Biomedical subjects

T M Peters

Publications and source records attributed to T M Peters.

At least 19 recordsLinked to original sources

PubMed2006

Distribution of molecular subtypes within Salmonella enterica serotype Enteritidis phage type 4 and S. Typhimurium definitive phage type 104 in nine European countries, 2000-2004: results of an international multi-centre study.

This study investigates the distribution of pulsed-field gel electrophoresis (PFGE) profiles within Salmonella enterica serotype Enteritidis phage type (PT) 4 and S. Typhimurium definitive phage type (DT) 104, from cases of human infection in nine European countries from 2000 to 2004. Isolates were subtyped using standardized methods and gel images submitted by each participating country to the coordinating centre (Health Protection Agency Centre for Infections, London, UK), where they were entered into a central database, developed within BioNumerics software, and designated using an agreed nomenclature. S. Enteritidis PT4 (n=3637) was differentiated into 38 different profiles. Simpson's index of diversity (D) of profiles ranged from 0.2 to 0.4. Profile SENTXB.0001 represented at least 80% of all profiles in each country. S. Typhimurium DT104 (n=1202) was differentiated into 28 different profile types. Simpson's D was at least 0.6 in all countries except in Austria and Italy. In both these countries over 74% of S. Typhimurium DT104 profiles were STYMXB.0013. Profile STYMXB.0061, was predominant in Denmark, Spain, Finland and England and Wales where it represented between 36% and 45% of profiles. Profile STYMXB.0001 represented nearly half of all profiles in Scotland and 23% in England and Wales. PFGE is proving useful for further discrimination within S. Enteritidis PT4 and S. Typhimurium DT104. Ascertainment of international outbreaks involving common serotypes and phage types may be increased by the timely pooling of PFGE profiles within a central database readily accessible to all participating countries.

Bacteriophage Typing↗

PubMed2004

Poly(vinyl alcohol) cryogel phantoms for use in ultrasound and MR imaging.

Poly(vinyl alcohol) cryogel, PVA-C, is presented as a tissue-mimicking material, suitable for application in magnetic resonance (MR) imaging and ultrasound imaging. A 10% by weight poly(vinyl alcohol) in water solution was used to form PVA-C, which is solidified through a freeze-thaw process. The number of freeze-thaw cycles affects the properties of the material. The ultrasound and MR imaging characteristics were investigated using cylindrical samples of PVA-C. The speed of sound was found to range from 1520 to 1540 m s(-1), and the attenuation coefficients were in the range of 0.075-0.28 dB (cm MHz)(-1). T1 and T2 relaxation values were found to be 718-1034 ms and 108-175 ms, respectively. We also present applications of this material in an anthropomorphic brain phantom, a multi-volume stenosed vessel phantom and breast biopsy phantoms. Some suggestions are made for how best to handle this material in the phantom design and development process.

Animals↗

PubMed2003

The Salm-gene project - a European collaboration for DNA fingerprinting for food-related salmonellosis.

An external quality assessment of PFGE method to discriminate between salmonella serotypes and lysotypes was carried out by the Salm-Gene project in Europe. A set of 16 strains of S. Enteritidis was sent to 9 national salmonella reference laboratories. By using a harmonised protocol, the PFGE profiles produced were comparable between each centre. In most cases, there was at least 90% similarity between isolates tested in the different European laboratories and there was usually >95% similarity. This suggests that PFGE analyses are reproducible and therefore can be used as a valuable investigation tool combined with epidemiological data.

DNA Fingerprinting↗

PubMed2002

Surveillance and clinical relevance of vacA genotypes of Helicobacter pylori infecting dyspeptic patients in mid-Essex.

The Helicobacter pylori vacuolating cytotoxin is a putative pathogenicity factor encoded by vacA, a mosaic gene with a global distribution. The vacA type prevalence and diversity of H. pylori isolated from antral gastric biopsies of 360 dyspeptic patients in mid-Essex, and of 79 patients from other locations, were investigated in order to test for links with disease severity. Mid (m)-region genotyping and subtyping by vacA HaeIII RFLP (restriction fragment length polymorphism) analysis showed that the m1 and m2 alleles were diverse, with 191 different subtypes. Variation in 44% of strains was accounted for by ten subtypes of which subtype v-1 represented a conserved core (33%) of the m1 form. Prevalence rates for combined mid and signal (s)-region genotypes were 40% for s1/m1, 46% for s1/m2, and 11% for s2/m2. Overall, vacA genotyping provided high typability and discrimination, but no specific RFLP markers could reliably predict a clinically significant presentation due to an H. pylori infection.

Alleles↗

PubMed2001

Temperature dosimetry using MR relaxation characteristics of poly(vinyl alcohol) cryogel (PVA-C).

Hyperthermic therapy is being used for a variety of medical treatments, such as tumor ablation and the enhancement of radiation therapy. Research in this area requires a tool to record the temperature distribution created by a heat source, similar to the dosimetry gels used in radiation therapy to record dose distribution. Poly(vinyl alcohol) cryogel (PVA-C) is presented as a material capable of recording temperature distributions between 45 and 70 degrees C, with less than a 1 degrees C error. An approximately linear, positive relationship between MR relaxation times and applied temperature is demonstrated, with a maximum of 16.3 ms/ degrees C change in T(1) and 10.2 ms/ degrees C in T(2) for a typical PVA-C gel. Applied heat reduces the amount of cross-linking in PVA-C, which is responsible for a predictable change in T(1) and T(2) times. Temperature distributions in PVA-C volumes may be determined by matching MR relaxation times across the volumes to calibration values produced in samples subjected to known temperatures. Factors such as thermotolerance, perfusion effects, and thermal conductivity of PVA-C are addressed for potentially extending this method to modeling thermal doses in tissue.

Gels↗

PubMed2001

Single-enzyme amplified fragment length polymorphism and its applicability for Salmonella epidemiology.

Amplified fragment length polymorphism (AFLP) is a PCR-based DNA fingerprinting technique whereby restriction fragments may be visualized without prior knowledge of nucleotide sequences. In AFLP analysis, bacterial genomic DNA is digested with a restriction enzyme and ligated to adapter oligonucleotides. A subset of DNA fragments are then amplified using primers which contain adapter-defined sequences. Selective amplification is achieved by the use of primers containing adapter-defined sequences with one additional arbitrary nucleotide. We used four primers complementary to the adapter sequence, but each differing in the final 3' base that extended into the fragment DNA. The usefulness of these primers for fingerprinting Salmonella enterica was assessed in a hierarchical manner. Using a single-enzyme approach (SAFLP) we have used this method to fingerprint 30 strains of S. enterica, belonging to 14 different serotypes. SAFLP profiles derived from Hind III fragments differentiated between the serotypes. In addition, SAFLP profiles for each serotype differentiated between the phage types and individual strains. The technique is significantly faster to perform than other DNA-based methods and has given reproducible and discriminatory results. This hierarchical SAFLP technique may provide a valuable addition to existing methods for the DNA fingerprinting of S. enterica for epidemiological studies.

DNA Fingerprinting↗

PubMed2001

Molecular epidemiology of Helicobacter pylori in England: prevalence of cag pathogenicity island markers and IS605 presence in relation to patient age and severity of gastric disease.

The cagA gene is a key marker for the Helicobacter pylori cag pathogenicity island (PAI), which may vary in composition in different strains with insertion sequence mediated interruptions and deletions of genes. While presence of cagA has been associated with increased risk for peptic ulcer disease and gastric cancer, the precise link with virulence is controversial. We investigated H. pylori from dyspeptics in one location in England (mid-Essex) with reference to the prevalence and distribution by age cohort of different cag PAI forms to determine if presence of the insertion element IS605 had a modifying effect on the severity of associated disease. H. pylori isolated from gastric biopsies over a 4-year period were screened by specific PCR assays for the presence of cagA, cagD, cagE and virD4 genes in the cag PAI, and for the presence of IS605 in the PAI and elsewhere in the genome. Most (68%) of the 166 isolates of H. pylori contained a PAI based on detection of cagA whereas 29% had no detectable PAI using multiple loci. The cagA+ genotype frequencies were similar in the peptic ulcer and non-ulcer dyspepsia-gastritis groups (79% vs. 74%) whereas frequencies in the NUD-oesophagitis and normal mucosa groups were lower (58%) but not significantly different (P>0.41). Genomic IS605 inserts were present at an overall frequency of 32% and were widely distributed with respect to patient age and disease severity. The combined cagA+/IS- strain genotype was common but not significantly associated with PUD compared to endoscopically normal mucosa (P> or =0.807). We concluded that presence of the IS605 element, whether in cagA+ or cagA- strains of H. pylori, did not systematically modify the severity of associated disease in the study population.

Adolescent↗

PubMed2001

Genetic diversity in the Helicobacter pylori cag pathogenicity island and effect on expression of anti-CagA serum antibody in UK patients with dyspepsia.

AIMS: To investigate variation within the cag pathogenicity island (PAI) of Helicobacter pylori isolated from patients with dyspepsia in mid-Essex, and to evaluate the effect on expression of anti-CagA antibody. METHODS: Sixty two isolates of H pylori cultured from gastric biopsies were screened by specific PCR assays for the presence of cagA and other gene markers (cagD and cagE, and virD4) in the cag PAI. An enzyme linked immunosorbent assay (ELISA) kit (Viva Diagnostica helicobacter p120) was used to test for anti-CagA IgG antibody in matching sera. Isolates were also genotyped by vacuolating cytotoxin polymerase chain reaction (PCR) analysis, and tested for absence of the complete cag PAI (empty site PCR assay). RESULTS: Forty one of the H pylori isolates had a cag PAI containing cagA. One strain had no cagA but other cag PAI loci were present, whereas the remaining 20 strains had no detectable cag PAI markers. Anti-CagA IgG antibody was detected in 34 sera by the ELISA assay, and when compared with the cag PAI genotype of the infecting strain, accuracy, sensitivity, and specificity were 92%, 87%, and 100%, respectively. The seven discrepant or borderline strains in the ELISA were all vacA s1 but differed in other genotypic markers. CONCLUSIONS: The cag PAI was widely distributed in H pylori from patients with dyspepsia in mid-Essex who had different gastric pathologies. Infection with a strain having an uninterrupted cag PAI was associated with the presence of anti-CagA antibody in most patients. Discrepant ELISA results, mostly for elderly patients with duodenal ulcers, were attributed to cagA associated variation, particularly to the presence of mixed cagA+/cagA- cell variants in the infecting strain population. Tests for anti-CagA serum antibody were unreliable for predicting severity of clinical disease associated with H pylori infection in this series of patients.

Adult↗

PubMed2000

An algorithmic overview of surface registration techniques for medical imaging.

This paper presents a literature survey of automatic 3D surface registration techniques emphasizing the mathematical and algorithmic underpinnings of the subject. The relevance of surface registration to medical imaging is that there is much useful anatomical information in the form of collected surface points which originate from complimentary modalities and which must be reconciled. Surface registration can be roughly partitioned into three issues: choice of transformation, elaboration of surface representation and similarity criterion, and matching and global optimization. The first issue concerns the assumptions made about the nature of relationships between the two modalities, e.g. whether a rigid-body assumption applies, and if not, what type and how general a relation optimally maps one modality onto the other. The second issue determines what type of information we extract from the 3D surfaces, which typically characterizes their local or global shape, and how we organize this information into a representation of the surface which will lead to improved efficiency and robustness in the last stage. The last issue pertains to how we exploit this information to estimate the transformation which best aligns local primitives in a globally consistent manner or which maximizes a measure of the similarity in global shape of two surfaces. Within this framework, this paper discusses in detail each surface registration issue and reviews the state-of-the-art among existing techniques.

Algorithms↗

PubMed2000

Image-guided surgery: from X-rays to virtual reality.

Since the discovery of X-rays, medical imaging has played a major role in the guidance of surgical procedures. While medical imaging began with simple X-ray plates to indicate the presence of foreign objects within the human body, the advent of the computer has been a major factor in the recent development of this field. Imaging techniques have grown greatly in their sophistication and can now provide the surgeon with high quality three-dimensional images depicting not only the normal anatomy and pathology, but also vascularity and function. One key factor in the advances in Image-Guided Surgery (IGS) is the ability not only to register images derived from the various imaging modalities amongst themselves, but also to register them to the patient. The other crucial aspect of IGS is the ability to track instruments in real time during the procedure, and to portray them as part of a realistic model of the operative volume. Stereoscopic and virtual-reality techniques can usefully enhance the visualization process. IGS nevertheless relies heavily on the assumption that the images acquired prior to surgery, and upon which the surgical guidance is based, accurately represent the morphology of the tissue during the surgical procedure. In many instances this assumption is invalid, and intra-operative real-time imaging, using interventional MRI, Ultrasound, and electrophysiological recordings are often employed to overcome this limitation. Although now in extensive clinical use, IGS is often currently perceived as an intrusion into the operating room. It must evolve towards becoming a routine surgical tool, but this will only happen if natural and intuitive human interfaces are developed for these systems.

Brain↗

PubMed2000

An inverse problem approach to the correction of distortion in EPI images.

Magnetic resonance imaging using the echo planar imaging (EPI) technique is particularly sensitive to main (B0) field inhomogeneities. The primary effect is geometrical distortion in the phase encoding direction. In this paper, we present a method based on the conjugate gradient algorithm to correct for this geometrical distortion, by solving the EPI imaging equation. Two versions are presented: one that attempts to solve the full four-dimensional (4-D) imaging equation, and one that independently solves for each profile along the blip encoding direction. Results are presented for both phantom and in vivo brain EPI images and compared with other proposed correction methods.

Algorithms↗

PubMed2000

Intraoperative ultrasound for guidance and tissue shift correction in image-guided neurosurgery.

We present a surgical guidance system that incorporates pre-operative image information (e.g., MRI) with intraoperative ultrasound (US) imaging to detect and correct for brain tissue deformation during image-guided neurosurgery (IGNS). Many interactive IGNS implementations employ pre-operative images as a guide to the surgeons throughout the procedure. However, when a craniotomy is involved, tissue movement during a procedure can be a significant source of error in these systems. By incorporating intraoperative US imaging, the target volume can be scanned at any time, and two-dimensional US images may be compared directly to the corresponding slice from the pre-operative image. Homologous points may be mapped from the intraoperative to the pre-operative image space with an accuracy of better than 2 mm, enabling the surgeon to use this information to assess the accuracy of the guidance system along with the progress of the procedure (e.g., extent of lesion removal) at any time during the operation. Anatomical features may be identified on both the pre-operative and intraoperative images and used to generate a deformation map, which can be used to warp the pre-operative image to match the intraoperative US image. System validation is achieved using a deformable multi-modality imaging phantom, and preliminary clinical results are presented.

Brain↗

PubMed2000

3-D image guidance for minimally invasive robotic coronary artery bypass.

BACKGROUND: The introduction of a robot-assisted microsurgical system has made endoscopic coronary artery bypass grafting (ECABG) possible. Despite the success of this approach, surgeons still require better visualization tools for pre-surgical planning and intra-operative image guidance. Such visualization tools could, for example, assist in the placement of thoracic ports to acquire optimum access to the target vessels. In this paper we discuss the essential steps toward image-guided completely endoscopic coronary bypass surgery with robot assistance, and we present our preliminary efforts toward the development of a three-dimensional (3-D) virtual cardiac surgical planning platform (VCSP) for ECABG. METHODS: Preoperative 3-D images of the thorax acquired with computed tomography and electrocardiogram-gated magnetic resonance imaging are imported into VCSP. Using VCSP, a user may interactively visualize and manipulate the simulated thoracic ports in 3-D within the reconstructed thoracic region. We have also implemented a virtual endoscope to simulate the endoscopic view observed by the surgeon during the operation. Once the port placements for optimal access to the target vessels are determined, the positions of the simulated tools can be recorded and marked on the patient to specify the positions for port incisions. RESULTS: A static thorax phantom was used to verify the port placements obtained from VCSP simulations. The angles and the distances between the ports, the endoscope and the markers that were placed on the surface of the phantom were measured, and the results were compared with those obtained from simulation. The physical measured distances and angles agreed with the simulated results with average errors of 4 mm and 2 degrees, respectively. CONCLUSIONS: The VCSP image-guided surgical system allows a surgeon to visualize a patient's thorax in a 3-D interactive environment for planning surgical procedures, and to determine the optimum port placement based on preoperative 3-D images. However, during an operation, the positions and orientation of the heart and the coronary arteries are changed from their corresponding locations in the preoperative images due to carbon-dioxide insufflation, lung deflation, and dynamic motions of the beating heart. One of our future goals of this project is the use of mathematical models that correct for these changes so that our system could be applied to intra-operative image guidance.

Adult↗

PubMed1999

Potential for aging female Aedes aegypti (Diptera: Culicidae) by gas chromatographic analysis of cuticular hydrocarbons, including a field evaluation.

Gas chromatography with flame-ionization detection was used to measure the time-associated, quantitative changes in the cuticular hydrocarbons of female Aedes aegypti (L.). Cohorts of unstressed Ae. aegypti, Rockefeller strain, were reared and held at 3 constant temperatures (24, 28, and 30 degrees C). Five females from each cohort were taken at 33 degree-day (DD) intervals from 0 to 231 DD (using 17 degrees C as the threshold temperature). Quantitative changes over time of cuticular hydrocarbons associated with gas chromatographic peaks 1 and 5 were identified as having promise for age grading. The relative abundance of peak 1 (pentacosane) decreased linearly from 0 to 132 DD, whereas peak 5 (nonacosane) increased linearly over the same period. Suboptimal larval conditions (crowded and starved), which resulted in physiological stress (decreased size), had negligible effect on the relative abundance of pentacosane and nonacosane. Additionally, the rate of change in the relative abundance of pentacosane and nonacosane were the same for both a recently colonized Chachoengsao (Thailand) strain of Ae. aegypti compared with the long-colonized Rockefeller (Caribbean) strain over a 0-99 DD interval. Two linear regression models, one based on the relative abundance of pentacosane and the other on the logit transformation of these values, were developed for aging female Ae. aegypti. A blind study using laboratory-reared mosquitoes and a mark-release-recapture experiment using field mosquitoes validated these age-grading models and produced promising results for aging females up to 132 DD (19, 12, and 10 calendar days at 24, 28 and 30 degrees C, respectively). Therefore the regression models, based on the relative abundance of these 2 cuticular hydrocarbons, appeared to be a useful approach for age-grading Ae. aegypti up to at least 12 d of age regardless of environmental conditions (temperature and stress) and population history (origin and colonization time).

Aedes↗

PubMed1999

Localization of somatosensory function by using positron emission tomography scanning: a comparison with intraoperative cortical stimulation.

OBJECT: To investigate the utility of [15O]H2O positron emission tomography (PET) activation studies in the presurgical mapping of primary somatosensory cortex, the authors compared the magnitude and location of activation foci obtained using PET scanning with the results of intraoperative cortical stimulation (ICS). METHODS: The authors used PET scanning and vibrotactile stimulation (of the face, hand, or foot) to localize the primary somatosensory cortex before surgical resection of mass lesions or epileptogenic foci affecting the central area in 20 patients. With the aid of image-guided surgical systems, the locations of significant activation foci on PET scanning were compared with those of positive ICS performed at craniotomy after the patient had received a local anesthetic agent. In addition, the relationship between the magnitude and statistical significance of blood flow changes and the presence of positive ICS was examined. In 22 (95.6%) of 23 statistically significant (p < 0.05) PET activation foci, spatially concordant sites on ICS were also observed. Intraoperative cortical stimulation was positive in 40% of the PET activation studies that did not result in statistically significant activation. In the patients showing these results, there was a clearly identifiable t-statistic peak that was spatially concordant with the site of positive ICS in the sensorimotor area. All PET activation foci with a t statistic greater than 4.75 were associated with spatially concordant sites of positive ICS. All PET activation foci with a t statistic less than 3.2 were associated with negative ICS. CONCLUSIONS: Positron emission tomography is an accurate method for mapping the primary somatosensory cortex before surgery. The need for ICS, which requires local anesthesia, may be eliminated when PET foci with high (> 4.75) or low (< 3.20) t-statistic peaks are elicited by vibrotactile stimulation.

Craniotomy↗

PubMed1998

Automated atlas integration and interactive three-dimensional visualization tools for planning and guidance in functional neurosurgery.

Many critical functionally distinct subcortical structures are not distinguishable on anatomical magnetic resonance imaging (MRI) scans. In order to provide the neurosurgeon with this missing information, a deformable volumetric atlas of the basal ganglia and thalamus has been created from the Schaltenbrand and Wahren atlas of cryogenic slices. The volumetric atlas can be automatically deformed to an individual patient's MRI. To facilitate the clinical use of the atlas, a visualization platform has been developed for preoperative and intraoperative use which permits manipulation of the merged atlas and MRI data sets in two- and three-dimensional views. The platform includes graphical tools which allow the visualization of projections of a leukotome and other surgical tools with respect to the atlas data, as well as preregistered images from any other imaging modality. In addition, a graphical interface has been designed to create custom virtual lesions using computer models of neurosurgical tools for intraoperative planning. To date this system has been employed as an adjunct to over 30 functional neurosurgical cases including surgery for movement disorders.

Algorithms↗

PubMed1998

Development of a scheme for genotyping Helicobacter pylori based on allelic variation in urease subunit genes.

Helicobacter pylori urease subunit genes in 383 isolates from 10 countries were investigated by PCR-restriction fragment length polymorphism (HaeIII) analysis. Eighty-two different ureAB profiles were documented by reference to known sequences. Variation among 51% of strains was accounted for by 10 predominant patterns, which provided a unique framework for categorizing isolates with geographically diverse origins.

Alleles↗

PubMed1996

Three-dimensional reconstruction of vascular trees. Theory and methodology.

In this paper we examine the few-view reconstruction problem as it applies to imaging vascular trees. A fully automated reconstruction algorithm is described that circumvents the traditional "correspondence problem," using only notions of consistency and connectivity. It is assumed that the vascular tree is a connected structure and that its centerlines have been identified in three or more images. The first of three steps in the procedure involves generating a connected structure that represents the multiplicity of solutions that are consistent with any two (different) projections. The second step assigns to each branch in this structure a measure of agreement based on its relationship with one or more additional views of the vasculature. The problem then becomes one of propagating this information, via connectivity relationships and consistency checks, throughout the above structure to distinguish between the branches comprising the imaged structure and the accompanying artifacts. In this paper we present the theory and methodology of the technique, while in a companion paper we address the issue of validation via simulations and experiments. Together, these papers shed some light on why ambiguities arise and often lead to errors in the few-view reconstruction problem. Strategies to handle these errors are described and results are presented that demonstrate the ability to obtain adequate reconstructions with as few as three distinct views.

Algorithms↗