Characterizing Exoplanets in the Visible and Infrared: A Spectrometer Concept for the EChO Space Mission

Transit-spectroscopy of exoplanets is one of the key observational techniques to characterize the extrasolar planet and its atmosphere. The observational challenges of these measurements require dedicated instrumentation and only the space environment allows an undisturbed access to earth-like atmospheric features such as water or carbon-dioxide. Therefore, several exoplanet-specific space missions are currently being studied. One of them is EChO, the Exoplanet Characterization Observatory, which is part of ESA's Cosmic Vision 2015-2025 program, and which is one of four candidates for the M3 launch slot in 2024. In this paper we present the results of our assessment study of the EChO spectrometer, the only science instrument onboard this spacecraft. The instrument is a multi-channel all-reflective dispersive spectrometer, covering the wavelength range from 400 nm to 16 microns simultaneously with a moderately low spectral resolution. We illustrate how the key technical challenge of the EChO mission - the high photometric stability - influences the choice of spectrometer concept and drives fundamentally the instrument design. First performance evaluations underline the fitness of the elaborated design solution for the needs of the EChO mission.Comment: 20 pages, 8 figures, accepted for publication in the Journal of Astronomical Instrumentatio

Concept and optical design of the cross-disperser module for CRIRES

This is the peer reviewed version of the following article: Oliva, Ernesto, A. Tozzi, D. Ferruzzi, L. Origlia, A. Hatzes, R. Follert, T. Loewinger et al. "Concept and optical design of the cross-disperser module for CRIRES+." In SPIE Astronomical Telescopes+ Instrumentation, pp. 91477R-91477R. International Society for Optics and Photonics, 2014, which has been published in final form at 10.1117/12.2054381

Comparison of the properties of two fossil groups of galaxies with the normal group NGC 6034 based on multiband imaging and optical spectroscopy

We collected multiband imaging and spectroscopy for two fossil groups (RX J1119.7+2126 and 1RXS J235814.4+150524) and one normal group (NGC 6034). We computed photometric redshifts in the central zones of each group, combining previous data with the SDSS five-band data. For each group we investigated the red sequence (RS) of the color-magnitude relation and computed the luminosity functions, stellar population ages and distributions of the group members. Spectroscopy allowed us to investigate the large-scale surroundings of these groups and the substructure levels in 1RXS J235814.4+150524 and NGC 6034. The large-scale environment of 1RXS J235814.4+150524 is poor, though its galaxy density map shows a clear signature of the surrounding cosmic web. RX J1119.7+2126 appears to be very isolated, while the cosmic environment of NGC 6034 is very rich. At the group scale, 1RXS J235814.4+150524 shows no substructure. Galaxies with recent stellar populations seem preferentially located in the group outskirts. A RS is discernable for all three groups in a color-magnitude diagram. The luminosity functions based on photometric redshift selection and on statistical background subtraction have comparable shapes, and agree with the few points obtained from spectroscopic redshifts. These luminosity functions show the expected dip between first and second brightest galaxies for the fossil groups only. Their shape is also regular and relatively flat at faint magnitudes down to the completeness level for RX J1119.7+2126 and NGC 6034, while there is a clear lack of faint galaxies for 1RXS J235814.4+150524. RX J1119.7+2126 is definitely classified as a fossil group; 1RXS J235814.4+150524 also has properties very close to those of a fossil group, while we confirm that NGC 6034 is a normal group.Comment: Accepted in A&A, english-improved, 5 jpeg figures, and shortened abstrac

A bispecific diabody directed against prostate-specific membrane antigen and CD3 induces T-cell mediated lysis of prostate cancer cells

BACKGROUND: Although cancer of the prostate is one of the most commonly diagnosed cancers in men, no curative treatment currently exists after its progression beyond resectable boundaries. Therefore, new agents for targeted treatment strategies are needed. Cross-linking of tumor antigens with T-cell associated antigens by bispecific monoclonal antibodies have been shown to increase antigen-specific cytotoxicity in T-cells. Since the prostate-specific membrane antigen (PSMA) represents an excellent tumor target, immunotherapy with bispecific diabodies could be a promising novel treatment option for prostate cancer. METHODS: A heterodimeric diabody specific for human PSMA and the T-cell antigen CD3 was constructed from the DNA of anti-CD3 and anti-PSMA single chain Fv fragments (scFv). It was expressed in E. coli using a vector containing a bicistronic operon for co-secretion of the hybrid scFv V_HCD3-V_LPSMA and V_HPSMA-V_LCD3. The resulting PSMAxCD3 diabody was purified from the periplasmic extract by immobilized metal affinity chromatography (IMAC). The binding properties were tested on PSMA-expressing prostate cancer cells and PSMA-negative cell lines as well as on Jurkat cells by flow cytometry. For in vitro functional analysis, a cell viability test (WST) was used. For in vivo evaluation the diabody was applied together with human peripheral blood lymphocytes (PBL) in a C4-2 xenograft-SCID mouse model. RESULTS: By Blue Native gel electrophoresis, it could be shown that the PSMAxCD3 diabody is mainly a tetramer. Specific binding both to CD3-expressing Jurkat cells and PSMA-expressing C4-2 cells was shown by flow cytometry. In vitro, the diabody proved to be a potent agent for retargeting PBL to lyze C4-2 prostate cancer cells. Treatment of SCID mice inoculated with C4-2 tumor xenografts with the diabody and PBL efficiently inhibited tumor growth. CONCLUSIONS: The PSMAxCD3 diabody bears the potential for facilitating immunotherapy of prostate cancer and for the elimination of minimal residual disease

Temporal development of the oral microbiome and prediction of early childhood caries

Human microbiomes are predicted to assemble in a reproducible and ordered manner yet there is limited knowledge on the development of the complex bacterial communities that constitute the oral microbiome. The oral microbiome plays major roles in many oral diseases including early childhood caries (ECC), which afflicts up to 70% of children in some countries. Saliva contains oral bacteria that are indicative of the whole oral microbiome and may have the ability to reflect the dysbiosis in supragingival plaque communities that initiates the clinical manifestations of ECC. The aim of this study was to determine the assembly of the oral microbiome during the first four years of life and compare it with the clinical development of ECC. The oral microbiomes of 134 children enrolled in a birth cohort study were determined at six ages between two months and four years-of-age and their mother’s oral microbiome was determined at a single time point. We identified and quantified 356 operational taxonomic units (OTUs) of bacteria in saliva by sequencing the V4 region of the bacterial 16S RNA genes. Bacterial alpha diversity increased from a mean of 31 OTUs in the saliva of infants at 1.9 months-of-age to 84 OTUs at 39 months-of-age. The oral microbiome showed a distinct shift in composition as the children matured. The microbiome data were compared with the clinical development of ECC in the cohort at 39, 48, and 60 months-of-age as determined by ICDAS-II assessment. Streptococcus mutans was the most discriminatory oral bacterial species between health and current disease, with an increased abundance in disease. Overall our study demonstrates an ordered temporal development of the oral microbiome, describes a limited core oral microbiome and indicates that saliva testing of infants may help predict ECC risk

Multi-band high resolution spectroscopy rules out the hot Jupiter BD+20 1790b - First data from the GIARPS Commissioning

Context. Stellar activity is currently challenging the detection of young planets via the radial velocity (RV) technique. Aims. We attempt to definitively discriminate the nature of the RV variations for the young active K5 star BD+20 1790, for which visible (VIS) RV measurements show divergent results on the existence of a substellar companion. Methods. We compare VIS data with high precision RVs in the near infrared (NIR) range by using the GIANO - B and IGRINS spectrographs. In addition, we present for the first time simultaneous VIS-NIR observations obtained with GIARPS (GIANO - B and HARPS - N) at Telescopio Nazionale Galileo (TNG). Orbital RVs are achromatic, so the RV amplitude does not change at different wavelengths, while stellar activity induces wavelength-dependent RV variations, which are significantly reduced in the NIR range with respect to the VIS. Results. The NIR radial velocity measurements from GIANO - B and IGRINS show an average amplitude of about one quarter with respect to previously published VIS data, as expected when the RV jitter is due to stellar activity. Coeval multi-band photometry surprisingly shows larger amplitudes in the NIR range, explainable with a mixture of cool and hot spots in the same active region. Conclusions. In this work, the claimed massive planet around BD+20 1790 is ruled out by our data. We exploited the crucial role of multi- wavelength spectroscopy when observing young active stars: thanks to facilities like GIARPS that provide simultaneous observations, this method can reach its maximum potential.Comment: 12 pages, 7 figure

CRIRES-POP: A library of high resolution spectra in the near-infrared

New instrumental capabilities and the wealth of astrophysical information extractable from the near-infrared wavelength region have led to a growing interest in the field of high resolution spectroscopy at 1-5 mu. We aim to provide a library of observed high-resolution and high signal-to-noise-ratio near-infrared spectra of stars of various types throughout the Hertzsprung-Russell diagram. This is needed for the exploration of spectral features in this wavelength range and for comparison of reference targets with observations and models. High quality spectra were obtained using the CRIRES near-infrared spectrograph at ESO's VLT covering the range from 0.97 to 5.3 mu at high spectral resolution. Accurate wavelength calibration and correction for of telluric lines were performed by fitting synthetic transmission spectra for the Earth's atmosphere to each spectrum individually. We describe the observational strategy and the current status and content of the library which includes 13 objects. The first examples of finally reduced spectra are presented. This publication will serve as a reference paper to introduce the library to the community and explore the extensive amount of material.Comment: accepted for publication in A&A; see also the project webpage http://www.univie.ac.at/crirespo

Best practice data life cycle approaches for the life sciences

Throughout history, the life sciences have been revolutionised by technological advances; in our era this is manifested by advances in instrumentation for data generation, and consequently researchers now routinely handle large amounts of heterogeneous data in digital formats. The simultaneous transitions towards biology as a data science and towards a ‘life cycle’ view of research data pose new challenges. Researchers face a bewildering landscape of data management requirements, recommendations and regulations, without necessarily being able to access data management training or possessing a clear understanding of practical approaches that can assist in data management in their particular research domain. Here we provide an overview of best practice data life cycle approaches for researchers in the life sciences/bioinformatics space with a particular focus on ‘omics’ datasets and computer-based data processing and analysis. We discuss the different stages of the data life cycle and provide practical suggestions for useful tools and resources to improve data management practices.Philippa C. Griffin, Jyoti Khadake, Kate S. LeMay, Suzanna E. Lewis, Sandra Orchard ... Nathan S. Watson-Haigh ... et al

Effects of Electrical and Structural Remodeling on Atrial Fibrillation Maintenance: A Simulation Study

Atrial fibrillation, a common cardiac arrhythmia, often progresses unfavourably: in patients with long-term atrial fibrillation, fibrillatory episodes are typically of increased duration and frequency of occurrence relative to healthy controls. This is due to electrical, structural, and contractile remodeling processes. We investigated mechanisms of how electrical and structural remodeling contribute to perpetuation of simulated atrial fibrillation, using a mathematical model of the human atrial action potential incorporated into an anatomically realistic three-dimensional structural model of the human atria. Electrical and structural remodeling both shortened the atrial wavelength - electrical remodeling primarily through a decrease in action potential duration, while structural remodeling primarily slowed conduction. The decrease in wavelength correlates with an increase in the average duration of atrial fibrillation/flutter episodes. The dependence of reentry duration on wavelength was the same for electrical vs. structural remodeling. However, the dynamics during atrial reentry varied between electrical, structural, and combined electrical and structural remodeling in several ways, including: (i) with structural remodeling there were more occurrences of fragmented wavefronts and hence more filaments than during electrical remodeling; (ii) dominant waves anchored around different anatomical obstacles in electrical vs. structural remodeling; (iii) dominant waves were often not anchored in combined electrical and structural remodeling. We conclude that, in simulated atrial fibrillation, the wavelength dependence of reentry duration is similar for electrical and structural remodeling, despite major differences in overall dynamics, including maximal number of filaments, wave fragmentation, restitution properties, and whether dominant waves are anchored to anatomical obstacles or spiralling freely