The lymphoma-associated NPM-ALK oncogene elicits a p16INKa/pRb-dependent tumour-suppressive pathway

Oncogene induced senescence (OIS) is a barrier for tumour development. Oncogene-dependent DNA damage and activation of the ARF/p53 pathway play a central role in OIS and, accordingly, ARF and p53 are frequently mutated in human cancer. A number of leukemia/lymphoma-initiating oncogenes, however, inhibit ARF/p53 and only infrequently select for ARF or p53 mutations, suggesting the involvement of other tumour-suppressive pathways. We report that NPM-ALK, the initiating oncogene of Anaplastic Large Cell Lymphomas (ALCLs), induces DNA-damage and irreversibly arrests the cell cycle of primary fibroblasts and hematopoietic progenitors. This effect is associated with inhibition of p53 and is due to activation of the p16INK4a/pRb tumour-suppressive pathway. Analysis of NPM-ALK lymphomagenesis in transgenic mice showed p16INK4a-dependent accumulation of senescent cells in pre-malignant lesions and decreased tumour latency in the absence of p16INK4a. Accordingly, human ALCLs showed no expression of either p16INK4a or pRb. Up-regulation of the histone-demethylase Jmjd3 and de-methylation at the p16INK4a promoter contributed to the effect of NPM-ALK on p16INK4a, which was transcriptionally regulated. These data demonstrate that p16INK4a/pRb may function as an alternative pathway of oncogene-induced senescence, and suggest that the reactivation of p16INK4a expression might be a novel strategy to restore the senescence program in some tumours

In(ter)dependência entre decisões judiciais e pareceres psicossociais nos juízos criminais: análise qualitativa

O parecer psicossocial consiste no principal meio de assessoramento aos operadores do Direito em processos judiciais que necessitam de uma análise psicossocial, sendo documento fundamental essa interdisciplinaridade. A partir da análise de aspectos qualitativos de 178 decisões judiciais proferidas entre 2010 e 2012, esta pesquisa objetivou verificar se juízes têm acolhido ou desconsiderado sugestões ou alusões de risco em pareceres psicossociais que avaliaram situações de violência doméstica contra crianças, adolescentes e mulheres. A interpretação qualitativa dos dados resultou na construção de três zonas de sentido: 1. O interesse da vítima no prosseguimento do feito é central para a decisão judicial; 2. A atuação psicossocial tem como objetivo realizar o acompanhamento ou tratamento das partes; e 3. A atuação psicossocial tem como objetivo assessorar a tomada de decisão judicial. Sugere-se investimento na interdisciplinaridade entre as ciências psicossociais e jurídica, com base nos paradigmas dos Direitos Humanos, redes sociais e reparação das vítimas.Palavras-chave: Psicologia Jurídica; Serviço Social na justiça; Parecer psicossocial; Violência doméstica e familiar

Deep generative modeling for single-cell transcriptomics.

Single-cell transcriptome measurements can reveal unexplored biological diversity, but they suffer from technical noise and bias that must be modeled to account for the resulting uncertainty in downstream analyses. Here we introduce single-cell variational inference (scVI), a ready-to-use scalable framework for the probabilistic representation and analysis of gene expression in single cells ( https://github.com/YosefLab/scVI ). scVI uses stochastic optimization and deep neural networks to aggregate information across similar cells and genes and to approximate the distributions that underlie observed expression values, while accounting for batch effects and limited sensitivity. We used scVI for a range of fundamental analysis tasks including batch correction, visualization, clustering, and differential expression, and achieved high accuracy for each task

In(ter)dependência entre decisões judiciais e pareceres psicossociais nos juízos criminais: análise qualitativa

O parecer psicossocial consiste no principal meio de assessoramento aos operadores do Direito em processos judiciais que necessitam de uma análise psicossocial, sendo documento fundamental essa interdisciplinaridade. A partir da análise de aspectos qualitativos de 178 decisões judiciais proferidas entre 2010 e 2012, esta pesquisa objetivou verificar se juízes têm acolhido ou desconsiderado sugestões ou alusões de risco em pareceres psicossociais que avaliaram situações de violência doméstica contra crianças, adolescentes e mulheres. A interpretação qualitativa dos dados resultou na construção de três zonas de sentido: 1. O interesse da vítima no prosseguimento do feito é central para a decisão judicial; 2. A atuação psicossocial tem como objetivo realizar o acompanhamento ou tratamento das partes; e 3. A atuação psicossocial tem como objetivo assessorar a tomada de decisão judicial. Sugere-se investimento na interdisciplinaridade entre as ciências psicossociais e jurídica, com base nos paradigmas dos Direitos Humanos, redes sociais e reparação das vítimas.Palavras-chave: Psicologia Jurídica; Serviço Social na justiça; Parecer psicossocial; Violência doméstica e familiar.

Anisotropy and chemical composition of ultra-high energy cosmic rays using arrival directions measured by the Pierre Auger Observatory

The Pierre Auger Collaboration has reported evidence for anisotropy in the distribution of arrival directions of the cosmic rays with energies $E>E_{th}=5.5\times 10^{19}$ eV. These show a correlation with the distribution of nearby extragalactic objects, including an apparent excess around the direction of Centaurus A. If the particles responsible for these excesses at $E>E_{th}$ are heavy nuclei with charge $Z$, the proton component of the sources should lead to excesses in the same regions at energies $E/Z$. We here report the lack of anisotropies in these directions at energies above $E_{th}/Z$ (for illustrative values of $Z=6,\ 13,\ 26$). If the anisotropies above $E_{th}$ are due to nuclei with charge $Z$, and under reasonable assumptions about the acceleration process, these observations imply stringent constraints on the allowed proton fraction at the lower energies

Update on the correlation of the highest energy cosmic rays with nearby extragalactic matter

Data collected by the Pierre Auger Observatory through 31 August 2007 showed evidence for anisotropy in the arrival directions of cosmic rays above the Greisen-Zatsepin-Kuz'min energy threshold, \nobreak{$6\times 10^{19}$eV}. The anisotropy was measured by the fraction of arrival directions that are less than $3.1^\circ$ from the position of an active galactic nucleus within 75 Mpc (using the V\'eron-Cetty and V\'eron $12^{\rm th}$ catalog). An updated measurement of this fraction is reported here using the arrival directions of cosmic rays recorded above the same energy threshold through 31 December 2009. The number of arrival directions has increased from 27 to 69, allowing a more precise measurement. The correlating fraction is $(38^{+7}_{-6})$, compared with $21$ expected for isotropic cosmic rays. This is down from the early estimate of $(69^{+11}_{-13})$. The enlarged set of arrival directions is examined also in relation to other populations of nearby extragalactic objects: galaxies in the 2 Microns All Sky Survey and active galactic nuclei detected in hard X-rays by the Swift Burst Alert Telescope. A celestial region around the position of the radiogalaxy Cen A has the largest excess of arrival directions relative to isotropic expectations. The 2-point autocorrelation function is shown for the enlarged set of arrival directions and compared to the isotropic expectation.Comment: Accepted for publication in Astroparticle Physics on 31 August 201

Phenotypic and molecular characterisation of CDK13-related congenital heart defects, dysmorphic facial features and intellectual developmental disorders

Background: De novo missense variants in CDK13 have been described as the cause of syndromic congenital heart defects in seven individuals ascertained from a large congenital cardiovascular malformations cohort. We aimed to further define the phenotypic and molecular spectrum of this newly described disorder. Methods: To minimise ascertainment bias, we recruited nine additional individuals with CDK13 pathogenic variants from clinical and research exome laboratory sequencing cohorts. Each individual underwent dysmorphology exam and comprehensive medical history review. Results: We demonstrate greater than expected phenotypic heterogeneity, including 33% (3/9) of individuals without structural heart disease on echocardiogram. There was a high penetrance for a unique constellation of facial dysmorphism and global developmental delay, as well as less frequently seen renal and sacral anomalies. Two individuals had novel CDK13 variants (p.Asn842Asp, p.Lys734Glu), while the remaining seven unrelated individuals had a recurrent, previously published p.Asn842Ser variant. Summary of all variants published to date demonstrates apparent restriction of pathogenic variants to the protein kinase domain with clustering in the ATP and magnesium binding sites. Conclusions: Here we provide detailed phenotypic and molecular characterisation of individuals with pathogenic variants in CDK13 and propose management guidelines based upon the estimated prevalence of anomalies identified. Keywords: CDK13, CHDFIDD, De novo variant, Neurodevelopmental disorders, Agenesis of the corpus callosum, Hypertelorism, Developmental delay, Cyclin-dependent kinase, Undiagnosed Diseases Networ

The Fluorescence Detector of the Pierre Auger Observatory

The Pierre Auger Observatory is a hybrid detector for ultra-high energy cosmic rays. It combines a surface array to measure secondary particles at ground level together with a fluorescence detector to measure the development of air showers in the atmosphere above the array. The fluorescence detector comprises 24 large telescopes specialized for measuring the nitrogen fluorescence caused by charged particles of cosmic ray air showers. In this paper we describe the components of the fluorescence detector including its optical system, the design of the camera, the electronics, and the systems for relative and absolute calibration. We also discuss the operation and the monitoring of the detector. Finally, we evaluate the detector performance and precision of shower reconstructions.Comment: 53 pages. Submitted to Nuclear Instruments and Methods in Physics Research Section