On tree decomposability of Henneberg graphs

In this work we describe an algorithm that generates well constrained geometric constraint graphs which are solvable by the tree-decomposition constructive technique. The algorithm is based on Henneberg constructions and would be of help in transforming underconstrained problems into well constrained problems as well as in exploring alternative constructions over a given set of geometric elements.Postprint (published version

A Henneberg-based algorithm for generating tree-decomposable minimally rigid graphs

In this work we describe an algorithm to generate tree-decomposable minimally rigid graphs on a given set of vertices V . The main idea is based on the well-known fact that all minimally rigid graphs, also known as Laman graphs, can be generated via Henneberg sequences. Given that not each minimally rigid graph is tree-decomposable, we identify a set of conditions on the way Henneberg steps are applied so that the resulting graph is tree-decomposable. We show that the worst case running time of the algorithm is O(|V|3).Postprint (author's final draft

Geometric constraint solving in a dynamic geometry framework.

Geometric constraint solving is a central topic in many fields such as parametric solid modeling, computer-aided design or chemical molecular docking. A geometric constraint problem consists of a set geometric objects on which a set of constraints is defined. Solving the geometric constraint problem means finding a placement for the geometric elements with respect to each other such that the set of constraints holds. Clearly, the primary goal of geometric constraint solving is to define rigid shapes. However an interesting problem arises when we ask whether allowing parameter constraint values to change with time makes sense. The answer is in the positive. Assuming a continuous change in the variant parameters, the result of the geometric constraint solving with variant parameters would result in the generation of families of different shapes built on top of the same geometric elements but governed by a fixed set of constraints. Considering the problem where several parameters change simultaneously would be a great accomplishment. However the potential combinatorial complexity make us to consider problems with just one variant parameter. Elaborating on work from other authors, we develop a new algorithm based on a new tool we have called h-graphs that properly solves the geometric constraint solving problem with one variant parameter. We offer a complete proof for the soundness of the approach which was missing in the original work. Dynamic geometry is a computer-based technology developed to teach geometry at secondary school, which provides the users with tools to define geometric constructions along with interaction tools such as drag-and-drop. The goal of the system is to show in the user's screen how the geometry changes in real time as the user interacts with the system. It is argued that this kind of interaction fosters students interest in experimenting and checking their ideas. The most important drawback of dynamic geometry is that it is the user who must know how the geometric problem is actually solved. Based on the fact that current user-computer interaction technology basically allows the user to drag just one geometric element at a time, we have developed a new dynamic geometry approach based on two ideas: 1) the underlying problem is just a geometric constraint problem with one variant parameter, which can be different for each drag-and-drop operation, and, 2) the burden of solving the geometric problem is left to the geometric constraint solver. Two classic and interesting problems in many computational models are the reachability and the tracing problems. Reachability consists in deciding whether a certain state of the system can be reached from a given initial state following a set of allowed transformations. This problem is paramount in many fields such as robotics, path finding, path planing, Petri Nets, etc. When translated to dynamic geometry two specific problems arise: 1) when intersecting geometric elements were at least one of them has degree two or higher, the solution is not unique and, 2) for given values assigned to constraint parameters, it may well be the case that the geometric problem is not realizable. For example computing the intersection of two parallel lines. Within our geometric constraint-based dynamic geometry system we have developed an specific approach that solves both the reachability and the tracing problems by properly applying tools from dynamic systems theory. Finally we consider Henneberg graphs, Laman graphs and tree-decomposable graphs which are fundamental tools in geometric constraint solving and its applications. We study which relationships can be established between them and show the conditions under which Henneberg constructions preserve graph tree-decomposability. Then we develop an algorithm to automatically generate tree-decomposable Laman graphs of a given order using Henneberg construction steps

The effects of death and post-mortem cold ischemia on human tissue transcriptomes

Post-mortem tissues samples are a key resource for investigating patterns of gene expression. However, the processes triggered by death and the post-mortem interval (PMI) can significantly alter physiologically normal RNA levels. We investigate the impact of PMI on gene expression using data from multiple tissues of post-mortem donors obtained from the GTEx project. We find that many genes change expression over relatively short PMIs in a tissue-specific manner, but this potentially confounding effect in a biological analysis can be minimized by taking into account appropriate covariates. By comparing ante- and post-mortem blood samples, we identify the cascade of transcriptional events triggered by death of the organism. These events do not appear to simply reflect stochastic variation resulting from mRNA degradation, but active and ongoing regulation of transcription. Finally, we develop a model to predict the time since death from the analysis of the transcriptome of a few readily accessible tissues.Peer ReviewedPostprint (published version

Functional signatures in non-small-cell lung cancer: a systematic review and meta-analysis of sex-based differences in transcriptomic studies

While studies have established the existence of differences in the epidemiological and clinical patterns of lung adenocarcinoma between male and female patients, we know relatively little regarding the molecular mechanisms underlying such sex-based differences. In this study, we explore said differences through a meta-analysis of transcriptomic data. We performed a meta-analysis of the functional profiling of nine public datasets that included 1366 samples from Gene Expression Omnibus and The Cancer Genome Atlas databases. Meta-analysis results from data merged, normalized, and corrected for batch effect show an enrichment for Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways related to the immune response, nucleic acid metabolism, and purinergic signaling. We discovered the overrepresentation of terms associated with the immune response, particularly with the acute inflammatory response, and purinergic signaling in female lung adenocarcinoma patients, which could influence reported clinical differences. Further evaluations of the identified differential biological processes and pathways could lead to the discovery of new biomarkers and therapeutic targets. Our findings also emphasize the relevance of sex-specific analyses in biomedicine, which represents a crucial aspect influencing biological variability in diseaseThis work was supported by Fondo de Investigación Sanitaria (ISCIII PI15-00209), GV/2020/ 186, and ISCIII PT17/0009/0015 FEDE

ICES. 2019. Working Group on Southern Horse Mackerel, Anchovy and Sardine (WGHANSA).

The Working Group on Southern Horse Mackerel, Anchovy and Sardine (WGHANSA1) met by correspondence from 3 to 7 June 2019, and in Madrid from the 25 to the 28 of November 2019, and was chaired by Alexandra Silva (Portugal). There were 13 participants from France, Portugal, Spain and UK. The main task of WGHANSA was to assess the status the stocks of sardine in the Celtic Seas and English Channel (pil.27.7), sardine in the Bay of Biscay (pil.27.8abd), sardine in the Cantabrian Sea and Atlantic Iberian waters (pil.27.8c9a), anchovy in the Bay of Biscay (ane.27.8), anchovy in Atlantic Iberian waters (ane.27.9a; components west and south), horse mackerel in Atlantic Iberian waters (hom.27.9a) and jack mackerel in the Azores (jaa.27.10). Assessments and short-term forecasts were updated according to the stock annexes. There is no assessment method adopted for pil.27.7 due to the lack of data. The stock of pil.27.8abd was assessed as category 1 for the first time, following an interbenchmark. Recruitment has been above the average, the spawning–stock biomass declined and fishing mortality steeply increased in 2010–2012. SSB is fluctuating above MSY Btrigger and F2018 is above FMSY and below Fpa. This year, the DEPM datapoint for 2017 was included in the pil.27.9a assessment for the first time, following a revision of the survey data. The stock has decreased since 2006 and stabilized to a historical low since 2012. The biomass of age 1 and older fish has been decreasing since 2006 and reached the lowest historical value in 2015. It has since increased slightly but is below Blim since 2011. Recruitment has been below the time-series average since 2005. Recruitment in 2018 was around the geometric mean of the last five years. Fishing mortality has been decreasing from a peak in 2011. In 2018, it was the lowest in the time-series and below Fpa and Flim. The stock size indicator for anchovy in 9a.west decreased 90% from 2018 to 2019 (4129 t), after a period of an increasing trend since 2014. The harvest rate decreased 67% from management year 2017 to 2018 being below the median of the historical time-series.The relative spawning–stock biomass of the south component of the anchovy 9.a stock has fluctuated without a trend over the time-series, with most of the values above Bpa. From 2018 to 2019, the relative SSB decreased 5% but is still well above Bpa. Relative Fishing mortality (F) has fluctuated with no clear trend. From management year 2017 to 2018, relative F decreased 93%. The SSB of horse mackerel in Division 9.a fluctuated from 1992, the beginning of the assessment period, to 2012–2013 and afterwards increased continuously to a historical maximum, in 2018. The consistently high recruitment since 2011 has contributed to the SSB increase. Fishing mortality was 0.029 year -1 in 2018, showing a 29% decrease compared to 2017. Fishing mortality has been below FMSY over the whole time-series. The spawning–stock biomass has been above MSY Btrigger over the whole time-series. The exploration of data on anchovy abundance-at-age from juvenile surveys IBERAS-JUVESAR and ECOCADIZ-RECLUTAS indicated the series are still short to conclude about their future incorporation into the assessments. The analyses of internal consistency of the indices and of their consistency with spring acoustic surveys showed promising results for ECOCADIZ-RECLUTAS and pointed out the need to revisit the results of some of the surveys, particularly the IBERAS_JUVESAR series. For sardine, 0-group abundance from IBERAS-JUVESAR (2013–2019) combined with data from an earlier autumn survey, SAR-PT-AUT (discontinued in 2008) covering the northwestern Iberian waters, showed a significant correlation with the abundance of age 1 individuals in surveys carried out in the following spring

El uso de una escape room como recurso docente en la Facultad de Farmacia

[EN] Escape Rooms are educational resources that are being used by many educators, fostering elements of collaboration that help in social skills development. In this study, a multidisciplinary Escape Room has been developed as an educational tool in order to improve students learning and prepare them for the future of professional practice. 145 students and 12 professors belonging to 8 different areas of knowledge from the Faculty of Pharmacy of the University of Seville participated in this activity. Through this innovation, a student-teacher feedback has been created, improving their relationship and learning from each other. The results obtained through satisfaction surveys show the great acceptance that the escape room had among the students, being the study valued with an overall score of 4.83/5. Although 93% of the students considered the activity of high/very high difficulty, 100% of them emphasize that this tool encourages teamwork and 86.9% consider that it reinforces knowledge. This study has awakened students motivation and interest in the subjects involved, strengthening learning and knowledge of the fundamental concepts acquired, and promoting teamwork and problem solving.[ES] Las Escape Rooms son un tipo de recurso que está siendo utilizado por muchos educadores, propiciando elementos de colaboración que ayudan a desarrollar habilidades sociales. En este estudio se ha desarrollado una Escape Room multidisciplinar como herramienta educativa con el fin de mejorar el aprendizaje de los estudiantes y prepararlos para el futuro de la práctica profesional. Participaron 145 alumnos y 12 profesores adscritos a 8 áreas de conocimiento distintas de la Facultad de Farmacia de la Universidad de Sevilla. Mediante esta innovación se ha producido una retroalimentación alumno-profesor, mejorando su relación y aprendiendo mutuamente. Los resultados obtenidos mediante encuestas de satisfacción muestran la gran aceptación que ha tenido la Escape Room entre los alumnos, siendo el estudio valorado con una puntuación general de 4,83/5. A pesar de que el 93% de los alumnos consideró la actividad de alta/muy alta dificultad, el 100% de los mismos destacan que esta herramienta fomenta el trabajo en equipo y el 86,9% considera que refuerza los conocimientos. Este estudio ha despertado en los alumnos la motivación e interés por las asignaturas implicadas, fortaleciendo el aprendizaje y conocimiento de los conceptos fundamentales adquiridos, y propiciando el trabajo en equipo y la resolución de problemas.Gutiérrez Praena, D.; Rios -Reina, R.; Ruiz, R.; Talero, E.; Callejón, R.; Callejón, RM.; Casas, M.... (2019). El uso de una escape room como recurso docente en la Facultad de Farmacia. En IN-RED 2019. V Congreso de Innovación Educativa y Docencia en Red. Editorial Universitat Politècnica de València. 1145-1155. https://doi.org/10.4995/INRED2019.2019.10356OCS1145115

Babelomics 5.0: functional interpretation for new generations of genomic data

This article has been accepted for publication in Nucleic Acids Research Published by Oxford University Press.Babelomics has been running for more than one decade offering a user-friendly interface for the functional analysis of gene expression and genomic data. Here we present its fifth release, which includes support for Next Generation Sequencing data including gene expression (RNA-seq), exome or genome resequencing. Babelomics has simplified its interface, being now more intuitive. Improved visualization options, such as a genome viewer as well as an interactive network viewer, have been implemented. New technical enhancements at both, client and server sides, makes the user experience faster and more dynamic. Babelomics offers user-friendly access to a full range of methods that cover: (i) primary data analysis, (ii) a variety of tests for different experimental designs and (iii) different enrichment and network analysis algorithms for the interpretation of the results of such tests in the proper functional context. In addition to the public server, local copies of Babelomics can be downloaded and installed. Babelomics is freely available at: http://www.babelomics.org.Spanish Ministry of Economy and Competitiveness [BIO2011-27069], Conselleria d'Educacio of the Valencian Community [PROMETEOII/2014/025]; EU FP7-PEOPLE Project MLPM [316861]; Fundació la Marató TV3 [151/C/2013]. Funding for open access charge: Spanish Ministry of Economy and Competitiveness [BIO2011-27069]

Role of Plant-Specific N-Terminal Domain of Maize CK2β1 Subunit in CK2β Functions and Holoenzyme Regulation

Protein kinase CK2 is a highly pleiotropic Ser/Thr kinase ubiquituous in eukaryotic organisms. CK2 is organized as a heterotetrameric enzyme composed of two types of subunits: the catalytic (CK2α) and the regulatory (CK2β). The CK2β subunits enhance the stability, activity and specificity of the holoenzyme, but they can also perform functions independently of the CK2 tetramer. CK2β regulatory subunits in plants differ from their animal or yeast counterparts, since they present an additional specific N-terminal extension of about 90 aminoacids that shares no homology with any previously characterized functional domain. Sequence analysis of the N-terminal domain of land plant CK2β subunit sequences reveals its arrangement through short, conserved motifs, some of them including CK2 autophosphorylation sites. By using maize CK2β1 and a deleted version (ΔNCK2β1) lacking the N-terminal domain, we have demonstrated that CK2β1 is autophosphorylated within the N-terminal domain. Moreover, the holoenzyme composed with CK2α1/ΔNCK2β1 is able to phosphorylate different substrates more efficiently than CK2α1/CK2β1 or CK2α alone. Transient overexpression of CK2β1 and ΔNCK2β1 fused to GFP in different plant systems show that the presence of N-terminal domain enhances aggregation in nuclear speckles and stabilizes the protein against proteasome degradation. Finally, bimolecular fluorescence complementation (BiFC) assays show the nuclear and cytoplasmic location of the plant CK2 holoenzyme, in contrast to the individual CK2α/β subunits mainly observed in the nucleus. All together, our results support the hypothesis that the plant-specific N-terminal domain of CK2β subunits is involved in the down-regulation of the CK2 holoenzyme activity and in the stabilization of CK2β1 protein. In summary, the whole amount of data shown in this work suggests that this domain was acquired by plants for regulatory purposes

Reference genome assessment from a population scale perspective: an accurate profile of variability and noise

This work was supported by grants [BIO2014-57291-R] from the Spanish Ministry of Economy and Competitiveness and ‘Plataforma de Recursos Biomoleculares y Bioinformáticos’ [PT13/0001/0007] from ISCIII, both co-funded with European Regional Development Funds (ERDF); and [EU H2020-INFRADEV-1-2015-1 ELIXIR-EXCELERATE (ref. 676559)]. David Conesa and Antonio López-Quílez would like to thank the Spanish Ministry of Economy and Competitiveness via research grant MTM2016-77501-P (jointly financed with the European Regional Development Fund)