3D Enhancement Color Maps in the Characterization of Intracranial Atherosclerotic Plaques.

BACKGROUND AND PURPOSE: High-resolution MR imaging allows the identification of culprit symptomatic plaques after the administration of gadolinium. Current high-resolution MR imaging methods are limited by 2D multiplanar views and manual sampling of ROIs. We analyzed a new 3D method to objectively quantify gadolinium plaque enhancement. MATERIALS AND METHODS: Patients with stroke due to intracranial atherosclerotic disease underwent 7T high-resolution MR imaging. 3D segmentations of the plaque and its parent vessel were generated. Signal intensity probes were automatically extended from the lumen into the plaque and the vessel wall to generate 3D enhancement color maps. Plaque gadolinium (Gd) uptake was quantified from 3D color maps as gadolinium uptake = (µPlaque T1 + Gd -µPlaque T1/SDPlaque T1). Additional metrics of enhancement such as enhancement ratio, variance, and plaque-versus-parent vessel enhancement were also calculated. Conventional 2D measures of enhancement were collected for comparison. RESULTS: Thirty-six culprit and 44 nonculprit plaques from 36 patients were analyzed. Culprit plaques had higher gadolinium uptake than nonculprit plaques (P < .001). Gadolinium uptake was the most accurate metric for identifying culprit plaques (OR, 3.9; 95% CI 2.1-8.3). Gadolinium uptake was more sensitive (86% versus 70%) and specific (71% versus 68%) in identifying culprit plaques than conventional 2D measurements. A multivariate model, including gadolinium uptake and plaque burden, identified culprit plaques with an 83% sensitivity and 86% specificity. CONCLUSIONS: The new 3D color map method of plaque-enhancement analysis is more accurate for identifying culprit plaques than conventional 2D methods. This new method generates a new set of metrics that could potentially be used to assess disease progression.

Demographic inference under a spatially continuous coalescent model.

In contrast with the classical population genetics theory that models population structure as discrete panmictic units connected by migration, many populations exhibit heterogeneous spatial gradients in population connectivity across semi-continuous habitats. The historical dynamics of such spatially structured populations can be captured by a spatially explicit coalescent model recently proposed by Etheridge (2008) and Barton et al. (2010a, 2010b) and whereby allelic lineages are distributed in a two-dimensional spatial continuum and move within this continuum based on extinction and coalescent events. Though theoretically rigorous, this model, which we here refer to as the continuum model, has not yet been implemented for demographic inference. To this end, here we introduce and demonstrate a statistical pipeline that couples the coalescent simulator of Kelleher et al. (2014) that simulates genealogies under the continuum model, with an approximate Bayesian computation (ABC) framework for parameter estimation of neighborhood size (that is, the number of locally breeding individuals) and dispersal ability (that is, the distance an offspring can travel within a generation). Using empirically informed simulations and simulation-based ABC cross-validation, we first show that neighborhood size can be accurately estimated. We then apply our pipeline to the South African endemic shrub species Berkheya cuneata to use the resulting estimates of dispersal ability and neighborhood size to infer the average population density of the species. More generally, we show that spatially explicit coalescent models can be successfully integrated into model-based demographic inference.

Phylogeography's past, present, and future: 10 years after Avise, 2000.

Approximately 20 years ago, Avise and colleagues proposed the integration of phylogenetics and population genetics for investigating the connection between micro- and macroevolutionary phenomena. The new field was termed phylogeography. Since the naming of the field, the statistical rigor of phylogeography has increased, in large part due to concurrent advances in coalescent theory which enabled model-based parameter estimation and hypothesis testing. The next phase will involve phylogeography increasingly becoming the integrative and comparative multi-taxon endeavor that it was originally conceived to be. This exciting convergence will likely involve combining spatially-explicit multiple taxon coalescent models, genomic studies of natural selection, ecological niche modeling, studies of ecological speciation, community assembly and functional trait evolution. This ambitious synthesis will allow us to determine the causal links between geography, climate change, ecological interactions and the evolution and composition of taxa across whole communities and assemblages. Although such integration presents analytical and computational challenges that will only be intensified by the growth of genomic data in non-model taxa, the rapid development of "likelihood-free" approximate Bayesian methods should permit parameter estimation and hypotheses testing using complex evolutionary demographic models and genomic phylogeographic data. We first review the conceptual beginnings of phylogeography and its accomplishments and then illustrate how it evolved into a statistically rigorous enterprise with the concurrent rise of coalescent theory. Subsequently, we discuss ways in which model-based phylogeography can interface with various subfields to become one of the most integrative fields in all of ecology and evolutionary biology.

Nearshore fish (Pholis gunnellus) persists across the North Atlantic through multiple glacial episodes.

The intertidal biota of the North Atlantic is characterized by two disjunct communities (North American and European) exposed to different climatic regimes during the Pleistocene and in the Holocene. We collect multilocus DNA sequence data from the nearshore fish Pholis gunnellus to help uncover processes determining biogeographical persistence during periodic coastal glaciations. Coalescent-based estimates from the multilocus DNA sequence data suggest that P. gunnellus persisted on both sides of the North Atlantic throughout the last two glacial maxima (> 202,000 years) with little trans-Atlantic gene flow since divergence, very little structure among populations within Europe (Phi(ST) < 0.05) and some structure within the North American coastline (Phi(ST) = 0.0-0.21). Although the ecological flexibility and high local migration of P. gunnellus could have enhanced this species' survival across the Atlantic, logistic regression did not find a significant determinant of trans-Atlantic persistence when considering 12 other North Atlantic phylogeographical studies from the literature.

Comparative phylogeographic summary statistics for testing simultaneous vicariance.

Testing for simultaneous vicariance across comparative phylogeographic data sets is a notoriously difficult problem hindered by mutational variance, the coalescent variance, and variability across pairs of sister taxa in parameters that affect genetic divergence. We simulate vicariance to characterize the behaviour of several commonly used summary statistics across a range of divergence times, and to characterize this behaviour in comparative phylogeographic datasets having multiple taxon-pairs. We found Tajima's D to be relatively uncorrelated with other summary statistics across divergence times, and using simple hypothesis testing of simultaneous vicariance given variable population sizes, we counter-intuitively found that the variance across taxon pairs in Nei and Li's net nucleotide divergence (pi(net)), a common measure of population divergence, is often inferior to using the variance in Tajima's D across taxon pairs as a test statistic to distinguish ancient simultaneous vicariance from variable vicariance histories. The opposite and more intuitive pattern is found for testing more recent simultaneous vicariance, and overall we found that depending on the timing of vicariance, one of these two test statistics can achieve high statistical power for rejecting simultaneous vicariance, given a reasonable number of intron loci (> 5 loci, 400 bp) and a range of conditions. These results suggest that components of these two composite summary statistics should be used in future simulation-based methods which can simultaneously use a pool of summary statistics to test comparative the phylogeographic hypotheses we consider here.

Dramatic mitochondrial gene rearrangements in the hermit crab Pagurus longicarpus (Crustacea, anomura).

The entire mitochondrial gene order of the crustacean Pagurus longicarpus was determined by sequencing all but approximately 300 bp of the mitochondrial genome. We report the first major gene rearrangements found in the clade including Crustacea and Insecta. At least eight mitochondrial gene rearrangements have dramatically altered the gene order of the hermit crab P. longicarpus relative to the putatively ancestral crustacean gene order. These include two rearrangements of protein-coding genes, the first reported for any nonchelicerate arthropod. Codon usage and amino acid sequences do not deviate substantially from those reported for other crustaceans. Investigating the phylogenetic distribution of these eight rearrangements will add additional characters to help resolve decapod phylogeny.

Characteristics of the nutrition provider in corporate and hospital wellness programs.

This two-phase research project was conducted to examine the content of corporate- and hospital-sponsored wellness programs and to determine the characteristics of the nutrition provider. In the first phase of the study, a questionnaire was sent to 150 wellness program directors located throughout the United States to determine the nature of their total wellness program. In the second phase, questionnaires were sent to the nutrition provider to elicit specific information on the characteristics and requirements for that position. Results indicated that corporate- and hospital-sponsored wellness programs offered a variety of activities. Those incorporating a nutrition component offered a range of events from nutrition assessment to individual counseling and disease awareness programs. The position of nutrition provider was most often held by a 26- to 46-year old woman with a master's degree and experience and educational background in an allied health field other than dietetics or nutrition. Registered dietitians were more likely to be responsible for the nutrition component of a hospital program than of a corporate program. Our results suggest that opportunities exist for registered dietitians in the field of health promotion and wellness.

Self-care and home dialysis-role of social work.

Social work intervention in Self-Care involves evaluation, preparation, crisis-intervention and ongoing assessment and support. Early introduction of this modality is considered vital and factors of age, education, socio-economic level, sensory and environmental conditions are considered in the evaluation process. The social work relationship with patients is described within the context of family and community supports. Experience has demonstrated that patients with pre-existing adaptation problems may require more concentrated social work counseling. The goals of independence and rehabilitation are shown to be effected by patient motivation and economic restrictions. The social worker participating in the team approach is described as contributing to the patients opportunity for self-determination through patient advocacy, supportive services and social action. Self-Care patients are considered as having high potential for achievement and satisfaction.

Dialysis and transplantation: a mothers' group.

Two social workers are helping mothers of transplant and dialysis patients to deal with the multiple reality and feeling problems posed by the unique situations encountered in the parenting of children with end-stage renal disease. The commonality of these problems indicated a group approach. The mothers' natural grouping was formalized into an effective supportive, educational, and helping experience.