1,133 research outputs found
Neutron depolarization studies of Pd-Ni-Fe-P alloy
Bulk metallic glasses based on the quaternary alloy Pd-Ni-Fe-P exhibit interesting phase behavior depending on temperature and applied magnetic field. Previous work has suggested that a range of magnetic phases including paramagnetic, superparamagnetic, ferromagnetic and spin glass can be observed in this system. We have applied one dimensional neutron depolarization to explore the correlation of magnetic moments in Pd40Ni22.5Fe17.5P20 alloy as a function of temperature and applied magnetic field. The results provided evidence for correlation lengths of ~ 200 Å. The nature of the correlations and the formation mechanism of the induced ferromagnetic phase are discusse
Real-time PCR based on SYBR-Green I fluorescence: An alternative to the TaqMan assay for a relative quantification of gene rearrangements, gene amplifications and micro gene deletions
BACKGROUND:
Real-time PCR is increasingly being adopted for RNA quantification and genetic analysis. At present the most popular real-time PCR assay is based on the hybridisation of a dual-labelled probe to the PCR product, and the development of a signal by loss of fluorescence quenching as PCR degrades the probe. Though this so-called 'TaqMan' approach has proved easy to optimise in practice, the dual-labelled probes are relatively expensive.
RESULTS:
We have designed a new assay based on SYBR-Green I binding that is quick, reliable, easily optimised and compares well with the published assay. Here we demonstrate its general applicability by measuring copy number in three different genetic contexts; the quantification of a gene rearrangement (T-cell receptor excision circles (TREC) in peripheral blood mononuclear cells); the detection and quantification of GLI, MYC-C and MYC-N gene amplification in cell lines and cancer biopsies; and detection of deletions in the OPA1 gene in dominant optic atrophy.
CONCLUSION:
Our assay has important clinical applications, providing accurate diagnostic results in less time, from less biopsy material and at less cost than assays currently employed such as FISH or Southern blotting
Dynamical aspects of mean field plane rotators and the Kuramoto model
The Kuramoto model has been introduced in order to describe synchronization
phenomena observed in groups of cells, individuals, circuits, etc... We look at
the Kuramoto model with white noise forces: in mathematical terms it is a set
of N oscillators, each driven by an independent Brownian motion with a constant
drift, that is each oscillator has its own frequency, which, in general,
changes from one oscillator to another (these frequencies are usually taken to
be random and they may be viewed as a quenched disorder). The interactions
between oscillators are of long range type (mean field). We review some results
on the Kuramoto model from a statistical mechanics standpoint: we give in
particular necessary and sufficient conditions for reversibility and we point
out a formal analogy, in the N to infinity limit, with local mean field models
with conservative dynamics (an analogy that is exploited to identify in
particular a Lyapunov functional in the reversible set-up). We then focus on
the reversible Kuramoto model with sinusoidal interactions in the N to infinity
limit and analyze the stability of the non-trivial stationary profiles arising
when the interaction parameter K is larger than its critical value K_c. We
provide an analysis of the linear operator describing the time evolution in a
neighborhood of the synchronized profile: we exhibit a Hilbert space in which
this operator has a self-adjoint extension and we establish, as our main
result, a spectral gap inequality for every K>K_c.Comment: 18 pages, 1 figur
Infection with the hepatitis C virus causes viral genotype-specific differences in cholesterol metabolism and hepatic steatosis
Lipids play essential roles in the hepatitis C virus (HCV) life cycle and patients with chronic HCV infection display disordered lipid metabolism which resolves following successful anti-viral therapy. It has been proposed that HCV genotype 3 (HCV-G3) infection is an independent risk factor for hepatocellular carcinoma and evidence suggests lipogenic proteins are involved in hepatocarcinogenesis. We aimed to characterise variation in host lipid metabolism between participants chronically infected with HCV genotype 1 (HCV-G1) and HCV-G3 to identify likely genotype-specific differences in lipid metabolism. We combined several lipidomic approaches: analysis was performed between participants infected with HCV-G1 and HCV-G3, both in the fasting and non-fasting states, and after sustained virological response (SVR) to treatment. Sera were obtained from 112 fasting patients (25% with cirrhosis). Serum lipids were measured using standard enzymatic methods. Lathosterol and desmosterol were measured by gas-chromatography mass spectrometry (MS). For further metabolic insight on lipid metabolism, ultra-performance liquid chromatography MS was performed on all samples. A subgroup of 13 participants had whole body fat distribution determined using in vivo magnetic resonance imaging and spectroscopy. A second cohort of (non-fasting) sera were obtained from HCV Research UK for comparative analyses: 150 treatment naïve patients and 100 non-viraemic patients post-SVR. HCV-G3 patients had significantly decreased serum apoB, non-HDL cholesterol concentrations, and more hepatic steatosis than those with HCV-G1. HCV-G3 patients also had significantly decreased serum levels of lathosterol, without significant reductions in desmosterol. Lipidomic analysis showed lipid species associated with reverse cholesterol transport pathway in HCV-G3. We demonstrated that compared to HCV-G1, HCV-G3 infection is characterised by low LDL cholesterol levels, with preferential suppression of cholesterol synthesis via lathosterol, associated with increasing hepatic steatosis. The genotype-specific lipid disturbances may shed light on genotypic variations in liver disease progression and promotion of hepatocellular cancer in HCV-G3
Infection with the hepatitis C virus causes viral genotype-specific differences in cholesterol metabolism and hepatic steatosis
Background: Lipids play essential roles in the hepatitis C virus (HCV) life cycle and patients with chronic HCV infection display disordered lipid metabolism which resolves following successful anti-viral therapy. It has been proposed that HCV genotype 3 (HCV-G3) infection is an independent risk factor for hepatocellular carcinoma and evidence suggests lipogenic proteins are involved in hepatocarcinogenesis. Aims: We aimed to characterise variation in host lipid metabolism between participants chronically infected with HCV genotype 1 (HCV-G1) and HCV-G3 to identify likely genotype-specific differences in lipid metabolism. Methods: We combined several lipidomic approaches: analysis was performed between participants infected with HCV-G1 and HCV-G3, both in the fasting and non-fasting states, and after sustained virological response (SVR) to treatment. Sera were obtained from 112 fasting patients (25% with cirrhosis). Serum lipids were measured using standard enzymatic methods. Lathosterol and desmosterol were measured by gas-chromatography mass spectrometry (MS). For further metabolic insight on lipid metabolism, ultra-performance liquid chromatography MS was performed on all samples. A subgroup of 13 participants had whole body fat distribution determined using in vivo magnetic resonance imaging and spectroscopy. A second cohort of (non-fasting) sera were obtained from HCV Research UK for comparative analyses: 150 treatment naïve patients and 100 non-viraemic patients post-SVR. Results: HCV-G3 patients had significantly decreased serum apoB, non-HDL cholesterol concentrations, and more hepatic steatosis than those with HCV-G1. HCV-G3 patients also had significantly decreased serum levels of lathosterol, without significant reductions in desmosterol. Lipidomic analysis showed lipid species associated with reverse cholesterol transport pathway in HCV-G3. Conclusions: We demonstrated that compared to HCV-G1, HCV-G3 infection is characterised by low LDL cholesterol levels, with preferential suppression of cholesterol synthesis via lathosterol, associated with increasing hepatic steatosis. The genotype-specific lipid disturbances may shed light on genotypic variations in liver disease progression and promotion of hepatocellular cancer in HCV-G3
Chaos in a double driven dissipative nonlinear oscillator
We propose an anharmonic oscillator driven by two periodic forces of
different frequencies as a new time-dependent model for investigating quantum
dissipative chaos. Our analysis is done in the frame of statistical ensemble of
quantum trajectories in quantum state diffusion approach. Quantum dynamical
manifestation of chaotic behavior, including the emergence of chaos, properties
of strange attractors, and quantum entanglement are studied by numerical
simulation of ensemble averaged Wigner function and von Neumann entropy.Comment: 9 pages, 18 figure
Dissipation and noise in adiabatic quantum pumps
We investigate the distribution function, the heat flow and the noise
properties of an adiabatic quantum pump for an arbitrary relation of pump
frequency and temperature. To achieve this we start with the
scattering matrix approach for ac-transport. This approach leads to expressions
for the quantities of interest in terms of the side bands of particles exiting
the pump. The side bands correspond to particles which have gained or lost a
modulation quantum . We find that our results for the pump
current, the heat flow and the noise can all be expressed in terms of a
parametric emissivity matrix. In particular we find that the current
cross-correlations of a multiterminal pump are directly related a to a
non-diagonal element of the parametric emissivity matrix. The approach allows a
description of the quantum statistical correlation properties (noise) of an
adiabatic quantum pump
<i>Pseudomonas aeruginosa</i> intensive care unit outbreak:winnowing of transmissions with molecular and genomic typing
Bioinformatics and computational biology analyses were supported by the University of St Andrews Bioinformatics Unit which is funded by a Wellcome Trust ISSF award [grant 097831/Z/11/Z]. BJP, KO, MP, MTGH, GP and SHG are funded by the Chief Scientist Office through the Scottish Infection Research Network, a part of the SHAIPI consortium grant reference number SIRN/10.Background: Pseudomonas aeruginosa healthcare outbreaks can be time consuming and difficult to investigate. Guidance does not specify which typing technique is most practical to base decisions on. Aim: We explore the usefulness of whole genome sequencing (WGS) in the investigation of a Pseudomonas aeruginosa outbreak describing how it compares with pulsed-field gel electrophoresis (PFGE) and variable number tandem repeat (VNTR) analysis. Methods: Six patient isolates and six environmental samples from an Intensive Care Unit (ICU) positive for P. aeruginosa over two years underwent VNTR, PFGE and WGS. Findings: VNTR and PFGE were required to fully determine the potential source of infection and rule out others. WGS results unambiguously distinguished linked isolates giving greater assurance of the transmission route between wash hand basin (WHB) water and two patients supporting control measures employed. Conclusion: WGS provided detailed information without need for further typing. When allied to epidemiological information it can be used to understand outbreak situations rapidly and with certainty. Implementation of WGS in real-time would be a major advance in day-to-day practice. It could become a standard of care as it becomes more widespread due to its reproducibility and reduction in costs.Publisher PDFPeer reviewe
Taub-NUT Black Holes in Third order Lovelock Gravity
We consider the existence of Taub-NUT solutions in third order Lovelock
gravity with cosmological constant, and obtain the general form of these
solutions in eight dimensions. We find that, as in the case of Gauss-Bonnet
gravity and in contrast with the Taub-NUT solutions of Einstein gravity, the
metric function depends on the specific form of the base factors on which one
constructs the circle fibration. Thus, one may say that the independence of the
NUT solutions on the geometry of the base space is not a robust feature of all
generally covariant theories of gravity and is peculiar to Einstein gravity. We
find that when Einstein gravity admits non-extremal NUT solutions with no
curvature singularity at , then there exists a non-extremal NUT solution
in third order Lovelock gravity. In 8-dimensional spacetime, this happens when
the metric of the base space is chosen to be . Indeed, third
order Lovelock gravity does not admit non-extreme NUT solutions with any other
base space. This is another property which is peculiar to Einstein gravity. We
also find that the third order Lovelock gravity admits extremal NUT solution
when the base space is or . We have extended these observations to two conjectures
about the existence of NUT solutions in Lovelock gravity in any
even-dimensional spacetime.Comment: 10 page
Black hole solutions in F(R) gravity with conformal anomaly
In this paper, we consider theory instead of Einstein gravity
with conformal anomaly and look for its analytical solutions. Depending on the
free parameters, one may obtain both uncharged and charged solutions for some
classes of models. Calculation of Kretschmann scalar shows that there is
a singularity located at , which the geometry of uncharged (charged)
solution is corresponding to the Schwarzschild (Reissner-Nordstr\"om)
singularity. Further, we discuss the viability of our models in details. We
show that these models can be stable depending on their parameters and in
different epoches of the universe.Comment: 12 pages, one figur
- …