Stabilization of diverged tandem repeats by mismatch repair: evidence for deletion formation via a misaligned replication intermediate.

A functional methyl-directed mismatch repair pathway in Escherichia coli prevents the formation of deletions between 101-bp tandem repeats with 4% sequence divergence. Deletions between perfectly homologous repeats are unaffected. Deletion in both cases occurs independently of the homologous recombination gene, recA. Because the methyl-directed mismatch repair pathway detects and excises one strand of a mispaired duplex, an intermediate for RecA-independent deletion of tandem repeats must therefore be a heteroduplex formed between strands of each repeat. We find that MutH endonuclease, which in vivo incises specifically the newly replicated strand of DNA, and the Dam methylase, the source of this strand-discrimination, are required absolutely for the exclusion of "homeologous" (imperfectly homologous) tandem deletion. This supports the idea that the heteroduplex intermediate for deletion occurs during or shortly after DNA replication in the context of hemi-methylation. Our findings confirm a "replication slippage" model for deletion formation whereby the displacement and misalignment of the nascent strand relative to the repeated sequence in the template strand accomplishes the deletion.

Forças, momentos e coeficiente de atrito em teste de três pontos e em teste de resistência ao deslizamento com braquetes autoligáveis e fios 0.014\" utilizando um novo dispositivo

O objetivo principal do estudo é comparar o teste em 3 pontos com braquetes com o teste de resistência ao deslizamento utilizando um novo dispositivo que realiza a mensuração simultânea do coeficiente de atrito, das forças e dos momentos nos braquetes de ancoragem e da força de desativação no braquete desalinhado, exercidos por fios ortodônticos. Os objetivos secundários foram desenvolver o dispositivo e comparar, no teste em 3 pontos: (i) a influência, nas grandezas e no coeficiente de atrito cinético, da variação da simetria nas distâncias inter-braquetes, do tipo de braquete de ancoragem (canino ou 2º pré-molar), do deslocamento (3 ou 5mm) do braquete central, do sentido do desalinhamento (vestibular ou lingual) do braquete central e da marca de fio-braquete; (ii) as 3 formas de cálculo do coeficiente de atrito cinético; (iii) os 10 ciclos, para vestibular ou lingual, para verificar se eles são semelhantes ou não entre si. Foram utilizados braquetes autoligáveis (dentes 13, 14 e 15) e fios 0.014\'\' NiTi e CuNiTi das marcas Aditek e Ormco. O teste de resistência ao deslizamento foi realizado no desalinhamento lingual, nos dois deslocamentos e na configuração simétrica. O teste em 3 pontos com braquetes foi realizado no desalinhamento lingual e vestibular, nos dois deslocamentos e na configuração simétrica e assimétrica. Por meio da ANOVA, foram comparados, entre os dois tipos de teste: (A) as grandezas e o coeficiente de atrito e (B) o coeficiente de atrito gerado apenas no braquete de 2º pré-molar. Utilizando-se do mesmo teste estatístico foram comparados, no teste em 3 pontos com braquetes: (A) na configuração simétrica, algumas grandezas e o coeficiente de atrito advindos da variação da marca de fio-braquete, do deslocamento, do desalinhamento e do tipo de braquete; (B) algumas grandezas e o coeficiente de atrito gerados na configuração simétrica e assimétrica; (C) os valores das 3 formas de cálculo do coeficiente de atrito na configuração simétrica; e (D) algumas grandezas e o coeficiente de atrito encontrados nos 10 ciclos. Resultados: (A) a maioria dos valores das grandezas e do coeficiente de atrito gerados pelos dois tipos de teste foram diferentes estatisticamente; (B) o braquete de 2º pré-molar apresentou valores de coeficiente de atrito diferentes entre os dois tipos de teste; (C) na configuração simétrica, as variáveis foram estatisticamente significantes na maioria dos casos para as grandezas analisadas e para o coeficiente de atrito; (D) houve diferença entre a configuração simétrica e assimétrica; (E) o coeficiente de atrito baseado nas duas normais e na força de atrito se aproximou mais da realidade clínica e foi sensível à variação da geometria da relação fio-braquete; e (F) os 10 ciclos para lingual foram semelhantes entre si em 70% dos casos e os 10 ciclos para vestibular foram diferentes em 57% dos casos. Conclusões: o teste em 3 pontos com braquetes é diferente do teste de resistência ao deslizamento; a variação das configurações geométricas e da marca de fio-braquete pode influenciar nos valores das grandezas e do coeficiente de atrito cinético; os 10 ciclos para lingual foram mais semelhantes entre si que os 10 ciclos para vestibular.

Chemical Sensor Based on a Long-Period Fibre Grating Modified by a Functionalized Polydimethylsiloxane Coating

A chemical sensor based on a coated long-period grating has been prepared and characterized. Designer coatings based on polydimethylsiloxane were prepared by the incorporation of diphenylsiloxane and titanium cross-linker in order to provide enhanced sensitivity for a variety of key environmental pollutants and optimal refractive index of the coating. Upon microextraction of the analyte into the polymer matrix, an increase in the refractive index of the coating resulted in a change in the attenuation spectrum of the long-period grating. The grating was interrogated using ring-down detection as a means to amplify the optical loss and to gain stability against misalignment and power fluctuations. Chemical differentiation of cyclohexane and xylene was achieved and a detection limit of 300 ppm of xylene vapour was realized.

EU-Mercosur trade relations: impacts of exchange rate misalignments on tariffs. CEPS Working Document No. 372, February 2013

The issue of “trade and exchange rate misalignments” is being discussed at the G20, IMF and WTO, following an initiative by Brazil. The main purpose of this paper is to apply the methodology developed by the authors to exam the impacts of misalignment on tariffs in order to analyse the impacts of misalignments on the trade relations between two customs unions – the EU and Mercosur, as well as to explain how tariff barriers are affected. It is divided into several sections: the first summarises the debate on exchange rates at the WTO; the second explains the methodology used to determine exchange rate misalignments; the third and fourth summarises the methodology applied to calculate the impacts of exchange rate misalignments on the level of tariff protection through an exercise of ‘misalignment tariffication’; the fifth reviews the effects of exchange rate misalignments on tariffs and its consequences for the trade negotiations between the two areas; and the last concludes and suggests a way to move the debate forward in the context of regional arrangements.

Operator-induced errors in Hartmann-Shack wavefront sensing:model eye study

Purpose: To evaluate the effects of instrument realignment and angular misalignment during the clinical determination of wavefront aberrations by simulation in model eyes. Setting: Aston Academy of Life Sciences, Aston University, Birmingham, United Kingdom. Methods: Six model eyes were examined with wavefront-aberration-supported cornea ablation (WASCA) (Carl Zeiss Meditec) in 4 sessions of 10 measurements each: sessions 1 and 2, consecutive repeated measures without realignment; session 3, realignment of the instrument between readings; session 4, measurements without realignment but with the model eye shifted 6 degrees angularly. Intersession repeatability and the effects of realignment and misalignment were obtained by comparing the measurements in the various sessions for coma, spherical aberration, and higher-order aberrations (HOAs). Results: The mean differences between the 2 sessions without realignment of the instrument were 0.020 μm ± 0.076 (SD) for Z3 - 1(P = .551), 0.009 ± 0.139 μm for Z3 1(P = .877), 0.004 ± 0.037 μm for Z4 0 (P = .820), and 0.005 ± 0.01 μm for HO root mean square (RMS) (P = .301). Differences between the nonrealigned and realigned instruments were -0.017 ± 0.026 μm for Z3 - 1(P = .159), 0.009 ± 0.028 μm for Z3 1 (P = .475), 0.007 ± 0.014 μm for Z4 0(P = .296), and 0.002 ± 0.007 μm for HO RMS (P = 0.529; differences between centered and misaligned instruments were -0.355 ± 0.149 μm for Z3 - 1 (P = .002), 0.007 ± 0.034 μm for Z3 1(P = .620), -0.005 ± 0.081 μm for Z4 0(P = .885), and 0.012 ± 0.020 μm for HO RMS (P = .195). Realignment increased the standard deviation by a factor of 3 compared with the first session without realignment. Conclusions: Repeatability of the WASCA was excellent in all situations tested. Realignment substantially increased the variance of the measurements. Angular misalignment can result in significant errors, particularly in the determination of coma. These findings are important when assessing highly aberrated eyes during follow-up or before surgery. © 2007 ASCRS and ESCRS.

Phakometric measurement of ocular surface radii of curvature, axial separations and alignment in relaxed and accommodated human eyes

Measurements (autokeratometry, A-scan ultrasonography and video ophthalmophakometry) of ocular surface radii, axial separations and alignment were made in the horizontal meridian of nine emmetropes (aged 20-38 years) with relaxed (cycloplegia) and active accommodation (mean ± 95% confidence interval: 3.7 ± 1.1 D). The anterior chamber depth (-1.5 ± 0.3 D) and both crystalline lens surfaces (front 3.1 ± 0.8 D; rear 2.1 ± 0.6 D) contributed to dioptric vergence changes that accompany accommodation. Accommodation did not alter ocular surface alignment. Ocular misalignment in relaxed eyes is mainly because of eye rotation (5.7 ± 1.6° temporally) with small amounts of lens tilt (0.2 ± 0.8° temporally) and decentration (0.1 ± 0.1 mm nasally) but these results must be viewed with caution as we did not account for corneal asymmetry. Comparison of calculated and empirically derived coefficients (upon which ocular surface alignment calculations depend) revealed that negligible inherent errors arose from neglect of ocular surface asphericity, lens gradient refractive index properties, surface astigmatism, effects of pupil size and centration, assumed eye rotation axis position and use of linear equations for analysing Purkinje image shifts. © 2004 The College of Optometrists.

Non-Linear oil firm force coefficients for a journal bearing operating under aligned and misaligned conditions

It is well established that hydrodynamic journal bearings are responsible for self-excited vibrations and have the effect of lowering the critical speeds of rotor systems. The forces within the oil film wedge, generated by the vibrating journal, may be represented by displacement and velocity coefficient~ thus allowing the dynamical behaviour of the rotor to be analysed both for stability purposes and for anticipating the response to unbalance. However, information describing these coefficients is sparse, misleading, and very often not applicable to industrial type bearings. Results of a combined analytical and experimental investigation into the hydrodynamic oil film coefficients operating in the laminar region are therefore presented, the analysis being applied to a 120 degree partial journal bearing having a 5.0 in diameter journal and a LID ratio of 1.0. The theoretical analysis shows that for this type of popular bearing, the eight linearized coefficients do not accurately describe the behaviour of the vibrating journal based on the theory of small perturbations, due to them being masked by the presence of nonlinearity. A method is developed using the second order terms of Taylor expansion whereby design charts are provided which predict the twentyeight force coefficients for both aligned, and for varying amounts of journal misalignment. The resulting non-linear equations of motion are solved using a modified Newton-Raphson method whereby the whirl trajectories are obtained, thus providing a physical appreciation of the bearing characteristics under dynamically loaded conditions.

Optimising the clinical analysis of retinal image quality in the human eye

Visual perception is dependent on both light transmission through the eye and neuronal conduction through the visual pathway. Advances in clinical diagnostics and treatment modalities over recent years have increased the opportunities to improve the optical path and retinal image quality. Higher order aberrations and retinal straylight are two major factors that influence light transmission through the eye and ultimately, visual outcome. Recent technological advancements have brought these important factors into the clinical domain, however the potential applications of these tools and considerations regarding interpretation of data are much underestimated. The purpose of this thesis was to validate and optimise wavefront analysers and a new clinical tool for the objective evaluation of intraocular scatter. The application of these methods in a clinical setting involving a range of conditions was also explored. The work was divided into two principal sections: 1. Wavefront Aberrometry: optimisation, validation and clinical application The main findings of this work were: • Observer manipulation of the aberrometer increases variability by a factor of 3. • Ocular misalignment can profoundly affect reliability, notably for off-axis aberrations. • Aberrations measured with wavefront analysers using different principles are not interchangeable, with poor relationships and significant differences between values. • Instrument myopia of around 0.30D is induced when performing wavefront analysis in non-cyclopleged eyes; values can be as high as 3D, being higher as the baseline level of myopia decreases. Associated accommodation changes may result in relevant changes to the aberration profile, particularly with respect to spherical aberration. • Young adult healthy Caucasian eyes have significantly more spherical aberration than Asian eyes when matched for age, gender, axial length and refractive error. Axial length is significantly correlated with most components of the aberration profile. 2. Intraocular light scatter: Evaluation of subjective measures and validation and application of a new objective method utilising clinically derived wavefront patterns. The main findings of this work were: • Subjective measures of clinical straylight are highly repeatable. Three measurements are suggested as the optimum number for increased reliability. • Significant differences in straylight values were found for contact lenses designed for contrast enhancement compared to clear lenses of the same design and material specifications. Specifically, grey/green tints induced significantly higher values of retinal straylight. • Wavefront patterns from a commercial Hartmann-Shack device can be used to obtain objective measures of scatter and are well correlated with subjective straylight values. • Perceived retinal stray light was similar in groups of patients implanted with monofocal and multi focal intraocular lenses. Correlation between objective and subjective measurements of scatter is poor, possibly due to different illumination conditions between the testing procedures, or a neural component which may alter with age. Careful acquisition results in highly reproducible in vivo measures of higher order aberrations; however, data from different devices are not interchangeable which brings the accuracy of measurement into question. Objective measures of intraocular straylight can be derived from clinical aberrometry and may be of great diagnostic and management importance in the future.

A low-cost remote sensing system for agricultural applications

This research develops a low cost remote sensing system for use in agricultural applications. The important features of the system are that it monitors the near infrared and it incorporates position and attitude measuring equipment allowing for geo-rectified images to be produced without the use of ground control points. The equipment is designed to be hand held and hence requires no structural modification to the aircraft. The portable remote sensing system consists of an inertia measurement unit (IMU), which is accelerometer based, a low-cost GPS device and a small format false colour composite digital camera. The total cost of producing such a system is below GBP 3000, which is far cheaper than equivalent existing systems. The design of the portable remote sensing device has eliminated bore sight misalignment errors from the direct geo-referencing process. A new processing technique has been introduced for the data obtained from these low-cost devices, and it is found that using this technique the image can be matched (overlaid) onto Ordnance Survey Master Maps at an accuracy compatible with precision agriculture requirements. The direct geo-referencing has also been improved by introducing an algorithm capable of correcting oblique images directly. This algorithm alters the pixels value, hence it is advised that image analysis is performed before image georectification. The drawback of this research is that the low-cost GPS device experienced bad checksum errors, which resulted in missing data. The Wide Area Augmented System (WAAS) correction could not be employed because the satellites could not be locked onto whilst flying. The best GPS data were obtained from the Garmin eTrex (15 m kinematic and 2 m static) instruments which have a highsensitivity receiver with good lock on capability. The limitation of this GPS device is the inability to effectively receive the P-Code wavelength, which is needed to gain the best accuracy when undertaking differential GPS processing. Pairing the carrier phase L1 with the pseudorange C/A-Code received, in order to determine the image coordinates by the differential technique, is still under investigation. To improve the position accuracy, it is recommended that a GPS base station should be established near the survey area, instead of using a permanent GPS base station established by the Ordnance Survey.

Clinical outcomes after implantation of a new hydrophobic acrylic toric IOL during routine cataract surgery

PURPOSE: To assess the clinical outcomes after implantation of a new hydrophobic acrylic toric intraocular lens (IOL) to correct preexisting corneal astigmatism in patients having routine cataract surgery. SETTING: Four hospital eye clinics throughout Europe. DESIGN: Cohort study. METHODS: This study included eyes with at least 0.75 diopter (D) of preexisting corneal astigmatism having routine cataract surgery. Phacoemulsification was performed followed by insertion and alignment of a Tecnis toric IOL. Patients were examined 4 to 8 weeks postoperatively; uncorrected distance visual acuity (UDVA), corrected distance visual acuity, manifest refraction, and keratometry were measured. Individual patient satisfaction with uncorrected vision and the surgeon’s assessment of ease of handling and performance of the IOL were also documented. The cylinder axis of the toric IOL was determined by dilated slitlamp examination. RESULTS: The study enrolled 67 eyes of 60 patients. Four to 8 weeks postoperatively, the mean UDVA was 0.15 logMAR G 0.17 (SD) and the UDVA was 20/40 or better in 88% of eyes. The mean refractive cylinder decreased significantly postoperatively, from -1.91 +/- 1.07 D to -0.67 +/- 0.54 D. No significant change in keratometric cylinder was observed. The mean absolute IOL misalignment from the intended axis was 3.4 degrees (range 0 to 12 degrees). The good UDVA resulted in high levels of patient satisfaction. CONCLUSION: Implantation of the new toric IOL was an effective, safe, and predictable method to manage corneal astigmatism in patients having routine cataract surgery.

Electronic dispersion compensation using full optical-field reconstruction in 10Gbit/s OOK based systems

We investigate the design of electronic dispersion compensation (EDC) using full optical-field reconstruction in 10Gbit/s on-off keyed transmission systems limited by optical signal-to-noise ratio (OSNR). By effectively suppressing the impairment due to low- frequency component amplification in phase reconstruction, properly designing the transmission system configuration to combat fiber nonlinearity, and successfully reducing the vulnerability to thermal noise, a 4.8dB OSNR margin can be achieved for 2160km single-mode fiber transmission without any optical dispersion compensation. We also investigate the performance sensitivity of the scheme to various system parameters, and propose a novel method to greatly enhance the tolerance to differential phase misalignment of the asymmetric Mach-Zehnder interferometer. This numerical study provides important design guidelines which will enable full optical-field EDC to become a cost-effective dispersion compensation solution for future transparent optical networks.

Full-field feed-forward equalizer with adaptive system optimization

We numerically investigate the combination of full-field detection and feed-forward equalizer (FFE) for adaptive chromatic dispersion compensation up to 2160 km in a 10 Gbit/s on-off keyed optical transmission system. The technique, with respect to earlier reports, incorporates several important implementation modules, including the algorithm for adaptive equalization of the gain imbalance between the two receiver chains, compensation of phase misalignment of the asymmetric Mach-Zehnder interferometer, and simplified implementation of field calculation. We also show that in addition to enabling fast adaptation and simplification of field calculation, full-field FFE exhibits enhanced tolerance to the sampling phase misalignment and reduced sampling rate when compared to the full-field implementation using a dispersive transmission line.

Evaluation of modern intraocular lenses

Accommodating Intraocular Lenses (IOLs), multifocal IOLs (MIOLs) and toric IOLs are designed to provide a greater level of spectacle independency post cataract surgery. All of these IOLs are reliant on the accurate calculation of intraocular lens power determined through reliable ocular biometry. A standardised defocus area metric and reading performance index metric were devised for the evaluation of the range of focus and the reading ability of subjects implanted with presbyopic correcting IOLs. The range of clear vision after implantation of an MIOL is extended by a second focal point; however, this results in the prevalence of dysphotopsia. A bespoke halometer was designed and validated to assess this photopic phenomenon. There is a lack of standardisation in the methods used for determining IOL orientation and thus rotation. A repeatable, objective method was developed to allow the accurate assessment of IOL rotation, which was used to determine the rotational and positional stability of a closed loop haptic IOL. A new commercially available biometry device was validated for use with subjects prior to cataract surgery. The optical low coherence reflectometry instrument proved to be a valid method for assessing ocular biometry and covered a wider range of ocular parameters in comparison with previous instruments. The advantages of MIOLs were shown to include an extended range of clear vision translating into greater reading ability. However, an increased prevalence of dysphotopsia was shown with a bespoke halometer, which was dependent on the MIOL optic design. Implantation of a single optic accommodating IOL did not improve reading ability but achieved high subjective ratings of near vision. The closed-loop haptic IOL displayed excellent rotational stability in the late period but relatively poor rotational stability in the early period post implantation. The orientation error was compounded by the high frequency of positional misalignment leading to an extensive overall misalignment of the IOL. This thesis demonstrates the functionality of new IOL lens designs and the importance of standardised testing methods, thus providing a greater understanding of the consequences of implanting these IOLs. Consequently, the findings of the thesis will influence future designs of IOLs and testing methods.

Induced vertical disparity effects on local and global stereopsis

Purpose: Although significant amounts of vertical misalignment could have a noticeable effect on visual performance, there is no conclusive evidence about the effect of very small amount of vertical disparity on stereopsis and binocular vision. Hence, the aim of this study was to investigate the effects of induced vertical disparity on local and global stereopsis at near. Materials and Methods: Ninety participants wearing best-corrected refraction had local and global stereopsis tested with 0.5 and 1.0 prism diopter (Δ) vertical prism in front of their dominant and non-dominant eye in turn. This was compared to local and global stereopsis in the same subjects without vertical prism. Data were analyzed in SPSS.17 software using the independent samples T and the repeated measures ANOVA tests. Results: Induced vertical disparity decreases local and global stereopsis. This reduction is greater when vertical disparity is induced in front of the non-dominant eye and affects global more than local stereopsis. Repeated measures ANOVA showed differences in the mean stereopsis between the different measured states for local and global values. Local stereopsis thresholds were reduced by 10s of arc or less on average with 1.0Δ of induced vertical prism in front of either eye. However, global stereopsis thresholds were reduced by over 100s of arc by the same 1.0Δ of induced vertical prism. Conclusion: Induced vertical disparity affects global stereopsis thresholds by an order of magnitude (or a factor of 10) more than local stereopsis. Hence, using a test that measures global stereopsis such as the TNO is more sensitive to vertical misalignment than a test such as the Stereofly that measures local stereopsis. © 2014 Informa Healthcare USA, Inc. All rights reserved: reproduction in whole or part not permitted.

Eye alignment:a novel approach

This thesis describes the design and development of an eye alignment/tracking system which allows self alignment of the eye’s optical axis with a measurement axis. Eye alignment is an area of research largely over-looked, yet it is a fundamental requirement in the acquisition of clinical data from the eye. New trends in the ophthalmic market, desiring portable hand-held apparatus, and the application of ophthalmic measurements in areas other than vision care have brought eye alignment under new scrutiny. Ophthalmic measurements taken in hand-held devices with out an clinician present requires alignment in an entirely new set of circumstances, requiring a novel solution. In order to solve this problem, the research has drawn upon eye tracking technology to monitor the eye, and a principle of self alignment to perform alignment correction. A handheld device naturally lends itself to the patient performing alignment, thus a technique has been designed to communicate raw eye tracking data to the user in a manner which allows the user to make the necessary corrections. The proposed technique is a novel methodology in which misalignment to the eye’s optical axis can be quantified, corrected and evaluated. The technique uses Purkinje Image tracking to monitor the eye’s movement as well as the orientation of the optical axis. The use of two sets of Purkinje Images allows quantification of the eye’s physical parameters needed for accurate Purkinje Image tracking, negating the need for prior anatomical data. An instrument employing the methodology was subsequently prototyped and validated, allowing a sample group to achieve self alignment of their optical axis with an imaging axis within 16.5-40.8 s, and with a rotational precision of 0.03-0.043°(95% confidence intervals). By encompassing all these factors the technique facilitates self alignment from an unaligned position on the visual axis to an aligned position on the optical axis. The consequence of this is that ophthalmic measurements, specifically pachymetric measurements, can be made in the absence of an optician, allowing the use of ophthalmic instrumentation and measurements in health professions other than vision care.