Digital reference object toolkit of breast DCE MRI for quantitative evaluation of image reconstruction and analysis methods.

PURPOSE: To develop a digital reference object (DRO) toolkit to generate realistic breast DCE-MRI data for quantitative assessment of image reconstruction and data analysis methods. METHODS: A simulation framework in a form of DRO toolkit has been developed using the ultrafast and conventional breast DCE-MRI data of 53 women with malignant (n = 25) or benign (n = 28) lesions. We segmented five anatomical regions and performed pharmacokinetic analysis to determine the ranges of pharmacokinetic parameters for each segmented region. A database of the segmentations and their pharmacokinetic parameters is included in the DRO toolkit that can generate a large number of realistic breast DCE-MRI data. We provide two potential examples for our DRO toolkit: assessing the accuracy of an image reconstruction method using undersampled simulated radial k-space data and assessing the impact of the B 1 + $$ {\mathrm{B}}_1^{+} $$ field inhomogeneity on estimated parameters. RESULTS: The estimated pharmacokinetic parameters for each region showed agreement with previously reported values. For the assessment of the reconstruction method, it was found that the temporal regularization resulted in significant underestimation of estimated parameters by up to 57% and 10% with the weighting factor λ = 0.1 and 0.01, respectively. We also demonstrated that spatial discrepancy of v p $$ {v}_p $$ and PS $$ \mathrm{PS} $$ increase to about 33% and 51% without correction for B 1 + $$ {\mathrm{B}}_1^{+} $$ field. CONCLUSION: We have developed a DRO toolkit that includes realistic morphology of tumor lesions along with the expected pharmacokinetic parameter ranges. This simulation framework can generate many images for quantitative assessment of DCE-MRI reconstruction and analysis methods.

Feasibility of measuring blood-brain barrier permeability using ultra-short echo time radial magnetic resonance imaging.

BACKGROUND AND PURPOSE: The purpose of this study is to evaluate the feasibility of using 3-dimensional (3D) ultra-short echo time (UTE) radial imaging method for measurement of the permeability of the blood-brain barrier (BBB) to gadolinium-based contrast agent. In this study, we propose to use the golden-angle radial sparse parallel (GRASP) method with 3D center-out trajectories for UTE, hence named as 3D UTE-GRASP. We first examined the feasibility of using 3D UTE-GRASP dynamic contrast-enhanced (DCE)-magnetic resonance imaging (MRI) for differentiating subtle BBB disruptions induced by focused ultrasound (FUS). Then, we examined the BBB permeability changes in Alzheimer's disease (AD) pathology using Alzheimer's disease transgenic mice (5xFAD) at different ages. METHODS: For FUS experiments, we used four Sprague Dawley rats at similar ages where we compared BBB permeability of each rat receiving the FUS sonication with different acoustic power (0.4-1.0 MPa). For AD transgenic mice experiments, we included three 5xFAD mice (6, 12, and 16 months old) and three wild-type mice (4, 8, and 12 months old). RESULTS: The result from FUS experiments showed a progressive increase in BBB permeability with increase of acoustic power (p < .05), demonstrating the sensitivity of DCE-MRI method for detecting subtle changes in BBB disruption. Our AD transgenic mice experiments suggest an early BBB disruption in 5xFAD mice, which is further impaired with aging. CONCLUSION: The results in this study substantiate the feasibility of using the proposed 3D UTE-GRASP method for detecting subtle BBB permeability changes expected in neurodegenerative diseases, such as AD.

Expression of Cholera Toxin (CT) and the Toxin Co-Regulated Pilus (TCP) by Variants of ToxT in Vibrio cholerae Strains.

The expression of the two major virulence genes of Vibrio cholerae-tcpA (the major subunit of the toxin co-regulated pilus) and ctxAB (cholera toxin)-is regulated by the ToxR regulon, which is triggered by environmental stimuli during infection within the human small intestine. Special culture methods are required to induce the expression of virulence genes in V. cholerae in the laboratory setting. In the present study, induction of the expression of virulence genes by two point mutations (65th and 139th amino acids) in toxT, which is produced by the ToxR regulon and activates the transcription of the virulence genes in V. cholerae, under laboratory culture conditions has been investigated. Each of the four toxT alleles assessed displayed different transcriptional activator functions in a given V. cholerae strain. Although the ToxR regulon has been known to not be expressed by El Tor biotype V. cholerae strains cultured under standard laboratory conditions, the variant toxT alleles that we assessed in this study enabled the expression virulence genes in El Tor biotype strains grown under simple culture conditions comprising shake culture in LB medium, suggesting that the regulation of virulence gene expression may be regulated more complexly than previously thought and may involve additional factors beyond the production of ToxT by the ToxR regulon.

Improving measurement of blood-brain barrier permeability with reduced scan time using deep-learning-derived capillary input function.

PURPOSE: In Dynamic contrast-enhanced MRI (DCE-MRI), Arterial Input Function (AIF) has been shown to be a significant contributor to uncertainty in the estimation of kinetic parameters. This study is to assess the feasibility of using a deep learning network to estimate local Capillary Input Function (CIF) to estimate blood-brain barrier (BBB) permeability, while reducing the required scan time. MATERIALS AND METHOD: A total of 13 healthy subjects (younger (<40 y/o): 8, older (> 67 y/o): 5) were recruited and underwent 25-min DCE-MRI scans. The 25 min data were retrospectively truncated to 10 min to simulate a reduced scan time of 10 min. A deep learning network was trained to predict the CIF using simulated tissue contrast dynamics with two vascular transport models. The BBB permeability (PS) was measured using 3 methods: (i) Ca-25min, using DCE-MRI data of 25 min with individually sampled AIF (Ca); (ii) Ca-10min, using truncated 10min data with AIF (Ca); and (iii) Cp-10min, using truncated 10 min data with CIF (Cp). The PS estimates from the Ca-25min method were used as reference standard values to assess the accuracy of the Ca-10min and Cp-10min methods in estimating the PS values. RESULTS: When compared to the reference method(Ca-25min), the Ca-10min and Cp-10min methods resulted in an overestimation of PS by 217 ± 241 % and 48.0 ± 30.2 %, respectively. The Bland Altman analysis showed that the mean difference from the reference was 8.85 ± 1.78 (x10-4 min-1) with the Ca-10min, while it was reduced to 1.63 ± 2.25 (x10-4 min-1) with the Cp-10min, resulting in an average reduction of 81%. The limits of agreement also reduced by up to 39.2% with the Cp-10min. We found a 75% increase of BBB permeability in the gray matter and a 35% increase in the white matter, when comparing the older group to the younger group. CONCLUSIONS: We demonstrated the feasibility of estimating the capillary-level input functions using a deep learning network. We also showed that this method can be used to estimate subtle age-related changes in BBB permeability with reduced scan time, without compromising accuracy. Moreover, the trained deep learning network can automatically select CIF, reducing the potential uncertainty resulting from manual user-intervention.

Intracellular Expression of CTB in Vibrio cholerae Strains in Laboratory Culture Conditions.

The introduction of the toxT-139F allele triggers the expression of TCP (toxin co-regulated pilus) and CT (cholera toxin) under simple laboratory culture conditions in most Vibrio cholerae strains. Such V. cholerae strains, especially strains that have been used in OCVs (oral cholera vaccines), can induce antibody responses against TCP in animal models. However, CT produced in these V. cholerae strains is secreted into the culture medium. In this study, V. cholerae strains that can express intracellular CTB under the control of the toxT-139F allele have been constructed for potential application in OCVs. First, we constructed a recombinant plasmid directly linking the ctxAB promoter to ctxB without ctxA and confirmed CTB expression from the plasmid in V. cholerae containing the toxT-139F allele. We constructed another recombinant plasmid to express NtrCTB, from which 14 internal amino acids-from the 7th to the 20th amino acid-of the leader peptide of CTB have been omitted, and we found that NtrCTB remained in the cells. Based on those results, we constructed V. cholerae strains in which chromosomal ctxAB is replaced by ntrctxB or ntrctxB-dimer. Both NtrCTB and NtrCTB-dimer remained in the bacterial cells, and 60% of the NtrCTB-dimer in the bacterial cells was maintained in a soluble form. To develop improved OCVs, these strains could be tested to see whether they induce immune responses against CTB in animal models.

Inactivated Vibrio cholerae Strains That Express TcpA via the toxT-139F Allele Induce Antibody Responses against TcpA.

Cholera remains a major global public health problem, for which oral cholera vaccines (OCVs) being a valuable strategy. Patients, who have recovered from cholera, develop antibody responses against LPS, cholera toxin (CT), toxin-coregulated pilus (TCP) major subunit A (TcpA) and other antigens; thus, these responses are potentially important contributors to immunity against Vibrio cholerae infection. However, assessments of the efficacy of current OCVs, especially inactivated OCVs, have focused primarily on O-antigen-specific antibody responses, suggesting that more sophisticated strategies are required for inactivated OCVs to induce immune responses against TCP, CT, and other antigens. Previously, we have shown that the toxT-139F allele enables V. cholerae strains to produce CT and TCP under simple laboratory culture conditions. Thus, we hypothesized that V. cholerae strains that express TCP via the toxT-139F allele induce TCP-specific antibody responses. As anticipated, V. cholerae strains that expressed TCP through the toxT-139F allele elicited antibody responses against TCP when the inactivated bacteria were delivered via a mouse model. We have further developed TCP-expressing V. cholerae strains that have been used in inactivated OCVs and shown that they effect an antibody response against TcpA in vivo, suggesting that V. cholerae strains with the toxT-139F allele are excellent candidates for cholera vaccines.

Estimation of the capillary level input function for dynamic contrast-enhanced MRI of the breast using a deep learning approach.

PURPOSE: To develop a deep learning approach to estimate the local capillary-level input function (CIF) for pharmacokinetic model analysis of DCE-MRI. METHODS: A deep convolutional network was trained with numerically simulated data to estimate the CIF. The trained network was tested using simulated lesion data and used to estimate voxel-wise CIF for pharmacokinetic model analysis of breast DCE-MRI data using an abbreviated protocol from women with malignant (n = 25) and benign (n = 28) lesions. The estimated parameters were used to build a logistic regression model to detect the malignancy. RESULT: The pharmacokinetic parameters estimated using the network-predicted CIF from our breast DCE data showed significant differences between the malignant and benign groups for all parameters. Testing the diagnostic performance with the estimated parameters, the conventional approach with arterial input function (AIF) showed an area under the curve (AUC) between 0.76 and 0.87, and the proposed approach with CIF demonstrated similar performance with an AUC between 0.79 and 0.81. CONCLUSION: This study shows the feasibility of estimating voxel-wise CIF using a deep neural network. The proposed approach could eliminate the need to measure AIF manually without compromising the diagnostic performance to detect the malignancy in the clinical setting.

Measurement of blood-brain barrier permeability using dynamic contrast-enhanced magnetic resonance imaging with reduced scan time.

PURPOSE: To investigate the feasibility of measuring the subtle disruption of blood-brain barrier (BBB) using DCE-MRI with a scan duration shorter than 10 min. METHODS: The extended Patlak-model (EPM) was introduced to include the effect of plasma flow (Fp ) in the estimation of vascular permeability-surface area product (PS). Numerical simulation studies were carried out to investigate how the reduction in scan time affects the accuracy in estimating contrast kinetic parameters. DCE-MRI studies of the rat brain were conducted with Fisher rats to confirm the results from the simulation. Intracranial F98 glioblastoma models were used to assess areas with different levels of permeability. In the normal brain tissues, the Patlak model (PM) and EPM were compared, whereas the 2-compartment-exchange-model (TCM) and EPM were assessed in the peri-tumor and the tumor regions. RESULTS: The simulation study results demonstrated that scan time reduction could lead to larger bias in PS estimated by PM (>2000%) than by EPM (<47%), especially when Fp is low. When Fp was high as in the gray matter, the bias in PM-PS (>900%) were larger than that in EPM-PS (<42%). The animal study also showed similar results, where the PM parameters were more sensitive to the scan duration than the EPM parameters. It was also demonstrated that, in the peri-tumor region, the EPM parameters showed less change by scan duration than the TCM parameters. CONCLUSION: The results of this study suggest that EPM can be used to measure PS with a scan duration of 10 min or less.