A standalone version of IsoFinder for the computational prediction of isochores in genome sequences

Isochores are long genome segments relatively homogeneous in G+C. A heuristic algorithm based on entropic segmentation has been developed by our group, and a web server implementing all the required components is available. However, a researcher may want to perform batch processing of many sequences simultaneously in its local machine, instead of analyzing them on one by one basis through the web. To this end, standalone versions are required. We report here the implementation of two standalone programs, able to predict isochores at the sequence level: 1) a command-line version (IsoFinder) for Windows and Linux systems; and 2) a user-friendly version (IsoFinderWin) running under Windows.Comment: 7 pages, 3 figure

Making sense of innovation by R&D and non-R&D innovators in low technology contexts: a forgotten lesson for policymakers

This paper attempts to use an integrated theory based on a firm’s internal and external sources of knowledge framework to analyze how different are R&D from non-R&D activities to innovate, specially in a context of low and medium low tech (LMT) sectors where most of the firms are SMEs. Simultaneously, the paper also explores the key differences between R&D and non-R&D innovators. The empirical analysis is based on a representative panel of 2023 Spanish manufacturing firms for 2005 and 2006 from the Spanish Ministry of Industry. Innovation in product and process is explained using non-R&D variables such as in Marketing, Design or hiring tertiary degree employees. Only innovation in product is explained by R&D expenditures. Addressing innovation in process, R&D variables work in few cases and neither R&D expenditures but occasionally R&D employees and are specially relevant the non-R&D variables. The interaction (moderating) effect is specially negative and significant, addressing the substitution effect with different implications regarding product or process innovation. Therefore, innovation can be explained using non-R&D variables such as investments in Marketing, Design, and other routines linked to human resources, technology monitoring committees or the existence of a formal plan to innovate. The firms with more internal resources, those which conduct R&D activities present a better AC and it leads to engage in cooperation agreements and access to external flows of knowledge. The paper has important implications for policymakers due to the fact that most of policies for R&D are based on R&D programmes, while there are other realities: non-R&D factors which also explain innovation, specially when considering low tech sector contexts. El presente artículo usa la teoría de recursos y capacidades para, a través de los recursos internos y externos de las empresas, analizar las actividades de R&D y las actividades de no-R&D en su impacto sobre la performance de innovación de la empresa, en un contexto sectorial de baja y media tecnología. Asimismo, el artículo explora el rol innovador de las empresas que hacen R&D y las que no lo hacen. Con una muestra de 2023 empresas manufactureras españolas, obtenemos un comportamiento innovador para la innovación en producto y en proceso y, sobre todo, observando que las actividades de R&D tienen muy poco peso explicativo sobre el resultado de innovación. El artículo presenta implicaciones para la Academia y los policymakers, sobre todo por el hecho de que la mayoría de las políticas de innovación se basan en actividades de R&D.fuentes de innovación, estrategias de búsqueda de conocimiento externo, cooperación tecnológica, capacidad de absorción. innovation sources, technology cooperation, absorptive capacity, search strategies.

DNA Methylation Profiling from High-Throughput Sequencing Data

In this chapter we will review the common steps in the analysis of whole genome singlebase-pair resolution methylation data including the pre-processing of the reads, the alignment and the read out of the methylation information of individual cytosines. We will specially focus on the possible error sources which need to be taken into account in order to generate high quality methylation maps. Several tools have been already developed to convert the sequencing data into knowledge about the methylation levels. We will review the most used tools discussing both technical aspects like user-friendliness and speed, but also biologically relevant questions as the quality control. For one of these tools, NGSmethPipe, we will give a step by step tutorial including installation and methylation profiling for different data types and species. We will conclude the chapter with a brief discussion of NGSmethDB, a database for the storage of single-base resolution methylation maps that can be used to further analyze the obtained methylation maps.This work was supported by the Ministry of Innovation and Science of the Spanish Government [BIO2010-20219 (M.H.), BIO2008-01353 (J.L.O.)]; ‘Juan de la Cierva’ grant (to M.H.) and Basque Country ‘Programa de formación de investigadores’ grant (to G.B.)

Phylogenetic distribution of large-scale genome patchiness

[Background] The phylogenetic distribution of large-scale genome structure (i.e. mosaic compositional patchiness) has been explored mainly by analytical ultracentrifugation of bulk DNA. However, with the availability of large, good-quality chromosome sequences, and the recently developed computational methods to directly analyze patchiness on the genome sequence, an evolutionary comparative analysis can be carried out at the sequence level. [Results] The local variations in the scaling exponent of the Detrended Fluctuation Analysis are used here to analyze large-scale genome structure and directly uncover the characteristic scales present in genome sequences. Furthermore, through shuffling experiments of selected genome regions, computationally-identified, isochore-like regions were identified as the biological source for the uncovered large-scale genome structure. The phylogenetic distribution of short- and large-scale patchiness was determined in the best-sequenced genome assemblies from eleven eukaryotic genomes: mammals (Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus, and Canis familiaris), birds (Gallus gallus), fishes (Danio rerio), invertebrates (Drosophila melanogaster and Caenorhabditis elegans), plants (Arabidopsis thaliana) and yeasts (Saccharomyces cerevisiae). We found large-scale patchiness of genome structure, associated with in silico determined, isochore-like regions, throughout this wide phylogenetic range. [Conclusion] Large-scale genome structure is detected by directly analyzing DNA sequences in a wide range of eukaryotic chromosome sequences, from human to yeast. In all these genomes, large-scale patchiness can be associated with the isochore-like regions, as directly detected in silico at the sequence level.This work was supported by the Spanish Government (BIO2005-09116-C03-01) and Plan Andaluz de Investigación (CVI-162, P06-FQM-01858, P07-FQM-03163 and TIC-640)

CpGcluster: a distance-based algorithm for CpG-island detection

BACKGROUND: Despite their involvement in the regulation of gene expression and their importance as genomic markers for promoter prediction, no objective standard exists for defining CpG islands (CGIs), since all current approaches rely on a large parameter space formed by the thresholds of length, CpG fraction and G+C content. RESULTS: Given the higher frequency of CpG dinucleotides at CGIs, as compared to bulk DNA, the distance distributions between neighboring CpGs should differ for bulk and island CpGs. A new algorithm (CpGcluster) is presented, based on the physical distance between neighboring CpGs on the chromosome and able to predict directly clusters of CpGs, while not depending on the subjective criteria mentioned above. By assigning a p-value to each of these clusters, the most statistically significant ones can be predicted as CGIs. CpGcluster was benchmarked against five other CGI finders by using a test sequence set assembled from an experimental CGI library. CpGcluster reached the highest overall accuracy values, while showing the lowest rate of false-positive predictions. Since a minimum-length threshold is not required, CpGcluster can find short but fully functional CGIs usually missed by other algorithms. The CGIs predicted by CpGcluster present the lowest degree of overlap with Alu retrotransposons and, simultaneously, the highest overlap with vertebrate Phylogenetic Conserved Elements (PhastCons). CpGcluster's CGIs overlapping with the Transcription Start Site (TSS) show the highest statistical significance, as compared to the islands in other genome locations, thus qualifying CpGcluster as a valuable tool in discriminating functional CGIs from the remaining islands in the bulk genome. CONCLUSION: CpGcluster uses only integer arithmetic, thus being a fast and computationally efficient algorithm able to predict statistically significant clusters of CpG dinucleotides. Another outstanding feature is that all predicted CGIs start and end with a CpG dinucleotide, which should be appropriate for a genomic feature whose functionality is based precisely on CpG dinucleotides. The only search parameter in CpGcluster is the distance between two consecutive CpGs, in contrast to previous algorithms. Therefore, none of the main statistical properties of CpG islands (neither G+C content, CpG fraction nor length threshold) are needed as search parameters, which may lead to the high specificity and low overlap with spurious Alu elements observed for CpGcluster predictions

Cochleates derived from Vibrio cholerae O1 proteoliposomes : The impact of structure transformation on mucosal immunisation

Cochleates are phospholipid-calcium precipitates derived from the interaction of anionic lipid vesicles with divalent cations. Proteoliposomes from bacteria may also be used as a source of negatively charged components, to induce calcium-cochleate formation. In this study, proteoliposomes from V. cholerae O1 (PLc) (sized 160.7±1.6 nm) were transformed into larger (16.3±4.6 µm) cochleate-like structures (named Adjuvant Finlay Cochleate 2, AFCo2) and evaluated by electron microscopy (EM). Measurements from transmission EM (TEM) showed the structures had a similar size to that previously reported using light microscopy, while observations from scanning electron microscopy (SEM) indicated that the structures were multilayered and of cochleate-like formation. The edges of the AFCo2 structures appeared to have spaces that allowed penetration of negative stain or Ovalbumin labeled with Texas Red (OVA-TR) observed by epi-fluorescence microscopy. In addition, freeze fracture electron microscopy confirmed that the AFCo2 structures consisted of multiple overlapping layers, which corresponds to previous descriptions of cochleates. TEM also showed that small vesicles co-existed with the larger cochleate structures, and in vitro treatment with a calcium chelator caused the AFCo2 to unfold and reassemble into small proteoliposome-like structures. Using OVA as a model antigen, we demonstrated the potential loading capacity of a heterologous antigen and in vivo studies showed that with simple admixing and administration via intragastric and intranasal routes AFCo2 provided enhanced adjuvant properties compared with PLc

Prediction of CpG-island function: CpG clustering vs. sliding-window methods

Background Unmethylated stretches of CpG dinucleotides (CpG islands) are an outstanding property of mammal genomes. Conventionally, these regions are detected by sliding window approaches using %G + C, CpG observed/expected ratio and length thresholds as main parameters. Recently, clustering methods directly detect clusters of CpG dinucleotides as a statistical property of the genome sequence. Results We compare sliding-window to clustering (i.e. CpGcluster) predictions by applying new ways to detect putative functionality of CpG islands. Analyzing the co-localization with several genomic regions as a function of window size vs. statistical significance (p-value), CpGcluster shows a higher overlap with promoter regions and highly conserved elements, at the same time showing less overlap with Alu retrotransposons. The major difference in the prediction was found for short islands (CpG islets), often exclusively predicted by CpGcluster. Many of these islets seem to be functional, as they are unmethylated, highly conserved and/or located within the promoter region. Finally, we show that window-based islands can spuriously overlap several, differentially regulated promoters as well as different methylation domains, which might indicate a wrong merge of several CpG islands into a single, very long island. The shorter CpGcluster islands seem to be much more specific when concerning the overlap with alternative transcription start sites or the detection of homogenous methylation domains. Conclusions The main difference between sliding-window approaches and clustering methods is the length of the predicted islands. Short islands, often differentially methylated, are almost exclusively predicted by CpGcluster. This suggests that CpGcluster may be the algorithm of choice to explore the function of these short, but putatively functional CpG islands

Linguistic validation of cystic fibrosis quality of life questionnaires

OBJECTIVE: The purpose of this study was to validate the Portuguese translations of four cystic fibrosis quality of life questionnaires (CFQ). The first three were developed for patients with cystic fibrosis aged from 6 to 11 years, from 12 to 13 years and 14 years or more, while the fourth was developed for the parents of patients aged 6 to 13 years. MATERIAL AND METHODS: The four CFQ translations contained from 35 to 50 questions covering nine domains and were validated as follows: translation from English to Portuguese, pilot application, back translation and then approval by the author of the English versions. The four translations were applied to 90 stable patients (30 from each age group) and the parents of patients aged 6-13 years (n = 60), on two occasions with a 13 to 17 day interval. Intraclass Correlation Coefficients (ICC) were used to measure reproducibility. This study was approved by the Commission for Ethics in Research at the institution. RESULTS:Reproducibility was good (ICC = 0.62 to 0.99) for the four translations in all domains, with the exceptions of the Digestion domain for the 6 to 11 and 12 to 13 years age groups with ICC = 0.59 and 0.47, respectively and the Social Role domain for the 14 and over age group (ICC = -0.19 ) CONCLUSION: The translation and cultural adaptation for Brazil resulted in four CFQ versions that are easy to understand and offer good reproducibility.OBJETIVO: O propósito deste estudo foi validar em português as quatro versões de questionários de qualidade de vida em fibrose cística, desenvolvidos para pacientes com fibrose cística de 6 a 11 anos, de 12 a 13 e mais de 14 anos, e para os pais de pacientes de 6 a 13 anos. MATERIAL E MÉTODOS: A validação das quatro versões de questionários de qualidade de vida em fibrose cística (de 35 e 50 questões, abrangendo nove domínios) constou de: versão inglês-português, aplicação-piloto, tradução retrógrada e aprovação da autora da versão inglesa. As quatro versões foram aplicadas a 90 pacientes estáveis (30 de cada grupo etário) e aos pais de doentes de 6-13 anos (n = 60), em duas entrevistas, com intervalo de 13-17 dias. Foi avaliada a reprodutibilidade pelo coeficiente de correlação intraclasse (CCI). O estudo foi aprovado pela comissão de ética em pesquisa da instituição. RESULTADOS: A reprodutibilidade foi boa (CCI = 0,62 a 0,99) para as quatro versões, em todos os domínios, exceto o digestivo (CCI = 0,59 e CCI = 0,47) para os grupos etários de 6 a 11 e 12 a 13 anos, respectivamente, e domínio papel social (CCI = -0,19 ) para o grupo acima de 14 anos. CONCLUSÃO: A tradução e a adaptação à língua e à cultura brasileiras das quatro versões de questionários de qualidade de vida em fibrose cística mostraram-se de fácil entendimento e boa reprodutibilidade.Universidade de São Paulo Faculdade de Medicina Departamento de PediatriaUniversidade Federal de São Paulo (UNIFESP) Escola Paulista de MedicinaFaculdade de Medicina do ABCUNIFESP-EPM Centro de Reabilitação PulmonarUniversidade de São Paulo Faculdade de Medicina Hospital das ClínicasUniversity of Miami Department of PsychologyUNIFESP, EPM, Centro de Reabilitação PulmonarSciEL

Combustion Recession after End of Injection in Diesel Spray

This work contributes to the understanding of physical mechanisms that control flashback, or more appropriately combustion recession, in diesel-like sprays. Combustion recession is the process whereby a lifted flame retreats back towards the injector after end-of-injection under conditions that favor autoignition. The motivation for this study is that failure of combustion recession can result in unburned hydrocarbon emissions. A large dataset, comprising many fuels, injection pressures, ambient temperatures, ambient oxygen concentrations, ambient densities, and nozzle diameters is used to explore experimental trends for the behavior of combustion recession. Then, a reduced-order model, capable of modeling non-reacting and reacting conditions, is used to help interpret the experimental trends. Finally, the reduced-order model is used to predict how a controlled ramp-down rate-ofinjection can enhance the likelihood of combustion recession for conditions that would not normally exhibit combustion recession. In general, fuel, ambient conditions, and the spray rate-of-injection transient during the end-of-injection determine the success or failure of combustion recession. The likelihood of combustion recession increases for higher ambient temperatures and oxygen concentrations as well as for higher reactivity fuels. In the transition between high and low ambient temperature (or oxygen concentration), the behavior of combustion recession changes from spatially sequential ignition to separated, or isolated, ignition sites that eventually merge. In contradistinction to typical diesel ignition delay trends where the autoignition times are longer for increasing injection pressure, the time required for combustion recession increases with injection pressure.Knox, BW.; Genzale, C.; Pickett, L.; García-Oliver, JM.; Vera-Tudela, WM. (2015). Combustion Recession after End of Injection in Diesel Spray. SAE International Journal of Fuel and Lubricants. 8(2):1-17. doi:10.4271/2015-01-0797S1178

Información mecanística en la evaluación de riesgos. Una aproximación desde las explicaciones basadas en mecanismos

RESUMENDesde la década pasada, en la evaluación de riesgos se ha propuesto utilizar la información mecanística con un doble propósito: seleccionar guías de inferencia y realizar extrapolaciones inter-químicas para establecer categorías de tóxicos. En este trabajo se utilizan aportaciones procedentes del análisis filosófico de las explicaciones mecanísticas para analizar el concepto de información mecanística utilizado en la evaluación de riesgos. Categorizamos la información mecanística de los modos de acción en términos de explicaciones etiológicas que emplean bosquejos de mecanismos. El grado de detalle que ha de incorporar la información mecanística en la evaluación de riesgos dependerá, entre otros factores, de consideraciones pragmáticas respecto del uso posterior de dicha información.PALABRAS CLAVEINFORMACIÓN MECANÍSTICA, EVAVALUACIÓN DE RIESGOS, MODELO, BOSQUEJO, EXPLICACIÓN.ABSTRACTSince the 2000s, in risk assessment studies it is usual to use mechanistic information with a double aim: to select inference guidelines and to make inter-chemical extrapolations to categorize toxics. Here, we use the contributions made in philosophical analysis of mechanistic explanations to analyze the concept of mechanistic information used in the risk assessment. We classify mechanistic information, specifically that concerning modes of action, in terms of etiological explanations employing sketches of mechanisms. The grade of the details that mechanistic information must incorporate to risk assessment depends on, among other factors, pragmatic considerations on the further use of such information.KEYWORDSMECHANISTIC INFORMATION, RISK ASSESSMENT, MODEL, SKETCH, EXPLANATION