A new approach to truncated regression for count data

Standard Poisson and negative binomial truncated regression models for count data include the regressors in the mean of the non-truncated distribution. In this paper, a new approach is proposed so that the explanatory variables determine directly the truncated mean. The main advantage is that the regression coefficients in the new models have a straightforward interpretation as the effect of a change in a covariate on the mean of the response variable. A simulation study has been carried out in order to analyze the performance of the proposed truncated regression models versus the standard ones showing that coefficient estimates are now more accurate in the sense that the standard errors are always lower. Also, the simulation study indicates that the estimates obtained with the standard models are biased. An application to real data illustrates the utility of the introduced truncated models in a hurdle model. Although in the example there are slight differences in the results between the two approaches, the proposed one provides a clear interpretation of the coefficient estimates

Effect of different media additives on capacitation of frozen-thawed ram spermatozoa as a potential replacement for estrous sheep serum

Capacitation is a key process through which spermatozoa acquire their fertilizing ability. This event is required for the successful application of assisted reproductive technologies such as IVF. The aim of the present study was to investigate the effect of using a synthetic oviductal fluid medium supplemented with either heparin–hypotaurine alone, in combination with progesterone (P4), 17β-estradiol (E2), or BSA, or just β-cyclodextrin, in replacement for estrous sheep serum (ESS) for ram sperm capacitation. After incubation in the corresponding media for 15 (time 0) or 60 minutes, sperm function was evaluated by computerized sperm motility analysis and flow cytometry (plasma membrane status and fluidity). Treatments rendering the best results in regards to sperm function parameters related to capacitation were used for an IVF test. Herein, neither heparin–hypotaurine (alone), or in combination with P4, or E2, nor β-cyclodextrin induced capacitation-related changes in frozen–thawed ram spermatozoa. Only the medium supplemented with heparin–hypotaurine–BSA was able to induce changes compatible with in vitro capacitation relating to sperm motility pattern and plasma membrane fluidity, comparable to those in ESS-containing medium. Both media yielded sperm parameter values that differed (P < 0.05) from those obtained in the rest of the media tested. However, after the IVF trial, BSA was unable to support cleavage rates (21.80%) comparable to those obtained with ESS (52.60%; P < 0.05). We conclude that heparin–hypotaurine, P4, E2, β-cyclodextrin, or BSA is not suitable for replacing ESS in capacitation and fertilization media for ram spermatozoa.M. Ramón was supported by the Research Recruitment Program from the National Institute for Agricultural and Food Research program.Peer Reviewe

CALIFA, the Calar Alto Legacy Integral Field Area survey: III. Second public data release

García-Benito, R. et. al.© ESO, 2015. This paper describes the Second Public Data Release (DR2) of the Calar Alto Legacy Integral Field Area (CALIFA) survey. The data for 200 objects are made public, including the 100 galaxies of the First Public Data Release (DR1). Data were obtained with the integral-field spectrograph PMAS/PPak mounted on the 3.5 m telescope at the Calar Alto observatory. Two different spectral setups are available for each galaxy, (i) a low-resolution V500 setup covering the wavelength range 3745-7500 Å with a spectral resolution of 6.0 Å (FWHM); and (ii) a medium-resolution V1200 setup covering the wavelength range 3650-4840 Å with a spectral resolution of 2.3 Å (FWHM). The sample covers a redshift range between 0.005 and 0.03, with a wide range of properties in the color-magnitude diagram, stellar mass, ionization conditions, and morphological types. All the cubes in the data release were reduced with the latest pipeline, which includes improvedspectrophotometric calibration, spatial registration, and spatial resolution. The spectrophotometric calibration is better than 6% and the median spatial resolution is 2.4. In total, the second data release contains over 1.5 million spectra.R.G.B., R.G.D., and E.P. are supported by the Spanish Ministerio de Ciencia e Innovacion under grant AYA2010-15081. S.Z. is supported by the EU Marie Curie Integration Grant >SteMaGE> Nr. PCIG12-GA-2012-326466 (Call Identifier: FP7-PEOPLE-2012 CIG). J.F.B. acknowledges support from grants AYA2010-21322-C03-02 and AIB-2010-DE-00227 from the Spanish Ministry of Economy and Competitiveness (MINECO), as well as from the FP7 Marie Curie Actions of the European Commission, via the Initial Training Network DAGAL under REA grant agreement number 289313. Support for L.G. is provided by the Ministry of Economy, Development, and Tourism's Millennium Science Initiative through grant IC12009, awarded to The Millennium Institute of Astrophysics, M.A.S.L.G. also acknowledges support by CONICYT through FONDECYT grant 3140566. A.G. acknowledges support from the FP7/2007-2013 under grant agreement n. 267251 (AstroFIt). J.M.G. acknowledges support from the Fundacao para a Ciencia e a Tecnologia (FCT) through the Fellowship SFRH/BPD/66958/2009 from FCT (Portugal) and research grant PTDC/FIS-AST/3214/2012. RAM was funded by the Spanish programme of International Campus of Excellence Moncloa (CEI). J.M.A. acknowledges support from the European Research Council Starting Grant (SEDmorph; P.I. V. Wild). I.M., J.M. and A.d.O. acknowledge the support by the projects AYA2010-15196 from the Spanish Ministerio de Ciencia e Innovacion and TIC 114 and PO08-TIC-3531 from Junta de Andalucia. AMI acknowledges support from Agence Nationale de la Recherche through the STILISM project (ANR-12-BS05-0016-02). M.M. acknowledges financial support from AYA2010-21887-C04-02 from the Ministerio de Economia y Competitividad. P.P. is supported by an FCT Investigador 2013 Contract, funded by FCT/MCTES (Portugal) and POPH/FSE (EC). P.P. acknowledges support by FCT under project FCOMP-01-0124-FEDER-029170 (Reference FCT PTDC/FIS-AST/3214/2012), funded by FCT-MEC (PIDDAC) and FEDER (COMPETE). T.R.L. thanks the support of the Spanish Ministerio de Educacion, Cultura y Deporte by means of the FPU fellowship. PSB acknowledges support from the Ramon y Cajal program, grant ATA2010-21322-C03-02 from the Spanish Ministry of Economy and Competitiveness (MINECO). C.J.W. acknowledges support through the Marie Curie Career Integration Grant 303912. V.W. acknowledges support from the European Research Council Starting Grant (SEDMorph P.I. V. Wild) and European Career Re-integration Grant (Phiz-Ev P.I.V. Wild). Y.A. acknowledges financial support from the Ramon y Cajal programme (RyC-2011-09461) and project AYA2013-47742-C4-3-P, both managed by the Ministerio de Economia y Competitividad, as well as the >Study of Emission-Line Galaxies with Integral-Field Spectroscopy> (SELGIFS) programme, funded by the EU (FP7-PEOPLE-2013-IRSES-612701) within the Marie-Sklodowska-Curie Actions schemePeer Reviewe

Galaxy clusters and groups in the ALHAMBRA Survey

We present a catalogue of 348 galaxy clusters and groups with $0.2<z<1.2$ selected in the 2.78 $deg^2$ ALHAMBRA Survey. The high precision of our photometric redshifts, close to $1\%$, and the wide spread of the seven ALHAMBRA pointings ensure that this catalogue has better mass sensitivity and is less affected by cosmic variance than comparable samples. The detection has been carried out with the Bayesian Cluster Finder (BCF), whose performance has been checked in ALHAMBRA-like light-cone mock catalogues. Great care has been taken to ensure that the observable properties of the mocks photometry accurately correspond to those of real catalogues. From our simulations, we expect to detect galaxy clusters and groups with both $70\%$ completeness and purity down to dark matter halo masses of $M_h\sim3\times10^{13}\rm M_{\odot}$ for $z<0.85$. Cluster redshifts are expected to be recovered with $\sim0.6\%$ precision for $z<1$. We also expect to measure cluster masses with $\sigma_{M_h|M^*_{CL}}\sim0.25-0.35\, dex$ precision down to $\sim3\times10^{13}\rm M_{\odot}$, masses which are $50\%$ smaller than those reached by similar work. We have compared these detections with previous optical, spectroscopic and X-rays work, finding an excellent agreement with the rates reported from the simulations. We have also explored the overall properties of these detections such as the presence of a colour-magnitude relation, the evolution of the photometric blue fraction and the clustering of these sources in the different ALHAMBRA fields. Despite the small numbers, we observe tentative evidence that, for a fixed stellar mass, the environment is playing a crucial role at lower redshifts (z$<$0.5).Comment: Accepted for publication in MNRAS. Catalogues and figures available online and under the following link: http://bascaso.net46.net/ALHAMBRA_clusters.htm

Predictores de riesgo en una cohorte española con cardiolaminopatías. Registro REDLAMINA

[Abstract] Introduction and objectives. According to sudden cardiac death guidelines, an implantable cardioverter-defibrillator (ICD) should be considered in patients with LMNA-related dilated cardiomyopathy (DCM) and ≥ 2 risk factors: male sex, left ventricular ejection fraction (LVEF) < 45%, nonsustained ventricular tachycardia (NSVT), and nonmissense genetic variants. In this study we aimed to describe the clinical characteristics of carriers of LMNA genetic variants among individuals from a Spanish cardiac-laminopathies cohort (REDLAMINA registry) and to assess previously reported risk criteria. Methods. The relationship between risk factors and cardiovascular events was evaluated in a cohort of 140 carriers (age ≥ 16 years) of pathogenic LMNA variants (54 probands, 86 relatives). We considered: a) major arrhythmic events (MAE) if there was appropriate ICD discharge or sudden cardiac death; b) heart failure death if there was heart transplant or death due to heart failure. Results. We identified 11 novel and 21 previously reported LMNA-related DCM variants. LVEF < 45% (P = .001) and NSVT (P < .001) were related to MAE, but not sex or type of genetic variant. The only factor independently related to heart failure death was LVEF < 45% (P < .001). Conclusions. In the REDLAMINA registry cohort, the only predictors independently associated with MAE were NSVT and LVEF < 45%. Therefore, female carriers of missense variants with either NSVT or LVEF < 45% should not be considered a low-risk group. It is important to individualize risk stratification in carriers of LMNA missense variants, because not all have the same prognosis.[Resumen] Introducción y objetivos. Según las guías de muerte súbita, se debe considerar un desfibrilador automático implantable (DAI) para los pacientes con miocardiopatía dilatada debida a variantes en el gen de la lamina (LMNA) con al menos 2 factores: varones, fracción de eyección del ventrículo izquierdo (FEVI) < 45%, taquicardia ventricular no sostenida (TVNS) y variantes no missense. Nuestro objetivo es describir las características clínicas de una cohorte española de pacientes con cardiolaminopatías (registro REDLAMINA) y evaluar los criterios de riesgo vigentes. Métodos. Se evaluó la relación entre factores de riesgo y eventos cardiovasculares en una cohorte de 140 portadores de variantes en LMNA (54 probandos, 86 familiares, edad ≥ 16 años). Se consideró: a) evento arrítmico mayor (EAM) si hubo descarga apropiada del DAI o muerte súbita, y b) muerte por insuficiencia cardiaca, incluidos los trasplantes. Resultados. Se identificaron 11 variantes nuevas y 21 previamente publicadas. La FEVI < 45% (p = 0,001) y la TVNS (p < 0,001) se relacionaron con los EAM, pero no el sexo o el tipo de variante (missense frente a no missense). La FEVI < 45% (p < 0,001) fue el único factor relacionado con la muerte por insuficiencia cardiaca. Conclusiones. En el registro REDLAMINA, los únicos 2 predictores asociados con EAM fueron la TVNS y la FEVI < 45%. No se debería considerar grupo de bajo riesgo a las portadoras de variantes missense con TVNS o FEVI < 45%. Es importante individualizar la estratificación del riesgo de los portadores de variantes missense en LMNA, porque no todas tienen el mismo pronóstico.This study received a grant from the Proyecto de investigación de la Sección de Insuficiencia Cardiaca 2017 from the Spanish Society of Cardiology and grants from the Instituto de Salud Carlos III (ISCIII) [PI14/0967, PI15/01551, AC16/0014] and ERA-CVD Joint Transnational Call 2016 (Genprovic). Grants from the ISCIII and the Ministerio de Economía y Competitividad de España (Spanish Department of Economy and Competitiveness) are supported by the Plan Estatal de I+D+i 2013-2016: Fondo Europeo de Desarrollo Regional (FEDER) “Una forma de hacer Europa”

The impact from survey depth and resolution on the morphological classification of galaxies

We consistently analyse for the first time the impact of survey depth and spatial resolution on the most used morphological parameters for classifying galaxies through non-parametric methods: Abraham and Conselice-Bershady concentration indices, Gini, M20moment of light, asymmetry, and smoothness. Three different non-local data sets are used, Advanced Large Homogeneous Area Medium Band Redshift Astronomical (ALHAMBRA) and Subaru/XMMNewton Deep Survey (SXDS, examples of deep ground-based surveys), and Cosmos Evolution Survey (COSMOS, deep space-based survey). We used a sample of 3000 local, visually classified galaxies, measuring their morphological parameters at their real redshifts (z ~ 0). Then we simulated them to match the redshift and magnitude distributions of galaxies in the non-local surveys. The comparisons of the two sets allow us to put constraints on the use of each parameter for morphological classification and evaluate the effectiveness of the commonly used morphological diagnostic diagrams. All analysed parameters suffer from biases related to spatial resolution and depth, the impact of the former being much stronger. When including asymmetry and smoothness in classification diagrams, the noise effects must be taken into account carefully, especially for ground-based surveys. M20 is significantly affected, changing both the shape and range of its distribution at all brightness levels. We suggest that diagnostic diagrams based on 2-3 parameters should be avoided when classifying galaxies in ground-based surveys, independently of their brightness; for COSMOS they should be avoided for galaxies fainter than F814 = 23.0. These results can be applied directly to surveys similar to ALHAMBRA, SXDS and COSMOS, and also can serve as an upper/lower limit for shallower/deeper ones.Ministerio de Economía y Competitividad AYA2010-15169, AYA2013-42227-P, AYA2013-4318

The impact from survey depth and resolution on the morphological classification of galaxies

We consistently analyse for the first time the impact of survey depth and spatial resolution on the most used morphological parameters for classifying galaxies through non-parametric methods: Abraham and Conselice-Bershady concentration indices, Gini, M20moment of light, asymmetry, and smoothness. Three different non-local data sets are used, Advanced Large Homogeneous Area Medium Band Redshift Astronomical (ALHAMBRA) and Subaru/XMMNewton Deep Survey (SXDS, examples of deep ground-based surveys), and Cosmos Evolution Survey (COSMOS, deep space-based survey). We used a sample of 3000 local, visually classified galaxies, measuring their morphological parameters at their real redshifts (z ~ 0). Then we simulated them to match the redshift and magnitude distributions of galaxies in the non-local surveys. The comparisons of the two sets allow us to put constraints on the use of each parameter for morphological classification and evaluate the effectiveness of the commonly used morphological diagnostic diagrams. All analysed parameters suffer from biases related to spatial resolution and depth, the impact of the former being much stronger. When including asymmetry and smoothness in classification diagrams, the noise effects must be taken into account carefully, especially for ground-based surveys. M20 is significantly affected, changing both the shape and range of its distribution at all brightness levels. We suggest that diagnostic diagrams based on 2-3 parameters should be avoided when classifying galaxies in ground-based surveys, independently of their brightness; for COSMOS they should be avoided for galaxies fainter than F814 = 23.0. These results can be applied directly to surveys similar to ALHAMBRA, SXDS and COSMOS, and also can serve as an upper/lower limit for shallower/deeper ones.MP acknowledge financial support from JAE-Doc programme of the Spanish National Research Council (CSIC), co-funded by the European Social Fund. This research was supported by the Junta de Andalucia through project TIC114, and the Spanish Ministry of Economy and Competitiveness (MINECO) through projects AYA2010-15169, AYA2013-42227-P, and AYA2013-43188-P.Peer Reviewe

The ALHAMBRA survey: accurate merger fractions derived by PDF analysis of photometrically close pairs

[Aims]: Our goal is to develop and test a novel methodology to compute accurate close-pair fractions with photometric redshifts. [Methods]: We improved the currently used methodologies to estimate the merger fraction fm from photometric redshifts by (i) using the full probability distribution functions (PDFs) of the sources in redshift space; (ii) including the variation in the luminosity of the sources with z in both the sample selection and the luminosity ratio constrain; and (iii) splitting individual PDFs into red and blue spectral templates to reliably work with colour selections.We tested the performance of our new methodology with the PDFs provided by the ALHAMBRA photometric survey. [Results]: The merger fractions and rates from the ALHAMBRA survey agree excellently well with those from spectroscopic work for both the general population and red and blue galaxies. With the merger rate of bright (MB ≤ -20 - 1:1z) galaxies evolving as (1 + z)n, the power-law index n is higher for blue galaxies (n = 2:7 0:5) than for red galaxies (n = 1:3 0:4), confirming previous results. Integrating the merger rate over cosmic time, we find that the average number of mergers per galaxy since z = 1 is Nm red = 0:57 0:05 for red galaxies and Nm blue = 0:26 0:02 for blue galaxies. [Conclusions]: Our new methodology statistically exploits all the available information provided by photometric redshift codes and yields accurate measurements of the merger fraction by close pairs from using photometric redshifts alone. Current and future photometric surveys will benefit from this new methodology.This work has been mainly funded by the FITE (Fondos de Inversiones de Teruel) and the projects AYA2012-30789, AYA2006-14056, and CSD2007-00060. We also acknowledge financial support from the Spanish Government grants AYA2010-15169, AYA2010-22111-C03-01, AYA2010-22111-C03-02, and AYA2013-48623-C2-2, from the Aragón Government through the Research Group E103, from the Junta de Andalucía through TIC-114 and the Excellence Project P08-TIC-03531, and from the Generalitat Valenciana through the projects Prometeo/2009/064 and PrometeoII/2014/060. A.J.C. is Ramón y Cajal fellow of the Spanish government. M.P. acknowledges the financial support from JAE-Doc program of the Spanish National Research Council (CSIC), co-funded by the European Social Fund.Peer Reviewe

The ALHAMBRA survey: Bayesian photometric redshifts with 23 bands for 3 deg2

A. Molino et al.The Advance Large Homogeneous Area Medium-Band Redshift Astronomical (ALHAMBRA) survey has observed eight different regions of the sky, including sections of the Cosmic Evolution Survey (COSMOS), DEEP2, European Large-Area Infrared Space Observatory Survey (ELAIS), Great Observatories Origins Deep Survey North (GOODS-N), Sloan Digital Sky Survey (SDSS) and Groth fields using a new photometric system with 20 optical, contiguous ~300-Å filters plus the JHKs bands. The filter system is designed to optimize the effective photometric redshift depth of the survey, while having enough wavelength resolution for the identification of faint emission lines. The observations, carried out with the Calar Alto 3.5-m telescope using the wide-field optical camera Large Area Imager for Calar Alto (LAICA) and the near-infrared (NIR) instrument Omega-2000, represent a total of ~700 h of on-target science images. Here we present multicolour point-spread function (PSF) corrected photometry and photometric redshifts for ~438 000 galaxies, detected in synthetic F814W images. The catalogues are complete down to a magnitude I~24.5AB and cover an effective area of 2.79 deg2. Photometric zero-points were calibrated using stellar transformation equations and refined internally, using a new technique based on the highly robust photometric redshifts measured for emission-line galaxies. We calculate Bayesian photometric redshifts with the Bayesian Photometric Redshift (BPZ)2.0 code, obtaining a precision of δz/(1+zs)=1 per cent for I<22.5 and δz/(1+zs)=1.4 per cent for 22.5<I<24.5. The global n(z) distribution shows a mean redshift 〈z〉=0.56 for I<22.5 AB and 〈z〉=0.86 for I<24.5 AB. Given its depth and small cosmic variance, ALHAMBRA is a unique data set for galaxy evolution studies. © 2014 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.We acknowledge financial support from the Spanish MICINN under the Consolider-Ingenio 2010 Program grant CSD2006-00070: First Science with the GTC. Part of this work was supported by Junta de Andalucía, through grant TIC-114 and the Excellence Project P08-TIC-3531, and by the Spanish Ministry for Science and Innovation through grants AYA2006-1456, AYA2010-15169, AYA2010-22111-C03-02, AYA2010-22111-C03-01 and Generalitat Valenciana project Prometeo 2009/064.Peer Reviewe

The ALHAMBRA survey: reliable morphological catalogue of 22 051 early- and late-type galaxies

Advanced Large Homogeneous Area Medium Band Redshift Astronomical (ALHAMBRA) is photometric survey designed to trace the cosmic evolution and cosmic variance. It covers a large area of ~4 deg2 in eight fields, where seven fields overlap with other surveys, allowing us to have complementary data in other wavelengths. All observations were carried out in 20 continuous, medium band (30 nm width) optical and 3 near-infrared (JHK) bands, providing the precise measurements of photometric redshifts. In addition, morphological classification of galaxies is crucial for any kind of galaxy formation and cosmic evolution studies, providing the information about star formation histories, their environment and interactions, internal perturbations, etc. We present a morphological classification of >40 000 galaxies in the ALHAMBRA survey. We associate to every galaxy a probability to be early type using the automated Bayesian code GALSVM. Despite of the spatial resolution of theALHAMBRAimages (~1 arcsec), for 22 051 galaxies, we obtained the contamination by other type of less than 10 per cent. Of those, 1640 and 10 322 galaxies are classified as early-(down to redshifts ~0.5) and late-type (down to redshifts ~1.0), respectively, with magnitudes F613W ≤ 22.0. In addition, for magnitude range 22.0 < F613W ≤ 23.0, we classified other 10 089 late-type galaxies with redshifts ≤1.3.We show that the classified objects populate the expected regions in the colour-mass and colour-magnitude planes. The presented data set is especially attractive given the homogeneous multiwavelength coverage available in the ALHAMBRA fields, and is intended to be used in a variety of scientific applications. The low-contamination catalogue (<10 per cent) is made publicly available with this paper. © 2013 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.This research was supported by the Junta de Andalucía through projects PO8-TIC-03531 and TIC114, the Spanish Ministry of Economy and Competitiveness (MINECO) through projects AYA2006-14046, AYA2010-15169, AYA2010-22111-C03-02, AYA2011-29517-C03-01, and the Generalitat Valenciana through project GV/Prometeo 2009/064. MP acknowledges financial support from JAE-Doc program of the Spanish National Research Council (CSIC), co-funded by the European Social Fund.Peer Reviewe