Balances: a new perspective for microbiome analysis

High-throughput sequencing technologies have revolutionized microbiome research by allowing the relative quantification of microbiome composition and function in different environments. In this work we focus on the identification of microbial signatures, groups of microbial taxa that are predictive of a phenotype of interest. We do this by acknowledging the compositional nature of the microbiome and the fact that it carries relative information. Thus, instead of defining a microbial signature as a linear combination in real space corresponding to the abundances of a group of taxa, we consider microbial signatures given by the geometric means of data from two groups of taxa whose relative abundances, or balance, are associated with the response variable of interest. In this work we present selbal, a greedy stepwise algorithm for selection of balances or microbial signatures that preserves the principles of compositional data analysis. We illustrate the algorithm with 16S rRNA abundance data from a Crohn’s microbiome study and an HIV microbiome study. We propose a new algorithm for the identification of microbial signatures. These microbial signatures can be used for diagnosis, prognosis, or prediction of therapeutic response based on an individual’s specific microbiota.Peer ReviewedPostprint (published version

Cytogenetic effects of irradiation on somatic and germ cells

This paper summarizes the results obtained in two of the research projects carried out in our laboratory within the radiation protection programs of the Consejo de Seguridad Nuclear and the European Union. These two research lines are fundamentally interconnected, since the analysis of the cytogenetic effects of radiation on somatic cells studies the consequences of occupational or accidental exposure to radiation for the individual, especially from the point of view of developing some type of malignancy, while the studies carried out in germ cells evaluate the risk of exposure for future generations, through the transmission of chromosome abnormalities via affected spermatozoa. In both cases these studies, which were mainly carried out during the last six years, in addition to providing basic data for the assessment of the consequences of radiation exposure and defining the steps to be taken to prevent the transmission of chromosome anomalies to the offspring in cases of therapeutic exposure, have also been fundamental in developing more effective techniques for the evaluation of the cytogenetic consequences of exposure to radiation

Morfologia i formació del complexe sinaptinèmic a espermatòcits i oòcits de Mus musculus

A method for the sequential study of synaptonemal complexes by light and electron microscopy has been used to characterize the synaptic process in mouse (Mus musculus) spermatocytes and oocytes. Pre- and post-synaptic figures can be easily identified

Comparison of polydrug use prevalences and typologies between men who have sex with men and general population men, in madrid and barcelona

Altres ajuts: Delegación del Gobierno para el Plan Nacional sobre Drogas (2019-017)This study compares the prevalence of drug use and the typologies of polydrug use (PDU) in men who have sex with men (MSM) and general population men (GPM). Participants were men aged 16-64, living in the provinces of Madrid and Barcelona: 1720 were recruited in a GPM survey, and 2658 were HIV-negative MSM from HIV/STIs diagnosis services. Lifetime and last-year prevalence of drug use and prevalence ratios (PRs) of MSM to GPM for the different drugs were calculated using Poisson regression. Latent class analysis (LCA) was performed to identify typologies of PDU. Lifetime use of the drugs considered was higher in MSM, and even higher for drug use in the last-year: PRs for cannabis, hallucinogens and cocaine ranged from 2-5; for amphetamine, ecstasy and methamphetamine 12-16; and above 60 for ketamine, GHB/GBL, inhalants and mephedrone. In the LCA for lifetime PDU four classes arose from the GPM (No-PDU (79.6%); Conventional PDU (13.8%); Intensive conventional PDU (4.9%); Heavy PDU (1.8%)) and four among MSM (No-PDU (57.7%); Conventional PDU plus poppers (18.8%); PDU preferring chemsex drugs (6.4%); Heavy PDU (17.2%)). For PDU during the last-year, three classes arose in the GPM: No-PDU (94.7%); Conventional PDU (4.3%); Heavy PDU (0.9%). For MSM, we identified four classes: No-PDU (64.7%); Conventional PDU plus poppers (15.6%); PDU preferring chemsex drugs (6.2%); Heavy PDU (13.5%). MSM should be considered a priority group for the prevention of the use of all drugs but the heterogeneity of PDU typologies regarding users' preference towards conventional and/or sexualised drugs needs to be taken into account

Estimating the evidence of selection and the reliability of inference in unigenic evolution

<p>Abstract</p> <p>Background</p> <p>Unigenic evolution is a large-scale mutagenesis experiment used to identify residues that are potentially important for protein function. Both currently-used methods for the analysis of unigenic evolution data analyze 'windows' of contiguous sites, a strategy that increases statistical power but incorrectly assumes that functionally-critical sites are contiguous. In addition, both methods require the questionable assumption of asymptotically-large sample size due to the presumption of approximate normality.</p> <p>Results</p> <p>We develop a novel approach, termed the Evidence of Selection (EoS), removing the assumption that functionally important sites are adjacent in sequence and and explicitly modelling the effects of limited sample-size. Precise statistical derivations show that the EoS score can be easily interpreted as an expected log-odds-ratio between two competing hypotheses, namely, the hypothetical presence or absence of functional selection for a given site. Using the EoS score, we then develop selection criteria by which functionally-important yet non-adjacent sites can be identified. An approximate power analysis is also developed to estimate the reliability of inference given the data. We validate and demonstrate the the practical utility of our method by analysis of the homing endonuclease <monospace>I-Bmol</monospace>, comparing our predictions with the results of existing methods.</p> <p>Conclusions</p> <p>Our method is able to assess both the evidence of selection at individual amino acid sites and estimate the reliability of those inferences. Experimental validation with <monospace>I-Bmol</monospace> proves its utility to identify functionally-important residues of poorly characterized proteins, demonstrating increased sensitivity over previous methods without loss of specificity. With the ability to guide the selection of precise experimental mutagenesis conditions, our method helps make unigenic analysis a more broadly applicable technique with which to probe protein function.</p> <p>Availability</p> <p>Software to compute, plot, and summarize EoS data is available as an open-source package called 'unigenic' for the 'R' programming language at <url>http://www.fernandes.org/txp/article/13/an-analytical-framework-for-unigenic-evolution</url>.</p

High-risk sex behavior and HIV prevalence among gay and bisexual men in the community of Madrid

BACKGROUND: To analyze high-risk sexual behavior as regards HIV, the use of preventive measures and the patient-reported prevalence of HIV infections among males belonging to one of the leading homosexual associations in the Region of Madrid. METHODS: Cross-sectional study conducted in 1997-1998 by way of mailed anonymous questionnaires. An analysis is made of the sociodemographic characteristics, how often condoms are used for different types of sexual intercourse with regular or casual partners, patient-reported prevalence of HIV and other related aspects. RESULTS: 157 questionnaires were returned by gay/bisexual males. These subjects averaged 32 years of age, 85% having a high school or college education, over the past 3 months, 56% had had intercourse with more than one man; 70.6% practiced insertive anal intercourse with a regular partner and 57.4% with casual partners, solely 32.5% and 61.1% of whom always used a condom. 69.7% had receptive anal intercourse with a regular partner and 39.4% with casual partners, 35.5% and 78.4% of whom respectively always used a condom. 86.6% had oral-genital intercourse, less than 10% having always used a condom. 137 were aware of their serological condition, and 15.2% were HIV positive. 10% had had some STD at some point during the previous year. CONCLUSIONS: A major percentage of those surveyed were involved in high-risk practices (several partners and unprotected high-risk sexual intercourse) which, in conjunction with the major prevalence of infection, can be said to be the same as a major seroconversion rate. ra la infección por VIH, el uso de medidas de preven- ción y la prevalencia autoinformada de infección por VIH en varones de una de las principales asociaciones de homo- sexuales de la Comunidad de Madrid. Métodos: Estudio tmnsversal realizado durante 1997- 1998. mediante un cuestionario anónimo remitido por correo. Se analizan las caructerísticas sociodemogrificas, la frecuen- cia de uso del preservativo en las distintas prklicas sexuales con la pareja estable y con las ocasionales. la prevalen& au- toinformada de VIH y otros aspectos relacionados. Resultados: Se obtuvieron 157 cuestionarios de varones homosexuales y bisexuales. Su edad media fue de 32 aiíos y el 85% tenía estudios medios o superiores. En los últimos 3 me- ses: el 56% tuvo relaciones con ~xí.s de un hombre; el 70.6% practicó la penetración anal insertiva con pareja estable y el 57,3% con conpactos ocasionales, de los que sólo el 33,510 y el 61,1% respectivamente utilizaron siempre el preservativo. La penetración anal receptiva la realizaron el 09.7% con pareja estable y el 39,4% con contactos ocasionales, utilizando siem- pre el preservativo el 355% y el 78,4% respectivamente. El 86.6% tuvieron relaciones oro-genitales y menos del 10% uti- lizaron siempre el preservativo. 137 hombres conocím su es- tado serológico y el 15,2% resultó VIH positivo. El 102% padeció alguna ETS durante el último aio. Conclusiones: Un importante porcentaje de entrevis- tndos mantiene prkticas de riesgo (varias parejas y relacio- nes sexuales de alto riesgo sin protección) que, asociado a una prevalencia de infección elevada, puede traducirse en unti importante tasa de seroconversión.Proyecto financiado por el Fondo de Investigación sanitaria ()

water chemistry are new challenges possible from coda compositional data analysis point of view

John Aitchison died in December 2016 leaving behind an important inheritance: to continue to explore the fascinating world of compositional data. However, notwithstanding the progress that we have made in this field of investigation and the diffusion of the CoDA theory in different researches, a lot of work has still to be done, particularly in geochemistry. In fact most of the papers published in international journals that manage compositional data ignore their nature and their consequent peculiar statistical properties. On the other hand, when CoDA principles are applied, several efforts are often made to continue to consider the log-ratio transformed variables, for example the centered log-ratio ones, as the original ones, demonstrating a sort of resistance to thinking in relative terms. This appears to be a very strange behavior since geochemists are used to ratios and their analysis is the base of the experimental calibration when standards are evolved to set the instruments. In this chapter some challenges are presented by exploring water chemistry data with the aim to invite people to capture the essence of thinking in a relative and multivariate way since this is the path to obtain a description of natural processes as complete as possible