Scoring Functions Based on Second Level Score for k-SAT with Long Clauses

It is widely acknowledged that stochastic local search (SLS) algorithms can efficiently find models for satisfiable instances of the satisfiability (SAT) problem, especially for random k-SAT instances. However, compared to random 3-SAT instances where SLS algorithms have shown great success, random k-SAT instances with long clauses remain very difficult. Recently, the notion of second level score, denoted as "score_2", was proposed for improving SLS algorithms on long-clause SAT instances, and was first used in the powerful CCASat solver as a tie breaker. In this paper, we propose three new scoring functions based on score_2. Despite their simplicity, these functions are very effective for solving random k-SAT with long clauses. The first function combines score and score_2, and the second one additionally integrates the diversification property "age". These two functions are used in developing a new SLS algorithm called CScoreSAT. Experimental results on large random 5-SAT and 7-SAT instances near phase transition show that CScoreSAT significantly outperforms previous SLS solvers. However, CScoreSAT cannot rival its competitors on random k-SAT instances at phase transition. We improve CScoreSAT for such instances by another scoring function which combines score_2 with age. The resulting algorithm HScoreSAT exhibits state-of-the-art performance on random k-SAT (k>3) instances at phase transition. We also study the computation of score_2, including its implementation and computational complexity.

Short communication: development and characterization of novel transcriptome-derived microsatellites for genetic analysis of persimmon

Oriental persimmon (Diospyros kaki Thunb.) (2n = 6x = 90) is a major commercial and deciduous fruit tree that is believed to have originated in China. However, rare transcriptomic and genomic information on persimmon is available. Using Roche 454 sequencing technology, the transcriptome from RNA of the flowers of D. kaki was analyzed. A total of 1,250,893 reads were generated and 83,898 unigenes were assembled. A total of 42,711 SSR loci were identified from 23,494 unigenes and 289 polymerase chain reaction primer pairs were designed. Of these 289 primers, 155 (53.6%) showed robust PCR amplification and 98 revealed polymorphism between 15 persimmon genotypes, indicating a polymorphic rate of 63.23% of the productive primers for characterization and genotyping of the genus Diospyros. Transcriptome sequence data generated from next-generation sequencing technology to identify microsatellite loci appears to be rapid and cost-efficient, particularly for species with no genomic sequence information available.

Accumulation of melanin in the peritoneum causes black abdomens in broilers

A suspected case of localized visceral hyperpigmentation was described for a breed of broiler in China. Using optical microscopy, the accumulation of pigments in the abdominal skin and visceral peritoneum was observed. Electron microscopy was used to further study the ultrastructure of the pigmented peritoneum, and pigment granules resembling melanosomes at different stages were found, and melanocytes were present in this tissue. Infrared spectroscopy was used to analyze the physical-chemical properties of pigments extracted from these broilers. Using synthetic melanin as a reference and the melanin from the peritoneum of Silkie fowls as a control, the pigments in the peritonea of these broilers were found to be melanin, and it had a chemical structure similar to that of melanin from the Silkie fowl peritoneum. In this way, the black abdomens of these broilers were found to have been caused by accumulation of melanin produced by melanocytes in visceral peritonea.

AKT2 expression in histopathologic grading and recurrence of meningiomas

BACKGROUND

AKT2 (protein kinase B), an important protein in PI3K signaling pathway, is overexpressed in a variety of malignant tumors. However, in patients with meningiomas, the potential correlation between AKT2 and clinical outcome remains unknown.

METHODS

The expression of AKT2 and Ki-67 in meningioma tissues were evaluated immunohistochemically in 94 patients with meningiomas. The correlation of AKT2 immunoreactivity with clinicopathological features and the prognostic value of AKT2 in patients were also analyzed.

RESULTS

In this study, we examined the expression of AKT2 in meningiomas and unveiled its possible relationship with the clinical outcome. Immunohistochemical analysis revealed high AKT2 expression in 46 patients (46/94, 48.9%) and low AKT2 expression in the remaining 48 patients (48/94, 51.1%). There was a positive correlation between AKT2 and Ki-67 immunoreactivity (r = 0.35, P = 0.01). Clinicopathological evaluation suggested that AKT2 expression was associated with pathological grade and recurrence (P < 0.05). Univariate and Cox analysis indicated a significant correlation between high levels of AKT2 immunoreactivity and high rates of tumor recurrence (P < 0.05).

CONCLUSIONS

We conclude that AKT2 may play an important role in the development of meningioma. High AKT2 labeling index indicates higher grade of meningioma, and therefore AKT2 may be a useful molecular marker for predicting the prognosis of meningioma.

195 EFFECTS OF GSK3 INHIBITOR ON THE PLURIPOTENCY MAINTENANCE OF BUFFALO EMBRYONIC STEM-CELL-LIKE CELLS

In this study, to explore the effects and mechanism of Wnt/β-catenin signalling pathway on the maintenance of pluripotency of buffalo embryonic stem-cell-like cells (buffalo ESC-like cells), the GSK3 inhibitors BIO and CHIR99021 were added throughout the experiment – i.e. from buffalo inner cell mass (ICM) culture to ESC-like line generation. The buffalo ICM were respectively cultured in the medium containing 0.5 μg mL–1 BIO and 5 mmol L–1 CHIR99021. The percentage of ICMs attachment and primary colony formation were observed, and found that there was no significant difference in the ICMs attachment rate among of the BIO, CHIR99021, and the control groups (91.18% and 92.98% v. 94.59%; P > 0.05). Treating ICMs with CHIR99021 resulted in more primary colony formation rate compared with the control group (77.71% v. 55.41%; P < 0.05). The proliferation rate of primary colonies of buffalo ESC-like cells was detected by bromodeoxyuridine immunofluorescence techniques. The results show that the proliferation rate of primary colonies in the group of buffalo ESC-like cells treated with CHIR99021 was significantly higher than that of the control group on Day 1, Day 3, Day 4, and Day 5 (P < 0.05), and it was also evidently higher than that of control group only on Day 1 (P < 0.05) in the group of BIO, but there was no significant difference in other days (P > 0.05). The mRNA expression level of proliferation marker PCNA of ESC-like cells was significantly up-regulated in both CHIR99021 and BIO treatment groups (P < 0.05), however, treating buffalo ESC-like cells with CHIR99021 significantly up-regulated the expression of pluripotent gene Oct4 and Sox2 (P < 0.05), but had no effect on pluripotent gene Nanog expression (P > 0.05). Oct4 expression was significantly increased (P < 0.05), and the expression of Sox2 and Nanog were significantly decreased (P < 0.05) in the group of BIO treatment. Furthermore, the relative protein level of β-catenin (the downstream effector of Wnt/β-catenin signalling pathway) and the mRNA expression level of c-Myc (the downstream target gene of Wnt/β-catenin signalling pathway) were significantly increased when buffalo ESC-like cells respectively treated with CHIR99021 and BIO (P < 0.05). In conclusion, treating buffalo ESC-like cells with GSK3 inhibitors CHIR99021 can promote proliferation of buffalo ESC-like cells, maintain their undifferentiated state, and up-regulate the expression levels of β-Catenin and c-Myc in buffalo ESC-like cells. These results indicate that Wnt/β-catenin signalling pathway plays an important role in regulation of self-renewal of buffalo ESC-like cells. This work was funded by the China High Technology Development Program (2011AA100607), China Natural Science Foundation (31072033), and Guangxi Science Foundation (2012GXNSFFA060004).

NuMVC: An Efficient Local Search Algorithm for Minimum Vertex Cover

The Minimum Vertex Cover (MVC) problem is a prominent NP-hard combinatorial optimization problem of great importance in both theory and application. Local search has proved successful for this problem. However, there are two main drawbacks in state-of-the-art MVC local search algorithms. First, they select a pair of vertices to exchange simultaneously, which is time-consuming. Secondly, although using edge weighting techniques to diversify the search, these algorithms lack mechanisms for decreasing the weights. To address these issues, we propose two new strategies: two-stage exchange and edge weighting with forgetting. The two-stage exchange strategy selects two vertices to exchange separately and performs the exchange in two stages. The strategy of edge weighting with forgetting not only increases weights of uncovered edges, but also decreases some weights for each edge periodically. These two strategies are used in designing a new MVC local search algorithm, which is referred to as NuMVC. We conduct extensive experimental studies on the standard benchmarks, namely DIMACS and BHOSLIB. The experiment comparing NuMVC with state-of-the-art heuristic algorithms show that NuMVC is at least competitive with the nearest competitor namely PLS on the DIMACS benchmark, and clearly dominates all competitors on the BHOSLIB benchmark. Also, experimental results indicate that NuMVC finds an optimal solution much faster than the current best exact algorithm for Maximum Clique on random instances as well as some structured ones. Moreover, we study the effectiveness of the two strategies and the run-time behaviour through experimental analysis.

Strain induced chemical potential difference between monolayer graphene sheets

Monolayer graphene sheets were deposited on a transparent and flexible polydimethylsiloxane (PDMS) substrate, and a tensile strain was loaded by stretching the substrate in one direction. It was found that an electric potential difference between stretched and static monolayer graphene sheets reached 8 mV when the strain was 5%. Theoretical calculations for the band structure and total energy revealed an alternative way to experimentally tune the band gap of monolayer graphene, and induce the generation of electricity.

Characterization and comparison of EST-SSR and TRAP markers for genetic analysis of the Japanese persimmon Diospyros kaki

We developed and characterized expressed sequence tags (ESTs)-simple sequence repeats (SSRs) and targeted region amplified polymorphism (TRAP) markers to examine genetic relationships in the persimmon genus Diospyros gene pool. In total, we characterized 14 EST-SSR primer pairs and 36 TRAP primer combinations, which were amplified across 20 germplasms of 4 species in the genus Diospyros. We used various genetic parameters, including effective multiplex ratio (EMR), diversity index (DI), and marker index (MI), to test the utility of these markers. TRAP markers gave higher EMR (24.85) but lower DI (0.33), compared to EST-SSRs (EMR = 3.65, DI = 0.34). TRAP gave a very high MI (8.08), which was about 8 times than the MI of EST-SSR (1.25). These markers were utilized for phylogenetic inference of 20 genotypes of Diospyros kaki Thunb. and allied species, with a result that all kaki genotypes clustered closely and 3 allied species formed an independent group. These markers could be further exploited for large-scale genetic relationship inference.

Abstract P2-05-21: Molecular subtypes of invasive breast cancers show differential expression of the proliferation marker Aurora Kinase A (AURKA)

Background: Invasive breast cancer (IBC) has been classified into four major subtypes based on gene expression profiling. The luminal A subtype (LA) has the best prognosis, when compared to luminal B (LB), HER2+, and basal-like (Basal). Ki67 by gene expression or immunohistochemistry (IHC) is commonly used as a proliferation index. The function of Ki67 in proliferation remains unknown. AURKA (STK15) is known to play an important role in mitosis, and is a component of the 21-gene recurrence score of the Oncotype Dx. With multiple platforms of molecular data available from hundreds of IBC tissues in The Cancer Genome Atlas project (TCGA), we sought to study the association of AURKA with different IBC subtypes and explore its use as a proliferation marker in IBCs.

Methods: Gene expression (Agilent, log2 transformed), relative DNA copy number (CN, Affymetrix SNP 6.0), and exome sequence mutation (Illumina) data for 459 IBC cases were downloaded from the TCGA data portal. PAM50 classification results of all samples were obtained from the TCGA breast cancer AWG group and included 203 LA, 113 LB, 51 HER2+, 84 Basal-like, and 8 Normal-like which were not used in this study due to the low numbers. Kruskal-Wallis tests were used to evaluate the differences among four subtypes on AURKA expression and CN, followed by Wilcoxon Mann-Whitney test with Bonferroni adjustment for pairwise analyses. Pearson's Correlation Coefficient was used for correlation analyses. All statistical analyses were performed using SAS and R, and two-sided, p values &lt;.05 were considered statistically significant.

Results: There was a significant difference among IBC subtypes, in gene expression as well as in CN (p values &lt; 0.0001). AURKA mRNA levels were significantly lower in LA (mean±SD, −2.61±0.63) compared to LB (−1.45±0.78), HER2+ (−1.38±0.61), and Basal (−1.26±0.62) subtypes (p values all &lt; 0.0001). No significant difference was detected between other subtype pairs. In CN analysis, Basal (0.09±0.22) was lower than HER2+ (0.32±0.308, p &lt; 0.0002) and LB (0.33±0.41, p &lt; 0.0001), and LA (0.14±0.28) is lower than HER2 (p &lt; 0.0016) and LB (p &lt; 0.0001), but no other significant CN difference between the subtypes were found. The means and SDs are provided for reference only. No correlation of p53 mutation status and AURKA expression were observed. However, AURKA gene expression level is correlated with MKI67 gene expression (R = 0.69, p &lt; 2.2e−16), and its correlation with PAM50 proliferation score is even higher (R = 0.80, p &lt; 2.2e−16).

Discussion: Using the TCGA data we observed that the mean gene expression level of AURKA is significantly lower in LA than the other IBC subtypes, by more than 50% (note the log2 transformation). This differential expression is not completely due to CN changes (especially for the Basal subtype). There is a strong association with other tumor cell proliferation markers such as the MKI67 gene and the PAM50 proliferation score. We are using computational and laboratorial studies to better understand the role of AURKA in the etiology of invasive breast cancers.

The views expressed in this article are those of the author and do not reflect the official policy of the Department of Defense, or U.S. Government.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P2-05-21.

Abstract P2-09-06: The structure design and biological activities of inhibitory peptides, which block the interactions among polycomb repressive complex 2

Polycomb repressive complex (PRC2) contains several proteins, including embryonic ectoderm development (EED), suppressor of zeste 12 (SUZ12) and enhancer of zeste homolog 2 (EZH2). Excessive EZH2 concentrations have been reported as a marker of aggressive breast cancer and associated with invasion and cancer progression. EZH2 levels were elevated in patients with invasive breast carcinoma relative to normal or atypical hyperplasia. Except for the C-terminal SET domain, which functions as a histone-lysine N-methyltransferases, EZH2 has an N-terminal alpha helix region, which forms tight complex with EED protein. The in vivo enzymatic activity of EZH2 relies on and be tightly regulated by the interaction with EED. We designed series of artificial peptides trying to block the interaction between EZH2 and EED. By using label-free surface plasmon resonance (SPR) technology, the dynamic binding capacities of these peptides were tested. There were 3 leading structures standing out from the screening of more 80 peptides. After several round of co-crystal structure based optimization, the binding capacity of one inhibitor was reached to several nM levels, which indicated the availability for being a drug candidate. Finally, the biological activities of the inhibitory peptides were tested in several breast cancer cell lines. The PRC2 inhibitory peptides in this study are the first time reported PRC2 targeting epigenetic molecules with biological activity in breast cancer.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P2-09-06.

Elevated serum antibodies against insulin-like growth factor-binding protein-2 allow detecting early-stage cancers: evidences from glioma and colorectal carcinoma studies

BACKGROUND

Tumor-specific immunity of insulin-like growth factor-binding protein-2 (IGFBP-2) has been reported in several cancers. We aimed to assess the role of serum IGFBP-2 antibodies (IGFBP-2 Abs) in early cancer detection.

PATIENTS AND METHODS

Glioma and colorectal carcinoma (CRC) were used as models. Serum IGFBP-2 and IGFBP-2 Abs were measured in 260 tumor patients (145 gliomas, 45 colorectal polyps, and 70 CRCs) and 141 controls. Receiver operating characteristic curves were applied.

RESULTS

Serum IGFBP-2 Ab levels were significantly elevated in tumors (mean: 82 ng/ml, median: 17 ng/ml, range: 0-1387 ng/ml) compared with controls (11, 0, 0-212 ng/ml) (P < 0.0001) and higher in early than advanced cancers opposite of serum IGFBP-2 levels. IGFBP-2 Abs effectively discriminated between controls and grade II and III gliomas [area under the curve (AUC): 0.821-0.864; 95% confidence interval (CI) = 0.762-0.936; P < 0.0001], and CRC I-II (AUC: 0.668; 95% CI = 0.566-0.770; P = 0.002) as well as indicative of advanced polyps at high risk of CRC (AUC: 0.72; 95% CI = 0.630-0.811; P < 0.0001). The sensitivity and specificity for diagnosing grade II-III gliomas reached 66%-84% and 81%. Combined serum IGFBP-2 and IGFBP-2 Abs augmented the discriminative power of all stage tumors (AUC: 0.823), gliomas (AUC: 0.800), and CRCs (AUC = 0.917).

CONCLUSION

Our results first demonstrate IGFBP-2 Abs for early cancer detection and in combination of serum IGFBP-2 for improved cancer diagnosis.