How to estimate the measurement error variance associated with ancestry proportion estimates

To show how the variance of the measurement error (ME) associated with individual ancestry proportion estimates can be estimated, especially when the number of ancestral populations (k) is greater than 2. We extend existing internal consistency measures to estimate the ME variance, and we compare these estimates with the ME variance estimated by use of the repeated measurement (RM) approach. Both approaches work by dividing the genotyped markers into subsets. We examine the effect of the number of subsets and of the allocation of markers to each subset on the performance of each approach. We used simulated data for all comparisons. Independently of the value of k, the measures of internal reliability provided less biased and more precise estimates of the ME variance than did those obtained with the RM approach. Both methods tend to perform better when a large number of subsets of markers with similar sizes are considered. Our results will facilitate the use of ME correction methods to address the ME problem in individual ancestry proportion estimates. Our method will improve the ability to control for type I error inflation and loss of power in association tests and other genomic research involving ancestry estimates

Health behavior modification after electron beam computed tomography and physician consultation

This study aimed to determine whether participants reported altering health behaviors (physical activity, diet, and alcohol consumption) after seeing results from an electron-beam computed tomography (EBCT) scan for coronary artery calcium and reviewing these results with a physician. Clinicians attempt to motivate patients to control cardiovascular risk factors by adopting healthy behaviors and reducing harmful actions. Asymptomatic patients (N = 510) were evaluated by EBCT for the extent of coronary artery calcium. Information pertaining to demographics, health history, and lifestyle/health behaviors was obtained from each participant at the time of the EBCT scan. Patients were given their numerical calcium score, shown images of their coronary arteries, and counseled by a physician for lifestyle and medical risk modification based on their coronary artery calcium score. Approximately 6 years after the scan, participants completed a follow-up questionnaire related to lifestyle modifications. In multivariable analysis, the presence and extent of coronary artery calcium was significantly associated with beneficial health behavior modifications. Specifically, the greater a patient’s coronary artery calcium score, the more likely they were to report increasing exercise (odds ratio = 1.34, P = 0.02), changing diet (odds ratio = 1.40, P < 0.01), and changing alcohol intake (odds ratio = 1.46, P = 0.05). This study suggests that seeing and being counseled on the presence and extent of coronary artery calcium is significantly associated with behavior change

Why don't serum vitamin D concentrations associate with BMD by DXA? A case of being 'bound' to the wrong assay? Implications for vitamin D screening.

BACKGROUND: The association between bone mineral density (BMD) and serum25-hydroxyvitamin D (25(OH)D) concentration is weak, particularly in certain races (eg, BlackAfrican vs Caucasian) and in athletic populations. We aimed to examine if bioavailable vitamin D rather than serum 25(OH)D was related to markers of bone health within a racially diverse athletic population. METHODS: In 604 male athletes (Arab (n=327), Asian (n=48), Black(n=108), Caucasian (n=53)and Hispanic (n=68)), we measured total 25(OH)D, vitamin D-binding protein and BMD by DXA. Bioavailable vitamin D was calculated using the free hormone hypothesis. RESULTS: From 604 athletes, 21.5% (n=130) demonstrated severe 25(OH)D deficiency, 37.1% (n=224) deficiency, 26% (n=157) insufficiency and 15.4% (n=93) sufficiency. Serum 25(OH)D concentrations were not associated with BMD at any site. After adjusting for age and race, bioavailable vitamin D was associated with BMD (spine, neck and hip). Mean serum vitamin D binding protein concentrations were not associated with 25(OH)D concentrations (p=0.392). CONCLUSION: Regardless of age or race, bioavailable vitamin D and not serum 25(OH)D was associated with BMD in a racially diverse athletic population. If vitamin D screening is warranted, clinicians should use appropriate assays to calculate vitamin D binding protein and bioavailable vitamin D levels concentrations than serum 25(OH)D. In turn, prophylactic vitamin D supplementation to 'correct' insufficient athletes should not be based on serum 25(OH)D measures

The Cambridge Sympathy Test: Self-reported sympathy and distress in autism

Abstract Background: Difficulties with aspects of social interaction, including empathy, comprise a core symptom of autism spectrum conditions (autism). Sympathy is a specific form of empathy and involves both cognitive and affective empathy. Data are presented from a new task of self-reported sympathy and personal distress. Methods: Participants with autism (93 males; 161 females) and controls (40 males, 93 females) took part in an online survey via the Autism Research Centre or Cambridge Psychology websites. Participants completed a task where they were asked to rate photographic images that were either of distressing, neutral or happy scenes, according to the amount of sympathy they had for the individual in the photo and the degree of personal distress they felt. All participants also completed the Empathy Quotient (EQ). Results: Significant differences were found between the autism and control groups for both self-reported sympathy and personal distress, with participants with autism giving lower ratings than controls. Control females scored significantly higher than control males in both sympathy and distress. Sympathy and distress ratings in the autism group did not differ significantly by sex. EQ showed positive correlations with sympathy and distress scores. Conclusions: Using a new measure of self-reported sympathy, we found that both males and females with autism gave lower ratings of sympathy when viewing people in distressing scenarios, compared to controls.The research leading to these results has received support from the Innovative Medicines Initiative Joint Undertaking under grant agreement n° 115300, resources of which are composed of financial contribution from the European Union's Seventh Framework Programme (FP7/2007 - 2013) and EFPIA companies' in kind contribution. The authors were also supported by Autism Research Trust, the MRC and the National Institute for Health Research (NIHR) Collaboration for Leadership in Applied Health Research and Care East of England at Cambridgeshire and Peterborough NHS Foundation Trust

Trace gases and CO2 isotope records from cabo de rama, India

Concentrations of carbon dioxide (CO2), methane (CH4), carbon monoxide (CO), nitrous oxide (N2O) and hydrogen (H2), and the stable carbon (δ 13C-CO2) and oxygen (δ 18O-CO2) isotopic composition of CO2 have been measured in air samples collected from Cabo de Rama (CRI), India, for the period 1993-2002. The observations show clear signatures of Northern and Southern Hemispheric (NH and SH) air masses, mixed with their regional fluxes and chemical loss mechanisms, resulting in complex seasonal variation of these gases. The CRI measurements are compared with remote marine sites at Seychelles and Mauna Loa. Simulations of two major anthropogenic greenhouse gases (CO2 and CH4) concentrations using a chemistry-transport model for the CRI site suggest that globally optimized fluxes can produce results comparable to the observations. We discuss that CRI observations have provided critical guidance in optimizing the fluxes to constrain the regional source/sinks balance

Functional diversity of marine ecosystems after the Late Permian mass extinction event

Article can be accessed from http://www.nature.com/ngeo/journal/v7/n3/full/ngeo2079.htmlThe Late Permian mass extinction event was the most severe such crisis of the past 500 million years and occurred during an episode of global warming. It is assumed to have had significant ecological impact, but its effects on marine ecosystem functioning are unknown and the patterns of marine recovery are debated. We analysed the fossil occurrences of all known Permian-Triassic benthic marine genera and assigned each to a functional group based on their inferred life habit. We show that despite the selective extinction of 62-74% of marine genera there was no significant loss of functional diversity at the global scale, and only one novel mode of life originated in the extinction aftermath. Early Triassic marine ecosystems were not as ecologically depauperate as widely assumed, which explains the absence of a Cambrian-style Triassic radiation in higher taxa. Functional diversity was, however, significantly reduced in particular regions and habitats, such as tropical reefs, and at these scales recovery varied spatially and temporally, probably driven by migration of surviving groups. Marine ecosystems did not return to their pre-extinction state, however, and radiation of previously subordinate groups such as motile, epifaunal grazers led to greater functional evenness by the Middle Triassic

The effects of supernovae on the dynamical evolution of binary stars and star clusters

In this chapter I review the effects of supernovae explosions on the dynamical evolution of (1) binary stars and (2) star clusters. (1) Supernovae in binaries can drastically alter the orbit of the system, sometimes disrupting it entirely, and are thought to be partially responsible for `runaway' massive stars - stars in the Galaxy with large peculiar velocities. The ejection of the lower-mass secondary component of a binary occurs often in the event of the more massive primary star exploding as a supernova. The orbital properties of binaries that contain massive stars mean that the observed velocities of runaway stars (10s - 100s km s$^{-1}$) are consistent with this scenario. (2) Star formation is an inherently inefficient process, and much of the potential in young star clusters remains in the form of gas. Supernovae can in principle expel this gas, which would drastically alter the dynamics of the cluster by unbinding the stars from the potential. However, recent numerical simulations, and observational evidence that gas-free clusters are observed to be bound, suggest that the effects of supernova explosions on the dynamics of star clusters are likely to be minimal.Comment: 16 pages, to appear in the 'Handbook of Supernovae', eds. Paul Murdin and Athem Alsabti. This version replaces an earlier version that contained several typo

Parametric study of EEG sensitivity to phase noise during face processing

&lt;b&gt;Background: &lt;/b&gt; The present paper examines the visual processing speed of complex objects, here faces, by mapping the relationship between object physical properties and single-trial brain responses. Measuring visual processing speed is challenging because uncontrolled physical differences that co-vary with object categories might affect brain measurements, thus biasing our speed estimates. Recently, we demonstrated that early event-related potential (ERP) differences between faces and objects are preserved even when images differ only in phase information, and amplitude spectra are equated across image categories. Here, we use a parametric design to study how early ERP to faces are shaped by phase information. Subjects performed a two-alternative force choice discrimination between two faces (Experiment 1) or textures (two control experiments). All stimuli had the same amplitude spectrum and were presented at 11 phase noise levels, varying from 0% to 100% in 10% increments, using a linear phase interpolation technique. Single-trial ERP data from each subject were analysed using a multiple linear regression model. &lt;b&gt;Results: &lt;/b&gt; Our results show that sensitivity to phase noise in faces emerges progressively in a short time window between the P1 and the N170 ERP visual components. The sensitivity to phase noise starts at about 120–130 ms after stimulus onset and continues for another 25–40 ms. This result was robust both within and across subjects. A control experiment using pink noise textures, which had the same second-order statistics as the faces used in Experiment 1, demonstrated that the sensitivity to phase noise observed for faces cannot be explained by the presence of global image structure alone. A second control experiment used wavelet textures that were matched to the face stimuli in terms of second- and higher-order image statistics. Results from this experiment suggest that higher-order statistics of faces are necessary but not sufficient to obtain the sensitivity to phase noise function observed in response to faces. &lt;b&gt;Conclusion: &lt;/b&gt; Our results constitute the first quantitative assessment of the time course of phase information processing by the human visual brain. We interpret our results in a framework that focuses on image statistics and single-trial analyses

The molecular basis of color vision in colorful fish: Four Long Wave-Sensitive (LWS) opsins in guppies (Poecilia reticulata) are defined by amino acid substitutions at key functional sites

<p>Abstract</p> <p>Background</p> <p>Comparisons of functionally important changes at the molecular level in model systems have identified key adaptations driving isolation and speciation. In cichlids, for example, long wavelength-sensitive (LWS) opsins appear to play a role in mate choice and male color variation within and among species. To test the hypothesis that the evolution of elaborate coloration in male guppies (<it>Poecilia reticulata</it>) is also associated with opsin gene diversity, we sequenced long wavelength-sensitive (LWS) opsin genes in six species of the family Poeciliidae.</p> <p>Results</p> <p>Sequences of four LWS opsin genes were amplified from the guppy genome and from mRNA isolated from adult guppy eyes. Variation in expression was quantified using qPCR. Three of the four genes encode opsins predicted to be most sensitive to different wavelengths of light because they vary at key amino acid positions. This family of LWS opsin genes was produced by a diversity of duplication events. One, an intronless gene, was produced prior to the divergence of families Fundulidae and Poeciliidae. Between-gene PCR and DNA sequencing show that two of the guppy LWS opsins are linked in an inverted orientation. This inverted tandem duplication event occurred near the base of the poeciliid tree in the common ancestor of <it>Poecilia </it>and <it>Xiphophorus</it>. The fourth sequence has been uncovered only in the genus <it>Poecilia</it>. In the guppies surveyed here, this sequence is a hybrid, with the 5' end most similar to one of the tandem duplicates and the 3' end identical to the other.</p> <p>Conclusion</p> <p>Enhanced wavelength discrimination, a possible consequence of opsin gene duplication and divergence, might have been an evolutionary prerequisite for color-based sexual selection and have led to the extraordinary coloration now observed in male guppies and in many other poeciliids.</p

Neural correlates of enhanced visual short-term memory for angry faces: An fMRI study

Copyright: © 2008 Jackson et al.Background: Fluid and effective social communication requires that both face identity and emotional expression information are encoded and maintained in visual short-term memory (VSTM) to enable a coherent, ongoing picture of the world and its players. This appears to be of particular evolutionary importance when confronted with potentially threatening displays of emotion - previous research has shown better VSTM for angry versus happy or neutral face identities.Methodology/Principal Findings: Using functional magnetic resonance imaging, here we investigated the neural correlates of this angry face benefit in VSTM. Participants were shown between one and four to-be-remembered angry, happy, or neutral faces, and after a short retention delay they stated whether a single probe face had been present or not in the previous display. All faces in any one display expressed the same emotion, and the task required memory for face identity. We find enhanced VSTM for angry face identities and describe the right hemisphere brain network underpinning this effect, which involves the globus pallidus, superior temporal sulcus, and frontal lobe. Increased activity in the globus pallidus was significantly correlated with the angry benefit in VSTM. Areas modulated by emotion were distinct from those modulated by memory load.Conclusions/Significance: Our results provide evidence for a key role of the basal ganglia as an interface between emotion and cognition, supported by a frontal, temporal, and occipital network.The authors were supported by a Wellcome Trust grant (grant number 077185/Z/05/Z) and by BBSRC (UK) grant BBS/B/16178