An experimental study: effects of boulder placement on hydraulic metrics of instream habitat complexity.

Boulder placement is a common method to restore degraded instream habitats by enhancing habitat complexity. This experimental study is the foremost attempt to systematically investigate the influence of rock-ramp boulder placement with varying boulder concentration and flow rate on habitat hydraulic complexity metrics, including the kinetic energy gradient and modified recirculation metrics. By adding boulders to a reach, the modified recirculation metric increased by one order of magnitude for all boulder concentrations. Based on the studied metrics, boulder placement with the highest boulder concentration (λ = 8.3%) resulted in the greatest habitat hydraulic complexity. A set of relationships of moderate strength were proposed to predict the metrics in reaches with boulders by having information about only boulder concentration, habitat characteristic size, and reach-averaged flow characteristics. Based on the available data from the literature, boulder placement especially at higher concentrations may provide suitable habitats for several riverine fish species. Further studies are needed to establish a reliable linkage between the metrics and instream species, to test a wider variety of parameters for verifying and improving the range of applicability of the proposed relationships, and to find the structural configuration at which the habitat complexity is maximized or optimized for a certain species.

Hybrid time-domain and continuous-wave diffuse optical tomography instrument with concurrent, clinical magnetic resonance imaging for breast cancer imaging.

Diffuse optical tomography has demonstrated significant potential for clinical utility in the diagnosis and prognosis of breast cancer, and its use in combination with other structural imaging modalities improves lesion localization and the quantification of functional tissue properties. Here, we introduce a hybrid diffuse optical imaging system that operates concurrently with magnetic resonance imaging (MRI) in the imaging suite, utilizing commercially available MR surface coils. The instrument acquires both continuous-wave and time-domain diffuse optical data in the parallel-plate geometry, permitting both absolute assignment of tissue optical properties and three-dimensional tomography; moreover, the instrument is designed to incorporate diffuse correlation spectroscopic measurements for probing tissue blood flow. The instrument is described in detail here. Image reconstructions of a tissue phantom are presented as an initial indicator of the system's ability to accurately reconstruct optical properties and the concrete benefits of the spatial constraints provided by concurrent MRI. Last, we briefly discuss how various data combinations that the instrument could facilitate, including tissue perfusion, can enable more comprehensive assessment of lesion physiology.

Cervical cancer outcome prediction to high-dose rate brachytherapy using quantitative magnetic resonance imaging analysis of tumor response to external beam radiotherapy.

BACKGROUND AND PURPOSE: In order to assess tumor regression and outcomes, a volumetric analysis was conducted for cervical cancer patients treated with magnetic resonance imaging (MRI)-based image-guided brachytherapy (IGBT). MATERIALS AND METHODS: Consecutive patients with FIGO stage IB1-IVA cervical cancer receiving chemoradiation from 2007 to 2013 were identified, excluding patients with perineal template-based interstitial brachytherapy or without undergoing MRI. A ring and tandem applicator±interstitial needles was used. T2-weighted imaging was completed following applicator insertion. Gross tumor volumes (GTVs) were retrospectively contoured: initial GTV (GTV(Pre-EBRT)), GTV at first brachytherapy (GTV(IGBT)) and percent residual GTV at first brachytherapy (% GTV(Residual)). RESULTS: Eighty-four patients were identified. With 20.8-month median follow-up, two-year estimates of local control (LC), disease-free survival (DFS) and overall survival (OS) were 91.3, 79.8, and 85.0%, respectively. Multivariate Cox regression revealed adenocarcinoma (HR 5.88, p=0.03) and GTV(IGBT) (HR 1.17, p<0.01) as predictors for local failure. GTV(IGBT)>7.5 cc was associated with inferior 2-year LC (75.0 vs. 96.6%, p<0.01), DFS (42.6 vs. 91.6%, p<0.01) and OS (65.2 vs. 91.5%, p<0.01). No difference in mean HRCTV D(90) EQD(2) was seen between the groups (p=0.61). CONCLUSION: Aside from known benefits of IGBT, MRI-based planning allows for assessment of tumor regression and prognosticates patients.

Optical bedside monitoring of cerebral blood flow in acute ischemic stroke patients during head-of-bed manipulation.

BACKGROUND AND PURPOSE: A primary goal of acute ischemic stroke (AIS) management is to maximize perfusion in the affected region and surrounding ischemic penumbra. However, interventions to maximize perfusion, such as flat head-of-bed (HOB) positioning, are currently prescribed empirically. Bedside monitoring of cerebral blood flow (CBF) allows the effects of interventions such as flat HOB to be monitored and may ultimately be used to guide clinical management. METHODS: Cerebral perfusion was measured during HOB manipulations in 17 patients with unilateral AIS affecting large cortical territories in the anterior circulation. Simultaneous measurements of frontal CBF and arterial flow velocity were performed with diffuse correlation spectroscopy and transcranial Doppler ultrasound, respectively. Results were analyzed in the context of available clinical data and a previous study. RESULTS: Frontal CBF, averaged over the patient cohort, decreased by 17% (P=0.034) and 15% (P=0.011) in the ipsilesional and contralesional hemispheres, respectively, when HOB was changed from flat to 30°. Significant (cohort-averaged) changes in blood velocity were not observed. Individually, varying responses to HOB manipulation were observed, including paradoxical increases in CBF with increasing HOB angle. Clinical features, stroke volume, and distance to the optical probe could not explain this paradoxical response. CONCLUSIONS: A lower HOB angle results in an increase in cortical CBF without a significant change in arterial flow velocity in AIS, but there is variability across patients in this response. Bedside CBF monitoring with diffuse correlation spectroscopy provides a potential means to individualize interventions designed to optimize CBF in AIS.

Influence of probe pressure on the diffuse correlation spectroscopy blood flow signal: extra-cerebral contributions.

A pilot study explores relative contributions of extra-cerebral (scalp/skull) versus brain (cerebral) tissues to the blood flow index determined by diffuse correlation spectroscopy (DCS). Microvascular DCS flow measurements were made on the head during baseline and breath-holding/hyperventilation tasks, both with and without pressure. Baseline (resting) data enabled estimation of extra-cerebral flow signals and their pressure dependencies. A simple two-component model was used to derive baseline and activated cerebral blood flow (CBF) signals, and the DCS flow indices were also cross-correlated with concurrent Transcranial Doppler Ultrasound (TCD) blood velocity measurements. The study suggests new pressure-dependent experimental paradigms for elucidation of blood flow contributions from extra-cerebral and cerebral tissues.

The optimal template effect in hippocampus studies of diseased populations.

We evaluate the impact of template choice on template-based segmentation of the hippocampus in epilepsy. Four dataset-specific strategies are quantitatively contrasted: the "closest to average" individual template, the average shape version of the closest to average template, a best appearance template and the best appearance and shape template proposed here and implemented in the open source toolkit Advanced Normalization Tools (ANTS). The cross-correlation similarity metric drives the correspondence model and is used consistently to determine the optimal appearance. Minimum shape distance in the diffeomorphic space determines optimal shape. Our evaluation results show that, with respect to gold-standard manual labeling of hippocampi in epilepsy, optimal shape and appearance template construction outperforms the other strategies for gaining data-derived templates. Our results also show the improvement is most significant on the diseased side and insignificant on the healthy side. Thus, the importance of the template increases when used to study pathology and may be less critical for normal control studies. Furthermore, explicit geometric optimization of the shape component of the unbiased template positively impacts the study of diseased hippocampi.

A high-resolution computational atlas of the human hippocampus from postmortem magnetic resonance imaging at 9.4 T.

This paper describes the construction of a computational anatomical atlas of the human hippocampus. The atlas is derived from high-resolution 9.4 Tesla MRI of postmortem samples. The main subfields of the hippocampus (cornu ammonis fields CA1, CA2/3; the dentate gyrus; and the vestigial hippocampal sulcus) are labeled in the images manually using a combination of distinguishable image features and geometrical features. A synthetic average image is derived from the MRI of the samples using shape and intensity averaging in the diffeomorphic non-linear registration framework, and a consensus labeling of the template is generated. The agreement of the consensus labeling with manual labeling of each sample is measured, and the effect of aiding registration with landmarks and manually generated mask images is evaluated. The atlas is provided as an online resource with the aim of supporting subfield segmentation in emerging hippocampus imaging and image analysis techniques. An example application examining subfield-level hippocampal atrophy in temporal lobe epilepsy demonstrates the application of the atlas to in vivo studies.

Shape-based alignment of hippocampal subfields: evaluation in postmortem MRI.

This paper estimates the accuracy of hippocampal subfield alignment via shape-based normalization. Evaluation takes place in postmortem MRI dataset acquired at 9.4 Tesla with many averages and approximately 0.01 mm3 voxel resolution. Continuous medial representations (cm-reps) are used to establish geometrical correspondences between hippocampal formations in different images; the extent to which these correspondences match up subfields is evaluated and compared to normalization driven by image forces. Shape-based normalization is shown to perform only slightly worse than image-based normalization; this is encouraging because the former is more applicable to in vivo MRI, which typically lacks features that distinguish hippocampal subfields.