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1.  JPEG2000 Still Image Coding Quality 
Journal of Digital Imaging  2013;26(5):866-874.
This work demonstrates the image qualities between two popular JPEG2000 programs. Two medical image compression algorithms are both coded using JPEG2000, but they are different regarding the interface, convenience, speed of computation, and their characteristic options influenced by the encoder, quantization, tiling, etc. The differences in image quality and compression ratio are also affected by the modality and compression algorithm implementation. Do they provide the same quality? The qualities of compressed medical images from two image compression programs named Apollo and JJ2000 were evaluated extensively using objective metrics. These algorithms were applied to three medical image modalities at various compression ratios ranging from 10:1 to 100:1. Following that, the quality of the reconstructed images was evaluated using five objective metrics. The Spearman rank correlation coefficients were measured under every metric in the two programs. We found that JJ2000 and Apollo exhibited indistinguishable image quality for all images evaluated using the above five metrics (r > 0.98, p < 0.001). It can be concluded that the image quality of the JJ2000 and Apollo algorithms is statistically equivalent for medical image compression.
doi:10.1007/s10278-013-9603-x
PMCID: PMC3782606  PMID: 23589187
Image compression; JPEG2000; Image quality
2.  Deriving Hounsfield units using grey levels in cone beam CT: a clinical application 
Dentomaxillofacial Radiology  2012;41(6):500-508.
Objective
To present a clinical study demonstrating a method to derive Hounsfield units from grey levels in cone beam CT (CBCT).
Methods
An acrylic intraoral reference object with aluminium, outer bone equivalent material (cortical bone), inner bone equivalent material (trabecular bone), polymethlymethacrylate and water equivalent material was used. Patients were asked if they would be willing to have an acrylic bite plate with the reference object placed in their mouth during a routine CBCT scan. There were 31 scans taken on the Asahi Alphard 3030 (Belmont Takara, Kyoto, Japan) and 30 scans taken on the Planmeca ProMax 3D (Planmeca, Helsinki, Finland) CBCT. Linear regression between the grey levels of the reference materials and their linear attenuation coefficients was performed for various photon energies. The energy with the highest regression coefficient was chosen as the effective energy. The attenuation coefficients for the five materials at the effective energy were scaled as Hounsfield units using the standard Hounsfield units equation and compared to those derived from the measured grey levels of the materials using the regression equation.
Results
In general, there was a satisfactory linear relation between the grey levels and the attenuation coefficients. This made it possible to calculate Hounsfield units from the measured grey levels. Uncertainty in determining effective energies resulted in unrealistic effective energies and significant variability of calculated CT numbers. Linear regression from grey levels directly to Hounsfield units at specified energies resulted in greater consistency.
Conclusions
The clinical application of a method for deriving Hounsfield units from grey levels in CBCT was demonstrated.
doi:10.1259/dmfr/31640433
PMCID: PMC3520389  PMID: 22752324
cone beam computed tomography; Hounsfield units; grey levels; bone density; linear attenuation coefficient
3.  Stress Echocardiography for the Diagnosis of Coronary Artery Disease 
Executive Summary
In July 2009, the Medical Advisory Secretariat (MAS) began work on Non-Invasive Cardiac Imaging Technologies for the Diagnosis of Coronary Artery Disease (CAD), an evidence-based review of the literature surrounding different cardiac imaging modalities to ensure that appropriate technologies are accessed by patients suspected of having CAD. This project came about when the Health Services Branch at the Ministry of Health and Long-Term Care asked MAS to provide an evidentiary platform on effectiveness and cost-effectiveness of non-invasive cardiac imaging modalities.
After an initial review of the strategy and consultation with experts, MAS identified five key non-invasive cardiac imaging technologies for the diagnosis of CAD. Evidence-based analyses have been prepared for each of these five imaging modalities: cardiac magnetic resonance imaging, single photon emission computed tomography, 64-slice computed tomographic angiography, stress echocardiography, and stress echocardiography with contrast. For each technology, an economic analysis was also completed (where appropriate). A summary decision analytic model was then developed to encapsulate the data from each of these reports (available on the OHTAC and MAS website).
The Non-Invasive Cardiac Imaging Technologies for the Diagnosis of Coronary Artery Disease series is made up of the following reports, which can be publicly accessed at the MAS website at: www.health.gov.on.ca/mas"> www.health.gov.on.ca/mas or at www.health.gov.on.ca/english/providers/program/mas/mas_about.html
Single Photon Emission Computed Tomography for the Diagnosis of Coronary Artery Disease: An Evidence-Based Analysis
Stress Echocardiography for the Diagnosis of Coronary Artery Disease: An Evidence-Based Analysis
Stress Echocardiography with Contrast for the Diagnosis of Coronary Artery Disease: An Evidence-Based Analysis
64-Slice Computed Tomographic Angiography for the Diagnosis of Coronary Artery Disease: An Evidence-Based Analysis
Cardiac Magnetic Resonance Imaging for the Diagnosis of Coronary Artery Disease: An Evidence-Based Analysis
Pease note that two related evidence-based analyses of non-invasive cardiac imaging technologies for the assessment of myocardial viability are also available on the MAS website:
Positron Emission Tomography for the Assessment of Myocardial Viability: An Evidence-Based Analysis
Magnetic Resonance Imaging for the Assessment of Myocardial Viability: an Evidence-Based Analysis
The Toronto Health Economics and Technology Assessment Collaborative has also produced an associated economic report entitled:
The Relative Cost-effectiveness of Five Non-invasive Cardiac Imaging Technologies for Diagnosing Coronary Artery Disease in Ontario [Internet]. Available from: http://theta.utoronto.ca/reports/?id=7
Objective
The objective of the analysis is to determine the diagnostic accuracy of stress echocardiography (ECHO) in the diagnosis of patients with suspected coronary artery disease (CAD) compared to coronary angiography (CA).
Stress Echocardiography
Stress ECHO is a non-invasive technology that images the heart using ultrasound. It is one of the most commonly employed imaging techniques for investigating a variety of cardiac abnormalities in both community and hospital settings. A complete ECHO exam includes M-mode, 2-dimensional (2-D) images and Doppler imaging.
In order to diagnosis CAD and assess whether myocardial ischemia is present, images obtained at rest are compared to those obtained during or immediately after stress. The most commonly used agents used to induce stress are exercise and pharmacological agents such as dobutamine and dipyridamole. The hallmark of stress-induced myocardial ischemia is worsening of wall motion abnormalities or the development of new wall motion abnormalities. A major challenge for stress ECHO is that the interpretation of wall motion contractility and function is subjective. This leads to inter-observer variability and reduced reproducibility. Further, it is estimated that approximately 30% of patients have sub-optimal stress ECHO exams. To overcome this limitation, contrast agents for LV opacification have been developed.
Although stress ECHO is a relatively easy to use technology that poses only a low risk of adverse events compared to other imaging technologies, it may potentially be overused and/or misused in CAD diagnosis. Several recent advances have been made focusing on quantitative methods for assessment, improved image quality and enhanced portability, however, evidence on the effectiveness and clinical utility of these enhancements is limited.
Evidence-Based Analysis
Research Questions
What is the diagnostic accuracy of stress ECHO for the diagnosis of patients with suspected CAD compared to the reference standard of CA?
What is the clinical utility1 of stress ECHO?
Literature Search
A literature search was performed on August 28, 2009 using OVID MEDLINE, MEDLINE In-Process and Other Non-Indexed Citations, EMBASE, the Cumulative Index to Nursing & Allied Health Literature (CINAHL), the Cochrane Library, and the International Agency for Health Technology Assessment (INAHTA) for studies published from January 1, 2004 until August 21, 2009. Abstracts were reviewed by a single reviewer and, for those studies meeting the eligibility criteria, full-text articles were obtained. Reference lists were also examined for any relevant studies not identified through the search.
Inclusion Criteria
Systematic reviews, meta-analyses, randomized controlled trials, prospective observational studies, retrospective analyses
Minimum sample size of 20 enrolled patients
Comparison to CA (reference standard)
Definition of CAD specified as either ≥50%, ≥70% or ≥75% coronary artery stenosis on CA
Reporting accuracy data on individual patients (rather than accuracy data stratified by segments of the heart)
English
Human
Exclusion Criteria
Duplicate studies
Non-systematic reviews, case reports
Grey literature (e.g., conference abstracts)
Insufficient data for independent calculation of sensitivity and specificity
Use of ECHO for purposes other than diagnosis of CAD (e.g., arrhythmia, valvular disease, mitral stenosis, pre-operative risk of MI)
Transesophageal ECHO since its primary use is for non-CAD indications such as endocarditis, intracardiac thrombi, valvular disorders
Only resting ECHO performed
Outcomes of Interest
Accuracy outcomes (sensitivity, specificity, positive predictive value, negative predictive value)
Costs
Summary of Findings
Given the vast amount of published literature on stress ECHO, it was decided to focus on the studies contained in the comprehensive 2007 review by Heijenbrok-Kal et al. (1) as a basis for the MAS evidence-based analysis. In applying our inclusion and exclusion criteria, 105 observational studies containing information on 13,035 patients were included. Six studies examined stress ECHO with adenosine, 26 with dipyridamole and 77 with dobutamine, the latter being the most commonly used pharmacological stress ECHO agent in Ontario. A further 18 studies employed exercise as the stressor.2 The prevalence of CAD ranged from 19% to 94% with a mean estimated prevalence of 70%. Based on the results of these studies the following conclusions were made:
Based on the available evidence, stress ECHO is a useful imaging modality for the diagnosis of CAD in patients with suspected disease. The overall pooled sensitivity is 0.80 (95% CI: 0.77 – 0.82) and the pooled specificity is 0.84 (95% CI: 0.82 – 0.87) using CA as the reference standard. The AUC derived from the sROC curve is 0.895 and the DOR is 20.64.
For pharmacological stress, the pooled sensitivity is 0.79 (95% CI: 0.71 – 0.87) and the pooled specificity is 0.85 (95% CI: 0.83 – 0.88). When exercise is employed as the stress agent, the pooled sensitivity is 0.81 (95% CI: 0.76– 0.86) and the pooled specificity is 0.79 (95% CI: 0.71 – 0.87). Although pharmacological stress and exercise stress would be indicated for different patient populations based on ability to exercise there were no significant differences in sensitivity and specificity.
Based on clinical experts, diagnostic accuracy on stress ECHO depends on the patient population, the expertise of the interpreter and the quality of the image.
PMCID: PMC3377563  PMID: 23074412
4.  Single Photon Emission Computed Tomography for the Diagnosis of Coronary Artery Disease 
Executive Summary
In July 2009, the Medical Advisory Secretariat (MAS) began work on Non-Invasive Cardiac Imaging Technologies for the Diagnosis of Coronary Artery Disease (CAD), an evidence-based review of the literature surrounding different cardiac imaging modalities to ensure that appropriate technologies are accessed by patients suspected of having CAD. This project came about when the Health Services Branch at the Ministry of Health and Long-Term Care asked MAS to provide an evidentiary platform on effectiveness and cost-effectiveness of non-invasive cardiac imaging modalities.
After an initial review of the strategy and consultation with experts, MAS identified five key non-invasive cardiac imaging technologies for the diagnosis of CAD. Evidence-based analyses have been prepared for each of these five imaging modalities: cardiac magnetic resonance imaging, single photon emission computed tomography, 64-slice computed tomographic angiography, stress echocardiography, and stress echocardiography with contrast. For each technology, an economic analysis was also completed (where appropriate). A summary decision analytic model was then developed to encapsulate the data from each of these reports (available on the OHTAC and MAS website).
The Non-Invasive Cardiac Imaging Technologies for the Diagnosis of Coronary Artery Disease series is made up of the following reports, which can be publicly accessed at the MAS website at: www.health.gov.on.ca/mas or at www.health.gov.on.ca/english/providers/program/mas/mas_about.html
Single Photon Emission Computed Tomography for the Diagnosis of Coronary Artery Disease: An Evidence-Based Analysis
Stress Echocardiography for the Diagnosis of Coronary Artery Disease: An Evidence-Based Analysis
Stress Echocardiography with Contrast for the Diagnosis of Coronary Artery Disease: An Evidence-Based Analysis
64-Slice Computed Tomographic Angiography for the Diagnosis of Coronary Artery Disease: An Evidence-Based Analysis
Cardiac Magnetic Resonance Imaging for the Diagnosis of Coronary Artery Disease: An Evidence-Based Analysis
Pease note that two related evidence-based analyses of non-invasive cardiac imaging technologies for the assessment of myocardial viability are also available on the MAS website:
Positron Emission Tomography for the Assessment of Myocardial Viability: An Evidence-Based Analysis
Magnetic Resonance Imaging for the Assessment of Myocardial Viability: an Evidence-Based Analysis
The Toronto Health Economics and Technology Assessment Collaborative has also produced an associated economic report entitled:
The Relative Cost-effectiveness of Five Non-invasive Cardiac Imaging Technologies for Diagnosing Coronary Artery Disease in Ontario [Internet]. Available from: http://theta.utoronto.ca/reports/?id=7
Objective
The objective of the analysis is to determine the diagnostic accuracy of single photon emission tomography (SPECT) in the diagnosis of coronary artery disease (CAD) compared to the reference standard of coronary angiography (CA). The analysis is primarily meant to allow for indirect comparisons between non-invasive strategies for the diagnosis of CAD, using CA as a reference standard.
SPECT
Cardiac SPECT, or myocardial perfusion scintigraphy (MPS), is a widely used nuclear, non-invasive image acquisition technique for investigating ischemic heart disease. SPECT is currently appropriate for all aspects of detecting and managing ischemic heart disease including diagnosis, risk assessment/stratification, assessment of myocardial viability, and the evaluation of left ventricular function. Myocardial perfusion scintigraphy was originally developed as a two-dimensional planar imaging technique, but SPECT acquisition has since become the clinical standard in current practice. Cardiac SPECT for the diagnosis of CAD uses an intravenously administered radiopharmaceutical tracer to evaluate regional coronary blood flow usually at rest and after stress. The radioactive tracers thallium (201Tl) or technetium-99m (99mTc), or both, may be used to visualize the SPECT acquisition. Exercise or a pharmacologic agent is used to achieve stress. After the administration of the tracer, its distribution within the myocardium (which is dependent on myocardial blood flow) is imaged using a gamma camera. In SPECT imaging, the gamma camera rotates around the patients for 10 to 20 minutes so that multiple two-dimensional projections are acquired from various angles. The raw data are then processed using computational algorithms to obtain three-dimensional tomographic images.
Since its inception, SPECT has evolved and its techniques/applications have become increasingly more complex and numerous. Accordingly, new techniques such as attenuation correction and ECG gating have been developed to correct for attenuation due to motion or soft-tissue artifact and to improve overall image clarity.
Research Questions
What is the diagnostic accuracy of SPECT for the diagnosis of CAD compared to the reference standard of CA?
Is SPECT cost-effective compared to other non-invasive cardiac imaging modalities for the diagnosis of CAD?
What are the major safety concerns with SPECT when used for the diagnosis of CAD?
Methods
A preliminary literature search was performed across OVID MEDLINE, MEDLINE In-Process and Other Non-Indexed Citations, EMBASE, the Cochrane Library, and the International Agency for Health Technology Assessment (INAHTA) for all systematic reviews/meta-analysis published between January 1, 2004 and August 22, 2009. A comprehensive systematic review was identified from this search and used as a basis for an updated search.
A second comprehensive literature search was then performed on October 30, 2009 across the same databases for studies published between January 1, 2002 and October 30, 2009. Abstracts were reviewed by a single reviewer and, for those studies meeting the eligibility criteria, full-text articles were obtained. Reference lists were also hand-searched for any additional studies.
Systematic reviews, meta-analyses, controlled clinical trials, and observational studies
Minimum sample size of 20 patients who completed coronary angiography
Use of CA as a reference standard for the diagnosis of CAD
Data available to calculate true positives (TP), false positives (FP), false negatives (FN) and true negatives (TN)
Accuracy data reported by patient not by segment
English language
Non-systematic reviews, case reports
Grey literature and abstracts
Trials using planar imaging only
Trials conducted in patients with non-ischemic heart disease
Studies done exclusively in special populations (e.g., patients with left branch bundle block, diabetics, minority populations) unless insufficient data available
Summary of Findings
Eighty-four observational studies, one non-randomized, single arm controlled clinical trial, and one poorly reported trial that appeared to be a randomized controlled trial (RCT) met the inclusion criteria for this review. All studies assessed the diagnostic accuracy of myocardial perfusion SPECT for the diagnosis of CAD using CA as a reference standard. Based on the results of these studies the following conclusions were made:
According to very low quality evidence, the addition of attenuation correction to traditional or ECG-gated SPECT greatly improves the specificity of SPECT for the diagnosis of CAD although this improvement is not statistically significant. A trend towards improvement of specificity was also observed with the addition of ECG gating to traditional SPECT.
According to very low quality evidence, neither the choice of stress agent (exercise or pharmacologic) nor the choice of radioactive tracer (technetium vs. thallium) significantly affect the diagnostic accuracy of SPECT for the diagnosis of CAD although a trend towards accuracy improvement was observed with the use of pharmacologic stress over exercise stress and technetium over thallium.
Considerably heterogeneity was observed both within and between trials. This heterogeneity may explain why some of the differences observed between accuracy estimates for various subgroups were not statistically significant.
More complex analytic techniques such as meta-regression may help to better understand which study characteristics significantly influence the diagnostic accuracy of SPECT.
PMCID: PMC3377554  PMID: 23074411
5.  Quality of Compressed Medical Images 
Journal of Digital Imaging  2007;20(2):149-159.
Previous studies have shown that Joint Photographic Experts Group (JPEG) 2000 compression is better than JPEG at higher compression ratio levels. However, some findings revealed that this is not valid at lower levels. In this study, the qualities of compressed medical images in these ratio areas (∼20), including computed radiography, computed tomography head and body, mammographic, and magnetic resonance T1 and T2 images, were estimated using both a pixel-based (peak signal to noise ratio) and two 8 × 8 window-based [Q index and Moran peak ratio (MPR)] metrics. To diminish the effects of blocking artifacts from JPEG, jump windows were used in both window-based metrics. Comparing the image quality indices between jump and sliding windows, the results showed that blocking artifacts were produced from JPEG compression, even at low compression ratios. However, even after the blocking artifacts were omitted in JPEG compressed images, JPEG2000 outperformed JPEG at low compression levels. We found in this study that the image contrast and the average gray level play important roles in image compression and quality evaluation. There were drawbacks in all metrics that we used. In the future, the image gray level and contrast effect should be considered in developing new objective metrics.
doi:10.1007/s10278-007-9013-z
PMCID: PMC3043905  PMID: 17318703
Image quality; JPEG; JPEG2000; image compression
6.  Cardiac Magnetic Resonance Imaging for the Diagnosis of Coronary Artery Disease 
Executive Summary
In July 2009, the Medical Advisory Secretariat (MAS) began work on Non-Invasive Cardiac Imaging Technologies for the Diagnosis of Coronary Artery Disease (CAD), an evidence-based review of the literature surrounding different cardiac imaging modalities to ensure that appropriate technologies are accessed by patients suspected of having CAD. This project came about when the Health Services Branch at the Ministry of Health and Long-Term Care asked MAS to provide an evidentiary platform on effectiveness and cost-effectiveness of non-invasive cardiac imaging modalities.
After an initial review of the strategy and consultation with experts, MAS identified five key non-invasive cardiac imaging technologies for the diagnosis of CAD. Evidence-based analyses have been prepared for each of these five imaging modalities: cardiac magnetic resonance imaging, single photon emission computed tomography, 64-slice computed tomographic angiography, stress echocardiography, and stress echocardiography with contrast. For each technology, an economic analysis was also completed (where appropriate). A summary decision analytic model was then developed to encapsulate the data from each of these reports (available on the OHTAC and MAS website).
The Non-Invasive Cardiac Imaging Technologies for the Diagnosis of Coronary Artery Disease series is made up of the following reports, which can be publicly accessed at the MAS website at: www.health.gov.on.ca/mas or at www.health.gov.on.ca/english/providers/program/mas/mas_about.html
Single Photon Emission Computed Tomography for the Diagnosis of Coronary Artery Disease: An Evidence-Based Analysis
Stress Echocardiography for the Diagnosis of Coronary Artery Disease: An Evidence-Based Analysis
Stress Echocardiography with Contrast for the Diagnosis of Coronary Artery Disease: An Evidence-Based Analysis
64-Slice Computed Tomographic Angiography for the Diagnosis of Coronary Artery Disease: An Evidence-Based Analysis
Cardiac Magnetic Resonance Imaging for the Diagnosis of Coronary Artery Disease: An Evidence-Based Analysis
Pease note that two related evidence-based analyses of non-invasive cardiac imaging technologies for the assessment of myocardial viability are also available on the MAS website:
Positron Emission Tomography for the Assessment of Myocardial Viability: An Evidence-Based Analysis
Magnetic Resonance Imaging for the Assessment of Myocardial Viability: an Evidence-Based Analysis
The Toronto Health Economics and Technology Assessment Collaborative has also produced an associated economic report entitled:
The Relative Cost-effectiveness of Five Non-invasive Cardiac Imaging Technologies for Diagnosing Coronary Artery Disease in Ontario [Internet]. Available from: http://theta.utoronto.ca/reports/?id=7
Objective
The objective of this analysis was to determine the diagnostic accuracy of cardiac magnetic resonance imaging (MRI) for the diagnosis of patients with known/suspected coronary artery disease (CAD) compared to coronary angiography.
Cardiac MRI
Stress cardiac MRI is a non-invasive, x-ray free imaging technique that takes approximately 30 to 45 minutes to complete and can be performed using to two different methods, a) perfusion imaging following a first pass of an intravenous bolus of gadolinium contrast, or b) wall motion imaging. Stress is induced pharmacologically with either dobutamine, dipyridamole, or adenosine, as physical exercise is difficult to perform within the magnet bore and often induces motion artifacts. Alternatives to stress cardiac perfusion MRI include stress single-photon emission computed tomography (SPECT) and stress echocardiography (ECHO). The advantage of cardiac MRI is that it does not pose the radiation burden associated with SPECT. During the same sitting, cardiac MRI can also assess left and right ventricular dimensions, viability, and cardiac mass. It may also mitigate the need for invasive diagnostic coronary angiography in patients with intermediate risk factors for CAD.
Evidence-Based Analysis
Literature Search
A literature search was performed on October 9, 2009 using OVID MEDLINE, MEDLINE In-Process and Other Non-Indexed Citations, EMBASE, the Cumulative Index to Nursing & Allied Health Literature (CINAHL), the Cochrane Library, and the International Agency for Health Technology Assessment (INAHTA) for studies published from January 1, 2005 to October 9, 2008. Abstracts were reviewed by a single reviewer and, for those studies meeting the eligibility criteria, full-text articles were obtained. Reference lists were also examined for any relevant studies not identified through the search. Articles with unknown eligibility were reviewed with a second clinical epidemiologist and then a group of epidemiologists until consensus was established. The quality of evidence was assessed as high, moderate, low or very low according to GRADE methodology.
Given the large amount of clinical heterogeneity of the articles meeting the inclusion criteria, as well as suggestions from an Expert Advisory Panel Meeting held on October 5, 2009, the inclusion criteria were revised to examine the effectiveness of cardiac MRI for the detection of CAD.
Heath technology assessments, systematic reviews, randomized controlled trials, observational studies
≥20 adult patients enrolled.
Published 2004-2009
Licensed by Health Canada
For diagnosis of CAD:
Reference standard is coronary angiography
Significant CAD defined as ≥ 50% coronary stenosis
Patients with suspected or known CAD
Reported results by patient, not segment
Non-English studies
Grey literature
Planar imaging
MUGA
Patients with recent MI (i.e., within 1 month)
Patients with non-ischemic heart disease
Studies done exclusively in special populations (e.g., women, diabetics)
Outcomes of Interest
Sensitivity and specificity
Area under the curve (AUC)
Diagnostic odds ratio (DOR)
Summary of Findings
Stress cardiac MRI using perfusion analysis yielded a pooled sensitivity of 0.91 (95% CI: 0.89 to 0.92) and specificity of 0.79 (95% CI: 0.76 to 0.82) for the detection of CAD.
Stress cardiac MRI using wall motion analysis yielded a pooled sensitivity of 0.81 (95% CI: 0.77 to 0.84) and specificity of 0.85 (95% CI: 0.81 to 0.89) for the detection of CAD.
Based on DORs, there was no significant difference between pooled stress cardiac MRI using perfusion analysis and pooled stress cardiac MRI using wall motion analysis (P=0.26) for the detection of CAD.
Pooled subgroup analysis of stress cardiac MRI using perfusion analysis showed no significant difference in the DORs between 1.5T and 3T MRI (P=0.72) for the detection of CAD.
One study (N=60) was identified that examined stress cardiac MRI using wall motion analysis with a 3T MRI. The sensitivity and specificity of 3T MRI were 0.64 (95% CI: 0.44 to 0.81) and 1.00 (95% CI: 0.89 to 1.00), respectively, for the detection of CAD.
The effectiveness of stress cardiac MRI for the detection of CAD in unstable patients with acute coronary syndrome was reported in only one study (N=35). Using perfusion analysis, the sensitivity and specificity were 0.72 (95% CI: 0.53 to 0.87) and 1.00 (95% CI: 0.54 to 1.00), respectively, for the detection of CAD.
Ontario Health System Impact Analysis
According to an expert consultant, in Ontario:
Stress first pass perfusion is currently performed in small numbers in London (London Health Sciences Centre) and Toronto (University Health Network at the Toronto General Hospital site and Sunnybrook Health Sciences Centre).
Stress wall motion is only performed as part of research protocols and not very often.
Cardiac MRI machines use 1.5T almost exclusively, with 3T used in research for first pass perfusion.
On November 25 2009, the Cardiac Imaging Expert Advisory Panel met and made the following comments about stress cardiac MRI for perfusion analysis:
Accessibility to cardiac MRI is limited and generally used to assess structural abnormalities. Most MRIs in Ontario are already in 24–hour, constant use and it would thus be difficult to add cardiac MRI for CAD diagnosis as an additional indication.
The performance of cardiac MRI for the diagnosis of CAD can be technically challenging.
GRADE Quality of Evidence for Cardiac MRI in the Diagnosis of CAD
The quality of the body of evidence was assessed according to the GRADE Working Group criteria for diagnostic tests. For perfusion analysis, the overall quality was determined to be low and for wall motion analysis the overall quality was very low.
PMCID: PMC3377522  PMID: 23074389
7.  Arterial stiffness, pressure and flow pulsatility and brain structure and function: the Age, Gene/Environment Susceptibility – Reykjavik Study 
Brain  2011;134(11):3398-3407.
Aortic stiffness increases with age and vascular risk factor exposure and is associated with increased risk for structural and functional abnormalities in the brain. High ambient flow and low impedance are thought to sensitize the cerebral microcirculation to harmful effects of excessive pressure and flow pulsatility. However, haemodynamic mechanisms contributing to structural brain lesions and cognitive impairment in the presence of high aortic stiffness remain unclear. We hypothesized that disproportionate stiffening of the proximal aorta as compared with the carotid arteries reduces wave reflection at this important interface and thereby facilitates transmission of excessive pulsatile energy into the cerebral microcirculation, leading to microvascular damage and impaired function. To assess this hypothesis, we evaluated carotid pressure and flow, carotid–femoral pulse wave velocity, brain magnetic resonance images and cognitive scores in participants in the community-based Age, Gene/Environment Susceptibility – Reykjavik study who had no history of stroke, transient ischaemic attack or dementia (n = 668, 378 females, 69–93 years of age). Aortic characteristic impedance was assessed in a random subset (n = 422) and the reflection coefficient at the aorta–carotid interface was computed. Carotid flow pulsatility index was negatively related to the aorta–carotid reflection coefficient (R = −0.66, P<0.001). Carotid pulse pressure, pulsatility index and carotid–femoral pulse wave velocity were each associated with increased risk for silent subcortical infarcts (hazard ratios of 1.62–1.71 per standard deviation, P<0.002). Carotid–femoral pulse wave velocity was associated with higher white matter hyperintensity volume (0.108 ± 0.045 SD/SD, P = 0.018). Pulsatility index was associated with lower whole brain (−0.127 ± 0.037 SD/SD, P<0.001), grey matter (−0.079 ± 0.038 SD/SD, P = 0.038) and white matter (−0.128 ± 0.039 SD/SD, P<0.001) volumes. Carotid–femoral pulse wave velocity (−0.095 ± 0.043 SD/SD, P = 0.028) and carotid pulse pressure (−0.114 ± 0.045 SD/SD, P = 0.013) were associated with lower memory scores. Pulsatility index was associated with lower memory scores (−0.165 ± 0.039 SD/SD, P<0.001), slower processing speed (−0.118 ± 0.033 SD/SD, P<0.001) and worse performance on tests assessing executive function (−0.155 ± 0.041 SD/SD, P<0.001). When magnetic resonance imaging measures (grey and white matter volumes, white matter hyperintensity volumes and prevalent subcortical infarcts) were included in cognitive models, haemodynamic associations were attenuated or no longer significant, consistent with the hypothesis that increased aortic stiffness and excessive flow pulsatility damage the microcirculation, leading to quantifiable tissue damage and reduced cognitive performance. Marked stiffening of the aorta is associated with reduced wave reflection at the interface between carotid and aorta, transmission of excessive flow pulsatility into the brain, microvascular structural brain damage and lower scores in various cognitive domains.
doi:10.1093/brain/awr253
PMCID: PMC3212721  PMID: 22075523
haemodynamics; aortic stiffness; magnetic resonance imaging; brain structure; cognitive function
8.  Deriving Hounsfield units using grey levels in cone beam computed tomography 
Dentomaxillofacial Radiology  2010;39(6):323-335.
Objectives
An in vitro study was performed to investigate the relationship between grey levels in dental cone beam CT (CBCT) and Hounsfield units (HU) in CBCT scanners.
Methods
A phantom containing 8 different materials of known composition and density was imaged with 11 different dental CBCT scanners and 2 medical CT scanners. The phantom was scanned under three conditions: phantom alone and phantom in a small and large water container. The reconstructed data were exported as Digital Imaging and Communications in Medicine (DICOM) and analysed with On Demand 3D® by Cybermed, Seoul, Korea. The relationship between grey levels and linear attenuation coefficients was investigated.
Results
It was demonstrated that a linear relationship between the grey levels and the attenuation coefficients of each of the materials exists at some “effective” energy. From the linear regression equation of the reference materials, attenuation coefficients were obtained for each of the materials and CT numbers in HU were derived using the standard equation.
Conclusions
HU can be derived from the grey levels in dental CBCT scanners using linear attenuation coefficients as an intermediate step.
doi:10.1259/dmfr/19603304
PMCID: PMC3520236  PMID: 20729181
Hounsfield units; cone beam computed tomography; grey levels
9.  Evaluation of multi-modal, multi-site neuroimaging measures in Huntington's disease: Baseline results from the PADDINGTON study☆ 
NeuroImage : Clinical  2012;2:204-211.
Background
Macro- and micro-structural neuroimaging measures provide valuable information on the pathophysiology of Huntington's disease (HD) and are proposed as biomarkers. Despite theoretical advantages of microstructural measures in terms of sensitivity to pathology, there is little evidence directly comparing the two.
Methods
40 controls and 61 early HD subjects underwent 3 T MRI (T1- and diffusion-weighted), as part of the PADDINGTON study. Macrostructural volumetrics were obtained for the whole brain, caudate, putamen, corpus callosum (CC) and ventricles. Microstructural diffusion metrics of fractional anisotropy (FA), mean-, radial- and axial-diffusivity (MD, RD, AD) were computed for white matter (WM), CC, caudate and putamen. Group differences were examined adjusting for age, gender and site. A formal comparison of effect sizes determined which modality and metrics provided a statistically significant advantage over others.
Results
Macrostructural measures showed decreased regional and global volume in HD (p < 0.001); except the ventricles which were enlarged (p < 0.01). In HD, FA was increased in the deep grey-matter structures (p < 0.001), and decreased in the WM (CC, p = 0.035; WM, p = 0.053); diffusivity metrics (MD, RD, AD) were increased for all brain regions (p < 0.001). The largest effect sizes were for putamen volume, caudate volume and putamen diffusivity (AD, RD and MD); each was significantly larger than those for all other metrics (p < 0.05).
Conclusion
The highest performing macro- and micro-structural metrics had similar sensitivity to HD pathology quantified via effect sizes. Region-of-interest may be more important than imaging modality, with deep grey-matter regions outperforming the CC and global measures, for both volume and diffusivity. FA appears to be relatively insensitive to disease effects.
Highlights
► Macro and microstructural metrics are sensitive to HD pathology cross-sectionally. ► Largest effect sizes for putamen volume, caudate volume and putamen diffusivity ► No significant advantage of highest performing macro over microstructural metrics ► Grey matter regions outperformed CC and global measures within each modality. ► FA appears to be relatively insensitive to disease effects.
doi:10.1016/j.nicl.2012.12.001
PMCID: PMC3777685  PMID: 24179770
Huntington's disease; MRI; Diffusion; Volumetric
10.  Medical Image Compression Based on Vector Quantization with Variable Block Sizes in Wavelet Domain 
An optimized medical image compression algorithm based on wavelet transform and improved vector quantization is introduced. The goal of the proposed method is to maintain the diagnostic-related information of the medical image at a high compression ratio. Wavelet transformation was first applied to the image. For the lowest-frequency subband of wavelet coefficients, a lossless compression method was exploited; for each of the high-frequency subbands, an optimized vector quantization with variable block size was implemented. In the novel vector quantization method, local fractal dimension (LFD) was used to analyze the local complexity of each wavelet coefficients, subband. Then an optimal quadtree method was employed to partition each wavelet coefficients, subband into several sizes of subblocks. After that, a modified K-means approach which is based on energy function was used in the codebook training phase. At last, vector quantization coding was implemented in different types of sub-blocks. In order to verify the effectiveness of the proposed algorithm, JPEG, JPEG2000, and fractal coding approach were chosen as contrast algorithms. Experimental results show that the proposed method can improve the compression performance and can achieve a balance between the compression ratio and the image visual quality.
doi:10.1155/2012/541890
PMCID: PMC3459264  PMID: 23049544
11.  Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations? 
Background
Cheminformaticians are equipped with a very rich toolbox when carrying out molecular similarity calculations. A large number of molecular representations exist, and there are several methods (similarity and distance metrics) to quantify the similarity of molecular representations. In this work, eight well-known similarity/distance metrics are compared on a large dataset of molecular fingerprints with sum of ranking differences (SRD) and ANOVA analysis. The effects of molecular size, selection methods and data pretreatment methods on the outcome of the comparison are also assessed.
Results
A supplier database (https://mcule.com/) was used as the source of compounds for the similarity calculations in this study. A large number of datasets, each consisting of one hundred compounds, were compiled, molecular fingerprints were generated and similarity values between a randomly chosen reference compound and the rest were calculated for each dataset. Similarity metrics were compared based on their ranking of the compounds within one experiment (one dataset) using sum of ranking differences (SRD), while the results of the entire set of experiments were summarized on box and whisker plots. Finally, the effects of various factors (data pretreatment, molecule size, selection method) were evaluated with analysis of variance (ANOVA).
Conclusions
This study complements previous efforts to examine and rank various metrics for molecular similarity calculations. Here, however, an entirely general approach was taken to neglect any a priori knowledge on the compounds involved, as well as any bias introduced by examining only one or a few specific scenarios. The Tanimoto index, Dice index, Cosine coefficient and Soergel distance were identified to be the best (and in some sense equivalent) metrics for similarity calculations, i.e. these metrics could produce the rankings closest to the composite (average) ranking of the eight metrics. The similarity metrics derived from Euclidean and Manhattan distances are not recommended on their own, although their variability and diversity from other similarity metrics might be advantageous in certain cases (e.g. for data fusion). Conclusions are also drawn regarding the effects of molecule size, selection method and data pretreatment on the ranking behavior of the studied metrics.
Graphical AbstractA visual summary of the comparison of similarity metrics with sum of ranking differences (SRD).
Electronic supplementary material
The online version of this article (doi:10.1186/s13321-015-0069-3) contains supplementary material, which is available to authorized users.
doi:10.1186/s13321-015-0069-3
PMCID: PMC4456712  PMID: 26052348
Fingerprint; Similarity; Ranking; Data fusion; Analysis of variance; Sum of ranking differences; Distance metrics
12.  Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations? 
Background
Cheminformaticians are equipped with a very rich toolbox when carrying out molecular similarity calculations. A large number of molecular representations exist, and there are several methods (similarity and distance metrics) to quantify the similarity of molecular representations. In this work, eight well-known similarity/distance metrics are compared on a large dataset of molecular fingerprints with sum of ranking differences (SRD) and ANOVA analysis. The effects of molecular size, selection methods and data pretreatment methods on the outcome of the comparison are also assessed.
Results
A supplier database (https://mcule.com/) was used as the source of compounds for the similarity calculations in this study. A large number of datasets, each consisting of one hundred compounds, were compiled, molecular fingerprints were generated and similarity values between a randomly chosen reference compound and the rest were calculated for each dataset. Similarity metrics were compared based on their ranking of the compounds within one experiment (one dataset) using sum of ranking differences (SRD), while the results of the entire set of experiments were summarized on box and whisker plots. Finally, the effects of various factors (data pretreatment, molecule size, selection method) were evaluated with analysis of variance (ANOVA).
Conclusions
This study complements previous efforts to examine and rank various metrics for molecular similarity calculations. Here, however, an entirely general approach was taken to neglect any a priori knowledge on the compounds involved, as well as any bias introduced by examining only one or a few specific scenarios. The Tanimoto index, Dice index, Cosine coefficient and Soergel distance were identified to be the best (and in some sense equivalent) metrics for similarity calculations, i.e. these metrics could produce the rankings closest to the composite (average) ranking of the eight metrics. The similarity metrics derived from Euclidean and Manhattan distances are not recommended on their own, although their variability and diversity from other similarity metrics might be advantageous in certain cases (e.g. for data fusion). Conclusions are also drawn regarding the effects of molecule size, selection method and data pretreatment on the ranking behavior of the studied metrics.
Graphical AbstractA visual summary of the comparison of similarity metrics with sum of ranking differences (SRD).
Electronic supplementary material
The online version of this article (doi:10.1186/s13321-015-0069-3) contains supplementary material, which is available to authorized users.
doi:10.1186/s13321-015-0069-3
PMCID: PMC4456712  PMID: 26052348
Fingerprint; Similarity; Ranking; Data fusion; Analysis of variance; Sum of ranking differences; Distance metrics
13.  Stress Echocardiography with Contrast for the Diagnosis of Coronary Artery Disease 
Executive Summary
In July 2009, the Medical Advisory Secretariat (MAS) began work on Non-Invasive Cardiac Imaging Technologies for the Diagnosis of Coronary Artery Disease (CAD), an evidence-based review of the literature surrounding different cardiac imaging modalities to ensure that appropriate technologies are accessed by patients suspected of having CAD. This project came about when the Health Services Branch at the Ministry of Health and Long-Term Care asked MAS to provide an evidentiary platform on effectiveness and cost-effectiveness of non-invasive cardiac imaging modalities.
After an initial review of the strategy and consultation with experts, MAS identified five key non-invasive cardiac imaging technologies for the diagnosis of CAD. Evidence-based analyses have been prepared for each of these five imaging modalities: cardiac magnetic resonance imaging, single photon emission computed tomography, 64-slice computed tomographic angiography, stress echocardiography, and stress echocardiography with contrast. For each technology, an economic analysis was also completed (where appropriate). A summary decision analytic model was then developed to encapsulate the data from each of these reports (available on the OHTAC and MAS website).
The Non-Invasive Cardiac Imaging Technologies for the Diagnosis of Coronary Artery Disease series is made up of the following reports, which can be publicly accessed at the MAS website at: www.health.gov.on.ca/mas or at www.health.gov.on.ca/english/providers/program/mas/mas_about.html
Single Photon Emission Computed Tomography for the Diagnosis of Coronary Artery Disease: An Evidence-Based Analysis
Stress Echocardiography for the Diagnosis of Coronary Artery Disease: An Evidence-Based Analysis
Stress Echocardiography with Contrast for the Diagnosis of Coronary Artery Disease: An Evidence-Based Analysis
64-Slice Computed Tomographic Angiography for the Diagnosis of Coronary Artery Disease: An Evidence-Based Analysis
Cardiac Magnetic Resonance Imaging for the Diagnosis of Coronary Artery Disease: An Evidence-Based Analysis
Pease note that two related evidence-based analyses of non-invasive cardiac imaging technologies for the assessment of myocardial viability are also available on the MAS website:
Positron Emission Tomography for the Assessment of Myocardial Viability: An Evidence-Based Analysis
Magnetic Resonance Imaging for the Assessment of Myocardial Viability: an Evidence-Based Analysis
The Toronto Health Economics and Technology Assessment Collaborative has also produced an associated economic report entitled:
The Relative Cost-effectiveness of Five Non-invasive Cardiac Imaging Technologies for Diagnosing Coronary Artery Disease in Ontario [Internet]. Available from: http://theta.utoronto.ca/reports/?id=7
Objective
The objective of this report is to compare echocardiography (ECHO) performed with microsphere contrast agents (contrast echocardiography) to ECHO performed without contrast and to single photon emission computed tomography (SPECT).
Contrast ECHO
Contrast agents for ECHO have been available since the technology was first introduced in the 1990s. Composed of tiny ‘microbubbles’ of an inert gas encapsulated within a lipid, protein, or polymer coat, these agents act to scatter incident ultrasound waves at the gas/liquid interface to increase the strength of a returning ECHO signal. When injected into a patient’s arm, they are transported throughout even the smallest capillaries to greatly enhance the blood pool signal, which would otherwise appear black on conventional two dimensional ECHO. The enhanced signal then helps cardiologists to determine what parts of the patient’s heart muscle are poorly perfused.
The first commercially available microsphere contrast agent was Albunex, which received approval by the Food and Drug Administration in the United States in 1994. This original microsphere agent was limited by its rapid gas volume loss which caused a decline in the ultrasound signal. It worked well in the right chambers of the heart, but dissolved when passing through the pulmonary capillaries and so was unable to provide contrast in the left side. Second generation agents employed different gases that prolonged the life of the microbubbles within the circulation and increased the reproducibility of results.
Today, the most common use for contrast ECHO is to enhance the definition of the left ventricular (LV) endocardial border for cases of LV opacification. The aim of contrast ECHO is to provide better quantification of LV volume and assessment of LV wall motion than ECHO alone. The newest area of development in the research of contrast ECHO is myocardial perfusion assessment, also known as myocardial contrast ECHO. Theoretically, since myocardial ischemia and infarction affect both perfusion and contractility (wall motion), contrast ECHO could be an ideal non-invasive imaging test as it could assess both perfusion and contractility, simultaneously and in real time.
Notably, critically ill patients on ventilators and those with lung problems are more likely to generate poor or ‘suboptimal’ echocardiograms than other patients, as are obese patients and those who’ve undergone recent chest operations. Contrast agents can potentially be used in 10% to 15% of all studies and in approximately 33% of stress tests due to from such suboptimal echocardiograms. Stress can be induced either pharmaceutically (e.g., through dobutamine, dipyrimidamole, adenosine) or with exercise. Generally, contrast agents are used more in pharmaceutical stress echocardiograms than in exercise stress echocardiograms.
Evidence-Based Analysis
This MAS analysis sought to address the following research questions:
Is contrast ECHO more effective than 99-technetium SPECT in terms its ability to detect CAD?
What is the effectiveness of contrast ECHO in assessing patients with suboptimal echocardiograms?
Is contrast ECHO safe compared to other cardiac imaging modalities?
Is contrast ECHO cost-effective compared to other cardiac imaging modalities?
Literature Search
Literature searches were performed on June 22, 2009 and July 27, 2009 using OVID MEDLINE, MEDLINE In-Process and Other Non-Indexed Citations, EMBASE, the Cochrane Library, and the International Agency for Health Technology Assessment (INAHTA) for studies published from January 1, 2004 until June 30, 2009. Abstracts were reviewed by a single reviewer and, for those studies meeting the eligibility criteria; full-text articles were obtained. Reference lists were also examined for any relevant studies not identified through the search.
Inclusion Criteria
Systematic reviews, meta-analyses, randomized controlled trials, prospective observational studies, retrospective analyses
Minimum sample size of 20 enrolled patients (human only)
The contrast agent used in the study must be licensed by Health Canada
Comparison to reference standard (coronary angiography for the diagnosis of coronary artery disease)
Reporting accuracy data on individual patients (rather than accuracy data stratified by segments of the heart)
English language
Exclusion Criteria
Non-systematic reviews, case reports
Grey literature (e.g. conference abstracts)
Outcomes of Interest
Accuracy outcomes (sensitivity, specificity, positive predictive value, negative predictive value)
Adverse events
Costs
Summary of Findings
Twenty-three observational studies were identified that assessed the diagnostic accuracy of contrast ECHO for the diagnosis of CAD. All of these studies used stress ECHO with contrast. In addition, nine retrospective chart reviews were identified, which assessed the safety of contrast ECHO at rest or stress. Based on the results of these studies the following conclusions were made:
Stress ECHO with contrast has a higher diagnostic accuracy in the diagnosis of CAD than stress ECHO (without contrast).
Stress ECHO with contrast seems to have a similar diagnostic accuracy to 99 technetium SPECT.
The addition of contrast to ECHO in patients with suboptimal ECHO results significantly improves interpretability of the results.
There is not a statistically significantly higher mortality rate in patients who receive contrast compared to those who do not.
PMCID: PMC3377574  PMID: 23074387
14.  An investigation into the use of MR imaging to determine the functional cross sectional area of lumbar paraspinal muscles 
European Spine Journal  2005;15(6):764-773.
The purpose of this study was to investigate the use of magnetic resonance (MR) imaging and image processing software to determine the functional cross-sectional area (FCSA) (the area of muscle isolated from fat) of the lumbar paraspinal muscles. The measurement of the morphology of the lumbar paraspinal muscles has become the focus of several recent investigations into the aetiology of low back pain. However, the reliability and validity of determining the FCSA of the lumbar paraspinal muscles using MR imaging are yet to be reported. T2 axial MR scans at the L1-S1 spinal levels of six subjects were obtained using identical MR systems and scanning parameters. Lean paraspinal muscle, vertebral body bone and intermuscular fat were manually segmented using image analysis software to assign a grey scale range to the MR signal intensity emitted by each tissue type. The resultant grey scale range for muscle was used to determine FCSA measurements for each of the paraspinal muscles, psoas, quadratus lumborum, erector spinae and lumbar multifidus on each scan slice. As various biological, instrument and measurement factors can affect MR signal intensity, a sensitivity analysis was conducted to determine the error associated in calculating FCSA for paraspinal muscle using a discrete grey scale range. Cross-sectional area and FCSA measurements were repeated three times and reliability indices for the FCSA measurements were obtained, showing excellent reliability, intra class correlation coefficient (mean=0.97, range 0.90–0.99) and %SEM (mean=2.6%, range 0.7–4.8%). In addition, the error associated with miscalculation of the grey scale range for the MR signal intensity of muscle was calculated and found to be low with an error of 20 grey scale units at the upper end of the muscle’s grey scale range resulting in a very small error in the measured muscle FCSA. The method presented in this paper has a variety of practical applications in areas such as evidence-based rehabilitation, biomechanical modelling and the determination of segmental inertial parameters.
doi:10.1007/s00586-005-0909-3
PMCID: PMC3489434  PMID: 15895259
Lumbar spine; Magnetic resonance imaging; Cross sectional area; Low back pain; Muscle morphology
15.  Genomic analysis for managing small and endangered populations: a case study in Tyrol Grey cattle 
Frontiers in Genetics  2015;6:173.
Analysis of genomic data is increasingly becoming part of the livestock industry. Therefore, the routine collection of genomic information would be an invaluable resource for effective management of breeding programs in small, endangered populations. The objective of the paper was to demonstrate how genomic data could be used to analyse (1) linkage disequlibrium (LD), LD decay and the effective population size (NeLD); (2) Inbreeding level and effective population size (NeROH) based on runs of homozygosity (ROH); (3) Prediction of genomic breeding values (GEBV) using small within-breed and genomic information from other breeds. The Tyrol Grey population was used as an example, with the goal to highlight the potential of genomic analyses for small breeds. In addition to our own results we discuss additional use of genomics to assess relatedness, admixture proportions, and inheritance of harmful variants. The example data set consisted of 218 Tyrol Grey bull genotypes, which were all available AI bulls in the population. After standard quality control restrictions 34,581 SNPs remained for the analysis. A separate quality control was applied to determine ROH levels based on Illumina GenCall and Illumina GenTrain scores, resulting into 211 bulls and 33,604 SNPs. LD was computed as the squared correlation coefficient between SNPs within a 10 mega base pair (Mb) region. ROHs were derived based on regions covering at least 4, 8, and 16 Mb, suggesting that animals had common ancestors approximately 12, 6, and 3 generations ago, respectively. The corresponding mean inbreeding coefficients (FROH) were 4.0% for 4 Mb, 2.9% for 8 Mb and 1.6% for 16 Mb runs. With an average generation interval of 5.66 years, estimated NeROH was 125 (NeROH>16 Mb), 186 (NeROH>8 Mb) and 370 (NeROH>4 Mb) indicating strict avoidance of close inbreeding in the population. The LD was used as an alternative method to infer the population history and the Ne. The results show a continuous decrease in NeLD, to 780, 120, and 80 for 100, 10, and 5 generations ago, respectively. Genomic selection was developed for and is working well in large breeds. The same methodology was applied in Tyrol Grey cattle, using different reference populations. Contrary to the expectations, the accuracy of GEBVs with very small within breed reference populations were very high, between 0.13–0.91 and 0.12–0.63, when estimated breeding values and deregressed breeding values were used as pseudo-phenotypes, respectively. Subsequent analyses confirmed the high accuracies being a consequence of low reliabilities of pseudo-phenotypes in the validation set, thus being heavily influenced by parent averages. Multi-breed and across breed reference sets gave inconsistent and lower accuracies. Genomic information may have a crucial role in management of small breeds, even if its primary usage differs from that of large breeds. It allows to assess relatedness between individuals, trends in inbreeding and to take decisions accordingly. These decisions would be based on the real genome architecture, rather than conventional pedigree information, which can be missing or incomplete. We strongly suggest the routine genotyping of all individuals that belong to a small breed in order to facilitate the effective management of endangered livestock populations.
doi:10.3389/fgene.2015.00173
PMCID: PMC4443735  PMID: 26074948
breed management; endangered breeds; SNP chip; linkage disequilibrium; runs of homozygosity; genomic selection
16.  Estimation of Tree Size Diversity Using Object Oriented Texture Analysis and Aster Imagery 
Sensors (Basel, Switzerland)  2008;8(8):4709-4724.
This study investigates the potential of object-based texture parameters extracted from 15m spatial resolution ASTER imagery for estimating tree size diversity in a Mediterranean forested landscape in Turkey. Tree size diversity based on tree basal area was determined using the Shannon index and Gini Coefficient at the sampling plot level. Image texture parameters were calculated based on the grey level co-occurrence matrix (GLCM) for various image segmentation levels. Analyses of relationships between tree size diversity and texture parameters found that relationships between the Gini Coefficient and the GLCM values were the most statistically significant, with the highest correlation (r=0.69) being with GLCM Homogeneity values. In contrast, Shannon Index values were weakly correlated with image derived texture parameters. The results suggest that 15m resolution Aster imagery has considerable potential in estimating tree size diversity based on the Gini Coefficient for heterogeneous Mediterranean forests.
doi:10.3390/s8084709
PMCID: PMC3705467
Tree size diversity; remote sensing; brutian pine; texture analysis; image segmentation
17.  Pressure and breast thickness in mammography—an exploratory calibration study 
The British Journal of Radiology  2013;86(1021):20120222.
Objective
To perform a calibration study to provide data to help improve consistency in the pressure that is applied during mammography.
Methods
Automatic readouts of breast thickness accuracy vary between mammography machines; therefore, one machine was selected for calibration. 250 randomly selected patients were invited to participate; 235 agreed, and 940 compression data sets were recorded (breast thickness, breast density and pressure). Pressure (measured in decanewtons) was increased from 5 daN through 1-daN intervals until the practitioner felt that the pressure was appropriate for imaging; at each pressure increment, breast thickness was recorded.
Results
Graphs were generated and equations derived; second-order polynomial trend lines were applied using the method of least squares. No difference existed between breast densities, but a difference did exist between “small” (15×29 cm) and “medium/large” (18×24/24×30 cm) paddles. Accordingly, data were combined. Graphs show changes in thickness from 5-daN pressure for craniocaudal and mediolateral oblique views for the small and medium/large paddles combined. Graphs were colour coded into three segments indicating high, intermediate and low gradients [≤−2 (light grey); −1.99 to −1 (mid-grey); and ≥−0.99 (dark grey)]. We propose that 13 daN could be an appropriate termination pressure on this mammography machine.
Conclusion
Using patient compression data we have calibrated a mammography machine to determine its breast compression characteristics. This calibration data could be used to guide practice to minimise pressure variations between practitioners, thereby improving patient experience and reducing potential variation in image quality.
Advances in knowledge
For the first time, pressure–thickness graphs are now available to help guide mammographers in the application of pressure.
doi:10.1259/bjr.20120222
PMCID: PMC3615392  PMID: 23239695
18.  Quality Degradation in Lossy Wavelet Image Compression  
Journal of Digital Imaging  2003;16(2):210-215.
The objective of this study was to develop a method for measuring quality degradation in lossy wavelet image compression. Quality degradation is due to denoising and edge blurring effects that cause smoothness in the compressed image. The peak Moran z histogram ratio between the reconstructed and original images is used as an index for degradation after image compression. The Moran test is applied to images randomly selected from each medical modality, computerized tomography, magnetic resonance imaging, and computed radiography and compressed using the wavelet compression at various levels. The relationship between the quality degradation and compression ratio for each image modality agrees with previous reports that showed a preference for mildly compressed images. Preliminary results show that the peak Moran z histogram ratio can be used to quantify the quality degradation in lossy image compression. The potential for this method is applications for determining the optimal compression ratio (the maximized compression without seriously degrading image quality) of an image for teleradiology.
doi:10.1007/s10278-003-1652-0
PMCID: PMC3046470  PMID: 14517721
Wavelet compression; quality evaluation; Moran test
19.  Temporal evolution of water diffusion parameters is different in grey and white matter in human ischaemic stroke 
Objectives: Our purpose was to investigate whether differences exist in the values and temporal evolution of mean diffusivity () and fractional anisotropy (FA) of grey and white matter after human ischaemic stroke.
Methods: Thirty two patients with lesions affecting both grey and white matter underwent serial diffusion tensor magnetic resonance imaging (DT-MRI) within 24 hours, and at 4–7 days, 10–14 days, 1 month, and 3 months after stroke. Multiple small circular regions of interest (ROI) were placed in the grey and white matter within the lesion and in the contralateral hemisphere. Values of {grey}, {white}, FA{grey} and FA{white} were measured in these ROI at each time point and the ratios of ischaemic to normal contralateral values (R and FAR) calculated.
Results: and FA showed different patterns of evolution after stroke. After an initial decline, the rate of increase of {grey} was faster than {white} from 4–7 to 10–14 days. FA{white} decreased more rapidly than FA{grey} during the first week, thereafter for both tissue types the FA decreased gradually. However, FA{white} was still higher than FA{grey} at three months indicating that some organised axonal structure remained. This effect was more marked in some patients than in others. R{grey} was significantly higher than R{white} within 24 hours and at 10–14 days (p<0.05), and FAR{white} was significantly more reduced than FAR{grey} at all time points (p<0.001).
Conclusions: The values and temporal evolution of and FA are different for grey and white matter after human ischaemic stroke. The observation that there is patient-to-patient variability in the degree of white matter structure remaining within the infarct at three months may have implications for predicting patient outcome.
doi:10.1136/jnnp.2003.033852
PMCID: PMC1738833  PMID: 15548489
20.  Automated measurement of heterogeneity in CT images of healthy and diseased rat lungs using variogram analysis of an octree decomposition 
BMC Medical Imaging  2014;14:1.
Background
Assessing heterogeneity in lung images can be an important diagnosis tool. We present a novel and objective method for assessing lung damage in a rat model of emphysema. We combined a three-dimensional (3D) computer graphics method–octree decomposition–with a geostatistics-based approach for assessing spatial relationships–the variogram–to evaluate disease in 3D computed tomography (CT) image volumes.
Methods
Male, Sprague-Dawley rats were dosed intratracheally with saline (control), or with elastase dissolved in saline to either the whole lung (for mild, global disease) or a single lobe (for severe, local disease). Gated 3D micro-CT images were acquired on the lungs of all rats at end expiration. Images were masked, and octree decomposition was performed on the images to reduce the lungs to homogeneous blocks of 2 × 2 × 2, 4 × 4 × 4, and 8 × 8 × 8 voxels. To focus on lung parenchyma, small blocks were ignored because they primarily defined boundaries and vascular features, and the spatial variance between all pairs of the 8 × 8 × 8 blocks was calculated as the square of the difference of signal intensity. Variograms–graphs of distance vs. variance–were constructed, and results of a least-squares-fit were compared. The robustness of the approach was tested on images prepared with various filtering protocols. Statistical assessment of the similarity of the three control rats was made with a Kruskal-Wallis rank sum test. A Mann-Whitney-Wilcoxon rank sum test was used to measure statistical distinction between individuals. For comparison with the variogram results, the coefficient of variation and the emphysema index were also calculated for all rats.
Results
Variogram analysis showed that the control rats were statistically indistinct (p = 0.12), but there were significant differences between control, mild global disease, and severe local disease groups (p < 0.0001). A heterogeneity index was calculated to describe the difference of an individual variogram from the control average. This metric also showed clear separation between dose groups. The coefficient of variation and the emphysema index, on the other hand, did not separate groups.
Conclusion
These results suggest the octree decomposition and variogram analysis approach may be a rapid, non-subjective, and sensitive imaging-based biomarker for characterizing lung disease.
doi:10.1186/1471-2342-14-1
PMCID: PMC3922839  PMID: 24393332
Lung imaging; Disease detection; COPD; Emphysema; Pulmonary; Octree; Variogram
21.  Airway Clearance Devices for Cystic Fibrosis 
Executive Summary
Objective
The purpose of this evidence-based analysis is to examine the safety and efficacy of airway clearance devices (ACDs) for cystic fibrosis and attempt to differentiate between devices, where possible, on grounds of clinical efficacy, quality of life, safety and/or patient preference.
Background
Cystic fibrosis (CF) is a common, inherited, life-limiting disease that affects multiple systems of the human body. Respiratory dysfunction is the primary complication and leading cause of death due to CF. CF causes abnormal mucus secretion in the airways, leading to airway obstruction and mucus plugging, which in turn can lead to bacterial infection and further mucous production. Over time, this almost cyclical process contributes to severe airway damage and loss of respiratory function. Removal of airway secretions, termed airway clearance, is thus an integral component of the management of CF.
A variety of methods are available for airway clearance, some requiring mechanical devices, others physical manipulation of the body (e.g. physiotherapy). Conventional chest physiotherapy (CCPT), through the assistance of a caregiver, is the current standard of care for achieving airway clearance, particularly in young patients up to the ages of six or seven. CF patients are, however, living much longer now than in decades past. The median age of survival in Canada has risen to 37.0 years for the period of 1998-2002 (5-year window), up from 22.8 years for the 5-year window ending in 1977. The prevalence has also risen accordingly, last recorded as 3,453 in Canada in 2002, up from 1,630 in 1977. With individuals living longer, there is a greater need for independent methods of airway clearance.
Airway Clearance Devices
There are at least three classes of airway clearance devices: positive expiratory pressure devices (PEP), airway oscillating devices (AOD; either handheld or stationary) and high frequency chest compression (HFCC)/mechanical percussion (MP) devices. Within these classes are numerous different brands of devices from various manufacturers, each with subtle iterations. At least 10 devices are licensed by Health Canada (ranging from Class 1 to Class 3 devices).
Evidence-Based Analysis of Effectiveness
Research Questions
Does long-term use of ACDs improve outcomes of interest in comparison to CCPT in patients with CF?
Does long-term use of one class of ACD improve outcomes of interest in comparison to another class of ACD in CF patients?
Literature Search
A comprehensive literature search was performed on March 7, 2009 using OVID MEDLINE, MEDLINE In-Process and Other Non-Indexed Citations, EMBASE, the Cumulative Index to Nursing & Allied Health Literature (CINAHL), the Cochrane Library, and the International Agency for Health Technology Assessment (INAHTA) for studies published from January 1, 1950 to March 7, 2009.
Inclusion Criteria
All randomized controlled trials including those of parallel and crossover design,
Systematic reviews and/or meta-analyses. Randomized controlled trials (RCTs), systematic reviews and meta-analyses
Exclusion Criteria
Abstracts were generally excluded because their methods could not be examined; however, abstract data was included in several Cochrane meta-analyses presented in this paper;
Studies of less than seven days duration (including single treatment studies);
Studies that did not report primary outcomes;
Studies in which less than 10 patients completed the study.
Outcomes of Interest
Primary outcomes under review were percent-predicted forced expiratory volume (FEV-1), forced vital capacity (FVC), and forced expiratory flow between 25%-75% (FEF25-75). Secondary outcomes included number of hospitalizations, adherence, patient preference, quality of life and adverse events. All outcomes were decided a priori.
Summary of Findings
Literature searching and back-searching identified 13 RCTs meeting the inclusion criteria, along with three Cochrane systematic reviews. The Cochrane reviews were identified in preliminary searching and used as the basis for formulating this review. Results were subgrouped by comparison and according to the available literature. For example, results from Cochrane meta-analyses included abstract data and therefore, additional meta-analyses were also performed on trials reported as full publications only (MAS generally excludes abstracted data when full publications are available as the methodological quality of trials reported in abstract cannot be properly assessed).
Executive Summary Table 1 summarizes the results across all comparisons and subgroupings for primary outcomes of pulmonary function. Only two comparisons yielded evidence of moderate or high quality according to GRADE criteria–the comparisons of CCPT vs. PEP and handheld AOD vs. PEP–but only the comparison of CCPT vs. PEP noted a significant difference between treatment groups. In comparison to CCPT, there was a significant difference in favour of PEP for % predicted FEV-1 and FVC according to one long-term, parallel RCT. This trial was accepted as the best available evidence for the comparison. The body of evidence for the remaining comparisons was low to very low, according to GRADE criteria, being downgraded most often because of poor methodological quality and low generalizability. Specifically, trials were likely not adequately powered (low sample sizes), did not conduct intention-to-treat analyses, were conducted primarily in children and young adolescents, and outdated (conducted more than 10 years ago).
Secondary outcomes were poorly or inconsistently reported, and were generally not of value to decision-making. Of note, there were a significantly higher number of hospitalizations among participants undergoing AOD therapy in comparison to PEP therapy.
Summarization of results for primary outcomes by comparison and subgroupings
Bolding indicates significant difference
Positive summary statistics favour the former intervention
Abbreviations: AOD, airway oscillating device; CCPT, conventional chest physiotherapy; CI, confidence interval; HFCC, high frequency chest compression; MP, mechanical percussion; N/A: not applicable; PEP, positive expiratory pressure
Economic Analysis
Devices ranged in cost from around $60 for PEP and handheld AODs to upwards of $18,000 for a HFCC vest device. Although the majority of device costs are paid out-of-pocket by the patients themselves, their parents, or covered by third-party medical insurance, Ontario did provide funding assistance through the Assistive Devices Program (ADP) for postural drainage boards and MP devices. These technologies, however, are either obsolete or their clinical efficacy is not supported by evidence. ADP provided roughly $16,000 in funding for the 2008/09 fiscal year. Using device costs and prevalent and incident cases of CF in Ontario, budget impact projections were generated for Ontario. Prevalence of CF in Ontario for patients from ages 6 to 71 was cited as 1,047 cases in 2002 while incidence was estimated at 46 new cases of CF diagnosed per year in 2002. Budget impact projections indicated that PEP and handheld AODs were highly economically feasible costing around $90,000 for the entire prevalent population and less than $3,000 per year to cover new incident cases. HFCC vest devices were by far the most expensive, costing in excess of $19 million to cover the prevalent population alone.
Conclusions
There is currently a lack of sufficiently powered, long-term, parallel randomized controlled trials investigating the use of ACDs in comparison to other airway clearance techniques. While much of the current evidence suggests no significant difference between various ACDs and alternative therapies/technologies, at least according to outcomes of pulmonary function, there is a strong possibility that past trials were not sufficiently powered to identify a difference. Unfortunately, it is unlikely that there will be any future trials comparing ACDs to CCPT as withholding therapy using an ACD may be seen as unethical at present.
Conclusions of clinical effectiveness are as follows:
Moderate quality evidence suggests that PEP is at least as effective as or more effective than CCPT, according to primary outcomes of pulmonary function.
Moderate quality evidence suggests that there is no significant difference between PEP and handheld AODs, according to primary outcomes of pulmonary function; however, secondary outcomes may favour PEP.
Low quality evidence suggests that there is no significant difference between AODs or HFCC/MP and CCPT, according to both primary and secondary outcomes.
Very low quality evidence suggests that there is no significant difference between handheld AOD and CCPT, according to primary outcomes of pulmonary function.
Budget impact projections show PEP and handheld AODs to be highly economically feasible.
PMCID: PMC3377547  PMID: 23074531
22.  Diffusion-weighted magnetic resonance imaging for predicting the clinical outcome of comatose survivors after cardiac arrest: a cohort study 
Critical Care  2010;14(1):R17.
Introduction
The aim of this study was to examine whether the patterns of diffusion-weighted imaging (DWI) abnormalities and quantitative regional apparent diffusion coefficient (ADC) values can predict the clinical outcome of comatose patients following cardiac arrest.
Methods
Thirty-nine patients resuscitated from out-of-hospital cardiac arrest were prospectively investigated. Within five days of resuscitation, axial DWIs were obtained and ADC maps were generated using two 1.5-T magnetic resonance scanners. The neurological outcomes of the patients were assessed using the Glasgow Outcome Scale (GOS) score at three months after the cardiac arrest. The brain injuries were categorised into four patterns: normal, isolated cortical injury, isolated deep grey nuclei injury, and mixed injuries (cortex and deep grey nuclei). Twenty-three subjects with normal DWIs served as controls. The ADC and percent ADC values (the ADC percentage as compared to the control data from the corresponding region) were obtained in various regions of the brains. We analysed the differences between the favourable (GOS score 4 to 5) and unfavourable (GOS score 1 to 3) groups with regard to clinical data, the DWI abnormalities, and the ADC and percent ADC values.
Results
The restricted diffusion abnormalities in the cerebral cortex, caudate nucleus, putamen and thalamus were significantly different between the favourable (n = 13) and unfavourable (n = 26) outcome groups. The cortical pattern of injury was seen in one patient (3%), the deep grey nuclei pattern in three patients (8%), the cortex and deep grey nuclei pattern in 21 patients (54%), and normal DWI findings in 14 patients (36%). The cortex and deep grey nuclei pattern was significantly associated with the unfavourable outcome (20 patients with unfavourable vs. 1 patient with favourable outcomes, P < 0.001). In the 22 patients with quantitative ADC analyses, severely reduced ADCs were noted in the unfavourable outcome group. The optimal cutoffs for the mean ADC and the percent ADC values determined by receiver operating characteristic (ROC) curve analysis in the cortex, caudate nucleus, putamen, and thalamus predicted the unfavourable outcome with sensitivities of 67 to 93% and a specificity of 100%.
Conclusions
The patterns of brain injury in early diffusion-weighted imaging (DWI) (less than or equal to five days after resuscitation) and the quantitative measurement of regional ADC may be useful for predicting the clinical outcome of comatose patients after cardiac arrest.
doi:10.1186/cc8874
PMCID: PMC2875532  PMID: 20152021
23.  Methods for CT Automatic Exposure Control Protocol Translation between Scanner Platforms 
Purpose
An imaging facility with a diverse fleet of CT scanners faces considerable challenges when propagating CT protocols with consistent image quality and patient dose across scanner makes and models. While some protocol parameters can comfortably remain constant between scanners (e.g. kV, gantry rotation time, etc.), the automatic exposure control parameter, which selects the overall mA level during tube current modulation, is difficult to match between scanners, especially from different CT manufacturers.
Method
Objective methods for converting tube-current-modulation protocols between CT scanners were developed. Three CT scanners were investigated, a GE LightSpeed 16 scanner, a GE VCT scanner, and a Siemens Definition AS+ scanner. Translation of the automatic exposure control (AEC) parameters such as noise index or quality reference mAs across CT scanners was specifically investigated. A variable-diameter polymethyl methacrylate (PMMA) phantom was imaged on the three scanners using a range of AEC parameters for each scanner. The phantom consisted of 5 cylindrical sections with diameters of 13 cm, 16 cm, 20 cm, 25 cm, and 32 cm. The protocol translation scheme was based upon matching either the CTDIvol or image noise (in HU) between two different CT scanners. A series of analytical fit functions, corresponding to different patient sizes (phantom diameters) were developed from the measured CT data. These functions relate the AEC metric of the reference scanner, the GE LightSpeed 16 in this case, to the AEC metric of a secondary scanner.
Results
When translating protocols between different models of CT scanners (from the GE LightSpeed 16 reference scanner to the GE VCT system), the translation functions were linear. However, a power-law function was necessary to convert the AEC functions of the GE LightSpeed 16 reference scanner to the Siemens Definition AS+ secondary scanner, due to differences in the AEC functionality designed by these two companies.
Conclusions
Protocol translation based on quantitative metrics – volume computed tomography dose index or measured image noise is feasible. Protocol translation has a dependency on patient size, especially between the GE and Siemens’ systems. Translation schemes that preserve dose levels may not produce identical image quality.
doi:10.1016/j.jacr.2013.10.014
PMCID: PMC3942665  PMID: 24589404
CT protocols; Automatic Exposure Control; Tube Current Modulation; Phantoms
24.  Total disc replacement using a tissue-engineered intervertebral disc in vivo: new animal model and initial results  
Study type: Basic science
Introduction: Chronic back pain due to degenerative disc disease (DDD) is among the most important medical conditions causing morbidity and significant health care costs. Surgical treatment options include disc replacement or fusion surgery, but are associated with significant short- and long-term risks.1 Biological tissue-engineering of human intervertebral discs (IVD) could offer an important alternative.2 Recent in vitro data from our group have shown successful engineering and growth of ovine intervertebral disc composites with circumferentially aligned collagen fibrils in the annulus fibrosus (AF) (Figure 1).3
Tissue-engineered composite disc a Experimental steps to generate composite tissue-engineered IVDs3 b Example of different AF formulations on collagen alignment in the AF. Second harmonic generation and two-photon excited fluorescence images of seeded collagen gels (for AF) of 1 and 2.5 mg/ml over time. At seeding, cells and collagen were homogenously distributed in the gels. Over time, AF cells elongated and collagen aligned parallel to cells. Less contraction and less alignment is noted after 3 days in the 2.5 mg/mL gel. c Imaging-based creation of a virtual disc model that will serve as template for the engineered disc. Total disc dimensions (AF and NP) were retrieved from micro-computer tomography (CT) (left images), and nucleus pulposus (NP) dimensions alone were retrieved from T2-weighted MRI images (right images). Merging of MRI and micro-CT models revealed a composite disc model (middle image)—Software: Microview, GE Healthcare Inc., Princeton, NJ; and slicOmatic v4.3, TomoVision, Montreal, Canada. d Flow chart describing the process for generating multi-lamellar tissue engineered IVDs. IVDs are produced by allowing cell-seeded collagen layers to contract around a cell-seeded alginate core (NP) over time
Objective: The next step is to investigate if biological disc implants survive, integrate, and restore function to the spine in vivo. A model will be developed that allows efficient in vivo testing of tissue-engineered discs of various compositions and characteristics.
Methods: Athymic rats were anesthetized and a dorsal approach was chosen to perform a microsurgical discectomy in the rat caudal spine (Fig. 2,Fig. 3). Control group I (n = 6) underwent discectomy only, Control group II (n = 6) underwent discectomy, followed by reimplantation of the autologous disc. Two treatment groups (group III, n = 6, 1 month survival; group IV, n = 6, 6 months survival) received a tissue-engineered composite disc implant. The rodents were followed clinically for signs of infection, pain level and wound healing. X-rays and magnetic resonance imaging (MRI) were assessed postoperatively and up to 6 months after surgery (Fig. 6,Fig. 7). A 7 Tesla MRI (Bruker) was implemented for assessment of the operated level as well as the adjacent disc (hydration). T2-weighted sequences were interpreted by a semiquantitative score (0 = no signal, 1 = weak signal, 2 = strong signal and anatomical features of a normal disc). Histology was performed with staining for proteoglycans (Alcian blue) and collagen (Picrosirius red) (Fig. 4,Fig. 5).
Disc replacement surgery a Operative situs with native disc that has been disassociated from both adjacent vertebrae b Native disc (left) and tissue-engineered implant (right) c Implant in situ before wound closureAF: Annulus fi brosus, nP: nucleus pulposus, eP: endplate, M: Muscle, T: Tendon, s: skin, art: artery, GP: Growth plate, B: Bone
Disc replacement surgery. Anatomy of the rat caudal disc space a Pircrosirius red stained axial cut of native disc space b Saffranin-O stained sagittal cut of native disc space
Histologies of three separate motion segments from three different rats. Animal one = native IVD, Animal two = status after discectomy, Animal three = tissue-engineered implant (1 month) a–c H&E (overall tissue staining for light micrsocopy) d–f Alcian blue (proteoglycans) g–i Picrosirius red (collagen I and II)
Histology from one motion segment four months after implantation of a bio-engineered disc construct a Picrosirius red staining (collagen) b Polarized light microscopy showing collagen staining and collagen organization in AF region c Increased Safranin-O staining (proteoglycans) in NP region of the disc implant d Higher magnification of figure 5c: Integration between implanted tissue-engineered total disc replacement and vertebral body bone
MRI a Disc space height measurements in flash/T1 sequence (top: implant (714.0 micrometer), bottom: native disc (823.5 micrometer) b T2 sequence, red circle surrounding the implant NP
7 Tesla MRI imaging of rat tail IVDs showing axial images (preliminary pilot data) a Diffusion tensor imaging (DTI) on two explanted rat tail discs in Formalin b Higher magnification of a, showing directional alignment of collagen fibers (red and green) when compared to the color ball on top which maps fibers' directional alignment (eg, fibers directing from left to right: red, from top to bottom: blue) c Native IVD in vivo (successful imaging of top and bottom of the IVD (red) d Gradient echo sequence (GE) showing differentiation between NP (light grey) and AF (dark margin) e GE of reimplanted tail IVD at the explantation level f T1Rho sequence demonstrating the NP (grey) within the AF (dark margin), containing the yellow marked region of interest for value acquisition (preliminary data are consistent with values reported in the literature). g T2 image of native IVD in vivo for monitoring of hydration (white: NP)
Results: The model allowed reproducible and complete discectomies as well as disc implantation in the rat tail spine without any surgical or postoperative complications. Discectomy resulted in immediate collapse of the disc space. Preliminary results indicate that disc space height was maintained after disc implantation in groups II, III and IV over time. MRI revealed high resolution images of normal intervertebral discs in vivo. Eight out of twelve animals (groups III and IV) showed a positive signal in T2-weighted images after 1 month (grade 0 = 4, grade 1 = 4, grade 2 = 4). Positive staining was seen for collagen as well as proteoglycans at the site of disc implantation after 1 month in each of the six animals with engineered implants (group III). Analysis of group IV showed positive T2 signal in five out of six animals and disc-height preservation in all animals after 6 months.
Conclusions: This study demonstrates for the first time that tissue-engineered composite IVDs with circumferentially aligned collagen fibrils survive and integrate with surrounding vertebral bodies when placed in the rat spine for up to 6 months. Tissue-engineered composite IVDs restored function to the rat spine as indicated by maintenance of disc height and vertebral alignment. A significant finding was that maintenance of the composite structure in group III was observed, with increased proteoglycan staining in the nucleus pulposus region (Figure 4d–f). Proteoglycan and collagen matrix as well as disc height preservation and positive T2 signals in MRI are promising parameters and indicate functionality of the implants.
doi:10.1055/s-0028-1100918
PMCID: PMC3623095  PMID: 23637671
25.  A Blurring Index for Medical Images 
Journal of Digital Imaging  2005;19(2):118-125.
This study was undertaken to investigate a useful image blurring index. This work is based on our previously developed method, the Moran peak ratio. Medical images are often deteriorated by noise or blurring. Image processing techniques are used to eliminate these two factors. The denoising process may improve image visibility with a trade-off of edge blurring and may introduce undesirable effects in an image. These effects also exist in images reconstructed using the lossy image compression technique. Blurring and degradation in image quality increases with an increase in the lossy image compression ratio. Objective image quality metrics [e.g., normalized mean square error (NMSE)] currently do not provide spatial information about image blurring. In this article, the Moran peak ratio is proposed for quantitative measurement of blurring in medical images. We show that the quantity of image blurring is dependent upon the ratio between the processed peak of Moran's Z histogram and the original image. The peak ratio of Moran's Z histogram can be used to quantify the degree of image blurring. This method produces better results than the standard gray level distribution deviation. The proposed method can also be used to discern blurriness in an image using different image compression algorithms.
doi:10.1007/s10278-005-8736-y
PMCID: PMC3045183  PMID: 16283091
Moran peak ratio; image blurring; image quality

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