Fast and robust quantification of uncertainty in non-linear diffusion MRI models.

Diffusion MRI (dMRI) allows for non-invasive investigation of brain tissue microstructure. By fitting a model to the dMRI signal, various quantitative measures can be derived from the data, such as fractional anisotropy, neurite density and axonal radii maps. We investigate the Fisher Information Matrix (FIM) and uncertainty propagation as a generally applicable method for quantifying the parameter uncertainties in linear and non-linear diffusion MRI models. In direct comparison with Markov Chain Monte Carlo (MCMC) sampling, the FIM produces similar uncertainty estimates at much lower computational cost. Using acquired and simulated data, we then list several characteristics that influence the parameter variances, including data complexity and signal-to-noise ratio. For practical purposes we investigate a possible use of uncertainty estimates in decreasing intra-group variance in group statistics by uncertainty-weighted group estimates. This has potential use cases for detection and suppression of imaging artifacts.

Ultra-high resolution and multi-shell diffusion MRI of intact ex vivo human brains using kT-dSTEAM at 9.4T.

Diffusion MRI (dMRI) in ex vivo human brain specimens is an important research tool for neuroanatomical investigations and the validation of dMRI techniques. Many ex vivo dMRI applications have benefited from very high dMRI resolutions achievable on small-bore preclinical or animal MRI scanners for small tissue samples. However, the investigation of entire human brains post mortem provides the important context of entire white matter (WM) network systems and entire gray matter (GM) areas connected through these systems. The investigation of intact ex vivo human brains in large bore systems creates challenges due to the limited gradient performance and transmit radio-frequency (B1+) inhomogeneities, specially at ultra-high field (UHF, 7T and higher). To overcome these issues, it is necessary to tailor ex vivo diffusion-weighted sequences specifically for high resolution and high diffusion-weighting. Here, we present kT-dSTEAM, which achieves B1+ homogenization across whole human brain specimens using parallel transmit (pTx) on a 9.4T MR system. We use kT-dSTEAM to obtain multi-shell high b-value and high resolution diffusion-weighted data in ex vivo whole human brains. Isotropic whole brain data can be acquired at high b-value (6000-8000 s/mm2) at high resolution (1000 µm) and at moderate b-value (3000 s/mm2) at ultra-high isotropic resolution (400 µm). As an illustration of the advantages of the ultra-high resolution, tractography across the WM/GM border shows less of the unwanted gyral crown bias, and more high-curvature paths connecting the sulcal wall than at lower resolution. The kT-dSTEAM also allows for acquisition of T1 and T2 weighted images suitable for estimating quantitative T1 and T2 maps. Finally, multi-shell analysis of kT-dSTEAM data at variable mixing time (TM) is shown as an approach for ex vivo data analysis which is adapted to the strengths of STEAM diffusion-weighting. Here, we use this gain for multi-orientation modelling and crossing-fiber tractography. We show that multi-shell data allows superior multiple orientation tractography of known crossing fiber structures in the brain stem.

High resolution anatomical and quantitative MRI of the entire human occipital lobe ex vivo at 9.4T.

Several magnetic resonance imaging (MRI) contrasts are sensitive to myelin content in gray matter in vivo which has ignited ambitions of MRI-based in vivo cortical histology. Ultra-high field (UHF) MRI, at fields of 7T and beyond, is crucial to provide the resolution and contrast needed to sample contrasts over the depth of the cortex and get closer to layer resolved imaging. Ex vivo MRI of human post mortem samples is an important stepping stone to investigate MRI contrast in the cortex, validate it against histology techniques applied in situ to the same tissue, and investigate the resolutions needed to translate ex vivo findings to in vivo UHF MRI. Here, we investigate key technology to extend such UHF studies to large human brain samples while maintaining high resolution, which allows investigation of the layered architecture of several cortical areas over their entire 3D extent and their complete borders where architecture changes. A 16 channel cylindrical phased array radiofrequency (RF) receive coil was constructed to image a large post mortem occipital lobe sample (~80×80×80mm3) in a wide-bore 9.4T human scanner with the aim of achieving high-resolution anatomical and quantitative MR images. Compared with a human head coil at 9.4T, the maximum Signal-to-Noise ratio (SNR) was increased by a factor of about five in the peripheral cortex. Although the transmit profile with a circularly polarized transmit mode at 9.4T is relatively inhomogeneous over the large sample, this challenge was successfully resolved with parallel transmit using the kT-points method. Using this setup, we achieved 60µm anatomical images for the entire occipital lobe showing increased spatial definition of cortical details compared to lower resolutions. In addition, we were able to achieve sufficient control over SNR, B0 and B1 homogeneity and multi-contrast sampling to perform quantitative T2* mapping over the same volume at 200µm. Markov Chain Monte Carlo sampling provided maximum posterior estimates of quantitative T2* and their uncertainty, allowing delineation of the stria of Gennari over the entire length and width of the calcarine sulcus. We discuss how custom RF receive coil arrays built to specific large post mortem sample sizes can provide a platform for UHF cortical layer-specific quantitative MRI over large fields of view.

Robust and fast nonlinear optimization of diffusion MRI microstructure models.

Advances in biophysical multi-compartment modeling for diffusion MRI (dMRI) have gained popularity because of greater specificity than DTI in relating the dMRI signal to underlying cellular microstructure. A large range of these diffusion microstructure models have been developed and each of the popular models comes with its own, often different, optimization algorithm, noise model and initialization strategy to estimate its parameter maps. Since data fit, accuracy and precision is hard to verify, this creates additional challenges to comparability and generalization of results from diffusion microstructure models. In addition, non-linear optimization is computationally expensive leading to very long run times, which can be prohibitive in large group or population studies. In this technical note we investigate the performance of several optimization algorithms and initialization strategies over a few of the most popular diffusion microstructure models, including NODDI and CHARMED. We evaluate whether a single well performing optimization approach exists that could be applied to many models and would equate both run time and fit aspects. All models, algorithms and strategies were implemented on the Graphics Processing Unit (GPU) to remove run time constraints, with which we achieve whole brain dataset fits in seconds to minutes. We then evaluated fit, accuracy, precision and run time for different models of differing complexity against three common optimization algorithms and three parameter initialization strategies. Variability of the achieved quality of fit in actual data was evaluated on ten subjects of each of two population studies with a different acquisition protocol. We find that optimization algorithms and multi-step optimization approaches have a considerable influence on performance and stability over subjects and over acquisition protocols. The gradient-free Powell conjugate-direction algorithm was found to outperform other common algorithms in terms of run time, fit, accuracy and precision. Parameter initialization approaches were found to be relevant especially for more complex models, such as those involving several fiber orientations per voxel. For these, a fitting cascade initializing or fixing parameter values in a later optimization step from simpler models in an earlier optimization step further improved run time, fit, accuracy and precision compared to a single step fit. This establishes and makes available standards by which robust fit and accuracy can be achieved in shorter run times. This is especially relevant for the use of diffusion microstructure modeling in large group or population studies and in combining microstructure parameter maps with tractography results.

Wisconsin wrestling minimum weight project.

Starting in the 1991-1992 school year, Wisconsin was the first state to have a mandatory minimum weight established for high school wrestlers, along with a comprehensive standardized nutrition education program. The minimum weight project was phased in over 2 years. The goal of the project is to scientifically predict a healthy minimum weight for high school wrestlers. No guidelines were previously set and unhealthy weight loss practices are sometimes used to achieve desired weights. A wrestler's weight is often determined by the need to fill a wrestling class and not on a good scientific basis. Many wrestling coaches across the state have tried to implement individual programs, but until this project there had been no coordinated, collective effort.

Characterization of human alpha fetoprotein charge microheterogeneity during fetal development.

Aliquotes of human amniotic fluid (AF), fetal serum (FS), and cord blood (CB) were obtained as by-products of routine clinical diagnostic procedures at term or in the second trimester of pregnancy. When samples of CB were applied to a pH 5.5-4 chromatofocusing gradient, three isoforms of AFP could be resolved; a pl 4.57 form (isoform IA, 52% AFP), a pl 4.27 form (isoform IB, 43% AFP), and one species that was bound to the column but could be eluted with 1.0 M NaCl (isoform II, pl less than 4.00, 5% AFP). Term AF displayed a profile similar to that observed in term CB. When samples of 15-20-week gestation AF were chromatofocused, the immunoreactive AFP recovered was distributed between isoform IA and IB (60%) and isoform II (40%). FS and AF obtained from same pregnancy (23-26 weeks) displayed an identical chromatofocusing profile. Aliquotes of AF subjected to conA revealed 83% reactive variants compared with greater than 95% reactive variants for CB. FS displayed a conA profile identical to CB. When individual CB charge isoforms were isolated and subjected to conA analysis, greater than 97% of the AFP bound to conA. In contrast, when AFP isoform IA and IB were isolated from midgestation AF, approximately 22% of the AFP did not bind to the lectin while 100% of isolated AFP isoform II eluted as the reactive variant. These data suggest that human AFP exists as at least three charge and two lectin variants and that the charge profile may change during fetal development.

Characterization of the acidic forms of ovine pituitary luteinizing hormone.

The naturally occurring acidic forms of ovine pituitary LH were examined by chromatofocusing. Immunoreactive oLH eluted as six variants (elutions pHs of greater than 7.4, 6.83, 6.59, 6.23, 5.5-4.0, and less than 4.0, designated as "basic forms" and variants II-VI, respectively). In rams, the percentage in each variant averaged 46, 9, 28, 10, 5 and 2, respectively, of the total LH recovered. oLH from non-implanted wethers or wethers implanted with dihydrotestosterone, E2 or dihydrotestosterone + E2 eluted as six similar variants but differences were noted in the distribution of oLH among the variants. Compared to rams, pituitary extracts from non-implanted and dihydrotestosterone-implanted wethers contained significantly higher percentages of oLH eluting as basic forms. In contrast, E2- or dihydrotestosterone-implanted wethers exhibited significantly higher percentages of oLH in the acidic variants. Each of these variants was demonstrated to contain biologically active oLH using an in vitro bioassay. Furthermore, the basic forms of oLH were the most abundant biologically active forms present in pituitary extracts. These results suggest that in addition to the seven basic forms of oLH previously described, there are at least five naturally occurring acidic forms of oLH in pituitary extracts which are biologically active, and the distribution of pituitary oLH among its isohormones, including the acidic forms, appears to be modified by steroids.

The charge characterization of native and deglycosylated thyrotropin.

Chromatofocusing was used to characterize the charge microheterogeneity of crude pituitary, highly purified native bovine (b) and deglycosylated (dg) thyrotropin (TSH) preparations. Greater than 90% of crude pituitary TSH and native bTSH-I-1 bound to concanavalin-A (conA) columns while dgbTSH was excluded from the column. Extracts of ovine (o) pituitaries contained at least nine species (isohormones) of immunoreactive TSH when chromatofocused on pH 7.5-4 gradients. Highly purified native bTSH-I-1 displayed a similar elution profile. In contrast, dgbTSH eluted as a single homogeneous species with an apparent pI greater than 7.5. When subjected to chromatofocusing on a pH 10.5-7 gradient, 68% of crude pituitary oTSH and 96% of native bTSH-I-1 was bound to the column but could be eluted with NaCl indicating acidic species, while at least three peaks of dgbTSH could be resolved having apparent pI's of 9.12, 9.03 and 8.98. These data suggest that although removal of the carbohydrate moieties markedly alters the isohormone pattern of TSH, chemical deglycosylation does not completely eliminate the charge microheterogeneity of bTSH.

Isolation and Characterization of Coproporphyrin Produced by Four Subspecies of Bacillus thuringiensis.

It was found by using spectrophotometric, spectrofluorometric, and high-pressure liquid chromatography that four subspecies of Bacillus thuringiensis produce coproporphyrin. The porphyrin isomer was identified as coproporphyrin I for B. thuringiensis subsp. kurstaki (HD1). The porphyrin was isolated both from spores and from a variety of spent growth media. The quantity of porphyrin released by each Bacillus subspecies differed. The rank order of porphyrin production follows: B. thuringiensis subsp. kurstaki HD1 > B. thuringiensis subsp. thuringiensis HD27 > B. thuringiensis subsp. thuringiensis HD41 > B. thuringiensis subsp. darmstadiensis HD199.