ScreenMill: A freely available software suite for growth measurement, analysis and visualization of high-throughput screen data

<p>Abstract</p> <p>Background</p> <p>Many high-throughput genomic experiments, such as Synthetic Genetic Array and yeast two-hybrid, use colony growth on solid media as a screen metric. These experiments routinely generate over 100,000 data points, making data analysis a time consuming and painstaking process. Here we describe <it>ScreenMill</it>, a new software suite that automates image analysis and simplifies data review and analysis for high-throughput biological experiments.</p> <p>Results</p> <p>The <it>ScreenMill</it>, software suite includes three software tools or "engines": an open source <it>Colony Measurement Engine </it>(<it>CM Engine</it>) to quantitate colony growth data from plate images, a web-based <it>Data Review Engine </it>(<it>DR Engine</it>) to validate and analyze quantitative screen data, and a web-based <it>Statistics Visualization Engine </it>(<it>SV Engine</it>) to visualize screen data with statistical information overlaid. The methods and software described here can be applied to any screen in which growth is measured by colony size. In addition, the <it>DR Engine </it>and <it>SV Engine </it>can be used to visualize and analyze other types of quantitative high-throughput data.</p> <p>Conclusions</p> <p><it>ScreenMill </it>automates quantification, analysis and visualization of high-throughput screen data. The algorithms implemented in S<it>creenMill </it>are transparent allowing users to be confident about the results <it>ScreenMill </it>produces. Taken together, the tools of <it>ScreenMill </it>offer biologists a simple and flexible way of analyzing their data, without requiring programming skills.</p

Spectral Classification; Old and Contemporary

Beginning with a historical account of the spectral classification, its refinement through additional criteria is presented. The line strengths and ratios used in two dimensional classifications of each spectral class are described. A parallel classification scheme for metal-poor stars and the standards used for classification are presented. The extension of spectral classification beyond M to L and T and spectroscopic classification criteria relevant to these classes are described. Contemporary methods of classifications based upon different automated approaches are introduced.Comment: To be published in "Principles and Perspectives in Cosmochemistry" Lecture Notes on Kodai School on Synthesis of Elements in Stars: Ed Aruna Goswami & Eswar Reddy, Springer Verlag, 2009, 17 pages, 10 figure

Skyrmion fluctuations at a first-order phase transition boundary

Magnetic skyrmions are topologically protected spin textures with promising prospects for applications in data storage. They can form a lattice state due to competing magnetic interactions and are commonly found in a small region of the temperature - magnetic field phase diagram. Recent work has demonstrated that these magnetic quasi-particles fluctuate at the μeV energy scale. Here, we use a coherent x-ray correlation method at an x-ray free-electron laser to investigate these fluctuations in a magnetic phase coexistence region near a first-order transition boundary where fluctuations are not expected to play a major role. Surprisingly, we find that the relaxation of the intermediate scattering function at this transition differs significantly compared to that deep in the skyrmion lattice phase. The observation of a compressed exponential behavior suggests solid-like dynamics, often associated with jamming. We assign this behavior to disorder and the phase coexistence observed in a narrow field-window near the transition, which can cause fluctuations that lead to glassy behavior

Community-based adaptation research in the Canadian Arctic

Community-based adaptation (CBA) has emerged over the last decade as an approach to empowering communities to plan for and cope with the impacts of climate change. While such approaches have been widely advocated, few have critically examined the tensions and challenges that CBA brings. Responding to this gap, this article critically examines the use of CBA approaches with Inuit communities in Canada. We suggest that CBA holds significant promise to make adaptation research more democratic and responsive to local needs, providing a basis for developing locally appropriate adaptations based on local/indigenous and Western knowledge. Yet, we argue that CBA is not a panacea, and its common portrayal as such obscures its limitations, nuances, and challenges. Indeed, if uncritically adopted, CBA can potentially lead to maladaptation, may be inappropriate in some instances, can legitimize outside intervention and control, and may further marginalize communities. We identify responsibilities for researchers engaging in CBA work to manage these challenges, emphasizing the centrality of how knowledge is generated, the need for project flexibility and openness to change, and the importance of ensuring partnerships between researchers and communities are transparent. Researchers also need to be realistic about what CBA can achieve, and should not assume that research has a positive role to play in community adaptation just because it utilizes participatory approaches

Detecting Regulatory Mechanisms in Endocrine Time Series Measurements

The regulatory mechanisms underlying pulsatile secretion are complex, especially as it is partly controlled by other hormones and the combined action of multiple agents. Regulatory relations between hormones are not directly observable but may be deduced from time series measurements of plasma hormone concentrations. Variation in plasma hormone levels are the resultant of secretion and clearance from the circulation. A strategy is proposed to extract inhibition, activation, thresholds and circadian synchronicity from concentration data, using particular association methods. Time delayed associations between hormone concentrations and/or extracted secretion pulse profiles reveal the information on regulatory mechanisms. The above mentioned regulatory mechanisms are illustrated with simulated data. Additionally, data from a lean cohort of healthy control subjects is used to illustrate activation (ACTH and cortisol) and circadian synchronicity (ACTH and TSH) in real data. The simulation and the real data both consist of 145 equidistant samples per individual, matching a 24-hr time span with 10 minute intervals. The results of the simulation and the real data are in concordance

Rubber Impact on 3D Textile Composites

A low velocity impact study of aircraft tire rubber on 3D textile-reinforced composite plates was performed experimentally and numerically. In contrast to regular unidirectional composite laminates, no delaminations occur in such a 3D textile composite. Yarn decohesions, matrix cracks and yarn ruptures have been identified as the major damage mechanisms under impact load. An increase in the number of 3D warp yarns is proposed to improve the impact damage resistance. The characteristic of a rubber impact is the high amount of elastic energy stored in the impactor during impact, which was more than 90% of the initial kinetic energy. This large geometrical deformation of the rubber during impact leads to a less localised loading of the target structure and poses great challenges for the numerical modelling. A hyperelastic Mooney-Rivlin constitutive law was used in Abaqus/Explicit based on a step-by-step validation with static rubber compression tests and low velocity impact tests on aluminium plates. Simulation models of the textile weave were developed on the meso- and macro-scale. The final correlation between impact simulation results on 3D textile-reinforced composite plates and impact test data was promising, highlighting the potential of such numerical simulation tools

SPECULOOS exoplanet search and its prototype on TRAPPIST

One of the most significant goals of modern science is establishing whether life exists around other suns. The most direct path towards its achievement is the detection and atmospheric characterization of terrestrial exoplanets with potentially habitable surface conditions. The nearest ultracool dwarfs (UCDs), i.e. very-low-mass stars and brown dwarfs with effective temperatures lower than 2700 K, represent a unique opportunity to reach this goal within the next decade. The potential of the transit method for detecting potentially habitable Earth-sized planets around these objects is drastically increased compared to Earth-Sun analogs. Furthermore, only a terrestrial planet transiting a nearby UCD would be amenable for a thorough atmospheric characterization, including the search for possible biosignatures, with near-future facilities such as the James Webb Space Telescope. In this chapter, we first describe the physical properties of UCDs as well as the unique potential they offer for the detection of potentially habitable Earth-sized planets suitable for atmospheric characterization. Then, we present the SPECULOOS ground-based transit survey, that will search for Earth-sized planets transiting the nearest UCDs, as well as its prototype survey on the TRAPPIST telescopes. We conclude by discussing the prospects offered by the recent detection by this prototype survey of a system of seven temperate Earth-sized planets transiting a nearby UCD, TRAPPIST-1.Comment: Submitted as a chapter in the "Handbook of Exoplanets" (editors: H. Deeg & J.A. Belmonte; Section Editor: N. Narita). 16 pages, 4 figure

Von Bezold assimilation effect reverses in stereoscopic conditions

Lightness contrast and lightness assimilation are opposite phenomena: in contrast, grey targets appear darker when bordering bright surfaces (inducers) rather than dark ones; in assimilation, the opposite occurs. The question is: which visual process favours the occurrence of one phenomenon over the other? Researchers provided three answers to this question. The first asserts that both phenomena are caused by peripheral processes; the second attributes their occurrence to central processes; and the third claims that contrast involves central processes, whilst assimilation involves peripheral ones. To test these hypotheses, an experiment on an IT system equipped with goggles for stereo vision was run. Observers were asked to evaluate the lightness of a grey target, and two variables were systematically manipulated: (i) the apparent distance of the inducers; and (ii) brightness of the inducers. The retinal stimulation was kept constant throughout, so that the peripheral processes remained the same. The results show that the lightness of the target depends on both variables. As the retinal stimulation was kept constant, we conclude that central mechanisms are involved in both lightness contrast and lightness assimilation

Assessment of a self-reported Drinks Diary for the estimation of drinks intake by care home residents: Fluid Intake Study in the Elderly (FISE)

Objectives: We evaluated the accuracy of a newly developed self-completed Drinks Diary in care home residents and compared it with direct observation and fluid intake charts. Design: Observational study. Setting: Residential care homes in Norfolk, UK. Participants: 22 elderly people (18 women, mean age 86.6 years SD 8.6, 12 with MMSE scores <27). Measurements: Participants recorded their own drinks intake over 24 hours using the Drinks Diary while care staff used the homes’ usual fluid intake chart to record drinks intake. These records were compared with drinks intake assessed by researcher direct observation (reference method), during waking hours (6am to 10pm), while drinks taken from 10pm to 6am were self-reported and checked with staff. Results: Drinks intake assessed by the Drinks Diary was highly correlated with researcher direct observation (Pearson correlation coefficient r=0.93, p<0.001, mean difference -163ml/day) while few staff-completed fluid charts were returned and correlation was low (r=0.122, p=0.818, mean difference 702ml/day). The Drinks Diary classified 19 of 22 participants correctly as drinking enough or not using both the European Food Safety Authority and US recommendations. Conclusion: The Drinks Diary estimate of drinks intake was comparable with direct observation and more accurate (and reliably completed) than staff records. The Drinks Diary can provide a reliable estimate of drinks intake in elderly care home residents physically and cognitively able to complete it. It may be useful for researchers, care staff and practitioners needing to monitor drinks intake of elderly people, to help them avoid dehydration