Gemini Planet Imager Observational Calibrations II: Detector Performance and Calibration

The Gemini Planet Imager is a newly commissioned facility instrument designed to measure the near-infrared spectra of young extrasolar planets in the solar neighborhood and obtain imaging polarimetry of circumstellar disks. GPI's science instrument is an integral field spectrograph that utilizes a HAWAII-2RG detector with a SIDECAR ASIC readout system. This paper describes the detector characterization and calibrations performed by the GPI Data Reduction Pipeline to compensate for effects including bad/hot/cold pixels, persistence, non-linearity, vibration induced microphonics and correlated read noise.Comment: 11 pages, 6 figures. Proceedings of the SPIE, 9147-28

Mesoscale modelling of polyelectrolyte electrophoresis

The electrophoretic behaviour of flexible polyelectrolyte chains ranging from single monomers up to long fragments of hundred repeat units is studied by a mesoscopic simulation approach. Abstracting from the atomistic details of the polyelectrolyte and the fluid, a coarse-grained molecular dynamics model connected to a mesoscopic fluid described by the Lattice Boltzmann approach is used to investigate free-solution electrophoresis. Our study demonstrates the importance of hydrodynamic interactions for the electrophoretic motion of polyelectrolytes and quantifies the influence of surrounding ions. The length-dependence of the electrophoretic mobility can be understood by evaluating the scaling behavior of the effective charge and the effective friction. The perfect agreement of our results with experimental measurements shows that all chemical details and fluid structure can be safely neglected, and a suitable coarse-grained approach can yield an accurate description of the physics of the problem, provided that electrostatic and hydrodynamic interactions between all entities in the system, i.e., the polyelectrolyte, dissociated counterions, additional salt and the solvent, are properly accounted for. Our model is able to bridge the single molecule regime of a few nm up to macromolecules with contour lengths of more than 100 nm, a length scale that is currently not accessible to atomistic simulations.Comment: 23 pages, 9 figures, to be presented at Faraday Discussion 14

Crystal growth of PbTe and (Pb, Sn)Te by the bridgman method and by THM

Synthesis and growth of PbTe and (Pb, Sn)Te single crystals by the Bridgman method and by the Travelling Heater Method (THM) from Te-rich solutions are described. It is to be seen from comparative investigations that seeded THM growth reproducibly provides oriented single-crystalline ingots free of low-angle grain boundaries and with etch pit densities of 8-12 × 104 cm-2. All the materials were p-type with carrier concentrations from 1 to 2 × 1018 cm-3

Automated segmentation of tissue images for computerized IHC analysis

This paper presents two automated methods for the segmentation ofimmunohistochemical tissue images that overcome the limitations of themanual approach aswell as of the existing computerized techniques. The first independent method, based on unsupervised color clustering, recognizes automatically the target cancerous areas in the specimen and disregards the stroma; the second method, based on colors separation and morphological processing, exploits automated segmentation of the nuclear membranes of the cancerous cells. Extensive experimental results on real tissue images demonstrate the accuracy of our techniques compared to manual segmentations; additional experiments show that our techniques are more effective in immunohistochemical images than popular approaches based on supervised learning or active contours. The proposed procedure can be exploited for any applications that require tissues and cells exploration and to perform reliable and standardized measures of the activity of specific proteins involved in multi-factorial genetic pathologie

The Optical Spectrum of the SN 1006 Supernova Remnant Revisited

We present the deepest optical spectrum acquired to date of Balmer-dominated shocks in the NW rim of SN 1006. We detect the broad and narrow components of H-alpha, H-beta and H-gamma and report the first detection of the He I 6678 emission line in this supernova remnant. We may have detected, at the 1.5-sigma level, faint He II 4686 emission. We measure a full width half maximum of 2290 +/- 80 km/s in the broad component H-alpha line, with broad-to-narrow flux ratios of 0.84^+(0.03)_(-0.01) and 0.93^(+0.18)_(-0.16) in H-alpha and H-beta, respectively. To match these observations, our nonradiative shock models require a low degree of electron-proton equilibration at the shock front, T_e/T_p <= 0.07, and a shock speed of 2890 +/- 100 km/s. These results agree well with an earlier analysis of ultraviolet lines from SN 1006. The He I/H-alpha and He I/He II flux ratios also indicate low equilibration. Furthermore, our models match the observations for mostly ionized (~ 90%) preshock H and mostly neutral (>~ 70%) preshock He, respectively. We conclude that the high H ionization fraction cannot be explained by either photoionization from the reverse shock or relic ionization from EUV photons released in the 1006 A.D. supernova. The most plausible explanation appears to be photoionization from the Galactic Lyman continuum.Comment: 7 pages, 7 figures, accepted for publication by Ap

Endothelial Cell-Astrocyte Interactions

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75690/1/j.1749-6632.1988.tb51417.x.pd

Adverse prognostic and predictive significance of low DNA-dependent protein kinase catalytic subunit (DNA-PKcs) expression in early-stage breast cancers

Background: DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a serine threonine kinase belonging to the PIKK family (phosphoinositide 3-kinase-like-family of protein kinase), is a critical component of the non-homologous end joining (NHEJ) pathway required for the repair of DNA double strand breaks. DNA-PKcs may be involved in breast cancer pathogenesis. Methods: We evaluated clinicopathological significance of DNA-PKcs protein expression in 1161 tumours and DNA-PKcs mRNA expression in 1950 tumours. We correlated DNA-PKcs to other markers of aggressive phenotypes, DNA repair, apoptosis and cell cycle regulation. Results: Low DNA-PKcs protein expression was associated with higher tumour grade, higher mitotic index, tumour de-differentiation and tumour type (ps<0.05). Absence of BRCA1, low XRCC1/SMUG1/APE1/Polβ were also more likely in low DNA-PKcs expressing tumours (ps<0.05). Low DNA-PKcs protein expression was significantly associated with worse breast cancer specific survival (BCCS) in univariate and multivariate analysis (ps<0.01). At the mRNA level, low DNA-PKcs was associated with PAM50.Her2 and PAM50.LumA molecular phenotypes (ps<0.01) and poor BCSS. In patients with ER positive tumours who received endocrine therapy, low DNA-PKcs (protein and mRNA) was associated with poor survival. In ER negative patients, low DNA-PKcs mRNA remains significantly associated with adverse outcome. Conclusions: Our study suggests that low DNA-PKcs expression may have prognostic and predictive significance in breast cancers

Quantification of genes and gene transcripts for microbial perchlorate reduction in fixed‐bed bioreactors

Aims:  Optimization of full‐scale, biological perchlorate treatment processes for drinking water would benefit from knowledge of the location and quantity of perchlorate‐reducing bacteria (PRB) and expression of perchlorate‐related genes in bioreactors. The aim of this study was to quantify perchlorate removal and perchlorate‐related genes ( pcrA and cld ) and their transcripts in bioreactors and to determine whether these genes or transcripts could serve as useful biomarkers for perchlorate treatment processes. Methods and Results:  Quantitative PCR (qPCR) assays targeting pcrA and cld were applied to two pilot‐scale, fixed‐bed bioreactors treating perchlorate‐contaminated groundwater. pcrA and cld genes per microgram of DNA were two‐ to threefold higher and three‐ to fourfold higher, respectively, in the bioreactor showing superior perchlorate‐removal performance. In a laboratory‐scale bioreactor, quantities of pcrA and cld genes and transcripts were compared under two distinct performance conditions ( c.  60 and 20% perchlorate removal) for a 5‐min empty bed contact time. cld genes per microgram of DNA were approximately threefold higher and cld transcripts per microgram of RNA were approximately sixfold higher under the higher perchlorate‐removal condition. No differences in pcrA genes or transcripts per microgram of DNA or RNA, respectively, were detected between the c.  60 and 20% perchlorate‐removal conditions, possibly because these assays did not accurately quantify pcrA genes and transcripts in the mixed culture present. Conclusions:  Quantities of cld genes and transcripts per microgram of DNA and RNA, respectively, were found to be higher when perchlorate removal was higher. However, quantities of pcrA and cld genes or transcripts were not found to directly correlate with perchlorate‐removal rates. Significance and Impact of the Study:  To our knowledge, this study represents the first application of qPCR assays to quantify perchlorate‐related genes and transcripts in continuous‐flow bioreactors. The results indicate that cld gene and transcript quantities can provide insights regarding the quantity, location and gene expression of PRB in bioreactors.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90307/1/JAM_5225_sm_FigS1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/90307/2/JAM_5225_sm_FigS2.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/90307/3/j.1365-2672.2011.05225.x.pd

Optimizing end-labeled free-solution electrophoresis by increasing the hydrodynamic friction of the drag-tag

We study the electrophoretic separation of polyelectrolytes of varying lengths by means of end-labeled free-solution electrophoresis (ELFSE). A coarse-grained molecular dynamics simulation model, using full electrostatic interactions and a mesoscopic Lattice Boltzmann fluid to account for hydrodynamic interactions, is used to characterize the drag coefficients of different label types: linear and branched polymeric labels, as well as transiently bound micelles. It is specifically shown that the label's drag coefficient is determined by its hydrodynamic size, and that the drag per label monomer is largest for linear labels. However, the addition of side chains to a linear label offers the possibility to increase the hydrodynamic size, and therefore the label efficiency, without having to increase the linear length of the label, thereby simplifying synthesis. The third class of labels investigated, transiently bound micelles, seems very promising for the usage in ELFSE, as they provide a significant higher hydrodynamic drag than the other label types. The results are compared to theoretical predictions, and we investigate how the efficiency of the ELFSE method can be improved by using smartly designed drag-tags.Comment: 32 pages, 11 figures, submitted to Macromolecule