Optimizing Dynamic Traces Using Symbolic Execution

Σε αυτή τη διπλωματική εργασία εξετάζουμε ίχνη εκτέλεσης διεργασιών και εκτελούμε βελτιστοποιήσεις πάνω σε αυτά. Εστιάζουμε στην πιθανότητα βελτιστοποίησης του κώδικα έχοντας κάνει υποθέσεις για την πρόσβαση στη μνήμη και τον έλεγχο ροής. Με βάση τις υποθέσεις μας, χρησιμοποιούμε συμβολική εκτέλεση ώστε (α) να βρούμε ευκαιρίες βελτιστοποίησης στο εύρος του ίχνους και (β) να εκτελέσουμε τις βελτιστοποιήσεις αυτές. Δείχνουμε ότι ευκαιρίες βελτιστοποίησης υπάρχουν σε ίχνη πραγματικών προγραμμάτων και θεωρούμε τρόπους για το πώς οι υποθέσεις μας μπορούν να προσαρμοστούν στις προϋποθέσεις ενός δυναμικού περιβάλλοντος.In this thesis we examine and optimize execution traces of binaries. We focus on the potential for optimization of machine code by making assumptions about memory accesses and control flow. Based on our assumptions, we use symbolic execution to (a) find optimization opportunities in the trace scope and (b) perform these optimizations. We show that optimization opportunities exist in traces found in real programs, and we suggest how our assumptions can be adapted to the needs of a dynamic environment

Immuno-Interface Score to Predict Outcome in Colorectal Cancer Independent of Microsatellite Instability Status

Tumor-associated immune cells have been shown to predict patient outcome in colorectal (CRC) and other cancers. Spatial digital image analysis-based cell quantification increases the informative power delivered by tumor microenvironment features and leads to new prognostic scoring systems. In this study we evaluated the intratumoral density of immunohistochemically stained CD8, CD20 and CD68 cells in 87 cases of CRC (48 were microsatellite stable, MSS, and 39 had microsatellite instability, MSI) in both the intratumoral tumor tissue and within the tumor-stroma interface zone (IZ) which was extracted by a previously developed unbiased hexagonal grid analytics method. Indicators of immune-cell gradients across the extracted IZ were computed and explored along with absolute cell densities, clinicopathological and molecular data, including gene mutation (BRAF, KRAS, PIK3CA) and MSI status. Multiple regression modeling identified (p < 0.0001) three independent prognostic factors: CD8+ and CD20+ Immunogradient indicators, that reflect cell migration towards the tumor, were associated with improved patient survival, while the infiltrative tumor growth pattern was linked to worse patient outcome. These features were combined into CD8-CD20 Immunogradient and immuno-interface scores which outperformed both tumor-node-metastasis (TNM) staging and molecular characteristics, and importantly, revealed high prognostic value both in MSS and MSI CRCs

Targeting gp100 and TRP-2 with a DNA vaccine: incorporating T cell epitopes with a human IgG1 antibody induces potent T cell responses that are associated with favourable clinical outcome in a phase I/II trial

A DNA vaccine, SCIB1, incorporating two CD8 and two CD4 epitopes from TRP-2/gp100 was evaluated in patients with metastatic melanoma. Each patient received SCIB1 via intramuscular injection with electroporation. The trial was designed to find the safest dose of SCIB1 which induced immune/clinical responses in patients with or without tumour. Fifteen patients with tumor received SCIB1 doses of 0.4-8 mg whilst 20 fully-resected patients received 2-8 mg doses. Twelve patients elected to continue immunization every 3 months for up to 39 months. SCIB1 induced dose-dependent T cell responses in 88% of patients with no serious adverse effects or dose limiting toxicities. The intensity of the T cell responses was significantly higher in patients receiving 4 mg doses without tumor when compared to those with tumor (p< 0.01). In contrast, patients with tumor showed a significantly higher response to the 8 mg dose than the 4 mg dose (p< 0.03) but there was no significant difference in the patients without tumor. One of 15 patients with measurable disease showed an objective tumor response and 7/15 showed stable disease. 5/20 fully-resected patients have experienced disease recurrence but all remained alive at the cut-off date with a median observation time of 37 months. A positive clinical outcome was associated with MHC-I and MHC-II expression on tumors prior to therapy (p=0.027). We conclude that SCIB1 is well tolerated and stimulates potent T cell responses in melanoma patients. It deserves further evaluation as a single agent adjuvant therapy or in combination with checkpoint inhibitors in advanced disease

N_LyST: a simple and rapid screening test for Lynch Syndrome

Aims: We sought to use PCR followed by high-resolution melting (HRM) analysis to develop a single closed-tube screening panel to screen for Lynch Syndrome. This comprises tests for microsatellite instability (MSI), MLH1 methylation promoter and BRAF mutation.Methods:For MSI-testing, 5 mononucleotide markers (BAT25, BAT26, BCAT25, MYB, EWSR1) were developed. In addition, primers were designed to interrogate Region C of the MLH1 promoter for methylation (using bisulphite-modified DNA) and to test for mutations in codon 600 of BRAF. Two separate cohorts from Nottingham (n = 99, 46 with MSI, 53 being microsatellite stable (MSS)) and Edinburgh (n=88, 45 MSI, 43 MSS). Results:All the cases (n=187) were blind tested for MSI and all were correctly characterised by our panel. The MLH1 promoter and BRAF were tested only in the Nottingham cohort. Successful blinded analysis was performed on the MLH1 promoter in 97 cases. All MSS cases showed a pattern of non-methylation whilst 41/44 cases with MSI showed full methylation. The three cases with MSI and a non-methylated pattern had aberrations in MSH2 and MSH6 expression. BRAF mutation was detected in 61% of MSI cases and 11% of MSS cases. Finally, 12 cases were blind screened by using the whole panel as a single test. Of these, 5 were identified as MSS, 4 as MSI/non-LS and 3 as MSI/possible LS. These results were concordant with the previous data.Conclusion: We describe the Nottingham Lynch Syndrome Test (N_LyST). This is a quick simple cheap method for screening for Lynch Syndrome

Fabry disease and incidence of cancer

Abstract Background Fabry disease is an X-linked lysosomal storage disorder caused by deficient activity of α-galactosidase A and the resulting accumulation of the glycosphingolipid globotriaosylceramide (Gb3) and its derivatives, including globotriaosylsphingosine (Lyso-Gb3). Increased cellular and plasma levels of Gb3 and Lyso-Gb3 affect multiple organs, with specific clinical consequences for the kidneys, heart and brain. There is growing evidence that alterations in glycosphingolipids may have an oncogenic role and this prompted a review of cases of cancer and benign lesions in a large single centre cohort of Fabry patients. We also explored whether there is a difference in the risk of cancer in Fabry patients compared to the general population. Results Our results suggest that Fabry patients may have a marginally reduced rate of all cancer (incidence rate ratio 0.61, 95% confidence interval 0.37 to 0.99) but possibly increased rates of melanoma, urological malignancies and meningiomas. Conclusion Greater knowledge and awareness of cancer in patients with Fabry disease may help identify at-risk individuals and elucidate cancer mechanisms in this rare inherited disease, which may potentially be relevant to the wider cancer population