Complete genome sequence of BK polyomavirus subtype Ib-1 detected in a kidney transplant patient with BK viremia using shotgun sequencing

We report here the complete genome sequence of polyomavirus BK subtype Ib-1, isolate AR11, identified in urine from a human kidney transplant recipient with a clinical diagnosis of BK viremia. The AR11 isolate is closely related to reference strain human polyomavirus 1 isolate J2B-2 with 99% identity

Can the United States Afford a “No-Fault” System of Compensation for Medical Injury?

One of the key issues separating US critics of a no-fault alternative to the tort system for compensating victims of medical injury from supporters is its anticipated cost. Results from a study are presented that estimate the costs of a no-fault system, one that is similar to the system now in operation in Sweden, within the context of the US health care system

An acoustic charge transport imager for high definition television applications

The primary goal of this research is to develop a solid-state television (HDTV) imager chip operating at a frame rate of about 170 frames/sec at 2 Megapixels/frame. This imager will offer an order of magnitude improvements in speed over CCD designs and will allow for monolithic imagers operating from the IR to UV. The technical approach of the project focuses on the development of the three basic components of the imager and their subsequent integration. The camera chip can be divided into three distinct functions: (1) image capture via an array of avalanche photodiodes (APD's); (2) charge collection, storage, and overflow control via a charge transfer transistor device (CTD); and (3) charge readout via an array of acoustic charge transport (ACT) channels. The use of APD's allows for front end gain at low noise and low operating voltages while the ACT readout enables concomitant high speed and high charge transfer efficiency. Currently work is progressing towards the optimization of each of these component devices. In addition to the development of each of the three distinct components, work towards their integration and manufacturability is also progressing. The component designs are considered not only to meet individual specifications but to provide overall system level performance suitable for HDTV operation upon integration. The ultimate manufacturability and reliability of the chip constrains the design as well. The progress made during this period is described in detail

An Integrated Circuit for Signal Processing of the AMS RICH Photmultipliers Tubes

An analog integrated circuit has been designed, in a BiCMOS 0.8 micron technology, for the feasability study of the signal processing of the AMS RICH photomultiplier tubes. This low power, three channel gated integrator includes its own gate and no external analog delay is requiered. It processes PMT pulses over a dynamic range of more than 100. A logic output that indicates whether the analog charge has to be considered is provided. This gated integrator is used with a compact DSP based acquisition system in a 132 channels RICH prototype. The charge calibration of each channel is carried out using a LED. The pedestal measurement is performed on activation of a dedicated input. The noise contribution study of the input RC network and amplifiers is presented.Comment: IEEE symp. on Nucl. Sci. and Med. Imaging, Toront

An integrated genomic analysis of lung cancer reveals loss of DUSP4 in EGFR-mutant tumors.

To address the biological heterogeneity of lung cancer, we studied 199 lung adenocarcinomas by integrating genome-wide data on copy number alterations and gene expression with full annotation for major known somatic mutations in this cancer. This showed non-random patterns of copy number alterations significantly linked to EGFR and KRAS mutation status and to distinct clinical outcomes, and led to the discovery of a striking association of EGFR mutations with underexpression of DUSP4, a gene within a broad region of frequent single-copy loss on 8p. DUSP4 is involved in negative feedback control of EGFR signaling, and we provide functional validation for its role as a growth suppressor in EGFR-mutant lung adenocarcinoma. DUSP4 loss also associates with p16/CDKN2A deletion and defines a distinct clinical subset of lung cancer patients. Another novel observation is that of a reciprocal relationship between EGFR and LKB1 mutations. These results highlight the power of integrated genomics to identify candidate driver genes within recurrent broad regions of copy number alteration and to delineate distinct oncogenetic pathways in genetically complex common epithelial cancers

An Acoustic Charge Transport Imager for High Definition Television Applications: Reliability Modeling and Parametric Yield Prediction of GaAs Multiple Quantum Well Avalanche Photodiodes

Reliability modeling and parametric yield prediction of GaAs/AlGaAs multiple quantum well (MQW) avalanche photodiodes (APDs), which are of interest as an ultra-low noise image capture mechanism for high definition systems, have been investigated. First, the effect of various doping methods on the reliability of GaAs/AlGaAs multiple quantum well (MQW) avalanche photodiode (APD) structures fabricated by molecular beam epitaxy is investigated. Reliability is examined by accelerated life tests by monitoring dark current and breakdown voltage. Median device lifetime and the activation energy of the degradation mechanism are computed for undoped, doped-barrier, and doped-well APD structures. Lifetimes for each device structure are examined via a statistically designed experiment. Analysis of variance shows that dark-current is affected primarily by device diameter, temperature and stressing time, and breakdown voltage depends on the diameter, stressing time and APD type. It is concluded that the undoped APD has the highest reliability, followed by the doped well and doped barrier devices, respectively. To determine the source of the degradation mechanism for each device structure, failure analysis using the electron-beam induced current method is performed. This analysis reveals some degree of device degradation caused by ionic impurities in the passivation layer, and energy-dispersive spectrometry subsequently verified the presence of ionic sodium as the primary contaminant. However, since all device structures are similarly passivated, sodium contamination alone does not account for the observed variation between the differently doped APDs. This effect is explained by the dopant migration during stressing, which is verified by free carrier concentration measurements using the capacitance-voltage technique

Developmental Basis of Pronephric Defects in Xenopus Body Plan Phenotypes

AbstractWe have used monoclonal antibodies that recognize the pronephric tubules or pronephric duct to explore the induction of the embryonic kidney in developing Xenopus embryos. Morphogenesis of the pronephros was examined in UV-ventralized and lithium-dorsalized embryos. We find that the pronephric tubules are present in all but the strongest UV-induced phenotypes, but absent from relatively moderate lithium phenotypes. Interestingly the pronephric duct, which develops from the ventroposterior portion of the pronephric anlage, is missing from more of the mild UV phenotypes than are pronephric tubules. The loss of the capacity to form pronephroi in UV-ventralized embryos is caused by the loss of tissues capable of inducing the pronephric mesoderm, as marginal zone explants from ventralized embryos are still competent to respond to pronephric-inductive signals. Explant recombination experiments indicate that the tissue responsible for both the loss of pronephroi in UV-ventralized embryos and the induction of pronephroi during normal development is the anterior somites. The absence of pronephroi in relatively mild lithium phenotypes has a developmental basis different from that of the UV phenotype, as explants from lithium-treated embryos are effective inducers of pronephroi in recombinants with competent mesoderm, even though they themselves do not form pronephroi in isolation. Together these data indicate that dorsal tissues, especially the anterior somites, are responsible for the establishment of the intermediate mesoderm and the induction of the embryonic kidneys and that even mild dorsalization destroys the capacity to form cells competent to receive this signal

Thymoglobulin Induction Dosing Strategies in a Low-Risk Kidney Transplant Population: Three or Four Days?

The optimal dose and duration of rabbit antithymocyte globulin (rATG) induction has not been defined. Methods. We compared the safety and efficacy of 2 dosing strategies, rATG 1.5 mg/kg for 4 days (n = 59) versus 2 mg/kg for 3 days (n = 59), in a retrospective, cohort study. Results. Two-year rejection-free survival was 95% in each group (P = .983). Renal function and infection rates were similar. The incidence of leucopenia was similar, although the 2 mg/kg group was more likely to be thrombocytopenic on day 2 (4% versus 28%, P = .04). Length of stay tended to be longer for the 1.5 mg/kg group (6.0 ± 3.7 versus 5.1 ± 1.9 days P = .104). A cost savings of $920 per patient for rATG were seen in the 2 mg/kg group (P = .122). Conclusions. Shorter, more intense dosing of rATG is safe and effective. The 3-day dose strategy resulted in a clinically shorter length of stay and may result in cost savings

drawProteins: a Bioconductor/R package for reproducible and programmatic generation of protein schematics

Protein schematics are valuable for research, teaching and knowledge communication. However, the tools used to automate the process are challenging. The purpose of the drawProteins package is to enable the generation of schematics of proteins in an automated fashion that can integrate with the Bioconductor/R suite of tools for bioinformatics and statistical analysis. Using UniProt accession numbers, the package uses the UniProt API to get the features of the protein from the UniProt database. The features are assembled into a data frame and visualized using adaptations of the ggplot2 package. Visualizations can be customised in many ways including adding additional protein features information from other data frames, altering colors and protein names and adding extra layers using other ggplot2 functions. This can be completed within a script that makes the workflow reproducible and sharable