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Owen MR, Clarkson MJ, Trees AJ. Diagnosis of toxoplasma abortion in ewes by polymerase chain reaction. Vet Rec 1998; 142:445-8. [PMID: 9602512 DOI: 10.1136/vr.142.17.445] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Eighteen oestrus-synchronised ewes were infected experimentally with 1500 sporulated oocysts of Toxoplasma gondii between 80 and 90 days of gestation. The infection induced pyrexia and specific antibody in all the ewes. One ewe resorbed its fetus, five ewes aborted and 12 delivered live, congenitally-infected lambs whose pre-colostral serum was antibody-positive. Tissues from the aborted fetuses and placentae from the live lambs were examined for toxoplasma infection by polymerase chain reaction (PCR) amplification of the B1 gene and by mouse inoculation. Using a simple protocol of tissue preparation without DNA extraction and a nested format, PCR was as sensitive as mouse inoculation. Placental cotyledon gave a higher sensitivity of detection than brain, lung or liver, and 16 of 19 placentae were positive by PCR compared with 13 of 18 by mouse inoculation. In mock-infected tissues, as few as 10 tachyzoites could be detected. The PCR could be applied to tissues unfit for mouse inoculation.
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Johnson-Saliba M, Siddon NA, Clarkson MJ, Tremethick DJ, Jans DA. Distinct importin recognition properties of histones and chromatin assembly factors. FEBS Lett 2000; 467:169-74. [PMID: 10675532 DOI: 10.1016/s0014-5793(00)01142-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Synthesis of the protein components of nuclear chromatin occurs in the cytoplasm, necessitating specific import into the nucleus. Here, we report the binding affinities of the nuclear localisation sequence (NLS)-binding importin subunits for a range of histones and chromatin assembly factors. The results suggest that import of histones to the nucleus may be mediated predominantly by importin beta1, whereas the import of the other components probably relies on the conventional alpha/beta1 import pathway. Differences in recognition by importin beta1 were observed between histone H2A and the variant H2AZ, as well as between histone H3/4 with or without acetylation. The results imply that different histone variants may possess distinct nuclear import properties, with acetylation possibly playing an inhibitory role through NLS masking.
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Abstract
Within 13 days of the experimental infection of 15 oestrus-synchronised ewes with 2000 sporulated oocysts of Toxoplasma gondii at 80 to 90 days of gestation 11 had aborted. The infection induced pyrexia and specific antibody in all the ewes. One ewe resorbed its fetus, 11 ewes aborted and three delivered, at full term, live congenitally infected lambs whose pre-colostral serum was antibody-positive. Tissues from the aborted fetuses and placentae from the live lambs were examined for toxoplasma infection by polymerase chain reaction (PCR) amplification of the B1 gene and by mouse inoculation. The live lambs were all shown to be infected by both methods, but there was no evidence of infection in any of the tissues from the acute phase abortions, suggesting that these fatalities occurred before the placenta or the fetus had been invaded by T gondii. Such toxoplasma-induced, acute-phase abortions are likely to be impossible to diagnose from fetal tissues. These results have implications not only for the diagnosis of naturally occurring ovine abortions but also for the understanding of the pathogenesis of toxoplasma-induced abortion.
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Clarkson MJ, Zombori G, Thompson S, Totz J, Song Y, Espak M, Johnsen S, Hawkes D, Ourselin S. The NifTK software platform for image-guided interventions: platform overview and NiftyLink messaging. Int J Comput Assist Radiol Surg 2014; 10:301-16. [PMID: 25408304 PMCID: PMC4338364 DOI: 10.1007/s11548-014-1124-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 10/17/2014] [Indexed: 11/24/2022]
Abstract
PURPOSE To perform research in image-guided interventions, researchers need a wide variety of software components, and assembling these components into a flexible and reliable system can be a challenging task. In this paper, the NifTK software platform is presented. A key focus has been high-performance streaming of stereo laparoscopic video data, ultrasound data and tracking data simultaneously. METHODS A new messaging library called NiftyLink is introduced that uses the OpenIGTLink protocol and provides the user with easy-to-use asynchronous two-way messaging, high reliability and comprehensive error reporting. A small suite of applications called NiftyGuide has been developed, containing lightweight applications for grabbing data, currently from position trackers and ultrasound scanners. These applications use NiftyLink to stream data into NiftyIGI, which is a workstation-based application, built on top of MITK, for visualisation and user interaction. Design decisions, performance characteristics and initial applications are described in detail. NiftyLink was tested for latency when transmitting images, tracking data, and interleaved imaging and tracking data. RESULTS NiftyLink can transmit tracking data at 1,024 frames per second (fps) with latency of 0.31 milliseconds, and 512 KB images with latency of 6.06 milliseconds at 32 fps. NiftyIGI was tested, receiving stereo high-definition laparoscopic video at 30 fps, tracking data from 4 rigid bodies at 20-30 fps and ultrasound data at 20 fps with rendering refresh rates between 2 and 20 Hz with no loss of user interaction. CONCLUSION These packages form part of the NifTK platform and have proven to be successful in a variety of image-guided surgery projects. Code and documentation for the NifTK platform are available from http://www.niftk.org . NiftyLink is provided open-source under a BSD license and available from http://github.com/NifTK/NiftyLink . The code for this paper is tagged IJCARS-2014.
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Research Support, Non-U.S. Gov't |
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Anderson IE, Baxter SI, Dunbar S, Rae AG, Philips HL, Clarkson MJ, Herring AJ. Analyses of the genomes of chlamydial isolates from ruminants and pigs support the adoption of the new species Chlamydia pecorum. INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY 1996; 46:245-51. [PMID: 8573503 DOI: 10.1099/00207713-46-1-245] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Analysis of the genomic DNAs of chlamydial isolates from sheep, cattle, and pigs was performed by Southern blot hybridization and by restriction endonuclease (RE) profiling of DNA amplified by PCR. The hybridization probes were derived from whole genomic DNA, the major outer membrane protein (MOMP) gene, the 16S rRNA gene, and an avian Chlamydia psittaci isolate plasmid. The PCR analysis used targets in the MOMP gene, the 16S rRNA gene, and the 60-kDa cysteine-rich protein gene. Together, the results showed that although there was considerable heterogeneity in the DNA sequence in the MOMP gene region, all the isolates had the same underlying total genomic RE profiles and yielded identical RE profiles for the rRNA and 60-kDa-protein gene regions. Most of the isolates were found to hybridize with the plasmid probe. Comparison of the MOMP sequence of one of the isolates (P787) with that of a known Chlamydia pecorum strain together with the results of the RE analyses allowed the conclusion that the isolates should all be classified within this new species.
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Pfeiffer M, Funke I, Robu MR, Bodenstedt S, Strenger L, Engelhardt S, Roß T, Clarkson MJ, Gurusamy K, Davidson BR, Maier-Hein L, Riediger C, Welsch T, Weitz J, Speidel S. Generating Large Labeled Data Sets for Laparoscopic Image Processing Tasks Using Unpaired Image-to-Image Translation. LECTURE NOTES IN COMPUTER SCIENCE 2019. [DOI: 10.1007/978-3-030-32254-0_14] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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Griffiths PC, Philips HL, Dawson M, Clarkson MJ. Antigenic and morphological differentiation of placental and intestinal isolates of Chlamydia psittaci of ovine origin. Vet Microbiol 1992; 30:165-77. [PMID: 1557895 DOI: 10.1016/0378-1135(92)90111-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Ewe placental and lamb intestinal isolates of Chlamydia psittaci recovered from flocks affected with ovine enzootic abortion were examined by inclusion morphology, indirect immunofluorescence (IIF) and immunoblot analysis. Chlamydiae recovered from the faeces of sheep from two flocks free of clinical disease were also examined. In cell culture ovine abortion (OA) and intestinal isolates were distinguishable by inclusion development and morphology. Similarly, in two-way IIF tests with one week mouse antisera isolates fell into two distinct groups: abortion or intestinal. Immunoblotting with convalescent sheep abortion antiserum identified 30 out of at least 40 silver staining polypeptides as antigenic both in OA and intestinal isolates. The serum produced a similar reaction pattern to the resolved proteins of each OA isolate, indicating a higher degree of antigenic conservation among these isolates. Considerable cross reactivity between the OA and intestinal isolates was identified, but the serum also showed apparent molecular weight differences between antigens of the two types in the 87-116 kDa, 38-44 kDa and 26-28 kDa regions. Furthermore, the immunoblotting analysis revealed heterogeneity among the intestinal isolates, particularly in antigens between 87-116 kDa and 38-44 kDa.
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Gutiérrez-Galve L, Lehmann M, Hobbs NZ, Clarkson MJ, Ridgway GR, Crutch S, Ourselin S, Schott JM, Fox NC, Barnes J. Patterns of cortical thickness according to APOE genotype in Alzheimer's disease. Dement Geriatr Cogn Disord 2010; 28:476-85. [PMID: 19940480 DOI: 10.1159/000258100] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/22/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Possession of one or more apolipoprotein E (APOE) epsilon4 alleles may influence the distribution of atrophy and clinical phenotype. We aimed to assess the influence of APOE genotype on cortical thickness and regional brain volumes in AD (Alzheimer's disease). METHODS We included 38 patients (9 epsilon4 non-carriers, 23 epsilon4 heterozygotes, 6 epsilon4 homozygotes) and 23 controls. Each subject had 2 magnetic resonance imaging (MRI) scans and a neuropsychological battery. Cortical thickness and isthmus cingulate volume were measured using FreeSurfer; the volumes of the hippocampus, whole brain, and lateral ventricles were calculated using manual and semi-automated volumetry. RESULTS Compared with controls, cortical thickness was significantly lower: in the bilateral temporal, posterior parietal and occipital regions in non-carriers, in the medial temporal and left parietal regions in heterozygotes, and in the medial temporal lobe in homozygotes. Comparisons between AD subgroups did not show significant differences. A trend for larger brain and isthmus cingulate volumes and smaller hippocampal and ventricular volumes with increasing epsilon4 dose were seen. These differences were supported by neuropsychological profiles. CONCLUSION These results suggest that APOE genotype may influence the topography of regional atrophy and cortical thinning in AD.
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Clarkson MJ, Philips HL. Isolation of faecal chlamydia from sheep in Britain and their characterization by cultural properties. Vet J 1997; 153:307-10. [PMID: 9232119 DOI: 10.1016/s1090-0233(97)80064-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Faeces samples were taken per rectum from sheep on 26 farms in England and Wales and examined for the presence of chlamydia by culture in McCoy cell monolayers. Thirteen of the farms were known to have had abortion outbreaks associated with Chlamydia psittaci (enzootic abortion) and 13 were free of this infection. The chlamydia isolated were characterized by cultural techniques. Chlamydia were isolated from the faeces of lambs on all 26 farms and the prevalence of infection varied form 5-50% on individual farms. There was no significant difference between the proportion of infected lambs on farms where enzootic abortion was present or absent. Lambs first showed infection when they were 3 months old and the prevalence rate of infection increased up to 9 months old. No chlamydia were isolated from the faeces of 316 adult ewes. The chlamydia were identified as enteric rather than abortion type and thus were C. pecorum rather than C. psittaci.
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Mansour MM, Dixon JB, Clarkson MJ, Carter SD, Rowan TG, Hammet NC. Bovine immune recognition of Ostertagia ostertagi larval antigens. Vet Immunol Immunopathol 1990; 24:361-71. [PMID: 2339503 DOI: 10.1016/0165-2427(90)90006-e] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Analysis of a detergent-solubilized somatic antigen of Ostertagia ostertagi 3rd stage larvae by SDS-PAGE and Western blotting has revealed two specific antigens with apparent molecular weights of 17 and 43 kD under reducing conditions. Probing of the Ostertagia ostertagi preparation with preinfection control sera has shown two cross-reacting antigens with apparent molecular weights of 67 and 81 kD. Both the 17 and the 43 kD antigens were recognised by IgG1 which was the predominant reactive subclass. FPLC fractionation of the crude extract with gel filtration and ion-exchange columns demonstrated immune reactivity in discrete peaks. Comparisons of ELISA and lymphocyte transformation showed antigenic components reactive with both antibodies and primed lymphocytes.
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Blewett DA, Gisemba F, Miller JK, Johnson FW, Clarkson MJ. Ovine enzootic abortion: the acquisition of infection and consequent abortion within a single lambing season. Vet Rec 1982; 111:499-501. [PMID: 7157609 DOI: 10.1136/vr.111.22.499] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The spread of enzootic abortion was observed in a flock of 37 unvaccinated Scottish blackface ewes, in mid-pregnancy at the start of the trial. Eight ewes were infected with the ZC 26 strain of chlamydia and allowed to run with 29 untreated controls until lambing was completed. All eight inoculated ewes aborted between 26 and 51 days after infection and chlamydial infection was demonstrated in seven of the abortions. Complement fixing antibodies were not detected in the controls until nine days after the first infected abortion, but within four weeks 69 per cent of the control ewes had developed significant complement fixation titres. Ten of the control ewes lost lambs, chlamydial infection was demonstrated in seven cases, two were undiagnosed and one was attributed to dystocia. The seven infected cases occurred between 69 and 87 days after the start of the trial and coincided with a further rise in the percentage of seropositive controls to a maximum of 90 per cent by the end of lambing.
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Granados A, Vakharia V, Rodionov R, Schweiger M, Vos SB, O'Keeffe AG, Li K, Wu C, Miserocchi A, McEvoy AW, Clarkson MJ, Duncan JS, Sparks R, Ourselin S. Automatic segmentation of stereoelectroencephalography (SEEG) electrodes post-implantation considering bending. Int J Comput Assist Radiol Surg 2018; 13:935-946. [PMID: 29736800 PMCID: PMC5973981 DOI: 10.1007/s11548-018-1740-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/15/2018] [Indexed: 11/26/2022]
Abstract
Purpose The accurate and automatic localisation of SEEG electrodes is crucial for determining the location of epileptic seizure onset. We propose an algorithm for the automatic segmentation of electrode bolts and contacts that accounts for electrode bending in relation to regional brain anatomy. Methods Co-registered post-implantation CT, pre-implantation MRI, and brain parcellation images are used to create regions of interest to automatically segment bolts and contacts. Contact search strategy is based on the direction of the bolt with distance and angle constraints, in addition to post-processing steps that assign remaining contacts and predict contact position. We measured the accuracy of contact position, bolt angle, and anatomical region at the tip of the electrode in 23 post-SEEG cases comprising two different surgical approaches when placing a guiding stylet close to and far from target point. Local and global bending are computed when modelling electrodes as elastic rods. Results Our approach executed on average in 36.17 s with a sensitivity of 98.81% and a positive predictive value (PPV) of 95.01%. Compared to manual segmentation, the position of contacts had a mean absolute error of 0.38 mm and the mean bolt angle difference of \documentclass[12pt]{minimal}
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\begin{document}$$0.59^{\circ }$$\end{document}0.59∘ resulted in a mean displacement error of 0.68 mm at the tip of the electrode. Anatomical regions at the tip of the electrode were in strong concordance with those selected manually by neurosurgeons, \documentclass[12pt]{minimal}
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\begin{document}$$ICC(3,k)=0.76$$\end{document}ICC(3,k)=0.76, with average distance between regions of 0.82 mm when in disagreement. Our approach performed equally in two surgical approaches regardless of the amount of electrode bending. Conclusion We present a method robust to electrode bending that can accurately segment contact positions and bolt orientation. The techniques presented in this paper will allow further characterisation of bending within different brain regions. Electronic supplementary material The online version of this article (10.1007/s11548-018-1740-8) contains supplementary material, which is available to authorized users.
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Journal Article |
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Faull WB, Clarkson MJ, Winter AC. Toxoplasmosis in a flock of sheep: some investigations into its source and control. Vet Rec 1986; 119:491-3. [PMID: 3811148 DOI: 10.1136/vr.119.20.491] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Toxoplasmosis was thought to be a minor problem on a lowland sheep farm purchasing some 200 ewe lambs annually. Serological investigations and production records suggested a more substantial problem with most of the ewe lambs seroconverting during their first pregnancy, many while still at grass and receiving no supplementary food. Only 60 live lambs were produced per 100 ewe lambs tupped. It was known that cats occasionally inhabited the sheep houses, from which straw bedding was spread onto the pastures after lambing. Trials over two years with ewe lambs grazing either 'clean' or 'dirty' pastures indicated that the straw bedding was the most likely source of infection. Serial serological studies not only defined the time of infection but also showed that the ewe lambs could be kept free of infection and produce more live lambs; 58 live births came from 81 'clean' ewe lambs compared with 21 from 50 'dirty' ewe lambs.
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Stallbaumer MF, Clarkson MJ, Bailey JW, Pritchard JE. The epidemiology of hydatid disease in England and Wales. J Hyg (Lond) 1986; 96:121-7. [PMID: 3950392 PMCID: PMC2129578 DOI: 10.1017/s0022172400062616] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The epidemiology of hydatid disease in man in England and Wales, based on the data collected between 1981 and 1983 at the Hydatid Reference Laboratory of the Public Health Laboratory Service, is presented. The incidence of hydatid disease was 42 cases per annum, with 2 cases per million population occurring in Wales and 0.2 per million in England. The highest prevalence was in London amongst the immigrant population. The incidence in the indigenous population was 15.5 cases per annum, with 5.6 cases per million occurring in South Powys, parts of South Wales and Herefordshire. The population most at risk is the rural, farming community in that area, but the West Midlands is also an apparent focus of the disease.
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research-article |
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Johnson FW, Clarkson MJ, Spencer WN. Direct isolation of the agent of enzootic abortion of ewes (Chlamydia psittaci) in cell cultures. Vet Rec 1983; 113:413-4. [PMID: 6649373 DOI: 10.1136/vr.113.18.413] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Isolation of Chlamydia psittaci in McCoy cell coverslip cultures from clinical material from field cases of enzootic abortion of ewes proved more sensitive than diagnosis by examination of smears stained by Ziehl-Neelsen. Enzootic abortion could be diagnosed in the absence of fetal membranes by culture of fetal lung or liver tissue.
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Abrams SE, Walsh KP, Coker SJ, Clarkson MJ. Responses of the post-term arterial duct to oxygen, prostaglandin E2, and the nitric oxide donor, 3-morpholinosydnonimine, in lambs and their clinical implications. BRITISH HEART JOURNAL 1995; 73:177-81. [PMID: 7696030 PMCID: PMC483787 DOI: 10.1136/hrt.73.2.177] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND Nitric oxide is a potent dilator of the pulmonary vasculature. There have been no previous reports on the action of nitric oxide on the arterial duct. OBJECTIVES To determine the responses of isolated post-term arterial duct rings from lambs to oxygen, prostaglandin E2 (PGE2) and the nitric oxide donor, 3-morpholinosydnonimine (SIN-1). SETTING Experimental laboratory. SUBJECTS Six neonatal lambs. METHODS Lambs aged 1-5 days were killed and the arterial duct and aorta excised and cut into rings. These were mounted on tension gauges in organ baths containing Krebs-Henseleit solution. Rings were exposed to increasing concentrations of oxygen, PGE2 and after preconstriction with potassium (40 mmol/l) to SIN-1. Tension and relaxation responses were recorded. RESULTS Increased oxygen tension resulted in increased tension in the ductal rings above 88.9 mm Hg as previously described. No response to PGE2 occurred before or after ductal rings were exposed to oxygen. SIN-1 caused relaxation of smooth muscle in the arterial duct to a similar degree as that in the aortic rings. CONCLUSIONS As previously shown, oxygen is a potent constrictor of the arterial duct. The post-term arterial duct does not relax in response to PGE2 possibly as a result of inactivation by oxygen of the special sensitivity of the duct to PGE2. SIN-1 is a potent smooth muscle relaxing agent in the term arterial duct and may have a role in the initial management of neonates with duct dependent pulmonary circulation.
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research-article |
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van Amsterdam B, Funke I, Edwards E, Speidel S, Collins J, Sridhar A, Kelly J, Clarkson MJ, Stoyanov D. Gesture Recognition in Robotic Surgery With Multimodal Attention. IEEE TRANSACTIONS ON MEDICAL IMAGING 2022; 41:1677-1687. [PMID: 35108200 PMCID: PMC7616924 DOI: 10.1109/tmi.2022.3147640] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Automatically recognising surgical gestures from surgical data is an important building block of automated activity recognition and analytics, technical skill assessment, intra-operative assistance and eventually robotic automation. The complexity of articulated instrument trajectories and the inherent variability due to surgical style and patient anatomy make analysis and fine-grained segmentation of surgical motion patterns from robot kinematics alone very difficult. Surgical video provides crucial information from the surgical site with context for the kinematic data and the interaction between the instruments and tissue. Yet sensor fusion between the robot data and surgical video stream is non-trivial because the data have different frequency, dimensions and discriminative capability. In this paper, we integrate multimodal attention mechanisms in a two-stream temporal convolutional network to compute relevance scores and weight kinematic and visual feature representations dynamically in time, aiming to aid multimodal network training and achieve effective sensor fusion. We report the results of our system on the JIGSAWS benchmark dataset and on a new in vivo dataset of suturing segments from robotic prostatectomy procedures. Our results are promising and obtain multimodal prediction sequences with higher accuracy and better temporal structure than corresponding unimodal solutions. Visualization of attention scores also gives physically interpretable insights on network understanding of strengths and weaknesses of each sensor.
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research-article |
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Morris DL, Richards KS, Clarkson MJ, Taylor DH. Comparison of Albendazole and Praziquantel therapy of Echinococcus granulosus in naturally infected sheep. Vet Parasitol 1990; 36:83-90. [PMID: 2382392 DOI: 10.1016/0304-4017(90)90096-t] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The effects of albendazole (10 mg kg-1 day-1) and praziquantel (50 mg kg-1 day-1) for 6 weeks on naturally infected sheep with pulmonary cysts of Echinococcus granulosus of proven viability were studied. Immediately following therapy, one of three sheep treated with praziquantel had viable cysts and 7 months later one of two sheep had viable cysts. One sheep died during albendazole therapy, but 7 months following therapy only one of five sheep had viable cysts. Electron microscopy demonstrated necrotic germinal layer tissue in most albendazole-treated cysts and praziquantel also had an effect on cyst ultrastructure. These data suggest that recurrence in humans treated with albendazole may be small. Whilst praziquantel was not particularly effective in this animal model, its clear effect on the ultrastructure suggests that an increased dose and combination therapy with albendazole may be more effective.
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Comparative Study |
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Clarkson MJ, Fraser SF, Bennett PN, McMahon LP, Brumby C, Warmington SA. Efficacy of blood flow restriction exercise during dialysis for end stage kidney disease patients: protocol of a randomised controlled trial. BMC Nephrol 2017; 18:294. [PMID: 28893206 PMCID: PMC5594594 DOI: 10.1186/s12882-017-0713-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 09/04/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Exercise during haemodialysis improves strength and physical function. However, both patients and clinicians are time poor, and current exercise recommendations add an excessive time burden making exercise a rare addition to standard care. Hypothetically, blood flow restriction exercise performed during haemodialysis can provide greater value for time spent exercising, reducing this time burden while producing similar or greater outcomes. This study will explore the efficacy of blood flow restriction exercise for enhancing strength and physical function among haemodialysis patients. METHODS This is a randomised controlled trial design. A total of 75 participants will be recruited from haemodialysis clinics. Participants will be allocated to a blood flow restriction cycling group, traditional cycling group or usual care control group. Both exercising groups will complete 3 months of cycling exercise, performed intradialytically, three times per week. The blood flow restriction cycling group will complete two 10-min cycling bouts separated by a 20-min rest at a subjective effort of 15 on a 6 to 20 rating scale. This will be done with pressurised cuffs fitted proximally on the active limbs during exercise at 50% of a pre-determined limb occlusion pressure. The traditional cycling group will perform a continuous 20-min bout of exercise at a subjective effort of 12 on the same subjective effort scale. These workloads and volumes are equivalent and allow for comparison of a common blood flow restriction aerobic exercise prescription and a traditional aerobic exercise prescription. The primary outcome measures are lower limb strength, assessed by a three repetition maximum leg extension test, as well as objective measures of physical function: six-minute walk test, 30-s sit to stand, and timed up and go. Secondary outcome measures include thigh muscle cross sectional area, body composition, routine pathology, quality of life, and physical activity engagement. DISCUSSION This study will determine the efficacy of blood flow restriction exercise among dialysis patients for improving key physiological outcomes that impact independence and quality of life, with reduced burden on patients. This may have broader implications for other clinical populations with similarly declining muscle health and physical function, and those contraindicated to higher intensities of exercise. TRIAL REGISTRATION Australian and New Zealand Clinical Trial Register: ACTRN12616000121460.
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Randomized Controlled Trial |
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Hill ER, Xia W, Clarkson MJ, Desjardins AE. Identification and removal of laser-induced noise in photoacoustic imaging using singular value decomposition. BIOMEDICAL OPTICS EXPRESS 2017; 8:68-77. [PMID: 28101402 PMCID: PMC5231316 DOI: 10.1364/boe.8.000068] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/28/2016] [Accepted: 11/11/2016] [Indexed: 05/20/2023]
Abstract
Singular value decomposition (SVD) was used to identify and remove laser-induced noise in photoacoustic images acquired with a clinical ultrasound scanner. This noise, which was prominent in the radiofrequency data acquired in parallel from multiple transducer elements, was induced by the excitation light source. It was modelled by truncating the SVD matrices so that only the first few largest singular value components were retained, and subtracted prior to image reconstruction. The dependency of the signal amplitude and the number of the largest singular value components used for noise modeling was investigated for different photoacoustic source geometries. Validation was performed with simulated data and measured noise, and with photoacoustic images acquired from the human forearm and finger in vivo using L14-5/38 and L40-8/12 linear array clinical imaging probes. The use of only one singular value component was found to be sufficient to achieve near-complete removal of laser-induced noise from reconstructed images. This method has strong potential to increase image quality for a wide range of photoacoustic imaging systems with parallel data acquisition.
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Clarkson MJ, May AK, Warmington SA. Is there rationale for the cuff pressures prescribed for blood flow restriction exercise? A systematic review. Scand J Med Sci Sports 2020; 30:1318-1336. [PMID: 32279391 DOI: 10.1111/sms.13676] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 03/12/2020] [Accepted: 03/27/2020] [Indexed: 01/10/2023]
Abstract
BACKGROUND Blood flow restriction exercise has increasingly broad applications among healthy and clinical populations. Ensuring the technique is applied in a safe, controlled, and beneficial way for target populations is essential. Individualized cuff pressures are a favored method for achieving this. However, there remains marked inconsistency in how individualized cuff pressures are applied. OBJECTIVES To quantify the cuff pressures used in the broader blood flow restriction exercise literature, and determine whether there is clear justification for the choice of pressure prescribed. METHODS Studies were included in this review from database searches if they employed an experimental design using original data, involved either acute or chronic exercise using blood flow restriction, and they assessed limb or arterial occlusion pressure to determine an individualized cuff pressure. Methodologies of the studies were evaluated using a bespoke quality assessment tool. RESULTS Fifty-one studies met the inclusion criteria. Individualized cuff pressures ranged from 30% to 100% arterial occlusion pressure. Only 7 out of 52 studies attempted to justify the individualized cuff pressure applied during exercise. The mean quality rating for all studies was 11.1 ± 1.2 out of 13. CONCLUSIONS The broader blood flow restriction exercise literature uses markedly heterogeneous prescription variables despite using individualized cuff pressures. This is problematic in the absence of any clear justification for the individualized cuff pressures selected. Systematically measuring and reporting all relevant acute responses and training adaptations to the full spectrum of BFR pressures alongside increased clarity around the methodology used during blood flow restriction exercise is paramount.
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Clarkson MJ, Awan MA. The immune response of sheep to Trypanosoma vivax. ANNALS OF TROPICAL MEDICINE AND PARASITOLOGY 1969; 63:515-27. [PMID: 4988736 DOI: 10.1080/00034983.1969.11686655] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Ortiz PL, Claxton JR, Clarkson MJ, McGarry J, Williams DJ. The specificity of antibody responses in cattle naturally exposed to Fasciola hepatica. Vet Parasitol 2000; 93:121-34. [PMID: 11035230 DOI: 10.1016/s0304-4017(00)00360-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fasciola hepatica causes significant morbidity and mortality in dairy cattle in the Andean region of Cajamarca, Peru, where prevalence of infection of up to 78% has been reported. ELISA and Western blot analyses were used to characterise antibody responses in dairy cattle to adult F. hepatica to excretory-secretory (E/S), somatic (SO) and surface (SU) antigens. Three groups of dairy cattle - calves, heifers and adult cows - naturally exposed to F. hepatica in this region, were monitored every 2 months over a 2-year period. Calves, heifers and adult cows all had antibodies which recognised a 28kDa protein in the SO preparation, whereas only adult cows had antibodies that recognised a 28kDa protein in E/S products. All three groups of cattle responded to a 60-66kDa group of proteins in E/S and SU preparations and a 17kDa antigen in SO products was recognised by antibodies from cows and heifers but not calves. The total antibody response to E/S antigens measured by ELISA, increased over time in calves and remained constantly high over the 2-year period in all three groups of cattle. Slight fluctuations in the antibody response occurred in the group of heifers and cows coinciding with seasonal changes in the level of challenge.
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Thompson S, Stoyanov D, Schneider C, Gurusamy K, Ourselin S, Davidson B, Hawkes D, Clarkson MJ. Hand-eye calibration for rigid laparoscopes using an invariant point. Int J Comput Assist Radiol Surg 2016; 11:1071-80. [PMID: 26995597 PMCID: PMC4893361 DOI: 10.1007/s11548-016-1364-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 02/24/2016] [Indexed: 01/22/2023]
Abstract
PURPOSE Laparoscopic liver resection has significant advantages over open surgery due to less patient trauma and faster recovery times, yet it can be difficult due to the restricted field of view and lack of haptic feedback. Image guidance provides a potential solution but one current challenge is in accurate "hand-eye" calibration, which determines the position and orientation of the laparoscope camera relative to the tracking markers. METHODS In this paper, we propose a simple and clinically feasible calibration method based on a single invariant point. The method requires no additional hardware, can be constructed by theatre staff during surgical setup, requires minimal image processing and can be visualised in real time. Real-time visualisation allows the surgical team to assess the calibration accuracy before use in surgery. In addition, in the laboratory, we have developed a laparoscope with an electromagnetic tracking sensor attached to the camera end and an optical tracking marker attached to the distal end. This enables a comparison of tracking performance. RESULTS We have evaluated our method in the laboratory and compared it to two widely used methods, "Tsai's method" and "direct" calibration. The new method is of comparable accuracy to existing methods, and we show RMS projected error due to calibration of 1.95 mm for optical tracking and 0.85 mm for EM tracking, versus 4.13 and 1.00 mm respectively, using existing methods. The new method has also been shown to be workable under sterile conditions in the operating room. CONCLUSION We have proposed a new method of hand-eye calibration, based on a single invariant point. Initial experience has shown that the method provides visual feedback, satisfactory accuracy and can be performed during surgery. We also show that an EM sensor placed near the camera would provide significantly improved image overlay accuracy.
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