Estimates of genetic differentiation measured by FST do not necessarily require large sample sizes when using many SNP markers

Population genetic studies provide insights into the evolutionary processes that influence the distribution of sequence variants within and among wild populations. FST is among the most widely used measures for genetic differentiation and plays a central role in ecological and evolutionary genetic studies. It is commonly thought that large sample sizes are required in order to precisely infer FST and that small sample sizes lead to overestimation of genetic differentiation. Until recently, studies in ecological model organisms incorporated a limited number of genetic markers, but since the emergence of next generation sequencing, the panel size of genetic markers available even in non-reference organisms has rapidly increased. In this study we examine whether a large number of genetic markers can substitute for small sample sizes when estimating FST. We tested the behavior of three different estimators that infer FST and that are commonly used in population genetic studies. By simulating populations, we assessed the effects of sample size and the number of markers on the various estimates of genetic differentiation. Furthermore, we tested the effect of ascertainment bias on these estimates. We show that the population sample size can be significantly reduced (as small as n = 4–6) when using an appropriate estimator and a large number of bi-allelic genetic markers (k.1,000). Therefore, conservation genetic studies can now obtain almost the same statistical power as studies performed on model organisms using markers developed with next-generation sequencing

Blind decomposition of Herschel-HIFI spectral maps of the NGC 7023 nebula

Large spatial-spectral surveys are more and more common in astronomy. This calls for the need of new methods to analyze such mega- to giga-pixel data-cubes. In this paper we present a method to decompose such observations into a limited and comprehensive set of components. The original data can then be interpreted in terms of linear combinations of these components. The method uses non-negative matrix factorization (NMF) to extract latent spectral end-members in the data. The number of needed end-members is estimated based on the level of noise in the data. A Monte-Carlo scheme is adopted to estimate the optimal end-members, and their standard deviations. Finally, the maps of linear coefficients are reconstructed using non-negative least squares. We apply this method to a set of hyperspectral data of the NGC 7023 nebula, obtained recently with the HIFI instrument onboard the Herschel space observatory, and provide a first interpretation of the results in terms of 3-dimensional dynamical structure of the region.Comment: Proceedings of the 2012 meeting of the french astronomical society (SF2A) in Nic

Charged particle detection performances of CMOS pixel sensors produced in a 0.18 um process with a high resistivity epitaxial layer

The apparatus of the ALICE experiment at CERN will be upgraded in 2017/18 during the second long shutdown of the LHC (LS2). A major motivation for this upgrade is to extend the physics reach for charmed and beauty particles down to low transverse momenta. This requires a substantial improvement of the spatial resolution and the data rate capability of the ALICE Inner Tracking System (ITS). To achieve this goal, the new ITS will be equipped with 50 um thin CMOS Pixel Sensors (CPS) covering either the 3 innermost layers or all the 7 layers of the detector. The CPS being developed for the ITS upgrade at IPHC (Strasbourg) is derived from the MIMOSA 28 sensor realised for the STAR-PXL at RHIC in a 0.35 um CMOS process. In order to satisfy the ITS upgrade requirements in terms of readout speed and radiation tolerance, a CMOS process with a reduced feature size and a high resistivity epitaxial layer should be exploited. In this respect, the charged particle detection performance and radiation hardness of the TowerJazz 0.18 um CMOS process were studied with the help of the first prototype chip MIMOSA 32. The beam tests performed with negative pions of 120 GeV/c at the CERN-SPS allowed to measure a signal-to-noise ratio (SNR) for the non-irradiated chip in the range between 22 and 32 depending on the pixel design. The chip irradiated with the combined dose of 1 MRad and 10^13 n_eq/cm^2 was observed to yield a SNR ranging between 11 and 23 for coolant temperatures varying from 15 C to 30 C. These SNR values were measured to result in particle detection efficiencies above 99.5% and 98% before and after irradiation respectively. These satisfactory results allow to validate the TowerJazz 0.18 um CMOS process for the ALICE ITS upgrade.Comment: (v2) Added hyper-links; (v3) A typo correcte

Towards equitable and trustworthy genomics research.

Funder: National Institutes of HealthThe representation of traditionally scientifically underserved groups in genomic research continues to be low despite concerns about equity and social justice and the scientific and clinical need. Among the factors that account for this are a lack of trust in the research community and limited diversity in this community. The success of the multiple initiatives that aim to improve representation relies on the willingness of underrepresented populations to make data and samples available for research and clinical use. In this narrative review, we propose that this requires building trust, and set out four approaches to demonstrating trustworthiness, including increasing diversity in the research workforce, and meaningful engagement with underrepresented communities in a culturally and linguistically appropriate manner. Capacity building globally will ensure that actual and perceived exploitation and 'helicopter' research could be eliminated

Development of CMOS Pixel Sensors fully adapted to the ILD Vertex Detector Requirements

CMOS Pixel Sensors are making steady progress towards the specifications of the ILD vertex detector. Recent developments are summarised, which show that these devices are close to comply with all major requirements, in particular the read-out speed needed to cope with the beam related background. This achievement is grounded on the double- sided ladder concept, which allows combining signals generated by a single particle in two different sensors, one devoted to spatial resolution and the other to time stamp, both assembled on the same mechanical support. The status of the development is overviewed as well as the plans to finalise it using an advanced CMOS process.Comment: 2011 International Workshop on Future Linear Colliders (LCWS11), Granada, Spain, 26-30 September 201

Seed Dispersal and Establishment of Endangered Plants on Oceanic Islands: The Janzen-Connell Model, and the Use of Ecological Analogues

BACKGROUND: The Janzen-Connell model states that plant-specific natural enemies may have a disproportionately large negative effect on progeny close to maternal trees. The majority of experimental and theoretical studies addressing the Janzen-Connell model have explored how it can explain existing patterns of species diversity in tropical mainland areas. Very few studies have investigated how the model's predictions apply to isolated oceanic islands, or to the conservation management of endangered plants. Here, we provide the first experimental investigation of the predictions of the Janzen-Connell model on an oceanic island, in a conservation context. In addition, we experimentally evaluate the use of ecological analogue animals to resurrect the functional component of extinct frugivores that could have dispersed seeds away from maternal trees. METHODOLOGY/PRINCIPAL FINDINGS: In Mauritius, we investigated seed germination and seedling survival patterns of the critically endangered endemic plant Syzygium mamillatum (Myrtaceae) in relation to proximity to maternal trees. We found strong negative effects of proximity to maternal trees on growth and survival of seedlings. We successfully used giant Aldabran tortoises as ecological analogues for extinct Mauritian frugivores. Effects of gut-passage were negative at the seed germination stage, but seedlings from gut-passed seeds grew taller, had more leaves, and suffered less damage from natural enemies than any of the other seedlings. CONCLUSIONS/SIGNIFICANCE: We provide the first experimental evidence of a distance-dependent Janzen-Connell effect on an oceanic island. Our results potentially have serious implications for the conservation management of rare plant species on oceanic islands, which harbour a disproportionately large fraction of the world's endemic and endangered plants. Furthermore, in contrast to recent controversy about the use of non-indigenous extant megafauna for re-wilding projects in North America and elsewhere, we argue that Mauritius and other oceanic islands are ideal study systems in which to empirically explore the use of ecological analogue species in restoration ecology

Symptoms and quality of life from patients undergoing hemodialysis in Switzerland

Background: Dialysis patients experience multiple symptoms impairing their quality of life. A relationship seems to exist between the cultural context and the burden of symptoms. In this study, the prevalence and severity of 30 symptoms and their relationship with quality of life among hemodialysis patients in Switzerland is explored. Methods: A cross-sectional correlation design was used with a convenience sample of 119 patients from five dialysis units. Presence and severity of symptoms were assessed with the Dialysis Symptom Index and quality of life with the WHOQOL-Bref questionnaire. Multivariate linear regressions were used to examine the relationship between the prevalence and severity of symptoms, respectively, and quality of life. T-tests and Fisher’s tests were used for the international comparison

Development of Single- and Double-sided Ladders for the ILD Vertex Detectors

We discuss two projects exploring the integration of thin CMOS pixel sensors in order to prototype ladders matching the geometry needed for the ILD vertex detector. The PLUME project has designed and fabricated full-size and fully functional double- sided layers which currently reach 0.6 % X0 and aim for 0.3 % X0 in mid-2012. Another approach, SERNWIETE, consists in wrapping the sensors in a polyimide-based micro-cable to obtain a supportless single-sided ladder with a material budget around 0.15 % X0. First promising samples have been produced and the full-size prototype is expected in spring 2012.Comment: International Workshop on Future Linear Colliders, LCWS 2011, Granada, Spain, 2011, 26-30 Septembe

Insulin clearance and the incidence of type 2 diabetes in Hispanics and African Americans: the IRAS Family Study.

ObjectiveWe aimed to identify factors that are independently associated with the metabolic clearance rate of insulin (MCRI) and to examine the association of MCRI with incident type 2 diabetes in nondiabetic Hispanics and African Americans.Research design and methodsWe investigated 1,116 participants in the Insulin Resistance Atherosclerosis Study (IRAS) Family Study with baseline examinations from 2000 to 2002 and follow-up examinations from 2005 to 2006. Insulin sensitivity (S(I)), acute insulin response (AIR), and MCRI were determined at baseline from frequently sampled intravenous glucose tolerance tests. MCRI was calculated as the ratio of the insulin dose over the incremental area under the curve of insulin. Incident diabetes was defined as fasting glucose ≥126 mg/dL or antidiabetic medication use by self-report.ResultsWe observed that S(I) and HDL cholesterol were independent positive correlates of MCRI, whereas fasting insulin, fasting glucose, subcutaneous adipose tissue, visceral adipose tissue, and AIR were independent negative correlates (all P < 0.05) at baseline. After 5 years of follow-up, 71 (6.4%) participants developed type 2 diabetes. Lower MCRI was associated with a higher risk of incident diabetes after adjusting for demographics, lifestyle factors, HDL cholesterol, indexes of obesity and adiposity, and insulin secretion (odds ratio 2.01 [95% CI 1.30-3.10], P = 0.0064, per one-SD decrease in loge-transformed MCRI).ConclusionsOur data showed that lower MCRI predicts the incidence of type 2 diabetes

Stock Composition of Some Sockeye Salmon, Oncorhynchus nerka, Catches in Southeast Alaska, Based on Incidence of Allozyme Variants, Freshwater Ages, and a Brain-Tissue Parasite

The incidence of four discrete characters of individual sockeye salmon -two genetically inherited proteins (PGM-1*and PGM-2*), freshwater age at migration, and the presence of the brain-tissue parasite Myxobolus arcticus-in weekly samples from two Alaskan fisheries (Noyes Island in 1986 and Sumner Strait in 1987) were used to infer stock composition of the catches based on corresponding character samples from 73 Alaskan and Canadian stocks. Estimated contributions of 13 stock groups, formed on the basis of character similarity of their members, were roughly consistent with expectations from tagging experiments, knowledge of stock magnitudes, and similar assessments from scales. Imprecision of the estimated contributions by the 13 stock groups limited their practical value; but variability was much reduced for combined estimated contributions by two inclusive categories, namely stock groups whose members had either high or low brainparasite prevalence. Noyes Island catches consisted predominantly of unparasitized fish, most of which were probably of Canadian origin. The majority of Sumner Strait catches consisted of parasitized fish, whose freshwater origins may have been in Alaska or Canada. (PDF file contains 27 pages.