Fully automated 3D segmentation of dopamine transporter SPECT images using an estimation-based approach

Quantitative measures of uptake in caudate, putamen, and globus pallidus in dopamine transporter (DaT) brain SPECT have potential as biomarkers for the severity of Parkinson disease. Reliable quantification of uptake requires accurate segmentation of these regions. However, segmentation is challenging in DaT SPECT due to partial-volume effects, system noise, physiological variability, and the small size of these regions. To address these challenges, we propose an estimation-based approach to segmentation. This approach estimates the posterior mean of the fractional volume occupied by caudate, putamen, and globus pallidus within each voxel of a 3D SPECT image. The estimate is obtained by minimizing a cost function based on the binary cross-entropy loss between the true and estimated fractional volumes over a population of SPECT images, where the distribution of the true fractional volumes is obtained from magnetic resonance images from clinical populations. The proposed method accounts for both the sources of partial-volume effects in SPECT, namely the limited system resolution and tissue-fraction effects. The method was implemented using an encoder-decoder network and evaluated using realistic clinically guided SPECT simulation studies, where the ground-truth fractional volumes were known. The method significantly outperformed all other considered segmentation methods and yielded accurate segmentation with dice similarity coefficients of ~ 0.80 for all regions. The method was relatively insensitive to changes in voxel size. Further, the method was relatively robust up to +/- 10 degrees of patient head tilt along transaxial, sagittal, and coronal planes. Overall, the results demonstrate the efficacy of the proposed method to yield accurate fully automated segmentation of caudate, putamen, and globus pallidus in 3D DaT-SPECT images

Weak Lensing from Space III: Cosmological Parameters

Weak gravitational lensing provides a unique method to directly map the dark matter in the universe and measure cosmological parameters. Current weak lensing surveys are limited by the atmospheric seeing from the ground and by the small field of view of existing space telescopes. We study how a future wide-field space telescope can measure the lensing power spectrum and skewness, and set constraints on cosmological parameters. The lensing sensitivity was calculated using detailed image simulations and instrumental specifications studied in earlier papers in this series. For instance, the planned SuperNova/Acceleration Probe (SNAP) mission will be able to measure the matter density parameter Omega_m and the dark energy equation of state parameter w with precisions comparable and nearly orthogonal to those derived with SNAP from supernovae. The constraints degrade by a factor of about 2 if redshift tomography is not used, but are little affected if the skewness only is dropped. We also study how the constraints on these parameters depend upon the survey geometry and define an optimal observing strategy.Comment: 12 pages, 11 figures. Accepted versio

Constraining dark energy with Sunyaev-Zel'dovich cluster surveys

We discuss the prospects of constraining the properties of a dark energy component, with particular reference to a time varying equation of state, using future cluster surveys selected by their Sunyaev-Zel'dovich effect. We compute the number of clusters expected for a given set of cosmological parameters and propogate the errors expected from a variety of surveys. In the short term they will constrain dark energy in conjunction with future observations of type Ia supernovae, but may in time do so in their own right.Comment: 5 pages, 3 figures, 1 table, version accepted for publication in PR

Circle of Willis variation in a complex stroke presentation: a case report

BACKGROUND: The impact of circle of Willis anatomical variation upon the presentation of stroke is probably underrecognised. CASE PRESENTATION: A 63-year-old right-handed woman developed a left hemiparesis and right leg weakness sequentially following a road traffic accident (RTA). Despite initial concern about the possibility of cervical spinal cord injury, the final diagnosis was bilateral artery-to-artery embolic cerebral infarction with dominant right internal carotid artery. CONCLUSION: The case illustrates the complex presentation of stroke as a pseudo-cervical cord lesion and the impact of circle of Willis anatomical variation upon the expression of large vessel cerebrovascular disease

Testing Models of Intrinsic Brightness Variations in Type Ia Supernovae, and their Impact on Measuring Cosmological Parameters

For spectroscopically confirmed Type Ia supernovae we evaluate models of intrinsic brightness variations with detailed data/Monte Carlo comparisons of the dispersion in the following quantities: Hubble-diagram scatter, color difference (B-V-c) between the true B-V color and the fitted color (c) from the SALT-II light curve model, and photometric redshift residual. The data sample includes 251 ugriz light curves from the 3-season Sloan Digital Sky Survey-II, and 191 griz light curves from the Supernova Legacy Survey 3-year data release. We find that the simplest model of a wavelength-independent (coherent) scatter is not adequate, and that to describe the data the intrinsic scatter model must have wavelength-dependent variations. We use Monte Carlo simulations to examine the standard approach of adding a coherent scatter term in quadrature to the distance-modulus uncertainty in order to bring the reduced chi2 to unity when fitting a Hubble diagram. If the light curve fits include model uncertainties with the correct wavelength dependence of the scatter, we find that the bias on the dark energy equation of state parameter $w$ is negligible. However, incorrect model uncertainties can lead to a significant bias on the distance moduli, with up to ~0.05 mag redshift-dependent variation. For the recent SNLS3 cosmology results we estimate that this effect introduces an additional systematic uncertainty on $w$ of ~0.02, well below the total uncertainty. However, this uncertainty depends on the samples used, and thus this small $w$-uncertainty is not guaranteed in future cosmology results.Comment: accepted by Ap

Cosmological parameter estimation using Very Small Array data out to l=1500

We estimate cosmological parameters using data obtained by the Very Small Array (VSA) in its extended configuration, in conjunction with a variety of other CMB data and external priors. Within the flat $\Lambda$CDM model, we find that the inclusion of high resolution data from the VSA modifies the limits on the cosmological parameters as compared to those suggested by WMAP alone, while still remaining compatible with their estimates. We find that $\Omega_{\rm b}h^2=0.0234^{+0.0012}_{-0.0014}$, $\Omega_{\rm dm}h^2=0.111^{+0.014}_{-0.016}$, $h=0.73^{+0.09}_{-0.05}$, $n_{\rm S}=0.97^{+0.06}_{-0.03}$, $10^{10}A_{\rm S}=23^{+7}_{-3}$ and $\tau=0.14^{+0.14}_{-0.07}$ for WMAP and VSA when no external prior is included.On extending the model to include a running spectral index of density fluctuations, we find that the inclusion of VSA data leads to a negative running at a level of more than 95% confidence ($n_{\rm run}=-0.069\pm 0.032$), something which is not significantly changed by the inclusion of a stringent prior on the Hubble constant. Inclusion of prior information from the 2dF galaxy redshift survey reduces the significance of the result by constraining the value of $\Omega_{\rm m}$. We discuss the veracity of this result in the context of various systematic effects and also a broken spectral index model. We also constrain the fraction of neutrinos and find that $f_{\nu}< 0.087$ at 95% confidence which corresponds to $m_\nu<0.32{\rm eV}$ when all neutrino masses are the equal. Finally, we consider the global best fit within a general cosmological model with 12 parameters and find consistency with other analyses available in the literature. The evidence for $n_{\rm run}<0$ is only marginal within this model

Identification of PKD1L1 Gene Variants in Children with the Biliary Atresia Splenic Malformation Syndrome

Biliary atresia (BA) is the most common cause of end‐stage liver disease in children and the primary indication for pediatric liver transplantation, yet underlying etiologies remain unknown. Approximately 10% of infants affected by BA exhibit various laterality defects (heterotaxy) including splenic abnormalities and complex cardiac malformations — a distinctive subgroup commonly referred to as the biliary atresia splenic malformation (BASM) syndrome. We hypothesized that genetic factors linking laterality features with the etiopathogenesis of BA in BASM patients could be identified through whole exome sequencing (WES) of an affected cohort. DNA specimens from 67 BASM subjects, including 58 patient‐parent trios, from the NIDDK‐supported Childhood Liver Disease Research Network (ChiLDReN) underwent WES. Candidate gene variants derived from a pre‐specified set of 2,016 genes associated with ciliary dysgenesis and/or dysfunction or cholestasis were prioritized according to pathogenicity, population frequency, and mode of inheritance. Five BASM subjects harbored rare and potentially deleterious bi‐allelic variants in polycystin 1‐like 1, PKD1L1, a gene associated with ciliary calcium signaling and embryonic laterality determination in fish, mice and humans. Heterozygous PKD1L1 variants were found in 3 additional subjects. Immunohistochemical analysis of liver from the one BASM subject available revealed decreased PKD1L1 expression in bile duct epithelium when compared to normal livers and livers affected by other non‐cholestatic diseases. Conclusion WES identified bi‐allelic and heterozygous PKD1L1 variants of interest in 8 BASM subjects from the ChiLDReN dataset. The dual roles for PKD1L1 in laterality determination and ciliary function suggest that PKD1L1 is a new, biologically plausible, cholangiocyte‐expressed candidate gene for the BASM syndrome

Postural directionality and head tremor in cervical dystonia

Background: Although abnormal head and neck postures are defining features of cervical dystonia (CD), head tremor (HT) is also common. However, little is known about the relationship between abnormal postures and HT in CD. Methods: We analyzed clinical data and video recordings from 185 patients enrolled by the Dystonia Coalition. We calculated the likelihood of their HT and HT type ( regular vs. jerky ) given directionality of abnormal head postures, disease duration, sex, and age. Results: Patients with retrocollis were more likely to have HT than patients with anterocollis (X Discussion: We found that HT is more likely for CD patients with a specific directionality in their predominant posture. Our finding that CD patients with longer disease duration have a higher likelihood of HT also raises the question of whether HT becomes more likely over time in individual patients

Cosmology with a long range repulsive force

We consider a class of cosmological models in which the universe is filled with a (non-electric) charge density that repels itself by means of a force carried by a vector boson with a tiny mass. When the vector's mass depends upon other fields, the repulsive interaction gives rise to an electromagnetic barrier which prevents these fields from driving the mass to zero. This can modify the cosmology dramatically. We present a very simple realization of this idea in which the vector's mass arises from a scalar field. The electromagnetic barrier prevents this field from rolling down its potential and thereby leads to accelerated expansion.Comment: 15 pages, 8 figures, LaTeX (version accepted for publication in PRD). 3 new figures, extended discussion of observational consequence

Comparison of an X-ray selected sample of massive lensing clusters with the MareNostrum Universe LCDM simulation

A long-standing problem of strong lensing by galaxy clusters regards the observed high rate of giant gravitational arcs as compared to the predictions in the framework of the "standard" cosmological model. Recently, few other inconsistencies between theoretical expectations and observations have been claimed which regard the large size of the Einstein rings and the high concentrations of few clusters with strong lensing features. All of these problems consistently indicate that observed galaxy clusters may be gravitational lenses stronger than expected. We use clusters extracted from the MareNostrum Universe to build up mock catalogs of galaxy clusters selected through their X-ray flux. We use these objects to estimate the probability distributions of lensing cross sections, Einstein rings, and concentrations for the sample of 12 MACS clusters at $z>0.5$ presented in Ebeling et al. (2007) and discussed in Zitrin et al. (2010). We find that simulated clusters produce $\sim 50$ less arcs than observed clusters do. The medians of the distributions of the Einstein ring sizes differ by $\sim 25$ between simulations and observations. We estimate that, due to cluster triaxiality and orientation biases affecting the lenses with the largest cross sections, the concentrations of the individual MACS clusters inferred from the lensing analysis should be up to a factor of $\sim 2$ larger than expected from the $\Lambda$CDM model. The arc statistics, the Einstein ring, and the concentration problems in strong lensing clusters are mitigated but not solved on the basis of our analysis. Nevertheless, due to the lack of redshifts for most of the multiple image systems used for modeling the MACS clusters, the results of this work will need to be verified with additional data. The upcoming CLASH program will provide an ideal sample for extending our comparison (abridged).Comment: 11 pages, 9 figures, accepted for publication on A&