6,367 research outputs found
A protein-based set of reference markers for liver tissues and hepatocellular carcinoma
Background: During the last decade, investigations have focused on revealing genes or proteins that are involved in HCC carcinogenesis using either genetic or proteomic techniques. However, these studies are overshadowed by a lack of good internal reference standards. The need to identify "housekeeping" markers, whose expression is stable in various experimental and clinical conditions, is therefore of the utmost clinical relevance in quantitative studies. This is the first study employed 2-DE analysis to screen for potential reference markers and aims to correlate the abundance of these proteins with their level of transcript expression. Methods: A Chinese cohort of 224 liver tissues samples (105 cancerous, 103 non-tumourous cirrhotic, and 16 normal) was profiled using 2-DE analysis. Expression of the potential reference markers was confirmed by western blot, immunohistochemistry and real-time quantitative PCR. geNorm algorithm was employed for gene stability measure of the identified reference markers. Results: The expression levels of three protein markers beta-actin (ACTB), heat shock protein 60 (HSP60), and protein disulphide isomerase (PDI) were found to be stable using p-values (p > 0.99) as a ranking tool in all 224 human liver tissues examined by 2-DE analysis. Of high importance, ACTB and HSP 60 were successfully validated at both protein and mRNA levels in human hepatic tissues by western blot, immunohistochemistry and real-time quantitative PCR. In addition, no significant correlation of these markers with any clinicopathological features of HCC and cirrhosis was found. Gene stability measure of these two markers with other conventionally applied housekeeping genes was assessed by the geNorm algorithm, which ranked ACTB and HSP60 as the most stable genes among this cohort of clinical samples. Conclusion: Our findings identified 2 reference markers that exhibited stable expression across human liver tissues with different conditions thus should be regarded as reliable reference moieties for normalisation of gene and protein expression in clinical research employing human hepatic tissues. © 2009 Sun et al; licensee BioMed Central Ltd.published_or_final_versio
Evidence for Two Superconducting Gaps in
We have measured the Raman spectra of polycrystalline MgB from 25 {\cm}
to 1200 {\cm}. When the temperature was decreased below the superconducting
transition temperature , we observed a superconductivity-induced
redistribution in the electronic Raman continuum. Two pair-breaking peaks
appear in the spectra, suggesting the presence of two superconducting gaps.
Furthermore, we have analyzed the measured spectra using a quasi
two-dimensional model in which two s-wave superconducting gaps open on two
sheets of Fermi surface. For the gap values we have obtained (2.7 meV) and (6.2 meV). Our results suggest
that a conventional phonon-mediated pairing mechanism occurs in the planar
boron bands and is responsible for the superconductivity of MgB.Comment: 3 figure
A glassy contribution to the heat capacity of hcp He solids
We model the low-temperature specific heat of solid He in the hexagonal
closed packed structure by invoking two-level tunneling states in addition to
the usual phonon contribution of a Debye crystal for temperatures far below the
Debye temperature, . By introducing a cutoff energy in the
two-level tunneling density of states, we can describe the excess specific heat
observed in solid hcp He, as well as the low-temperature linear term in the
specific heat. Agreement is found with recent measurements of the temperature
behavior of both specific heat and pressure. These results suggest the presence
of a very small fraction, at the parts-per-million (ppm) level, of two-level
tunneling systems in solid He, irrespective of the existence of
supersolidity.Comment: 11 pages, 4 figure
Functional emulation of high resolution tsunami modelling over Cascadia
he rarity of tsunamis impels the scientific community to rely on numerical simulation for planning and risk assessment purposes because of the low availability of actual data from historic events. Numerical models, also called simulators, typically produce time series of outputs. Due to the large computational cost of such simulators, statistical emulation is required to carry out uncertainty quantification tasks, as emulators efficiently approximate simulators. There is thus a need to create emulators that respect the nature of time series outputs. We introduce here a novel statistical emulation of the input-output dependence of these computer models. We employ the Outer Product Emulator with two enhancements. Functional registration and Functional Principal Components techniques improve the predictions of the emulator. Our phase registration method captures fine variations in amplitude. Smoothness in the time series of outputs is modelled, and we are thus able to select more representative, and more parsimonious, regression functions than a fixed basis method such as a Fourier basis. We apply this approach to the high resolution tsunami wave propagation and coastal inundation for the Cascadia region in the Pacific Northwest. The coseismic representation in this analysis is novel, and more realistic than in previous studies. With the help of the emulator, we can carry out sensitivity analysis of the maximum wave elevation with respect to the source characteristics, and we are able to propagate uncertainties from the source characteristics to wave heights in order to issue probabilistic statements about tsunami hazard for Cascadia
Glide and Superclimb of Dislocations in Solid He
Glide and climb of quantum dislocations under finite external stress,
variation of chemical potential and bias (geometrical slanting) in Peierls
potential are studied by Monte Carlo simulations of the effective string model.
We treat on unified ground quantum effects at finite temperatures . Climb at
low is assisted by superflow along dislocation core -- {\it superclimb}.
Above some critical stress avalanche-type creation of kinks is found. It is
characterized by hysteretic behavior at low . At finite biases gliding
dislocation remains rough even at lowest -- the behavior opposite to
non-slanted dislocations. In contrast to glide, superclimb is characterized by
quantum smooth state at low temperatures even for finite bias. In some
intermediate -range giant values of the compressibility as well as
non-Luttinger type behavior of the core superfluid are observed.Comment: Updated version submitted to JLTP as QFS2010 proceedings; 11 pages, 6
figure
NIKA: A millimeter-wave kinetic inductance camera
Current generation millimeter wavelength detectors suffer from scaling limits
imposed by complex cryogenic readout electronics. To circumvent this it is
imperative to investigate technologies that intrinsically incorporate strong
multiplexing. One possible solution is the kinetic inductance detector (KID).
In order to assess the potential of this nascent technology, a prototype
instrument optimized for the 2 mm atmospheric window was constructed. Known as
the N\'eel IRAM KIDs Array (NIKA), it was recently tested at the Institute for
Millimetric Radio Astronomy (IRAM) 30-meter telescope at Pico Veleta, Spain.
The measurement resulted in the imaging of a number of sources, including
planets, quasars, and galaxies. The images for Mars, radio star MWC349, quasar
3C345, and galaxy M87 are presented. From these results, the optical NEP was
calculated to be around WHz. A factor of 10
improvement is expected to be readily feasible by improvements in the detector
materials and reduction of performance-degrading spurious radiation.Comment: Accepted for publication in Astronomy & Astrophysic
Quantum Monte Carlo calculations of the one-body density matrix and excitation energies of silicon
Quantum Monte Carlo (QMC) techniques are used to calculate the one-body
density matrix and excitation energies for the valence electrons of bulk
silicon. The one-body density matrix and energies are obtained from a
Slater-Jastrow wave function with a determinant of local density approximation
(LDA) orbitals. The QMC density matrix evaluated in a basis of LDA orbitals is
strongly diagonally dominant. The natural orbitals obtained by diagonalizing
the QMC density matrix resemble the LDA orbitals very closely. Replacing the
determinant of LDA orbitals in the wave function by a determinant of natural
orbitals makes no significant difference to the quality of the wave function's
nodal surface, leaving the diffusion Monte Carlo energy unchanged. The Extended
Koopmans' Theorem for correlated wave functions is used to calculate excitation
energies for silicon, which are in reasonable agreement with the available
experimental data. A diagonal approximation to the theorem, evaluated in the
basis of LDA orbitals, works quite well for both the quasihole and
quasielectron states. We have found that this approximation has an advantageous
scaling with system size, allowing more efficient studies of larger systems.Comment: 13 pages, 4 figures. To appear in Phys. Rev.
Sensitive detection of colorectal cancer in peripheral blood by septin 9 DNA methylation assay
BACKGROUND: Colorectal cancer (CRC) is the second leading cause of cancer deaths despite the fact that detection of this cancer in early stages results in over 90% survival rate. Currently less than 45% of at-risk individuals in the US are screened regularly, exposing a need for better screening tests. We performed two case-control studies to validate a blood-based test that identifies methylated DNA in plasma from all stages of CRC. METHODOLOGY/PRINCIPAL FINDINGS: Using a PCR assay for analysis of Septin 9 (SEPT9) hypermethylation in DNA extracted from plasma, clinical performance was optimized on 354 samples (252 CRC, 102 controls) and validated in a blinded, independent study of 309 samples (126 CRC, 183 controls). 168 polyps and 411 additional disease controls were also evaluated. Based on the training study SEPT9-based classification detected 120/252 CRCs (48%) and 7/102 controls (7%). In the test study 73/126 CRCs (58%) and 18/183 control samples (10%) were positive for SEPT9 validating the training set results. Inclusion of an additional measurement replicate increased the sensitivity of the assay in the testing set to 72% (90/125 CRCs detected) while maintaining 90% specificity (19/183 for controls). Positive rates for plasmas from the other cancers (11/96) and non-cancerous conditions (41/315) were low. The rate of polyp detection (>1 cm) was approximately 20%. CONCLUSIONS/SIGNIFICANCE: Analysis of SEPT9 DNA methylation in plasma represents a straightforward, minimally invasive method to detect all stages of CRC with potential to satisfy unmet needs for increased compliance in the screening population. Further clinical testing is warranted
The Green Bank Northern Celestial Cap Pulsar Survey - I: Survey Description, Data Analysis, and Initial Results
We describe an ongoing search for pulsars and dispersed pulses of radio
emission, such as those from rotating radio transients (RRATs) and fast radio
bursts (FRBs), at 350 MHz using the Green Bank Telescope. With the Green Bank
Ultimate Pulsar Processing Instrument, we record 100 MHz of bandwidth divided
into 4,096 channels every 81.92 . This survey will cover the entire sky
visible to the Green Bank Telescope (, or 82% of the sky)
and outside of the Galactic Plane will be sensitive enough to detect slow
pulsars and low dispersion measure (30 ) millisecond
pulsars (MSPs) with a 0.08 duty cycle down to 1.1 mJy. For pulsars with a
spectral index of 1.6, we will be 2.5 times more sensitive than previous and
ongoing surveys over much of our survey region. Here we describe the survey,
the data analysis pipeline, initial discovery parameters for 62 pulsars, and
timing solutions for 5 new pulsars. PSR J02145222 is an MSP in a long-period
(512 days) orbit and has an optical counterpart identified in archival data.
PSR J06365129 is an MSP in a very short-period (96 minutes) orbit with a
very low mass companion (8 ). PSR J06455158 is an isolated MSP
with a timing residual RMS of 500 ns and has been added to pulsar timing array
experiments. PSR J14347257 is an isolated, intermediate-period pulsar that
has been partially recycled. PSR J18164510 is an eclipsing MSP in a
short-period orbit (8.7 hours) and may have recently completed its spin-up
phase.Comment: 18 pages, 10 figures, 5 tables, accepted by Ap
Defects and glassy dynamics in solid He-4: Perspectives and current status
We review the anomalous behavior of solid He-4 at low temperatures with
particular attention to the role of structural defects present in solid. The
discussion centers around the possible role of two level systems and structural
glassy components for inducing the observed anomalies. We propose that the
origin of glassy behavior is due to the dynamics of defects like dislocations
formed in He-4. Within the developed framework of glassy components in a solid,
we give a summary of the results and predictions for the effects that cover the
mechanical, thermodynamic, viscoelastic, and electro-elastic contributions of
the glassy response of solid He-4. Our proposed glass model for solid He-4 has
several implications: (1) The anomalous properties of He-4 can be accounted for
by allowing defects to freeze out at lowest temperatures. The dynamics of solid
He-4 is governed by glasslike (glassy) relaxation processes and the
distribution of relaxation times varies significantly between different
torsional oscillator, shear modulus, and dielectric function experiments. (2)
Any defect freeze-out will be accompanied by thermodynamic signatures
consistent with entropy contributions from defects. It follows that such
entropy contribution is much smaller than the required superfluid fraction, yet
it is sufficient to account for excess entropy at lowest temperatures. (3) We
predict a Cole-Cole type relation between the real and imaginary part of the
response functions for rotational and planar shear that is occurring due to the
dynamics of defects. Similar results apply for other response functions. (4)
Using the framework of glassy dynamics, we predict low-frequency yet to be
measured electro-elastic features in defect rich He-4 crystals. These
predictions allow one to directly test the ideas and very presence of glassy
contributions in He-4.Comment: 33 pages, 13 figure
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