Pipe3d, a pipeline to analyze integral field spectroscopy data: II Analysis sequence and califa dataproducts

Presentamos una version mejorada de FIT3D, una herramienta de ajuste para el analisis de las poblaciones estelares y el gas ionizado en espectros de galaxias de resolucion intermedia. La misma se desarrollo para el análisis de datos de espectroscopía de campo integral y es la base de Pipe3D, un dataducto usado en el analisis de datos de los muestreos CALIFA, MaNGA y SAMI. Describimos la filosof´ıa y los pasos seguidos en el ajuste, presentando un conjunto amplio de simulaciones con el fin de estimar la precisión de los parametros derivados, mostrando el resultado de dichas simulaciones. Finalmente, comparamos el resultado del analisis con FIT3D y el obtenido mediante otros paquetes de uso frecuente, encontrando que los parametros derivados son totalmente compatibles.We present Pipe3D, an analysis pipeline based on the FIT3D fitting tool, developed to explore the properties of the stellar populations and ionized gas of integral field spectroscopy (IFS) data. Pipe3D was created to provide coherent, simple to distribute, and comparable dataproducts, independently of the origin of the data, focused on the data of the most recent IFU surveys (e.g., CALIFA, MaNGA, and SAMI), and the last generation IFS instruments (e.g., MUSE). In this article we describe the di fferent steps involved in the analysis of the data, illustrating them by showing the dataproducts derived for NGC 2916, observed by CALIFA and P-MaNGA. As a practical example of the pipeline we present the complete set of dataproducts derived for the 200 datacubes that comprises the V500 setup of the CALIFA Data Release 2 (DR2), making them freely available through the network. Finally, we explore the hypothesis that the properties of the stellar populations and ionized gas of galaxies at the e ffective radius are representative of the overall average ones, finding that this is indeed the case.Fil: Sánchez, S. F.. Universidad Nacional Autonoma de Mexico. Instituto de Astronomia; MéxicoFil: Pérez, E.. Instituto de Astrofísica de Andalucía; España. Consejo Superior de Investigaciones Científicas; EspañaFil: Sanchez Blazquez, P.. Departamento de Fisica Teorica ; Facultad de Ciencias ; Universidad Autonoma de Madrid;Fil: García Benito, Rubén. Instituto de Astrofísica de Andalucía; España. Consejo Superior de Investigaciones Científicas; EspañaFil: Ibarra Mede, H. J.. Space Telescope Science Institute; Estados UnidosFil: González, J. J.. Universidad Nacional Autonoma de Mexico. Instituto de Astronomia; MéxicoFil: Rosales Ortega, F. F.. Instituto Nacional de Astrofísica, Optica y Electrónica ; MéxicoFil: Sánchez Menguiano, L.. Instituto de Astrofísica de Andalucía; España. Consejo Superior de Investigaciones Científicas; EspañaFil: Ascasibar, Y.. Universidad Autónoma de Barcelona. Facultad de Física. Departamento Astronomía y Meteorología; EspañaFil: Bitsakis, T.. Universidad Nacional Autonoma de Mexico. Instituto de Astronomia; MéxicoFil: Law, D.. Space Telescope Science Institute; Estados UnidosFil: Cano Díaz, M.. Universidad Nacional Autonoma de Mexico. Instituto de Astronomia; MéxicoFil: López Cobá, C.. Universidad Nacional Autonoma de Mexico. Instituto de Astronomia; MéxicoFil: Marino, R. A.. Universidad Complutense de Madrid; EspañaFil: Gil de Paz, A.. Australian Astronomical Observatory; AustraliaFil: López Sánchez, A.. Instituto de Astrofísica de Canarias (iac); EspañaFil: Barrera Ballesteros, Jorge K.. Instituto de Astrofísica de Canarias; EspañaFil: Galbany, Lluís. Millennium Institute Of Astrophysics; Chile. Universidad de Chile; ChileFil: Mast, Damian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Astronomía Teórica y Experimental. Universidad Nacional de Córdoba. Observatorio Astronómico de Córdoba. Instituto de Astronomía Teórica y Experimental; ArgentinaFil: Abril Malgarejo, V.. Universidad Nacional Autonoma de Mexico. Instituto de Astronomia; MéxicoFil: Roman Lopes, A.. Universidad de La Serena; Chil

The Mass-Metallicity relation explored with CALIFA: I. Is there a dependence on the star formation rate?

We present the results on the study of the global and local M-Z relation based on the first data available from the CALIFA survey (150 galaxies). This survey provides integral field spectroscopy of the complete optical extent of each galaxy (up to 2-3 effective radii), with enough resolution to separate individual HII regions and/or aggregations. Nearly $\sim$3000 individual HII regions have been detected. The spectra cover the wavelength range between [OII]3727 and [SII]6731, with a sufficient signal-to-noise to derive the oxygen abundance and star-formation rate associated with each region. In addition, we have computed the integrated and spatially resolved stellar masses (and surface densities), based on SDSS photometric data. We explore the relations between the stellar mass, oxygen abundance and star-formation rate using this dataset. We derive a tight relation between the integrated stellar mass and the gas-phase abundance, with a dispersion smaller than the one already reported in the literature ($\sigma_{\Delta{\rm log(O/H)}}=$0.07 dex). Indeed, this dispersion is only slightly larger than the typical error derived for our oxygen abundances. However, we do not find any secondary relation with the star-formation rate, other than the one induced due to the primary relation of this quantity with the stellar mass. We confirm the result using the $\sim$3000 individual HII regions, for the corresponding local relations. Our results agree with the scenario in which gas recycling in galaxies, both locally and globally, is much faster than other typical timescales, like that of gas accretion by inflow and/or metal loss due to outflows. In essence, late-type/disk dominated galaxies seem to be in a quasi-steady situation, with a behavior similar to the one expected from an instantaneous recycling/closed-box model.Comment: 19 Pages, 8 figures, Accepted for Publishing in Astronomy and Astrophysics (A&A

Uso de compuestos nutracéuticos en nuevas formulaciones de piensos acuícolas

Trabajo presentado en las X Jornadas de Acuicultura en el Litoral Suratlántico: Nuevos retos y perspectivas para la sostenibilidad de la acuicultura, celebrado entre el 22 y 23 de noviembre de 2023 en Huelva.[EN] Different strategies have been followed to improve the aquaculture of main European farmed fish, such as genetic selection, refinements in culture conditions or enhanced feed formulation and management. However, more knowledge is required to exploit fish phenotypic plasticity to obtain those that better match aquaculture or market conditions. The overall objective of this mini-review is to identify the latest productive traits recently performed, mainly in commercial carnivorous species, and underlying biological processes that would be susceptible to improve the competitivity of aquaculture sector through nutritional issues. Thus, this work is framed within the concepts of Circular Economy and Blue Growth, where it is intended to point out the use of natural compounds extracted from seaweeds, microalgae and by-products of the industry for their inclusion in aquafeeds, allowing a more efficient use of more sustainable vegetable protein sources, and also to evaluate if these nutraceutical compounds counteract detrimental effects observed by nutritional interventions or environmentally challenged.[ES] La producción acuícola ha seguido diferentes estrategias para su optimización a lo largo de las últimas décadas, como el desarrollo de la selección genética, la mejora de las condiciones de cultivo, o el avance en la formulación y gestión de los piensos. Sin embargo, se requiere más conocimiento para explotar la plasticidad fenotípica de los peces para obtener aquellos que se ajusten mejor a las condiciones de la acuicultura o del mercado. El objetivo general de esta mini-revisión es identificar los últimos avances realizados recientemente, principalmente en especies carnívoras comerciales, y los procesos biológicos subyacentes que serían susceptibles de mejorar la competitividad del sector acuícola a través de intervenciones nutricionales. Así, este trabajo se enmarca dentro de los conceptos de Economía Circular y Crecimiento Azul, donde se pretende señalar el uso de compuestos naturales extraídos de algas, microalgas y subproductos de la industria para su inclusión en alimentos acuícolas, permitiendo un uso más eficiente de fuentes de proteínas vegetales más sostenibles, y también evaluar si estos compuestos nutracéuticos son capaces de contrarrestar los efectos perjudiciales observados por las formulaciones inadecuadas o desafiados por factores ambientales estresantes.This work was supported by the Projects “FEDER-UCA18-107182”, “FisioBream-II Call for Young Researchers CEI⋅MAR 2019”, “ALGAE4FISH-CEI·MAR Empresa 2018”, “VALINVA-CEI·MAR Empresa 2019”, “SeriBlue-CEI·MAR Empresa 2020”, and co-financed by the spin-off LifeBioencapsulation S.L. (Almería) and Biotechnology Biopolym S.A. (Granada)

SALMANTICOR study. Rationale and design of a population-based study to identify structural heart disease abnormalities: a spatial and machine learning analysis

[EN]Introduction: This study aims to obtain data on the prevalence and incidence of structural heart disease in a population setting and, to analyse and present those data on the application of spatial and machine learning methods that, although known to geography and statistics, need to become used for healthcare research and for political commitment to obtain resources and support effective public health programme implementation. Methods and analysis: We will perform a cross-sectional survey of randomly selected residents of Salamanca (Spain). 2400 individuals stratified by age and sex and by place of residence (rural and urban) will be studied. The variables to analyse will be obtained from the clinical history, different surveys including social status, Mediterranean diet, functional capacity, ECG, echocardiogram, VASERA and biochemical as well as genetic analysis. Ethics and dissemination: The study has been approved by the ethical committee of the healthcare community. All study participants will sign an informed consent for participation in the study. The results of this study will allow the understanding of the relationship between the different influencing factors and their relative importance weights in the development of structural heart disease

Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies

Background: Genome-wide association studies (GWAS) in Parkinson's disease have increased the scope of biological knowledge about the disease over the past decade. We aimed to use the largest aggregate of GWAS data to identify novel risk loci and gain further insight into the causes of Parkinson's disease. / Methods: We did a meta-analysis of 17 datasets from Parkinson's disease GWAS available from European ancestry samples to nominate novel loci for disease risk. These datasets incorporated all available data. We then used these data to estimate heritable risk and develop predictive models of this heritability. We also used large gene expression and methylation resources to examine possible functional consequences as well as tissue, cell type, and biological pathway enrichments for the identified risk factors. Additionally, we examined shared genetic risk between Parkinson's disease and other phenotypes of interest via genetic correlations followed by Mendelian randomisation. / Findings: Between Oct 1, 2017, and Aug 9, 2018, we analysed 7·8 million single nucleotide polymorphisms in 37 688 cases, 18 618 UK Biobank proxy-cases (ie, individuals who do not have Parkinson's disease but have a first degree relative that does), and 1·4 million controls. We identified 90 independent genome-wide significant risk signals across 78 genomic regions, including 38 novel independent risk signals in 37 loci. These 90 variants explained 16–36% of the heritable risk of Parkinson's disease depending on prevalence. Integrating methylation and expression data within a Mendelian randomisation framework identified putatively associated genes at 70 risk signals underlying GWAS loci for follow-up functional studies. Tissue-specific expression enrichment analyses suggested Parkinson's disease loci were heavily brain-enriched, with specific neuronal cell types being implicated from single cell data. We found significant genetic correlations with brain volumes (false discovery rate-adjusted p=0·0035 for intracranial volume, p=0·024 for putamen volume), smoking status (p=0·024), and educational attainment (p=0·038). Mendelian randomisation between cognitive performance and Parkinson's disease risk showed a robust association (p=8·00 × 10−7). / Interpretation: These data provide the most comprehensive survey of genetic risk within Parkinson's disease to date, to the best of our knowledge, by revealing many additional Parkinson's disease risk loci, providing a biological context for these risk factors, and showing that a considerable genetic component of this disease remains unidentified. These associations derived from European ancestry datasets will need to be followed-up with more diverse data. / Funding: The National Institute on Aging at the National Institutes of Health (USA), The Michael J Fox Foundation, and The Parkinson's Foundation (see appendix for full list of funding sources)

Identification of Candidate Parkinson Disease Genes by Integrating Genome-Wide Association Study, Expression, and Epigenetic Data Sets

Importance Substantial genome-wide association study (GWAS) work in Parkinson disease (PD) has led to the discovery of an increasing number of loci shown reliably to be associated with increased risk of disease. Improved understanding of the underlying genes and mechanisms at these loci will be key to understanding the pathogenesis of PD. / Objective To investigate what genes and genomic processes underlie the risk of sporadic PD. / Design and Setting This genetic association study used the bioinformatic tools Coloc and transcriptome-wide association study (TWAS) to integrate PD case-control GWAS data published in 2017 with expression data (from Braineac, the Genotype-Tissue Expression [GTEx], and CommonMind) and methylation data (derived from UK Parkinson brain samples) to uncover putative gene expression and splicing mechanisms associated with PD GWAS signals. Candidate genes were further characterized using cell-type specificity, weighted gene coexpression networks, and weighted protein-protein interaction networks. / Main Outcomes and Measures It was hypothesized a priori that some genes underlying PD loci would alter PD risk through changes to expression, splicing, or methylation. Candidate genes are presented whose change in expression, splicing, or methylation are associated with risk of PD as well as the functional pathways and cell types in which these genes have an important role. / Results Gene-level analysis of expression revealed 5 genes (WDR6 [OMIM 606031], CD38 [OMIM 107270], GPNMB [OMIM 604368], RAB29 [OMIM 603949], and TMEM163 [OMIM 618978]) that replicated using both Coloc and TWAS analyses in both the GTEx and Braineac expression data sets. A further 6 genes (ZRANB3 [OMIM 615655], PCGF3 [OMIM 617543], NEK1 [OMIM 604588], NUPL2 [NCBI 11097], GALC [OMIM 606890], and CTSB [OMIM 116810]) showed evidence of disease-associated splicing effects. Cell-type specificity analysis revealed that gene expression was overall more prevalent in glial cell types compared with neurons. The weighted gene coexpression performed on the GTEx data set showed that NUPL2 is a key gene in 3 modules implicated in catabolic processes associated with protein ubiquitination and in the ubiquitin-dependent protein catabolic process in the nucleus accumbens, caudate, and putamen. TMEM163 and ZRANB3 were both important in modules in the frontal cortex and caudate, respectively, indicating regulation of signaling and cell communication. Protein interactor analysis and simulations using random networks demonstrated that the candidate genes interact significantly more with known mendelian PD and parkinsonism proteins than would be expected by chance. / Conclusions and Relevance Together, these results suggest that several candidate genes and pathways are associated with the findings observed in PD GWAS studies

Identification of sixteen novel candidate genes for late onset Parkinson’s disease

Background Parkinson’s disease (PD) is a neurodegenerative movement disorder affecting 1–5% of the general population for which neither effective cure nor early diagnostic tools are available that could tackle the pathology in the early phase. Here we report a multi-stage procedure to identify candidate genes likely involved in the etiopathogenesis of PD. Methods The study includes a discovery stage based on the analysis of whole exome data from 26 dominant late onset PD families, a validation analysis performed on 1542 independent PD patients and 706 controls from different cohorts and the assessment of polygenic variants load in the Italian cohort (394 unrelated patients and 203 controls). Results Family-based approach identified 28 disrupting variants in 26 candidate genes for PD including PARK2, PINK1, DJ-1(PARK7), LRRK2, HTRA2, FBXO7, EIF4G1, DNAJC6, DNAJC13, SNCAIP, AIMP2, CHMP1A, GIPC1, HMOX2, HSPA8, IMMT, KIF21B, KIF24, MAN2C1, RHOT2, SLC25A39, SPTBN1, TMEM175, TOMM22, TVP23A and ZSCAN21. Sixteen of them have not been associated to PD before, were expressed in mesencephalon and were involved in pathways potentially deregulated in PD. Mutation analysis in independent cohorts disclosed a significant excess of highly deleterious variants in cases (p = 0.0001), supporting their role in PD. Moreover, we demonstrated that the co-inheritance of multiple rare variants (≥ 2) in the 26 genes may predict PD occurrence in about 20% of patients, both familial and sporadic cases, with high specificity (> 93%; p = 4.4 × 10− 5). Moreover, our data highlight the fact that the genetic landmarks of late onset PD does not systematically differ between sporadic and familial forms, especially in the case of small nuclear families and underline the importance of rare variants in the genetics of sporadic PD. Furthermore, patients carrying multiple rare variants showed higher risk of manifesting dyskinesia induced by levodopa treatment. Conclusions Besides confirming the extreme genetic heterogeneity of PD, these data provide novel insights into the genetic of the disease and may be relevant for its prediction, diagnosis and treatment

The management of acute venous thromboembolism in clinical practice. Results from the European PREFER in VTE Registry

Venous thromboembolism (VTE) is a significant cause of morbidity and mortality in Europe. Data from real-world registries are necessary, as clinical trials do not represent the full spectrum of VTE patients seen in clinical practice. We aimed to document the epidemiology, management and outcomes of VTE using data from a large, observational database. PREFER in VTE was an international, non-interventional disease registry conducted between January 2013 and July 2015 in primary and secondary care across seven European countries. Consecutive patients with acute VTE were documented and followed up over 12 months. PREFER in VTE included 3,455 patients with a mean age of 60.8 ± 17.0 years. Overall, 53.0 % were male. The majority of patients were assessed in the hospital setting as inpatients or outpatients (78.5 %). The diagnosis was deep-vein thrombosis (DVT) in 59.5 % and pulmonary embolism (PE) in 40.5 %. The most common comorbidities were the various types of cardiovascular disease (excluding hypertension; 45.5 %), hypertension (42.3 %) and dyslipidaemia (21.1 %). Following the index VTE, a large proportion of patients received initial therapy with heparin (73.2 %), almost half received a vitamin K antagonist (48.7 %) and nearly a quarter received a DOAC (24.5 %). Almost a quarter of all presentations were for recurrent VTE, with >80 % of previous episodes having occurred more than 12 months prior to baseline. In conclusion, PREFER in VTE has provided contemporary insights into VTE patients and their real-world management, including their baseline characteristics, risk factors, disease history, symptoms and signs, initial therapy and outcomes

Sensitivity of the Cherenkov Telescope Array for probing cosmology and fundamental physics with gamma-ray propagation

The Cherenkov Telescope Array (CTA), the new-generation ground-based observatory for $\gamma$-ray astronomy, provides unique capabilities to address significant open questions in astrophysics, cosmology, and fundamental physics. We study some of the salient areas of $\gamma$-ray cosmology that can be explored as part of the Key Science Projects of CTA, through simulated observations of active galactic nuclei (AGN) and of their relativistic jets. Observations of AGN with CTA will enable a measurement of $\gamma$-ray absorption on the extragalactic background light with a statistical uncertainty below 15% up to a redshift $z=2$ and to constrain or detect $\gamma$-ray halos up to intergalactic-magnetic-field strengths of at least 0.3pG. Extragalactic observations with CTA also show promising potential to probe physics beyond the Standard Model. The best limits on Lorentz invariance violation from $\gamma$-ray astronomy will be improved by a factor of at least two to three. CTA will also probe the parameter space in which axion-like particles could constitute a significant fraction, if not all, of dark matter. We conclude on the synergies between CTA and other upcoming facilities that will foster the growth of $\gamma$-ray cosmology

Sensitivity of the Cherenkov Telescope Array to a dark matter signal from the Galactic centre

We provide an updated assessment of the power of the Cherenkov Telescope Array (CTA) to search for thermally produced dark matter at the TeV scale, via the associated gamma-ray signal from pair-annihilating dark matter particles in the region around the Galactic centre. We find that CTA will open a new window of discovery potential, significantly extending the range of robustly testable models given a standard cuspy profile of the dark matter density distribution. Importantly, even for a cored profile, the projected sensitivity of CTA will be sufficient to probe various well-motivated models of thermally produced dark matter at the TeV scale. This is due to CTA's unprecedented sensitivity, angular and energy resolutions, and the planned observational strategy. The survey of the inner Galaxy will cover a much larger region than corresponding previous observational campaigns with imaging atmospheric Cherenkov telescopes. CTA will map with unprecedented precision the large-scale diffuse emission in high-energy gamma rays, constituting a background for dark matter searches for which we adopt state-of-the-art models based on current data. Throughout our analysis, we use up-to-date event reconstruction Monte Carlo tools developed by the CTA consortium, and pay special attention to quantifying the level of instrumental systematic uncertainties, as well as background template systematic errors, required to probe thermally produced dark matter at these energies.</p