A fast parallel algorithm for finding the largest common 4-connected component from two matrices

Opisujemo novi dizajn paralelnog algoritma za rješavanje problema dvodimenzionalnog najduljeg zajedničkog podniza (2D LCS), iskoristivši arhitekturu grafičke obradne jedinice s više jezgri (multi-core graphic processing unit) ponuđene od Compute Unified Device Architecture (CUDA). U ovom radu također definiramo 2D LCS problem pronalaženjem najveće zajedničke 4-spojene komponente iz dvije ulazne matrice i predstavljamo algoritam koji može točno riješiti ovaj problem u 0 (mnst/P) vremenu s P-core GPU.We describe a new design of parallel algorithm for solving the two-dimensional longest common substring (2D LCS) problem, taking advantage of the multi-core graphic processing unit architecture offered by Compute Unified Device Architecture (CUDA). In this article we also define the 2D LCS problem as finding the largest common 4-connected component from two input matrices and present an algorithm which can exactly solve this problem in 0 (mnst/P) time with a P-core GPU

Extensive analysis of D7S486 in primary gastric cancer supports TESTIN as a candidate tumor suppressor gene

<p>Abstract</p> <p>Background</p> <p>High frequency of loss of heterozygosity (LOH) was found at D7S486 in primary gastric cancer (GC). And we found a high frequency of LOH region on 7q31 in primary GC from China, and identified D7S486 to be the most frequent LOH locus. This study was aimed to determine what genes were affected by the LOH and served as tumor suppressor genes (TSGs) in this region. Here, a high-throughput single nucleotide polymorphisms (SNPs) microarray fabricated in-house was used to analyze the LOH status around D7S486 on 7q31 in 75 patients with primary GC. Western blot, immunohistochemistry, and RT-PCR were used to assess the protein and mRNA expression of TESTIN (TES) in 50 and 140 primary GC samples, respectively. MTS assay was used to investigate the effect of TES overexpression on the proliferation of GC cell lines. Mutation and methylation analysis were performed to explore possible mechanisms of TES inactivation in GC.</p> <p>Results</p> <p>LOH analysis discovered five candidate genes (<it>ST7</it>, <it>FOXP2</it>, <it>MDFIC</it>, <it>TES </it>and <it>CAV1</it>) whose frequencies of LOH were higher than 30%. However, only <it>TES </it>showed the potential to be a TSG associated with GC. Among 140 pairs of GC samples, decreased <it>TES </it>mRNA level was found in 96 (68.6%) tumor tissues when compared with matched non-tumor tissues (<it>p </it>< 0.001). Also, reduced TES protein level was detected in 36 (72.0%) of all 50 tumor tissues by Western blot (<it>p </it>= 0.001). In addition, immunohistochemical staining result was in agreement with that of RT-PCR and Western blot. Down regulation of TES was shown to be correlated with tumor differentiation (<it>p </it>= 0.035) and prognosis (<it>p </it>= 0.035, log-rank test). Its overexpression inhibited the growth of three GC cell lines. Hypermethylation of <it>TES </it>promoter was a frequent event in primary GC and GC cell lines. However, no specific gene mutation was observed in the coding region of the <it>TES </it>gene.</p> <p>Conclusions</p> <p>Collectively, all results support the role of <it>TES </it>as a TSG in gastric carcinogenesis and that <it>TES </it>is inactivated primarily by LOH and CpG island methylation.</p

Radiomic signature of the FOWARC trial predicts pathological response to neoadjuvant treatment in rectal cancer

Background We aimed to develop a radiomic model based on pre-treatment computed tomography (CT) to predict the pathological complete response (pCR) in patients with rectal cancer after neoadjuvant treatment and tried to integrate our model with magnetic resonance imaging (MRI)-based radiomic signature. Methods This was a secondary analysis of the FOWARC randomized controlled trial. Radiomic features were extracted from pre-treatment portal venous-phase contrast-enhanced CT images of 177 patients with rectal cancer. Patients were randomly allocated to the primary and validation cohort. The least absolute shrinkage and selection operator regression was applied to select predictive features to build a radiomic signature for pCR prediction (rad-score). This CT-based rad-score was integrated with clinicopathological variables using gradient boosting machine (GBM) or MRI-based rad-score to construct comprehensive models for pCR prediction. The performance of CT-based model was evaluated and compared by receiver operator characteristic (ROC) curve analysis. The LR (likelihood ratio) test and AIC (Akaike information criterion) were applied to compare CT-based rad-score, MRI-based rad-score and the combined rad-score. Results We developed a CT-based rad-score for pCR prediction and a gradient boosting machine (GBM) model was built after clinicopathological variables were incorporated, with improved AUCs of 0.997 [95% CI 0.990–1.000] and 0.822 [95% CI 0.649–0.995] in the primary and validation cohort, respectively. Moreover, we constructed a combined model of CT- and MRI-based radiomic signatures that achieve better AIC (75.49 vs. 81.34 vs.82.39) than CT-based rad-score (P = 0.005) and MRI-based rad-score (P = 0.003) alone did. Conclusions The CT-based radiomic models we constructed may provide a useful and reliable tool to predict pCR after neoadjuvant treatment, identify patients that are appropriate for a 'watch and wait' approach, and thus avoid overtreatment. Moreover, the CT-based radiomic signature may add predictive value to the MRI-based models for clinical decision making

Perfluorocarbon nanodrug induced oxygen self-enriching sonodynamic therapy improves cancer immunotherapy after insufficient radiofrequency ablation

Residual lesions and undetectable metastasis after insufficient radiofrequency ablation (iRFA) are associated with earlier new metastases and poor survival in cancer patients, for induced aggressive tumor phenotype and immunosuppression. Programmed cell death protein 1(PD-1) blockade has been reported to enhance the radiofrequency ablation-elicited antitumor immunity, but its ability to eliminate incompletely ablated residual lesions has been questioned. Here, we report a combined treatment modality post iRFA based on integrating an oxygen self-enriching nanodrug PFH-Ce6 liposome@O2 nanodroplets (PCL@O2)-augmented noninvasive sonodynamic therapy (SDT) with PD-1 blockade. PCL@O2 containing Ce6 as the sonosensitizer and PFH as O2 reservoir, was synthesized as an augmented SDT nanoplatform and showed increased ROS generation to raise effective apoptosis of tumor cells, which also exposed more calreticulin to induce stronger immunogenic cell death (ICD). Combining with PD-1 blockade post iRFA, this optimized SDT induced a better anti-tumor response in MC38 tumor bearing mouse model, which not only arrested residual primary tumor progression, but also inhibited the growth of distant tumor, therefore prolonging the survival. Profiling of immune populations within the tumor draining lymph nodes and tumors further revealed that combination therapy effectively induced ICD, and promoted the maturation of dendritic cells, tumor infiltration of T cells, as well as activation of cytotoxic T lymphocytes. While iRFA alone could result in an increase of regulatory T cells (Tregs) in the residual tumors, SDT plus PD-1 blockade post iRFA reduced the number of Tregs in both primary and distant tumors. Moreover, the combined treatment could significantly initiate long-term immune memory, manifesting as elevated levels of CD8+ and CD4+ central memory cells. Therefore, this study establishes the preclinical proof of concept to apply oxygen self-enriching SDT to augment cancer immunotherapy after iRFA

Research and Application of Heat Treatment Process with 20Cr13 Martensitic Stainless Steel Material for Chain

View of the fracture problem of the chain in the 20Cr13 material of martensitic stainless steel,the scheme of improving the heat treatment process is put forward. Through the test of the different parameters of heat treatment,comprehensive the hardness and Charpy impact test,the appropriate heat treatment process is determined. The practice shows that,according to the results of the above scheme,the design of the chain meets the requirements of corrosion resistance,wear resistance and higher strength