Dimensionality Reduction of Longitudinal 'Omics Data using Modern Tensor Factorization

Precision medicine is a clinical approach for disease prevention, detection and treatment, which considers each individual's genetic background, environment and lifestyle. The development of this tailored avenue has been driven by the increased availability of omics methods, large cohorts of temporal samples, and their integration with clinical data. Despite the immense progression, existing computational methods for data analysis fail to provide appropriate solutions for this complex, high-dimensional and longitudinal data. In this work we have developed a new method termed TCAM, a dimensionality reduction technique for multi-way data, that overcomes major limitations when doing trajectory analysis of longitudinal omics data. Using real-world data, we show that TCAM outperforms traditional methods, as well as state-of-the-art tensor-based approaches for longitudinal microbiome data analysis. Moreover, we demonstrate the versatility of TCAM by applying it to several different omics datasets, and the applicability of it as a drop-in replacement within straightforward ML tasks

Differential actions of eplerenone and spironolactone on the protective effect of testosterone against cardiomyocyte apoptosis in vitro

©2010. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/ This document is the Accepted version of a Published Work that appeared in final form in Revista Española de cardiología. To access the final edited and published work see https://doi.org/10.1016/s1885-5857(10)70162-6Introduction and objectives: Testosterone deficiency is associated with a poor prognosis in patients with heart failure. It is not clear whether testosterone reduces cardiomyocyte apoptosis or whether the effect of spironolactone, an aldosterone receptor blocker with progestogenic and anti-androgen activity, differs from that of the selective aldosterone blocker eplerenone. Methods: Apoptosis induced by hyperosmotic stress in the embryonic rat heart cell line H9c2 was monitored by measuring cell viability, DNA fragmentation and caspase-3, -8 and -9 activation. The effect of testosterone was investigated in the presence or absence of spironolactone and eplerenone. Results: Exposure to sorbitol (0.6 M, 3 h) decreased cell viability and increased DNA fragmentation and caspase-3, -8 and -9 activation. These effects were all significantly reduced by testosterone, 100 nM (P< .01). Pretreatment with spironolactone, 10 .M, blocked the effects of testosterone, decreased cell viability (P< .01) and increased caspase activation (P< .01). In contrast, eplerenone, 10 .M, increased cell viability (P< .001) without altering the effect on caspase activation. These actions were not modified by the androgen receptor blocker flutamide. They were mediated by SAPK/JNK and ERK1/2 signaling pathways (P< .01). Conclusions: Testosterone appears to have a protective effect against cardiomyocyte apoptosis which is antagonized by spironolactone but not by eplerenone. These effects await confirmation in in vivo models, but their presence could have clinical and therapeutic implications

Ferritin heavy chain as main mediator of preventive effect of metformin against mitochondrial damage induced by doxorubicin in cardiomyocytes

©2014. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/ This document is the Accepted version of a Published Work that appeared in final form inFree Radical Biology and Medicine. To access the final edited and published work see https://doi.org/10.1016/j.freeradbiomed.2013.11.003The efficacy of doxorubicin (DOX) as an antitumor agent is greatly limited by the induction of cardiomyopathy, which results from mitochondrial dysfunction and iron-catalyzed oxidative stress in the cardiomyocyte. Metformin (MET) has been seen to have a protective effect against the oxidative stress induced by DOX in cardiomyocytes through its modulation of ferritin heavy chain (FHC), the main iron-storage protein. This study aimed to assess the involvement of FHC as a pivotal molecule in the mitochondrial protection offered by MET against DOX cardiotoxicity. The addition of DOX to adult mouse cardiomyocytes (HL-1 cell line) increased the cytosolic and mitochondrial free iron pools in a time-dependent manner. Simultaneously, DOX inhibited complex I activity and ATP generation and induced the loss of mitochondrial membrane potential. The mitochondrial dysfunction induced by DOX was associated with the release of cytochrome c to the cytosol, the activation of caspase 3, and DNA fragmentation. The loss of iron homeostasis, mitochondrial dysfunction, and apoptosis induced by DOX were prevented by treatment with MET 24h before the addition of DOX. The involvement of FHC and NF-κB was determined through siRNA-mediated knockdown. Interestingly, the presilencing of FHC or NF-κB with specific siRNAs blocked the protective effect induced by MET against DOX cardiotoxicity. These findings were confirmed in isolated primary neonatal rat cardiomyocytes. In conclusion, these results deepen our knowledge of the protective action of MET against DOX-induced cardiotoxicity and suggest that therapeutic strategies based on FHC modulation could protect cardiomyocytes from the mitochondrial damage induced by DOX by restoring iron homeostasi

Filamin C Truncation Mutations Are Associated With Arrhythmogenic Dilated Cardiomyopathy and Changes in the Cell-Cell Adhesion Structures.

OBJECTIVES: The purpose of this study was to assess the phenotype of Filamin C (FLNC) truncating variants in dilated cardiomyopathy (DCM) and understand the mechanism leading to an arrhythmogenic phenotype. BACKGROUND: Mutations in FLNC are known to lead to skeletal myopathies, which may have an associated cardiac component. Recently, the clinical spectrum of FLNC mutations has been recognized to include a cardiac-restricted presentation in the absence of skeletal muscle involvement. METHODS: A population of 319 U.S. and European DCM cardiomyopathy families was evaluated using whole-exome and targeted next-generation sequencing. FLNC truncation probands were identified and evaluated by clinical examination, histology, transmission electron microscopy, and immunohistochemistry. RESULTS: A total of 13 individuals in 7 families (2.2%) were found to harbor 6 different FLNC truncation variants (2 stopgain, 1 frameshift, and 3 splicing). Of the 13 FLNC truncation carriers, 11 (85%) had either ventricular arrhythmias or sudden cardiac death, and 5 (38%) presented with evidence of right ventricular dilation. Pathology analysis of 2 explanted hearts from affected FLNC truncation carriers showed interstitial fibrosis in the right ventricle and epicardial fibrofatty infiltration in the left ventricle. Ultrastructural findings included occasional disarray of Z-discs within the sarcomere. Immunohistochemistry showed normal plakoglobin signal at cell-cell junctions, but decreased signals for desmoplakin and synapse-associated protein 97 in the myocardium and buccal mucosa. CONCLUSIONS: We found FLNC truncating variants, present in 2.2% of DCM families, to be associated with a cardiac-restricted arrhythmogenic DCM phenotype characterized by a high risk of life-threatening ventricular arrhythmias and a pathological cellular phenotype partially overlapping with arrhythmogenic right ventricular cardiomyopathy

An ultraviolet-selected galaxy redshift survey - III: Multicolour imaging and non-uniform star formation histories

(abridged) We present panoramic u' and optical ground-based imaging observations of a complete sample of low-redshift (0<z<0.4) galaxies selected in the ultraviolet (UV) at 2000A using the balloon-borne FOCA instrument of Milliard et al. This survey is highly sensitive to newly-formed massive stars, and hence to actively star-forming galaxies. We use the new data to further investigate the stellar population and star formation properties of this sample. When combined with our earlier spectroscopic surveys, these new data allow us to compare star-formation measures derived from aperture-corrected Ha line fluxes, UV(2000A) and u'(3600A) continuum fluxes on a galaxy-by-galaxy basis. As expected from our earlier studies, we find broad correlations between the dust-corrected star-formation diagnostics, though the scatter is larger than that from observational errors, with significant offsets from trends expected according to simple star-formation history (SFH) models. Varying metallicities and/or initial mass functions seem unable to explain the observed discrepancies. We investigate the star-formation properties further by modelling the observed spectroscopic and photometric properties of the galaxies in our survey. Nearly half of the galaxies surveyed possess features that appear incompatible with simple constant or smoothly declining SFHs, favouring instead irregular or temporally-varying SFHs. We demonstrate how this can reconcile the majority of our observations, and determine empirical corrections to calculate intrinsic star formation rates from measures based on UV (or u') observations alone. We discuss the broader implications of our finding that a significant fraction of star-forming galaxies have complex SFHs, particularly in the context of recent determinations of the cosmic SFH.Comment: MNRAS; post-referee report version. 16 pages, 10 figure

Desenvolvimento de Um Sistema Web Para Gestão de Simulações Dosimétricas Para Radiodiagnóstico / Development of a Web System to Manage Dosimetric Simulations for Radiodiagnosis

Este trabalho descreve a implementação de uma plataforma Web de forma automatizada para a criação, gestão, acompanhamento e análise de simulações dosimetricas para Radiodiagnóstico. Utilizando o codigo GATE/Geant4 baseado em Monte Carlo o sistema realiza simulações computacionais de exames médicos envolvendo raios-X. A estrutura da plataforma permeteu uma redução do tempo de geração e processamento das simulações. O sistema proporsiona no final as dosis aos quais os pacientes são submetidos em radiodiagnóstico, magnitude necesaria para a evaluação do risco de câncer radioinduzido com exames que utilizam raios-X

Circulating tumor cells for comprehensive and multiregional non-invasive genetic characterization of multiple myeloma

Multiple myeloma (MM) patients undergo repetitive bone marrow (BM) aspirates for genetic characterization. Circulating tumor cells (CTCs) are detectable in peripheral blood (PB) of virtually all MM cases and are prognostic, but their applicability for noninvasive screening has been poorly investigated. Here, we used next-generation flow (NGF) cytometry to isolate matched CTCs and BM tumor cells from 53 patients and compared their genetic profile. In eight cases, tumor cells from extramedullary (EM) plasmacytomas were also sorted and whole-exome sequencing was performed in the three spatially distributed tumor samples. CTCs were detectable by NGF in the PB of all patients with MM. Based on the cancer cell fraction of clonal and subclonal mutations, we found that ~22% of CTCs egressed from a BM (or EM) site distant from the matched BM aspirate. Concordance between BM tumor cells and CTCs was high for chromosome arm-level copy number alterations (≥95%) though not for translocations (39%). All high-risk genetic abnormalities except one t(4;14) were detected in CTCs whenever present in BM tumor cells. Noteworthy, ≥82% mutations present in BM and EM clones were detectable in CTCs. Altogether, these results support CTCs for noninvasive risk-stratification of MM patients based on their numbers and genetic profile.This study was supported by the Centro de Investigación Biomédica en Red—Área de Oncología—del Instituto de Salud Carlos III (CIBERONC; CB16/12/00236, CB16/12/00369, CB16/12/00489, and CB16/12/00400); by Cancer Research UK [C355/A26819] and FC AECC and AIRC under the Accelerator Award Program; by the Instituto de Salud Carlos III, FCAECC and co-financed by FEDER (ERANET-TRANSCAN-2 iMMunocell AC17/00101); the Spanish Ministry of Science and Innovation and co-financed by FSE (Torres Quevedo fellowship, PTQ-16-08623); the Black Swan Research Initiative of the International Myeloma Foundation; European Research Council (ERC) under the European Commission’s H2020 Framework Programme (MYELOMANEXT, 680200); the Qatar National Research Fund (QNRF) Award No. 7-916-3-237; the AACR-Millennium Fellowship in Multiple Myeloma Research (15-40-38-PAIV); the Leukemia Research Foundation; and the Multiple Myeloma Research Foundation (MMRF) under the 2019 Research Fellowship Award

Sex Differences in Frequency, Severity, and Distribution of Cerebral Microbleeds

Peer reviewe

Sloan Digital Sky Survey IV: Mapping the Milky Way, Nearby Galaxies, and the Distant Universe

We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and high signal-to-noise ratios in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially resolved spectroscopy for thousands of nearby galaxies (median $z\sim 0.03$). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between $z\sim 0.6$ and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGNs and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5 m Sloan Foundation Telescope at the Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5 m du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in 2016 July