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Search Results: 1 - 10 of 67101 matches for " Paul-Michael Agapow "
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Phylogenetic biodiversity assessment based on systematic nomenclature
Ross H Crozier,Lisa J Dunnett,Paul-Michael Agapow
Evolutionary Bioinformatics , 2005,
Abstract: Biodiversity assessment demands objective measures, because ultimately conservation decisions must prioritize the use of limited resources for preserving taxa. The most general framework for the objective assessment of conservation worth are those that assess evolutionary distinctiveness, e.g. Genetic (Crozier 1992) and Phylogenetic Diversity (Faith 1992), and Evolutionary History (Nee & May 1997). These measures all attempt to assess the conservation worth of any scheme based on how much of the encompassing phylogeny of organisms is preserved. However, their general applicability is limited by the small proportion of taxa that have been reliably placed in a phylogeny. Given that phylogenizaton of many interesting taxa or important is unlikely to occur soon, we present a framework for using taxonomy as a reasonable surrogate for phylogeny. Combining this framework with exhaustive searches for combinations of sites containing maximal diversity, we provide a proof-of-concept for assessing conservation schemes for systematized but un-phylogenised taxa spread over a series of sites. This is illustrated with data from four studies, on North Queensland flightless insects (Yeates et al. 2002), ants from a Florida Transect (Lubertazzi & Tschinkel 2003), New England bog ants (Gotelli & Ellison 2002) and a simulated distribution of the known New Zealand Lepidosauria (Daugherty et al. 1994). The results support this approach, indicating that species, genus and site numbers predict evolutionary history, to a degree depending on the size of the data set.
Phylogenetic biodiversity assessment based on systematic nomenclature
Ross H Crozier,Lisa J Dunnett,Paul-Michael Agapow
Evolutionary Bioinformatics , 2006,
Abstract: Biodiversity assessment demands objective measures, because ultimately conservation decisions must prioritize the use of limited resources for preserving taxa. The most general framework for the objective assessment of conservation worth are those that assess evolutionary distinctiveness, e.g. Genetic (Crozier 1992) and Phylogenetic Diversity (Faith 1992), and Evolutionary History (Nee & May 1997). These measures all attempt to assess the conservation worth of any scheme based on how much of the encompassing phylogeny of organisms is preserved. However, their general applicability is limited by the small proportion of taxa that have been reliably placed in a phylogeny. Given that phylogenizaton of many interesting taxa or important is unlikely to occur soon, we present a framework for using taxonomy as a reasonable surrogate for phylogeny. Combining this framework with exhaustive searches for combinations of sites containing maximal diversity, we provide a proof-of-concept for assessing conservation schemes for systematized but un-phylogenised taxa spread over a series of sites. This is illustrated with data from four studies, on North Queensland flightless insects (Yeates et al. 2002), ants from a Florida Transect (Lubertazzi & Tschinkel 2003), New England bog ants (Gotelli & Ellison 2002) and a simulated distribution of the known New Zealand Lepidosauria (Daugherty et al. 1994). The results support this approach, indicating that species, genus and site numbers predict evolutionary history, to a degree depending on the size of the data set.
A Comparison of the Effects of Random and Selective Mass Extinctions on Erosion of Evolutionary History in Communities of Digital Organisms
Gabriel Yedid, Jason Stredwick, Charles A. Ofria, Paul-Michael Agapow
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0037233
Abstract: The effect of mass extinctions on phylogenetic diversity and branching history of clades remains poorly understood in paleobiology. We examined the phylogenies of communities of digital organisms undergoing open-ended evolution as we subjected them to instantaneous “pulse” extinctions, choosing survivors at random, and to prolonged “press” extinctions involving a period of low resource availability. We measured age of the phylogenetic root and tree stemminess, and evaluated how branching history of the phylogenetic trees was affected by the extinction treatments. We found that strong random (pulse) and strong selective extinction (press) both left clear long-term signatures in root age distribution and tree stemminess, and eroded deep branching history to a greater degree than did weak extinction and control treatments. The widely-used Pybus-Harvey gamma statistic showed a clear short-term response to extinction and recovery, but differences between treatments diminished over time and did not show a long-term signature. The characteristics of post-extinction phylogenies were often affected as much by the recovery interval as by the extinction episode itself.
Evolutionary Pathways of the Pandemic Influenza A (H1N1) 2009 in the UK
Monica Galiano, Paul-Michael Agapow, Catherine Thompson, Steven Platt, Anthony Underwood, Joanna Ellis, Richard Myers, Jonathan Green, Maria Zambon
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0023779
Abstract: The emergence of the influenza (H1N1) 2009 virus provided a unique opportunity to study the evolution of a pandemic virus following its introduction into the human population. Virological and clinical surveillance in the UK were comprehensive during the first and second waves of the pandemic in 2009, with extensive laboratory confirmation of infection allowing a detailed sampling of representative circulating viruses. We sequenced the complete coding region of the haemagglutinin (HA) segment of 685 H1N1 pandemic viruses selected without bias during two waves of pandemic in the UK (April-December 2009). Phylogenetic analysis showed that although temporal accumulation of amino acid changes was observed in the HA sequences, the overall diversity was less than that typically seen for seasonal influenza A H1N1 or H3N2. There was co-circulation of multiple variants as characterised by signature amino acid changes in the HA. A specific substitution (S203T) became predominant both in UK and global isolates. No antigenic drift occurred during 2009 as viruses with greater than four-fold reduction in their haemagglutination inhibition (HI) titre (“low reactors”) were detected in a low proportion (3%) and occurred sporadically. Although some limited antigenic divergence in viruses with four-fold reduction in HI titre might be related to the presence of 203T, additional studies are needed to test this hypothesis.
Influence of rub-in technique on required application time and hand coverage in hygienic hand disinfection
Günter Kampf, Mirja Reichel, Yvonne Feil, Sven Eggerstedt, Paul-Michael Kaulfers
BMC Infectious Diseases , 2008, DOI: 10.1186/1471-2334-8-149
Abstract: The reference procedure lasted on average 75 s and resulted in 53% of subjects with at least one untreated area on the hands. Five repetitions of the rub-in steps lasted on average 37 s with 67% of subjects having incompletely treated hands. One repetition lasted on average 17 s, and all subjects had at least one untreated area. Repeating the sequence of steps lasted longer, but did not yield a better result. "Responsible application" was quite fast, lasting 25 s among non-healthcare worker subjects and 28 s among healthcare workers. It was also effective, with 53% and 55% of hands being incompletely treated. New techniques were as fast and effective as "responsible application". Large untreated areas were found only with short applications. Fingertips and palms were often covered completely.In clinical practice, hand disinfection is apparently better than practitioners of infection control often anticipate. Based on our data, a high-quality hygienic hand disinfection is not possible within 15 s. A 30 s application time can, however, be recommended for clinical practice. The currently recommended six steps of EN 1500 are not really suitable for clinical practice, because they yield comparably poor results. The most appropriate application procedure may be "responsible application", or one of the other new techniques.In many European countries the commonly recommended application time for hygienic hand disinfection is 30 seconds (s), based on efficacy data obtained according to EN 1500 [1]. Well-formulated hand rubs, however, may show in vitro bactericidal activity in only 15 seconds [2]. Therefore, a sufficient efficacy according to EN 1500 might also be achieved in vivo in an application time shorter than 30 seconds. One major concern, however, is that a 15 s treatment would not ensure that the hands are entirely covered with the hand disinfectant. The Centers for Disease Control and Prevention (CDC) guidelines for hand rub use recommend a very general technique wh
The Impact of Criminal Code Training on Eyewitness Identification Accuracy  [PDF]
Michael Storozuk, Paul Dupuis
Psychology (PSYCH) , 2013, DOI: 10.4236/psych.2013.412149
Abstract:

Eyewitness identification accuracy of offenders (persons who committed a crime) is generally unreliable. In this study, we implemented a training approach to examine the impact of a brief criminal law training session on the identification accuracy of eyewitnesses viewing a simulated violent altercation between two males. Participants provided with prior training on how to appropriately apply specific criminal law definitions relevant to a violent altercation (assault and self-defense provisions) were more accurate in their identifications of the offender when compared to participants provided with irrelevant training (a riot and the unlawful assembly of a riot), and participants provided with no training, when observing the same violent altercation. Potential implications and limitations are discussed.

Elimination of Pollution of Groundwater by On-Site Sanitation Systems  [PDF]
Michael Kyakula, Simon Okiror, Paul Kawesa
Journal of Water Resource and Protection (JWARP) , 2015, DOI: 10.4236/jwarp.2015.717118
Abstract: About half the population in developing countries lack safe excreta disposal facilities. Improper wastewater disposal contaminates groundwater resulting in spread of water related diseases such as typhoid, cholera, dysentery. This research experimentally tested the applicability of charcoal and saw dust packed membranes as sewage purifiers for on-site sanitation systems like, septic tanks, cesspool, pit latrines, pour-flush pit excreta systems. Tests for E. coli, COD and BOD of the influent which was raw sewerage from sewers and effluent from layered saw dust and charcoal purifying materials experimental setup were separately carried out. The layers were varied from 150 mm, 200 mm and 300 mm with 150 mm layers of gravel in between. The experimental tests showed that 300 mm charcoal layers with a 150 mm gravel middle layer, reduced E. coli from 4800×1014 CFU/100ml to 1.08×104 CFU/100ml, BOD5 from 698 mg/l to 0.5 mg/l, COD from 1492 mg/l to 3.0 mg/l against environmental standards of 1.0×104 CFU/100ml, 50 mg/l, and 100 mg/l respectively and its efficiency is directly proportional to thickness of charcoal dust layers. In conclusion, introducing a lined purification chamber with layers of charcoal dust between the on-site sanitation system and soak pit will eliminate the pollution of ground water.
Development of a Wireless Environmental Data Acquisition Prototype Adopting Agile Practices: An Experience Report  [PDF]
Paul Celicourt, Richard Sam, Michael Piasecki
Journal of Software Engineering and Applications (JSEA) , 2016, DOI: 10.4236/jsea.2016.910031
Abstract: The traditional software development model commonly named “waterfall” is unable to cope with the increasing functionality and complexity of modern embedded systems. In addition, it is unable to support the ability for businesses to quickly respond to new market opportunities due to changing requirements. As a response, the software development community developed the Agile Methodologies (e.g., extreme Programming, Scrum) which were also adopted by the Embedded System community. However, failures and bad experiences in applying Agile Methodologies to the development of embedded systems have not been reported in the literature. Therefore, this paper contributes a detailed account of our first-time experiences adopting an agile approach in the prototype development of a wireless environment data acquisition system in an academic environment. We successfully applied a subset of the extreme Programming (XP) methodology to our software development using the Python programming language, an experience that demonstrated its benefits in shaping the design of the software and also increasing productivity. We used an incremental development approach for the hardware components and adopted a “cumulative testing” approach. For the overall development process management, however, we concluded that the Promise/Commitment-Based Project Management (PB-PM/CBPM) was better suited. We discovered that software and hardware components of embedded systems are best developed in parallel or near-parallel. We learned that software components that pass automated tests may not survive in the tests against the hardware. Throughout this rapid prototyping effort, factors like team size and our availability as graduate students were major obstacles to fully apply the XP methodology.
Holographic Dark Information Energy
Michael Paul Gough
Entropy , 2011, DOI: 10.3390/e13040924
Abstract: Landauer’s principle and the Holographic principle are used to derive the holographic information energy contribution to the Universe. Information energy density has increased with star formation until sufficient to start accelerating the expansion of the universe. The resulting reduction in the rate of star formation due to the accelerated expansion may provide a feedback that limits the information energy density to a constant level. The characteristics of the universe’s holographic information energy then closely match those required to explain dark energy and also answer the cosmic coincidence problem. Furthermore the era of acceleration will be clearly limited in time.
Technical development of PubMed Interact: an improved interface for MEDLINE/PubMed searches
Michael Muin, Paul Fontelo
BMC Medical Informatics and Decision Making , 2006, DOI: 10.1186/1472-6947-6-36
Abstract: PubMed Interact is a Web-based MEDLINE/PubMed search application built with HTML, JavaScript and PHP. It is implemented on a Windows Server 2003 with Apache 2.0.52, PHP 4.4.1 and MySQL 4.1.18. PHP scripts provide the backend engine that connects with E-Utilities and parses XML files. JavaScript manages client-side functionalities and converts Web pages into interactive platforms using dynamic HTML (DHTML), Document Object Model (DOM) tree manipulation and Ajax methods. With PubMed Interact, users can limit searches with JavaScript slider bars, preview result counts, delete citations from the list, display and add related articles and create relevance lists. Many interactive features occur at client-side, which allow instant feedback without reloading or refreshing the page resulting in a more efficient user experience.PubMed Interact is a highly interactive Web-based search application for MEDLINE/PubMed that explores recent trends in Web technologies like DOM tree manipulation and Ajax. It may become a valuable technical development for online medical search applications.This research continues to investigate innovations in user-computer interface for online storage and retrieval systems in medical research. The goal of the project is to advance the development of a Web-based medical search tool that can enhance user interaction with the MEDLINE/PubMed database and push to the forefront the different strategies and filters in Entrez PubMed that often remain hidden from novice users, such as age groups, clinical study filters and systematic reviews. The long-term objective is to study and implement clean and effective user interfaces for MEDLINE/PubMed that increases utilization and improves search outcomes without overwhelming novice users and limiting the workflow of advanced users. This manuscript reports the development, implementation and technical evaluation of the research application, PubMed Interact.An earlier version of this project is the Slider Interface
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