Improving fluid registration through white matter segmentation in a twin study design

Robust and automatic non-rigid registration depends on many parameters that have not yet been systematically explored. Here we determined how tissue classification influences non-linear fluid registration of brain MRI. Twin data is ideal for studying this question, as volumetric correlations between corresponding brain regions that are under genetic control should be higher in monozygotic twins (MZ) who share 100% of their genes when compared to dizygotic twins (DZ) who share half their genes on average. When these substructure volumes are quantified using tensor-based morphometry, improved registration can be defined based on which method gives higher MZ twin correlations when compared to DZs, as registration errors tend to deplete these correlations. In a study of 92 subjects, higher effect sizes were found in cumulative distribution functions derived from statistical maps when performing tissue classification before fluid registration, versus fluidly registering the raw images. This gives empirical evidence in favor of pre-segmenting images for tensor-based morphometry.

Mapping genetic influences on ventricular structure in twins

Despite substantial progress in measuring the anatomical and functional variability of the human brain, little is known about the genetic and environmental causes of these variations. Here we developed an automated system to visualize genetic and environmental effects on brain structure in large brain MRI databases. We applied our multi-template segmentation approach termed "Multi-Atlas Fluid Image Alignment" to fluidly propagate hand-labeled parameterized surface meshes, labeling the lateral ventricles, in 3D volumetric MRI scans of 76 identical (monozygotic, MZ) twins (38 pairs; mean age = 24.6 (SD = 1.7)); and 56 same-sex fraternal (dizygotic, DZ) twins (28 pairs; mean age = 23.0 (SD = 1.8)), scanned as part of a 5-year research study that will eventually study over 1000 subjects. Mesh surfaces were averaged within subjects to minimize segmentation error. We fitted quantitative genetic models at each of 30,000 surface points to measure the proportion of shape variance attributable to (1) genetic differences among subjects, (2) environmental influences unique to each individual, and (3) shared environmental effects. Surface-based statistical maps, derived from path analysis, revealed patterns of heritability, and their significance, in 3D. Path coefficients for the 'ACE' model that best fitted the data indicated significant contributions from genetic factors (A = 7.3%), common environment (C = 38.9%) and unique environment (E = 53.8%) to lateral ventricular volume. Earlier-maturing occipital horn regions may also be more genetically influenced than later-maturing frontal regions. Maps visualized spatially-varying profiles of environmental versus genetic influences. The approach shows promise for automatically measuring gene-environment effects in large image databases.

Common genetic variants influence human subcortical brain structures

The highly complex structure of the human brain is strongly shaped by genetic influences. Subcortical brain regions form circuits with cortical areas to coordinate movement, learning, memory and motivation, and altered circuits can lead to abnormal behaviour and disease. To investigate how common genetic variants affect the structure of these brain regions, here we conduct genome-wide association studies of the volumes of seven subcortical regions and the intracranial volume derived from magnetic resonance images of 30,717 individuals from 50 cohorts. We identify five novel genetic variants influencing the volumes of the putamen and caudate nucleus. We also find stronger evidence for three loci with previously established influences on hippocampal volume and intracranial volume. These variants show specific volumetric effects on brain structures rather than global effects across structures. The strongest effects were found for the putamen, where a novel intergenic locus with replicable influence on volume (rs945270; P = 1.08×10 -33; 0.52% variance explained) showed evidence of altering the expression of the KTN1 gene in both brain and blood tissue. Variants influencing putamen volume clustered near developmental genes that regulate apoptosis, axon guidance and vesicle transport. Identification of these genetic variants provides insight into the causes of variability in human brain development, and may help to determine mechanisms of neuropsychiatric dysfunction.

A new combined surface and volume registration

3D registration of brain MRI data is vital for many medical imaging applications. However, purely intensitybased approaches for inter-subject matching of brain structure are generally inaccurate in cortical regions, due to the highly complex network of sulci and gyri, which vary widely across subjects. Here we combine a surfacebased cortical registration with a 3D fluid one for the first time, enabling precise matching of cortical folds, but allowing large deformations in the enclosed brain volume, which guarantee diffeomorphisms. This greatly improves the matching of anatomy in cortical areas. The cortices are segmented and registered with the software Freesurfer. The deformation field is initially extended to the full 3D brain volume using a 3D harmonic mapping that preserves the matching between cortical surfaces. Finally, these deformation fields are used to initialize a 3D Riemannian fluid registration algorithm, that improves the alignment of subcortical brain regions. We validate this method on an MRI dataset from 92 healthy adult twins. Results are compared to those based on volumetric registration without surface constraints; the resulting mean templates resolve consistent anatomical features both subcortically and at the cortex, suggesting that the approach is well-suited for cross-subject integration of functional and anatomic data.

Neuroimaging and genetics: Exploring, searching, and finding

This issue on the genetics of brain imaging phenotypes is a celebration of the happy marriage between two of science's highly interesting fields: neuroscience and genetics. The articles collected here are ample evidence that a good deal of synergy exists in this marriage. A wide selection of papers is presented that provide many different perspectives on how genes cause variation in brain structure and function, which in turn influence behavioral phenotypes (including psychopathology). They are examples of the many different methodologies in contemporary genetics and neuroscience research. Genetic methodology includes genome-wide association (GWA), candidate-gene association, and twin studies. Sources of data on brain phenotypes include cortical gray matter (GM) structural/volumetric measures from magnetic resonance imaging (MRI); white matter (WM) measures from diffusion tensor imaging (DTI), such as fractional anisotropy; functional- (activity-) based measures from electroencephalography (EEG), and functional MRI (fMRI). Together, they reflect a combination of scientific fields that have seen great technological advances, whether it is the single-nucleotide polymorphism (SNP) array in genetics, the increasingly high-resolution MRI imaging, or high angular resolution diffusion imaging technique for measuring WM connective properties.

The presence of executive deficits in patients with Obstructive Sleep Apnoea

Obstructive sleep apnoea (OSA) is a chronic condition in which the upper airways collapse repeatedly during sleep, completely or partially obstructing breathing. This obstruction leads to chronic intermittent hypoxia and severe sleep fragmentation, disrupting the restorative functions of sleep. Beebe and Gozal (2002)a developed a theory which hypothesises that disruption of the restorative functions of sleep lead to a chronic low level brain damage most evident in executive functions (EF). Neuropsychological testing of EF, volumetric MRI, magnetic resonance spectroscopy, event related potentials and CSF biomarkers all provide support for this theory. Little research has been done to explore the nature of the subjective complaint and it’s impact on the activities of daily living.

RNASeqBrowser: A genome browser for simultaneous visualization of raw strand specific RNAseq reads and UCSC genome browser custom tracks

Background Strand specific RNAseq data is now more common in RNAseq projects. Visualizing RNAseq data has become an important matter in Analysis of sequencing data. The most widely used visualization tool is the UCSC genome browser that introduced the custom track concept that enabled researchers to simultaneously visualize gene expression at a particular locus from multiple experiments. Our objective of the software tool is to provide friendly interface for visualization of RNAseq datasets. Results This paper introduces a visualization tool (RNASeqBrowser) that incorporates and extends the functionality of the UCSC genome browser. For example, RNASeqBrowser simultaneously displays read coverage, SNPs, InDels and raw read tracks with other BED and wiggle tracks -- all being dynamically built from the BAM file. Paired reads are also connected in the browser to enable easier identification of novel exon/intron borders and chimaeric transcripts. Strand specific RNAseq data is also supported by RNASeqBrowser that displays reads above (positive strand transcript) or below (negative strand transcripts) a central line. Finally, RNASeqBrowser was designed for ease of use for users with few bioinformatic skills, and incorporates the features of many genome browsers into one platform. Conclusions The features of RNASeqBrowser: (1) RNASeqBrowser integrates UCSC genome browser and NGS visualization tools such as IGV. It extends the functionality of the UCSC genome browser by adding several new types of tracks to show NGS data such as individual raw reads, SNPs and InDels. (2) RNASeqBrowser can dynamically generate RNA secondary structure. It is useful for identifying non-coding RNA such as miRNA. (3) Overlaying NGS wiggle data is helpful in displaying differential expression and is simple to implement in RNASeqBrowser. (4) NGS data accumulates a lot of raw reads. Thus, RNASeqBrowser collapses exact duplicate reads to reduce visualization space. Normal PC’s can show many windows of NGS individual raw reads without much delay. (5) Multiple popup windows of individual raw reads provide users with more viewing space. This avoids existing approaches (such as IGV) which squeeze all raw reads into one window. This will be helpful for visualizing multiple datasets simultaneously. RNASeqBrowser and its manual are freely available at http://www.australianprostatecentre.org/research/software/rnaseqbrowser webcite or http://sourceforge.net/projects/rnaseqbrowser/ webcite

ITO-free top emitting organic light emitting diodes with enhanced light out-coupling

Bottom emitting organic light emitting diodes (OLEDs) can suffer from lower external quantum efficiencies (EQE) due to inefficient out-coupling of the generated light. Herein, it is demonstrated that the current efficiency and EQE of red, yellow, and blue fluorescent single layer polymer OLEDs is significantly enhanced when a MoOx(5 nm)/Ag(10 nm)/MoOx(40 nm) stack is used as the transparent anode in a top emitting OLED structure. A maximum current efficiency and EQE of 21.2 cd/A and 6.7%, respectively, was achieved for a yellow OLED, while a blue OLED achieved a maximum of 16.5 cd/A and 10.1%, respectively. The increase in light out-coupling from the top-emitting OLEDs led to increase in efficiency by a factor of up to 2.2 relative to the optimised bottom emitting devices, which is the best out-coupling reported using solution processed polymers in a simple architecture and a significant step forward for their use in large area lighting and displays.

Media futures: A review essay on'The Future of Reputation','TV Futures', and'The Future of the Internet and How to Stop It'

In his 1987 book, The Media Lab: Inventing the Future at MIT, Stewart Brand provides an insight into the visions of the future of the media in the 1970s and 1980s. 1 He notes that Nicolas Negroponte made a compelling case for the foundation of a media laboratory at MIT with diagrams detailing the convergence of three sectors of the media—the broadcast and motion picture industry; the print and publishing industry; and the computer industry. Stewart Brand commented: ‘If Negroponte was right and communications technologies really are converging, you would look for signs that technological homogenisation was dissolving old boundaries out of existence, and you would expect an explosion of new media where those boundaries used to be’. Two decades later, technology developers, media analysts and lawyers have become excited about the latest phase of media convergence. In 2006, the faddish Time Magazine heralded the arrival of various Web 2.0 social networking services: You can learn more about how Americans live just by looking at the backgrounds of YouTube videos—those rumpled bedrooms and toy‐strewn basement rec rooms—than you could from 1,000 hours of network television. And we didn’t just watch, we also worked. Like crazy. We made Facebook profiles and Second Life avatars and reviewed books at Amazon and recorded podcasts. We blogged about our candidates losing and wrote songs about getting dumped. We camcordered bombing runs and built open‐source software. America loves its solitary geniuses—its Einsteins, its Edisons, its Jobses—but those lonely dreamers may have to learn to play with others. Car companies are running open design contests. Reuters is carrying blog postings alongside its regular news feed. Microsoft is working overtime to fend off user‐created Linux. We’re looking at an explosion of productivity and innovation, and it’s just getting started, as millions of minds that would otherwise have drowned in obscurity get backhauled into the global intellectual economy. The magazine announced that Time’s Person of the Year was ‘You’, the everyman and everywoman consumer ‘for seizing the reins of the global media, for founding and framing the new digital democracy, for working for nothing and beating the pros at their own game’. This review essay considers three recent books, which have explored the legal dimensions of new media. In contrast to the unbridled exuberance of Time Magazine, this series of legal works displays an anxious trepidation about the legal ramifications associated with the rise of social networking services. In his tour de force, The Future of Reputation: Gossip, Rumor, and Privacy on the Internet, Daniel Solove considers the implications of social networking services, such as Facebook and YouTube, for the legal protection of reputation under privacy law and defamation law. Andrew Kenyon’s edited collection, TV Futures: Digital Television Policy in Australia, explores the intersection between media law and copyright law in the regulation of digital television and Internet videos. In The Future of the Internet and How to Stop It, Jonathan Zittrain explores the impact of ‘generative’ technologies and ‘tethered applications’—considering everything from the Apple Mac and the iPhone to the One Laptop per Child programme.

Settling behaviours of low alumina/caustic ratios during seawater neutralisation of Bayer liquor

Factors that affect the settleability of seawater neutralised bauxite refinery residues are poorly understood, in particular, the settleability of precipitates in the absence of red mud and those formed with different alumina/caustic (AC) ratios. The influence of temperature, AC ratio, caustic concentration and the volumetric ratio of seawater on the settleability of seawater neutralisation precipitates and their respective compositions and stabilities have been determined. An array of techniques have been used to determine the composition and stability of precipitates and include pH, conductivity, inductively coupled plasma optical emission spectroscopy, infrared spectroscopy and X-ray diffraction. Temperature has been shown to have a significant influence on the settleability and calcium carbonate phase distributions in precipitates, as well as the overall stability of the precipitates. More complex phase compositions have also been found for Bayer liquors with lower AC ratios. The caustic concentration and temperature of the reaction have the greatest influence on the settling efficiency of the precipitates. Assessments on the chemical stability of the precipitates, precipitate settleability and discharge water quality have been made. In addition, productivity and environmental impacts caused by changes in precipitate settleability have also been considered.

Solution chemistry impacts on the seawater neutralisation process: Benefits of nanofiltered seawater and reverse osmosis brine

It is well known that the neutralisation of Bayer liquor with seawater causes the precipitation of stable alkaline products and a reduction in pH and dissolved metal concentrations in the effluent. However, there is limited information available on solution chemistry effects on the stability and reaction kinetics of these precipitates. This investigation shows the influence of reactive species (magnesium and calcium) in seawater on precipitate stabilities and volumetric efficiencies during the neutralisation of bauxite refinery residues. Correlations between synthetic seawater solutions and real samples of seawater (filtered seawater, nanofiltered seawater and reverse osmosis brine) have been made. These investigations have been used to confirm that alternative seawater sources can be used to increase the productivity potential of the neutralisation process with minimal implications on the composition and stability of precipitates formed. The volume efficiency of the neutralisation process using synthetic analogues has been shown to be almost directly proportional with the concentration of magnesium. This was further confirmed in the nanofiltered seawater and reverse osmosis brine that showed increases in the efficiency of neutralisation by factors of 3 and 2 compared to seawater, which corresponds with relatively the same increase in the concentration of magnesium in these alternative seawater sources. An assessment of the chemical stability of the precipitates, volumetric efficiency, and discharge water quality have been determined using numerous techniques that include pH, conductivity, inductively coupled plasma optical emission spectroscopy, infrared spectroscopy, thermogravimetric analysis coupled to mass spectrometry and X-ray diffraction. Correlations between synthetic solution compositions and alternative seawater sources have been used to determine if alternative seawater sources are potential substitutes for seawater based on improvements in productivity, implementation costs, savings to operations and environmental benefits.

Commercial friendships between gay sales associates and straight female customers in luxury settings: A proposed theoretical framework

This study investigates friendships between gay sales associates and heterosexual female customers in luxury retail settings. By employing grounded theory methodology, the study integrates theories and findings from diverse literature streams into an original conceptual framework to illustrate the resources gay sales associates and straight female customers receive from and provide to each other during retail exchanges. The study explains why gay male–straight female friendships are uniquely suited for luxury consumption settings. Female customers characterize their friendships with gay sales associates as providing honesty, security, trust, and comfort, which stems from the absence of sexual interest and a lack of inter-female competition. Gay sales associates receive acceptance for who they are and for their displays of unconventional masculinity in retail settings. They also obtain a temporary rite from their female customers, a so-called mandate of privacy, which permits both parties to ignore the bounds of modesty and accept a degree of intimacy. Such intimacy facilitates transactions that require both personalization and customer–employee closeness, such as the selling of high-end apparel, accessories, and jewelry.

Digital design interventions for creating new presentations of self in public urban places

During everyday urban life, people spend time in public urban places waiting for specific events to occur. During these times, people sometimes tend to engage with their information and communication technology (ICT) devices in a way that shuts off interactions with collocated people. These devices could also be used to better connect with the urban space and collocated people within. This chapter presents and discusses the impact of three design interventions on the urban user experience enabling collocated people to share lightweight, non-privacy-sensitive data in the urban space. We investigate and discuss the impact on the urban experience under the notions of people, place, and technology with an emphasis on how the sharing of non-privacy-sensitive data can positively transform anonymous public urban places in various ways through anonymous digital augmentations.

Meta-analysis of structural imaging findings in Attention-Deficit/Hyperactivity Disorder

Background Although there are many structural neuroimaging studies of attention-deficit/hyperactivity disorder (ADHD) in children, there are inconsistencies across studies and no consensus regarding which brain regions show the most robust area or volumetric reductions relative to control subjects. Our goal was to statistically analyze structural imaging data via a meta-analysis to help resolve these issues. Methods We searched the MEDLINE and PsycINFO databases through January 2005. Studies must have been written in English, used magnetic resonance imaging, and presented the means and standard deviations of regions assessed. Data were extracted by one of the authors and verified independently by another author. Results Analyses were performed using STATA with metan, metabias, and metainf programs. A meta-analysis including all regions across all studies indicated global reductions for ADHD subjects compared with control subjects, standardized mean difference equal to .408, p less than .001. Regions most frequently assessed and showing the largest differences included cerebellar regions, the splenium of the corpus callosum, total and right cerebral volume, and right caudate. Several frontal regions assessed in only two studies also showed large significant differences. Conclusions This meta-analysis provides a quantitative analysis of neuroanatomical abnormalities in ADHD and information that can be used to guide future studies.

Shaping development through mechanical strain: The transcriptional basis of diet-induced phenotypic plasticity in a cichlid fish

Adaptive phenotypic plasticity, the ability of an organism to change its phenotype to match local environments, is increasingly recognized for its contribution to evolution. However, few empirical studies have explored the molecular basis of plastic traits. The East African cichlid fish Astatoreochromis alluaudi displays adaptive phenotypic plasticity in its pharyngeal jaw apparatus, a structure that is widely seen as an evolutionary key innovation that has contributed to the remarkable diversity of cichlid fishes. It has previously been shown that in response to different diets, the pharyngeal jaws change their size, shape and dentition: hard diets induce an adaptive robust molariform tooth phenotype with short jaws and strong internal bone structures, while soft diets induce a gracile papilliform tooth phenotype with elongated jaws and slender internal bone structures. To gain insight into the molecular underpinnings of these adaptations and enable future investigations of the role that phenotypic plasticity plays during the formation of adaptive radiations, the transcriptomes of the two divergent jaw phenotypes were examined. Our study identified a total of 187 genes whose expression differs in response to hard and soft diets, including immediate early genes, extracellular matrix genes and inflammatory factors. Transcriptome results are interpreted in light of expression of candidate genesmarkers for tooth size and shape, bone cells and mechanically sensitive pathways. This study opens up new avenues of research at new levels of biological organization into the roles of phenotypic plasticity during speciation and radiation of cichlid fishes.