Development of real-time PCR assay for the early diagnosis, treatment response prediction and monitoring of nasopharyngeal carcinoma (NPC) disease

Nasopharyngeal carcinoma (NPC) is a non-lymphomatous squamous cell carcinoma that develops in the epithelial cells layer covering the surface of the nasopharynx. NPC is considered a diagnostic challenge to clinicians due to the difficulty in nasopharynx examination, and non-specific symptoms. The Epstein–Barr virus (EBV) is well-associated with NPC. In addition, EBV LMP1 30 bp deletion was shown to play a vital role in enhanced oncogenic behaviour of EBV infected cells and results in more aggressive EBV-related tumour phenotypes. Therefore, this study intended to develop an innovative Taqman hydrolysis probe-based qPCR to detect the EBV's LMP1 30 bp deletion using whole blood samples from NPC patients. This developed assay will help the clinicians in early diagnosis, treatment response prediction, understand the extent of treatment effectiveness, and follow-up monitoring of NPC patients after treatment. In this developed i-qPCR, the mutant-specific primers, probes and multi-points degenerative blocker were designed. The Taqman hydrolysis probe-based qPCR parameters to detect the EBV's LMP1 30 bp deletion were also optimised. Internal control (IAC) was incorporated to rule out the false negative result. The demographic data of NPC patients were collected and used in the statistical analysis of this study. The assay validation was accomplished based on MIQE guidelines. The developed assay's analytical sensitivity was performed using 10-fold serial dilutions of MT gBLOCK (synthetic DNA). The analytical specificity was evaluated using 48 bacterial, fungal and virus genomic DNA and 12 extracted genomic DNA from archived biopsy tissue and fine-needle aspiration samples of NPC patients. The diagnostic evaluation of the developed assay was performed on 109 prospective specimens from NPC patients, non-NPC cancer patients and healthy individuals. The LOD of this developed assay was 173 copies/assay. The diagnostic evaluation showed 100% specificity, 83.3% sensitivity, 100% PPV and 98.7% NPV. A significant association was found between clinician treatment response prediction and Cq values of 30 bp deletion in this study (P-value= 0.033). In conclusion, this study was effective in developing an i-qPCR assay for early detection of 30 bp deletion tumour marker with high specificity and sensitivity, to help clinicians in treatment response prediction, and determine treatment effectiveness among NPC patients

Comparing the Preventive Measures of Prophet Muhammads Teachings to Preventive Medicine in Combating COVID-19

This study follows the partial inductive approach to identify the Prophetic Sayings pertaining to the subject. By comparing with contemporary preventive medicine principles, this study aims to present the most salient preventive measures found in the teachings of Prophet Muhammad and which can be useful in preventing COVID-19 epidemic. In addition, it follows the analytical approach in studying the subjects which could be related to the protection against infection transmission and compare them with well-established principles of preventive medicine. And the study follows a deductive approach to identify the most important rules and instructions pertaining to the subject from the Prophetic Sayings. The study found that the most preventive principles found in the Prophetic sayings are daily hand washing while massaging them, ensuring the cleanliness of the mouth and nose, encouraging the use of available means such as handkerchiefs to prevent the spread of coughing and sneezing droplets, burying the secretions of the nose and mouth if handkerchiefs are not available, and the frequent use of toothpicks to brush the teeth and tongue. Furthermore, the study found that the Prophetic Sayings accentuate the importance of strictly enforced isolation and quarantine during an epidemic. Such measures are found to coincide with the teachings of Islamic faith

Lower Bounds on the Time/Memory Tradeoff of Function Inversion

We study time/memory tradeoffs of function inversion: an algorithm, i.e., an inverter, equipped with an $s$-bit advice on a randomly chosen function $f\colon [n] \mapsto [n]$ and using $q$ oracle queries to $f$, tries to invert a randomly chosen output $y$ of $f$, i.e., to find $x\in f^{-1}(y)$. Much progress was done regarding adaptive function inversion - the inverter is allowed to make adaptive oracle queries. Hellman [IEEE transactions on Information Theory \u2780] presented an adaptive inverter that inverts with high probability a random $f$. Fiat and Naor [SICOMP \u2700] proved that for any $s,q$ with $s^3 q = n^3$ (ignoring low-order terms), an $s$-advice, $q$-query variant of Hellman\u27s algorithm inverts a constant fraction of the image points of any function. Yao [STOC \u2790] proved a lower bound of $sq\ge n$ for this problem. Closing the gap between the above lower and upper bounds is a long-standing open question. Very little is known for the non-adaptive variant of the question - the inverter chooses its queries in advance. The only known upper bounds, i.e., inverters, are the trivial ones (with $s+q= n$), and the only lower bound is the above bound of Yao. In a recent work, Corrigan-Gibbs and Kogan [TCC \u2719] partially justified the difficulty of finding lower bounds on non-adaptive inverters, showing that a lower bound on the time/memory tradeoff of non-adaptive inverters implies a lower bound on low-depth Boolean circuits. Bounds that, for a strong enough choice of parameters, are notoriously hard to prove. We make progress on the above intriguing question, both for the adaptive and the non-adaptive case, proving the following lower bounds on restricted families of inverters: - Linear-advice (adaptive inverter): If the advice string is a linear function of $f$ (e.g., $A\times f$, for some matrix $A$, viewing $f$ as a vector in $[n]^n$), then $s+q \in \Omega(n)$. The bound generalizes to the case where the advice string of $f_1 + f_2$, i.e., the coordinate-wise addition of the truth tables of $f_1$ and $f_2$, can be computed from the description of $f_1$ and $f_2$ by a low communication protocol. - Affine non-adaptive decoders: If the non-adaptive inverter has an affine decoder - it outputs a linear function, determined by the advice string and the element to invert, of the query answers - then $s \in \Omega(n)$ (regardless of $q$). - Affine non-adaptive decision trees: If the non-adaptive inversion algorithm is a $d$-depth affine decision tree - it outputs the evaluation of a decision tree whose nodes compute a linear function of the answers to the queries - and $q 0$, then $s\in \Omega(n/d \log n)$

Offline Witness Encryption with Semi-Adaptive Security

The first construction of Witness Encryption (WE) by Garg et al. (STOC 2013) has led to many exciting avenues of research in the past years. A particularly interesting variant is Offline WE (OWE) by Abusalah et al. (ACNS 2016), as the encryption algorithm uses neither obfuscation nor multilinear maps. Current OWE schemes provide only selective security. That is, the adversary must commit to their challenge messages $m_0$ and $m_1$ before seeing the public parameters. We provide a new, generic framework to construct OWE, which achieves adaptive security in the sense that the adversary may choose their challenge messages adaptively. We call this semi-adaptive security, because - as in prior work - the instance of the considered NP language that is used to create the challenge ciphertext must be fixed before the parameters are generated in the security proof. We show that our framework gives the first OWE scheme with constant ciphertext overhead even for messages of polynomially-bounded size. We achieve this by introducing a new variant of puncturable encryption defined by Green and Miers (S&P 2015) and combining it with the iO-based approach of Abusalah et al. Finally, we show that our framework can be easily extended to construct the first Extractable Offline Witness Encryption (EOWE), by using extractability obfuscation of Boyle et al. (TCC 2014) in place of iO, opening up even more possible applications. The obfuscation is needed only for our public parameters, but its functionality can be realised with a Trusted Execution Environment (TEE), which means we have a very efficient scheme with ciphertexts consisting of only 5 group elements

Game theoretic path selection to support security in device-to-device communications

Device-to-Device (D2D) communication is expected to be a key feature sup- ported by 5G networks, especially due to the proliferation of Mobile Edge Computing (MEC), which has a prominent role in reducing network stress by shifting computational tasks from the Internet to the mobile edge. Apart from being part of MEC, D2D can extend cellular coverage allowing users to communicate directly when telecommunication infrastructure is highly congested or absent. This significant departure from the typical cellular paradigm imposes the need for de- centralised network routing protocols. Moreover, enhanced capabilities of mobile devices and D2D networking will likely result in proliferation of new malware types and epidemics. Although the literature is rich in terms of D2D routing protocols that enhance quality-of-service and energy consumption, they provide only basic security support, e.g., in the form of encryption. Routing decisions can, however, contribute to collaborative detection of mobile malware by leveraging different kinds of anti-malware software installed on mobile devices. Benefiting from the cooperative nature of D2D communications, devices can rely on each other’s contributions to detect malware. The impact of our work is geared to- wards having more malware-free D2D networks. To achieve this, we designed and implemented a novel routing protocol for D2D communications that optimises routing decisions for explicitly improving malware detection. The protocol identifies optimal network paths, in terms of malware mitigation and energy spent for malware detection, based on a game theoretic model. Diverse capabilities of network devices running different types of anti-malware software and their potential for inspecting messages relayed towards an intended destination device are leveraged using game theoretic tools. An optimality analysis of both Nash and Stackelberg security games is undertaken, including both zero and non-zero sum variants, and the Defender’s equilibrium strategies. By undertaking network simulations, theoretical results obtained are illustrated through randomly generated network scenarios showing how our protocol outperforms conventional routing protocols, in terms of expected payoff, which consists of: security damage inflicted by malware and malware detection cost

Accelerated sparse matrix-based computation of electromagnetic transients

202207 bckwVersion of RecordOthersNatural Sciences and Engineering Research Council of CanadaPublishe

CPU based parallel computation of electromagnetic transients for large power grids

202307 bckwAccepted ManuscriptSelf-fundedPublishe