Spatiospectral image processing workflow considerations for advanced MR spectroscopy of the brain.

Magnetic resonance spectroscopy (MRS) is one of the few non-invasive imaging modalities capable of making neurochemical and metabolic measurements in vivo. Traditionally, the clinical utility of MRS has been narrow. The most common use has been the "single-voxel spectroscopy" variant to discern the presence of a lactate peak in the spectra in one location in the brain, typically to evaluate for ischemia in neonates. Thus, the reduction of rich spectral data to a binary variable has not classically necessitated much signal processing. However, scanners have become more powerful and MRS sequences more advanced, increasing data complexity and adding 2 to 3 spatial dimensions in addition to the spectral one. The result is a spatially- and spectrally-variant MRS image ripe for image processing innovation. Despite this potential, the logistics for robustly accessing and manipulating MRS data across different scanners, data formats, and software standards remain unclear. Thus, as research into MRS advances, there is a clear need to better characterize its image processing considerations to facilitate innovation from scientists and engineers. Building on established neuroimaging standards, we describe a framework for manipulating these images that generalizes to the voxel, spectral, and metabolite level across space and multiple imaging sites while integrating with LCModel, a widely used quantitative MRS peak-fitting platform. In doing so, we provide examples to demonstrate the advantages of such a workflow in relation to recent publications and with new data. Overall, we hope our characterizations will lower the barrier of entry to MRS processing for neuroimaging researchers.

Deep whole brain segmentation of 7T structural MRI.

7T magnetic resonance imaging (MRI) has the potential to drive our understanding of human brain function through new contrast and enhanced resolution. Whole brain segmentation is a key neuroimaging technique that allows for region-by-region analysis of the brain. Segmentation is also an important preliminary step that provides spatial and volumetric information for running other neuroimaging pipelines. Spatially localized atlas network tiles (SLANT) is a popular 3D convolutional neural network (CNN) tool that breaks the whole brain segmentation task into localized sub-tasks. Each sub-task involves a specific spatial location handled by an independent 3D convolutional network to provide high resolution whole brain segmentation results. SLANT has been widely used to generate whole brain segmentations from structural scans acquired on 3T MRI. However, the use of SLANT for whole brain segmentation from structural 7T MRI scans has not been successful due to the inhomogeneous image contrast usually seen across the brain in 7T MRI. For instance, we demonstrate the mean percent difference of SLANT label volumes between a 3T scan-rescan is approximately 1.73%, whereas its 3T-7T scan-rescan counterpart has higher differences around 15.13%. Our approach to address this problem is to register the whole brain segmentation performed on 3T MRI to 7T MRI and use this information to finetune SLANT for structural 7T MRI. With the finetuned SLANT pipeline, we observe a lower mean relative difference in the label volumes of ~8.43% acquired from structural 7T MRI data. Dice similarity coefficient between SLANT segmentation on the 3T MRI scan and the after finetuning SLANT segmentation on the 7T MRI increased from 0.79 to 0.83 with p<0.01. These results suggest finetuning of SLANT is a viable solution for improving whole brain segmentation on high resolution 7T structural imaging.

Examination of common and unique brain regions for atypical reading and math: a meta-analysis.

The purpose of this study is to identify consistencies across functional neuroimaging studies regarding common and unique brain regions/networks for individuals with reading difficulties (RD) and math difficulties (MD) compared to typically developing (TD) individuals. A systematic search of the literature, utilizing multiple databases, yielded 116 functional magnetic resonance imaging and positron emission tomography studies that met the criteria. Coordinates that directly compared TD with either RD or MD were entered into GingerALE (Brainmap.org). An activation likelihood estimate (ALE) meta-analysis was conducted to examine common and unique brain regions for RD and MD. Overall, more studies examined RD (n = 96) than MD (n = 20). Across studies, overactivation for reading and math occurred in the right insula and inferior frontal gyrus for atypically developing (AD) > TD comparisons, albeit in slightly different areas of these regions; however, inherent threshold variability across imaging studies could diminish overlying regions. For TD > AD comparisons, there were no similar or overlapping brain regions. Results indicate there were domain-specific differences for RD and MD; however, there were some similarities in the ancillary recruitment of executive functioning skills. Theoretical and practical implications for researchers and educators are discussed.

Using a semi-automated approach to quantify Unidentified Bright Objects in Neurofibromatosis type 1 and linkages to cognitive and academic outcomes.

Neurofibromatosis type 1 (NF1) is an autosomal dominant neurocutaneous syndrome that affects multiple organ systems resulting in widespread symptoms, including cognitive deficits. In addition to the criteria required for an NF1 diagnosis, approximately 70% of children with NF1 present with Unidentified Bright Objects (UBOs) or Focal Areas of Signal Intensity, which are hyperintense bright spots seen on T2-weighted magnetic resonance images and seen more prominently on FLAIR magnetic resonance images (Sabol et al., 2011). Current findings relating the presence/absence, quantities, sizes, and locations of these bright spots to cognitive abilities are mixed. To contribute to and hopefully disentangle some of these mixed findings, we explored potential relationships between metrics related to UBOs and cognitive abilities in a sample of 28 children and adolescents with NF1 (M=12.52 years; SD=3.18 years; 16 male). We used the Lesion Segmentation Tool (LST) to automatically detect and segment the UBOs. The LST was able to qualitatively and quantitatively reliably detect UBOs in images of children with NF1. Using these automatically detected and segmented lesions, we found that while controlling for age, biological sex, perceptual IQ, study, and scanner, "total UBO volume", defined as the sum of all the voxels representing all of the UBOs for each participant, helped explain differences in word reading, phonological awareness, and visuospatial skills. These findings contribute to the emerging NF1 literature and help parse the specific deficits that children with NF1 have, to then help improve the efficacy of reading interventions for children with NF1.

Ultra-high-resolution Mapping of Cortical Layers 3T-Guided 7T MRI.

7T MRI provides unprecedented resolution for examining human brain anatomy in vivo. For example, 7T MRI enables deep thickness measurement of laminar subdivisions in the right fusiform area. Existing laminar thickness measurement on 7T is labor intensive, and error prone since the visual inspection of the image is typically along one of the three orthogonal planes (axial, coronal, or sagittal view). To overcome this, we propose a new analytics tool that allows flexible quantification of cortical thickness on a 2D plane that is orthogonal to the cortical surface (beyond axial, coronal, and sagittal views) based on the 3D computational surface reconstruction. The proposed method further distinguishes high quality 2D planes and the low-quality ones by automatically inspecting the angles between the surface normals and slice direction. In our approach, we acquired a pair of 3T and 7T scans (same subject). We extracted the brain surfaces from the 3T scan using MaCRUISE and projected the surface to the 7T scan's space. After computing the angles between the surface normals and axial direction vector, we found that 18.58% of surface points were angled at more than 80° with the axial direction vector and had 2D axial planes with visually distinguishable cortical layers. 15.12% of the surface points with normal vectors angled at 30° or lesser with the axial direction, had poor 2D axial slices for visual inspection of the cortical layers. This effort promises to dramatically extend the area of cortex that can be quantified with ultra-high resolution in-plane imaging methods.

Cortical Morphology in Autism: Findings from a Cortical Shape-Adaptive Approach to Local Gyrification Indexing.

It has been challenging to elucidate the differences in brain structure that underlie behavioral features of autism. Prior studies have begun to identify patterns of changes in autism across multiple structural indices, including cortical thickness, local gyrification, and sulcal depth. However, common approaches to local gyrification indexing used in prior studies have been limited by low spatial resolution relative to functional brain topography. In this study, we analyze the aforementioned structural indices, utilizing a new method of local gyrification indexing that quantifies this index adaptively in relation to specific sulci/gyri, improving interpretation with respect to functional organization. Our sample included n = 115 autistic and n = 254 neurotypical participants aged 5-54, and we investigated structural patterns by group, age, and autism-related behaviors. Differing structural patterns by group emerged in many regions, with age moderating group differences particularly in frontal and limbic regions. There were also several regions, particularly in sensory areas, in which one or more of the structural indices of interest either positively or negatively covaried with autism-related behaviors. Given the advantages of this approach, future studies may benefit from its application in hypothesis-driven examinations of specific brain regions and/or longitudinal studies to assess brain development in autism.

The relationship between cognitive skills and reading comprehension of narrative and expository texts: A longitudinal study from Grade 1 to Grade 4.

Following the increased emphasis on expository text in early grades, this study examined narrative and expository reading comprehension growth in a sample of children who were followed longitudinally from grades 1 to 4, with the goals of explaining potential differences in children's overall performance and growth of narrative and expository text comprehension and identifying the cognitive factors that distinctly contribute to comprehension for each text type. We hypothesized that differences in reading comprehension growth of narrative and expository texts would be explained by various cognitive factors, specifically those related to executive functions (EF; e.g., working memory, planning/organization, shifting, and inhibition). At four annual time points, children (n= 94) read, retold (Recall), and answered questions (CompQ) about expository and narrative passages. Growth curve modeling was used to explore reading comprehension development across the two types of text. On average, results showed that children scored better on reading comprehension of narrative passages than they did on expository passages across all time points. After controlling for socioeconomic status (SES), vocabulary in 1st grade predicted 4th grade comprehension scores (Recall) for both narrative and expository passages, while word reading efficiency (WRE) in 1st grade predicted 4th grade comprehension scores (CompQ) for expository passages only. Additionally, WRE was associated with the growth of expository reading comprehension: children with higher WRE showed a faster growth rate for expository CompQ. The contribution of EF to text comprehension was largely confined to expository text, although planning and organization (measured using a direct cognitive assessment) in 1st grade also predicted 4th grade comprehension scores for narrative text Recall. For expository text comprehens ion, working memory, planning and organization, shifting, and inhibition (measured using a parent rating scale), predicted reading comprehension outcomes. Critically, 1st grade shifting and inhibition not only predicted 4th grade expository text comprehension (CompQ), but also modulated its growth rate: children with stronger shifting and inhibition had faster rates of growth. Together, these findings suggest that expository reading comprehension is (1) more difficult than narrative reading comprehension and (2) is associated with unique cognitive skills.

Fairy Tales versus Facts: Genre Matters to the Developing Brain.

Neurobiological studies of discourse comprehension have almost exclusively focused on narrative comprehension. However, successful engagement in modern society, particularly in educational settings, also requires comprehension with an aim to learn new information (i.e., "expository comprehension"). Despite its prevalence, no studies to date have neurobiologically characterized expository comprehension as compared with narrative. In the current study, we used functional magnetic resonance imaging in typically developing children to test whether different genres require specialized brain networks. In addition to expected activations in language and comprehension areas in the default mode network (DMN), expository comprehension required significantly greater activation in the frontoparietal control network (FPN) than narrative comprehension, and relied significantly less on posterior regions in the DMN. Functional connectivity analysis revealed that, compared with narrative, the FPN robustly correlated with the DMN, and this inter-network communication was higher with increased reading expertise. These findings suggest that, relative to narrative comprehension, expository comprehension shows (1) a unique configuration of the DMN, potentially to support non-social comprehension processes, and (2) increased utilization of top-down regions to help support goal-directed comprehension processes in the DMN. More generally, our findings reveal that different types of discourse-level comprehension place diverse neural demands on the developing brain.

Prefrontal mediation of the reading network predicts intervention response in dyslexia.

A primary challenge facing the development of interventions for dyslexia is identifying effective predictors of intervention response. While behavioral literature has identified core cognitive characteristics of response, the distinction of reading versus executive cognitive contributions to response profiles remains unclear, due in part to the difficulty of segregating these constructs using behavioral outputs. In the current study we used functional neuroimaging to piece apart the mechanisms of how/whether executive and reading network relationships are predictive of intervention response. We found that readers who are responsive to intervention have more typical pre-intervention functional interactions between executive and reading systems compared to nonresponsive readers. These findings suggest that intervention response in dyslexia is influenced not only by domain-specific reading regions, but also by contributions from intervening domain-general networks. Our results make a significant gain in identifying predictive bio-markers of outcomes in dyslexia, and have important implications for the development of personalized clinical interventions.

Teaching reading to children with neurofibromatosis type 1: a clinical trial with random assignment to different approaches.

AIM: Neurofibromatosis type 1 (NF1) is a genetic disorder with a cognitive profile that includes visual-spatial perception deficits and a high incidence of reading disability. There is a paucity of information about how this cognitively complex population responds to mainstream reading interventions. The clinical trial goals were to determine whether children and adolescents with NF1 and reading deficits (NF+RD) benefit from mainstream remedial reading programs and whether responsiveness varies with differences in program-related visual-spatial demands. METHOD: Forty-nine participants (28 males, 21 females; aged 8-14y) with either NF+RD (n=17, 11 males, six females) or idiopathic reading deficit (IRD) (n=32, 17 males, 15 females) were randomly assigned to intensive remedial teaching using one of two multisensory reading programs: one with greater kinesthetic demands and the other with greater visual-spatial demands. Two control groups - wait-list IRD (n=14, 11 males, three females) and typically developing readers (n=26, 13 males, 13 females) - received no treatment. Repeated measures and multivariate ANOVA analyses compared each group's growth in reading achievement from pre- to post-testing. RESULTS: Treated groups showed significant growth whereas untreated groups did not. Comparing treated groups, the IRD group responded equally well to both interventions, whereas the NF+RD group showed a better response to the more kinesthetic approach. INTERPRETATION: Results suggest that multisensory remedial reading teaching that emphasizes kinesthetic demands more than visual-spatial demands is suitable for students with NF+RD.

Neuroimaging of reading intervention: a systematic review and activation likelihood estimate meta-analysis.

A growing number of studies examine instructional training and brain activity. The purpose of this paper is to review the literature regarding neuroimaging of reading intervention, with a particular focus on reading difficulties (RD). To locate relevant studies, searches of peer-reviewed literature were conducted using electronic databases to search for studies from the imaging modalities of fMRI and MEG (including MSI) that explored reading intervention. Of the 96 identified studies, 22 met the inclusion criteria for descriptive analysis. A subset of these (8 fMRI experiments with post-intervention data) was subjected to activation likelihood estimate (ALE) meta-analysis to investigate differences in functional activation following reading intervention. Findings from the literature review suggest differences in functional activation of numerous brain regions associated with reading intervention, including bilateral inferior frontal, superior temporal, middle temporal, middle frontal, superior frontal, and postcentral gyri, as well as bilateral occipital cortex, inferior parietal lobules, thalami, and insulae. Findings from the meta-analysis indicate change in functional activation following reading intervention in the left thalamus, right insula/inferior frontal, left inferior frontal, right posterior cingulate, and left middle occipital gyri. Though these findings should be interpreted with caution due to the small number of studies and the disparate methodologies used, this paper is an effort to synthesize across studies and to guide future exploration of neuroimaging and reading intervention.

Accelerating chronically unresponsive children to tier 3 instruction: what level of data is necessary to ensure selection accuracy?

Response-to-intervention (RTI) approaches to disability identification are meant to put an end to the so-called wait-to-fail requirement associated with IQ discrepancy. However, in an unfortunate irony, there is a group of children who wait to fail in RTI frameworks. That is, they must fail both general classroom instruction (Tier 1) and small-group intervention (Tier 2) before becoming eligible for the most intensive intervention (Tier 3). The purpose of this article was to determine how to predict accurately which at-risk children will be unresponsive to Tiers 1 and 2, thereby allowing unresponsive children to move directly from Tier 1 to Tier 3. As part of an efficacy study of a multitier RTI approach to prevention and identification of reading disabilities (RD), 129 first-grade children who were unresponsive to classroom reading instruction were randomly assigned to 14 weeks of small-group, Tier 2 intervention. Nonresponders to this instruction (n = 33) were identified using local norms on first-grade word identification fluency growth linked to a distal outcome of RD at the end of second grade. Logistic regression models were used to predict membership in responder and nonresponder groups. Predictors were entered as blocks of data from least to most difficult to obtain: universal screening data, Tier 1 response data, norm referenced tests, and Tier 2 response data. Tier 2 response data were not necessary to classify students as responders and nonresponders to Tier 2 instruction, suggesting that some children can be accurately identified as eligible for Tier 3 intervention using only Tier 1 data, thereby avoiding prolonged periods of failure to instruction.

Functional correlates of children's responsiveness to intervention.

Functional imaging research has yielded evidence of changes in poor readers after instructional intervention. Although it is well established that within the group of children with poor reading there are differences in behavioral response to intervention, little is know about the functional correlates of responsiveness. Therefore, we acquired functional magnetic resonance imaging (MRI) data from children identified as "at risk for reading disability" who responded differently to a reading intervention (5 responders; 5 nonresponders; 4 controls). Groups differed in activation level of the left hemisphere posterior superior temporal and the middle temporal gyri, suggesting that future imaging studies should consider responders and nonresponders separately.

Selecting At-Risk First-Grade Readers for Early Intervention: Eliminating False Positives and Exploring the Promise of a Two-Stage Gated Screening Process.

The purposes of this study were (a) to identify measures that when added to a base 1(st)-grade screening battery help eliminate false positives and (b) to investigate gains in efficiency associated with a 2-stage gated screening procedure. We tested 355 children in the fall of 1(st) grade, and assessed for reading difficulty at the end of 2(nd) grade. The base screening model, included measures of phonemic awareness, rapid naming skill, oral vocabulary, and initial word identification fluency (WIF). Short-term WIF progress monitoring (intercept and slope), dynamic assessment, running records, and oral reading fluency were each considered as an additional screening measure in contrasting models. Results indicated that the addition of WIF progress monitoring and dynamic assessment, but not running records or oral reading fluency, significantly decreased false positives. The 2-stage gated screening process using phonemic decoding efficiency in the first stage significantly reduced the number of children requiring the full screening battery.

Curcumin, a Curcuma longa constituent, acts on MAPK p38 pathway modulating COX-2 and iNOS expression in chronic experimental colitis.

Ulcerative colitis (UC) is a nonspecific inflammatory disorder characterized by oxidative and nitrosative stress, leucocyte infiltration and up-regulation of pro-inflammatory cytokines. Mitogen-activated protein kinases (MAPKs), such as the p38 and the c-Jun N-terminal kinase (JNK) modulate the transcription of many genes involved in the inflammatory process. Curcumin is a polyphenol derived from Curcuma longa, which is known to have anti-inflammatory activity. The aim of this study was to study the effects and mechanisms of action of curcumin, on chronic colitis in rats. Inflammation response was assessed by histology and myeloperoxidase activity (MPO). We determined the production of Th1 and Th2 cytokines and nitrites in colon mucosa, as well as the expression of inducible nitric oxide synthase (iNOS), cyclo-oxygenase(COX)-1 and-2 by western blotting and inmmunohistochemistry. Finally, we studied the involvement of MAPKs signaling in the protective effect of curcumin in chronic colonic inflammation. Curcumin (50-100 mg/kg/day) were administered by oral gavage 24 h after trinitrobenzensulfonic acid (TNBS) instillation, and daily during 2 weeks before sacrifice. Curcumin significantly attenuated the damage and caused substantial reductions of the rise in MPO activity and tumour necrosis factor alpha (TNF)-alpha. Also curcumine was able to reduce nitrites colonic levels and induced down-regulation of COX-2 and iNOS expression, and a reduction in the activation of p38 MAPK; however, no changes in the activation of JNK could be observed. In conclusion, we suggest that inhibition of p38 MAPK signaling by curcumin could explain the reduced COX-2 and iNOS immunosignals and the nitrite production in colonic mucosa reducing the development of chronic experimental colitis.

Constitutively active K-cyclin/cdk6 kinase in Kaposi sarcoma-associated herpesvirus-infected cells.

BACKGROUND: Kaposi sarcoma-associated human herpesvirus (KSHV) encodes K-cyclin, a homologue of D-type cellular cyclins, which binds cyclin-dependent kinases to phosphorylate various substrates. K-cyclin/cdk phosphorylates a subset of substrates normally targeted by cyclins D, E, and A. We used cells naturally infected with KSHV to further characterize the biochemical features of K-cyclin. METHODS: We used immunoprecipitation with K-cyclin antibodies to examine the association of K-cyclin with cdk2, cdk6, p21Cip1, and p27Kip1 proteins in BC3 cells. We separated populations of BC3 cells enriched in cells in G1, S, or G2/M phases by elutriation and measured K-cyclin protein and the kinase activity of K-cyclin/cdk6 complexes. The half-life of K-cyclin and cyclin D2 proteins was determined by blocking protein synthesis with cycloheximide and measuring proteins in cell lysates by western blot analysis. We fused the entire K-cyclin sequence to the carboxyl-terminal sequence of cellular cyclin D that contains the PEST degradation sequence to produce K-cyclin/D2 and transfected K-cyclin/D2 into K-cyclin-negative cells to investigate the effect of the PEST sequence on K-cyclin's stability. RESULTS: Viral K-cyclin interacted with cyclin-dependent kinases cdk2, cdk4, and cdk6 and with the cyclin/cdk inhibitory proteins p21Cip1 and p27Kip1 in BC3 cell lysates. Unlike D-type cyclins, whose expression is cell cycle dependent, the level of K-cyclin was stable throughout the cell cycle, and the kinase associated with the K-cyclin/cdk6 complex was constitutively active. The half-life of K-cyclin (6.9 hours) was much longer than that of cellular cyclin D2 (0.6 hour) and that of K-cyclin/D2 (0.5 hour), probably because K-cyclin lacks the PEST degradation sequence present in D-type cyclins. CONCLUSION: The constitutive activation of K-cyclin/cdk complexes in KSHV-infected cells appears to result from the extended half-life of K-cyclin and may explain its role in Kaposi sarcoma.