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Search Results: 1 - 10 of 229983 matches for " Philip C. Gregory "
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Additional Keplerian Signals in the HARPS data for Gliese 667C from a Bayesian Re-analysis
Philip C. Gregory
Physics , 2012,
Abstract: A re-analysis of Gliese 667C HARPS precision radial velocity data was carried out with a Bayesian multi-planet Kepler periodogram (from 0 to 7 planets) based on a fusion Markov chain Monte Carlo algorithm. The most probable number of signals detected is 6 with a Bayesian false alarm probability of 0.012. The residuals are shown to be consistent with white noise. The 6 signals detected include two previously reported with periods of 7.198 (b) and 28.14 (c) days, plus additional periods of 30.82 (d), 38.82 (e), 53.22, and 91.3 (f) days. The 53 day signal is probably the second harmonic of the stellar rotation period and is likely the result of surface activity. The existence of the additonal Keplerian signals suggest the possibilty of further planets, two of which (d and e) could join Gl 667Cc in the central region of the habitable zone. N-body simulations are required to determine which of these signals are consistent with a stable planetary system. $M \sin i$ values corresponding to signals b, c, d, e, and f are $\sim$ 5.4, 4.8, 3.1, 2.4, and 5.4 M$_{\earth}$, respectively.
Bayesian Re-analysis of the Gliese 581 Exoplanet System
Philip C. Gregory
Physics , 2011, DOI: 10.1111/j.1365-2966.2011.18877.x
Abstract: A re-analysis of Gliese 581 HARPS and HIRES precision radial velocity data was carried out with a Bayesian multi-planet Kepler periodogram (from 1 to 6 planets) based on a fusion Markov chain Monte Carlo algorithm. In all cases the analysis included an unknown parameterized stellar jitter noise term. For the HARPS data set the most probable number of planetary signals detected is 5 with a Bayesian false alarm probability of 0.01. These include the $3.1498\pm0.0005$, $5.3687\pm0.0002$, $12.927_{-0.004}^{+0.006}$, and $66.9\pm0.2$d periods reported previously plus a $399_{-16}^{+14}$d period. The orbital eccentricities are $0.0_{-0.0}^{+0.2}$, $0.00_{-0.00}^{+0.02}$, $0.10_{-0.10}^{+0.06}$, $0.33_{-0.10}^{+0.09}$, and $0.02_{-0.02}^{+0.30}$, respectively. The semi-major axis and $M sin i$ of the 5 planets are ($0.0285\pm0.0006$ au, $1.9\pm0.3$M$_{\earth}$), ($0.0406\pm0.0009$ au, $15.7\pm0.7$M$_{\earth}$), ($0.073\pm0.002$ au, $5.3\pm0.4$M$_{\earth}$), ($0.218\pm0.005$ au, $6.7\pm0.8$M$_{\earth}$), and ($0.7\pm0.2$ au, $6.6_{-2.7}^{+2.0}$M$_{\earth}$), respectively. The analysis of the HIRES data set yielded a reliable detection of only the strongest 5.37 and 12.9 day periods. The analysis of the combined HIRES/HARPS data again only reliably detected the 5.37 and 12.9d periods. Detection of 4 planetary signals with periods of 3.15, 5.37, 12.9, and 66.9d was only achieved by including an additional unknown but parameterized Gaussian error term added in quadrature to the HIRES quoted errors. The marginal distribution for the sigma of this additional error term has a well defined peak at $1.8\pm0.4$m s$^{-1}$. It is possible that this additional error arises from unidentified systematic effects. We did not find clear evidence for a fifth planetary signal in the combined HIRES/HARPS data set.
A Bayesian Periodogram Finds Evidence for Three Planets in 47 Ursae Majoris
Philip C. Gregory,Debra A. Fischer
Physics , 2010, DOI: 10.1111/j.1365-2966.2009.16233.x
Abstract: A Bayesian analysis of 47 Ursae Majoris (47 UMa) radial velocity data confirms and refines the properties of two previously reported planets with periods of 1079 and 2325 days and finds evidence for an additional long period planet with a period of approximately 10000 days. The three planet model is found to be 10^5 times more probable than the next most probable model which is a two planet model. The nonlinear model fitting is accomplished with a new hybrid Markov chain Monte Carlo (HMCMC) algorithm which incorporates parallel tempering, simulated annealing and genetic crossover operations. Each of these features facilitate the detection of a global minimum in chi-squared. By combining all three, the HMCMC greatly increases the probability of realizing this goal. When applied to the Kepler problem it acts as a powerful multi-planet Kepler periodogram. The measured periods are 1078 \pm 2, 2391{+100}{-87}, and 14002{+4018}{-5095}d, and the corresponding eccentricities are 0.032 \pm 0.014, 0.098{+.047}{-.096}, and 0.16{+.09}{-.16}. The results favor low eccentricity orbits for all three. Assuming the three signals (each one consistent with a Keplerian orbit) are caused by planets, the corresponding limits on planetary mass (M sin i) and semi-major axis are (2.53{+.07}{-.06}MJ, 2.10\pm0.02au), (0.54\pm0.07MJ, 3.6\pm0.1au), and (1.6{+0.3}{-0.5}MJ, 11.6{+2.1}{-2.9}au), respectively. We have also characterized a noise induced eccentricity bias and designed a correction filter that can be used as an alternate prior for eccentricity, to enhance the detection of planetary orbits of low or moderate eccentricity.
Rapid and Accurate Prediction and Scoring of Water Molecules in Protein Binding Sites
Gregory A. Ross, Garrett M. Morris, Philip C. Biggin
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0032036
Abstract: Water plays a critical role in ligand-protein interactions. However, it is still challenging to predict accurately not only where water molecules prefer to bind, but also which of those water molecules might be displaceable. The latter is often seen as a route to optimizing affinity of potential drug candidates. Using a protocol we call WaterDock, we show that the freely available AutoDock Vina tool can be used to predict accurately the binding sites of water molecules. WaterDock was validated using data from X-ray crystallography, neutron diffraction and molecular dynamics simulations and correctly predicted 97% of the water molecules in the test set. In addition, we combined data-mining, heuristic and machine learning techniques to develop probabilistic water molecule classifiers. When applied to WaterDock predictions in the Astex Diverse Set of protein ligand complexes, we could identify whether a water molecule was conserved or displaced to an accuracy of 75%. A second model predicted whether water molecules were displaced by polar groups or by non-polar groups to an accuracy of 80%. These results should prove useful for anyone wishing to undertake rational design of new compounds where the displacement of water molecules is being considered as a route to improved affinity.
Towards Open Access
Gregory C Ippolito, Christian Schmidt, Chhaya Das, Philip W Tucker
Molecular Cancer , 2005, DOI: 10.1186/1476-4598-4-20
Abstract: Publications are perhaps the sole currency of scientific research--for it is publications which beget funding, and in turn, funding which begets more publications--and as such they are vitally important to the career of any research scientist. How, when, and where the research is published can be as significant as the research results themselves since the influence of a research article may only be as potent as its ability to attract an audience of readers and thereby disseminate through the field.Indeed, the root of the word publication implies its dissemination to a public readership generally, and in this way the progress of science is archived in the historical record. True to this spirit, the NIH has initiated the Public Access Policy [1,2] and has created a single repository (PubMed Central, or PMC) to archive the corpus of biomedical research--past, present, and future. This Public Access Policy follows on the heels of a similar initiative in the United Kingdom last year when the House of Commons Science and Technology Committee recommended the promotion of Open Access in the UK to all publicly funded scientific research [4].The NIH proposal mandates Open Access, but only to those research articles deriving in part or whole from direct costs provided by NIH grants. Nonetheless, this policy will likely apply to a major fraction of all research publications. By its own estimation, the NIH currently funds at least ten percent (65,000 articles) of all biomedical literature annually [5]. Moreover, PubMed Central will further expand due to the continuing submission (since its inception in 2000) of all final articles published in Open Access journals. To date, PubMed Central [6] archives approximately 100,000 articles from over 130 biomedical journals. Such a single repository, covering the full spectrum of research literature and freely available to the world, is revolutionary. The NIH directive, although strongly encouraged, was issued merely as a "request," and s
Validation of the Edinburgh Claudication Questionnaire in 1st generation Black African-Caribbean and South Asian UK migrants: A sub-study to the Ethnic-Echocardiographic Heart of England Screening (E-ECHOES) study
Philip C Bennett, Gregory YH Lip, Stanley Silverman, Andrew D Blann, Paramjit S Gill
BMC Medical Research Methodology , 2011, DOI: 10.1186/1471-2288-11-85
Abstract: Subjects were recruited from the Ethnic-Echocardiographic Heart of England Screening (E-ECHOES) study, a community based screening survey for heart failure in minority ethnic groups. Translated versions of the ECQ were prepared following a recognised protocol. All participants attending screening between October 2007 and February 2009 were asked to complete the ECQ in the language of their choice (English, Punjabi, Bengali, Urdu, Hindi or Gujarati). Subjects answering positively to experiencing leg pain or discomfort on walking were asked to return to have Ankle Brachial Pressure Index (ABPI) measured.154 out of 2831 subjects participating in E-ECHOES (5.4%) were eligible to participate in this sub-study, for which 74.3% returned for ABPI assessment. Non-responders were younger than participants (59[9] vs. 65[11] years; p = 0.015). Punjabi, English and Bengali questionnaires identified participants with Intermittent Claudication, so these questionnaires were assessed. The sensitivities (SN), specificities (SP), positive (PPV) and negative (NPV) predictive values were calculated. English: SN: 50%; SP: 68%; PPV: 43%; NPV: 74%. Punjabi: SN: 50%; SP: 87%; PPV: 43%; NPV: 90%. Bengali: SN: 33%; SP: 50%; PPV: 13%; NPV: 73%. There were significant differences in diagnostic accuracy between the 3 versions (Punjabi: 83.8%; Bengali: 45%; English: 62.2%; p < 0.0001). No significant differences were found in sensitivity and specificity between illiterate and literate participants in any of the questionnaires and there was no significant different difference between those under and over 60 years of age.Our findings suggest that the ECQ is not as sensitive or specific a diagnostic tool in 1st generation Black African-Caribbean and South Asian UK migrants than in the Edinburgh Artery Study, reflecting the findings of other diagnostic questionnaires in these minority ethnic groups. However this study is limited by sample size so conclusions should be interpreted with caution.Periphe
Bright/ARID3A contributes to chromatin accessibility of the immunoglobulin heavy chain enhancer
Danjuan Lin, Gregory C Ippolito, Rui-Ting Zong, James Bryant, Janet Koslovsky, Philip Tucker
Molecular Cancer , 2007, DOI: 10.1186/1476-4598-6-23
Abstract: Numerous studies have demonstrated the requirement of the intronic enhancer (Eμ) in transcription of immunoglobulin heavy chains (reviewed in [1]). In vivo, Eμ is required for successful B-cell development, and in its absence, completion of antigen receptor assembly through VDJ recombination is blocked [2,3]. Based on chromatin immunoprecipitation (ChIP) measurements of its histone modification status, Eμ assumes an accessible chromatin configuration specifically in B cells [4-6]. Conventional transcription factors may seize upon this B cell-accessible state to bind to Eμ for transactivation via VDJ-associated promoters (Fig. 1A). Transcriptional activators further exploit increasingly accessible chromatin structures to enhance their binding as B cells progress through development [7].The Eμ core is flanked on both sides by nuclear matrix associating regions (MARs) (Fig. 1A,B) [8]. As proposed for MARs in general, the Eμ MARs are thought to anchor higher order chromatin into discrete looped domains and to attach them to the nuclear matrix – a site where proteins essential for transcription might reside [9]. While the importance of the Eμ core is universally accepted, the role of their associated MARs remains controversial. The Eμ MARs were initially implicated in locus down-regulation [10-12], an argument strengthened by the observation that the enhancer core alone will activate gene expression in non-B cells [12]. Conversely, the Eμ MARs have been shown to stimulate IgH transcription in B cells (reviewed in [13]), perhaps by impacting chromatin structure of the enhancer [14-17]. For example, targeted in vivo deletion of both intronic MARs reduced IgH transcription 5–10 fold [17]. However, deletion of the endogenous MARs in a hybridoma cell line had modest effects, implying a redundant function for the MARs and the core enhancer in maintaining IgH expression [18]. Studies which examined the Eμ MARs in VDJ rearrangement have had variable outcomes, largely depending o
Laser Ranging for Gravitational, Lunar, and Planetary Science
Stephen M. Merkowitz,Philip W. Dabney,Jeffrey C. Livas,Jan F. McGarry,Gregory A. Neumann,Thomas W. Zagwodzki
Physics , 2007, DOI: 10.1142/S0218271807011565
Abstract: More precise lunar and Martian ranging will enable unprecedented tests of Einstein's theory of General Relativity and well as lunar and planetary science. NASA is currently planning several missions to return to the Moon, and it is natural to consider if precision laser ranging instruments should be included. New advanced retroreflector arrays at carefully chosen landing sites would have an immediate positive impact on lunar and gravitational studies. Laser transponders are currently being developed that may offer an advantage over passive ranging, and could be adapted for use on Mars and other distant objects. Precision ranging capability can also be combined with optical communications for an extremely versatile instrument. In this paper we discuss the science that can be gained by improved lunar and Martian ranging along with several technologies that can be used for this purpose.
Modeling Mid-Infrared Diagnostics of Obscured Quasars and Starbursts
Gregory F. Snyder,Christopher C. Hayward,Anna Sajina,Patrik Jonsson,Thomas J. Cox,Lars Hernquist,Philip F. Hopkins,Lin Yan
Physics , 2012, DOI: 10.1088/0004-637X/768/2/168
Abstract: We analyze the link between active galactic nuclei (AGN) and mid-infrared flux using dust radiative transfer calculations of starbursts realized in hydrodynamical simulations. Focusing on the effects of galaxy dust, we evaluate diagnostics commonly used to disentangle AGN and star formation in ultraluminous infrared galaxies (ULIRGs). We examine these quantities as a function of time, viewing angle, dust model, AGN spectrum, and AGN strength in merger simulations representing two possible extremes of the ULIRG population: one is a typical gas-rich merger at z ~ 0, and the other is characteristic of extremely obscured starbursts at z ~ 2 to 4. This highly obscured burst begins star-formation-dominated with significant PAH emission, and ends with a ~10^9 yr period of red near-IR colors. At coalescence, when the AGN is most luminous, dust obscures the near-infrared AGN signature, reduces the relative emission from polycyclic aromatic hydrocarbons (PAHs), and enhances the 9.7 micron absorption by silicate grains. Although generally consistent with previous interpretations, our results imply none of these indicators can unambiguously estimate the AGN luminosity fraction in all cases. Motivated by the simulations, we show that a combination of the extinction feature at 9.7 micron, the PAH strength, and a near-infrared slope can simultaneously constrain the AGN fraction and dust grain distribution for a wide range of obscuration. We find that this indicator, accessible to the James Webb Space Telescope, may estimate the AGN power as tightly as the hard X-ray flux alone, thereby providing a valuable future cross-check and constraint for large samples of distant ULIRGs.
Tylor vs. Westermarck: Explaining the Incest Taboo  [PDF]
Gregory C. Leavitt
Sociology Mind (SM) , 2013, DOI: 10.4236/sm.2013.31008
Abstract:

In the late 19th century arguments explaining incest avoidance were framed separately by Edward Tylor and Edward Westermarck. Tylor offered an environmental theory asserting that people have to marry outside of their own kin and communities or die out from the detrimental effects of isolation. Westermarck turned to Darwin’s theory to explain that harmful inbreeding had been selected against in the human genome. By the late 20th and early 21st centuries explanations of human behaviors have become increasingly encompassed by natural selection theory. The debate concerning the productiveness of evolutionary biology for explaining complex human behaviors is highly contentious and continues unabated. Although human evolutionists repeatedly say that environment is important for understanding human behavior they often do not develop this part of the equation. Behind the prestige of evolutionary biology selection models of human behavior have passed into popular science and the public psyche. Often heard today from a wide range of highly visible media sources is an assortment of topics on human behaviors which are framed by Darwinian assumptions. Contemplations about incest and inbreeding avoidance fall into this category and are presented by Darwinian social science as the best case example demonstrating evolutionary suppositions about human behavior. In the article that follows these issues are framed and examined. The argument is offered that evolutionary approaches are not always the most compelling and that convincing environmental explanations are overlooked.

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