Doctoral Program: Analysis and Mitigation of Risks in Infrastructures, INFRARISK- (http://infrarisk.tecnico.ulisboa.pt)

Magnetoliposomes incorporated in peptide-based hydrogels: towards development of magnetolipogels

A major problem with magnetogels is the encapsulation of hydrophobic drugs. Magnetoliposomes not only provide these domains but also improve drug stability and avert the aggregation of the magnetic nanoparticles. In this work, two magnetoliposome architectures, solid and aqueous, were combined with supramolecular peptide-based hydrogels, which are of biomedical interest owing to their biocompatibility, easy tunability, and wide array of applications. This proof-of-concept was carried out through combination of magnetoliposomes (loaded with the model drug curcumin and the lipid probe Nile Red) with the hydrogels prior to pH triggered gelation, and fluorescence spectroscopy was used to assess the dynamics of the encapsulated molecules. These systems allow for the encapsulation of a wider array of drugs. Further, the local environment of the encapsulated molecules after gelation is unaffected by the used magnetoliposome architecture. This system design is promising for future developments on drug delivery as it provides a means to independently modify the components and adapt and optimize the design according to the required conditions.FCT -Fundação para a Ciência e a Tecnologia(UIDB/00686/2020

Fluorescence properties of a potential antitumoral benzothieno[3,2-b]pyrrole in solution and lipid membranes

Fluorescence properties of the antitumoral methyl 3-(benzo[b]thien-2-yl)-benzothieno[3,2-b]pyrrole-2-carboxylate (BTP) were studied in solution and in lipid bilayers of dipalmitoyl phosphatidylcholine (DPPC), dioleoyl phosphatidylethanolamine (DOPE) and egg yolk phosphatidylcholine (Egg-PC). BTP presents good fluorescence quantum yields in all solvents studied (0.20 ≤ ΦF ≤ 0.32) and a bathochromic shift in polar solvents. The results indicate an ICT character of the excited state, with an estimated dipole moment of μe = 7.38 D. Fluorescence (steady-state) anisotropy measurements of BTP incorporated in lipid membranes of DPPC, DOPE and Egg-PC indicate that this compound is deeply located in the lipid bilayer, feeling the difference between the rigid gel phase and fluid phases. BTP inhibits the growth of three human tumour cell lines, MCF-7 (breast adenocarcinoma), SF-268 (glioma) and NCI-H460 (non-small cell lung cancer), being significantly more potent against the NCI-H460 tumour cells.European Communitarian Fund (FEDER)Fundação para a Ciência e a Tecnologia (FCT) – projecto SeARCH (ref. REEQ/443/EEI/2005), bolsa SFRH/BPD/24548/2005, projecto PTDC/QUI/81238/200

Magnetogels based on iron oxide nanoparticles and peptide hydrogels containing Naproxen and/or RGD

In this work, iron oxide nanoparticles, with diameters around 12 nm, were synthesized by coprecipitation method in aqueous solution. These nanoparticles exhibit a superparamagnetic behavior, with a coercive field of 9.7 Oe and a blocking temperature of 118 K. The nanoparticles were successfully incorporated in peptide-based hydrogels containing naproxen (Npx) and/or RGD. The ability of these magnetogels to act as drug nanocarriers is being investigated, aiming at developing multifunctional therapeutic nanosystems.info:eu-repo/semantics/publishedVersio