Incidence and mechanism of the pivot shift. An in vitro study.

Accepted versio

Identifying the impact of G-quadruplexes on Affymetrix 3' arrays using cloud computing.

A tetramer quadruplex structure is formed by four parallel strands of DNA/ RNA containing runs of guanine. These quadruplexes are able to form because guanine can Hoogsteen hydrogen bond to other guanines, and a tetrad of guanines can form a stable arrangement. Recently we have discovered that probes on Affymetrix GeneChips that contain runs of guanine do not measure gene expression reliably. We associate this finding with the likelihood that quadruplexes are forming on the surface of GeneChips. In order to cope with the rapidly expanding size of GeneChip array datasets in the public domain, we are exploring the use of cloud computing to replicate our experiments on 3' arrays to look at the effect of the location of G-spots (runs of guanines). Cloud computing is a recently introduced high-performance solution that takes advantage of the computational infrastructure of large organisations such as Amazon and Google. We expect that cloud computing will become widely adopted because it enables bioinformaticians to avoid capital expenditure on expensive computing resources and to only pay a cloud computing provider for what is used. Moreover, as well as financial efficiency, cloud computing is an ecologically-friendly technology, it enables efficient data-sharing and we expect it to be faster for development purposes. Here we propose the advantageous use of cloud computing to perform a large data-mining analysis of public domain 3' arrays

First principles simulations of 2D Cu superlattices on the MgO(001) surface

First principles slab simulations of copper 2D superlattices of different densities on the perfect MgO(0 0 1) surface are performed using the DFT method as implemented into the CRYSTAL98 computer code. In order to clarify the nature of interfacial bonding, we consider regular 1/4, 1/2 and I monolayer (ML) coverages and compare results of our calculations with various experimental and theoretical data. Our general conclusion is that the physical adhesion associated with a Cu polarization and charge redistribution gives the predominant contribution to the bonding of the regular Cu 2D layer on the MgO(0 0 1) surface. (C) 2003 Elsevier B.V. All rights reserved

Wilson Loop Renormalization Group Flows

The locally BPS Wilson loop and the pure gauge Wilson loop map under AdS/CFT duality to string world-sheet boundaries with standard and alternate quantizations of the world-sheet fields. This implies an RG flow between the two operators, which we verify at weak coupling. Many additional loop operators exist at strong coupling, with a rich pattern of RG flows.Comment: 10 p, 2 figures. v3: Title change, expanded treatment of RG flow

The effective string spectrum in the orthogonal gauge

The low-energy effective action on long string-like objects in quantum field theory, such as confining strings, includes the Nambu-Goto action and then higher-derivative corrections. This action is diffeomorphism-invariant, and can be analyzed in various gauges. Polchinski and Strominger suggested a specific way to analyze this effective action in the orthogonal gauge, in which the induced metric on the worldsheet is conformally equivalent to a flat metric. Their suggestion leads to a specific term at the next order beyond the Nambu-Goto action. We compute the leading correction to the Nambu-Goto spectrum using the action that includes this term, and we show that it agrees with the leading correction previously computed in the static gauge. This gives a consistency check for the framework of Polchinski and Strominger, and helps to understand its relation to the theory in the static gauge.Comment: 21 page

Effective String Theory and Nonlinear Lorentz Invariance

We study the low-energy effective action governing the transverse fluctuations of a long string, such as a confining flux tube in QCD. We work in the static gauge where this action contains only the transverse excitations of the string. The static gauge action is strongly constrained by the requirement that the Lorentz symmetry, that is spontaneously broken by the long string vacuum, is nonlinearly realized on the Nambu-Goldstone bosons. One solution to the constraints (at the classical level) is the Nambu-Goto action, and the general solution contains higher derivative corrections to this. We show that in 2+1 dimensions, the first allowed correction to the Nambu-Goto action is proportional to the squared curvature of the induced metric on the worldsheet. In higher dimensions, there is a more complicated allowed correction that appears at lower order than the curvature squared. We argue that this leading correction is similar to, but not identical to, the one-loop determinant (\sqrt{-h} R \Box^{-1} R) computed by Polyakov for the bosonic fundamental string.Comment: 15 page

Demographic and clinical profile of patients with juvenile onset open angle glaucoma in southwestern Nigeria

Background: This was a non-comparative, retrospective review of patients diagnosed with juvenile open angle glaucoma (JOAG) in the eye clinic of a tertiary hospital in southwestern Nigeria.Objective: To document the demographic characteristics, clinical features and treatment outcome of the patients diagnosed with JOAG.Materials and Methods: Data were extracted from the clinical record of patients diagnosed with JOAG in the eye clinic of the University College Hospital, Ibadan, Nigeria, between January 2001 and December 2005. Such data included the basic demographic data, the clinical characteristic of the patients and the outcome of their treatment.Results: Twenty-nine patients were reviewed, which represents 3.4% of all newly diagnosed glaucoma patients seen in the out-patient section of the eye clinic of the University College Hospital, Ibadan, over the period reviewed. Eight (27.6%) patients were aged 20 years and below. The mean age was 25.1 ± SD 6.0 years. Eighteen (62.1%) had visual acuity of 6/18 or worse in the better eye at the time of presentation. The mean intraocular pressure (IOP) of the patients at presentation was 32.3 ± SD 15.2 mmHg. Eight (27.6%) patients defaulted within 6 months of presentation. The mean IOP for the 21 patients who were followed up on treatment for a mean period of 9.6 months was 17.0 ± SD 6.0 mmHg.Conclusion: Most patients with JOAG in this review presented with advanced form of the disease. Early detection through parent-driven school eye health program and community-based case detection could help in reducing the scourge arising from JOAG among our population

Effective String Theory Revisited

We revisit the effective field theory of long relativistic strings such as confining flux tubes in QCD. We derive the Polchinski-Strominger interaction by a calculation in static gauge. This interaction implies that a non-critical string which initially oscillates in one direction gets excited in orthogonal directions as well. In static gauge no additional term in the effective action is needed to obtain this effect. It results from a one-loop calculation using the Nambu-Goto action. Non-linearly realized Lorentz symmetry is manifest at all stages in dimensional regularization. We also explain that independent of the number of dimensions non-covariant counterterms have to be added to the action in the commonly used zeta-function regularization.Comment: 21 pages, 4 figures, v2: typo corrected, references added, published versio

Rapid IoT device identification at the edge

Consumer Internet of Things (IoT) devices are increasingly common in everyday homes, from smart speakers to security cameras. Along with their benefits come potential privacy and security threats. To limit these threats we must implement solutions to filter IoT traffic at the edge. To this end the identification of the IoT device is the first natural step. In this paper we demonstrate a novel method of rapid IoT device identification that uses neural networks trained on device DNS traffic that can be captured from a DNS server on the local network. The method identifies devices by fitting a model to the first seconds of DNS second-level-domain traffic following their first connection. Since security and privacy threat detection often operate at a device specific level, rapid identification allows these strategies to be implemented immediately. Through a total of 51,000 rigorous automated experiments, we classify 30 consumer IoT devices from 27 different manufacturers with 82% and 93% accuracy for product type and device manufacturers respectively

The impact of industries on surface water quality of River Ona and River Alaro in Oluyole Industrial Estate, Ibadan, Nigeria

Samples of water from two rivers (River Ona and River Alaro) in Oluyole Industrial Estate, Ibadan, Nigeria were analysed to evaluate the impact of industrial discharges on the surface water quality. The results obtained indicated that most of the parameters analysed (pH, total hardness, sulphate, chloride, nitrate and dissolved solids) were lower than the World Health Organisation (WHO) maximum permissible limit for drinking water. However, the levels of nitrate, chloride, total phosphorus, total solids and oil and grease were higher in the industrial zones than those found in the upstream of both rivers. These ranged between 3.00 – 8.55, 7.48 – 11.78, 2.14 – 3.57, 260 – 520 mg/l and 381.20 – 430.80 mg/l, respectively. Nitrate and total phosphorus which are essential nutrients for plants were the most accumulated in both rivers. The gross organic pollution indicators monitored (chemical oxygen demand and oil and grease) revealed that River Alaro was more polluted than River Ona. It was established from the results of this study that industrial discharges had negative impact on the surface water qualities of both rivers. Hence, extraction of water from both rivers for domestic and agricultural purposes requires some forms of physical and chemical treatment.Key words: River Ona, River Alaro, industrial discharges, surface water quality