Comparability of Microarray Data between Amplified and Non Amplified RNA in Colorectal Carcinoma

Microarray analysis reaches increasing popularity during the investigation of prognostic gene clusters in oncology. The standardisation of technical procedures will be essential to compare various datasets produced by different research groups. In several projects the amount of available tissue is limited. In such cases the preamplification of RNA might be necessary prior to microarray hybridisation. To evaluate the comparability of microarray results generated either by amplified or non amplified RNA we isolated RNA from colorectal cancer samples (stage UICC IV) following tumour tissue enrichment by macroscopic manual dissection (CMD). One part of the RNA was directly labelled and hybridised to GeneChips (HG-U133A, Affymetrix), the other part of the RNA was amplified according to the ?Eberwine? protocol and was then hybridised to the microarrays. During unsupervised hierarchical clustering the samples were divided in groups regarding the RNA pre-treatment and 5.726 differentially expressed genes were identified. Using independent microarray data of 31 amplified vs. 24 non amplified RNA samples from colon carcinomas (stage UICC III) in a set of 50 predictive genes we validated the amplification bias. In conclusion microarray data resulting from different pre-processing regarding RNA pre-amplification can not be compared within one analysis

Light-cone Distribution Amplitudes of the Nucleon and Negative Parity Nucleon Resonances from Lattice QCD

We present the results of a lattice study of light-cone distribution amplitudes (DAs) of the nucleon and negative parity nucleon resonances using two flavors of dynamical (clover) fermions on lattices of different volumes and pion masses down to m_pi = 150 MeV. We find that the three valence quarks in the proton share their momentum in the proportion 37% : 31% : 31%, where the larger fraction corresponds to the u-quark that carries proton helicity, and determine the value of the wave function at the origin in position space, which turns out to be small compared to the existing estimates based on QCD sum rules. Higher-order moments are constrained by our data and are all compatible with zero within our uncertainties. We also calculate the normalization constants of the higher-twist DAs that are related to the distribution of quark angular momentum. Furthermore, we use the variational method and customized parity projection operators to study the states with negative parity. In this way we are able to separate the contributions of the two lowest states that, as we argue, possibly correspond to N*(1535) and a mixture of N*(1650) and the pion-nucleon continuum, respectively. It turns out that the state that we identify with N*(1535) has a very different DA as compared to both the second observed negative parity state and the nucleon, which may explain the difference in the decay patterns of N*(1535) and N*(1650) observed in experiment.Comment: 19 pages, 11 figure

Mars Spacecraft Power System Development Final Report

Development of optimum Mariner spacecraft power system for application to future flyby and orbiter mission

Histotripsy Homogenization of the Prostate: Thresholds for Cavitation Damage of Periprostatic Structures

Background and Purpose: Histotripsy is a noninvasive, pulsed ultrasound technology that produces mechanically homogenized tissue within targeted volumes. Previous work has demonstrated prostatic tissue debulking in a canine model. The aim was to establish safety thresholds by evaluating histologic changes of urinary sphincter, neurovascular bundle (NVB), and rectum after targeted histotripsy treatment of these critical structures. Materials and Methods: Rectum, urinary sphincter, and NVB in five anesthetized canines were targeted for histotripsy treatment (50 total points). Locations received 1k, 10k, or 100k acoustic pulses (4 microsecond, 1-MHz) at a repetition frequency of 500-Hz. Canine subjects were euthanized immediately (2), survived 3 days (1), or 2 weeks (3) after treatment. Prostates, periprostatic tissue, and rectum were harvested and processed for histology. Results: The sphincter was structurally intact with minimal muscle fiber disruption even after 100k pulses (n=10). Undamaged nerves, arteries, and veins of the NVB were seen despite mechanical homogenization of surrounding loose connective tissue (n=19). The rectum, however, exhibited dose-dependent damage (n=20). 1k pulses yielded mild submucosal hemorrhage. 10k pulses resulted in moderate collagen disruption and focal mucosal homogenization. 100k pulses produced damage to the mucosa and muscularis propria with extensive hemorrhage and collagen disruption. One canine treated with 100k pulses needed early euthanasia (day 3) because of complications from a urine leak. Conclusions: Histotripsy histologic tissue effect varied based on targeted structure with substantial structural preservation of NVB and sphincter. Rectal subclinical damage was apparent after 1k pulses and increased in extent and severity with escalating doses. Future work will include assessment of functional outcomes and refinement of these initial safety thresholds.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90446/1/end-2E2010-2E0648.pd

Incidence and drug treatment of emotional distress after cancer diagnosis : a matched primary care case-control study

Notes This work is published under the standard license to publish agreement. After 12 months the work will become freely available and the license terms will switch to a Creative Commons Attribution-NonCommercial-Share Alike 3.0 Unported License.Peer reviewedPublisher PD

Increasing Resiliency to Natural Hazards—A Strategic Plan for the Multi-Hazards Demonstration Project in Southern California

The U.S. Geological Survey (USGS) is initiating a new project designed to improve resiliency to natural hazards in southern California through the application of science to community decision making and emergency response. The Multi-Hazards Demonstration Project will assist the region’s communities to reduce their risk from natural hazards by directing new and existing research towards the community’s needs, improving monitoring technology, producing innovative products, and improving dissemination of the results. The natural hazards to be investigated in this project include coastal erosion, earthquakes, floods, landslides, tsunamis, and wildfires. Americans are more at risk from natural hazards now than at any other time in our Nation’s history. Southern California, in particular, has one of the Nation’s highest potentials for extreme catastrophic losses due to natural hazards, with estimates of expected losses exceeding $3 billion per year. These losses can only be reduced through the decisions of the southern California community itself. To be effective, these decisions must be guided by the best information about hazards, risk, and the cost-effectiveness of mitigation technologies. The USGS will work with collaborators to set the direction of the research and to create multi-hazard risk frameworks where communities can apply the results of scientific research to their decision-making processes. Partners include state, county, city, and public-lands government agencies, public and private utilities, companies with a significant impact and presence in southern California, academic researchers, the Federal Emergency Management Agency (FEMA), National Oceanic and Atmospheric Administration (NOAA), and local emergency response agencies. Prior to the writing of this strategic plan document, three strategic planning workshops were held in February and March 2006 at the USGS office in Pasadena to explore potential relationships. The goal of these planning sessions was to determine the external organizations’ needs for mitigation efforts before potential natural hazard events, and response efforts during and after the event. On the basis of input from workshop participants, four priority areas were identified for future research to address. They are (1) helping decision makers design planning scenarios, (2) improving upon the mapping of multiple hazards in urban areas, (3) providing real-time information from monitoring networks, and (4) integrating information in a risk and decision-making analysis. Towards this end, short-term and out-year goals have been outlined with the priorities in mind. First-year goals are (1) to engage the user community to establish the structures and processes for communications and interactions, (2) to develop a program to create scenarios of anticipated disasters, beginning in the first year with a scenario of a southern San Andreas earthquake that triggers secondary hazards, (3) to compile existing datasets of geospatial data, and (4) to target research efforts to support more complete and robust products in future years. Both the first-year and out-year goals have been formulated around a working-group structure that builds on existing research strengths within the USGS. The project is intended to demonstrate how developments in methodology and products can lead to improvement in our management of natural hazards in an urban environment for application across the Nation

The ρ-meson light-cone distribution amplitudes from lattice QCD

We present the results of a lattice study of the normalization constants and second moments of the light-cone distribution amplitudes of longitudinally and transversely polarized $\rho$ mesons. The calculation is performed using two flavors of dynamical clover fermions at lattice spacings between $0.060\,\text{fm}$ and $0.081\,\text{fm}$, different lattice volumes up to $m_\pi L = 6.7$ and pion masses down to $m_\pi=150\,\text{MeV}$. Bare lattice results are renormalized non-perturbatively using a variant of the RI'-MOM scheme and converted to the $\overline{\text{MS}}$ scheme. The necessary conversion coefficients, which are not available in the literature, are calculated. The chiral extrapolation for the relevant decay constants is worked out in detail. We obtain for the ratio of the tensor and vector coupling constants $f_\rho^T/f_\rho^{\vphantom{T}} = 0.629(8)$ and the values of the second Gegenbauer moments $a_2^\parallel = 0.132(27)$ and $a_2^\perp = 0.101(22)$ at the scale $\mu = 2\,\text{GeV}$ for the longitudinally and transversely polarized $\rho$ mesons, respectively. The errors include the statistical uncertainty and estimates of the systematics arising from renormalization. Discretization errors cannot be estimated reliably and are not included. In this calculation the possibility of $\rho\to\pi\pi$ decay at the smaller pion masses is not taken into account