A 16-Channel Receive,Forced Current Excitation Dual-Transmit Coil for Breast Imaging at 7T

Purpose

To enable high spatial and temporal breast imaging resolution via combined use of high field MRI, array coils, and forced current excitation (FCE) multi channel transmit.

Materials and Methods

A unilateral 16-channel receive array insert was designed for use in a transmit volume coil optimized for quadrature operation with dual-transmit RF shimming at 7T. Signal-to-noise ratio (SNR) maps, g-factor maps, and high spatial and temporal resolution in vivo images were acquired to demonstrate the utility of the coil architecture.

Results

The dual-transmit FCE coil provided homogeneous excitation and the array provided an increase in average SNR of 3.3 times (max 10.8, min 1.5) compared to the volume coil in transmit/receive mode. High resolution accelerated in vivo breast imaging demonstrated the ability to achieve isotropic spatial resolution of 0.5 mm within clinically relevant 90 s scan times, as well as the ability to perform 1.0 mm isotropic resolution imaging, 7 s per dynamics, with the use of bidirectional SENSE acceleration of up to R = 9.

Conclusion

The FCE design of the transmit coil easily accommodates the addition of a sixteen channel array coil. The improved spatial and temporal resolution provided by the high-field array coil with FCE dual-channel transmit will ultimately be beneficial in lesion detection and characterization.     

Novel X-ray image noise reduction technology reduces patient radiation dose while maintaining image quality in coronary angiography

Aims

The consequences of high radiation dose for patient and staff demand constant improvements in X-ray dose reduction technology. This study assessed non-inferiority of image quality and quantified patient dose reduction in interventional cardiology for an anatomy-specific optimised cine acquisition chain combined with advanced real-time image noise reduction algorithms referred to as ‘study cine’, compared with conventional angiography.

Methods

Fifty patients underwent two coronary angiographic acquisitions: one with advanced image processing and optimised exposure system settings to enable dose reduction (study cine) and one with standard image processing and exposure settings (reference cine). The image sets of 39 patients (18 females, 21 males) were rated by six experienced independent reviewers, blinded to the patient and image characteristics. The image pairs were randomly presented. Overall 85 % of the study cine images were rated as better or equal quality compared with the reference cine (95 % CI 0.81–0.90). The median dose area product per frame decreased from 55 to 26 mGy.cm²/frame (53 % reduction, p < 0.001).

Conclusion

This study demonstrates that the novel X-ray imaging technology provides non-inferior image quality compared with conventional angiographic systems for interventional cardiology with a 53 % patient dose reduction.     

An Augmented Lagrangian Based Compressed Sensing Reconstruction for Non-Cartesian Magnetic Resonance Imaging without Gridding and Regridding at Every Iteration

Background

Non-Cartesian trajectories are used in a variety of fast imaging applications, due to the incoherent image domain artifacts they create when undersampled. While the gridding technique is commonly utilized for reconstruction, the incoherent artifacts may be further removed using compressed sensing (CS). CS reconstruction is typically done using conjugate-gradient (CG) type algorithms, which require gridding and regridding to be performed at every iteration. This leads to a large computational overhead that hinders its applicability.

Methods

We sought to develop an alternative method for CS reconstruction that only requires two gridding and one regridding operation in total, irrespective of the number of iterations. This proposed technique is evaluated on phantom images and whole-heart coronary MRI acquired using 3D radial trajectories, and compared to conventional CS reconstruction using CG algorithms in terms of quantitative vessel sharpness, vessel length, computation time, and convergence rate.

Results

Both CS reconstructions result in similar vessel length (P = 0.30) and vessel sharpness (P = 0.62). The per-iteration complexity of the proposed technique is approximately 3-fold lower than the conventional CS reconstruction (17.55 vs. 52.48 seconds in C++). Furthermore, for in-vivo datasets, the convergence rate of the proposed technique is faster (60±13 vs. 455±320 iterations) leading to a ∼23-fold reduction in reconstruction time.

Conclusions

The proposed reconstruction provides images of similar quality to the conventional CS technique in terms of removing artifacts, but at a much lower computational complexity.     

Implementation of dual-source RF excitation in 3 T MR-scanners allows for nearly identical ADC values compared to 1.5 T MR scanners in the abdomen

Background

To retrospectively and prospectively compare abdominal apparent diffusion coefficient (ADC) values obtained within in a 1.5 T system and 3 T systems with and without dual-source parallel RF excitation techniques.

Methodology/Principal Findings

After IRB approval, diffusion-weighted (DW) images of the abdomen were obtained on three different MR systems (1.5 T, a first generation 3 T, and a second generation 3 T which incorporates dual-source parallel RF excitation) on 150 patients retrospectively and 19 volunteers (57 examinations total) prospectively. Seven regions of interest (ROI) were throughout the abdomen were selected to measure the ADC. Statistical analysis included independent two-sided t-tests, Mann-Whitney U tests and correlation analysis. In the DW images of the abdomen, mean ADC values were nearly identical with nonsignificant differences when comparing the 1.5 T and second generation 3 T systems in all seven anatomical regions in the patient population and six of the seven in the volunteer population (p>0.05 in all distributions). The strength of correlation measured in the volunteer population between the two scanners in the kidneys ranged from r = 0.64–0.88 and in the remaining regions (besides the spleen), r>0.85. In the patient population the first generation 3 T scanner had different mean ADC values with significant differences (p<0.05) compared to the other two scanners in each of the seven distributions. In the volunteer population, the kidneys shared similar ADC mean values in comparison to the other two scanners with nonsignificant differences.

Conclusions/Significance

A second generation 3 T scanner with dual-source parallel RF excitation provides nearly identical ADC values compared with the 1.5 T imaging system in abdominal imaging.     

Study of Oxidative Stress in Human Lens Epithelial Cells Exposed to 1.8 GHz Radiofrequency Fields

Objectives

The aims of the present study were to determine oxidative stress and to explore possible reasons of reactive oxygen species (ROS) increase in human lens epithelial (HLE) B3 cells exposed to low intensity 1.8 GHz radiofrequency fields (RF).

Methods

The HLE B3 cells were divided into RF exposure and RF sham-exposure groups. The RF exposure intensity was at specific absorption rate (SAR) of 2, 3, or 4 W/kg. The ROS levels were measured by a fluorescent probe 2′7′-dichlorofluorescin diacetate (DCFH-DA) assay in the HLE B3 cells exposed to 1.8 GHz RF for 0.5, 1, and 1.5 h. Lipid peroxidation and cellular viability were detected by an MDA test and Cell Counting Kit-8 (CCK-8) assays, respectively, in the HLE B3 cells exposed to 1.8 GHz RF for 6, 12, and 24 h, respectively. The mRNA expression of SOD1, SOD2, CAT, and GPx1 genes and the expression of SOD1, SOD2, CAT, and GPx1 proteins was measured by qRT-PCR and Western blot assays in the HLE B3 cells exposed to 1.8 GHz RF for 1 h.

Results

The ROS and MDA levels significantly increased (P<0.05) in the RF exposure group and that the cellular viability, mRNA expression of four genes, and expression of four proteins significantly decreased (P<0.05) compared with the RF sham-exposure group.

Conclusions

Oxidative stress is present in HLE B3 cells exposed to 1.8 GHz low-intensity RF and that the increased production of ROS may be related to down-regulation of four antioxidant enzyme genes induced by RF exposure.     

MicroPure Imaging for the Evaluation of Microcalcifications in Gouty Arthritis Involving the First Metatarsophalangeal Joint: A Preliminary Study

Objective

To assess the value of MicroPure, a new ultrasound image processing technique, in identifying microcalcifications (formed by monosodium urate crystals) in the first metatarsophalangeal joints attacked by gout compared to gray-scale ultrasound images.

Materials and Methods

Thirty-six patients who fulfilled the study inclusion criteria underwent gray-scale ultrasound and MicroPure examinations of the first metatarsophalangeal joints attacked by gout. Static images of the target areas were acquired using gray-scale ultrasound and MicroPure. Two independent and blinded investigators analyzed the images to determine the number of microcalcifications and to score for image quality and artifacts.

Results

The two investigators observed significantly more microcalcifications with MicroPure compared to gray-scale ultrasound (ρ<0.001). The level of agreement between the investigators consistently increased from gray-scale ultrasound to MicroPure imaging (gray-scale interclass correlation coefficient of 0.69 vs. MicroPure interclass correlation coefficient of 0.81). One investigator preferred the MicroPure image quality over gray-scale ultrasound (ρ<0.001), but the other investigator disagreed (ρ<0.001). Both investigators observed fewer artifacts with MicroPure than with gray-scale ultrasound (ρ<0.009).

Conclusion

MicroPure imaging identified significantly more microcalcifications than gray-scale ultrasound.     

Adaptive Iterative Dose Reduction Using Three Dimensional Processing (AIDR3D) Improves Chest CT Image Quality and Reduces Radiation Exposure

Objective

To assess the advantages of Adaptive Iterative Dose Reduction using Three Dimensional Processing (AIDR3D) for image quality improvement and dose reduction for chest computed tomography (CT).

Methods

Institutional Review Boards approved this study and informed consent was obtained. Eighty-eight subjects underwent chest CT at five institutions using identical scanners and protocols. During a single visit, each subject was scanned using different tube currents: 240, 120, and 60 mA. Scan data were converted to images using AIDR3D and a conventional reconstruction mode (without AIDR3D). Using a 5-point scale from 1 (non-diagnostic) to 5 (excellent), three blinded observers independently evaluated image quality for three lung zones, four patterns of lung disease (nodule/mass, emphysema, bronchiolitis, and diffuse lung disease), and three mediastinal measurements (small structure visibility, streak artifacts, and shoulder artifacts). Differences in these scores were assessed by Scheffe''s test.

Results

At each tube current, scans using AIDR3D had higher scores than those without AIDR3D, which were significant for lung zones (p<0.0001) and all mediastinal measurements (p<0.01). For lung diseases, significant improvements with AIDR3D were frequently observed at 120 and 60 mA. Scans with AIDR3D at 120 mA had significantly higher scores than those without AIDR3D at 240 mA for lung zones and mediastinal streak artifacts (p<0.0001), and slightly higher or equal scores for all other measurements. Scans with AIDR3D at 60 mA were also judged superior or equivalent to those without AIDR3D at 120 mA.

Conclusion

For chest CT, AIDR3D provides better image quality and can reduce radiation exposure by 50%.     

A Simple Sign for Recognizing Off–Axis OCT Measurement Beam Placement in the Context of Multicentre Studies

Purpose

Optical coherence tomography (OCT) allows quantification of the thickness of the retinal nerve fibre layer (RNFL) thickness, a potential biomarker for neurodegeneration. The estimated annual RNFL loss in multiple sclerosis amounts to 2 μm using time domain OCT. The recognition of measurement artifacts exceeding this limit is relevant for the successful use of OCT as a secondary outcome measure in clinical trials.

Methods

Prospective study design. An exploratory pilot study (ring and volume scans) followed by a cohort study (1,980 OCT ring scans). The OCT measurement beam was placed off–axis to the left, right, top and bottom of the subjects pupil and RNFL thickness of these scans were compared to the centrally placed reference scans.

Results

Off–axis placement of the OCT measurement beam resulted in significant artifacts in RNFL thickness measurements (95%CI 9μm, maximal size of error 42μm). Off–axis placement gave characteristic patterns of the OCT live images which are not necessarily saved for review. Off–axis placement also causes regional inhomogeneity of reflectivity in the outer nuclear (ONL) and outer plexiform layers (OPL) which remains visible on scans saved for review.

Conclusion

Off–axis beam placement introduces measurement artifacts at a magnitude which may mask recognition of RNFL loss due to neurodegeneration in multiple sclerosis. The resulting pattern in the OCT live image can only be recognised by the technician capturing the scans. Once the averaged scans have been aligned this pattern is lost. Retrospective identification of this artifact is however possible by presence of regional inhomogeneity of ONL/OPL reflectivity. This simple and robust sign may be considered for quality control criteria in the setting of multicentre OCT studies. The practical advice of this study is to keep the OCT image in the acquisition window horizontally aligned whenever possible.     

Artifacts in magnetic resonance imaging and computed tomography caused by dental materials

Background

Artifacts caused by dental restorations, such as dental crowns, dental fillings and orthodontic appliances, are a common problem in MRI and CT scans of the head and neck. The aim of this in-vitro study was to identify and evaluate the artifacts produced by different dental restoration materials in CT and MRI images.

Methods

Test samples of 44 materials (Metal and Non-Metal) commonly used in dental restorations were fabricated and embedded with reference specimens in gelatin moulds. MRI imaging of 1.5T and CT scan were performed on the samples and evaluated in two dimensions. Artifact size and distortions were measured using a digital image analysis software.

Results

In MRI, 13 out of 44 materials produced artifacts, while in CT 41 out of 44 materials showed artifacts. Artifacts produced in both MRI and CT images were categorized according to the size of the artifact.

Significance

Metal based restoration materials had strong influence on CT and less artifacts in MRI images. Rare earth elements such as Ytterbium trifluoride found in composites caused artifacts in both MRI and CT. Recognizing these findings would help dental materials manufacturers and developers to produce materials which can cause less artifacts in MRI and CT images.     

Association between Sjogren's Syndrome and Respiratory Failure: Put Airway,Interstitia, and Vessels Close Together: A National Cohort Study

Objectives

Few studies have evaluated the association between Sjogren''s syndrome (SS) and respiratory failure (RF). Thus, we conducted a retrospective national cohort study to investigate whether Sjogren''s syndrome (SS) increases the risk of respiratory failure (RF).

Methods

The cohort consisted of 4954 newly diagnosed patients with SS but without a previous diagnosis of RF, and 19816 patients as the comparison cohort from the catastrophic illnesses registry, obtained from the 2000–2005 period. All of the study participants were followed from the index date to December 31, 2011. We analyzed the association between the risk of RF and SS by using a Cox proportional hazards regression model, controlling for sex, age, and comorbidities.

Results

The overall incidence rate of RF showed a 3.21-fold increase in the SS cohort compared with the comparison cohort. The adjusted HR of RF was 3.04 for the SS cohort compared with the comparison cohort, after we adjusted for sex, age, and comorbidities. The HRs of RF for patients with primary SS and secondary SS compared with the comparison cohort were 2.99 and 3.93, respectively (P for trend <.001). The HRs of RF increased as the severity of SS increased, from 2.34 for those with no inpatient care experience to 5.15 for those with inpatient care experience (P for trend <.001).

Conclusion

This study indicates that clinical physicians should not only consider secondary SS but also primary SS as a critical factor that increases the risk of RF.     

A Robust Post-Processing Workflow for Datasets with Motion Artifacts in Diffusion Kurtosis Imaging

Purpose

The aim of this study was to develop a robust post-processing workflow for motion-corrupted datasets in diffusion kurtosis imaging (DKI).

Materials and methods

The proposed workflow consisted of brain extraction, rigid registration, distortion correction, artifacts rejection, spatial smoothing and tensor estimation. Rigid registration was utilized to correct misalignments. Motion artifacts were rejected by using local Pearson correlation coefficient (LPCC). The performance of LPCC in characterizing relative differences between artifacts and artifact-free images was compared with that of the conventional correlation coefficient in 10 randomly selected DKI datasets. The influence of rejected artifacts with information of gradient directions and b values for the parameter estimation was investigated by using mean square error (MSE). The variance of noise was used as the criterion for MSEs. The clinical practicality of the proposed workflow was evaluated by the image quality and measurements in regions of interest on 36 DKI datasets, including 18 artifact-free (18 pediatric subjects) and 18 motion-corrupted datasets (15 pediatric subjects and 3 essential tremor patients).

Results

The relative difference between artifacts and artifact-free images calculated by LPCC was larger than that of the conventional correlation coefficient (p<0.05). It indicated that LPCC was more sensitive in detecting motion artifacts. MSEs of all derived parameters from the reserved data after the artifacts rejection were smaller than the variance of the noise. It suggested that influence of rejected artifacts was less than influence of noise on the precision of derived parameters. The proposed workflow improved the image quality and reduced the measurement biases significantly on motion-corrupted datasets (p<0.05).

Conclusion

The proposed post-processing workflow was reliable to improve the image quality and the measurement precision of the derived parameters on motion-corrupted DKI datasets. The workflow provided an effective post-processing method for clinical applications of DKI in subjects with involuntary movements.     

128-Slice Acceletated-Pitch Dual Energy CT Angiography of the Head and Neck: Comparison of Different Low Contrast Medium Volumes

Background

Our study aims to evaluate the image quality and feasibility of 128-slice dual-energy CTA (DE-CTA) for supra-aortic arteries using reduced amounts of contrast medium (CM).

Methods

A prospective study was performed in 54 patients receiving CTA of the head and neck with a 128-slice dual-source CT system. Patients were randomized into two groups with a volume of either 40 mL of CM (Group I) or 50 mL of CM (Group II). Arterial and venous enhancements were recorded for quantitative assessment. Qualitative assessments for images without bone removal (BR) were based on a) the visualization of the circle of Willis and b) streak artifacts due to residual CM in the subclavian or internal jugular veins ipsilateral to injection of CM. Qualitative assessment of dual-energy images using BR was based on the presence of bone remnants and vessel integrity. Quantitative data was compared using the Student t test. The χ² test was used for the qualitative measurements of streak artifacts in veins while the Mann-Whitney U test was used for the qualitative measurements of images with BR.

Results

Arterial and venous attenuation was significantly higher in Group II (P=0.000). Image quality regarding the circle of Willis was excellent in both groups (3.90±0.30 for Group I and 4.00±0 for Group II) . Imaging of the internal jugular veins was scored higher in Group I (1.87±0.72) compared with Group II (1.48±0.51) (P=0.021). Within Group I using BR, mean scores for bone remnants did not differ significantly (P>0.05) but mean scores of vessel integrity (P<0.05) did.

Conclusions

Contrast-enhanced head and neck CTA is feasible using a scan protocol with low amounts of contrast medium (40 mL) on a 128-slice dual-energy CTA. The 40-mL protocol provides satisfactory image quality before and after dual-energy bone-removal post-processing.     

High-Pitch CT Pulmonary Angiography in Third Generation Dual-Source CT: Image Quality in an Unselected Patient Population

Objectives

To investigate the feasibility of high-pitch CT pulmonary angiography (CTPA) in 3^rd generation dual-source CT (DSCT) in unselected patients.

Methods

Forty-seven patients with suspected pulmonary embolism underwent high-pitch CTPA on a 3^rd generation dual-source CT scanner. CT dose index (CTDI_vol) and dose length product (DLP) were obtained. Objective image quality was analyzed by calculating signal-to-noise-ratio (SNR) and contrast-to-noise ratio (CNR). Subjective image quality on the central, lobar, segmental and subsegmental level was rated by two experienced radiologists.

Results

Median CTDI was 8.1 mGy and median DLP was 274 mGy*cm. Median SNR was 32.9 in the central and 31.9 in the segmental pulmonary arteries. CNR was 29.2 in the central and 28.2 in the segmental pulmonary arteries. Median image quality was “excellent” in central and lobar arteries and “good” in subsegmental arteries according to both readers. Segmental arteries varied between “excellent” and “good”. Image quality was non-diagnostic in one case (2%), beginning in the lobar arteries. Thirteen patients (28%) showed minor motion artifacts.

Conclusions

In third-generation dual-source CT, high-pitch CTPA is feasible for unselected patients. It yields excellent image quality with minimal motion artifacts. However, compared to standard-pitch cohorts, no distinct decrease in radiation dose was observed.     

Low-Dose Prospectively Electrocardiogram-Gated Axial Dual-Source CT Angiography in Patients with Pulsatile Bilateral Bidirectional Glenn Shunt: An Alternative Noninvasive Method for Postoperative Morphological Estimation

Objective

To explore the clinical value of low-dose prospectively electrocardiogram-gated axial dual-source CT angiography (low-dose PGA scanning, CTA) in patients with pulsatile bilateral bidirectional Glenn shunt (bBDG) as an alternative noninvasive method for postoperative morphological estimation.

Methods

Twenty patients with pulsatile bBDG (mean age 4.2±1.6 years) underwent both low-dose PGA scanning and conventional cardiac angiography (CCA) for the morphological changes. The morphological evaluation included the anatomy of superior vena cava (SVC) and pulmonary artery (PA), the anastomotic location, thrombosis, aorto-pulmonary collateral circulation, pulmonary arteriovenous malformations, etc. Objective and subjective image quality was assessed. Bland–Altman analysis and linear regression analyses were used to evaluate the correlation on measurements between CTA and CCA. Effective radiation dose of both modalities was calculated.

Results

The CT attenuation value of bilateral SVC and PA was higher than 300 HU. The average subjective image quality score was 4.05±0.69. The morphology of bilateral SVC and PA was displayed completely and intuitively by CTA images. There were 24 SVC above PA and 15 SVC beside PA. Thrombosis was found in 1 patient. Collateral vessels were detected in 13 patients. No pulmonary arteriovenous malformation was found in our study. A strong correlation (R²>0.8, P<0.001) was observed between the measurements on CTA images and on CCA images. Bland–Altman analysis demonstrated a systematic overestimation of the measurements by CTA (the mean value of bias>0).The mean effective dose of CTA and CCA was 0.50±0.17 mSv and 4.85±1.34 mSv respectively.

Conclusion

CT angiography with a low-dose PGA scanning is an accurate and reliable noninvasive examination in the assessment of morphological changes in patients with pulsatile bBDG.     

Respiratory Motion Reduction in PET/CT Using Abdominal Compression for Lung Cancer Patients

Purpose

Respiratory motion causes substantial artifacts in reconstructed PET images when using helical CT as the attenuation map in PET/CT imaging. In this study, we aimed to reduce the respiratory artifacts in PET/CT images of patients with lung tumors using an abdominal compression device.

Methods

Twelve patients with lung cancer located in the middle or lower lobe of the lung were recruited. The patients were injected with 370 MBq of ¹⁸F-FDG. During PET, the patients assumed two bed positions for 1.5 min/bed. After conducting free-breathing imaging, we obtained images of the patients with abdominal compression by applying the same setup used in the free-breathing scan. The differences in the standardized uptake value (SUV)_max, SUV_mean, tumor volume, and the centroid of the tumors between PET and various CT schemes were measured.

Results

The SUV_max and SUV_mean derived from PET/CT imaging using an abdominal compression device increased for all the lesions, compared with those obtained using the conventional approach. The percentage increases were 18.1% ±14% and 17% ±16.8% for SUV_max and SUV_mean, respectively. PET/CT imaging combined with abdominal compression generally reduced the tumor mismatch between CT and the corresponding attenuation corrected PET images, with an average decrease of 1.9±1.7 mm over all the cases.

Conclusions

PET/CT imaging combined with abdominal compression reduces respiratory artifacts and PET/CT misregistration, and enhances quantitative SUV in tumor. Abdominal compression is easy to set up and is an effective method used in PET/CT imaging for clinical oncology, especially in the thoracic region.     

Separating Drought Effects from Roof Artifacts on Ecosystem Processes in a Grassland Drought Experiment

1

Given the predictions of increased drought probabilities under various climate change scenarios, there have been numerous experimental field studies simulating drought using transparent roofs in different ecosystems and regions. Such roofs may, however, have unknown side effects, called artifacts, on the measured variables potentially confounding the experimental results. A roofed control allows the quantification of potential artifacts, which is lacking in most experiments.

2

We conducted a drought experiment in experimental grasslands to study artifacts of transparent roofs and the resulting effects of artifacts on ecosystems relative to drought on three response variables (aboveground biomass, litter decomposition and plant metabolite profiles). We established three drought treatments, using (1) transparent roofs to exclude rainfall, (2) an unroofed control treatment receiving natural rainfall and (3) a roofed control, nested in the drought treatment but with rain water reapplied according to ambient conditions.

3

Roofs had a slight impact on air (+0.14°C during night) and soil temperatures (−0.45°C on warm days, +0.25°C on cold nights), while photosynthetically active radiation was decreased significantly (−16%). Aboveground plant community biomass was reduced in the drought treatment (−41%), but there was no significant difference between the roofed and unroofed control, i.e., there were no measurable roof artifact effects.

4

Compared to the unroofed control, litter decomposition was decreased significantly both in the drought treatment (−26%) and in the roofed control treatment (−18%), suggesting artifact effects of the transparent roofs. Moreover, aboveground metabolite profiles in the model plant species Medicago x varia were different from the unroofed control in both the drought and roofed control treatments, and roof artifact effects were of comparable magnitude as drought effects.

5

Our results stress the need for roofed control treatments when using transparent roofs for studying drought effects, because roofs can cause significant side effects.     

Use of Whole Genome Sequencing to Determine the Microevolution of Mycobacterium tuberculosis during an Outbreak

Rationale

Current tools available to study the molecular epidemiology of tuberculosis do not provide information about the directionality and sequence of transmission for tuberculosis cases occurring over a short period of time, such as during an outbreak. Recently, whole genome sequencing has been used to study molecular epidemiology of Mycobacterium tuberculosis over short time periods.

Objective

To describe the microevolution of M. tuberculosis during an outbreak caused by one drug-susceptible strain.

Method and Measurements

We included 9 patients with tuberculosis diagnosed during a period of 22 months, from a population-based study of the molecular epidemiology in San Francisco. Whole genome sequencing was performed using Illumina’s sequencing by synthesis technology. A custom program written in Python was used to determine single nucleotide polymorphisms which were confirmed by PCR product Sanger sequencing.

Main results

We obtained an average of 95.7% (94.1–96.9%) coverage for each isolate and an average fold read depth of 73 (1 to 250). We found 7 single nucleotide polymorphisms among the 9 isolates. The single nucleotide polymorphisms data confirmed all except one known epidemiological link. The outbreak strain resulted in 5 bacterial variants originating from the index case A1 with 0–2 mutations per transmission event that resulted in a secondary case.

Conclusions

Whole genome sequencing analysis from a recent outbreak of tuberculosis enabled us to identify microevolutionary events observable during transmission, to determine 0–2 single nucleotide polymorphisms per transmission event that resulted in a secondary case, and to identify new epidemiologic links in the chain of transmission.     

Anatomy-corresponding method of IMRT verification

Background

During a proper execution of dMLC plans, there occurs an undesired but frequent effect of the dose locally accumulated by tissue being significantly different than expected. The conventional dosimetric QA procedures give only a partial picture of the quality of IMRT treatment, because their solely quantitative outcomes usually correspond more to the total area of the detector than the actually irradiated volume.

Aim

The aim of this investigation was to develop a procedure of dynamic plans verification which would be able to visualize the potential anomalies of dose distribution and specify which tissue they exactly refer to.

Materials & methods

The paper presents a method discovered and clinically examined in our department. It is based on a Gamma Evaluation concept and allows accurate localization of deviations between predicted and acquired dose distributions, which were registered by portal as well as film dosimetry. All the calculations were performed on the self-made software GammaEval, the γ-images (2-dimensional distribution of γ-values) and γ-histograms were created as quantitative outcomes of verification.

Results

Over 150 maps of dose distribution have been analyzed and the cross-examination of the gamma images with DRRs was performed.

Conclusions

It seems, that the complex monitoring of treatment would be possible owing to the images obtained as a cross-examination of γ-images and corresponding DRRs.     

A rheumatoid factor paradox: inhibition of rituximab effector function

Introduction

Rituximab (RTX) therapy of rheumatoid arthritis (RA) exhibits enhanced effectiveness in seropositive patients. Using patient sera, we tested if this improved efficacy was associated with enhanced RTX mediated complement-dependent cytotoxicity (RTX-CDC).

Methods

We developed an in vitro assay for RTX-CDC using patient sera and the Daudi human B cell line. Using propidium iodide uptake and flow cytometry, we compared RTX-CDC with rheumatoid factor (RF)+ sera relative to normal volunteer, non-RA and RF- sera. Additional studies examined mixing studies of RF+ and RF- sera, as well as the effect of monoclonal IgA or IgM RF. Finally, the effect of RF on RTX mediated trogocytosis of normal B cells was evaluated.

Results

Using human sera, addition of RTX resulted in rapid and profound (> 50%) Daudi cell death that was complement dependent. Surprisingly, RF+ patient sera exhibited reduced RTX-CDC relative to RF- sera, with an inverse relationship of RTX-CDC and RF titer. Mixing studies indicated the presence of an inhibitor of RTX-CDC in RF+ sera. The addition of monoclonal IgM or IgA RF to RF- sera markedly inhibited RTX-CDC. This effect was specific for RF binding to the Fc portion of RTX as it was not apparent with the F(ab)'' domains of RTX engineered onto IgG3 heavy chain. RF also modestly inhibited RTX mediated trogocytosis.

Conclusions

Contrary to expectations, RF+ sera exhibits reduced RTX-CDC due to the presence of RF. The enhanced efficacy of RTX in seropositive RA patients cannot be attributed to improved B cell depletion through CDC. This result indicates that high RF levels may potentially modulate the efficacy of any therapeutic monoclonal antibody dependent on Fc effector function.     

Comparison of Total Variation with a Motion Estimation Based Compressed Sensing Approach for Self-Gated Cardiac Cine MRI in Small Animal Studies

Purpose

Compressed sensing (CS) has been widely applied to prospective cardiac cine MRI. The aim of this work is to study the benefits obtained by including motion estimation in the CS framework for small-animal retrospective cardiac cine.

Methods

We propose a novel B-spline-based compressed sensing method (SPLICS) that includes motion estimation and generalizes previous spatiotemporal total variation (ST-TV) methods by taking into account motion between frames. In addition, we assess the effect of an optimum weighting between spatial and temporal sparsity to further improve results. Both methods were implemented using the efficient Split Bregman methodology and were evaluated on rat data comparing animals with myocardial infarction with controls for several acceleration factors.

Results

ST-TV with optimum selection of the weighting sparsity parameter led to results similar to those of SPLICS; ST-TV with large relative temporal sparsity led to temporal blurring effects. However, SPLICS always properly corrected temporal blurring, independently of the weighting parameter. At acceleration factors of 15, SPLICS did not distort temporal intensity information but led to some artefacts and slight over-smoothing. At an acceleration factor of 7, images were reconstructed without significant loss of quality.

Conclusion

We have validated SPLICS for retrospective cardiac cine in small animal, achieving high acceleration factors. In addition, we have shown that motion modelling may not be essential for retrospective cine and that similar results can be obtained by using ST-TV provided that an optimum selection of the spatiotemporal sparsity weighting parameter is performed.