Contextualizing genetic risk score for disease screening and rare variant discovery.

Studies of the genetic basis of complex traits have demonstrated a substantial role for common, small-effect variant polygenic burden (PB) as well as large-effect variants (LEV, primarily rare). We identify sufficient conditions in which GWAS-derived PB may be used for well-powered rare pathogenic variant discovery or as a sample prioritization tool for whole-genome or exome sequencing. Through extensive simulations of genetic architectures and generative models of disease liability with parameters informed by empirical data, we quantify the power to detect, among cases, a lower PB in LEV carriers than in non-carriers. Furthermore, we uncover clinically useful conditions wherein the risk derived from the PB is comparable to the LEV-derived risk. The resulting summary-statistics-based methodology (with publicly available software, PB-LEV-SCAN) makes predictions on PB-based LEV screening for 36 complex traits, which we confirm in several disease datasets with available LEV information in the UK Biobank, with important implications on clinical decision-making

Rare Copy Number Variants in \u3cem\u3eNRXN1\u3c/em\u3e and \u3cem\u3eCNTN6\u3c/em\u3e Increase Risk for Tourette Syndrome

Tourette syndrome (TS) is a model neuropsychiatric disorder thought to arise from abnormal development and/or maintenance of cortico-striato-thalamo-cortical circuits. TS is highly heritable, but its underlying genetic causes are still elusive, and no genome-wide significant loci have been discovered to date. We analyzed a European ancestry sample of 2,434 TS cases and 4,093 ancestry-matched controls for rare (\u3c 1% frequency) copy-number variants (CNVs) using SNP microarray data. We observed an enrichment of global CNV burden that was prominent for large (\u3e 1 Mb), singleton events (OR = 2.28, 95% CI [1.39–3.79], p = 1.2 × 10−3) and known, pathogenic CNVs (OR = 3.03 [1.85–5.07], p = 1.5 × 10−5). We also identified two individual, genome-wide significant loci, each conferring a substantial increase in TS risk (NRXN1 deletions, OR = 20.3, 95% CI [2.6–156.2]; CNTN6 duplications, OR = 10.1, 95% CI [2.3–45.4]). Approximately 1% of TS cases carry one of these CNVs, indicating that rare structural variation contributes significantly to the genetic architecture of TS

Technology Innovation Enabling Falls Risk Assessment in a Community Setting

Approximately one in three people over the age of 65 will fall each year, resulting in significant financial, physical, and emotional cost on the individual, their family, and society. Currently, falls are managed using on-body sensors and alarm pendants to notify others when a falls event occurs. However these technologies do not prevent a fall from occurring. There is now a growing focus on falls risk assessment and preventative interventions. Falls risk is currently assessed in a clinical setting by expert physiotherapists, geriatricians, or occupational therapists following the occurrence of an injurious fall. As the population ages, this reactive model of care will become increasingly unsatisfactory, and a proactive community-based prevention strategy will be required. Recent advances in technology can support this new model of care by enabling community-based practitioners to perform tests that previously required expensive technology or expert interpretation. Gait and balance impairment is one of the most common risk factors for falls. This paper reviews the current technical and non-technical gait and balance assessments, discusses how low-cost technology can be applied to objectively administer and interpret these tests in the community, and reports on recent research where body-worn sensors have been utilized. It also discusses the barriers to adoption in the community and proposes ethnographic research as a method to investigate solutions to these barriers

On the Nature of Stars with Planets

We consider the metallicities and kinematics of nearby stars known to have planetary-mass companions in the general context of the overall properties of the local Galactic Disk. We have used Stromgren photometry to determine abundances for both the extrasolar-planet host stars and for a volume-limited sample of 486 F, G and K stars selected from the Hipparcos catalogue. The latter data show that the Sun lies near the modal abundance of the disk, with over 45% of local stars having super-solar metallicities. Twenty of the latter stars (4.1%) are known to have planetary-mass companions. Using that ratio to scale data for the complete sample of planetary host stars, we find that the fraction of stars with extrasolar planets rises sharply with increasing abundance, confirming previous results. However, the frequency remains at the 3-4% level for stars within 0.15 dex of solar abundance, and falls to ~1% only for stars with abundances less than half solar. Given the present observational constraints, both in velocity precision and in the available time baseline, these numbers represent a lower limit to the frequency of extrasolar planetary systems. A comparison between the kinematics of the planetary host stars and a representative sample of disk stars suggests that the former have an average age which is ~60% of the latter.Comment: 46 pages, 13 figures; accepted for PAS

Development and Evaluation of SENSE-ational Mealtimes: a Book for Families with Mealtime Difficulties

Many families with young children experience mealtime difficulties whereby the child eats a limited range of foods and/or refuses new food. Clinical interventions typically include behaviour training, enhancement of parenting skills and nutrition education. Clinical experience and a review of the literature across several domains suggested that interventions that optimise reflective functioning and understandings about sensory preferences at mealtimes are needed for both mild and complex mealtime difficulties. This study describes the development of the SENSE-ational Mealtimes book for families with mealtime difficulties and reports the findings of the initial evaluation. A questionnaire was used to assess the change in the frequency of difficult mealtimes, level of concern, understandings, feelings and goals of mothers 2 months after the book was distributed in a community setting. Mothers also provided feedback regarding helpfulness of the book, needs of families and recommendations. There was a statistically significant improvement in all aspects, namely frequency of mealtime difficulties, level of concern, understandings, feelings and goals. The subjective data indicated that the concepts instrumental in enhancing most mothers' understandings were how sensory preferences and past experiences of all members of the family had an impact on mealtime interactions. Initial evaluation suggests that wide-spread access to the SENSE-ational Mealtimes book could be an inexpensive approach to reduce the costs of adverse effects of mealtime difficulties on the emotional well-being of families and dietary intake of children. Mothers unanimously recommended the SENSE-ational Mealtimes book for both targeted prevention of and early intervention with mealtime difficulties in families

Anti-cancer effects and mechanism of actions of aspirin analogues in the treatment of glioma cancer

INTRODUCTION: In the past 25 years only modest advancements in glioma treatment have been made, with patient prognosis and median survival time following diagnosis only increasing from 3 to 7 months. A substantial body of clinical and preclinical evidence has suggested a role for aspirin in the treatment of cancer with multiple mechanisms of action proposed including COX 2 inhibition, down regulation of EGFR expression, and NF-κB signaling affecting Bcl-2 expression. However, with serious side effects such as stroke and gastrointestinal bleeding, aspirin analogues with improved potency and side effect profiles are being developed. METHOD: Effects on cell viability following 24 hr incubation of four aspirin derivatives (PN508, 517, 526 and 529) were compared to cisplatin, aspirin and di-aspirin in four glioma cell lines (U87 MG, SVG P12, GOS – 3, and 1321N1), using the PrestoBlue assay, establishing IC50 and examining the time course of drug effects. RESULTS: All compounds were found to decrease cell viability in a concentration and time dependant manner. Significantly, the analogue PN517 (IC50 2mM) showed approximately a twofold increase in potency when compared to aspirin (3.7mM) and cisplatin (4.3mM) in U87 cells, with similar increased potency in SVG P12 cells. Other analogues demonstrated similar potency to aspirin and cisplatin. CONCLUSION: These results support the further development and characterization of novel NSAID derivatives for the treatment of glioma

Sleep deprivation impairs and caffeine enhances my performance, but not always our performance: how acting in a group can change the effects of impairments and enhancements

What effects do factors that impair or enhance performance in individuals have when these individuals act in groups? We provide a framework, called the GIE ("Effects of Grouping on Impairments and Enhancements”) framework, for investigating this question. As prominent examples for individual-level impairments and enhancements, we discuss sleep deprivation and caffeine. Based on previous research, we derive hypotheses on how they influence performance in groups, specifically process gains and losses in motivation, individual capability, and coordination. We conclude that the effect an impairment or enhancement has on individual-level performance is not necessarily mirrored in group performance: grouping can help or hurt. We provide recommendations on how to estimate empirically the effects individual-level performance impairments and enhancements have in groups. By comparing sleep deprivation to stress and caffeine to pharmacological cognitive enhancement, we illustrate that we cannot readily generalize from group results on one impairment or enhancement to another, even if they have similar effects on individual-level performance

A Study of Time-Dependent CP-Violating Asymmetries and Flavor Oscillations in Neutral B Decays at the Upsilon(4S)

We present a measurement of time-dependent CP-violating asymmetries in neutral B meson decays collected with the BABAR detector at the PEP-II asymmetric-energy B Factory at the Stanford Linear Accelerator Center. The data sample consists of 29.7 ${\rm fb}^{-1}$ recorded at the $\Upsilon(4S)$ resonance and 3.9 ${\rm fb}^{-1}$ off-resonance. One of the neutral B mesons, which are produced in pairs at the $\Upsilon(4S)$, is fully reconstructed in the CP decay modes $J/\psi K^0_S$, $\psi(2S) K^0_S$, $\chi_{c1} K^0_S$, $J/\psi K^{*0}$ ($K^{*0}\to K^0_S\pi^0$) and $J/\psi K^0_L$, or in flavor-eigenstate modes involving $D^{(*)}\pi/\rho/a_1$ and $J/\psi K^{*0}$ ($K^{*0}\to K^+\pi^-$). The flavor of the other neutral B meson is tagged at the time of its decay, mainly with the charge of identified leptons and kaons. The proper time elapsed between the decays is determined by measuring the distance between the decay vertices. A maximum-likelihood fit to this flavor eigenstate sample finds $\Delta m_d = 0.516\pm 0.016 {\rm (stat)} \pm 0.010 {\rm (syst)} {\rm ps}^{-1}$. The value of the asymmetry amplitude $\sin2\beta$ is determined from a simultaneous maximum-likelihood fit to the time-difference distribution of the flavor-eigenstate sample and about 642 tagged $B^0$ decays in the CP-eigenstate modes. We find $\sin2\beta=0.59\pm 0.14 {\rm (stat)} \pm 0.05 {\rm (syst)}$, demonstrating that CP violation exists in the neutral B meson system. (abridged)Comment: 58 pages, 35 figures, submitted to Physical Review

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.

BACKGROUND: We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. RESULTS: The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. CONCLUSIONS: Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution