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Search Results: 1 - 10 of 463853 matches for " Todd A. Gibson "
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The Roots of Bioinformatics in ISMB
Todd A. Gibson
PLOS Computational Biology , 2012, DOI: 10.1371/journal.pcbi.1002679
Abstract:
Questioning the Ubiquity of Neofunctionalization
Todd A. Gibson ,Debra S. Goldberg
PLOS Computational Biology , 2009, DOI: 10.1371/journal.pcbi.1000252
Abstract: Gene duplication provides much of the raw material from which functional diversity evolves. Two evolutionary mechanisms have been proposed that generate functional diversity: neofunctionalization, the de novo acquisition of function by one duplicate, and subfunctionalization, the partitioning of ancestral functions between gene duplicates. With protein interactions as a surrogate for protein functions, evidence of prodigious neofunctionalization and subfunctionalization has been identified in analyses of empirical protein interactions and evolutionary models of protein interactions. However, we have identified three phenomena that have contributed to neofunctionalization being erroneously identified as a significant factor in protein interaction network evolution. First, self-interacting proteins are underreported in interaction data due to biological artifacts and design limitations in the two most common high-throughput protein interaction assays. Second, evolutionary inferences have been drawn from paralog analysis without consideration for concurrent and subsequent duplication events. Third, the theoretical model of prodigious neofunctionalization is unable to reproduce empirical network clustering and relies on untenable parameter requirements. In light of these findings, we believe that protein interaction evolution is more persuasively characterized by subfunctionalization and self-interactions.
A transit timing analysis of nine RISE light curves of the exoplanet system TrES-3
N. P. Gibson,D. Pollacco,I. Skillen,E. K. Simpson,S. Barros,Y. C. Joshi,I. Todd,C. Benn,D. Christian,M. Hrudková,F. P. Keenan,I. A. Steele
Physics , 2009, DOI: 10.1088/0004-637X/700/2/1078
Abstract: We present nine newly observed transits of TrES-3, taken as part of a transit timing program using the RISE instrument on the Liverpool Telescope. A Markov-Chain Monte-Carlo analysis was used to determine the planet-star radius ratio and inclination of the system, which were found to be Rp/Rstar=0.1664^{+0.0011}_{-0.0018} and i = 81.73^{+0.13}_{-0.04} respectively, consistent with previous results. The central transit times and uncertainties were also calculated, using a residual-permutation algorithm as an independent check on the errors. A re-analysis of eight previously published TrES-3 light curves was conducted to determine the transit times and uncertainties using consistent techniques. Whilst the transit times were not found to be in agreement with a linear ephemeris, giving chi^2 = 35.07 for 15 degrees of freedom, we interpret this to be the result of systematics in the light curves rather than a real transit timing variation. This is because the light curves that show the largest deviation from a constant period either have relatively little out-of-transit coverage, or have clear systematics. A new ephemeris was calculated using the transit times, and was found to be T_c(0) = 2454632.62610 +- 0.00006 HJD and P = 1.3061864 +- 0.0000005 days. The transit times were then used to place upper mass limits as a function of the period ratio of a potential perturbing planet, showing that our data are sufficiently sensitive to have probed for sub-Earth mass planets in both interior and exterior 2:1 resonances, assuming the additional planet is in an initially circular orbit.
A transit timing analysis of seven RISE light curves of the exoplanet system HAT-P-3
N. P. Gibson,D. Pollacco,S. Barros,C. Benn,D. Christian,M. Hrudková,Y. C. Joshi,F. P. Keenan,E. K. Simpson,I. Skillen,I. A. Steele,I. Todd
Physics , 2009, DOI: 10.1111/j.1365-2966.2009.15770.x
Abstract: We present seven light curves of the exoplanet system HAT-P-3, taken as part of a transit timing program using the RISE instrument on the Liverpool Telescope. The light curves are analysed using a Markov-Chain Monte-Carlo algorithm to update the parameters of the system. The inclination is found to be i = 86.75^{+0.22}_{-0.21} deg, the planet-star radius ratio to be R_p/R_star = 0.1098^{+0.0010}_{-0.0012}, and the stellar radius to be R_star = 0.834^{+0.018}_{-0.026} R_sun, consistent with previous results but with a significant improvement in the precision. Central transit times and uncertainties for each light curve are also determined, and a residual permutation algorithm used as an independent check on the errors. The transit times are found to be consistent with a linear ephemeris, and a new ephemeris is calculated as T_c(0) = 2454856.70118 +- 0.00018 HJD and P = 2.899738 +- 0.000007 days. Model timing residuals are fitted to the measured timing residuals to place upper mass limits for a hypothetical perturbing planet as a function of the period ratio. These show that we have probed for planets with masses as low as 0.33 M_earth and 1.81 M_earth in the interior and exterior 2:1 resonances, respectively, assuming the planets are initially in circular orbits.
Validating New Technologies to Treat Depression, Pain and the Feeling of Sentient Beings: A Reply to “Neuroscience for the Soul”  [PDF]
Michael A. Persinger, Todd R. Murphy
Neuroscience & Medicine (NM) , 2016, DOI: 10.4236/nm.2016.71004
Abstract: The primary assumption of Neuroscience is that all experiences are strongly correlated with or caused by the specifics of brain structures and their particular dynamics. The profound experiences attributed to the “sensed presence” and their cultural anthropomorphisms such as deities and gods are persistent reports in human populations that are frequently associated with permanent changes in behavior, reduced depression and alleviation of pain. The majority of traditional clinical observations and modern imaging techniques have emphasized the central role of right temporal lobe structures and their directly related networks. The experimental simulation of sensed presences which can result in attributions to spiritual, deity-based or mystical sources within the clinical laboratory by the application of physiologically-patterned magnetic fields across the temporal lobes through our God Helmet requires the same precision of technology that is essential for synthesizing molecular treatments for modifying anomalous behavior, depression and pain. Despite the clinical utility of these simulated conditions within Neuroscience and Medicine, misinformation concerning the bases and efficacy of this new technology persist. Here we present detailed technical clarifications and rebuttals to refute these misconceptions. A Hegelian approach to this delay of development and impedance provides a context through which the ultimate synthesis and application of this technology may be accommodated in the near future.
Atmospheric PSF Interpolation for Weak Lensing in Short Exposure Imaging Data
C. Chang,P. J. Marshall,J. G. Jernigan,J. R. Peterson,S. M. Kahn,S. F. Gull,Y. AlSayyad,Z. Ahmad,J. Bankert,D. Bard,A. Connolly,R. R. Gibson,K. Gilmore,E. Grace,M. Hannel,M. A. Hodge,L. Jones,S. Krughoff,S. Lorenz,S. Marshall,A. Meert,S. Nagarajan,E. Peng,A. P. Rasmussen,M. Shmakova,N. Sylvestre,N. Todd,M. Young
Physics , 2012, DOI: 10.1111/j.1365-2966.2012.22134.x
Abstract: A main science goal for the Large Synoptic Survey Telescope (LSST) is to measure the cosmic shear signal from weak lensing to extreme accuracy. One difficulty, however, is that with the short exposure time ($\simeq$15 seconds) proposed, the spatial variation of the Point Spread Function (PSF) shapes may be dominated by the atmosphere, in addition to optics errors. While optics errors mainly cause the PSF to vary on angular scales similar or larger than a single CCD sensor, the atmosphere generates stochastic structures on a wide range of angular scales. It thus becomes a challenge to infer the multi-scale, complex atmospheric PSF patterns by interpolating the sparsely sampled stars in the field. In this paper we present a new method, PSFent, for interpolating the PSF shape parameters, based on reconstructing underlying shape parameter maps with a multi-scale maximum entropy algorithm. We demonstrate, using images from the LSST Photon Simulator, the performance of our approach relative to a 5th-order polynomial fit (representing the current standard) and a simple boxcar smoothing technique. Quantitatively, PSFent predicts more accurate PSF models in all scenarios and the residual PSF errors are spatially less correlated. This improvement in PSF interpolation leads to a factor of 3.5 lower systematic errors in the shear power spectrum on scales smaller than $\sim13'$, compared to polynomial fitting. We estimate that with PSFent and for stellar densities greater than $\simeq1/{\rm arcmin}^{2}$, the spurious shear correlation from PSF interpolation, after combining a complete 10-year dataset from LSST, is lower than the corresponding statistical uncertainties on the cosmic shear power spectrum, even under a conservative scenario.
Spurious Shear in Weak Lensing with LSST
C. Chang,S. M. Kahn,J. G. Jernigan,J. R. Peterson,Y. AlSayyad,Z. Ahmad,J. Bankert,D. Bard,A. Connolly,R. R. Gibson,K. Gilmore,E. Grace,M. Hannel,M. A. Hodge,M. J. Jee,L. Jones,S. Krughoff,S. Lorenz,P. J. Marshall,S. Marshall,A. Meert,S. Nagarajan,E. Peng,A. P. Rasmussen,M. Shmakova,N. Sylvestre,N. Todd,M. Young
Physics , 2012, DOI: 10.1093/mnras/sts223
Abstract: The complete 10-year survey from the Large Synoptic Survey Telescope (LSST) will image $\sim$ 20,000 square degrees of sky in six filter bands every few nights, bringing the final survey depth to $r\sim27.5$, with over 4 billion well measured galaxies. To take full advantage of this unprecedented statistical power, the systematic errors associated with weak lensing measurements need to be controlled to a level similar to the statistical errors. This work is the first attempt to quantitatively estimate the absolute level and statistical properties of the systematic errors on weak lensing shear measurements due to the most important physical effects in the LSST system via high fidelity ray-tracing simulations. We identify and isolate the different sources of algorithm-independent, \textit{additive} systematic errors on shear measurements for LSST and predict their impact on the final cosmic shear measurements using conventional weak lensing analysis techniques. We find that the main source of the errors comes from an inability to adequately characterise the atmospheric point spread function (PSF) due to its high frequency spatial variation on angular scales smaller than $\sim10'$ in the single short exposures, which propagates into a spurious shear correlation function at the $10^{-4}$--$10^{-3}$ level on these scales. With the large multi-epoch dataset that will be acquired by LSST, the stochastic errors average out, bringing the final spurious shear correlation function to a level very close to the statistical errors. Our results imply that the cosmological constraints from LSST will not be severely limited by these algorithm-independent, additive systematic effects.
Effect of Measurement Errors on Predicted Cosmological Constraints from Shear Peak Statistics with LSST
D. Bard,J. M. Kratochvil,C. Chang,M. May,S. M. Kahn,Y. AlSayyad,Z. Ahmad,J. Bankert,A. Connolly,R. R. Gibson,K. Gilmore,E. Grace,Z. Haiman,M. Hannel,K. M. Huffenberger,J. G. Jernigan,L. Jones,S. Krughoff,S. Lorenz,S. Marshall,A. Meert,S. Nagarajan,E. Peng,J. Peterson,A. P. Rasmussen,M. Shmakova,N. Sylvestre,N. Todd,M. Young
Physics , 2013, DOI: 10.1088/0004-637X/774/1/49
Abstract: The statistics of peak counts in reconstructed shear maps contain information beyond the power spectrum, and can improve cosmological constraints from measurements of the power spectrum alone if systematic errors can be controlled. We study the effect of galaxy shape measurement errors on predicted cosmological constraints from the statistics of shear peak counts with the Large Synoptic Survey Telescope (LSST). We use the LSST image simulator in combination with cosmological N-body simulations to model realistic shear maps for different cosmological models. We include both galaxy shape noise and, for the first time, measurement errors on galaxy shapes. We find that the measurement errors considered have relatively little impact on the constraining power of shear peak counts for LSST.
Genetic variation in DNA-repair pathways and response to radiochemotherapy in esophageal adenocarcinoma: a retrospective cohort study of the Eastern Cooperative Oncology Group
Harry H Yoon, Paul J Catalano, Kathleen M Murphy, Todd C Skaar, Santosh Philips, Mark Powell, Elizabeth A Montgomery, Michael J Hafez, Steven M Offer, Geoffrey Liu, Stephen J Meltzer, Xifeng Wu, Arlene A Forastiere, Al B Benson, Lawrence R Kleinberg, Michael K Gibson
BMC Cancer , 2011, DOI: 10.1186/1471-2407-11-176
Abstract: Eighty-one eligible treatment-na?ve subjects with newly diagnosed resectable esophageal adenocarcinoma received radiotherapy (45 Gy) concurrent with cisplatin-based chemotherapy, with planned subsequent surgical resection. The primary endpoint was pCR, defined as complete absence of tumor in the surgical specimen after radiochemotherapy. Using germline DNA from 60 subjects, we examined the base-excision repair SNP, XRCC1 Arg399Gln, and 4 other SNPs in nucleotide excision (XPD Lys751Gln and Asp312Asn, ERCC1 3' flank) and double-stranded break (XRCC2 5' flank) repair pathways, and correlated genotype with pCR rate. Paired tumor tissue was used to estimate the frequency of allelic imbalance at the XRCC1 SNP.The variant allele of the XRCC1 SNP (399Gln) was detected in 52% of subjects. Only 6% of subjects with the variant allele experienced a pCR, compared to 28% of subjects without the variant allele (odds ratio 5.37 for failing to achieve pCR, p = 0.062). Allelic imbalance at this locus was found in only 10% of informative subjects, suggesting that germline genotype may reflect tumor genotype at this locus. No significant association with pCR was noted for other SNPs.Assessed for the first time in a prospective, interventional trial cohort of esophageal adenocarcinoma, XRCC1 399Gln was associated with resistance to radiochemotherapy. Further investigation of this genetic variation is warranted in larger cohorts. In addition, these data indicate that germline genotype may serve as a surrogate for tumor genotype at this locus.Esophageal adenocarcinoma (EAC) is one of the fastest rising cancers in the West, particularly among white men[1]. Survival remains poor despite experimentation with numerous cytotoxic agents and therapeutic approaches, as well as improvements in diagnostic, surgical, and radiation technique[2]. In the U.S., a widely used standard to attempt to cure locally advanced disease, which is a common stage at presentation, is to provide concurrent radiochem
Interkulturelle Online-Kommunikation: Konversationsanalyse und die Analyse asynchroner schriftlichter Diskussionen Intercultural Communication Online: Conversation Analysis and the Investigation of Asynchronous Written Discourse Comunicación intercultural en línea: Análisis de conversación y la investigación de discurso escrito asincrónico
Will Gibson
Forum : Qualitative Social Research , 2008,
Abstract: Der vorliegende Artikel arbeitet methodologische Probleme heraus, die entstehen, wenn bei der Analyse von schriftlichen, asynchronen Online-Diskussionen "Kultur" und "Interkulturalit t" als interaktiv darstellbare und beobachtbare Ph nomene behandelt werden. Insbesondere wird untersucht, wie die Konversationsanalyse mit ihrem Fokus auf Sequenzialit t und das Konzept der Zugeh rigkeitskategorisierungen die Analyse von Kultur als verschriftlichte, interaktive Leistung unterstützen k nnte. Im Beitrag wird dargelegt, dass trotz der offensichtlichen Unterschiede zwischen sequenziellen mündlichen Gespr chen und verschriftlichten Online-Diskussionen durch die Konversationsanalyse interessante Methoden bereitgestellt werden, um Online-Diskussionen zu analysieren. Die beiden Aspekte der Sequenzialit t und der Zugeh rigkeitskategorien sind dabei hilfreich, um anhand von Verschriftlichungen in Online-Foren die Konstruktion sichtbarer und als solche erkennbare, interkulturelle Diskurspraktiken nachzuzeichnen. URN: urn:nbn:de:0114-fqs0901493 This paper works through the methodological issues involved in treating "culture" and "interculturality" as interactionally demonstrable and observable phenomena in written online asynchronous discourse. In particular, the paper explores the ways that conversation analysis (CA) and its focus on sequentiality and membership categorization analysis might aid the analysis of culture as a textural interactional achievement. The paper argues that, while there are some clear differences between sequential talk and written asynchronous discourse, there are still interesting ways in which CA's analytic foci may be worked through in relation to online discourse. Both the concern with sequentiality and with membership categories may well help us to see how the construction of visible and recognizable intercultural discourse practices are accomplished through written modes in online forums. URN: urn:nbn:de:0114-fqs0901493 Este artículo aborda los temas metodológicos involucrados al tratar la "cultura" y la "interculturalidad" como fenómenos interactivamente observables y demostrables en el discurso escrito asincrónico. En particular, explora las formas en que el análisis de conversación (AC) y su foco en la secuencialidad y el análisis de categorización de membresía pueden ayudar al análisis de la cultura como una realización interactiva textual. Se argumenta que, aunque hay algunas claras diferencias entre el habla secuencial y el discurso escrito asincrónico, hay todavía formas interesantes en las que los focos analíticos del AC pueden a
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