NGS4Cloud: Cloud-based NGS Data Processing

Motivation and challenges: Next-Generation Sequencing (NGS) technologies are greatly increasing the amount of genomic computer data, revolutionizing the biosciences field and leading to the development of more complex NGS Data Analysis techniques [2]. These techniques, known as pipelines or workflows, consist of running and refining a series of intertwined computational analysis and visualization tasks on large amounts of data. These pipelines involve the use of multiple software tools and data resources in a staged fashion, with the output of one tool being passed as input to the next one. To simplify the design and execution of biomedical workflows by end users, especially those that use multiple software tools and data resources, a number of scientific workflow systems have been developed over the past decade. Examples include Galaxy [1] and Swift [3]. However, most of these scientific workflow systems cannot be easily deployed and most of the times are only available to users with access to specialized IT support. There are two main issues to address in the design of an execution environment to these pipelines. First, due to the complexity of configuring and parametrizing pipelines, the use of NGS Data Analysis techniques is not an easy task for a user without IT knowledge. Second, knowing input data can be as much as terabytes and petabytes, pipelines execution require, in general, a great amount of computational resources.info:eu-repo/semantics/publishedVersio

A hybrid meta-heuristic for the generation of feasible large-scale course timetables using instance decomposition

This study introduces a hybrid meta-heuristic for generating feasible course timetables in large-scale scenarios. We conducted tests using our university's instances. The current commercial software often struggles to meet constraints and takes hours to find satisfactory solutions. Our methodology combines adaptive large neighbourhood search, guided local search, variable neighbourhood search, and an innovative instance decomposition technique. Constraint violations from various groups are treated as objective functions to minimize. The search focuses on time slots with the most violations, and if no improvements are observed after a certain number of iterations, the most challenging constraint groups receive new weights to guide the search towards non-dominated solutions, even if the total sum of violations increases. In cases where this approach fails, a shaking phase is employed. The decomposition mechanism works by iteratively introducing curricula to the problem and finding new feasible solutions while considering an expanding set of lectures. Assignments from each iteration can be adjusted in subsequent iterations. Our methodology is tested on real-world instances from our university and random subdivisions. For subdivisions with 400 curricula timetables, decomposition reduced solution times by up to 27%. In real-world instances with 1,288 curricula timetables, the reduction was 18%. Clustering curricula with more common lectures and professors during increments improved solution times by 18% compared to random increments. Using our methodology, viable solutions for real-world instances are found in an average of 21 minutes, whereas the commercial software takes several hours

Incorporation of strawberry into yoghurt: effects on the phytochemical composition

Yogurt has high nutritional value as source of calcium, protein, and provides the beneficial effects of living bacteria. Fruit preparations can be added to yogurt to create new products and combine the nutritional value of dairy and fruit matrices. Interactions of plant phenolics with proteins may lead to the formation of soluble or insoluble complexes. These interactions may have a detrimental effect on the in vivo bioavailability of both phenolics and proteins. The aims of this study were to establish evaluate the protein profiles of yogurt before and after the addition of strawberry and to assess the antioxidant properties and phytochemical of the fruit yogurt, in order to evaluate the possible interaction between protein and phenolic compounds therein. Industrial strawberry preparates containing 50% of fruit, 23% sucrose, 8% glucose-fructose syrup, starch (2%) were incorporated in natural yogurt and kept during 28 days at 2ºC. Extracts were obtained with methanol: formic acid (9:1 v/v) and stored at -20°C for 1 h to facilitate protein precipitation. Extracts was centrifuged and supernatant filtered with 3 kDa membrane. Total antioxidant activity was assessed by the ABTS method, total phenolics by Folin Ciocalteu’s method, and total anthocyanins by pH-differential method. Individual phenolics and anthocyanins were analysed by HPLC-DAD and proteins profile were analyzed by FPLC, SDS-PAGE and Urea-PAGE. An immediate decrease in total antioxidant activity and total phenolics was observed after addition of fruit preparate to yogurt. Antioxidant activity, decrease from 0.84±0.08 to 0.65±0.06 mg ascorbic acid equivalents/g fw. Total phenolics decrease from 1.14±0.05 to 0.98±0.03 mg gallic acid equivalents/g fw and anthocyanins did not change significantly (0.060±0.008 to 0.067±0.017 mg pelargonidin-3-glucoside/g fw). After 28 days at 2°C, the antioxidant activity decrease 18%, total phenolics 11% and anthocyanins 25%. Ellagic acid decreased 20%, while (+)-catechin, (-)-epicatechin, rutin and kaempferol increased 7, 5, 18 and 12%, respectively. Anthocyanins decreased by 18, 48 and 21% for cyanidin-3-glucoside, pelargonidin-3-glucoside and pelargonidin-3-rutinoside, respectively, during the 28-day shelf-life period. (+)-Catechin, (-)-epicatechin, rutin and pelargonidin-3-glucoside were always present in yogurt in lower concentration than in the original fruit (accounted for dilution effects), suggesting strong interaction of these phenolics with the dairy matrix. The only soluble protein detected was alfa-lactalbumin present at 0.22 mg/mL, which decrease 47% when fruit is added. This strong reduction suggests an immediate formation of complexes upon incorporation of strawberry preparate. Free alfa-lactalbumin continued to decrease (48%) during shelf-life, being less available to absorption. These results suggest that interactions between strawberry and yogurt components may affect nutritional availability.info:eu-repo/semantics/publishedVersio

Resonant Lepton-Gluon Collisions at the Large Hadron Collider

We study the lepton-induced resonant production of color-adjoint leptons (leptogluons) at the LHC employing the lepton parton density function of the proton. We demonstrate that this production mechanism can be useful to extend the LHC ability to search for leptogluons beyond purely quark/gluon initiated production processes up to ~ 3.5 TeV leptogluon masses and O(1) TeV compositeness scales. Discerning leptogluons from scalar and vector leptoquarks is also possible in this channel, given a data sample containing the order of 100 signal events. We argue that the resonant channel can be combined with leptogluon pair and associated leptogluon-lepton productions to boost exclusion limits and discovery prospects at the LHC.Comment: 15 pages, 8 figure

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

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

Leucodermia Adquirida num Doente com Dermatite de Contacto Alérgica ao FreeStyle Libre®

In the past few years, the glucose sensor FreeStyle Libre® has been associated with several cases of allergic contact dermatitis. The allergen responsible for most of these cases is isobornyl acrylate, a substance present within the sensor that migrates through the adhesive, thereby reaching the skin. Acquired leukoderma, which may occur in an area previously affected by allergic contact dermatitis, has been described in several medical devices with adhesives. However, until the present, only one case of leukoderma induced by allergic contact dermatitis to FreeStyle Libre® has been described. We report the case of a 41-year-old woman with diabetes mellitus type 1, who developed leukoderma in association with allergic contact dermatitis to this glucose sensor.Nos últimos anos, os sensores de glicose FreeStyle Libre® têm sido associados a inúmeros casos de dermatite de contato alérgica. O alérgenio responsável pela maioria destes casos é o acrilato de isobornilo, uma substância presente no sensor que migra através adesivo, atingindo assim a pele. A leucoderma adquirida pode surgir em áreas previamente afetada por uma dermatite de contato alérgica, tendo sido descrita em associação a vários dispositivos médicos com adesivos. No entanto, até ao momento, foi descrito apenas um caso de leucoderma induzida por sensibilização de contato ao FreeStyle Libre®. Descrevemos o caso de uma mulher de 41 anos com diabetes mellitus tipo 1, que desenvolveu leucoderma em associação a uma dermatite de contato alérgica a este sensor de glicose

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