A population study of binocular function

As part of a genome-wide association study (GWAS) of perceptual traits in healthy adults, we measured stereo acuity, the duration of alternative percepts in binocular rivalry and the extent of dichoptic masking in 1060 participants. We present the distributions of the measures, the correlations between measures, and their relationships to other psychophysical traits. We report sex differences, and correlations with age, interpupillary distance, eye dominance, phorias, visual acuity and personality. The GWAS, using data from 988 participants, yielded one genetic association that passed a permutation test for significance: The variant rs1022907 in the gene VTI1A was associated with self-reported ability to see autostereograms. We list a number of other suggestive genetic associations (p<10^-5).

The BRUTUS Automatic Cryptanalytic Framework: Testing CAESAR Authenticated Encryption Candidates for Weaknesses

This report summarizes our results from security analysis covering all 57 competitions for authenticated encryption: security, applicability, and robustness (CAESAR) first-round candidates and over 210 implementations. We have manually identified security issues with three candidates, two of which are more serious, and these ciphers have been withdrawn from the competition. We have developed a testing framework, BRUTUS, to facilitate automatic detection of simple security lapses and susceptible statistical structures across all ciphers. From this testing, we have security usage notes on four submissions and statistical notes on a further four. We highlight that some of the CAESAR algorithms pose an elevated risk if employed in real-life protocols due to a class of adaptive-chosen-plaintext attacks. Although authenticated encryption with associated data are often defined (and are best used) as discrete primitives that authenticate and transmit only complete messages, in practice, these algorithms are easily implemented in a fashion that outputs observable ciphertext data when the algorithm has not received all of the (attacker-controlled) plaintext. For an implementor, this strategy appears to offer seemingly harmless and compliant storage and latency advantages. If the algorithm uses the same state for secret keying information, encryption, and integrity protection, and the internal mixing permutation is not cryptographically strong, an attacker can exploit the ciphertext–plaintext feedback loop to reveal secret state information or even keying material. We conclude that the main advantages of exhaustive, automated cryptanalysis are that it acts as a very necessary sanity check for implementations and gives the cryptanalyst insights that can be used to focus more specific attack methods on given candidates.

ANRIL Variants and Aggressive Periodontitis in European and African Populations

Introduction: The chromosome 9p21 locus has been identified as a marker of coronary artery disease. In this locus studies have focused on variations in the ANRIL gene that has also been identified as a strong candidate for association with aggressive periodontitis (AgP).
Objective: To investigate possible associations between gene variants of ANRIL and AgP in European and African populations.
Methods: European AgP cases (n= 213) and age-matched periodontally healthy controls (n= 81) were recruited from centres in the United Kingdom (Belfast, Glasgow, Newcastle and London). African AgP cases (n= 95) and controls (n= 105) were recruited in Khartoum, Sudan. Five single nucleotide polymorphisms (SNPs) in ANRIL were genotyped using Sequenom and analysed using Haploview with permutation testing to correct for multiple candidates. Odds ratios (OR) and 95% confidence intervals (95%CI) were calculated.
Results: In the European subjects there was a significant association between rs518394 (p=0.0013; OR = 1.81, 95%CI 1.26-2.61) and rs1333049 (p=0.0028; OR = 1.75, 95%CI 1.21-2.52) and AgP. These associations remained significant after permutation testing. In addition there was an association between rs 1360590 (p=0.035) and AgP in females. In the African subjects there was a significant association between only one SNP rs1537415 and AgP (p=0.036; OR = 1.59, 95%CI 1.04-2.43), however, this was not significant following permutation testing. There were no significant associations with rs3217992 in either population.
Conclusions: SNP variants in the ANRIL locus were shown to be significantly associated with AgP in a European population and for the first time in an African population confirming this as the best replicated locus for aggressive periodontitis.

Building Support Vector Machines in the Context of Regularised Least Squares

This paper formulates a linear kernel support vector machine (SVM) as a regularized least-squares (RLS) problem. By defining a set of indicator variables of the errors, the solution to the RLS problem is represented as an equation that relates the error vector to the indicator variables. Through partitioning the training set, the SVM weights and bias are expressed analytically using the support vectors. It is also shown how this approach naturally extends to Sums with nonlinear kernels whilst avoiding the need to make use of Lagrange multipliers and duality theory. A fast iterative solution algorithm based on Cholesky decomposition with permutation of the support vectors is suggested as a solution method. The properties of our SVM formulation are analyzed and compared with standard SVMs using a simple example that can be illustrated graphically. The correctness and behavior of our solution (merely derived in the primal context of RLS) is demonstrated using a set of public benchmarking problems for both linear and nonlinear SVMs.