Measuring Symmetry in Children With Unrepaired Cleft Lip: Defining a Standard for the Three-Dimensional Midfacial Reference Plane.

OBJECTIVE: Quantitative measures of facial form to evaluate treatment outcomes for cleft lip (CL) are currently limited. Computer-based analysis of three-dimensional (3D) images provides an opportunity for efficient and objective analysis. The purpose of this study was to define a computer-based standard of identifying the 3D midfacial reference plane of the face in children with unrepaired cleft lip for measurement of facial symmetry. PARTICIPANTS: The 3D images of 50 subjects (35 with unilateral CL, 10 with bilateral CL, five controls) were included in this study. INTERVENTIONS: Five methods of defining a midfacial plane were applied to each image, including two human-based (Direct Placement, Manual Landmark) and three computer-based (Mirror, Deformation, Learning) methods. MAIN OUTCOME MEASURE: Six blinded raters (three cleft surgeons, two craniofacial pediatricians, and one craniofacial researcher) independently ranked and rated the accuracy of the defined planes. RESULTS: Among computer-based methods, the Deformation method performed significantly better than the others. Although human-based methods performed best, there was no significant difference compared with the Deformation method. The average correlation coefficient among raters was .4; however, it was .7 and .9 when the angular difference between planes was greater than 6° and 8°, respectively. CONCLUSIONS: Raters can agree on the 3D midfacial reference plane in children with unrepaired CL using digital surface mesh. The Deformation method performed best among computer-based methods evaluated and can be considered a useful tool to carry out automated measurements of facial symmetry in children with unrepaired cleft lip.

Morphological simulation tests the limits on phenotype discovery in 3D image analysis.

In the past few decades, advances in 3D imaging have created new opportunities for reverse genetic screens. Rapidly growing datasets of 3D images of genetic knockouts require high-throughput, automated computational approaches for identifying and characterizing new phenotypes. However, exploratory, discovery-oriented image analysis pipelines used to discover these phenotypes can be difficult to validate because, by their nature, the expected outcome is not known a priori . Introducing known morphological variation through simulation can help distinguish between real phenotypic differences and random variation; elucidate the effects of sample size; and test the sensitivity and reproducibility of morphometric analyses. Here we present a novel approach for 3D morphological simulation that uses open-source, open-access tools available in 3D Slicer, SlicerMorph, and Advanced Normalization Tools in R (ANTsR). While we focus on diffusible-iodine contrast-enhanced micro-CT (diceCT) images, this approach can be used on any volumetric image. We then use our simulated datasets to test whether tensor-based morphometry (TBM) can recover our introduced differences; to test how effect size and sample size affect detectability; and to determine the reproducibility of our results. In our approach to morphological simulation, we first generate a simulated deformation based on a reference image and then propagate this deformation to subjects using inverse transforms obtained from the registration of subjects to the reference. This produces a new dataset with a shifted population mean while retaining individual variability because each sample deforms more or less based on how different or similar it is from the reference. TBM is a widely-used technique that statistically compares local volume differences associated with local deformations. Our results showed that TBM recovered our introduced morphological differences, but that detectability was dependent on the effect size, the sample size, and the region of interest (ROI) included in the analysis. Detectability of subtle phenotypes can be improved both by increasing the sample size and by limiting analyses to specific body regions. However, it is not always feasible to increase sample sizes in screens of essential genes. Therefore, methodical use of ROIs is a promising way to increase the power of TBM to detect subtle phenotypes. Generating known morphological variation through simulation has broad applicability in developmental, evolutionary, and biomedical morphometrics and is a useful way to distinguish between a failure to detect morphological difference and a true lack of morphological difference. Morphological simulation can also be applied to AI-based supervised learning to augment datasets and overcome dataset limitations.

Maternal ethanol consumption alters the epigenotype and the phenotype of offspring in a mouse model.

Recent studies have shown that exposure to some nutritional supplements and chemicals in utero can affect the epigenome of the developing mouse embryo, resulting in adult disease. Our hypothesis is that epigenetics is also involved in the gestational programming of adult phenotype by alcohol. We have developed a model of gestational ethanol exposure in the mouse based on maternal ad libitum ingestion of 10% (v/v) ethanol between gestational days 0.5-8.5 and observed changes in the expression of an epigenetically-sensitive allele, Agouti viable yellow (A(vy)), in the offspring. We found that exposure to ethanol increases the probability of transcriptional silencing at this locus, resulting in more mice with an agouti-colored coat. As expected, transcriptional silencing correlated with hypermethylation at A(vy). This demonstrates, for the first time, that ethanol can affect adult phenotype by altering the epigenotype of the early embryo. Interestingly, we also detected postnatal growth restriction and craniofacial dysmorphology reminiscent of fetal alcohol syndrome, in congenic a/a siblings of the A(vy) mice. These findings suggest that moderate ethanol exposure in utero is capable of inducing changes in the expression of genes other than A(vy), a conclusion supported by our genome-wide analysis of gene expression in these mice. In addition, offspring of female mice given free access to 10% (v/v) ethanol for four days per week for ten weeks prior to conception also showed increased transcriptional silencing of the A(vy) allele. Our work raises the possibility of a role for epigenetics in the etiology of fetal alcohol spectrum disorders, and it provides a mouse model that will be a useful resource in the continued efforts to understand the consequences of gestational alcohol exposure at the molecular level.

Oligocene mammals from Ethiopia and faunal exchange between Afro-Arabia and Eurasia.

Afro-Arabian mammalian communities underwent a marked transition near the Oligocene/Miocene boundary at approximately 24 million years (Myr) ago. Although it is well documented that the endemic paenungulate taxa were replaced by migrants from the Northern Hemisphere, the timing and evolutionary dynamics of this transition have long been a mystery because faunas from about 32 to 24 Myr ago are largely unknown. Here we report a late Oligocene fossil assemblage from Ethiopia, which constrains the migration to postdate 27 Myr ago, and yields new insight into the indigenous faunal dynamics that preceded this event. The fauna is composed of large paenungulate herbivores and reveals not only which earlier taxa persisted into the late Oligocene epoch but also demonstrates that one group, the Proboscidea, underwent a marked diversification. When Eurasian immigrants entered Afro-Arabia, a pattern of winners and losers among the endemics emerged: less diverse taxa such as arsinoitheres became extinct, moderately species-rich groups such as hyracoids continued into the Miocene with reduced diversity, whereas the proboscideans successfully carried their adaptive radiation out of Afro-Arabia and across the world.

High-resolution X-ray computed tomography scanning of primate copulatory plugs.

In this study, high-resolution computed tomography X-ray scanning was used to scan ring-tailed lemur (Lemur catta) copulatory plugs. This method produced accurate measures of plug volume and surface area, but was not useful for visualizing plug internal structure. Copulatory plug size was of interest because it may relate to male fertilization success. Copulatory plugs form from coagulated ejaculate, and are routinely displaced in this species by the penis of a subsequent mate during copulation (Parga [2003] Int. J. Primatol. 24:889-899). Because one potential function of these plugs may be to preclude or delay other males' successful insemination of females, we tested the hypothesis that larger plugs are more difficult for subsequent males to displace. Plugs were collected opportunistically upon displacement during data collection on L. catta mating behavior on St. Catherines Island, Georgia (USA) during two subsequent breeding seasons. Copulatory plugs exhibited a wide range of volumes: 1,758-5,013.6 mm3 (n = 9). Intraindividual differences in plug volume were sometimes greater than interindividual differences. Contrary to predictions, larger plugs were not more time-consuming for males to displace via penile intromission during copulation. Nor were plugs with longer vaginal residence times notably smaller than plugs with shorter residence times, as might be expected if plugs disintegrate while releasing sperm (Asdell [1946] Patterns of Mammalian Reproduction; Ithaca: Comstock). We found a significant inverse correlation between number of copulatory mounts leading to ejaculation and copulatory plug volume. This may indicate that if males are sufficiently sexually aroused to reach ejaculation in fewer mounts, they tend to produce ejaculates of greater volume.

Preliminary observations on the calcaneal trabecular microarchitecture of extant large-bodied hominoids.

In this pilot study, we point out potential differences between calcaneal trabecular microarchitecture in humans and nonhuman large apes, such as increased degree of anisotropy, reduced bone volume fraction, and very stereotypical orientation of the trabeculae. Even though sample size does not permit us to investigate the issue statistically, the observed differences between humans and other hominoids warrants further in-depth investigation. We also show that some measurements of the trabecular network might be dependent on sampling density, which can be difficult to deal with in the case of animals of different body masses. We also present a new visualization technique that summarizes the trabecular network orientation, and makes it more readily interpretable than the summary statistics of the underlying fabric tensor of the orientation matrix.