Convex optimization problem prototyping for image reconstruction in computed tomography with the Chambolle-Pock algorithm

The primal-dual optimization algorithm developed in Chambolle and Pock (CP), 2011 is applied to various convex optimization problems of interest in computed tomography (CT) image reconstruction. This algorithm allows for rapid prototyping of optimization problems for the purpose of designing iterative image reconstruction algorithms for CT. The primal-dual algorithm is briefly summarized in the article, and its potential for prototyping is demonstrated by explicitly deriving CP algorithm instances for many optimization problems relevant to CT. An example application modeling breast CT with low-intensity X-ray illumination is presented.Comment: Resubmitted to Physics in Medicine and Biology. Text has been modified according to referee comments, and typos in the equations have been correcte

Superconductivity-enhanced bias spectroscopy in carbon nanotube quantum dots

We study low-temperature transport through carbon nanotube quantum dots in the Coulomb blockade regime coupled to niobium-based superconducting leads. We observe pronounced conductance peaks at finite source-drain bias, which we ascribe to elastic and inelastic cotunneling processes enhanced by the coherence peaks in the density of states of the superconducting leads. The inelastic cotunneling lines display a marked dependence on the applied gate voltage which we relate to different tunneling-renormalizations of the two subbands in the nanotube. Finally, we discuss the origin of an especially pronounced sub-gap structure observed in every fourth Coulomb diamond

Methanol maps of low-mass protostellar systems: the Serpens Molecular Core

Observations of Serpens have been performed at the JCMT using Harp-B. Maps over a 4.5'x5.4' region were made in a frequency window around 338 GHz, covering the 7-6 transitions of methanol. Emission is extended over each source, following the column density of H2 but showing up also particularly strongly around outflows. The rotational temperature is low, 15-20 K, and does not vary with position within each source. The abundance is typically 10^-9 - 10^-8 with respect to H2 in the outer envelope, whereas "jumps" by factors of up to 10^2 -10^3 inside the region where the dust temperature exceeds 100 K are not excluded. A factor of up to ~ 10^3 enhancement is seen in outflow gas. In one object, SMM4, the ice abundance has been measured to be ~ 3x10^-5 with respect to H2 in the outer envelope, i.e., a factor of 10^3 larger than the gas-phase abundance. Comparison with C18O J=3-2 emission shows that strong CO depletion leads to a high gas-phase abundance of CH3OH not just for the Serpens sources, but for a larger sample of protostars. The observations illustrate the large-scale, low-level desorption of CH3OH from dust grains, extending out to and beyond 7500 AU from each source, a scenario which is consistent with non-thermal (photo-)desorption from the ice. The observations also illustrate the usefulness of CH3OH as a tracer of energetic input in the form of outflows, where methanol is sputtered from the grain surfaces. Finally, the observations provide further evidence of CH3OH formation through CO hydrogenation proceeding on grain surfaces in low-mass envelopes.Comment: Accepted for publication in A&A

BCR-ABL activity and its response to drugs can be determined in CD34+ CML stem cells by CrkL phosphorylation status using flow cytometry.

In chronic myeloid leukaemia, CD34(+) stem/progenitor cells appear resistant to imatinib mesylate (IM) in vitro and in vivo. To investigate the underlying mechanism(s) of IM resistance, it is essential to quantify Bcr-Abl kinase status at the stem cell level. We developed a flow cytometry method to measure CrkL phosphorylation (P-CrkL) in samples with <10(4) cells. The method was first validated in wild-type (K562) and mutant (BAF3) BCR-ABL(+) as well as BCR-ABL(-) (HL60) cell lines. In response to increasing IM concentration, there was a linear reduction in P-CrkL, which was Bcr-Abl specific and correlated with known resistance. The results were comparable to those from Western blotting. The method also proved to be reproducible with small samples of normal and Ph(+) CD34(+) cells and was able to discriminate between Ph(-), sensitive and resistant Ph(+) cells. This assay should now enable investigators to unravel the mechanism(s) of IM resistance in stem cells

Linking ice and gas in the Serpens low-mass star-forming region

The interaction between dust, ice, and gas during the formation of stars produces complex organic molecules. While observations indicate that several species are formed on ice-covered dust grains and are released into the gas phase, the exact chemical interplay between solid and gas phases and their relative importance remain unclear. Our goal is to study the interplay in regions of low-mass star formation through ice- and gas-mapping and by directly measuring gas-to-ice ratios. This provides constraints on the routes that lead to the chemical complexity that is observed in both phases. We present observations of gas-phase methanol (CH$_3$OH) and carbon monoxide at 1.3 mm towards ten low-mass young protostars in the Serpens SVS4 cluster from the SubMillimeter Array and the Atacama Pathfinder EXperiment telescope. We used archival data from the Very Large Telescope to derive abundances of ice H$_2$O, CO, and CH$_3$OH towards the same region. Finally, we constructed gas-ice maps of SVS4 and directly measured CO and CH$_3$OH gas-to-ice ratios. The CH$_3$OH gas-to-ice ratio agrees with values that were previously reported for embedded Class 0/I low-mass protostars. The CO gas-maps trace an extended gaseous component that is not sensitive to the effect of freeze-out. We find that there is no straightforward correlation between CO and CH$_3$OH gas with their ice counterparts in the cluster. This is likely related to the complex morphology of SVS4: the Class 0 protostar SMM4 and its envelope lie in the vicinity, and the outflow associated with SMM4 intersects the cluster. This study serves as a pathfinder for future observations with ALMA and the James Webb Space Telescope that will provide high-sensitivity gas-ice maps of molecules more complex than methanol. Such comparative maps will be essential to constrain the chemical routes that regulate the chemical complexity in star-forming regions.Comment: 25 pages, 20 figures, accepted for publication by A&

Rhythm in the speech of a person with right hemisphere damage: Applying the pairwise variability index

Although several aspects of prosody have been studied in speakers with right hemisphere damage (RHD), rhythm remains largely uninvestigated. This study compares the rhythm of an Australian English speaker with right hemisphere damage (due to a stroke, but with no concomitant dysarthria) to that of a neurologically unimpaired individual. The speakers' rhythm is compared using the pairwise variability index (PVI) which allows for an acoustic characterization of rhythm by comparing the duration of successive vocalic and intervocalic intervals. A sample of speech from a structured interview between a speech and language therapist and each participant was analysed. Previous research has shown that speakers with RHD may have difficulties with intonation production, and therefore it was hypothesized that there may also be rhythmic disturbance. Results show that the neurologically normal control uses a similar rhythm to that reported for British English (there are no previous studies available for Australian English), whilst the speaker with RHD produces speech with a less strongly stress-timed rhythm. This finding was statistically significant for the intervocalic intervals measured (t(8) = 4.7, p < .01), and suggests that some aspects of prosody may be right lateralized for this speaker. The findings are discussed in relation to previous findings of dysprosody in RHD populations, and in relation to syllable-timed speech of people with other neurological conditions

ESO Imaging Survey: Infrared Deep Public Survey

This paper presents new J and Ks data obtained from observations conducted at the ESO 3.5m New Technology Telescope using the SOFI camera. These data were taken as part of the ESO Imaging Survey Deep Public Survey (DPS) and significantly extend the earlier optical/infrared EIS-DEEP survey presented in a previous paper. The DPS-IR survey comprises two observing strategies: shallow Ks observations providing nearly full coverage of pointings with complementary multi-band optical data and deeper J and Ks observations of the central parts of these fields. The DPS-IR survey provides a coverage of roughly 2.1 square degrees in Ks with 0.63 square degrees to fainter magnitudes and also covered in J, over three independent regions of the sky. The goal of the present paper is to describe the observations, the data reduction procedures, and to present the final survey products. The astrometric solution with an estimated accuracy of <0.15" is based on the USNO catalog. The final stacked images presented here number 89 and 272, in J and Ks, respectively, the latter reflecting the larger surveyed area. The J and Ks images were taken with a median seeing of 0.77" and 0.8". The images reach a median 5sigma limiting magnitude of J_AB~23.06 in an aperture of 2", while the corresponding limiting magnitude in Ks_AB is ~21.41 and ~22.16 mag for the shallow and deep strategies. Overall, the observed limiting magnitudes are consistent with those originally proposed. The quality of the data has been assessed by comparing the measured magnitude of sources at the bright end directly with those reported by the 2MASS survey and at the faint end by comparing the counts of galaxies and stars with those of other surveys to comparable depth and to model predictions. The final science-grade catalogs and images are available at CDS.Comment: Accepted for publication in A&A, 14 pages, 8 figures, a full resolution version of the paper is available from http://www.astro.ku.dk/~lisbeth/eisdata/papers/5019.pd

SCUBA Mapping of Spitzer c2d Small Clouds and Cores

We present submillimeter observations of dark clouds that are part of the Spitzer Legacy Program, From Molecular Cores to Planet-Forming Disks (c2d). We used the Submillimetre Common User's Bolometer Array to map the regions observed by Spitzer by the c2d program to create a census of dense molecular cores including data from the infrared to the submillimeter. In this paper, we present the basic data from these observations: maps, fluxes, and source attributes. We also show data for an object just outside the Perseus cloud that was serendipitously observed in our program. We propose that this object is a newly discovered, evolved protostar.Comment: 37 pages, accepted to The Astronomical Journa