Whole blood assessment of antigen specific cellular immune response by real time quantitative PCR: a versatile monitoring and discovery tool

BACKGROUND: Monitoring of cellular immune responses is indispensable in a number of clinical research areas, including microbiology, virology, oncology and autoimmunity. Purification and culture of peripheral blood mononuclear cells and rapid access to specialized equipment are usually required. We developed a whole blood (WB) technique monitoring antigen specific cellular immune response in vaccinated or naturally sensitized individuals. METHODS: WB (300 microl) was incubated at 37 degrees C with specific antigens, in the form of peptides or commercial vaccines for 5-16 hours. Following RNAlater addition to stabilize RNA, the mixture could be stored over one week at room temperature or at 4 degrees C. Total RNA was then extracted, reverse transcribed and amplified in quantitative real-time PCR (qRT-PCR) assays with primers and probes specific for cytokine and/or chemokine genes. RESULTS: Spiking experiments demonstrated that this technique could detect antigen specific cytokine gene expression from 50 cytotoxic T lymphocytes (CTL) diluted in 300 microl WB. Furthermore, the high sensitivity of this method could be confirmed ex-vivo by the successful detection of CD8+ T cell responses against HCMV, EBV and influenza virus derived HLA-A0201 restricted epitopes, which was significantly correlated with specific multimer staining. Importantly, a highly significant (p = 0.000009) correlation between hepatitis B surface antigen (HBsAg) stimulated IL-2 gene expression, as detectable in WB, and specific antibody titers was observed in donors vaccinated against hepatitis B virus (HBV) between six months and twenty years before the tests. To identify additional markers of potential clinical relevance, expression of chemokine genes was also evaluated. Indeed, HBsAg stimulated expression of MIP-1beta (CCL4) gene was highly significantly (p = 0.0006) correlated with specific antibody titers. Moreover, a longitudinal study on response to influenza vaccine demonstrated a significant increase of antigen specific IFN-gamma gene expression two weeks after immunization, declining thereafter, whereas increased IL-2 gene expression was still detectable four months after vaccination. CONCLUSION: This method, easily amenable to automation, might qualify as technology of choice for high throughput screening of immune responses to large panels of antigens from cohorts of donors. Although analysis of cytokine gene expression requires adequate laboratory infrastructure, initial antigen stimulation and storage of test probes can be performed with minimal equipment and time requirements. This might prove important in "field" studies with difficult access to laboratory facilities

Translating Video Content to Natural Language Descriptions

Humans use rich natural language to describe and communicate visual perceptions. In order to provide natural language descriptions for visual content, this paper combines two important ingredients. First, we generate a rich semantic representation of the visual content including e.g. object and activity labels. To predict the semantic representation we learn a CRF to model the relationships between different components of the visual input. And second, we propose to formulate the generation of natural language as a machine translation problem using the semantic representation as source language and the generated sentences as target language. For this we exploit the power of a parallel corpus of videos and textual descriptions and adapt statistical machine translation to translate between our two languages. We evaluate our video descriptions on the TACoS dataset, which contains video snippets aligned with sentence descriptions. Using automatic evaluation and human judgments we show significant improvements over several base line approaches, motivated by prior work. Our translation approach also shows improvements over related work on an image description task

NY-ESO-1 tumour associated antigen is a cytoplasmic protein detectable by specific monoclonal antibodies in cell lines and clinical specimens

NY-ESO-1 gene encodes a novel member of the cancer/testis (CT) family of human tumour-associated antigens (TAA). Specific monoclonal antibodies (mAb) have identified the corresponding gene product in lysates of tumour cell lines as a 22 kDa protein but no data are available concerning its intracellular location or distribution within neoplastic tissues. We have generated NY-ESO-1 specific mAbs recognizing the target molecule in cytospin preparations and in sections from clinical tumour specimens. These reagents identify NY-ESO-1 TAA in melanoma cell lines expressing the specific gene as a cytoplasmic protein, sharing the intracellular location of most MAGE TAA. In a series of 12 melanoma specimens, specific staining, limited to neoplastic cells, was detectable in the five cases where NY-ESO-1 gene expression was observed. In two of them over 90% of tumour cells showed evidence of positive staining. Lower percentages of positive neoplastic cells ranging between single cells and 50% were observed in the remaining tumours. These data suggest that active specific immunotherapies targeting NY-ESO-1, alone or in combination with other TAA could be of high clinical relevance in sizeable subgroups of melanoma patients. © 2000 Cancer Research Campaig

Cross-checking SMBH mass estimates in NGC 6958-I. Stellar dynamics from adaptive optics-assisted MUSE observations

Supermassive black hole masses (M (BH)) can dynamically be estimated with various methods and using different kinematic tracers. Different methods have only been cross-checked for a small number of galaxies and often show discrepancies. To understand these discrepancies, detailed cross-comparisons of additional galaxies are needed. We present the first part of our cross-comparison between stellar- and gas-based M-BH estimates in the nearby fast-rotating early-type galaxy NGC 6958. The measurements presented here are based on ground-layer adaptive optics-assisted Multi-Unit Spectroscopic Explorer (MUSE) science verification data at around 0."6 spatial resolution. The spatial resolution is a key ingredient for the measurement and we provide a Gaussian parametrization of the adaptive optics-assisted point spread function for various wavelengths. From the MUSE data, we extracted the stellar kinematics and constructed dynamical models. Using an axisymmetric Schwarzschild technique, we measured an M-BH of (3.6(-2.4)(+2.7)) x10(8) M-circle dot at 3 sigma significance taking kinematical and dynamical systematics (e.g. radially varying mass-to-light ratio) into account. We also added a dark halo, but our data do not allow us to constrain the dark matter fraction. Adding dark matter with an abundance matching prior results in a 25 per cent more massive black hole. Jeans anisotropic models return M-BH of (4.6(-2.7)(+2.5)) x10(8) and (8.6(-0.8)(+0.8)) x10(8) M-circle dot at 3 sigma confidence for spherical and cylindrical alignments of the velocity ellipsoid, respectively. In a follow-up study, we will compare the stellar-based M (BH) with those from cold and warm gas tracers, which will provide additional constraints for the M-BH for NGC 6958, and insights into assumptions that lead to potential systematic uncertainty

Six new supermassive black hole mass determinations from adaptive-optics assisted SINFONI observations

Different massive black hole mass – host galaxy scaling relations suggest that the growth of massive black holes is entangled with the evolution of their host galaxies. The number of measured black hole masses is still limited and additional measurements are necessary to understand the underlying physics of this apparent coevolution. We add six new black hole mass (MBH) measurements of nearby fast rotating early-type galaxies to the known black hole mass sample, namely NGC 584, NGC 2784, NGC 3640, NGC 4570, NGC 4281, and NGC 7049. Our target galaxies have effective velocity dispersions (σe) between 170 and 245 km s−1, and thus this work provides additional insight into the black hole properties of intermediate-mass early-type galaxies. We combined high-resolution adaptive-optics SINFONI data with large-scale MUSE, VIMOS and SAURON data from ATLAS3D to derive two-dimensional stellar kinematics maps. We then built both Jeans Anisotropic Models and axisymmetric Schwarzschild models to measure the central black hole masses. Our Schwarzschild models provide black hole masses of (1.3 ± 0.5) × 108 M⊙ for NGC 584, (1.0 ± 0.6) × 108 M⊙ for NGC 2784, (7.7 ± 5) × 107 M⊙ for NGC 3640, (5.4 ± 0.8) × 108 M⊙ for NGC 4281, (6.8 ± 2.0) × 107 M⊙ for NGC 4570, and (3.2 ± 0.8) × 108 M⊙ for NGC 7049 at 3σ confidence level, which are consistent with recent MBH−σe scaling relations. NGC 3640 has a velocity dispersion dip and NGC 7049 a constant velocity dispersion in the center, but we can clearly constrain their lower black hole mass limit. We conclude our analysis with a test on NGC 4570 taking into account a variable mass-to-light ratio (M/L) when constructing dynamical models. When considering M/L variations linked mostly to radial changes in the stellar metallicity, we find that the dynamically determined black hole mass from NGC 4570 decreases by 30%. Further investigations are needed in the future to account for the impact of radial M/L gradients on dynamical modeling

A low upper mass limit for the central black hole in the late-type galaxy NGC 4414

We present our mass estimate of the central black hole in the isolated spiral galaxy NGC 4414. Using natural guide star adaptive optics assisted observations with the Gemini Near-Infrared Integral Field Spectrometer (NIFS) and the natural seeing Gemini Multi-Object Spectrographs-North (GMOS), we derived two-dimensional stellar kinematic maps of NGC 4414 covering the central 1.5 arcsec and 10 arcsec, respectively, at a NIFS spatial resolution of 0.13 arcsec. The kinematic maps reveal a regular rotation pattern and a central velocity dispersion dip down to around 105 km s$^{-1}$. We constructed dynamical models using two different methods: Jeans anisotropic dynamical modeling and axisymmetric Schwarzschild modeling. Both modeling methods give consistent results, but we cannot constrain the lower mass limit and only measure an upper limit for the black hole mass of M$_{BH}$ = 1.56 × 10$^{6}$M⊙ (at 3σ level) which is at least 1σ below the recent M$_{BH}$−σe relations. Further tests with dark matter, mass-to-light ratio variation and different light models confirm that our results are not dominated by uncertainties. The derived upper limit mass is not only below the M$_{BH}$−σe relation, but is also five times lower than the lower limit black hole mass anticipated from the resolution limit of the sphere of influence. This proves that via high quality integral field data we are now able to push black hole measurements down to at least five times less than the resolution limit.The authors want to thank Tony Wong for providing the CO data of NGC 4414 and Remco Van den Bosch for fruitful discussions regarding the MGE model of NGC 4414. M.C. acknowledges support from a Royal Society University Research Fellowship. Based on observations obtained at the Gemini Observatory, which is operated by the Association of Universities for Research in Astronomy, Inc., under a cooperative agreement with the NSF on behalf of the Gemini partnership: the National Science Foundation (United States), the National Research Council (Canada), CONICYT (Chile), the Australian Research Council (Australia), Ministério da Ciência, Tecnologia e Inovação (Brazil) and Ministerio de Ciencia, Tecnología e Innovación Productiva (Argentina), under program GN-2007A-Q-45. Based on observations made with the NASA/ESA Hubble Space Telescope, obtained from the ESA Hubble Science Archive at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. Funding for SDSS-III has been provided by the Alfred P. Sloan Foundation, the Participating Institutions, the National Science Foundation, and the U.S. Department of Energy Office of Science. The SDSS-III web site is http://www.sdss3.org/. SDSS-III is managed by the Astrophysical Research Consortium for the Participating Institutions of the SDSS-III Collaboration including the University of Arizona, the Brazilian Participation Group, Brookhaven National Laboratory, Carnegie Mellon University, University of Florida, the French Participation Group, the German Participation Group, Harvard University, the Instituto de Astrofisica de Canarias, the Michigan State/Notre Dame/JINA Participation Group, Johns Hopkins University, Lawrence Berkeley National Laboratory, Max Planck Institute for Astrophysics, Max Planck Institute for Extraterrestrial Physics, New Mexico State University, New York University, Ohio State University, Pennsylvania State University, University of Portsmouth, Princeton University, the Spanish Participation Group, University of Tokyo, University of Utah, Vanderbilt University, University of Virginia, University of Washington, and Yale University. This research made use of Montage. It is funded by the National Science Foundation under Grant Number ACI-1440620, and was previously funded by the National Aeronautics and Space Administration’s Earth Science Technology Office, Computation Technologies Project, under Cooperative Agreement Number NCC5-626 between NASA and the California Institute of Technology. This research has made use of the NASA/IPAC Extragalactic Database (NED) which is operated by the Jet Propulsion Laboratory, California Institute of Technology, under contract with the National Aeronautics and Space Administration. We acknowledge the usage of the HyperLeda database (http://leda.univ-lyon1.fr

The MBHBM Project-I: measurement of the central black hole mass in spiral galaxy NGC 3504 using molecular gas kinematics

We present a dynamical mass measurement of the supermassive black hole (SMBH) in the nearby double-barred spiral galaxy NGC 3504 as part of the Measuring Black Holes in below Milky Way (M sstarf) Mass Galaxies Project. Our analysis is based on Atacama Large Millimeter/submillimeter Array cycle 5 observations of the ${}^{12}\mathrm{CO}(2-1)$ emission line. These observations probe NGC 3504's circumnuclear gas disk (CND). Our dynamical model of the CND simultaneously constrains a black hole (BH) mass of ${1.6}_{-0.4}^{+0.6}\times {10}^{7}$ M ⊙, which is consistent with the empirical BH–galaxy scaling relations and a mass-to-light ratio in the H band of 0.44 ± 0.12 (M ⊙/${L}_{\odot }$). This measurement also relies on our new estimation of the distance to the galaxy of 32.4 ± 2.1 Mpc using the surface brightness fluctuation method, which is much further than the existing distance estimates. Additionally, our observations detect a central deficit in the ${}^{12}\mathrm{CO}(2-1)$ integrated intensity map with a diameter of 6.3 pc at the putative position of the SMBH. However, we find that a dense gas tracer CS(5 − 4) peaks at the galaxy center, filling in the 12CO(2 − 1)-attenuated hole. Holes like this one are observed in other galaxies, and our observations suggest these may be caused by changing excitation conditions rather than a true absence of molecular gas around the nucleus

The MAGPI Survey: Drivers of kinematic asymmetries in the ionised gas of z∼0.3z\sim0.3 star-forming galaxies

Galaxy gas kinematics are sensitive to the physical processes that contribute to a galaxy's evolution. It is expected that external processes will cause more significant kinematic disturbances in the outer regions, while internal processes will cause more disturbances for the inner regions. Using a subsample of 47 galaxies ($0.27<z<0.36$) from the Middle Ages Galaxy Properties with Integral Field Spectroscopy (MAGPI) survey, we conduct a study into the source of kinematic disturbances by measuring the asymmetry present in the ionised gas line-of-sight velocity maps at the $0.5R_e$ (inner regions) and $1.5R_e$ (outer regions) elliptical annuli. By comparing the inner and outer kinematic asymmetries, we aim to better understand what physical processes are driving the asymmetries in galaxies. We find the local environment plays a role in kinematic disturbance, in agreement with other integral field spectroscopy studies of the local universe, with most asymmetric systems being in close proximity to a more massive neighbour. We do not find evidence suggesting that hosting an Active Galactic Nucleus (AGN) contributes to asymmetry within the inner regions, with some caveats due to emission line modelling. In contrast to previous studies, we do not find evidence that processes leading to asymmetry also enhance star formation in MAGPI galaxies. Finally, we find a weak anti-correlation between stellar mass and asymmetry (ie. high stellar mass galaxies are less asymmetric). We conclude by discussing possible sources driving the asymmetry in the ionised gas, such as disturbances being present in the colder gas phase (either molecular or atomic) prior to the gas being ionised, and non-axisymmetric features (e.g., a bar) being present in the galactic disk. Our results highlight the complex interplay between ionised gas kinematic disturbances and physical processes involved in galaxy evolution.Comment: e.g., 20 pages, 19 figure