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

Does the `Higgs' have Spin Zero?

The Higgs boson is predicted to have spin zero. The ATLAS and CMS experiments have recently reported of an excess of events with mass ~ 125 GeV that has some of the characteristics expected for a Higgs boson. We address the questions whether there is already any evidence that this excess has spin zero, and how this possibility could be confirmed in the near future. The excess observed in the gamma gamma final state could not have spin one, leaving zero and two as open possibilities. We calculate the angular distribution of gamma gamma pairs from the decays of a spin-two boson produced in gluon-gluon collisions, showing that is unique and distinct from the spin-zero case. We also calculate the distributions for lepton pairs that would be produced in the W W* decays of a spin-two boson, which are very different from those in Higgs decays, and note that the kinematics of the event selection used to produce the excess observed in the W W* final state have reduced efficiency for spin two.Comment: 22 pages, 22 figures, Version accepted for publication in JHEP, includes additional plots of dilepton mass distribution

Sec24p and Sec16p cooperate to regulate the GTP cycle of the COPII coat

Vesicle budding from the endoplasmic reticulum (ER) employs a cycle of GTP binding and hydrolysis to regulate assembly of the COPII coat. We have identified a novel mutation (sec24‐m11) in the cargo‐binding subunit, Sec24p, that specifically impacts the GTP‐dependent generation of vesicles in vitro. Using a high‐throughput approach, we defined genetic interactions between sec24‐m11 and a variety of trafficking components of the early secretory pathway, including the candidate COPII regulators, Sed4p and Sec16p. We defined a fragment of Sec16p that markedly inhibits the Sec23p‐ and Sec31p‐stimulated GTPase activity of Sar1p, and demonstrated that the Sec24p‐m11 mutation diminished this inhibitory activity, likely by perturbing the interaction of Sec24p with Sec16p. The consequence of the heightened GTPase activity when Sec24p‐m11 is present is the generation of smaller vesicles, leading to accumulation of ER membranes and more stable ER exit sites. We propose that association of Sec24p with Sec16p creates a novel regulatory complex that retards the GTPase activity of the COPII coat to prevent premature vesicle scission, pointing to a fundamental role for GTP hydrolysis in vesicle release rather than in coat assembly/disassembly

Interventions for preventing occupational irritant hand dermatitis (Review)

Background: Occupational irritant hand dermatitis (OIHD) causes significant functional impairment, disruption of work, and discomfort in the working population. Different preventive measures such as protective gloves, barrier creams and moisturisers can be used, but it is not clear how effective these are. This is an update of a Cochrane review which was previously published in 2010. Objectives: To assess the effects of primary preventive interventions and strategies (physical and behavioural) for preventing OIHD in healthy people (who have no hand dermatitis) who work in occupations where the skin is at risk of damage due to contact with water, detergents, chemicals or other irritants, or from wearing gloves. Search methods: We updated our searches of the following databases to January 2018: the Cochrane Skin Specialised Register, CENTRAL, MEDLlNE, and Embase. We also searched five trials registers and checked the bibliographies of included studies for further references to relevant trials. We handsearched two sets of conference proceedings. Selection criteria: We included parallel and cross-over randomised controlled trials (RCTs) which examined the effectiveness of barrier creams, moisturisers, gloves, or educational interventions compared to no intervention for the primary prevention of OIHD under field conditions. Data collection and analysis: We used the standard methodological procedures expected by Cochrane. The primary outcomes were signs and symptoms of OIHD developed during the trials, and the frequency of treatment discontinuation due to adverse effects

Pathways to the medieval hospital : Collective osteobiographies of poverty and charity

Medieval hospitals were founded to provide charity, but poverty and infirmity were broad and socially determined categories and little is known about the residents of these institutions and the pathways that led them there. Combining skeletal, isotopic and genetic data, the authors weave a collective biography of individuals buried at the Hospital of St John the Evangelist, Cambridge. By starting with the physical remains, rather than historical expectations, they demonstrate the varied life courses of those who were ultimately buried in the hospital's cemetery, illustrating the diverse faces of medieval poverty and institutional notions of charity. The findings highlight the value of collective osteobiography when reconstructing the social landscapes of the past

Gluon-gluon contributions to W+ W- production and Higgs interference effects

In this paper we complete our re-assessment of the production of W boson pairs at the LHC, by calculating analytic results for the gg -> W+ W- -> (\nu l l\nu) process including the effect of massive quarks circulating in the loop. Together with the one-loop amplitudes containing the first two generations of massless quarks propagating in the loop, these diagrams can give a significant contribution with a large flux of gluons. One of the component parts of this calculation is the production of a standard model Higgs boson, gg -> H and its subsequent decay, H -> W+(-> \nu l) W-(-> l \nu). We will quantify the importance of the interference between the Higgs boson production process and the gluon-induced continuum production in the context of searches for the Higgs boson at the Tevatron and the LHC. For instance, for mH < 140 GeV the effect of the interference typically results in around a 10% reduction in the expected number of Higgs signal events. The majority of this interference is due to non-resonant contributions. Therefore cuts on the transverse mass such as those currently used by the ATLAS collaboration reduce the destructive interference to about a 1% effect. We advocate that a cut on the maximum transverse mass be used in future Higgs searches in this channel

Search for the standard model Higgs boson in the H to ZZ to 2l 2nu channel in pp collisions at sqrt(s) = 7 TeV

A search for the standard model Higgs boson in the H to ZZ to 2l 2nu decay channel, where l = e or mu, in pp collisions at a center-of-mass energy of 7 TeV is presented. The data were collected at the LHC, with the CMS detector, and correspond to an integrated luminosity of 4.6 inverse femtobarns. No significant excess is observed above the background expectation, and upper limits are set on the Higgs boson production cross section. The presence of the standard model Higgs boson with a mass in the 270-440 GeV range is excluded at 95% confidence level.Comment: Submitted to JHE

Search for New Physics with Jets and Missing Transverse Momentum in pp collisions at sqrt(s) = 7 TeV

A search for new physics is presented based on an event signature of at least three jets accompanied by large missing transverse momentum, using a data sample corresponding to an integrated luminosity of 36 inverse picobarns collected in proton--proton collisions at sqrt(s)=7 TeV with the CMS detector at the LHC. No excess of events is observed above the expected standard model backgrounds, which are all estimated from the data. Exclusion limits are presented for the constrained minimal supersymmetric extension of the standard model. Cross section limits are also presented using simplified models with new particles decaying to an undetected particle and one or two jets

Combined search for the quarks of a sequential fourth generation

Results are presented from a search for a fourth generation of quarks produced singly or in pairs in a data set corresponding to an integrated luminosity of 5 inverse femtobarns recorded by the CMS experiment at the LHC in 2011. A novel strategy has been developed for a combined search for quarks of the up and down type in decay channels with at least one isolated muon or electron. Limits on the mass of the fourth-generation quarks and the relevant Cabibbo-Kobayashi-Maskawa matrix elements are derived in the context of a simple extension of the standard model with a sequential fourth generation of fermions. The existence of mass-degenerate fourth-generation quarks with masses below 685 GeV is excluded at 95% confidence level for minimal off-diagonal mixing between the third- and the fourth-generation quarks. With a mass difference of 25 GeV between the quark masses, the obtained limit on the masses of the fourth-generation quarks shifts by about +/- 20 GeV. These results significantly reduce the allowed parameter space for a fourth generation of fermions.Comment: Replaced with published version. Added journal reference and DO

Measurement of the t t-bar production cross section in the dilepton channel in pp collisions at sqrt(s) = 7 TeV

The t t-bar production cross section (sigma[t t-bar]) is measured in proton-proton collisions at sqrt(s) = 7 TeV in data collected by the CMS experiment, corresponding to an integrated luminosity of 2.3 inverse femtobarns. The measurement is performed in events with two leptons (electrons or muons) in the final state, at least two jets identified as jets originating from b quarks, and the presence of an imbalance in transverse momentum. The measured value of sigma[t t-bar] for a top-quark mass of 172.5 GeV is 161.9 +/- 2.5 (stat.) +5.1/-5.0 (syst.) +/- 3.6(lumi.) pb, consistent with the prediction of the standard model.Comment: Replaced with published version. Included journal reference and DO