Efficient Planning under Uncertainty with Macro-actions

Deciding how to act in partially observable environments remains an active area of research. Identifying good sequences of decisions is particularly challenging when good control performance requires planning multiple steps into the future in domains with many states. Towards addressing this challenge, we present an online, forward-search algorithm called the Posterior Belief Distribution (PBD). PBD leverages a novel method for calculating the posterior distribution over beliefs that result after a sequence of actions is taken, given the set of observation sequences that could be received during this process. This method allows us to efficiently evaluate the expected reward of a sequence of primitive actions, which we refer to as macro-actions. We present a formal analysis of our approach, and examine its performance on two very large simulation experiments: scientific exploration and a target monitoring domain. We also demonstrate our algorithm being used to control a real robotic helicopter in a target monitoring experiment, which suggests that our approach has practical potential for planning in real-world, large partially observable domains where a multi-step lookahead is required to achieve good performance.

Heterogeneity of gene expression in stromal fibroblasts of human breast carcinomas and normal breast

Breast carcinoma invasion is associated with prominent alterations in stromal fibroblasts. Carcinoma-associated fibroblasts (CAF) support and promote tumorigenesis, whereas normal mammary fibroblasts (NF) are thought to suppress tumor progression. Little is known about the difference in gene expression between CAF and NF or the patient-to-patient variability in gene expression. Paired CAF and NF were isolated from six primary human breast carcinoma specimens. RNA was extracted from low-passage cultures of CAF and NF and analyzed with Affymetrix Human Genome U133 Plus 2.0 arrays. The array data were examined with an empirical Bayes model and filtered according to the posterior probability of equivalent expression and fold difference in expression. Twenty-one genes (27 probe sets) were up-regulated in CAF, as compared to NF. Known functions of these genes relate to paracrine or intracellular signaling, transcriptional regulation, extracellular matrix and cell adhesion/migration. Ten genes (14 probe sets) were down-regulated in CAF, including the pluripotency transcription factor KLF4. Quantitative RT-PCR analysis of 10 genes validated the array results. Immunohistochemical staining for three gene products confirmed stromal expression in terms of location and relative quantity. Surprisingly, the variability of gene expression was slightly higher in NF than in CAF, suggesting inter-individual heterogeneity of normal stroma.

Progesterone Receptor (PR) Promoter Methylation – Role as a Predictive and Prognostic Marker in Breast Cancer

Estrogen receptor α expression is a well known and clinically utilized predictor of endocrine treatment response. In addition, loss of expression of the progesterone receptor (PR), an estrogen induced gene, has been shown to be associated with resistance to endocrine therapy. PR is known to be epigenetically regulated by DNA methylation, but only a few studies have correlated PR DNA methylation with its expression in breast cancer. Previous studies are contradictory and have been limited by small sample size. There is also evidence that differential expression of the two PR isoforms, PRA and PRB, might contribute to breast tumorigenesis, and altered hormone response. Whether PRA and/or PRB DNA methylation could predict response to endocrine therapy remains an open question. Further, there are no published studies so far testing whether PRA and/or PRB methylation have prognostic significance.Our objective was 1) to determine whether there was an association between PRA and/or PRB methylation levels with total PR expression in breast tumors, and 2) to determine if PRA and/or PRB methylation would have predictive and/or prognostic value. For this study, we utilized tumor DNA from patients with ER-positive breast tumors which were treated with adjuvant tamoxifen after surgery (n=500), and from patients treated with surgery only (n=500). PR expression was determined by ligand binding assay, and PRA and PRB promoter methylation was measured by bisulfite pyrosequencing.Both PRA and PRB methylation were significantly (p<0.0001) associated with PR expression, in an inverse relationship. Low PR expression was significantly (p=0.02) associated with worse overall survival (OS), and there was a trend towards shorter disease free survival (DFS) in the tamoxifen treated group. There was no association between PR expression and survival in the untreated group. PRA methylation was significantly (p<0.0001) associated with PRB methylation. Intriguingly, increased PRA methylation was significantly associated with shorter DFS (p=0.047) and OS (p=0.0067) in tamoxifen treated patients, and with shorter OS (p=0.008) in the untreated patients. In contrast, there was no significant association between PRB methylation and survival in either tamoxifen treated or untreated patients.Our results show that PR expression is significantly associated with PR methylation. The data suggest that PRA methylation is a predictive marker for tamoxifen response and also a prognostic marker for breast cancer progression. This is the largest study so far to elucidate the association of PRA and PRB methylation with PR status, response to tamoxifen, and tumor prognosis, and we believe that it provides useful insights into the role of PR methylation in breast tumorigenesis.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 2002.

Heterogeneity of gene expression in stromal fibroblasts of breast carcinomas and normal breast

Abstract #105

Background: The cancer microenvironment plays a critical role in tumor development and progression. Cancer associated fibroblasts (CAF) constitute a significant component of the tumor stroma and participate in reciprocal communication with the tumor cells. Information on differential gene expression specifically in stromal fibroblasts is sparse and data describing the variability of gene expression in CAF and normal fibroblasts (NF) is currently lacking. The purpose of this study was to identify genes differentially expressed in CAF and matched NF and to analyze the heterogeneity of gene expression profiles in the two cell types.
 Materials and methods: Fibroblast cell cultures were established from 6 patients with primary invasive breast cancer. Gene expression profiles were generated using oligonucleotide microarrays (Affymetrix HG-U133 Plus 2.0). Differentially expressed genes were ranked using Empirical Bayes modeling. A cut-off value of 0.005 was chosen for the posterior probability of equivalent expression. Lists of overexpressed genes were generated after eliminating genes with less than two-fold overexpression.
 Results: 17 genes were overexpressed in CAF compared to NF with known functions in paracrine and intracellular signaling, transcription regulation and extracellular matrix production. Using the same posterior probability cut-off, we identified 7 genes which were expressed at least two-fold higher in NF than in CAF. These genes have purported roles in steroid hormone metabolism, transcription, migration and cell signaling. Using semiquantitative RT-PCR and immunohistochemistry, we confirmed the over- and underexpression of a subset of 10 differentially expressed genes. The heterogeneity of gene expression in CAF vs. NF was compared with F-tests to determine variances. The estimated probability of NF gene expression variance being higher than CAF gene expression variance was 0.547 with a 95% confidence interval of 0.543 to 0.551 (p<0.0001), indicating that gene expression is more variable in NF than in CAF. By ranking the q-values of individual genes we identified 3 known genes, which show a significant difference in variance between CAF and NF (p<0.05).
 Conclusion: Altered gene expression in fibroblasts likely contributes to tumor growth and progression by enhancing ECM production, promoting stromal-epithelial paracrine signaling and altering steroid hormone metabolism. The inter-individual heterogeneity of gene expression in NF may indicate that the mammary stroma varies between individuals, supporting the hypothesis that the ability of the stroma to act as a barrier to cancer development and tumor progression may also be variable. Conversely, the heterogeneous gene expression in NF may be a reflection of a relative synchronization and uniformity of gene expression in CAF.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 105.

Effect of Ultrasonic Degradation on In Vitro Antioxidant Activity of Polysaccharides from Porphyra yezoensis (Rhodophyta)

This article aims to study the effect of ultrasonic degradation on antioxidant activity of polysaccharides from Porphyra yezoensis (Rhodophyta) (PSPY), and to look for the relationship between molecular structure of fractions (F1, F2, and F3) from ultrasonic-degraded PSPY (UDPSPY) and their activities of scavenging hydroxyl and superoxide anion radicals, chelating ability of iron ion and reducing power. Results of antioxidant assays indicated that the UDPSPY had higher antioxidant activity of scavenging superoxide anion radical and hydroxyl radical than that of the PSPY. As antioxidant activities of the fractions are concerned, this result might suggest that decreasing molecular weight and increasing sulfate group content in the molecule were vital and necessary factors for improving antioxidant activity of PSPY. Decrease of molecular weight was the dominant reason for increasing activities of scavenging non-site and site specific hydroxyl radical and reducing power of F1, F2, and F3, and increase of sulfate group content in the molecule was the dominant reason for increasing activities of scavenging superoxide anion radical and chelating ferrous ions of F1, F2, and F3. It was possible that ultrasonic treatment could be a new and effective method for enhancing PSPY's antioxidant activity.

Significant alterations of biodistribution and immune responses in Balb/c mice administered with adenovirus targeted to CD40(+) cells

CD40 ligation has been shown to promote antigen-presenting functions of dendritic cells, which express CD40 receptor. Here we reported significantly altered biodistribution and immune responses with the use of CD40-targeted adenovirus. Compared with unmodified adenovirus 5, the CD40-targeted adenovirus following intravenous administration (i.v.) resulted in increased transgene expressions in the lung and thymus, which normally do not take up significant amounts of adenovirus. Intradermal injection saw modified adenovirus being mainly processed in local draining lymph nodes and skin. Following intranasal administration (i.n.), neither unmodified nor targeted viruses were found to be in the liver or spleen, which predominantly took up the virus following i.v. administration. However, inadvertent infection of the brain was found with unmodified adenoviruses, with the second highest gene expression among 14 tissues examined. Importantly, such undesirable effects were largely ablated with the use of targeted vector. Moreover, the targeted adenovirus elicited more sustained antigen-specific cellular immune responses (up to 17-fold) at later time points (30 days post boosting), but also significantly hampered humoral responses irrespective of administration routes. Additional data suggest the skewed immune responses induced by the targeted adenoviruses were not due to the identity of the transgene but more likely a combination of overall transgene load and CD40 stimulation.

A unified approach for lesion segmentation on MRI of multiple sclerosis

Accurate determination of lesion volumes on brain MR images is hampered by the presence of a large number of false positive and negative classifications. A strategy that combines parametric and nonparametric techniques is developed and implemented for minimizing the false classifications. Initially, CSF and lesions are segmented using Parzen window classifier. Image processing, morphological operations, and ratio map of proton density (PD) and T2 weighted images are used for minimizing false positives. Lesions are delineated using fuzzy connectedness principle. Contextual information was used for minimizing false negative lesion classifications. Gray and white matter classification is realized using HMRF-EM algorithm.

The relationship between polymorphisms of HCMV UL144 ORF and clinical manifestations in 73 strains with congenital and/or perinatal HCMV infection

Human cytomegalovirus (HCMV) displays genetic variability and can cause a wide range of diseases in neonates. To explore the relationship between polymorphisms and clinical manifestations, the UL144 genes from 73 clinical strains were sequenced. All of the strains, which came from 70 infants with suspected congenital and/or perinatal HCMV infection, were non-passage strains. Among them, 23 strains were from surgery specimens, and the others were from urine samples. Clinically, 12 infants displayed asymptomatic infection and 58 patients displayed symptomatic infection. The results showed that 36 patients (49.3%) were infected with strains belonging to UL144 group G1 (G1a 33/36, G1b 3/36), 19 patients (28.8%) were infected with strains belonging to group G2, and 15 patients (21.9%) were infected with strains belonging to group G3. This result indicated that UL144 group G1 was the predominant genotype in congenital and/or perinatal HCMV infection in northern China. Compared with the distribution pattern of strains in UL144 genotypes of data from Chicago, Iowa and Texas, and Japan by chi-square test, the difference was statistically significant. This suggested that the distribution pattern of strains in UL144 genotype was related to geographic location. However, no linkage was observed between the UL144 genotypes and the severity and/or outcome of HCMV disease.

Sequence variability of the human cytomegalovirus UL141 Open Reading Frame in clinical strains

Human cytomegalovirus (HCMV) displays genetic polymorphisms. HCMV disease and tissue tropism may be related to specific genomic variability among strains. This work analyzed the genetic polymorphism of UL141 open reading frame (ORF), one of the genes in HCMV UL/b' region, from 21 clinical strains. 8 previously published UL141 sequences in the GenBank were used for sequence comparison. Detailed sequence analysis showed that the UL141 gene was highly conserved at both the nucleotide and amino acid level. The coding regions were identical in size. The nucleotide and amino acid sequence identities among all strains were 96.9-100% and 97.6-100%, respectively.