Characterisation of a candidate dual AGN

We present Chandra and optical observations of a candidate dual AGN discovered serendipitously while searching for recoiling black holes via a cross-correlation between the serendipitous XMM source catalog (2XMMi) and SDSS-DR7 galaxies with a separation no larger than ten times the sum of their Petrosian radii. The system has a stellar mass ratio M$_{1}$/M$_{2}\approx 0.7$. One of the galaxies (Source 1) shows clear evidence for AGN activity in the form of hard X-ray emission and optical emission-line diagnostics typical of AGN ionisation. The nucleus of the other galaxy (Source 2) has a soft X-ray spectrum, bluer colours, and optical emission line ratios dominated by stellar photoionisation with a "composite" signature, which might indicate the presence of a weak AGN. When plotted on a diagram with X-ray luminosity vs [OIII] luminosity both nuclei fall within the locus defined by local Seyfert galaxies. From the optical spectrum we estimate the electron densities finding n$_{1} < 27$ e$^{-}$ cm$^{-3}$ and n$_{2} \approx 200$ e$^{-}$ cm$^{-3}$. From a 2D decomposition of the surface brightness distribution we infer that both galaxies host rotationally supported bulges (Sersic index $< 1$). While the active nature of Source 1 can be established with confidence, whether the nucleus of Source 2 is active remains a matter of debate. Evidence that a faint AGN might reside in its nucleus is, however, tantalising.Comment: 16 pages, 9 figures. Accepted for publication on MNRAS. Comments welcom

Dissipative dynamics and cooling rates of trapped impurity atoms immersed in a reservoir gas

We study the dissipative dynamics of neutral atoms in anisotropic harmonic potentials, immersed in a reservoir species that is not trapped by the harmonic potential. Considering initial motional excitation of the atoms along one direction, we explore the resulting spontaneous emission of reservoir excitations, across a range of trap parameters from strong to weak radial confinement. In different limits these processes are useful as a basis for analogies to laser cooling, or as a means to introduce controlled dissipation to many-body dynamics. For realistic experimental parameters, we analyze the distribution of the atoms during the decay and determine the effects of heating arising from a finite temperature reservoir

GRAVITY: The AO-Assisted, Two-Object Beam-Combiner Instrument

We present the proposal for the infrared adaptive optics (AO) assisted, two-object, high-throughput, multiple-beam-combiner GRAVITY for the VLTI. This instrument will be optimized for phase-referenced interferometric imaging and narrow-angle astrometry of faint, red objects. Following the scientific drivers, we analyze the VLTI infrastructure, and subsequently derive the requirements and concept for the optimum instrument. The analysis can be summarized with the need for highest sensitivity, phase referenced imaging and astrometry of two objects in the VLTI beam, and infrared wavefront-sensing. Consequently our proposed instrument allows the observations of faint, red objects with its internal infrared wavefront sensor, pushes the optical throughput by restricting observations to K-band at low and medium spectral resolution, and is fully enclosed in a cryostat for optimum background suppression and stability. Our instrument will thus increase the sensitivity of the VLTI significantly beyond the present capabilities. With its two fibers per telescope beam, GRAVITY will not only allow the simultaneous observations of two objects, but will also push the astrometric accuracy for UTs to 10 micro-arcsec, and provide simultaneous astrometry for up to six baselines.Comment: 12 pages, to be published in the Proceedings of the ESO Workshop on "The Power of Optical/IR Interferometry: Recent Scientific Results and 2nd Generation VLTI Instrumentation", eds. F. Paresce, A. Richichi, A. Chelli and F. Delplancke, held in Garching, Germany, 4-8 April 200

ANATOMICAL VARIATIONS OF THE INTERNAL JUGULAR VEIN: THE ROLE OF ULTRASONOGRAPHY

Purpose: In many places, especially in emergency department, central venous catheter is still inserted using anatomical landmark guidance with a success rate up to 97.6% and complications up to 15%. This study was aimed to determine by the support of ultrasono-graphy (US) the anatomical variations of the internal jugular vein (IJV) in relation with other structures of the neck, such as the common carotid artery (CCA). Material and Methods: 830 patients requiring central vein catheterization (CVC) were in-cluded in the analysis. The position of the IJV in relation to the other structures of the neck was demonstrated by portable ultrasonography. Results: The mean diameter of IJV was 10.3 mm in right and 10.5 mm in left side of neck, in male (p > 0.05) and 9.1 mm in right and 10.5 mm in left side of neck, in female (p > 0.05). The mean distance between IJV and CCA was 1.9 mm in right and 1.7 mm in left side of neck in male, and 2.0 mm in right and 2.2 mm in left side of neck in female. The mean distance of IJV from the skin surface was 9.8 mm in right and 10.0 mm in left side of neck in male, and 12.1 mm in right and 12.5 mm in left side of neck in female. On 25.54 % we observed variations of internal jugular vein site. On 3.97 % we observed a small caliber of internal jugular vein that could complicate the catheterization of the vein. On 1.8 % was diagnosed a thrombus of internal jugular vein, that is considered as an ab-solute contraindication for a CVC. Conclusion: Different patients had anatomical variations that are important and should be knowed, in order to reduce the possibility of severe complication

Evaluation of pre-processing on the meta-analysis of DNA methylation data from the Illumina HumanMethylation450 BeadChip platform

Introduction Meta-analysis is a powerful means for leveraging the hundreds of experiments being run worldwide into more statistically powerful analyses. This is also true for the analysis of omic data, including genome-wide DNA methylation. In particular, thousands of DNA methylation profiles generated using the Illumina 450k are stored in the publicly accessible Gene Expression Omnibus (GEO) repository. Often, however, the intensity values produced by the BeadChip (raw data) are not deposited, therefore only pre-processed values -obtained after computational manipulation- are available. Pre-processing is possibly different among studies and may then affect meta-analysis by introducing non-biological sources of variability. Material and methods To systematically investigate the effect of pre-processing on meta-analysis, we analysed four different collections of DNA methylation samples (datasets), each composed of two subsets, for which raw data from controls (i.e. healthy subjects) and cases (i.e. patients) are available. We pre-processed the data from each dataset with nine among the most common pipelines found in literature. Moreover, we evaluated the performance of regRCPqn, a modification of the RCP algorithm that aims to improve data consistency. For each combination of pre-processing (9 7 9), we first evaluated the between-sample variability among control subjects and, then, we identified genomic positions that are differentially methylated between cases and controls (differential analysis). Results and conclusion The pre-processing of DNA methylation data affects both the between-sample variability and the loci identified as differentially methylated, and the effects of pre-processing are strongly dataset-dependent. By contrast, application of our renormalization algorithm regRCPqn: (i) reduces variability and (ii) increases agreement between meta-analysed datasets, both critical components of data harmonization

Expression of apoptosis-related markers and clinical outcome in patients with advanced colorectal cancer

The clinical relevance of bax and bcl-2 protein expression has been investigated in 84 patients with recurrent or metastatic colorectal cancer submitted to a chemotherapy regimen including methotrexate and fluorouracil/leucovorin. Cytoplasmic immunostaining of bax and bcl-2 was present in 65.5% and 38%, respectively, of the tumours. No association was found between bax and bcl-2 or between p53 and bax or bcl-2 protein expression. Moreover, the biomarkers were unrelated to patient and tumour characteristics known to affect the clinical outcome of colorectal cancer patients. In general, the apoptosis-related markers did not appear indicative of short- and long-term clinical response nor of prognosis. Bcl-2-negative lesions were more frequent among patients who reached an objective clinical response, which is in agreement with previously reported data regarding other tumour types. When the interrelationship between p53 and bax expression was examined, a better response rate (40%) was found for patients whose tumours did not express p53 and bax, and a better prognosis (2-year probability of overall survival 75%) for patients with p53-positive and bax-negative tumours. In the present series of patients with advanced colorectal cancer submitted to systemic chemotherapy we did not find a clear association between expression of apoptosis-related markers and clinical outcome, even in the subset of patients in which the apoptotic index as determined by the TUNEL approach was investigated. © 2001 Cancer Research Campaign http://www.bjcancer.co

Lipoatrophy of the footpad in HIV-treated patients is associated with increased PAI-1

Purpose: To describe lipoatrophy of the plantar pedis fat pads in HIV patients with or without long-term antiretroviral therapy (ART); to compare the characteristics of ART patients with and without plantar pedis lipoatrophy; and to examine the effects of HIV and metabolic/cardiovascular risk parameters and treatment history on plantar pedis lipoatrophy. Design: One hundred and thirty four patients who started PI-ART in 1996 and 49 treatment naïve patients, recruited 2004, were examined and graded for lipoatrophy of five body compartments including the plantar fat pads eight years after start of ART. Baseline HIV- and ART-related factors were documented together with follow up metabolic/cardiovascular risk parameters. Results: Plantar pedis lipoatrophy occurred more often among ART patients (60%) than among treatment naïve patients (12%; p <0.001). ART patients with plantar lipoatrophy were older, had higher PAI-1 values, a higher prevalence of lipoatrophy in other body compartments, and longer stavudine and didanosine treatment history as compared to patients without plantar lipoatrophy. In multiple logistic regression, the best predictive model for plantar lipoatrophy was increased PAI-1 when HIV and metabolic/cardiovascular risk parameters were studied and treatment with didanosine when treatment history was studied. Increased PAI-1 was not associated to lioatrophy in any other location. Conclusions: Plantar lipoatrophy is common among patients on long-term ART and, although often overlooked, may cause significant discomfort. The association to PAI-1, a well known marker of increased cardiovascular risk, is intriguing and further focuses on the need of an active approach to evaluating and lowering cardiovascular risk factors in long-term HIV treatment

Convolutional LSTM Networks for Subcellular Localization of Proteins

Machine learning is widely used to analyze biological sequence data. Non-sequential models such as SVMs or feed-forward neural networks are often used although they have no natural way of handling sequences of varying length. Recurrent neural networks such as the long short term memory (LSTM) model on the other hand are designed to handle sequences. In this study we demonstrate that LSTM networks predict the subcellular location of proteins given only the protein sequence with high accuracy (0.902) outperforming current state of the art algorithms. We further improve the performance by introducing convolutional filters and experiment with an attention mechanism which lets the LSTM focus on specific parts of the protein. Lastly we introduce new visualizations of both the convolutional filters and the attention mechanisms and show how they can be used to extract biological relevant knowledge from the LSTM networks