Vacuolating cytotoxin (vacA) alleles of Helicobacter pylori comprise two geographically widespread types, m1 and m2, and have evolved through limited recombination

Vacuolating cytotoxin (vacA) alleles of Helicobacter pylori vary, particularly in their mid region (which may be type m1 or m2) and their signal peptide coding region (type s1 or s2). We investigated nucleotide diversity among vacA alleles in strains from several locales in Asia, South America, and the USA. Phylogenetic analysis of vacA mid region sequences from 18 strains validated the division into two main groups (m1 and m2) and showed further significant divisions within these groups. Informative site analysis demonstrated one example of recombination between m1 and m2 alleles, and several examples of recombination among alleles within these groups. Recombination was not sufficiently extensive to destroy phylogenetic structure entirely. Synonymous nucleotide substitution rates were markedly different between regions of vacA, suggesting different evolutionary divergence times and implying horizontal transfer of genetic elements within vacA. Non-synonymous/synonymous rate ratios were greater between m1 and m2 sequences than among m1 sequences, consistent with m1 and m2 alleles encoding functions fitting strains for slightly different ecological niches

Accuracy Analysis of an Image Guided Robotic Urology Surgery System

We present an evaluation of the accuracy of a system for image guided radical prostatectomy using the daVinci telemanipulator. The system is split into components and ten sources of error identified. The magnitude of three of these error sources; segmentation of bone from MRI, registration to patient using intraoperative ultrasound, and endoscope tracking error is determined experimentally. The remaining errors are estimated from the literature. We demonstrate that the distribution of ultrasound slices used for registration can reduce the system error by up to 0.7mm. Our results show that our system can localise the prostate to within 3.7mm RMS, and that the largest component of the this error is the segmentation of the pelvic bone from MRI

Image Guidance in Telemanipulator Assisted Urology Surgery

This thesis outlines the development of an image guided surgery system, intended for use in \davinci assisted radical prostatectomy but more generally applicable to laparoscopic urology surgery. We defined the key performance parameter of the system as the accuracy of overlaying modelled anatomy onto the surgical scene. This thesis is primarily concerned with determining the system accuracy based on an analysis of the system's components. A common error measure was defined for all system components. This is an on screen error (measured in pixels) based on the error in projecting a single point lying near the apex of the prostate with the endoscope in a typical surgical pose. In this case the projected point was approximately 200 mm from the endoscope lens. An intraoperative coordinate system is first defined as the coordinate system of an optical tracking system used to track the endoscope. The MRI image of the patient is transformed into the intraoperative coordinate system. Prior to surgery the endoscope is calibrated and during surgery the endoscope is tracked, defining a transform from the coordinates of the optical tracking system to the endoscope screen. This transform is used to project the MRI image onto the endoscope video display. The early part of the thesis describes a novel algorithm for registering MRI to ultrasound images of the bone which was used to put the MRI image into the intraoperative coordinate system. Using this algorithm avoids the need for fiducial markers. The table below shows the errors (as on screen pixel RMS) due to using this algorithm. An approximate value as RMS distance error at the prostate apex point is also included

Normothermic machine perfusion for the assessment and transplantation of declined human kidneys from donation after circulatory death donors.

BACKGROUND: A significant proportion of donation after circulatory death (DCD) kidneys are declined for transplantation because of concerns over their quality. Ex vivo normothermic machine perfusion (NMP) provides a unique opportunity to assess the quality of a kidney and determine its suitability for transplantation. METHODS: In phase 1 of this study, declined human DCD kidneys underwent NMP assessment for 60 min. Kidneys were graded 1-5 using a quality assessment score (QAS) based on macroscopic perfusion, renal blood flow and urine output during NMP. In phase 2 of the study, declined DCD kidneys were assessed by NMP with an intention to transplant them. RESULTS: In phase 1, 18 of 42 DCD kidneys were declined owing to poor in situ perfusion. After NMP, 28 kidneys had a QAS of 1-3, and were considered suitable for transplantation. In phase 2, ten of 55 declined DCD kidneys underwent assessment by NMP. Eight kidneys had been declined because of poor in situ flushing in the donor and five of these were transplanted successfully. Four of the five kidneys had initial graft function. CONCLUSION: NMP technology can be used to increase the number of DCD kidney transplants by assessing their quality before transplantation

Nonmethane hydrocarbon measurements in the North Atlantic Flight Corridor during the Subsonic Assessment Ozone and Nitrogen Oxide Experiment

Mixing ratios of nonmethane hydrocarbons (NMHCs) were not enhanced in whole air samples collected within the North Atlantic Flight Corridor (NAFC) during the fall of 1997. The investigation was conducted aboard NASA's DC-8 research aircraft, as part of the Subsonic Assessment (SASS) Ozone and Nitrogen Oxide Experiment (SONEX). NMHC enhancements were not detected within the general organized tracking system of the NAFC, nor during two tail chases of the DC-8's own exhaust. Because positive evidence of aircraft emissions was demonstrated by enhancements in both nitrogen oxides and condensation nuclei during SONEX, the NMHC results suggest that the commercial air traffic fleet operating in the North Atlantic region does not contribute at all or contributes negligibly to NMHCs in the NAFC. Copyright 2000 by the American Geophysical Union

Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment

Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult to assess in those analyses. To compare the performance of different aligners and help detect systematic errors in alignments, a number of benchmarking strategies have been pursued. Here we present an overview of the main strategies--based on simulation, consistency, protein structure, and phylogeny--and discuss their different advantages and associated risks. We outline a set of desirable characteristics for effective benchmarking, and evaluate each strategy in light of them. We conclude that there is currently no universally applicable means of benchmarking MSA, and that developers and users of alignment tools should base their choice of benchmark depending on the context of application--with a keen awareness of the assumptions underlying each benchmarking strategy.Comment: Revie

Modulation of adipocyte G-protein expression in cancer cachexia by a lipid-mobilizing factor (LMF)

Adipocytes isolated from cachectic mice bearing the MAC 16 tumour showed over a 3-fold increase in lipolytic response to both low concentrations of isoprenaline and a tumour-derived lipid mobilizing factor (LMF). This was reflected by an enhanced stimulation of adenylate cyclase in plasma membrane fractions of adipocytes in the presence of both factors. There was no up-regulation of adenylate cyclase in response to forskolin, suggesting that the effect arose from a change in receptor number or G-protein expression. Immunoblotting of adipocyte membranes from mice bearing the MAC16 tumour showed an increased expression of Gαs up to 10% weight loss and a reciprocal decrease in Gα. There was also an increased expression of Gαs and a decrease in Gα in adipose tissue from a patient with cancer-associated weight loss compared with a non-cachectic cancer patient. The changes in G-protein expression were also seen in adipose tissue of normal mice administered pure LMF as well as in 3T3L1 adipocytes in vitro. The changes in G-protein expression induced by LMF were attenuated by the polyunsaturated fatty acid, eicosapentaenoic acid (EPA). This suggests that this tumour-derived lipolytic factor acts to sensitize adipose tissue to lipolytic stimuli, and that this effect is attenuated by EPA, which is known to preserve adipose tissue in cancer cachexia. © 2001 Cancer Research Campaig

Variability of Quasilinear Diffusion Coefficients for Plasmaspheric Hiss

In the outer radiation belt, the acceleration and loss of high‐energy electrons is largely controlled by wave‐particle interactions. Quasilinear diffusion coefficients are an efficient way to capture the small‐scale physics of wave‐particle interactions due to magnetospheric wave modes such as plasmaspheric hiss. The strength of quasilinear diffusion coefficients as a function of energy and pitch angle depends on both wave parameters and plasma parameters such as ambient magnetic field strength, plasma number density, and composition. For plasmaspheric hiss in the magnetosphere, observations indicate large variations in the wave intensity and wave normal angle, but less is known about the simultaneous variability of the magnetic field and number density. We use in situ measurements from the Van Allen Probe mission to demonstrate the variability of selected factors that control the size and shape of pitch angle diffusion coefficients: wave intensity, magnetic field strength, and electron number density. We then compare with the variability of diffusion coefficients calculated individually from colocated and simultaneous groups of measurements. We show that the distribution of the plasmaspheric hiss diffusion coefficients is highly non‐Gaussian with large variance and that the distributions themselves vary strongly across the three phase space bins studied. In most bins studied, the plasmaspheric hiss diffusion coefficients tend to increase with geomagnetic activity, but our results indicate that new approaches that include natural variability may yield improved parameterizations. We suggest methods like stochastic parameterization of wave‐particle interactions could use variability information to improve modeling of the outer radiation belt

Cognitive outcomes of temporal lobe epilepsy surgery in older patients

Purpose: To examine the cognitive risks of temporal lobe surgery in patients aged 50 years and older. / Methods: We analysed data from 55 patients who underwent temporal lobe surgery (26 left-sided:29 right sided) from 1988 to 2012 at our centre. Pre-surgical and one year post-operative memory and naming capacity were compared to data obtained from two younger cohorts; 185 aged 18–30 and 220 aged 31–49. / Results: Pre-operative memory impairments were most marked for the oldest cohort and were associated with a longer duration of epilepsy. Naming capacity improved with age and better performance was associated with a later age at epilepsy onset. Post-operative declines were largest in older patients, achieving statistical significance for verbal memory, naming and subjective ratings. Left temporal lobe resections carried the greatest risk of memory and naming decline. Cognitive outcomes were unrelated to seizure outcome, VIQ or mood. / Conclusion: Our findings indicate the cognitive risks of TLE surgery are greater for older patients. Cognitive outcomes need to be considered when assessing the efficacy of epilepsy surgery in older cohorts and pre-operative performance levels need to be taken into account