Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis

This work was partially supported by FCT through the PIDDAC Program funds (INESC-ID multiannual funding) and under grant PEst-OE/EEI/LA0008/2011 (IT multiannual funding). In addition, it was also partially funded by projects HIVCONTROL (PTDC/EEA-CRO/100128/2008, S. Vinga, PI), TAGS (PTDC/EIA-EIA/112283/2009) and NEUROCLINOMICS (PTDC/EIA-EIA/111239/2009) from FCT (Portugal).Background: Chaos Game Representation (CGR) is an iterated function that bijectively maps discrete sequences into a continuous domain. As a result, discrete sequences can be object of statistical and topological analyses otherwise reserved to numerical systems. Characteristically, CGR coordinates of substrings sharing an L-long suffix will be located within 2(-L) distance of each other. In the two decades since its original proposal, CGR has been generalized beyond its original focus on genomic sequences and has been successfully applied to a wide range of problems in bioinformatics. This report explores the possibility that it can be further extended to approach algorithms that rely on discrete, graph-based representations. Results: The exploratory analysis described here consisted of selecting foundational string problems and refactoring them using CGR-based algorithms. We found that CGR can take the role of suffix trees and emulate sophisticated string algorithms, efficiently solving exact and approximate string matching problems such as finding all palindromes and tandem repeats, and matching with mismatches. The common feature of these problems is that they use longest common extension (LCE) queries as subtasks of their procedures, which we show to have a constant time solution with CGR. Additionally, we show that CGR can be used as a rolling hash function within the Rabin-Karp algorithm. Conclusions: The analysis of biological sequences relies on algorithmic foundations facing mounting challenges, both logistic (performance) and analytical (lack of unifying mathematical framework). CGR is found to provide the latter and to promise the former: graph-based data structures for sequence analysis operations are entailed by numerical-based data structures produced by CGR maps, providing a unifying analytical framework for a diversity of pattern matching problems.publishersversionpublishe

Dissecting the stellar content of Leo:A dwarf irregular caught in transition

Leo I is considered one of the youngest dwarf spheroidals (dSph) in the Local Group. Its isolation, extended star formation history (SFH), and recent perigalacticon passage (~1 Gyr ago) make Leo~I one of the most interesting nearby stellar systems. Here, we analyse deep photometric Hubble Space Telescope data via colour-magnitude diagram fitting techniques to study its global and radially-resolved SFH. We find global star formation enhancements in Leo I ~13, 5.5, 2.0, and 1.0 Gyr ago, after which it was substantially quenched. Within the context of previous works focused on Leo I, we interpret the most ancient and the youngest ones as being linked to an early formation (surviving reionisation) and the latest perigalacticon passage (transition from dIrr to dSph), respectively. We clearly identify the presence of very metal poor stars ([Fe/H]~-2) ageing ~5-6 and ~13 Gyr old. We speculate with the possibility that this metal-poor population in Leo I is related to the merging with a low mass system (possibly an ultra-faint dwarf). This event would have triggered star formation (peak of star formation ~5.5 Gyr ago) and accumulated old, metal poor stars from the accreted system in LeoI. Some of the stars born during this event would also form from accreted gas of low-metallicity (giving rise to the 5-6 Gyr low-metallicity tail). Given the intensity and extension of the 2.0 Gyr burst, we hypothesise that this enhancement could also have an external origin. Despite the quenching of star formation around 1 Gyr ago (most probably induced by ram pressure stripping with the Milky Way halo at pericentre), we report the existence of stars as young as 300-500 Myr. We also distinguish two clear spatial regions: the inner ~190 pc presents an homogeneous stellar content (size of the gaseous star forming disc in LeoI from ~4.5 to 1 Gyr ago), whereas the outer regions display a clear positive age gradient.Comment: 20 pages, 11+5 figures, accepted for publication in MNRA

An example of localized D-branes solution on PP-wave backgrounds

In this note we provide an explicit example of type IIB supersymmetric D3-branes solution on a pp-wave like background, consisting in the product of an eight-dimensional pp-wave times a two-dimensional flat space. An interesting property of our solution is the fully localization of the D3-branes (i.e. the solution depends on all the transverse coordinates). Then we show the generalization to other Dp-branes and to the D1/D5 system.Comment: 14 pages, 1 table; v2. references adde

Dual-energy X-ray absorptiometry study of body composition in patients with lipodystrophy

Inst Estadual Diabet & Endocrinol, Metab Unit, Rio de Janeiro, BrazilUniversidade Federal de São Paulo, Dept Endocrinol & Metab, São Paulo, BrazilDENSSO, Rio de Janeiro, BrazilUniversidade Federal de São Paulo, Dept Endocrinol & Metab, São Paulo, BrazilWeb of Scienc

Dairy consumption at snack meal occasions and the overall quality of diet during childhood. Prospective and cross-sectional analyses from the IDEFICS/I.Family cohort

There is scarce information on the influence of dairy consumption between main meals on the overall diet quality through childhood, constituting the main aim of this research. From the Identification and prevention of Dietary-and lifestyle induced health EFfects In Children and infantS (IDEFICS) study, and based on the data availability in each period due to drop outs, 8807 children aged 2 to 9.9 years from eight European countries at baseline (T0: 2007–2008); 5085 children after two years (T1); and 1991 after four years (T3), were included in these analyses. Dietary intake and the Diet Quality Index (DQI) were assessed by two 24 hours dietary recalls (24-HDR) and food frequency questionnaire. Consumption of milk and yogurt (p = 0.04) and cheese (p < 0.001) at snack meal occasions was associated with higher DQI scores in T0; milk and yogurt (p < 0.001), and cheese (p < 0.001) in T1; and cheese (p = 0.05) in T3. Consumers of milk (p = 0.02), yogurt (p < 0.001), or cheese (p < 0.001) throughout T0 and T1 at all snack moments had significantly higher scores of DQI compared to non-consumers. This was also observed with the consumption of cheese between T1 and T3 (p = 0.03). Consumption of dairy products at snack moments through childhood is associated with a better overall diet quality, being a good strategy to improve it in this period

Green-Schwarz Strings in TsT-transformed backgrounds

We consider classical strings propagating in a background generated by a sequence of TsT transformations. We describe a general procedure to derive the Green-Schwarz action for strings. We show that the U(1) isometry variables of the TsT-transformed background are related to the isometry variables of the initial background in a universal way independent of the details of the background. This allows us to prove that strings in the TsT-transformed background are described by the Green-Schwarz action for strings in the initial background subject to twisted boundary conditions. Our construction implies that a TsT transformation preserves integrability properties of the string sigma model. We discuss in detail type IIB strings propagating in the \g_i-deformed AdS_5 x S^5 space-time, find the twisted boundary conditions for bosons and fermions, and use them to write down an explicit expression for the monodromy matrix. We also discuss string zero modes whose dynamics is governed by a fermionicgeneralization of the integrable Neumann model.Comment: 33 pages, latex, v2: typos correcte

Integrated quantitative PIXE analysis and EDX spectroscopy using a laser-driven particle source

Among the existing elemental characterization techniques, Particle Induced X-ray Emission (PIXE) and Energy Dispersive X-ray (EDX) spectroscopy are two of the most widely used in different scientific and technological fields. Here we present the first quantitative laser-driven PIXE and laser-driven EDX experimental investigation performed at the Centro de L\'aseres Pulsados in Salamanca. Thanks to their potential for compactness and portability, laser-driven particle sources are very appealing for materials science applications, especially for materials analysis techniques. We demonstrate the possibility to exploit the X-ray signal produced by the co-irradiation with both electrons and protons to identify the elements in the sample. We show that, using the proton beam only, we can successfully obtain quantitative information about the sample structure through laser-driven PIXE analysis. These results pave the way towards the development of a compact and multi-functional apparatus for the elemental analysis of materials based on a laser-driven particle source.Comment: This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (ENSURE grant agreement No. 647554). Submitted to Science Advances on 20th May 2

Permanent Neonatal Diabetes Caused by Creation of an Ectopic Splice Site within the INS Gene

PublishedCase ReportsJournal ArticleResearch Support, Non-U.S. Gov'tBACKGROUND: The aim of this study was to characterize the genetic etiology in a patient who presented with permanent neonatal diabetes at 2 months of age. METHODOLOGY/PRINCIPAL FINDINGS: Regulatory elements and coding exons 2 and 3 of the INS gene were amplified and sequenced from genomic and complementary DNA samples. A novel heterozygous INS mutation within the terminal intron of the gene was identified in the proband and her affected father. This mutation introduces an ectopic splice site leading to the insertion of 29 nucleotides from the intronic sequence into the mature mRNA, which results in a longer and abnormal transcript. CONCLUSIONS/SIGNIFICANCE: This study highlights the importance of routinely sequencing the exon-intron boundaries and the need to carry out additional studies to confirm the pathogenicity of any identified intronic genetic variants.Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas (CIBERDEM)Instituto de Salud Carlos III of the Spanish Ministry of HealthFIS-programsWellcome Trus

The Mediterranean fishery management: A call for shifting the current paradigm from duplication to synergy

Independence of science and best available science are fundamental pillars of the UN-FAO code of conduct for responsible fisheries and are also applied to the European Union (EU) Common Fishery Policy (CFP), with the overarching objective being the sustainable exploitation of the fisheries resources. CFP is developed by DG MARE, the department of the European Commission responsible for EU policy on maritime affairs and fisheries, which has the Scientific, Technical and Economic Committee for Fisheries (STECF) as consultant body. In the Mediterranean and Black Sea, the General Fisheries Commission for the Mediterranean (FAO-GFCM), with its own Scientific Advisory Committee on Fisheries (GFCM-SAC), plays a critical role in fisheries governance, having the authority to adopt binding recommendations for fisheries conservation and management. During the last years, advice on the status of the main stocks in the Mediterranean and Black Sea has been provided both by GFCM-SAC and EU-STECF, often without a clear coordination and a lack of shared rules and practices. This has led in the past to: i) duplications of the advice on the status of the stocks thus adding confusion in the management process and, ii) a continuous managers’ interference in the scientific process by DG MARE officials hindering its transparency and independence. Thus, it is imperative that this stalemate is rapidly resolved and that the free role of science in Mediterranean fisheries assessment and management is urgently restored to assure the sustainable exploitation of Mediterranean marine resources in the future.En prens