YAC contigs of the Rab1 and wobbler (wr) spinal muscular atrophy gene region on proximal mouse chromosome 11 and of the homologous region on human chromosome 2p

powerful tool to advance the identi®cation of gene com-Despite rapid progress in the physical characteriza- plexes and of disease genes. In this respect, the analysis tion of murine and human genomes, little molecular in- of human chromosomes 16 and 19 (Nowak, 1995) and formation is available on certain regions, e.g., proximal mouse chromosomes 1 (Hunter et al., 1994) and 17 (Cox mouse chromosome 11 (Chr 11) and human chromosome et al., 1993) as well as of human and murine X chromo-2p (Chr 2p). We have localized the wobbler spinal atrophy somes is particularly far advanced (Hamvas et al., 1993). gene wr to proximal mouse Chr 11, tightly linked toRab1, On the other hand, such extensive information is not a gene coding for a small GTP-binding protein, and Glns- available for mouse proximal chromosome 11 (Chr 11) ps1, an intronless pseudogene of the glutamine synthe- and human chromosome 2p (Chr 2p) (Fig. 1; cf. Berry et tase gene. We have now used these markers to construct al., 1995; Nowak, 1995), known to share at least the genesa 1.3-Mb yeast arti®cial chromosome (YAC) contig of the for the reticuloendotheliosis oncogene (Brownell et al.,Rab1 region on mouse Chr 11. Four YAC clones isolated 1985), for a brain-speci®cb-spectrin isoform (Bloom et al.,from two independent YAC libraries were characterized 1992), and for cytoplasmic malate dehydrogenase (Ball etby rare-cutting analysis, ¯uorescence in situ hybridiza-al., 1994). However, comparing the segregation map oftion (FISH), and sequence-tagged site (STS) isolation and the mouse with the human cytogenetic map, a colinearmapping. Rab1 and Glns-ps1 were found to be only 20

Impact of granulation effects on the use of Balmer lines as temperature indicators

Balmer lines serve as important indicators of stellar effective temperatures in late-type stellar spectra. One of their modelling uncertainties is the influence of convective flows on their shape. We aim to characterize the influence of convection on the wings of Balmer lines. We perform a differential comparison of synthetic Balmer line profiles obtained from 3D hydrodynamical model atmospheres and 1D hydrostatic standard ones. The model parameters are appropriate for F,G,K dwarf and subgiant stars of metallicity ranging from solar to 1/1000 solar. The shape of the Balmer lines predicted by 3D models can never be exactly reproduced by a 1D model, irrespective of its effective temperature. We introduce the concept of a 3D temperature correction, as the effective temperature difference between a 3D model and a 1D model which provides the closest match to the 3D profile. The temperature correction is different for the different members of the Balmer series and depends on the adopted mixing-length parameter in the 1D model. Among the investigated models, the 3D correction ranges from -300K to +300K. Horizontal temperature fluctuations tend to reduce the 3D correction. Accurate effective temperatures cannot be derived from the wings of Balmer lines, unless the effects of convection are properly accounted for. The 3D models offer a physically well justified way of doing so. The use of 1D models treating convection with the mixing-length theory do not appear to be suitable for this purpose. In particular, there are indications that it is not possible to determine a single value of the mixing-length parameter which will optimally reproduce the Balmer lines for any choice of atmospheric parameters.Comment: 6 pages, 3 figures, accepted for publication in A&

CRANKITE: a fast polypeptide backbone conformation sampler

Background: CRANKITE is a suite of programs for simulating backbone conformations of polypeptides and proteins. The core of the suite is an efficient Metropolis Monte Carlo sampler of backbone conformations in continuous three-dimensional space in atomic details. Methods: In contrast to other programs relying on local Metropolis moves in the space of dihedral angles, our sampler utilizes local crankshaft rotations of rigid peptide bonds in Cartesian space. Results: The sampler allows fast simulation and analysis of secondary structure formation and conformational changes for proteins of average length

Main-Sequence and sub-giant stars in the Globular Cluster NGC6397: The complex evolution of the lithium abundance

Thanks to the high multiplex and efficiency of Giraffe at the VLT we have been able for the first time to observe the Li I doublet in the Main Sequence (MS) stars of a Globular Cluster. At the same time we observed Li in a sample of Sub-Giant (SG) stars of the same B-V colour. Our final sample is composed of 84 SG stars and 79 MS stars. In spite of the fact that SG and MS span the same temperature range we find that the equivalent widths of the Li I doublet in SG stars are systematically larger than those in MS stars, suggesting a higher Li content among SG stars. This is confirmed by our quantitative analysis. We derived the effective temperatures, from H$\alpha$ fitting, and NLTE Li abundances of the stars in our the sample, using 3D and 1D models. We find that SG stars have a mean Li abundance higher by 0.1dex than MS stars, using both 1D and 3D models. We also detect a positive slope of Li abundance with effective temperature. These results provide an unambiguous evidence that the Li abundance changes with evolutionary status. The physical mechanisms responsible for this behaviour are not yet clear, and none of the existing models seems to describe accurately these observations. Based on these conclusions, we believe that the cosmological lithium problem still remains an open question.Comment: Proceedings of the contributed talk presented at the IAU Symposium 26

Combination of Conservative and Interventional Therapy Strategies for Intra- and Extrahepatic Cholangiocellular Carcinoma: A Retrospective Survival Analysis

Background. Due to the predominantly advanced stage at the time of diagnosis treatment of cholangiocarcinoma is difficult. Apart from surgical resection, interventional treatment strategies are increasingly used in advanced stage tumours. The aim of the study was a retrospective comparison of the effect of the various forms of treatment on morbidity and mortality. Method. A total of 195 patients, received either chemotherapy or a combination of photodynamic therapy (PDT) or transarterial chemoembolization (TACE) and chemotherapy. Results. The median survival rate for all patients was 15.6 months, 50.8% were still alive 1 year after diagnosis. Patients, who had previously undergone surgery, survived 17.1 months longer than those without surgical treatment (P < .01). Chemotherapy prolonged the survival by 9.2 months (P = .47). Palliative patients under combination of chemotherapy and PDT survived on average 1.8 months longer (P = .28), with chemotherapy and TACE 9.8 months longer (P = .04) compared to chemotherapy alone. Conclusions. It appears that surgical treatment and chemotherapy combined with PDT or TACE may prolong survival

On the Formation Height of the SDO/HMI Fe 6173 Doppler Signal

The Helioseismic and Magnetic Imager (HMI) onboard the Solar Dynamics Observatory (SDO) is designed to study oscillations and the mag- netic field in the solar photosphere. It observes the full solar disk in the Fe I absorption line at 6173\AA . We use the output of a high-resolution 3D, time- dependent, radiation-hydrodynamic simulation based on the CO5BOLD code to calculate profiles F({\lambda},x,y,t) for the Fe I 6173{\AA} line. The emerging profiles F({\lambda},x,y,t) are multiplied by a representative set of HMI filter transmission profiles R_i({\lambda},1 \leq i \leq 6) and filtergrams I_i(x,y,t;1 \leq i \leq 6) are constructed for six wavelengths. Doppler velocities V_HMI(x,y,t) are determined from these filtergrams using a simplified version of the HMI pipeline. The Doppler velocities are correlated with the original velocities in the simulated atmosphere. The cross- correlation peaks near 100 km, suggesting that the HMI Doppler velocity signal is formed rather low in the solar atmosphere. The same analysis is performed for the SOHO/MDI Ni I line at 6768\AA . The MDI Doppler signal is formed slightly higher at around 125 km. Taking into account the limited spatial resolution of the instruments, the apparent formation height of both the HMI and MDI Doppler signal increases by 40 to 50 km. We also study how uncertainties in the HMI filter-transmission profiles affect the calculated velocities.Comment: 15 pages, 11 Figure

The solar photospheric abundance of hafnium and thorium. Results from CO5BOLD 3D hydrodynamic model atmospheres

Context: The stable element hafnium (Hf) and the radioactive element thorium (Th) were recently suggested as a suitable pair for radioactive dating of stars. The applicability of this elemental pair needs to be established for stellar spectroscopy. Aims: We aim at a spectroscopic determination of the abundance of Hf and Th in the solar photosphere based on a \cobold 3D hydrodynamical model atmosphere. We put this into a wider context by investigating 3D abundance corrections for a set of G- and F-type dwarfs. Method: High-resolution, high signal-to-noise solar spectra were compared to line synthesis calculations performed on a solar CO5BOLD model. For the other atmospheres, we compared synthetic spectra of CO5BOLD 3D and associated 1D models. Results: For Hf we find a photospheric abundance A(Hf)=0.87+-0.04, in good agreement with a previous analysis, based on 1D model atmospheres. The weak Th ii 401.9 nm line constitutes the only Th abundance indicator available in the solar spectrum. It lies in the red wing of an Ni-Fe blend exhibiting a non-negligible convective asymmetry. Accounting for the asymmetry-related additional absorption, we obtain A(Th)=0.09+-0.03, consistent with the meteoritic abundance, and about 0.1 dex lower than obtained in previous photospheric abundance determinations. Conclusions: Only for the second time, to our knowledge, has am non-negligible effect of convective line asymmetries on an abundance derivation been highlighted. Three-dimensional hydrodynamical simulations should be employed to measure Th abundances in dwarfs if similar blending is present, as in the solar case. In contrast, 3D effects on Hf abundances are small in G- to mid F-type dwarfs and sub-giants, and 1D model atmospheres can be conveniently used.Comment: A&A, in pres

Vortex Motions in the Solar Atmosphere: Definitions, Theory, Observations, and Modelling

Vortex flows, related to solar convective turbulent dynamics at granular scales and their interplay with magnetic fields within intergranular lanes, occur abundantly on the solar surface and in the atmosphere above. Their presence is revealed in high-resolution and high-cadence solar observations from the ground and from space and with state-of-the-art magnetoconvection simulations. Vortical flows exhibit complex characteristics and dynamics, excite a wide range of different waves, and couple different layers of the solar atmosphere, which facilitates the channeling and transfer of mass, momentum and energy from the solar surface up to the low corona. Here we provide a comprehensive review of documented research and new developments in theory, observations, and modelling of vortices over the past couple of decades after their observational discovery, including recent observations in Hα, innovative detection techniques, diverse hydrostatic modelling of waves and forefront magnetohydrodynamic simulations incorporating effects of a non-ideal plasma. It is the first systematic overview of solar vortex flows at granular scales, a field with a plethora of names for phenomena that exhibit similarities and differences and often interconnect and rely on the same physics. With the advent of the 4-m Daniel K. Inouye Solar Telescope and the forthcoming European Solar Telescope, the ongoing Solar Orbiter mission, and the development of cutting-edge simulations, this review timely addresses the state-of-the-art on vortex flows and outlines both theoretical and observational future research directions

Observing the Sun with Atacama Large Millimeter/submillimeter Array (ALMA): High Resolution Interferometric Imaging

Observations of the Sun at millimeter and submillimeter wavelengths offer a unique probe into the structure, dynamics, and heating of the chromosphere; the structure of sunspots; the formation and eruption of prominences and filaments; and energetic phenomena such as jets and flares. High-resolution observations of the Sun at millimeter and submillimeter wavelengths are challenging due to the intense, extended, low- contrast, and dynamic nature of emission from the quiet Sun, and the extremely intense and variable nature of emissions associated with energetic phenomena. The Atacama Large Millimeter/submillimeter Array (ALMA) was designed with solar observations in mind. The requirements for solar observations are significantly different from observations of sidereal sources and special measures are necessary to successfully carry out this type of observations. We describe the commissioning efforts that enable the use of two frequency bands, the 3 mm band (Band 3) and the 1.25 mm band (Band 6), for continuum interferometric-imaging observations of the Sun with ALMA. Examples of high-resolution synthesized images obtained using the newly commissioned modes during the solar commissioning campaign held in December 2015 are presented. Although only 30 of the eventual 66 ALMA antennas were used for the campaign, the solar images synthesized from the ALMA commissioning data reveal new features of the solar atmosphere that demonstrate the potential power of ALMA solar observations. The ongoing expansion of ALMA and solar-commissioning efforts will continue to enable new and unique solar observing capabilities.Comment: 22 pages, 12 figures, accepted for publication in Solar Physic

Magnetic Coupling in the Quiet Solar Atmosphere

Three kinds of magnetic couplings in the quiet solar atmosphere are highlighted and discussed, all fundamentally connected to the Lorentz force. First the coupling of the convecting and overshooting fluid in the surface layers of the Sun with the magnetic field. Here, the plasma motion provides the dominant force, which shapes the magnetic field and drives the surface dynamo. Progress in the understanding of the horizontal magnetic field is summarized and discussed. Second, the coupling between acoustic waves and the magnetic field, in particular the phenomenon of wave conversion and wave refraction. It is described how measurements of wave travel times in the atmosphere can provide information about the topography of the wave conversion zone, i.e., the surface of equal Alfv\'en and sound speed. In quiet regions, this surface separates a highly dynamic magnetic field with fast moving magnetosonic waves and shocks around and above it from the more slowly evolving field of high-beta plasma below it. Third, the magnetic field also couples to the radiation field, which leads to radiative flux channeling and increased anisotropy in the radiation field. It is shown how faculae can be understood in terms of this effect. The article starts with an introduction to the magnetic field of the quiet Sun in the light of new results from the Hinode space observatory and with a brief survey of measurements of the turbulent magnetic field with the help of the Hanle effect.Comment: To appear in "Magnetic Coupling between the Interior and the Atmosphere of the Sun", eds. S.S. Hasan and R.J. Rutten, Astrophysics and Space Science Proceedings, Springer-Verlag, Heidelberg, Berlin, 200