PyDesigner v1.0: A Pythonic Implementation of the DESIGNER Pipeline for Diffusion Magnetic Resonance Imaging.

PyDesigner is a Python-based software package based on the original Diffusion parameter EStImation with Gibbs and NoisE Removal (DESIGNER) pipeline (Dv1) for dMRI preprocessing and tensor estimation. This software is openly provided for non-commercial research and may not be used for clinical care. PyDesigner combines tools from FSL and MRtrix3 to perform denoising, Gibbs ringing correction, eddy current motion correction, brain masking, image smoothing, and Rician bias correction to optimize the estimation of multiple diffusion measures. It can be used across platforms on Windows, Mac, and Linux to accurately derive commonly used metrics from DKI, DTI, WMTI, FBI, and FBWM datasets as well as tractography ODFs and .fib files. It is also file-format agnostic, accepting inputs in the form of .nii, .nii.gz, .mif, and dicom format. User-friendly and easy to install, this software also outputs quality control metrics illustrating signal-to-noise ratio graphs, outlier voxels, and head motion to evaluate data integrity. Additionally, this dMRI processing pipeline supports multiple echo-time dataset processing and features pipeline customization, allowing the user to specify which processes are employed and which outputs are produced to meet a variety of user needs.

Comparison of three magnetic resonance imaging measures of brain iron in healthy and cocaine use disorder participants.

Several magnetic resonance imaging (MRI) measures for quantifying endogenous nonheme brain iron have been proposed. These correspond to distinct physical properties with varying sensitivities and specificities to iron. Moreover, they may depend not only on tissue iron concentration, but also on the intravoxel spatial pattern of iron deposition, which is complex in many brain regions. Here, the three MRI brain iron measures of R 2 * , magnetic field correlation (MFC), and magnetic susceptibility are compared in several deep gray matter regions for both healthy participants (HPs) and individuals with cocaine use disorder (CUD). Their concordance is assessed from their correlations with each other and their relative dependencies on age. In addition, associations between the iron measures and microstructure in adjacent white matter regions are investigated by calculating their correlations with diffusion MRI measures from the internal capsule, and associations with cognition are determined by using results from a battery of standardized tests relevant to CUD. It is found that all three iron measures are strongly correlated with each other for the considered gray matter regions, but with correlation coefficients substantially less than one indicating important differences. The age dependencies of all three measures are qualitatively similar in most regions, except for the red nucleus, where the susceptibility has a significantly stronger correlation with age than R 2 * . Weak to moderate correlations are seen for the iron measures with several of the diffusion and cognitive measures, with the strongest correlations being obtained for R 2 * . The iron measures differ little between the HP and CUD groups, although susceptibility is significantly lower in the red nucleus for the CUD group. For the comparisons made, the iron measures behave similarly in most respects, but with notable quantitative differences. It is suggested that these differences may be, in part, attributable to a higher sensitivity to the spatial pattern of iron deposition for R 2 * and MFC than for susceptibility. This is supported most strongly by a sharp contrast between the values of the iron measures in the globus pallidus relative to those in the red nucleus. The observed correlations of the iron measures with diffusion and cognitive scores point to possible connections between gray matter iron, white matter microstructure, and cognition.

A digital assay for programmed death-ligand 1 (22C3) quantification combined with immune cell recognition algorithms in non-small cell lung cancer.

PD-L1 (22C3) checkpoint inhibitor therapy represents a mainstay of modern cancer immunotherapy for non-small cell lung cancer (NSCLC). In vitro diagnostic (IVD) PD-L1 antibody staining is widely used to predict clinical intervention efficacy. However, pathologist interpretation of this assay is cumbersome and variable, resulting in poor positive predictive value concerning patient therapy response. To address this, we developed a digital assay (DA) termed Tissue Insight (TI) 22C3 NSCLC, for the quantification of PD-L1 in NSCLC tissues, including digital recognition of macrophages and lymphocytes. We completed clinical validation of this digital image analysis solution in 66 NSCLC patient samples, followed by concordance studies (comparison of PD-L1 manual and digital scores) in an additional 99 patient samples. We then combined this DA with three distinct immune cell recognition algorithms for detecting tissue macrophages, alveolar macrophages, and lymphocytes to aid in sample interpretation. Our PD-L1 (22C3) DA was successfully validated and had a scoring agreement (digital to manual) higher than the inter-pathologist scoring. Furthermore, the number of algorithm-identified immune cells showed significant correlation when compared with those identified by immunohistochemistry in serial sections stained by double immunofluorescence. Here, we demonstrated that TI 22C3 NSCLC DA yields comparable results to pathologist interpretation while eliminating the intra- and inter-pathologist variability associated with manual scoring while providing characterization of the immune microenvironment, which can aid in clinical treatment decisions.

Validation of a DKK1 RNAscope chromogenic in situ hybridization assay for gastric and gastroesophageal junction adenocarcinoma tumors.

Dickkopf-1 (DKK1) is a secreted modulator of Wnt signaling that is frequently overexpressed in tumors and associated with poor clinical outcomes. DKN-01 is a humanized monoclonal therapeutic antibody that binds DKK1 with high affinity and has demonstrated clinical activity in gastric/gastroesophageal junction (G/GEJ) patients with elevated tumoral expression of DKK1. Here we report on the validation of a DKK1 RNAscope chromogenic in situ hybridization assay to assess DKK1 expression in G/GEJ tumor tissue. To reduce pathologist time, potential pathologist variability from manual scoring and support pathologist decision making, a digital image analysis algorithm that identifies tumor cells and quantifies the DKK1 signal was developed. Following CLIA guidelines the DKK1 RNAscope chromogenic in situ hybridization assay and digital image analysis algorithm were successfully validated for sensitivity, specificity, accuracy, and precision. The DKK1 RNAscope assay in conjunction with the digital image analysis solution is acceptable for prospective screening of G/GEJ adenocarcinoma patients. The work described here will further advance the companion diagnostic development of our DKK1 RNAscope assay and could generally be used as a guide for the validation of RNAscope assays with digital image quantification.

Brain iron levels in attention-deficit/hyperactivity disorder normalize as a function of psychostimulant treatment duration.

Brain iron homeostasis is a dopamine-related mechanism that may be modified with long-term psychostimulant treatment in attention-deficit/hyperactivity disorder (ADHD). We previously reported that while medication-naïve youth with ADHD have reduced brain iron compared to controls and psychostimulant-medicated patients, no differences were detected between the latter groups. In this follow-up study, we examined whether the duration of psychostimulant treatment correlates with the degree of iron normalization. Brain iron was indexed with MRI using an advanced method called magnetic field correlation (MFC) imaging and the conventional R2* proton transverse relaxation rate method. MFC was acquired in 30 psychostimulant-medicated youth with comorbid-free ADHD and 29 age-matched controls (all males). R2* was acquired in a subset of these individuals. Region-of-interest analyses for MFC and R2* group differences and within-group correlations with age and years of psychostimulant treatment were conducted in the globus pallidus (GP), putamen (PUT), caudate nucleus (CN), thalamus (THL) and red nucleus. No significant MFC and R2* group differences were detected. However, while all regional MFC and R2* significantly increased with age in the control group, MFC and R2* increased in the GP, PUT, CN and THL with psychostimulant treatment duration in the ADHD group to a greater degree than with age. Our findings suggest that while youth with ADHD may have less prominent age-related brain iron increases than that seen in typical development, long-term use of psychostimulant medications may compensate through a normalizing effect on basal ganglia iron. Longitudinal studies following ADHD patients before and after long-term psychostimulant treatment are needed to confirm these findings.

Elevated Brain Iron in Cocaine Use Disorder as Indexed by Magnetic Field Correlation Imaging.

BACKGROUND: Iron homeostasis is a critical biological process that may be disrupted in cocaine use disorder (CUD). In the brain, iron is required for neural processes involved in addiction and can be lethal to cells if unbound, especially in excess. Moreover, recent studies have implicated elevated brain iron in conditions of prolonged psychostimulant exposure. Thus, the purpose of this study was to examine iron in basal ganglia reward regions of individuals with CUD using an advanced imaging method called magnetic field correlation (MFC) imaging. METHODS: MFC imaging was acquired in 19 non-treatment-seeking individuals with CUD and 19 healthy control individuals (both male and female). Region-of-interest analyses for MFC group differences and within-group correlations with age and years of cocaine use were conducted in the globus pallidus internal segment (GPi), globus pallidus external segment, putamen, caudate nucleus, thalamus, and red nucleus. RESULTS: Individuals with CUD had significantly elevated MFC compared with control individuals within the GPi. In control individuals, MFC significantly increased with age in the GPi, globus pallidus external segment, putamen, and caudate nucleus. Conversely, there were no significant MFC within-group correlations in the CUD group. CONCLUSIONS: Individuals with CUD have excess iron in the GPi, as indexed by MFC, and lack the age-related gradual iron deposition seen in normal aging. Because the globus pallidus is critical for the transition of goal-directed behavior to compulsive behavior, significantly elevated iron in the GPi may contribute to the persistence of CUD. These findings implicate dysregulation of brain iron homeostasis in CUD and support pursuing this new line of research.

Revealing the Structural Neural Circuitry of Attention Deficit Hyperactivity Disorder With Diffusion MRI: Implications for Future Diagnosis and Treatment.

OBJECTIVE: Rates of attention deficit hyperactivity disorder (ADHD) diagnosis and psychostimulant prescriptions continue to rise, yet there are no clear diagnostic tests or biomarkers for the disorder. The purpose of this article is to highlight the role of diffusion MRI in bolstering a neurobiologic conceptualization of ADHD and how this holds promise for optimizing future diagnosis. CONCLUSION: Diffusion MRI is a powerful neuroimaging tool for noninvasive assessment of the structural neural circuitry underlying brain function and behavior. Though the modality is still in its infancy, diffusion MRI studies are showing neural network disruption in ADHD consistent with findings from other imaging modalities. Given the mounting evidence of brain-behavior correlates in ADHD, it is likely that imaging-based biomarkers will one day be incorporated into clinical diagnosis and treatment evaluation. Until then, diffusion MRI findings serve to validate ADHD as a brain-based disorder with immediate public health implications for individuals with ADHD.

Neuroimaging the neural correlates of increased risk for substance use disorders in attention-deficit/hyperactivity disorder-A systematic review.

BACKGROUND/OBJECTIVES: Children with attention-deficit/hyperactivity disorder (ADHD) are nearly three times more likely to develop substance use disorders (SUD) than their typically developing peers. Our objective was to review the existing neuroimaging research on high-risk ADHD (ie, ADHD with disruptive behavior disorders, familial SUD and/or early substance use), focusing on impulsivity as one possible mechanism underlying SUD risk. METHODS: A PubMed literature search was conducted using combinations of the keywords "ADHD," "substance use," "substance use disorder," "SUD," "addiction," "dependence," "abuse," "risk," "brain" "MRI," "imaging" and "neuroimaging." Studies had to include cohorts that met diagnostic criteria for ADHD; studies of individuals with ADHD who all met criteria for SUD were excluded. Eight studies met the search criteria. RESULTS: Individuals with high-risk ADHD have hyperactivation in the motivation-reward processing brain network during tasks of impulsive choice, emotion processing, and risky decision-making. During response inhibition tasks, they have hypoactivation in the inhibitory control brain network. However, studies focusing on this latter circuit found hypoactivation during inhibitory control tasks, decreased white matter microstructure coherence and reduced cortical thickness in ADHD independent of substance use history. DISCUSSION/CONCLUSIONS: An exaggerated imbalance between the inhibitory control network and the motivation-reward processing network is theorized to distinguish individuals with high-risk ADHD. Preliminary findings suggest that an exaggerated aberrant reward processing network may be the driving neural correlate of increased SUD risk in ADHD. SCIENTIFIC SIGNIFICANCE: Neural biomarkers of increased SUD risk in ADHD could help clinicians identify which patients may benefit most from SUD prevention. Thus, more neuroimaging research on this vulnerable population is needed. (Am J Addict 2017;26:99-111).

Alcohol use during a trial of N-acetylcysteine for adolescent marijuana cessation.

AIMS: Current adolescent alcohol treatments have modest effects and high relapse rates. Evaluation of novel pharmacotherapy treatment is warranted. N-acetylcysteine (NAC), an over-the-counter antioxidant supplement with glutamatergic properties, is a promising treatment for marijuana cessation in adolescents; however, its effects on adolescent drinking have not been examined. To that end, this secondary analysis evaluated: (1) the effect of NAC vs. placebo on alcohol use over an eight-week adolescent marijuana cessation trial and (2) the role of marijuana cessation and reduction on subsequent alcohol use. METHODS: Marijuana-dependent adolescents (ages 15-21; N=116) interested in treatment were randomized to NAC 1200mg or matched placebo twice daily for eightweeks. Participants were not required to be alcohol users or interested in alcohol cessation to qualify. RESULTS: There were no demographic or baseline alcohol use differences between participants randomized to NAC vs. placebo (ps>0.05). Of the 89 participants returning for ≥one visit following randomization, 77 reported ≥one alcoholic drink in the 30days prior to study entry and averaged 1.3 (SD=1.4) binge drinking days per week. During treatment, less marijuana use (measured via urine cannabinoid levels) was associated with less alcohol use in the NAC-treated group but not in the placebo-treated group (p=0.016). CONCLUSIONS: There was no evidence of compensatory alcohol use during marijuana treatment. In fact, in the NAC group, lower levels of marijuana use were associated with less alcohol use, suggesting NAC effects may generalize to other substances and could be useful in decreasing adolescent alcohol use. NAC trials specifically focused on alcohol-using adolescents are warranted.

One diffusion acquisition and different white matter models: how does microstructure change in human early development based on WMTI and NODDI?

White matter microstructural changes during the first three years of healthy brain development are characterized using two different models developed for limited clinical diffusion data: White Matter Tract Integrity (WMTI) metrics from Diffusional Kurtosis Imaging (DKI) and Neurite Orientation Dispersion and Density Imaging (NODDI). Both models reveal a non-linear increase in intra-axonal water fraction and in tortuosity of the extra-axonal space as a function of age, in the genu and splenium of the corpus callosum and the posterior limb of the internal capsule. The changes are consistent with expected behavior related to myelination and asynchrony of fiber development. The intra- and extracellular axial diffusivities as estimated with WMTI do not change appreciably in normal brain development. The quantitative differences in parameter estimates between models are examined and explained in the light of each model's assumptions and consequent biases, as highlighted in simulations. Finally, we discuss the feasibility of a model with fewer assumptions.

Multimodal MR imaging of brain iron in attention deficit hyperactivity disorder: a noninvasive biomarker that responds to psychostimulant treatment?

PURPOSE: To comprehensively assess brain iron levels in typically developing control subjects and patients with attention deficit hyperactivity disorder (ADHD) when psychostimulant medication history is accounted for. MATERIALS AND METHODS: This prospective study was approved by the institutional review board, and informed consent was obtained. Brain iron was indexed noninvasively by using magnetic resonance (MR) imaging relaxation rates (R2, R2*, R2') and magnetic field correlation (MFC) in the globus pallidus, putamen, caudate nucleus, and thalamus for 22 patients with ADHD (12 medication-naïve patients and 10 with a history of psychostimulant treatment) and 27 control subjects (age range, 8-18 years). Serum iron measures were also collected. Subgroup differences were analyzed with data-appropriate omnibus tests followed by post hoc pairwise comparisons; false discovery rate correction was conducted to control for multiple comparisons. RESULTS: Medication-naïve ADHD patients had significantly lower striatal and thalamic MFC indexes of brain iron than did control subjects (putamen, P = .012; caudate nucleus, P = .008; thalamus, P = .012) and psychostimulant-medicated ADHD patients (putamen, P = .006; caudate nucleus, P = .010; thalamus, P = .021). Conversely, the MFC indexes in medicated patients were comparable to those in control subjects. No significant differences were detected with R2, R2*, R2', or serum measures. CONCLUSION: Lower MFC indexes of striatal and thalamic brain iron in medication-naïve ADHD patients and lack of differences in psychostimulant-medicated patients suggest that MFC indexes of brain iron may represent a noninvasive diagnostic biomarker that responds to psychostimulant treatment.

Attention-deficit/hyperactivity disorder without comorbidity is associated with distinct atypical patterns of cerebral microstructural development.

Differential core symptoms and treatment responses are associated with the pure versus comorbid forms of attention-deficit/hyperactivity disorder (ADHD). However, comorbidity has largely been unaccounted for in neuroimaging studies of ADHD. We used diffusional kurtosis imaging to investigate gray matter (GM) and white matter (WM) microstructure of children and adolescents with ADHD (n = 22) compared to typically developing controls (TDC, n = 27) and examined whether differing developmental patterns are related to comorbidity. The ADHD group (ADHD-mixed) consisted of subgroups with and without comorbidity (ADHD-comorbid, n = 11; ADHD-pure, n = 11, respectively). Age-related changes and group differences in cerebral microstructure of the ADHD-mixed group and each ADHD subgroup were compared to TDC. Whole-brain voxel-based analyses with mean kurtosis (MK) and mean diffusivity (MD) metrics were conducted to probe GM and WM. Tract-based spatial statistics analyses of WM were performed with MK, MD, fractional anisotropy, and directional (axial, radial) kurtosis and diffusivity metrics. ADHD-pure patients lacked significant age-related changes in GM and WM microstructure that were observed globally in TDC and had significantly greater WM microstructural complexity than TDC in bilateral frontal and parietal lobes, insula, corpus callosum, and right external and internal capsules. Including ADHD patients with diverse comorbidities in analyses masked these findings. A distinct atypical age-related trajectory and aberrant regional differences in brain microstructure were detected in ADHD without comorbidity. Our results suggest that different phenotypic manifestations of ADHD, defined by the presence or absence of comorbidity, differ in cerebral microstructural markers.

In vivo assessment of age-related brain iron differences by magnetic field correlation imaging.

PURPOSE: To assess a recently developed magnetic resonance imaging (MRI) technique called magnetic field correlation (MFC) imaging along with a conventional imaging method, the transverse relaxation rate (R2), for estimating age-related brain iron concentration in adolescents and adults. Brain region measures were compared with nonheme iron concentrations (C(PM) ) based on a prior postmortem study. MATERIALS AND METHODS: Asymmetric spin echo (ASE) images were acquired at 3T from 26 healthy individuals (16 adolescents, 10 adults). Regions of interest (ROIs) were placed in areas in which age-related iron content was estimated postmortem: globus pallidus (GP), putamen (PUT), caudate nucleus (CN), thalamus (THL), and frontal white matter (FWM). Regression and group analyses were conducted on ROI means. RESULTS: MFC and R2 displayed significant linear relationships to C(PM) when all regions were combined. Whereas MFC was significantly correlated with C(PM) for every individual region except FWM and detected significantly lower means in adolescents than adults for each region, R2 detected significant correlation and lower means for only PUT and CN. CONCLUSION: Our results support the hypothesis that MFC is sensitive to brain iron in GM regions and detects age-related iron increases known to occur from adolescence to adulthood. MFC may be more sensitive than R2 to iron-related changes occurring within specific brain regions.

Preliminary evidence of altered gray and white matter microstructural development in the frontal lobe of adolescents with attention-deficit hyperactivity disorder: a diffusional kurtosis imaging study.

PURPOSE: To investigate non-Gaussian water diffusion using diffusional kurtosis imaging (DKI) to assess age effects on gray matter (GM) and white matter (WM) microstructural changes in the prefrontal cortex (PFC) of adolescents with attention-deficit hyperactivity disorder (ADHD) compared to typically developing controls (TDC). MATERIALS AND METHODS: In this preliminary cross-sectional study, T1-weighted magnetization-prepared rapid gradient echo (MPRAGE) and DKI images were acquired at 3T from TDC (n = 13) and adolescents with ADHD (n = 12). Regression analysis of the PFC region of interest (ROI) was conducted. RESULTS: TDC show a significant kurtosis increase of WM microstructural complexity from 12 to 18 years of age, particularly in the radial direction, whereas WM microstructure in ADHD is stagnant in both the axial and radial directions. In ADHD, GM microstructure also lacked a significant age-related increase in complexity as seen in TDC; only kurtosis measures were able to detect this difference. CONCLUSION: These findings support the prevailing theory that ADHD is a disorder affecting frontostriatal WM. Our study is the first to directly quantify an aberrant age-related trajectory in ADHD within GM microstructure, suggesting that the assessment of non-Gaussian directional diffusion using DKI provides more sensitive and complementary information about tissue microstructural changes than conventional diffusion imaging methods.

Construction of a 3D probabilistic atlas of human cortical structures.

We describe the construction of a digital brain atlas composed of data from manually delineated MRI data. A total of 56 structures were labeled in MRI of 40 healthy, normal volunteers. This labeling was performed according to a set of protocols developed for this project. Pairs of raters were assigned to each structure and trained on the protocol for that structure. Each rater pair was tested for concordance on 6 of the 40 brains; once they had achieved reliability standards, they divided the task of delineating the remaining 34 brains. The data were then spatially normalized to well-known templates using 3 popular algorithms: AIR5.2.5's nonlinear warp (Woods et al., 1998) paired with the ICBM452 Warp 5 atlas (Rex et al., 2003), FSL's FLIRT (Smith et al., 2004) was paired with its own template, a skull-stripped version of the ICBM152 T1 average; and SPM5's unified segmentation method (Ashburner and Friston, 2005) was paired with its canonical brain, the whole head ICBM152 T1 average. We thus produced 3 variants of our atlas, where each was constructed from 40 representative samples of a data processing stream that one might use for analysis. For each normalization algorithm, the individual structure delineations were then resampled according to the computed transformations. We next computed averages at each voxel location to estimate the probability of that voxel belonging to each of the 56 structures. Each version of the atlas contains, for every voxel, probability densities for each region, thus providing a resource for automated probabilistic labeling of external data types registered into standard spaces; we also computed average intensity images and tissue density maps based on the three methods and target spaces. These atlases will serve as a resource for diverse applications including meta-analysis of functional and structural imaging data and other bioinformatics applications where display of arbitrary labels in probabilistically defined anatomic space will facilitate both knowledge-based development and visualization of findings from multiple disciplines.