Quantitative magnetic resonance image analysis via the EM algorithm with stochastic variation

Quantitative Magnetic Resonance Imaging (qMRI) provides researchers insight into pathological and physiological alterations of living tissue, with the help of which researchers hope to predict (local) therapeutic efficacy early and determine optimal treatment schedule. However, the analysis of qMRI has been limited to ad-hoc heuristic methods. Our research provides a powerful statistical framework for image analysis and sheds light on future localized adaptive treatment regimes tailored to the individual's response. We assume in an imperfect world we only observe a blurred and noisy version of the underlying pathological/physiological changes via qMRI, due to measurement errors or unpredictable influences. We use a hidden Markov random field to model the spatial dependence in the data and develop a maximum likelihood approach via the Expectation--Maximization algorithm with stochastic variation. An important improvement over previous work is the assessment of variability in parameter estimation, which is the valid basis for statistical inference. More importantly, we focus on the expected changes rather than image segmentation. Our research has shown that the approach is powerful in both simulation studies and on a real dataset, while quite robust in the presence of some model assumption violations.Comment: Published in at http://dx.doi.org/10.1214/07-AOAS157 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Single-Calf Heifer System Profitability Compared to Other North Dakota Beef Production Systems

Production Economics, Productivity Analysis,

Longitudinal image analysis of tumour–healthy brain change in contrast uptake induced by radiation

The work is motivated by a quantitative magnetic resonance imaging study of the differential tumour–healthy tissue change in contrast uptake induced by radiation. The goal is to determine the time in which there is maximal contrast uptake (a surrogate for permeability) in the tumour relative to healthy tissue. A notable feature of the data is its spatial heterogeneity. Zhang and co-workers have discussed two parallel approaches to ‘denoise’ a single image of change in contrast uptake from baseline to one follow-up visit of interest. In this work we extend the image model to explore the longitudinal profile of the tumour–healthy tissue contrast uptake in multiple images over time. We fit a two-stage model. First, we propose a longitudinal image model for each subject. This model simultaneously accounts for the spatial and temporal correlation and denoises the observed images by borrowing strength both across neighbouring pixels and over time. We propose to use the Mann–Whitney U -statistic to summarize the tumour contrast uptake relative to healthy tissue. In the second stage, we fit a population model to the U -statistic and estimate when it achieves its maximum. Our initial findings suggest that the maximal contrast uptake of the tumour core relative to healthy tissue peaks around 3 weeks after initiation of radiotherapy, though this warrants further investigation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/79255/1/j.1467-9876.2010.00718.x.pd

Impact of historical gold mining activities on marine sediments in Wine Harbour, Nova Scotia, Canada

Past investigations at historical gold (Au) districts in Nova Scotia, Canada have identified elevated concentrations of arsenic (As) and mercury (Hg) in nearby sediments and waters. These metal(loid)s are derived from erosion of mineralized bedrock, and the disposal of mine tailings into the environment during early operations. The Wine Harbour gold district is located along the eastern shore of Nova Scotia, and produced 1329 kg of Au from 75 581 tonnes of crushed rock from 1862 to 1939.The gold occurs in arsenopyrite-bearing quartz-carbonate veins and was extracted using stamp milling and Hg amalgamation. Historical maps document tailings deposits near former stamp mill sites; however, the extent to which these mine wastes influence environmental quality in the adjacent marine environment is uncertain. In this study, we measured metal(loid) concentrations in tailings, marine sediments, and surface waters to assess the lateral and vertical extent of mining-related impacts on Wine Harbour. Chemical analyses of terrestrial and intertidal tailings reveal high concentrations of both As (86–196 000 mg/kg) and Hg (444–320 000 µg/kg). Analyses of marine sediments show a wide range in both As (4–568 mg/kg) and Hg (<5–7430 µg/kg) concentrations. In general, the highest metal(loid) concentrations in sediments were recorded down-gradient of stamp mill sites. Elevated concentrations were also detected in sediments underlying an active mussel aquaculture operation at the western end of the harbour. Results from this study have been used to help assess potential ecosystem and human health risks associated with historical gold mine wastes in the Wine Harbour area

Quaternary Deformation Along the Wharekauhau Fault System, North Island, New Zealand: Implications for an Unstable Linkage Between Active Strike-Slip and Thrust Faults

The southern Wairarapa region of the North Island of New Zealand preserves a variably deformed late Quaternary stratigraphic sequence that provides insight into the temporal variability in the partitioning of contraction onto faults in the upper plate of an obliquely convergent margin. Detailed mapping, stratigraphic data, and new radiocarbon and optically stimulated luminescence ages from Quaternary units reveal the interaction between tectonics and sedimentation from ∼125 ka to(i.e., Wharekauhau fault system) at the southern end of the Wairarapa fault zone, a major oblique-slip fault in the upper plate of the Hikurangi Margin. The Wharekauhau thrust accommodated a minimum of 280 ± 60 m of horizontal shortening from ∼70 to 20 ka. The inferred shortening rate, 3.5–8.4 mm/yr, may have accounted for 11–30% of margin-normal plate motion. By ∼20 ka, the thrust was abandoned. Subsequent deformation at shallow levels occurred on a segmented fault system that accommodated/yr shortening. Active deformation in the region is partitioned between slip on (1) the more western Wairarapa-Mukamuka fault system (dominantly dextral slip but also causing local uplift of the coast); (2) a series of discontinuously expressed strike-slip faults and linking blind oblique-reverse thrusts near the trace of the inactive Wharekauhau thrust; and (3) a blind thrust fault farther to the east. The spatial and temporal complexity of the Wharekauhau fault system and the importance it has had in accommodating upper plate deformation argue for an unsteady linkage between upper plate faults and between these faults and the plate interface

Phase-stepping interferometry of GaAs nanowires: determining nano-wire radius

Phase stepping interferometry is used to measure the size of near-cylindrical nanowires. Nanowires with nominal radii of 25 nm and 50 nm were used to test this by comparing specific measured optical phase profile values with theoretical values calculated using a wave-optic model of the Phase stepping interferometry (PSI) system. Agreement within 10% was found, which enabled nanowire radii to be predicted within 4% of the nominal value. This demonstration highlights the potential capability for phase stepping interferometry to characterize single nanoparticles of known geometry in the optical far-field.This research was supported by Australian Research Council Grant Nos. LE110100024 and DP130102674, a Macquarie University Research Development Grant, and the Australian National Fabrication Facility (ANFF)

Multi-night cortico-basal recordings reveal mechanisms of NREM slow-wave suppression and spontaneous awakenings in Parkinson's disease

Sleep disturbance is a prevalent and disabling comorbidity in Parkinson’s disease (PD). We performed multi-night (n = 57) at-home intracranial recordings from electrocorticography and subcortical electrodes using sensing-enabled Deep Brain Stimulation (DBS), paired with portable polysomnography in four PD participants and one with cervical dystonia (clinical trial: NCT03582891). Cortico-basal activity in delta increased and in beta decreased during NREM (N2 + N3) versus wakefulness in PD. DBS caused further elevation in cortical delta and decrease in alpha and low-beta compared to DBS OFF state. Our primary outcome demonstrated an inverse interaction between subcortical beta and cortical slow-wave during NREM. Our secondary outcome revealed subcortical beta increases prior to spontaneous awakenings in PD. We classified NREM vs. wakefulness with high accuracy in both traditional (30 s: 92.6 ± 1.7%) and rapid (5 s: 88.3 ± 2.1%) data epochs of intracranial signals. Our findings elucidate sleep neurophysiology and impacts of DBS on sleep in PD informing adaptive DBS for sleep dysfunction

Aging reduces left atrial performance during adrenergic stress in middle aged and older patients

Background: During adrenergic stress, the influence of age on left atrial (LA) function is unknown. We hypothesized that aging decreases LA total emptying fraction (LAEF) during maximal adrenergic stress. The aim of the study was to determine the influence of aging on LA function during adrenergic stress in middle aged and older patients. Methods: We enrolled 167 middle aged and elderly participants, and measured LA and left ventricular (LV) volumes using a multi-slice three-dimensional cine white blood cardiovascular magnetic resonance (CMR) technique before and during intravenous dobutamine infused to achieve 80% of the maximum heart rate response for age. Paired sample t-test was used to detect differences in LA and LV volumes between baseline and peak dose stage of dobutamine stress CMR, and multivariable linear regression was used to identify predictors of LA function. Results: Participants averaged 68 ± 8 years in age, 53% were men, 25% exhibited coronary artery disease, 35% had diabetes, 9% had a remote history of atrial fibrillation, 90% had hypertension, and 11% had inducible LV wall motion abnormalities indicative of ischemia during dobutamine CMR. Increasing age correlated with LA volumes (maximal and minimal) and inversely correlated with LAEF at rest and after peak adrenergic stress. Age was an independent predictor of LAEF during adrenergic stress, even after accounting for gender, LV volumes, and other co-morbidities including inducible ischemia. Conclusions: Age is associated with a decrease in LA function during adrenergic stress even after adjusting for co-morbidities associated with cardiovascular disease and LV function. (Cardiol J 2012; 19, 1: 45–52

Detection of Bacterial Antigens and Alzheimer\u27s Disease-like Pathology in the Central Nervous System of BALB/c Mice Following Intranasal Infection with a Laboratory Isolate of Chlamydia pneumoniae

Pathology consistent with that observed in Alzheimer’s disease (AD) has previously been documented following intranasal infection of normal wild-type mice with Chlamydia pneumoniae (Cpn) isolated from an AD brain (96-41). In the current study, BALB/c mice were intranasally infected with a laboratory strain of Cpn, AR-39, and brain and olfactory bulbs were obtained at 1-4 months post-infection (pi). Immunohistochemistry for amyloid beta or Cpn antigens was performed on sections from brains of infected or mock-infected mice. Chlamydia-specific immunolabeling was identified in olfactory bulb tissues and in cerebrum of AR-39 infected mice. The Cpn specific labeling was most prominent at 1 month pi and the greatest burden of amyloid deposition was noted at 2 months pi, whereas both decreased at 3 and 4 months. Viable Cpn was recovered from olfactory bulbs of 3 of 3 experimentally infected mice at 1 and 3 months pi, and in 2 of 3 mice at 4 months pi. In contrast, in cortical tissues of infected mice at 1 and 4 months pi no viable organism was obtained. At 3 months pi, only 1 of 3 mice had a measurable burden of viable Cpn from the cortical tissues. Mock-infected mice (0 of 3) had no detectable Cpn in either olfactory bulbs or cortical tissues. These data indicate that the AR-39 isolate of Cpn establishes a limited infection predominantly in the olfactory bulbs of BALB/c mice. Although infection with the laboratory strain of Cpn promotes deposition of amyloid beta, this appears to resolve following reduction of the Cpn antigen burden over time. Our data suggest that infection with the AR-39 laboratory isolate of Cpn results in a different course of amyloid beta deposition and ultimate resolution than that observed following infection with the human AD-brain Cpn isolate, 96-41. These data further support that there may be differences, possibly in virulence factors, between Cpn isolates in the generation of sustainable AD pathology