Automated ventricular mapping with multi-atlas fluid image alignment reveals genetic effects in Alzheimer's disease

We developed and validated a new method to create automated 3D parametric surface models of the lateral ventricles in brain MRI scans, providing an efficient approach to monitor degenerative disease in clinical studies and drug trials. First, we used a set of parameterized surfaces to represent the ventricles in four subjects' manually labeled brain MRI scans (atlases). We fluidly registered each atlas and mesh model to MRIs from 17 Alzheimer's disease (AD) patients and 13 age- and gender-matched healthy elderly control subjects, and 18 asymptomatic ApoE4-carriers and 18 age- and gender-matched non-carriers. We examined genotyped healthy subjects with the goal of detecting subtle effects of a gene that confers heightened risk for Alzheimer's disease. We averaged the meshes extracted for each 3D MR data set, and combined the automated segmentations with a radial mapping approach to localize ventricular shape differences in patients. Validation experiments comparing automated and expert manual segmentations showed that (1) the Hausdorff labeling error rapidly decreased, and (2) the power to detect disease- and gene-related alterations improved, as the number of atlases, N, was increased from 1 to 9. In surface-based statistical maps, we detected more widespread and intense anatomical deficits as we increased the number of atlases. We formulated a statistical stopping criterion to determine the optimal number of atlases to use. Healthy ApoE4-carriers and those with AD showed local ventricular abnormalities. This high-throughput method for morphometric studies further motivates the combination of genetic and neuroimaging strategies in predicting AD progression and treatment response. © 2007 Elsevier Inc. All rights reserved.

Automated 3D mapping & shape analysis of the lateral ventricles via fluid registration of multiple surface-based atlases

We developed and validated a new method to create automated 3D parametric surface models of the lateral ventricles, designed for monitoring degenerative disease effects in clinical neuroscience studies and drug trials. First we used a set of parameterized surfaces to represent the ventricles in a manually labeled set of 9 subjects' MRIs (atlases). We fluidly registered each of these atlases and mesh models to a set of MRIs from 12 Alzheimer's disease (AD) patients and 14 matched healthy elderly subjects, and we averaged the resulting meshes for each of these images. Validation experiments on expert segmentations showed that (1) the Hausdorff labeling error rapidly decreased, and (2) the power to detect disease-related alterations monotonically improved as the number of atlases, N, was increased from 1 to 9. We then combined the segmentations with a radial mapping approach to localize ventricular shape differences in patients. In surface-based statistical maps, we detected more widespread and intense anatomical deficits as we increased the number of atlases, and we formulated a statistical stopping criterion to determine the optimal value of N. Anterior horn anomalies in Alzheimer's patients were only detected with the multi-atlas segmentation, which clearly outperformed the standard single-atlas approach.

Direct mapping of hippocampal surfaces with intrinsic shape context

We propose in this paper a new method for the mapping of hippocampal (HC) surfaces to establish correspondences between points on HC surfaces and enable localized HC shape analysis. A novel geometric feature, the intrinsic shape context, is defined to capture the global characteristics of the HC shapes. Based on this intrinsic feature, an automatic algorithm is developed to detect a set of landmark curves that are stable across population. The direct map between a source and target HC surface is then solved as the minimizer of a harmonic energy function defined on the source surface with landmark constraints. For numerical solutions, we compute the map with the approach of solving partial differential equations on implicit surfaces. The direct mapping method has the following properties: (1) it has the advantage of being automatic; (2) it is invariant to the pose of HC shapes. In our experiments, we apply the direct mapping method to study temporal changes of HC asymmetry in Alzheimer's disease (AD) using HC surfaces from 12 AD patients and 14 normal controls. Our results show that the AD group has a different trend in temporal changes of HC asymmetry than the group of normal controls. We also demonstrate the flexibility of the direct mapping method by applying it to construct spherical maps of HC surfaces. Spherical harmonics (SPHARM) analysis is then applied and it confirms our results on temporal changes of HC asymmetry in AD.

Mapping hippocampal and ventricular change in Alzheimer disease

We developed an anatomical mapping technique to detect hippocampal and ventricular changes in Alzheimer disease (AD). The resulting maps are sensitive to longitudinal changes in brain structure as the disease progresses. An anatomical surface modeling approach was combined with surface-based statistics to visualize the region and rate of atrophy in serial MRI scans and isolate where these changes link with cognitive decline. Fifty-two high-resolution MRI scans were acquired from 12 AD patients (age: 68.4 ± 1.9 years) and 14 matched controls (age: 71.4 ± 0.9 years), each scanned twice (2.1 ± 0.4 years apart). 3D parametric mesh models of the hippocampus and temporal horns were created in sequential scans and averaged across subjects to identify systematic patterns of atrophy. As an index of radial atrophy, 3D distance fields were generated relating each anatomical surface point to a medial curve threading down the medial axis of each structure. Hippocampal atrophic rates and ventricular expansion were assessed statistically using surface-based permutation testing and were faster in AD than in controls. Using color-coded maps and video sequences, these changes were visualized as they progressed anatomically over time. Additional maps localized regions where atrophic changes linked with cognitive decline. Temporal horn expansion maps were more sensitive to AD progression than maps of hippocampal atrophy, but both maps correlated with clinical deterioration. These quantitative, dynamic visualizations of hippocampal atrophy and ventricular expansion rates in aging and AD may provide a promising measure to track AD progression in drug trials.

Corrigendum to "Mapping hippocampal and ventricular change in Alzheimer disease" [NeuroImage 22 (2004) 1754-1766] (DOI:10.1016/j.neuroimage.2004.03.040)

We recently noticed an error in the demographic data in this article. The validity of the findings and the conclusions of the paper is not affected. However, there is an error in the reported sample size and in the means and standard deviations of the subjects’ ages and MMSE scores. We would like to correct this error, which came to light when we were re-analyzing the data for a meta-analysis. The error occurred because an older version of a spreadsheet was incorrectly used when reporting the sample composition. Instead of examining 12 Alzheimer's disease patients and 14 healthy elderly controls, we in fact examined 17 Alzheimer’s disease patients and 14 healthy elderly controls. All maps and morphometric data reported in the paper are correct, except that the sample size was in fact slightly higher than that originally reported, and the maps computed in the paper were based on the larger sample (which included five more subjects in the Alzheimer’s disease group). All of the maps and figures in the paper are correct, and the conclusions of the paper are unchanged. We apologize for this error, which falls under the sole responsibility of the first author. The corrected demographic information appears below.

Mapping cortical change in Alzheimer's disease, brain development, and schizophrenia

This paper describes algorithms that can identify patterns of brain structure and function associated with Alzheimer's disease, schizophrenia, normal aging, and abnormal brain development based on imaging data collected in large human populations. Extraordinary information can be discovered with these techniques: dynamic brain maps reveal how the brain grows in childhood, how it changes in disease, and how it responds to medication. Genetic brain maps can reveal genetic influences on brain structure, shedding light on the nature-nurture debate, and the mechanisms underlying inherited neurobehavioral disorders. Recently, we created time-lapse movies of brain structure for a variety of diseases. These identify complex, shifting patterns of brain structural deficits, revealing where, and at what rate, the path of brain deterioration in illness deviates from normal. Statistical criteria can then identify situations in which these changes are abnormally accelerated, or when medication or other interventions slow them. In this paper, we focus on describing our approaches to map structural changes in the cortex. These methods have already been used to reveal the profile of brain anomalies in studies of dementia, epilepsy, depression, childhood- and adult-onset schizophrenia, bipolar disorder, attention-deficit/hyperactivity disorder, fetal alcohol syndrome, Tourette syndrome, Williams syndrome, and in methamphetamine abusers. Specifically, we describe an image analysis pipeline known as cortical pattern matching that helps compare and pool cortical data over time and across subjects. Statistics are then defined to identify brain structural differences between groups, including localized alterations in cortical thickness, gray matter density (GMD), and asymmetries in cortical organization. Subtle features, not seen in individual brain scans, often emerge when population-based brain data are averaged in this way. Illustrative examples are presented to show the profound effects of development and various diseases on the human cortex. Dynamically spreading waves of gray matter loss are tracked in dementia and schizophrenia, and these sequences are related to normally occurring changes in healthy subjects of various ages.

Mapping teacher-faces

This paper uses Deleuze and Guattari's concept of faciality to analyse the teacher's face. According to Deleuze and Guattari, the teacher-face is a special type of face because it is an 'overcoded' face produced in specific landscapes. This paper suggests four limit-faces for teacher faciality that actualise different mixes of signifiance and subjectification in a classroom in which individualisation and massifications are affected. Understanding these limit-faces suggests new ways to conceive the affects actualised in the classroom that are subjected to increasing levels of surveillance from education policy makers. Through this ‘partial mapping’ new possibilities emerge to “escape the face”.

Learned ultra-wideband RADAR sensor model for augmented LIDAR-based traversability mapping in vegetated environments

In vegetated environments, reliable obstacle detection remains a challenge for state-of-the-art methods, which are usually based on geometrical representations of the environment built from LIDAR and/or visual data. In many cases, in practice field robots could safely traverse through vegetation, thereby avoiding costly detours. However, it is often mistakenly interpreted as an obstacle. Classifying vegetation is insufficient since there might be an obstacle hidden behind or within it. Some Ultra-wide band (UWB) radars can penetrate through vegetation to help distinguish actual obstacles from obstacle-free vegetation. However, these sensors provide noisy and low-accuracy data. Therefore, in this work we address the problem of reliable traversability estimation in vegetation by augmenting LIDAR-based traversability mapping with UWB radar data. A sensor model is learned from experimental data using a support vector machine to convert the radar data into occupancy probabilities. These are then fused with LIDAR-based traversability data. The resulting augmented traversability maps capture the fine resolution of LIDAR-based maps but clear safely traversable foliage from being interpreted as obstacle. We validate the approach experimentally using sensors mounted on two different mobile robots, navigating in two different environments.

Associations between individual socioeconomic position, neighbourhood disadvantage, and transport mode: Baseline results from the HABITAT multilevel study

Background Understanding how different socioeconomic indicators are associated with transport modes provide insight into which interventions might contribute to reducing socioeconomic inequalities in health. The purpose of this study was to examine associations between neighbourhood-level socioeconomic disadvantage, individual-level socioeconomic position (SEP) and usual transport mode. Methods This investigation included 11,036 residents from 200 neighbourhoods in Brisbane, Australia. Respondents self-reported their usual transport mode (car or motorbike, public transport, walking or cycling). Indicators for individual-level SEP were education, occupation, and household income; and neighbourhood disadvantage was measured using a census-derived index. Data were analysed using multilevel multinomial logistic regression. High SEP respondents and residents of the most advantaged neighbourhoods who used a private motor vehicle as their usual form of transport was the reference category. Results Compared with driving a motor vehicle, the odds of using public transport were higher for white collar employees (OR1.68, 95%CrI 1.41-2.01), members of lower income households (OR 1.71 95%CrI 1.25-2.30), and residents of more disadvantaged neighbourhoods (OR 1.93, 95%CrI 1.46-2.54); and lower for respondents with a certificate-level education (OR 0.60, 95%CrI 0.49-0.74) and blue collar workers (OR 0.63, 95%CrI 0.50-0.81). The odds of walking for transport were higher for the least educated (OR 1.58, 95%CrI 1.18-2.11), those not in the labour force (OR 1.94, 95%CrI 1.38-2.72), members of lower income households (OR 2.10, 95%CrI 1.23-3.64), and residents of more disadvantaged neighbourhoods (OR 2.73, 95%CrI 1.46-5.24). The odds of cycling were lower among less educated groups (OR 0.31, 95% CrI 0.19-0.48). Conclusion The relationships between socioeconomic characteristics and transport modes are complex, and provide challenges for those attempting to encourage active forms of transportation. Further work is required exploring the individual- and neighbourhood-level mechanisms behind transport mode choice, and what factors might influence individuals from different socioeconomic backgrounds to change to more active transport modes.

Development of polymorphic microsatellite markers suitable for genetic linkage mapping of olive flounder Paralichthys olivaceus

Microsatellite markers are important for gene mapping and for marker-assisted selection. Sixty-five polymorphic microsatellite markers were developed with an enriched partial genomic library from olive flounder Paralichthys olivaceus an important commercial fish species in Korea. The variability of these markers was tested in 30 individuals collected from the East Sea (Korea). The number of alleles for each locus ranged from 2 to 33 (mean, 17.1). Observed and expected heterozygosity as well as polymorphism information content varied from 0.313 to 1.000 (mean, 0.788), from 0.323 to 0.977 (mean, 0.820), and from 0.277 to 0.960 (mean, 0.787), respectively. Nine loci showed significant deviation from the Hardy-Weinberg equilibrium after sequential Bonferroni correction. Analysis with MICROCHECKER suggested the presence of null alleles at five of these loci with estimated null allele frequencies of 0.126-0.285. These new microsatellite markers from genomic libraries will be useful for constructing a P. olivaceus linkage map.

Identity-by-Descent Mapping to Detect Rare Variants Conferring Susceptibility to Multiple Sclerosis

Genome-wide association studies (GWAS) have identified around 60 common variants associated with multiple sclerosis (MS), but these loci only explain a fraction of the heritability of MS. Some missing heritability may be caused by rare variants that have been suggested to play an important role in the aetiology of complex diseases such as MS. However current genetic and statistical methods for detecting rare variants are expensive and time consuming. 'Population-based linkage analysis' (PBLA) or so called identity-by-descent (IBD) mapping is a novel way to detect rare variants in extant GWAS datasets. We employed BEAGLE fastIBD to search for rare MS variants utilising IBD mapping in a large GWAS dataset of 3,543 cases and 5,898 controls. We identified a genome-wide significant linkage signal on chromosome 19 (LOD = 4.65; p = 1.9×10-6). Network analysis of cases and controls sharing haplotypes on chromosome 19 further strengthened the association as there are more large networks of cases sharing haplotypes than controls. This linkage region includes a cluster of zinc finger genes of unknown function. Analysis of genome wide transcriptome data suggests that genes in this zinc finger cluster may be involved in very early developmental regulation of the CNS. Our study also indicates that BEAGLE fastIBD allowed identification of rare variants in large unrelated population with moderate computational intensity. Even with the development of whole-genome sequencing, IBD mapping still may be a promising way to narrow down the region of interest for sequencing priority. © 2013 Lin et al.

Introduction: Mapping the Contours of East Asian Commercial Law for the Asian Century

The centre of economic gravity in the new century is shifting to the East. Since 200 1, according to the International Monetary Fund (IMF), Asia's contribution to world economic growth has matched that of the United States and Europe combined, and, since 2006, has even exceeded it (IMF, 20 I I; Neumann and Arora, 20 II ). This surge is easy to explain: China has emerged as a global super-power; Japan remains the third-largest world economy, despite only recently emerging from over twenty years of economic stagnation (The Age, 2013); South Korea and the ' tiger ' economies of Taiwan, Hong Kong and Singapore have achieved high-level economic development through capital investment and technological innovation; and Indonesia, Thailand, the Philippines and Malaysia have supplied riches in labour and resources to the regional economy (Macintyre and Naughton, 2005, p. 78). A growing middle class is lifting consumption. ‘Billions of Asians,' writes Mahbubani (2008, p. 3), 'are marching to modernity.’ This book examines scholarly interpretations for the role commercial law has played in East Asia's economic rise. At first blush, this might seem a daunting task. After all, as some theorists have argued, the East Asian experience is largely neglected in writings on Jaw generally and commercial law more broadly (Wolff, 20 12). This is because law, as a discipline, was largely forged in the prior European and American centuries; these 'Anglo-American moorings' ill-serve legal analysis in the new Asian Century (Cossman, 1997, p. 539).

Mapping genes for osteoporosis-Old dogs and new tricks

In stark contrast to its horticultural origins, modern genetics is an extremely technology-driven field. Almost all the major advances in the field over the past 20 years have followed technological developments that have permitted change in study designs. The development of PCR in the 1980s led to RFLP mapping of monogenic diseases. The development of fluorescent-tagged genotyping methods led to linkage mapping approaches for common diseases that dominated the 1990s. The development of microarray SNP genotyping has led to the genome-wide association study era of the new millennium. And now the development of next-generation sequencing technologies is about to open up a new era of gene-mapping, enabling many potential new study designs. This review aims to present the strengths and weaknesses of the current approaches, and present some new ideas about gene-mapping approaches that are likely to advance our knowledge of the genes involved in heritable bone traits such as bone mineral density (BMD) and fracture.