Initial results of multilevel principal components analysis of facial shape

Traditionally, active shape models (ASMs) do not make a distinction between groups in the subject population and they rely on methods such as (single-level) principal components analysis (PCA). Multilevel principal components analysis (PCA) allows one to model between-group effects and within-group effects explicitly. Three dimensional (3D) laser scans were taken from 240 subjects (38 Croatian female, 35 Croatian male, 40 English female, 40 English male, 23 Welsh female, 27 Welsh male, 23 Finnish female, and 24 Finnish male) and 21 landmark points were created subsequently for each scan. After Procrustes transformation, eigenvalues from mPCA and from single-level PCA based on these points were examined. mPCA indicated that the first two eigenvalues of largest magnitude related to within-groups components, but that the next largest eigenvalue related to between-groups components. Eigenvalues from single-level PCA always had a larger magnitude than either within-group or between-group eigenvectors at equivalent eigenvalue number. An examination of the first mode of variation indicated possible mixing of between-group and within-group effects in single-level PCA. Component scores for mPCA indicated clustering with country and gender for the between-groups components (as ex-pected), but not for the within-group terms (also as expected). Clustering of component scores for single-level PCA was harder to resolve. In conclusion, mPCA is viable method of forming shape models that offers distinct advantages over single-level PCA when groups occur naturally in the subject population

What’s in a Smile? Initial results of multilevel principal components analysis of facial shape and image texture

Multilevel principal components analysis (mPCA) has previously been shown to provide a simple and straightforward method of forming point distribution models that can be used in (active) shape models. Here we extend the mPCA approach to model image texture as well as shape. As a test case, we consider a set of (2D frontal) facial images from a group of 80 Finnish subjects (34 male; 46 female) with two different facial expressions (smiling and neutral) per subject. Shape (in terms of landmark points) and image texture are considered separately in this initial analysis. Three-level models are constructed that contain levels for biological sex, “within-subject” variation (i.e., facial expression), and “between-subject” variation (i.e., all other sources of variation). By considering eigenvalues, we find that the order of importance as sources of variation for facial shape is: facial expression (47.5%), between-subject variations (45.1%), and then biological sex (7.4%). By contrast, the order for image texture is: between-subject variations (55.5%), facial expression (37.1%), and then biological sex (7.4%). The major modes for the facial expression level of the mPCA models clearly reflect changes in increased mouth size and increased prominence of cheeks during smiling for both shape and texture. Even subtle effects such as changes to eyes and nose shape during smile are seen clearly. The major mode for the biological sex level of the mPCA models similarly relates clearly to changes between male and female. Model fits yield “scores” for each principal component that show strong clustering for both shape and texture by biological sex and facial expression at appropriate levels of the model. We conclude that mPCA correctly decomposes sources of variation due to biological sex and facial expression (etc.) and that it provides a reliable method of forming models of both shape and image texture

Transport of Explosive Residue Surrogates in Saturated Porous Media

Department of Defense operational ranges may become contaminated by particles of explosives residues (ER) as a result of low-order detonations of munitions. The goal of this study was to determine the extent to which particles of ER could migrate through columns of sandy sediment, representing model aquifer materials. Transport experiments were conducted in saturated columns (2 × 20 cm) packed with different grain sizes of clean sand or glass beads. Fine particles (approximately 2 to 50 μm) of 2,6-dinitrotoluene (DNT) were used as a surrogate for ER. DNT particles were applied to the top 1 cm of sand or beads in the columns, and the columns were subsequently leached with artificial groundwater solutions. DNT migration occurred as both dissolved and particulate phases. Concentration differences between unfiltered and filtered samples indicate that particulate DNT accounted for up to 41% of the mass recovered in effluent samples. Proportionally, more particulate than dissolved DNT was recovered in effluent solutions from columns with larger grain sizes, while total concentrations of DNT in effluent were inversely related to grain size. Of the total DNT mass applied to the uppermost layer of the column, <3% was recovered in the effluent with the bulk remaining in the top 2 cm of the column. Our results suggest there is some potential for subsurface migration of ER particles and that most of the particles will be retained over relatively short transport distances

An optimized TOPS+ comparison method for enhanced TOPS models

This article has been made available through the Brunel Open Access Publishing Fund.Background Although methods based on highly abstract descriptions of protein structures, such as VAST and TOPS, can perform very fast protein structure comparison, the results can lack a high degree of biological significance. Previously we have discussed the basic mechanisms of our novel method for structure comparison based on our TOPS+ model (Topological descriptions of Protein Structures Enhanced with Ligand Information). In this paper we show how these results can be significantly improved using parameter optimization, and we call the resulting optimised TOPS+ method as advanced TOPS+ comparison method i.e. advTOPS+. Results We have developed a TOPS+ string model as an improvement to the TOPS [1-3] graph model by considering loops as secondary structure elements (SSEs) in addition to helices and strands, representing ligands as first class objects, and describing interactions between SSEs, and SSEs and ligands, by incoming and outgoing arcs, annotating SSEs with the interaction direction and type. Benchmarking results of an all-against-all pairwise comparison using a large dataset of 2,620 non-redundant structures from the PDB40 dataset [4] demonstrate the biological significance, in terms of SCOP classification at the superfamily level, of our TOPS+ comparison method. Conclusions Our advanced TOPS+ comparison shows better performance on the PDB40 dataset [4] compared to our basic TOPS+ method, giving 90 percent accuracy for SCOP alpha+beta; a 6 percent increase in accuracy compared to the TOPS and basic TOPS+ methods. It also outperforms the TOPS, basic TOPS+ and SSAP comparison methods on the Chew-Kedem dataset [5], achieving 98 percent accuracy. Software Availability: The TOPS+ comparison server is available at http://balabio.dcs.gla.ac.uk/mallika/WebTOPS/.This article is available through the Brunel Open Access Publishing Fun

Ecological Release and Venom Evolution of a Predatory Marine Snail at Easter Island

BACKGROUND:Ecological release is coupled with adaptive radiation and ecological diversification yet little is known about the molecular basis of phenotypic changes associated with this phenomenon. The venomous, predatory marine gastropod Conus miliaris has undergone ecological release and exhibits increased dietary breadth at Easter Island. METHODOLOGY/PRINCIPAL FINDINGS:We examined the extent of genetic differentiation of two genes expressed in the venom of C. miliaris among samples from Easter Island, American Samoa and Guam. The population from Easter Island exhibits unique frequencies of alleles that encode distinct peptides at both loci. Levels of divergence at these loci exceed observed levels of divergence observed at a mitochondrial gene region at Easter Island. CONCLUSIONS/SIGNIFICANCE:Patterns of genetic variation at two genes expressed in the venom of this C. miliaris suggest that selection has operated at these genes and contributed to the divergence of venom composition at Easter Island. These results show that ecological release is associated with strong selection pressures that promote the evolution of new phenotypes

MS4a4B, a CD20 Homologue in T Cells, Inhibits T Cell Propagation by Modulation of Cell Cycle

MS4a4B, a CD20 homologue in T cells, is a novel member of the MS4A gene family in mice. The MS4A family includes CD20, FcεRIβ, HTm4 and at least 26 novel members that are characterized by their structural features: with four membrane-spanning domains, two extracellular domains and two cytoplasmic regions. CD20, FcεRIβ and HTm4 have been found to function in B cells, mast cells and hematopoietic cells respectively. However, little is known about the function of MS4a4B in T cell regulation. We demonstrate here that MS4a4B negatively regulates mouse T cell proliferation. MS4a4B is highly expressed in primary T cells, natural killer cells (NK) and some T cell lines. But its expression in all malignant T cells, including thymoma and T hybridoma tested, was silenced. Interestingly, its expression was regulated during T cell activation. Viral vector-driven overexpression of MS4a4B in primary T cells and EL4 thymoma cells reduced cell proliferation. In contrast, knockdown of MS4a4B accelerated T cell proliferation. Cell cycle analysis showed that MS4a4B regulated T cell proliferation by inhibiting entry of the cells into S-G2/M phase. MS4a4B-mediated inhibition of cell cycle was correlated with upregulation of Cdk inhibitory proteins and decreased levels of Cdk2 activity, subsequently leading to inhibition of cell cycle progression. Our data indicate that MS4a4B negatively regulates T cell proliferation. MS4a4B, therefore, may serve as a modulator in the negative-feedback regulatory loop of activated T cell

Understanding Society Innovation Panel Wave 11: Results from Methodological Experiments

This is the final version. Available from the University of Essex via the link in this recordThis paper presents some preliminary findings from Wave 11 of the Innovation Panel (IP11) of Understanding Society: The UK Household Longitudinal Study. Understanding Society is a major panel survey in the UK. In May 2018, the eleventh wave of the Innovation Panel went into the field. IP11 used a mixed-mode design, using on-line interviews and face-to-face interviews. This paper describes the design of IP11, the experiments carried and the preliminary findings from early analysis of the data

Trends in the perceived body size of adolescent males and females in Scotland, 1990–2014: changing associations with mental well-being

Objectives: This paper explores trends in Scottish adolescents’ body size perceptions and associated mental well-being outcomes. Methods: Data were collected on Scottish 11, 13 and 15-year olds by the Health Behaviour in School-aged Children study between 1990 and 2014 (n=42,312). Logistic regression was used to examine changes in the prevalence of over- and underweight perceptions. Ordinal and linear regression was used to examine changes in the association between body perception and mental well-being. Results: Little change was observed in over- or under-weight perceptions between 1990 and 2014. However, relative to those perceiving their body as ‘about right’, those perceiving themselves as overweight reported decreasing confidence (all groups), decreasing happiness (11- and 13-year old girls) and increasing psychological symptoms (all girls and 15 year-old boys). Perceived underweight is associated with poor well-being, especially in males, but we present little evidence that this is a recent phenomenon. Conclusions: We present evidence suggesting that the influence of body image on adolescent mental health is increasing over time. This may play a role in the recently observed worsening of mental well-being in Scottish adolescents.Publisher PDFPeer reviewe

Impact of race pace on development of hyponatraemia in full- and half-marathoners

Objective. Prior studies of full-marathon participants have demonstrated a higher incidence of hyponatraemia in runners with completion times of 4 hours or more. Our primary aim was to determine if slower pace is associated with increased prevalence of hyponatraemia. Secondly, we evaluated the prevalence of hyponatraemia in full-marathoners v. halfmarathoners.Methods. This observational, cross-sectional study comprised consenting runners in the 26.2 With Donna, The National Marathon to Finish Breast Cancer, in Jacksonville Beach, Florida, February 2008. On race day, participants completed a questionnaire, provided finger-stick blood samples, and were weighed both pre- and post-race.Results. A significant negative association was found between pace and post-race sodium level (p&lt;0.001). A negative correlation was found between finishing time and post-race sodium level (p&lt;0.001). The prevalence of post-race hyponatraemia was 4% (4/106) among half-marathoners and 13% (12/89) among full-marathoners (P=0.02). An inverse correlation was found between sodium change and weight change, significant in fullmarathoners (r=-0.55, p&lt;0.001) but not half-marathoners (r=- 0.23, p=0.042).Conclusions. Slower race pace and longer finishing times were associated with lower post-race sodium levels. Full-marathoners had a significantly higher prevalence of hyponatraemia. The development of hyponatraemia was associated with weight gain. Our data indicate that the relationship between post-race sodium concentration and pace differs according to the distance of the event. We can extrapolate from this data that longer racedistance with increased availability of fluid stations combined with a slower pace may increase the risk of developing exerciseinduced hyponatraemia

Atmospheric Ice‐Nucleating Particles in the Dusty Tropical Atlantic

Desert dust is one of the most important atmospheric ice-nucleating aerosol species around the globe. However, there have been very few measurements of ice-nucleating particle (INP) concentrations in dusty air close to desert sources. In this study we report the concentration of INPs in dust laden air over the tropical Atlantic within a few days' transport of one of the world's most important atmospheric sources of desert dust, the Sahara. These measurements were performed as part of the Ice in Clouds Experiment-Dust campaign based in Cape Verde, during August 2015. INP concentrations active in the immersion mode, determined using a droplet-on-filter technique, ranged from around 10² m⁻³ at -12°C to around 10⁵ m⁻³ at -23°C. There is about 2 orders of magnitude variability in INP concentration for a particular temperature, which is determined largely by the variability in atmospheric dust loading. These measurements were made at altitudes from 30 to 3,500 m in air containing a range of dust loadings. The ice active site density (n s ) for desert dust dominated aerosol derived from our measurements agrees with several laboratory-based parameterizations for ice nucleation by desert dust within 1 to 2 orders of magnitude. The small variability in n s values determined from our measurements (within about 1 order of magnitude) is striking given that the back trajectory analysis suggests that the sources of dust were geographically diverse. This is consistent with previous work, which indicates that desert dust's ice-nucleating activity is only weakly dependent on source