3,985 research outputs found
A combined approach to data mining of textual and structured data to identify cancer-related targets
BACKGROUND: We present an effective, rapid, systematic data mining approach for identifying genes or proteins related to a particular interest. A selected combination of programs exploring PubMed abstracts, universal gene/protein databases (UniProt, InterPro, NCBI Entrez), and state-of-the-art pathway knowledge bases (LSGraph and Ingenuity Pathway Analysis) was assembled to distinguish enzymes with hydrolytic activities that are expressed in the extracellular space of cancer cells. Proteins were identified with respect to six types of cancer occurring in the prostate, breast, lung, colon, ovary, and pancreas. RESULTS: The data mining method identified previously undetected targets. Our combined strategy applied to each cancer type identified a minimum of 375 proteins expressed within the extracellular space and/or attached to the plasma membrane. The method led to the recognition of human cancer-related hydrolases (on average, ~35 per cancer type), among which were prostatic acid phosphatase, prostate-specific antigen, and sulfatase 1. CONCLUSION: The combined data mining of several databases overcame many of the limitations of querying a single database and enabled the facile identification of gene products. In the case of cancer-related targets, it produced a list of putative extracellular, hydrolytic enzymes that merit additional study as candidates for cancer radioimaging and radiotherapy. The proposed data mining strategy is of a general nature and can be applied to other biological databases for understanding biological functions and diseases
Penetrating particle ANalyzer (PAN)
PAN is a scientific instrument suitable for deep space and interplanetary
missions. It can precisely measure and monitor the flux, composition, and
direction of highly penetrating particles (100 MeV/nucleon) in deep
space, over at least one full solar cycle (~11 years). The science program of
PAN is multi- and cross-disciplinary, covering cosmic ray physics, solar
physics, space weather and space travel. PAN will fill an observation gap of
galactic cosmic rays in the GeV region, and provide precise information of the
spectrum, composition and emission time of energetic particle originated from
the Sun. The precise measurement and monitoring of the energetic particles is
also a unique contribution to space weather studies. PAN will map the flux and
composition of penetrating particles, which cannot be shielded effectively,
precisely and continuously, providing valuable input for the assessment of the
related health risk, and for the development of an adequate mitigation
strategy. PAN has the potential to become a standard on-board instrument for
deep space human travel.
PAN is based on the proven detection principle of a magnetic spectrometer,
but with novel layout and detection concept. It will adopt advanced particle
detection technologies and industrial processes optimized for deep space
application. The device will require limited mass (~20 kg) and power (~20 W)
budget. Dipole magnet sectors built from high field permanent magnet Halbach
arrays, instrumented in a modular fashion with high resolution silicon strip
detectors, allow to reach an energy resolution better than 10\% for nuclei from
H to Fe at 1 GeV/n
Design, Implementation and First Measurements with the Medipix Neutron Camera in CMS
The Medipix detector is the first device dedicated to measuring mixed-field
radiation in the CMS cavern and able to distinguish between different particle
types. Medipix2-MXR chips bump bonded to silicon sensors with various neutron
conversion layers developed by the IEAP CTU in Prague were successfully
installed for the 2008 LHC start-up in the CMS experimental and services
caverns to measure the flux of various particle types, in particular neutrons.
They have operated almost continuously during the 2010 run period, and the
results shown here are from the proton run between the beginning of July and
the end of October 2010. Clear signals are seen and different particle types
have been observed during regular LHC luminosity running, and an agreement in
the measured flux rate is found with the simulations. These initial results are
promising, and indicate that these devices have the potential for further and
future LHC and high energy physics applications as radiation monitoring devices
for mixed field environments, including neutron flux monitoring. Further
extensions are foreseen in the near future to increase the performance of the
detector and its coverage for monitoring in CMS.Comment: 15 pages, 16 figures, submitted to JINS
Fluids of hard ellipsoids: Phase diagram including a nematic instability from Percus-Yevick theory
An important aspect of molecular fluids is the relation between orientation
and translation parts of the two-particle correlations. Especially the detailed
knowledge of the influence of orientation correlations is needed to explain and
calculate in detail the occurrence of a nematic phase.
The simplest model system which shows both orientation and translation
correlations is a system of hard ellipsoids. We investigate an isotropic fluid
formed of hard ellipsoids with Percus-Yevick theory.
Solving the Percus-Yevick equations self-consistently in the high density
regime gives a clear criterion for a nematic instability. We calculate in
detail the equilibrium phase diagram for a fluid of hard ellipsoids of
revolution. Our results compare well with Monte Carlo Simulations and density
functional theory.Comment: 7 pages including 4 figure
Hole Hopping Across a Protein-Protein Interface.
We have investigated photoinduced hole hopping in a Pseudomonas aeruginosa azurin mutant Re126WWCuI, where two adjacent tryptophan residues (W124 and W122) are inserted between the CuI center and a Re photosensitizer coordinated to a H126 imidazole (Re = ReI(H126)(CO)3(dmp)+, dmp = 4,7-dimethyl-1,10-phenanthroline). Optical excitation of this mutant in aqueous media (//(CuII)' back ET that occurs over 12 Ă
, in contrast to the 23 Ă
, 120 us step in Re126WWCuI. Importantly, dimerization makes Re126FWCuI photoreactive and, in the case of {Re126WWCuI}2, channels the photoproduced "hole" to the molecule that was not initially photoexcited, thereby shortening the lifetime of ReI(H126)(CO)3(dmpâą-)//CuII. Whereas two adjacent W124 and W122 indoles dramatically enhance CuI->*Re intramolecular multistep ET, the tryptophan quadruplex in {Re126WWCuI}2 does not accelerate intermolecular electron transport; instead, it acts as a hole storage and crossover unit between inter- and intramolecular ET pathways. Irradiation of {Re126WWCuII}2 or {Re126FWCuII}2 also triggers intermolecular *Re////(W122âą+)' intermolecular charge recombination. Our findings shed light on the factors that control interfacial hole/electron hopping in protein complexes and on the role of aromatic amino acids in accelerating long-range electron transport
Constraints on Low-Mass WIMP Interactions on 19F from PICASSO
Recent results from the PICASSO dark matter search experiment at SNOLAB are
reported. These results were obtained using a subset of 10 detectors with a
total target mass of 0.72 kg of 19F and an exposure of 114 kgd. The low
backgrounds in PICASSO allow recoil energy thresholds as low as 1.7 keV to be
obtained which results in an increased sensitivity to interactions from Weakly
Interacting Massive Particles (WIMPs) with masses below 10 GeV/c^2. No dark
matter signal was found. Best exclusion limits in the spin dependent sector
were obtained for WIMP masses of 20 GeV/c^2 with a cross section on protons of
sigma_p^SD = 0.032 pb (90% C.L.). In the spin independent sector close to the
low mass region of 7 GeV/c2 favoured by CoGeNT and DAMA/LIBRA, cross sections
larger than sigma_p^SI = 1.41x10^-4 pb (90% C.L.) are excluded.Comment: 23 pages, 7 figures, to be published in Phys. Lett.
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