Secondary curve behaviour in Lenke IC class adolescent idiopathic scoliosis following video assisted thoracoscopic spinal fusion

Introduction. Ideally after selective thoracic fusion for Lenke Class IC (i.e. major thoracic / secondary lumbar) curves, the lumbar spine will spontaneously accommodate to the corrected position of the thoracic curve, thereby achieving a balanced spine, avoiding the need for fusion of lumbar spinal segments1. The purpose of this study was to evaluate the behaviour of the lumbar curve in Lenke IC class adolescent idiopathic scoliosis (AIS) following video-assisted thoracoscopic spinal fusion and instrumentation (VATS) of the major thoracic curve. Methods. A retrospective review of 22 consecutive patients with AIS who underwent VATS by a single surgeon was conducted. The results were compared to published literature examining the behaviour of the secondary lumbar curve where other surgical approaches were employed. Results. Twenty-two patients (all female) with AIS underwent VATS. All major thoracic curves were right convex. The average age at surgery was 14 years (range 10 to 22 years). On average 6.7 levels (6 to 8) were instrumented. The mean follow-up was 25.1 months (6 to 36). The pre-operative major thoracic Cobb angle mean was 53.8° (40° to 75°). The pre-operative secondary lumbar Cobb angle mean was 43.9° (34° to 55°). On bending radiographs, the secondary curve corrected to 11.3° (0° to 35°). The rib hump mean measurement was 15.0° (7° to 21°). At latest follow-up the major thoracic Cobb angle measured on average 27.2° (20° to 41°) (p<0.001 – univariate ANOVA) and the mean secondary lumbar curve was 27.3° (15° to 42°) (p<0.001). This represented an uninstrumented secondary curve correction factor of 37.8%. The mean rib hump measured was 6.5° (2° to 15°) (p<0.001). The results above were comparable to published series when open surgery was performed. Discussion. VATS is an effective method of correcting major thoracic curves with secondary lumbar curves. The behaviour of the secondary lumbar curve is consistent with published series when open surgery, both anterior and posterior, is performed.

Elliptic curves, group law, and efficient computation

This thesis is about the derivation of the addition law on an arbitrary elliptic curve and efficiently adding points on this elliptic curve using the derived addition law. The outcomes of this research guarantee practical speedups in higher level operations which depend on point additions. In particular, the contributions immediately find applications in cryptology. Mastered by the 19th century mathematicians, the study of the theory of elliptic curves has been active for decades. Elliptic curves over finite fields made their way into public key cryptography in late 1980’s with independent proposals by Miller [Mil86] and Koblitz [Kob87]. Elliptic Curve Cryptography (ECC), following Miller’s and Koblitz’s proposals, employs the group of rational points on an elliptic curve in building discrete logarithm based public key cryptosystems. Starting from late 1990’s, the emergence of the ECC market has boosted the research in computational aspects of elliptic curves. This thesis falls into this same area of research where the main aim is to speed up the additions of rational points on an arbitrary elliptic curve (over a field of large characteristic). The outcomes of this work can be used to speed up applications which are based on elliptic curves, including cryptographic applications in ECC. The aforementioned goals of this thesis are achieved in five main steps. As the first step, this thesis brings together several algebraic tools in order to derive the unique group law of an elliptic curve. This step also includes an investigation of recent computer algebra packages relating to their capabilities. Although the group law is unique, its evaluation can be performed using abundant (in fact infinitely many) formulae. As the second step, this thesis progresses the finding of the best formulae for efficient addition of points. In the third step, the group law is stated explicitly by handling all possible summands. The fourth step presents the algorithms to be used for efficient point additions. In the fifth and final step, optimized software implementations of the proposed algorithms are presented in order to show that theoretical speedups of step four can be practically obtained. In each of the five steps, this thesis focuses on five forms of elliptic curves over finite fields of large characteristic. A list of these forms and their defining equations are given as follows: (a) Short Weierstrass form, y2 = x3 + ax + b, (b) Extended Jacobi quartic form, y2 = dx4 + 2ax2 + 1, (c) Twisted Hessian form, ax3 + y3 + 1 = dxy, (d) Twisted Edwards form, ax2 + y2 = 1 + dx2y2, (e) Twisted Jacobi intersection form, bs2 + c2 = 1, as2 + d2 = 1, These forms are the most promising candidates for efficient computations and thus considered in this work. Nevertheless, the methods employed in this thesis are capable of handling arbitrary elliptic curves. From a high level point of view, the following outcomes are achieved in this thesis. - Related literature results are brought together and further revisited. For most of the cases several missed formulae, algorithms, and efficient point representations are discovered. - Analogies are made among all studied forms. For instance, it is shown that two sets of affine addition formulae are sufficient to cover all possible affine inputs as long as the output is also an affine point in any of these forms. In the literature, many special cases, especially interactions with points at infinity were omitted from discussion. This thesis handles all of the possibilities. - Several new point doubling/addition formulae and algorithms are introduced, which are more efficient than the existing alternatives in the literature. Most notably, the speed of extended Jacobi quartic, twisted Edwards, and Jacobi intersection forms are improved. New unified addition formulae are proposed for short Weierstrass form. New coordinate systems are studied for the first time. - An optimized implementation is developed using a combination of generic x86-64 assembly instructions and the plain C language. The practical advantages of the proposed algorithms are supported by computer experiments. - All formulae, presented in the body of this thesis, are checked for correctness using computer algebra scripts together with details on register allocations.

Exponential asymptotics with multiple stokes lines

When asymptotic series methods are applied in order to solve problems that arise in applied mathematics in the limit that some parameter becomes small, they are unable to demonstrate behaviour that occurs on a scale that is exponentially small compared to the algebraic terms of the asymptotic series. There are many examples of physical systems where behaviour on this scale has important effects and, as such, a range of techniques known as exponential asymptotic techniques were developed that may be used to examinine behaviour on this exponentially small scale. Many problems in applied mathematics may be represented by behaviour within the complex plane, which may subsequently be examined using asymptotic methods. These problems frequently demonstrate behaviour known as Stokes phenomenon, which involves the rapid switches of behaviour on an exponentially small scale in the neighbourhood of some curve known as a Stokes line. Exponential asymptotic techniques have been applied in order to obtain an expression for this exponentially small switching behaviour in the solutions to orginary and partial differential equations. The problem of potential flow over a submerged obstacle has been previously considered in this manner by Chapman & Vanden-Broeck (2006). By representing the problem in the complex plane and applying an exponential asymptotic technique, they were able to detect the switching, and subsequent behaviour, of exponentially small waves on the free surface of the flow in the limit of small Froude number, specifically considering the case of flow over a step with one Stokes line present in the complex plane. We consider an extension of this work to flow configurations with multiple Stokes lines, such as flow over an inclined step, or flow over a bump or trench. The resultant expressions are analysed, and demonstrate interesting implications, such as the presence of exponentially sub-subdominant intermediate waves and the possibility of trapped surface waves for flow over a bump or trench. We then consider the effect of multiple Stokes lines in higher order equations, particu- larly investigating the behaviour of higher-order Stokes lines in the solutions to partial differential equations. These higher-order Stokes lines switch off the ordinary Stokes lines themselves, adding a layer of complexity to the overall Stokes structure of the solution. Specifically, we consider the different approaches taken by Howls et al. (2004) and Chap- man & Mortimer (2005) in applying exponential asymptotic techniques to determine the higher-order Stokes phenomenon behaviour in the solution to a particular partial differ- ential equation.

Algebraic analysis of small scale LEX-BES

This paper examines the algebraic cryptanalysis of small scale variants of the LEX-BES. LEX-BES is a stream cipher based on the Advanced Encryption Standard (AES) block cipher. LEX is a generic method proposed for constructing a stream cipher from a block cipher, initially introduced by Biryukov at eSTREAM, the ECRYPT Stream Cipher project in 2005. The Big Encryption System (BES) is a block cipher introduced at CRYPTO 2002 which facilitates the algebraic analysis of the AES block cipher. In this paper, experiments were conducted to find solution of the equation system describing small scale LEX-BES using Gröbner Basis computations. This follows a similar approach to the work by Cid, Murphy and Robshaw at FSE 2005 that investigated algebraic cryptanalysis on small scale variants of the BES. The difference between LEX-BES and BES is that due to the way the keystream is extracted, the number of unknowns in LEX-BES equations is fewer than the number in BES. As far as the author knows, this attempt is the first at creating solvable equation systems for stream ciphers based on the LEX method using Gröbner Basis computations.

An analysis of the RC4 family of stream ciphers against algebraic attacks

To date, most applications of algebraic analysis and attacks on stream ciphers are on those based on lin- ear feedback shift registers (LFSRs). In this paper, we extend algebraic analysis to non-LFSR based stream ciphers. Specifically, we perform an algebraic analysis on the RC4 family of stream ciphers, an example of stream ciphers based on dynamic tables, and inves- tigate its implications to potential algebraic attacks on the cipher. This is, to our knowledge, the first pa- per that evaluates the security of RC4 against alge- braic attacks through providing a full set of equations that describe the complex word manipulations in the system. For an arbitrary word size, we derive alge- braic representations for the three main operations used in RC4, namely state extraction, word addition and state permutation. Equations relating the inter- nal states and keystream of RC4 are then obtained from each component of the cipher based on these al- gebraic representations, and analysed in terms of their contributions to the security of RC4 against algebraic attacks. Interestingly, it is shown that each of the three main operations contained in the components has its own unique algebraic properties, and when their respective equations are combined, the resulting system becomes infeasible to solve. This results in a high level of security being achieved by RC4 against algebraic attacks. On the other hand, the removal of an operation from the cipher could compromise this security. Experiments on reduced versions of RC4 have been performed, which confirms the validity of our algebraic analysis and the conclusion that the full RC4 stream cipher seems to be immune to algebraic attacks at present.

Improved algebraic cryptanalysis of QUAD, Bivium and Trivium via graph partitioning on equation systems

We present a novel approach for preprocessing systems of polynomial equations via graph partitioning. The variable-sharing graph of a system of polynomial equations is defined. If such graph is disconnected, then the corresponding system of equations can be split into smaller ones that can be solved individually. This can provide a tremendous speed-up in computing the solution to the system, but is unlikely to occur either randomly or in applications. However, by deleting certain vertices on the graph, the variable-sharing graph could be disconnected in a balanced fashion, and in turn the system of polynomial equations would be separated into smaller systems of near-equal sizes. In graph theory terms, this process is equivalent to finding balanced vertex partitions with minimum-weight vertex separators. The techniques of finding these vertex partitions are discussed, and experiments are performed to evaluate its practicality for general graphs and systems of polynomial equations. Applications of this approach in algebraic cryptanalysis on symmetric ciphers are presented: For the QUAD family of stream ciphers, we show how a malicious party can manufacture conforming systems that can be easily broken. For the stream ciphers Bivium and Trivium, we nachieve significant speedups in algebraic attacks against them, mainly in a partial key guess scenario. In each of these cases, the systems of polynomial equations involved are well-suited to our graph partitioning method. These results may open a new avenue for evaluating the security of symmetric ciphers against algebraic attacks.

Algebraic attacks on clock-controlled stream ciphers

Stream ciphers are encryption algorithms used for ensuring the privacy of digital telecommunications. They have been widely used for encrypting military communications, satellite communications, pay TV encryption and for voice encryption of both fixed lined and wireless networks. The current multi year European project eSTREAM, which aims to select stream ciphers suitable for widespread adoptation, reflects the importance of this area of research. Stream ciphers consist of a keystream generator and an output function. Keystream generators produce a sequence that appears to be random, which is combined with the plaintext message using the output function. Most commonly, the output function is binary addition modulo two. Cryptanalysis of these ciphers focuses largely on analysis of the keystream generators and of relationships between the generator and the keystream it produces. Linear feedback shift registers are widely used components in building keystream generators, as the sequences they produce are well understood. Many types of attack have been proposed for breaking various LFSR based stream ciphers. A recent attack type is known as an algebraic attack. Algebraic attacks transform the problem of recovering the key into a problem of solving multivariate system of equations, which eventually recover the internal state bits or the key bits. This type of attack has been shown to be effective on a number of regularly clocked LFSR based stream ciphers. In this thesis, algebraic attacks are extended to a number of well known stream ciphers where at least one LFSR in the system is irregularly clocked. Applying algebriac attacks to these ciphers has only been discussed previously in the open literature for LILI-128. In this thesis, algebraic attacks are first applied to keystream generators using stop-and go clocking. Four ciphers belonging to this group are investigated: the Beth-Piper stop-and-go generator, the alternating step generator, the Gollmann cascade generator and the eSTREAM candidate: the Pomaranch cipher. It is shown that algebraic attacks are very effective on the first three of these ciphers. Although no effective algebraic attack was found for Pomaranch, the algebraic analysis lead to some interesting findings including weaknesses that may be exploited in future attacks. Algebraic attacks are then applied to keystream generators using (p; q) clocking. Two well known examples of such ciphers, the step1/step2 generator and the self decimated generator are investigated. Algebraic attacks are shown to be very powerful attack in recovering the internal state of these generators. A more complex clocking mechanism than either stop-and-go or the (p; q) clocking keystream generators is known as mutual clock control. In mutual clock control generators, the LFSRs control the clocking of each other. Four well known stream ciphers belonging to this group are investigated with respect to algebraic attacks: the Bilateral-stop-and-go generator, A5/1 stream cipher, Alpha 1 stream cipher, and the more recent eSTREAM proposal, the MICKEY stream ciphers. Some theoretical results with regards to the complexity of algebraic attacks on these ciphers are presented. The algebraic analysis of these ciphers showed that generally, it is hard to generate the system of equations required for an algebraic attack on these ciphers. As the algebraic attack could not be applied directly on these ciphers, a different approach was used, namely guessing some bits of the internal state, in order to reduce the degree of the equations. Finally, an algebraic attack on Alpha 1 that requires only 128 bits of keystream to recover the 128 internal state bits is presented. An essential process associated with stream cipher proposals is key initialization. Many recently proposed stream ciphers use an algorithm to initialize the large internal state with a smaller key and possibly publicly known initialization vectors. The effect of key initialization on the performance of algebraic attacks is also investigated in this thesis. The relationships between the two have not been investigated before in the open literature. The investigation is conducted on Trivium and Grain-128, two eSTREAM ciphers. It is shown that the key initialization process has an effect on the success of algebraic attacks, unlike other conventional attacks. In particular, the key initialization process allows an attacker to firstly generate a small number of equations of low degree and then perform an algebraic attack using multiple keystreams. The effect of the number of iterations performed during key initialization is investigated. It is shown that both the number of iterations and the maximum number of initialization vectors to be used with one key should be carefully chosen. Some experimental results on Trivium and Grain-128 are then presented. Finally, the security with respect to algebraic attacks of the well known LILI family of stream ciphers, including the unbroken LILI-II, is investigated. These are irregularly clock- controlled nonlinear filtered generators. While the structure is defined for the LILI family, a particular paramater choice defines a specific instance. Two well known such instances are LILI-128 and LILI-II. The security of these and other instances is investigated to identify which instances are vulnerable to algebraic attacks. The feasibility of recovering the key bits using algebraic attacks is then investigated for both LILI- 128 and LILI-II. Algebraic attacks which recover the internal state with less effort than exhaustive key search are possible for LILI-128 but not for LILI-II. Given the internal state at some point in time, the feasibility of recovering the key bits is also investigated, showing that the parameters used in the key initialization process, if poorly chosen, can lead to a key recovery using algebraic attacks.

Algebraic analysis of small Scale LEX-BES

This work examines the algebraic cryptanalysis of small scale variants of the LEX-BES. LEX-BES is a stream cipher based on the Advanced Encryption Standard (AES) block cipher. LEX is a generic method proposed for constructing a stream cipher from a block cipher, initially introduced by Biryukov at eSTREAM, the ECRYPT Stream Cipher project in 2005. The Big Encryption System (BES) is a block cipher introduced at CRYPTO 2002 which facilitates the algebraic analysis of the AES block cipher. In this article, experiments were conducted to find solutions of equation systems describing small scale LEX-BES using Gröbner Basis computations. This follows a similar approach to the work by Cid, Murphy and Robshaw at FSE 2005 that investigated algebraic cryptanalysis on small scale variants of the BES. The difference between LEX-BES and BES is that due to the way the keystream is extracted, the number of unknowns in LEX-BES equations is fewer than the number in BES. As far as the authors know, this attempt is the first at creating solvable equation systems for stream ciphers based on the LEX method using Gröbner Basis computations.

Stochastic analysis of the VEGF receptor response curve

Recently, an analysis of the response curve of the vascular endothelial growth factor (VEGF) receptor and its application to cancer therapy was described in [T. Alarcón, and K. Page, J. R. Soc. Lond. Interface 4, 283–304 (2007)]. The analysis is significantly extended here by demonstrating that an alternative computational strategy, namely the Krylov FSP algorithm for the direct solution of the chemical master equation, is feasible for the study of the receptor model. The new method allows us to further investigate the hypothesis of symmetry in the stochastic fluctuations of the response. Also, by augmenting the original model with a single reversible reaction we formulate a plausible mechanism capable of realizing a bimodal response, which is reported experimentally but which is not exhibited by the original model. The significance of these findings for mechanisms of tumour resistance to antiangiogenic therapy is discussed.

A different algebraic analysis of the ZUC stream cipher

Existing algebraic analyses of the ZUC cipher indicate that the cipher should be secure against algebraic attacks. In this paper, we present an alternative algebraic analysis method for the ZUC stream cipher, where a combiner is used to represent the nonlinear function and to derive equations representing the cipher. Using this approach, the initial states of ZUC can be recovered from 2^97 observed words of keystream, with a complexity of 2^282 operations. This method is more successful when applied to a modified version of ZUC, where the number of output words per clock is increased. If the cipher outputs 120 bits of keystream per clock, the attack can succeed with 219 observed keystream bits and 2^47 operations. Therefore, the security of ZUC against algebraic attack could be significantly reduced if its throughput was to be increased for efficiency.

Algebraic analysis of the SSS stream cipher

Both the SSS and SOBER-t32 stream cipher designs use a single word-based shift register and a nonlinear filter function to produce keystream. In this paper we show that the algebraic attack method previously applied to SOBER-t32 is prevented from succeeding on SSS by the use of the key dependent substitution box (SBox) in the nonlinear filter of SSS. Additional assumptions and modifications to the SSS cipher in an attempt to enable algebraic analysis result in other difficulties that also render the algebraic attack infeasible. Based on these results, we conclude that a well chosen key-dependent substitution box used in the nonlinear filter of the stream cipher provides resistance against such algebraic attacks.

High-resolution DNA melt curve analysis of the clustered, regularly interspaced short-palindromic-repeat locus of Campylobacter jejuni

A novel method for genotyping the clustered, regularly interspaced short-palindromic-repeat (CRISPR) locus of Campylobacter jejuni is described. Following real-time PCR, CRISPR products were subjected to high-resolution melt (HRM) analysis, a new technology that allows precise melt profile determination of amplicons. This investigation shows that the CRISPR HRM assay provides a powerful addition to existing C. jejuni genotyping methods and emphasizes the potential of HRM for genotyping short sequence repeats in other species