248 research outputs found
Lower Critical Dimension of Ising Spin Glasses
Exact ground states of two-dimensional Ising spin glasses with Gaussian and
bimodal (+- J) distributions of the disorder are calculated using a
``matching'' algorithm, which allows large system sizes of up to N=480^2 spins
to be investigated. We study domain walls induced by two rather different types
of boundary-condition changes, and, in each case, analyze the system-size
dependence of an appropriately defined ``defect energy'', which we denote by
DE. For Gaussian disorder, we find a power-law behavior DE ~ L^\theta, with
\theta=-0.266(2) and \theta=-0.282(2) for the two types of boundary condition
changes. These results are in reasonable agreement with each other, allowing
for small systematic effects. They also agree well with earlier work on smaller
sizes. The negative value indicates that two dimensions is below the lower
critical dimension d_c. For the +-J model, we obtain a different result, namely
the domain-wall energy saturates at a nonzero value for L\to \infty, so \theta
= 0, indicating that the lower critical dimension for the +-J model exactly
d_c=2.Comment: 4 pages, 4 figures, 1 table, revte
Generating droplets in two-dimensional Ising spin glasses by using matching algorithms
We study the behavior of droplets for two dimensional Ising spin glasses with
Gaussian interactions. We use an exact matching algorithm which enables study
of systems with linear dimension L up to 240, which is larger than is possible
with other approaches. But the method only allows certain classes of droplets
to be generated. We study single-bond, cross and a category of fixed volume
droplets as well as first excitations. By comparison with similar or equivalent
droplets generated in previous works, the advantages but also the limitations
of this approach are revealed. In particular we have studied the scaling
behavior of the droplet energies and droplet sizes. In most cases, a crossover
of the data can be observed such that for large sizes the behavior is
compatible with the one-exponent scenario of the droplet theory. Only for the
case of first excitations, no clear conclusion can be reached, probably because
even with the matching approach the accessible system sizes are still too
small.Comment: 11 pages, 16 figures, revte
Energetics of clusters in the two-dimensional Ising spin glass
We study numerically the properties of local low-energy excitations in the
two-dimensional Ising spin glass. Given the ground state, we determine the
lowest-lying connected cluster of flipped spins containing one given spin,
either with a fixed volume, or with a volume constrained to lie in a certain
range. Our aim is to understand corrections to the scaling predicted by the
droplet picture of spin glasses and to resolve contradictory results reported
in the literature for the stiffness exponent. We find no clear trace of
corrections to scaling, and the obtained stiffness exponent is in relatively
good agreement with standard domain wall calculations.Comment: 8 pages, 9 figure
Prostate-Specific Ets (PSE) factor: a novel marker for detection of metastatic breast cancer in axillary lymph nodes
Prostate Specific Ets factor is a recently identified transcriptional activator that is overexpressed in prostate cancer. To determine whether this gene is overexpressed in breast cancer, we performed a virtual Northern blot using data available online at the Cancer Genome Anatomy Project website. Ninety-five SAGE libraries were probed with a unique sequence tag to the Prostate Specific Ets gene. The results indicate that Prostate Specific Ets is expressed in 14 out of 15 breast cancer libraries (93%), nine out of 10 prostate cancer libraries (90%), three out of 40 libraries from other cancers (7.5%), and four out of 30 normal tissue libraries (13%). To determine the possibility that the Prostate Specific Ets gene is a novel marker for detection of metastatic breast cancer in axillary lymph nodes, quantitative real-time RT–PCR analyses were performed. The mean level of Prostate Specific Ets expression in lymph nodes containing metastatic breast cancer (n=22) was 410-fold higher than in normal lymph node (n=51). A receiver operator characteristic curve analysis indicated that Prostate Specific Ets was overexpressed in 18 out of 22 lymph nodes containing metastatic breast cancer (82%). The receiver operator characteristic curve analysis also indicated that the diagnostic accuracy of the Prostate Specific Ets gene for detection of metastatic breast cancer in axillary lymph nodes was 0.949. These results provide evidence that Prostate Specific Ets is a potentially informative novel marker for detection of metastatic breast cancer in axillary lymph nodes, and should be included in any study that involves molecular profiling of breast cancer
Ground states of two-dimensional J Edwards-Anderson spin glasses
We present an exact algorithm for finding all the ground states of the
two-dimensional Edwards-Anderson spin glass and characterize its
performance. We investigate how the ground states change with increasing system
size and and with increasing antiferromagnetic bond ratio . We find that
that some system properties have very large and strongly non-Gaussian
variations between realizations.Comment: 15 pages, 21 figures, 2 tables, uses revtex4 macro
Identification of 5 novel genes methylated in breast and other epithelial cancers
<p>Abstract</p> <p>Background</p> <p>There are several high throughput approaches to identify methylated genes in cancer. We utilized one such recently developed approach, MIRA (methylated-CpG island recovery assay) combined with CpG island arrays to identify novel genes that are epigenetically inactivated in breast cancer.</p> <p>Results</p> <p>Using this approach we identified numerous CpG islands that demonstrated aberrant DNA methylation in breast cancer cell lines. Using a combination of COBRA and sequencing of bisulphite modified DNA, we confirmed 5 novel genes frequently methylated in breast tumours; <it>EMILIN2, SALL1</it>, <it>DBC1</it>, <it>FBLN2 </it>and <it>CIDE-A</it>. Methylation frequencies ranged from between 25% and 63% in primary breast tumours, whilst matched normal breast tissue DNA was either unmethylated or demonstrated a much lower frequency of methylation compared to malignant breast tissue DNA. Furthermore expression of the above 5 genes was shown to be restored following treatment with a demethylating agent in methylated breast cancer cell lines. We have expanded this analysis across three other common epithelial cancers (lung, colorectal, prostate). We demonstrate that the above genes show varying levels of methylation in these cancers. Lastly and most importantly methylation of <it>EMILIN2 </it>was associated with poorer clinical outcome in breast cancer and was strongly associated with estrogen receptor as well as progesterone receptor positive breast cancers.</p> <p>Conclusion</p> <p>The combination of the MIRA assay with CpG island arrays is a very useful technique for identifying epigenetically inactivated genes in cancer genomes and can provide molecular markers for early cancer diagnosis, prognosis and epigenetic therapy.</p
Marker genes for circulating tumour cells predict survival in metastasized breast cancer patients
We investigated the prognostic significance of circulating breast cancer cells in peripheral blood detected by quantitative RT-PCR of marker genes in patients with advanced breast cancer. Blood samples from 94 breast cancer patients with metastatic disease (M1) were examined for circulating tumour cells by studying the mRNA expression of CK19, p1B, PS2 and EGP2 by real-time PCR. Using a score function, developed for predicting circulating tumour cells by quadratic discriminant analysis (QDA), the four expression levels were combined into a single discriminant value. Tumour cells were present in 24 out of 94 (31%) of the patients. In 77% (72 out of 94) of the patients distant metastatic disease was localised in the bone. In 36% (26 out of 72) of the patients with bone metastases at the time of blood sampling, a positive QDA for the four genes was found, in contrast to only 14% (three out of 22) without bone involvement. Overall survival rates by Kaplan-Meier revealed no prognostic effect for the presence of bone metastases (P=0.93). However, patients with a positive QDA value did have a progression-free survival at 1 year of 3% and overall survival at 2 years of 17%, against 22 and 36% for patients with a negative QDA value (P=0.015 and 0.0053, respectively). Breast cancer patients with metastatic disease have a significantly worse progression-free and overall survival when circulating tumour cells can be detected in their peripheral bloo
Clinicopathological and biological significance of mitotic centromere-associated kinesin overexpression in human gastric cancer
Mitotic centromere-associated kinesin (MCAK) is a microtubule (MT) depolymerase necessary for ensuring proper kinetochore MT attachment during spindle formation. To determine MCAK expression status and its clinicopathological significance, real-time reverse transcriptase–polymerase chain reaction was used in 65 cases of gastric cancer. MCAK gene expression in cancer tissue was significantly higher than expression in non-malignant tissue (P<0.05). Elevated MCAK expression was significantly associated with lymphatic invasion (P=0.01) and lymph node metastasis (P=0.04). Furthermore, patients with high MCAK expression had a significantly poorer survival rate than those with low MCAK expression (P=0.008). Immunohistochemical study revealed that expression of MCAK was primarily observed in cancer cells. Additionally, a gastric cancer cell line (AZ521) that stably expressed MCAK was established and used to investigate the biological effects of the MCAK gene. In vitro results showed that cells transfected with MCAK had a high rate of proliferation (P<0.001) and increased migratory ability (P<0.001) compared to mock-transfected cells. This study demonstrated that elevated expression of MCAK may be associated with lymphatic invasion, lymph node metastasis, and poor prognosis. These characteristics may be due in part to the increased proliferative and migratory ability of cells expressing MCAK
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