Quantitative proteomics in resected renal cancer tissue for biomarker discovery and profiling

<b>Background:</b>  Proteomics-based approaches for biomarker discovery are promising strategies used in cancer research. We present state-of-art label-free quantitative proteomics method to assess proteome of renal cell carcinoma (RCC) compared with noncancer renal tissues.<p></p> <b>Methods:</b>  Fresh frozen tissue samples from eight primary RCC lesions and autologous adjacent normal renal tissues were obtained from surgically resected tumour-bearing kidneys. Proteins were extracted by complete solubilisation of tissues using filter-aided sample preparation (FASP) method. Trypsin digested proteins were analysed using quantitative label-free proteomics approach followed by data interpretation and pathways analysis.<p></p> <b>Results:</b>  A total of 1761 proteins were identified and quantified with high confidence (MASCOT ion score threshold of 35 and P-value <0.05). Of these, 596 proteins were identified as differentially expressed between cancer and noncancer tissues. Two upregulated proteins in tumour samples (adipose differentiation-related protein and Coronin 1A) were further validated by immunohistochemistry. Pathway analysis using IPA, KOBAS 2.0, DAVID functional annotation and FLink tools showed enrichment of many cancer-related biological processes and pathways such as oxidative phosphorylation, glycolysis and amino acid synthetic pathways.<p></p> <b>Conclusions:<b>  Our study identified a number of differentially expressed proteins and pathways using label-free proteomics approach in RCC compared with normal tissue samples. Two proteins validated in this study are the focus of on-going research in a large cohort of patients.<p></p&gt

Summary and Recommendations from the Review of LTI and CNGS Controls held at CERN on July 10th, 2001

The Review of LHC Transfer lines and Injection (LTI) and CERN Neutrinos to Gran Sasso (CNGS) Controls was the first overview of requirements and preparations for the control of these facilities. Participants were asked to outline work that was already underway or planned in order to build an account of activities and responsibilities. The control of CNGS facilities downstream of the primary target was not included

Experience with the LHC beam dump post-operational checks system

After each beam dump in the LHC automatic post-operational checks are made to guarantee that the last beam dump has been executed correctly and that the system can be declared to be ‘as good as new’ before the next injection is allowed. The analysis scope comprises the kicker waveforms, redundancy in kicker generator signal paths and different beam instrumentation measurements. This paper describes the implementation and the operational experience of the internal and external post-operational checks of the LHC beam dumping system during the commissioning of the LHC without beam and during the first days of beam operation

Beam commissioning of injection into the LHC

The LHC injection tests and first turn beam commissioning took place in late summer 2008, after detailed and thorough preparation. The beam commissioning of the downstream sections of the SPS-to-LHC transfer lines and the LHC injection systems is described. The details of the aperture measurements in the injection regions are presented together with the performance of the injection related equipment. The measured injection stability is compared to the expectations. The operational issues encountered are discussed

myTunes: Digital music library users and their self-images

This investigation explored the relationships between individuals’ self-images and their interactions with their digital music collections via the commercially predominant program iTunes. Sixty-nine university students completed an internet-based Musical Self-Images Questionnaire (MSIQ) along with a series of questions concerning their iTunes collections. The majority of participants were highly engaged with music, regardless of their varied musical backgrounds. Factor analysis of the MSIQ data revealed two distinct self-image groups, which we label as ‘musical practitioner’ (linking ‘overall musician’, ‘performer’, ‘composer’, ‘teacher’, and ‘listener’) and ‘music consumer’ (linking ‘listener’, ‘fan’, and ‘technology user’). Participants used an average of seven attributes to categorize their music, and most consistently used one in particular to sort their collections. Those who rated themselves as higher level performers and fans used the playlist function (which involves compiling sequences of selected tracks) more often than those with lower self-ratings on those scales

Strange prospects for LHC energies

Strange quark and hadron production will be studied at the Large Hadron Collider (LHC) energies in order to explore the properties of both pp and heavy-ion collisions. The ALICE experiment will be specifically efficient in the strange sector with the identification of baryons and mesons over a wide range of transverse momentum. Dedicated measurements are proposed for investigating chemical equilibration and bulk properties. Strange particles can also help to probe kinematical regions where hard processes and pQCD dominate. We try to anticipate here several ALICE analyses to be performed as the first Pb--Pb and pp data will be available.Comment: 5 pages, 2 figures. To appear in the proceedings of Hot Quarks 2006, Villasimius, Italy, 15-20 May 200

Probabilistic classification of acute myocardial infarction from multiple cardiac markers

Logistic regression and Gaussian mixture model (GMM) classifiers have been trained to estimate the probability of acute myocardial infarction (AMI) in patients based upon the concentrations of a panel of cardiac markers. The panel consists of two new markers, fatty acid binding protein (FABP) and glycogen phosphorylase BB (GPBB), in addition to the traditional cardiac troponin I (cTnI), creatine kinase MB (CKMB) and myoglobin. The effect of using principal component analysis (PCA) and Fisher discriminant analysis (FDA) to preprocess the marker concentrations was also investigated. The need for classifiers to give an accurate estimate of the probability of AMI is argued and three categories of performance measure are described, namely discriminatory ability, sharpness, and reliability. Numerical performance measures for each category are given and applied. The optimum classifier, based solely upon the samples take on admission, was the logistic regression classifier using FDA preprocessing. This gave an accuracy of 0.85 (95% confidence interval: 0.78–0.91) and a normalised Brier score of 0.89. When samples at both admission and a further time, 1–6 h later, were included, the performance increased significantly, showing that logistic regression classifiers can indeed use the information from the five cardiac markers to accurately and reliably estimate the probability AMI

Photoelectron diffraction investigation of the structure of the clean TiO2(110)(1×1) surface

The surface relaxations of the rutile TiO2(110)(1×1) clean surface have been determined by O 1 s and Ti 2p3∕2 scanned-energy mode photoelectron diffraction. The results are in excellent agreement with recent low-energy electron diffraction (LEED) and medium energy ion scattering (MEIS) results, but in conflict with the results of some earlier investigations including one by surface x-ray diffraction. In particular, the bridging O atoms at the surface are found to relax outward, rather than inward, relative to the underlying bulk. Combined with the recent LEED and MEIS results, a consistent picture of the structure of this surface is provided. While the results of the most recent theoretical total-energy calculations are qualitatively consistent with this experimental consensus, significant quantitative differences remain

Large-scale variations in ozone and polar stratospheric clouds measured with airborne lidar during formation of the 1987 ozone hole over Antarctica

A joint field experiment between NASA and NOAA was conducted during August to September 1987 to obtain in situ and remote measurements of key gases and aerosols from aircraft platforms during the formation of the ozone (O3) hole over Antarctica. The ER-2 (advanced U-2) and DC-8 aircraft from the NASA Ames Research Center were used in this field experiment. The NASA Langley Research Center's airborne differential absorption lidar (DIAL) system was operated from the DC-8 to obtain profiles of O3 and polar stratospheric clouds in the lower stratosphere during long-range flights over Antarctica from August 28 to September 29, 1987. The airborne DIAL system was configured to transmit simultaneously four laser wavelengths (301, 311, 622, and 1064 nm) above the DC-8 for DIAL measurements of O3 profiles between 11 to 20 km ASL (geometric altitude above sea level) and multiple wavelength aerosol backscatter measurements between 11 to 24 km ASL. A total of 13 DC-8 flights were made over Antarctica with 2 flights reaching the South Pole. Polar stratospheric clouds (PSC's) were detected in multiple thin layers in the 11 to 21 km ASL altitude range with each layer having a typical thickness of less than 1 km. Two types of PSC's were found based on aerosol backscattering ratios: predominantly water ice clouds (type 2) and clouds with scattering characteristics consistent with binary solid nitric acid/water clouds (type 1). Large-scale cross sections of O3 distributions were obtained. The data provides additional information about a potentially important transport mechanism that may influence the O3 budget inside the vortex. There is also some evidence that strong low pressure systems in the troposphere are associated with regions of lower stratospheric O3. This paper discusses the spatial and temporal variations of O3 inside and outside the polar vortex region during the development of the O3 hole and relates these data to other measurements obtained during this field experiment

The local adsorption structure of benzene on Si(001)-(2 × 1): a photoelectron diffraction investigation

Scanned-energy mode C 1s photoelectron diffraction has been used to investigate the local adsorption geometry of benzene on Si(001) at saturation coverage and room temperature. The results show that two different local bonding geometries coexist, namely the 'standard butterfly' (SB) and 'tilted bridge' (TB) forms, with a composition of 58 ± 29% of the SB species. Detailed structural parameter values are presented for both species including Si–C bond lengths. On the basis of published measurements of the rate of conversion of the SB to the TB form on this surface, we estimate that the timescale of our experiment is sufficient for achieving equilibrium, and in this case our results indicate that the difference in the Gibbs free energy of adsorption, ΔG(TB)−ΔG(SB), is in the range −0.023 to +0.049 eV. We suggest, however, that the relative concentration of the two species may also be influenced by a combination of steric effects influencing the kinetics, and a sensitivity of the adsorption energies of the adsorbed SB and TB forms to the nature of the surrounding benzene molecules