Supercomputació al CSUC

Aquest article descriu el servei de supercomputació que proporciona el Consorci de Serveis Universitaris de Catalunya (CSUC) a la comunitat acadèmica i de recerca. Repassa breument les activitats del Consorci, els projectes i usuaris que utilitzen aquest servei i el tipus de simulacions científiques que s'hi porten a terme. A més, es fa un repàs dels projectes de física i dels nous reptes en supercomputació al Consorci

Global discovery and characterization of small non-coding RNAs in marine microalgae

Background Marine phytoplankton are responsible for 50% of the CO2 that is fixed annually worldwide and contribute massively to other biogeochemical cycles in the oceans. Diatoms and coccolithophores play a significant role as the base of the marine food web and they sequester carbon due to their ability to form blooms and to biomineralise. To discover the presence and regulation of short non-coding RNAs (sRNAs) in these two important phytoplankton groups, we sequenced short RNA transcriptomes of two diatom species (Thalassiosira pseudonana, Fragilariopsis cylindrus) and validated them by Northern blots along with the coccolithophore Emiliania huxleyi. Results Despite an exhaustive search, we did not find canonical miRNAs in diatoms. The most prominent classes of sRNAs in diatoms were repeat-associated sRNAs and tRNA-derived sRNAs. The latter were also present in E. huxleyi. tRNA-derived sRNAs in diatoms were induced under important environmental stress conditions (iron and silicate limitation, oxidative stress, alkaline pH), and they were very abundant especially in the polar diatom F. cylindrus (20.7% of all sRNAs) even under optimal growth conditions. Conclusions This study provides first experimental evidence for the existence of short non-coding RNAs in marine microalgae. Our data suggest that canonical miRNAs are absent from diatoms. However, the group of tRNA-derived sRNAs seems to be very prominent in diatoms and coccolithophores and maybe used for acclimation to environmental conditions

Intervención a través de Conocimiento Constructivo en Ferrol Vello, Galicia

A arquitectura anónima constitui um património de elevada relevância no contexto nacional, sobretudo pela sua presença predominante em sítios históricos. Os edifícios que os constituem, têm características construtivas específicas e são um testemunho significativo das culturas construtivas. É grande a falta de atenção a este tipo de arquitetura, bem como a falta de uma posição concreta sobre a sua salvaguarda. Esta situação coloca em risco a sua preservação e conservação. A estes problemas junta-se o abandono e a falta de manutenção, de que resulta que qualquer intervenção que tire os edifícios do seu estado de ruína seja socialmente aceite como benéfica. Este fator marca as intervenções a que estes edifícios estão vinculados e, dominam as abordagens que levam consigo uma forte descaracterização e perda de valores culturais e construtivos. Este fator constitui os objetivos da presente investigação. A primeira é o estudo das diferentes etapas que constituem o processo de intervenção através dos diferentes métodos, juntamente com a análise dos valores e significados que estabelecem os princípios de intervenção nas identidades construtivas que constituem a tipologia de habitação. A dissertação tem como objetivo verificar a relevância da preservação do conhecimento construtivo em relação às diferentes diretrizes de atuação baseadas nas teorias da Conservação, que ajudam a evitar a descaracterização de sítios históricos. A metodologia utilizada vai desde a revisão da história e das teorias da conservação e restauração, até os estudos de caso de natureza qualitativa. O primeiro deles centra-se no campo teórico, base desta investigação que permite contribuir para estabelecer pilares rígidos, a partir dos quais se estabelecem e esclarecem conceitos-chave que marcam as diferentes fases que constituem as etapas da intervenção. O segundo método é utilizado como método de análise do processo de atuação de casos exemplares de boas práticas. A procura de diferentes decisões de ação em relação à condição e significado das identidades construtivas, permite a conclusão numa análise comparativa e a reflexão sobre os princípios e critérios obtidos. A investigação prossegue estabelecendo um caso exemplar de atuação no complexo histórico de Ferrol Vello. Através da análise contextual construtiva histórica, identifica-se a materialidade e técnica das identidades construtivas do edifício 29 localizado entre a Rúa Castro e Benito Vicetto. Pelos pontos estratégicos e pelas conclusões tiradas após a observação com base na identidade construtiva obtida, bem como a consideração do Plano Especial de Reabilitação e Conservação; é estabelecido o programa e a estratégia de intervenção no referido edifício.La arquitectura anónima constituye un patrimonio de elevada relevancia en el contexto nacional, sobre todo por su presencia predominante en los conjuntos históricos. Los edificios que los conforman, poseen características constructivas específicas y son un significativo testimonio de las culturas constructivas. La falta de atención sobre este tipo de arquitectura es elevada, así como, la falta de posición concreta sobre su salvaguarda. Esta situación coloca en riesgo su preservación y conservación. A estas problemáticas hay que añadir el abandono y la falta de mantenimiento, que deriva en el resultado de que cualquier intervención que retire los edificios de su estado de ruina, es socialmente aceptada como beneficiosa. Este factor, marca las intervenciones a la que estos edificios están atados y, dominan los abordajes que llevan consigo una fuerte descaracterización y pérdida de valores culturales y constructivos. Este factor conforma los objetivos de la presente investigación. Siendo el primero, el estudio de las distintas etapas que conforman el proceso de intervención a través de los diferentes métodos establecidos, en conjunto con el análisis de los valores y significados que establecen los principios de intervención en las identidades constructivas que conforman la tipología arquitectónica habitacional. La disertación pretende verificar la relevancia de la preservación del conocimiento constructivo en relación con las diferentes directrices de actuación fundamentadas en las teorías de conservación, que contribuyen a evitar descaracterizar los conjuntos históricos. La metodología utilizada es mixta y engloba desde la revisión de la historia y las teorías de conservación y restauración, hasta el estudio de casos múltiples de naturaleza cualitativa. Primeramente, se estudia el ámbito teórico, fundamento para esta investigación que permite contribuir en establecer unos pilares rígidos, a partir de los cuales son establecidos y aclarados conceptos clave que marcan las diferentes fases que conforman las etapas de intervención. A continuación, se aborda el análisis del proceso de actuación de casos ejemplares de buenas prácticas. La búsqueda de las diferentes decisiones de actuación en relación con la condición y significado de las identidades constructivas, permite la conclusión en un análisis comparativo y la reflexión sobre los principios y criterios obtenidos. El segundo objetivo es el estudio de un caso de ejemplo de actuación en el conjunto histórico de Ferrol Vello. A través del análisis contextual histórico constructivo se identifican la materialidad y técnica de las identidades constructivas del edificio 29 situado entre las rúas Castro y Benito Vicetto. A través de los puntos estratégicos y de las conclusiones realizadas tras la observación en base a la identidad constructiva obtenida, así como también la consideración del Plan Especial de Rehabilitación y Conservación, se establecen el programa y la estrategia de intervención en dicha edificación.Anonymous architecture constitutes a high relevance heritage on the national context, above all because of its predominant presence in historical complex. The buildings that make them up have specific constructive characteristics and are a significant testimony of constructive cultures. The lack of attention to this type of architecture is high, as well it is the position on its safeguarding. This situation puts its preservation and conservation at risk. To these problems must be added abandon and lack of maintenance, which results that in any intervention that removes buildings from their state of ruin, is socially accepted as beneficial. This factor marks the interventions to which these buildings are attached, dominating strong decharacterization and loss of cultural and constructive values approaches. This approach reflects on the direction of this investigation. The first being the study of the different stages that put up together the intervention process through the different established methods, integrating the values and meanings analysis that establish the principles of intervention in the constructive identities that constitute this architectural housing typology. The dissertation seeks to verify the preservation relevance of constructive knowledge in relation to the different guidelines for action based on Conservation Theories, which help to avoid decharacterizing historical sites. The methodology used is mixed and ranges from the review of the history and the theories of conservation and restoration, to the multiple case study of a qualitative nature. First of all, the investigation focuses on the theorical field, wich allows to establish solid groundings. This research leaves the contribution for establishing and clarifing key concepts that consolidate the process of intervention. Consecutively the analysis approachs is made by the intervention process study of exemplary good practices cases. The search for different action decisions in relation to the condition and meaning of constructive identities, allows the conclusion in one synthesis and reflection on the principles and criteria obtained. The investigation continues by establishing an example case of action in the historical complex of Ferrol Vello. Through the historical constructive contextual analysis, the materiality and technique of the constructive identities of the Building 29 located between Rúa Castro and Benito Vicetto are identified. Through the strategic points and the conclusions made after the observation based on the constructive identity obtained, as well as the consideration of the Special Rehabilitation and Conservation Plan; the intervention program and strategy is established

Validation of a self-reported work disability questionnaire for ulcerative colitis

Ulcerative colitis (UC) may severely limit patients'' capacity to work. Recently, we validated a work disability questionnaire (WDQ) for Crohn disease. As UC shares clinical characteristics with Crohn disease, we hypothesized that the questionnaire might also be useful for UC. The study was aimed to validate the WDQ for use in UC. Consecutive patients with UC (n = 142, 67 women; age 48 +/- 1) completed the UC-WDQ and the inflammatory bowel disease questionnaire-9 (IBDQ-9), and EuroQoL-5D quality-of-life questionnaires. Validation of the UC-WDQ included an assessment of its construct validity, including: discriminant validity, convergent validity, and reproducibility (test-retest). We also calculated the intraclass correlation and the Cronbach alpha. 1. Discriminant validity: Mean UC-WDQ scores were 12.8 +/- 4.4 (remission phase) and 17.2 +/- 6.1 (with clinical activity) (P < .05). 2. Convergent validity: The correlations of UC-WDQ were r = 0.74 (P < .001) with IBDQ, r = 0.44 (P < .01) with disease activity, r = 0.56 (P < .01) with EuroQoL-5D, and r = 0.60 (P < .01) with the EuroQoL-5D visual scale. 3. Reproducibility: Test-retest reproducibility: UC-WDQ scores obtained after a 2-week interval were similar (15.8 vs 15.1), (r = 0.91, P < .01). Intraclass correlation was 0.93 (95% confidence interval 0.92-0.95). Cronbach alpha was 0.94. The UC-WDQ is a valid and reliable tool for measuring work disability in patients with UC

Photon-Counting Detector CT Angiography for Endoleak Detection After Endovascular Aortic Repair: Triphasic CT With True Noncontrast Versus Biphasic CT With Virtual Noniodine Imaging

OBJECTIVES: The aim of this study was to compare image quality and endoleak detection after endovascular abdominal aortic aneurysm repair between a triphasic computed tomography (CT) with true noncontrast (TNC) and a biphasic CT with virtual noniodine (VNI) images on photon-counting detector CT (PCD-CT). MATERIALS AND METHODS: Adult patients after endovascular abdominal aortic aneurysm repair who received a triphasic examination (TNC, arterial, venous phase) on a PCD-CT between August 2021 and July 2022 were retrospectively included. Endoleak detection was evaluated by 2 blinded radiologists on 2 different readout sets (triphasic CT with TNC-arterial-venous vs biphasic CT with VNI-arterial-venous). Virtual noniodine images were reconstructed from the venous phase. The radiologic report with additional confirmation by an expert reader served as reference standard for endoleak presence. Sensitivity, specificity, and interreader agreement (Krippendorf α) were calculated. Image noise was assessed subjectively in patients using a 5-point scale and objectively calculating the noise power spectrum in a phantom. RESULTS: One hundred ten patients (7 women; age, 76 ± 8 years) with 41 endoleaks were included. Endoleak detection was comparable between both readout sets with a sensitivity and specificity of 0.95/0.84 (TNC) versus 0.95/0.86 (VNI) for reader 1 and 0.88/0.98 (TNC) versus 0.88/0.94 (VNI) for reader 2. Interreader agreement for endoleak detection was substantial (TNC: 0.716, VNI: 0.756). Subjective image noise was comparable between TNC and VNI (4; IQR [4, 5] vs 4; IQR [4, 5], P = 0.44). In the phantom, noise power spectrum peak spatial frequency was similar between TNC and VNI (both f peak = 0.16 mm -1 ). Objective image noise was higher in TNC (12.7 HU) as compared with VNI (11.5 HU). CONCLUSIONS: Endoleak detection and image quality were comparable using VNI images in biphasic CT as compared with TNC images in triphasic CT offering the possibility to reduce scan phases and radiation exposure

A database of microRNA expression patterns in Xenopus laevis

MicroRNAs (miRNAs) are short, non-coding RNAs around 22 nucleotides long. They inhibit gene expression either by translational repression or by causing the degradation of the mRNAs they bind to. Many are highly conserved amongst diverse organisms and have restricted spatio-temporal expression patterns during embryonic development where they are thought to be involved in generating accuracy of developmental timing and in supporting cell fate decisions and tissue identity. We determined the expression patterns of 180 miRNAs in Xenopus laevis embryos using LNA oligonucleotides. In addition we carried out small RNA-seq on different stages of early Xenopus development, identified 44 miRNAs belonging to 29 new families and characterized the expression of 5 of these. Our analyses identified miRNA expression in many organs of the developing embryo. In particular a large number were expressed in neural tissue and in the somites. Surprisingly none of the miRNAs we have looked at show expression in the heart. Our results have been made freely available as a resource in both XenMARK and Xenbase

Characterisation and expression of microRNAs in developing wings of the neotropical butterfly Heliconius melpomene.

BACKGROUND: Heliconius butterflies are an excellent system for studies of adaptive convergent and divergent phenotypic traits. Wing colour patterns are used as signals to both predators and potential mates and are inherited in a Mendelian manner. The underlying genetic mechanisms of pattern formation have been studied for many years and shed light on broad issues, such as the repeatability of evolution. In Heliconius melpomene, the yellow hindwing bar is controlled by the HmYb locus. MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that have key roles in many biological processes, including development. miRNAs could act as regulators of genes involved in wing development, patterning and pigmentation. For this reason we characterised miRNAs in developing butterfly wings and examined differences in their expression between colour pattern races. RESULTS: We sequenced small RNA libraries from two colour pattern races and detected 142 Heliconius miRNAs with homology to others found in miRBase. Several highly abundant miRNAs were differentially represented in the libraries between colour pattern races. These candidates were tested further using Northern blots, showing that differences in expression were primarily due to developmental stage rather than colour pattern. Assembly of sequenced reads to the HmYb region identified hme-miR-193 and hme-miR-2788; located 2380 bp apart in an intergenic region. These two miRNAs are expressed in wings and show an upregulation between 24 and 72 hours post-pupation, indicating a potential role in butterfly wing development. A search for miRNAs in all available H. melpomene BAC sequences (~2.5 Mb) did not reveal any other miRNAs and no novel miRNAs were predicted. CONCLUSIONS: Here we describe the first butterfly miRNAs and characterise their expression in developing wings. Some show differences in expression across developing pupal stages and may have important functions in butterfly wing development. Two miRNAs were located in the HmYb region and were expressed in developing pupal wings. Future work will examine the expression of these miRNAs in different colour pattern races and identify miRNA targets among wing patterning genes.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

The combination of quantitative faecal occult blood test and faecal calprotectin is a cost-effective strategy to avoid colonoscopies in symptomatic patients without relevant pathology

Background: Faecal occult blood test (FOBT) has demonstrated effectiveness in colorectal cancer (CRC) screening. Faecal calprotectin (FC) has proven efficient for evaluating activity in inflammatory bowel disease (IBD), but its value in CRC detection is less established. Most symptomatic patients have benign pathologies, but still undergo colonoscopy in many settings. Aims: To evaluate the diagnostic accuracy and cost-effectiveness of the combination of FOBT plus FC in symptomatic patients. Methods: Patients who completed colonic investigations and returned stool samples, on which FOBT and FC were performed, were recruited prospectively. CRC, advanced adenoma, IBD and angiodysplasia were considered as relevant pathologies. Results: A total of 404 patients were included, of whom 87 (21.5%) had relevant pathologies. Sensitivity and specificity were 50.6% and 69.6% for FOBT, 78.2% and 54.4% for FC. Negative predictive value (NPV) was 90.1% for FC and 86.9% for FOBT. NPV for the combination of FOBT and FC was 94.1%, with a sensitivity and specificity of 88.5% and 50.3%. The area under ROC (receiver operator curve) (AUC) was 0.741 for FOBT, 0.736 for FC and 0.816 for the combination. The total cost for visits and procedures was €233, 016 (€577/patient). Using a combination of FOBT and FC as pre-endoscopic tool allows colonoscopies to be reduced by 39.4%, reducing total costs by 20.5%. Conclusion: The combination of FOBT and FC has a better diagnostic accuracy compared with each test alone. Performing both tests before colonoscopy is a less costly and more effective strategy, reducing unnecessary procedures and complications

Predicted efficacy of a pharmacogenetic passport for inflammatory bowel disease

BACKGROUND: High inter-individual variability in therapeutic response to drugs used in the management of Inflammatory Bowel Disease (IBD) leads to high morbidity and high costs. Genetic variants predictive of thiopurine-induced myelosuppression, thiopurine-induced pancreatitis and immunogenicity of Tumour Necrosis Factor alpha (TNFα) antagonists have been identified, but uptake of pre-treatment pharmacogenetic testing into clinical guidelines has been slow. AIM: To explore the efficacy of a pharmacogenetic passport for IBD that includes multiple pharmacogenetic predictors of response. METHODS: Patients with IBD exposed to thiopurines and/or TNFα antagonists were retrospectively evaluated for the presence of thiopurine toxicity and/or immunogenicity of TNFα antagonists. All patients were genotyped using both whole-exome sequencing and the Illumina Global Screening Array. An in-house-developed computational pipeline translated genetic data into an IBD pharmacogenetic passport that predicted risks for thiopurine toxicity and immunogenicity of TNFα antagonists per patient. Using pharmacogenetic-guided treatment guidelines, we calculated clinical efficacy estimates for pharmacogenetic testing for IBD. RESULTS: Among 710 patients with IBD exposed to thiopurines and/or TNFα antagonists, 150 adverse drug responses occurred and our pharmacogenetic passport would have predicted 54 (36%) of these. Using a pharmacogenetic passport for IBD that includes genetic variants predictive of thiopurine-induced myelosuppression, thiopurine-induced pancreatitis, and immunogenicity of TNFα antagonists, 24 patients need to be genotyped to prevent one of these adverse drug responses. CONCLUSIONS: This study highlights the clinical efficacy of a pharmacogenetic passport for IBD. Implementation of such a pharmacogenetic passport into clinical management of IBD may contribute to a reduction in adverse drug responses

Environmental and epigenetic regulation of Rider retrotransposons in tomato.

Transposable elements in crop plants are the powerful drivers of phenotypic variation that has been selected during domestication and breeding programs. In tomato, transpositions of the LTR (long terminal repeat) retrotransposon family Rider have contributed to various phenotypes of agronomical interest, such as fruit shape and colour. However, the mechanisms regulating Rider activity are largely unknown. We have developed a bioinformatics pipeline for the functional annotation of retrotransposons containing LTRs and defined all full-length Rider elements in the tomato genome. Subsequently, we showed that accumulation of Rider transcripts and transposition intermediates in the form of extrachromosomal DNA is triggered by drought stress and relies on abscisic acid signalling. We provide evidence that residual activity of Rider is controlled by epigenetic mechanisms involving siRNAs and the RNA-dependent DNA methylation pathway. Finally, we demonstrate the broad distribution of Rider-like elements in other plant species, including crops. Our work identifies Rider as an environment-responsive element and a potential source of genetic and epigenetic variation in plants