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Search Results: 1 - 10 of 176601 matches for " Marc E Colosimo "
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TreeViewJ: An application for viewing and analyzing phylogenetic trees
Matthew W Peterson, Marc E Colosimo
Source Code for Biology and Medicine , 2007, DOI: 10.1186/1751-0473-2-7
Abstract: We present TreeViewJ, a Java tool for visualizing, editing and analyzing phylogenetic trees. The software allows researchers to color and change the width of branches that they wish to highlight, and add names to nodes. If collection dates are available for taxa, the software can map them onto a timeline, and sort the tree in ascending or descending date order.TreeViewJ is a tool for researchers to visualize, edit, "decorate," and produce publication-ready images of phylogenetic trees. It is open-source, and released under an GPL license, and available at http://treeviewj.sourceforge.net webcite.Phylogenetic trees are widely used to visualize evolutionary relationships between different organisms or samples of the same organism. There is a variety of both free and commercial tree visualization software [1-5] available, but limitations in these programs often require the user to use multiple programs for analysis, annotation, and display for publication. For some applications, such as epidemiological studies, the visualization of sample collection dates along with the tree would provide further insight into relationships. However, no currently available visualization packages provide this functionality.A variety of file formats exist for the storage of phylogenetic trees. Some, like the New Hampshire[6] format store only the node name and branch length information. Others, like the New Hampshire Extended [5] and Nexus[7] formats, can be used to store other data such as formatting and sequence data. Other file formats, such as the Lucid [8] and Structure of Descriptive Data (SDD) [9] formats have been used for the description of taxonomic data. Recently, a draft standard for an XML-based format, PhyloXML [10], has been released. XML-based formats are ideal for storing phylogenetic data because they can be easily interpreted by readily available general purpose software (thus eliminating the need for customized parsers), easily allow for annotation, and are extensible.
Nephele: genotyping via complete composition vectors and MapReduce
Marc E Colosimo, Matthew W Peterson, Scott Mardis, Lynette Hirschman
Source Code for Biology and Medicine , 2011, DOI: 10.1186/1751-0473-6-13
Abstract: Nephele is a suite of tools that uses the complete composition vector algorithm to represent each sequence in the dataset as a vector derived from its constituent k-mers by passing the need for multiple sequence alignment, and affinity propagation clustering to group the sequences into genotypes based on a distance measure over the vectors. Our methods produce results that correlate well with expert-defined clades or genotypes, at a fraction of the computational cost of traditional phylogenetic methods run on traditional hardware. Nephele can use the open-source Hadoop implementation of MapReduce to parallelize execution using multiple compute nodes. We were able to generate a neighbour-joined tree of over 10,000 16S samples in less than 2 hours.We conclude that using Nephele can substantially decrease the processing time required for generating genotype trees of tens to hundreds of organisms at genome scale sequence coverage.In the post-genomic era, as sequencing becomes ever cheaper and more routine, biological sequence analysis has provided many useful tools for the study and combat of infectious disease. These tools, which can include both experimental and computational methods, are important for molecular epidemiological studies [1-3], vaccine development [4-6], and microbial forensics [7-9]. One such method is genotyping, the grouping of samples based on their genetic sequence. This can be done experimentally [10-12] or computationally, either by identifying genetic signatures (nucleotide substrings which are only found in a single group of sequences) [13], or on the basis of genetic distance among the sequences [14-16]. These methods allow a researcher to split a group of sequences into distinct partitions for further analysis. In a forensics context, genotyping a sequence can yield clues on where the sequence comes from. In surveillance, genotyping can be used to examine the evolutionary footprint of a pathogen, for example, to identify areas where certain v
Overview of BioCreAtIvE task 1B: normalized gene lists
Hirschman Lynette,Colosimo Marc,Morgan Alexander,Yeh Alexander
BMC Bioinformatics , 2005, DOI: 10.1186/1471-2105-6-s1-s11
Abstract: Background Our goal in BioCreAtIve has been to assess the state of the art in text mining, with emphasis on applications that reflect real biological applications, e.g., the curation process for model organism databases. This paper summarizes the BioCreAtIvE task 1B, the "Normalized Gene List" task, which was inspired by the gene list supplied for each curated paper in a model organism database. The task was to produce the correct list of unique gene identifiers for the genes and gene products mentioned in sets of abstracts from three model organisms (Yeast, Fly, and Mouse). Results Eight groups fielded systems for three data sets (Yeast, Fly, and Mouse). For Yeast, the top scoring system (out of 15) achieved 0.92 F-measure (harmonic mean of precision and recall); for Mouse and Fly, the task was more difficult, due to larger numbers of genes, more ambiguity in the gene naming conventions (particularly for Fly), and complex gene names (for Mouse). For Fly, the top F-measure was 0.82 out of 11 systems and for Mouse, it was 0.79 out of 16 systems. Conclusion This assessment demonstrates that multiple groups were able to perform a real biological task across a range of organisms. The performance was dependent on the organism, and specifically on the naming conventions associated with each organism. These results hold out promise that the technology can provide partial automation of the curation process in the near future.
Profile: April Colosimo
April Colosimo
Partnership : the Canadian Journal of Library and Information Practice and Research , 2009,
Abstract:
How the Brain Process Stimulus-Response Conflict? New Insights from Lateralized Readiness Potentials Scalp Topography and Reaction Times  [PDF]
Marc E. Lavoie, Johannes E. A. Stauder
Journal of Behavioral and Brain Science (JBBS) , 2013, DOI: 10.4236/jbbs.2013.31014
Abstract:
Stimulus-Response Compatibility (SRC) refers to the fact that some tasks are performed easier and better than others because of the way stimuli and responses are paired with each other. To assess the brain responses to stimulus-response conflicts, we investigated the behavioral (accuracy and Reaction Times: RTs) as well as the physiological response (Lateralized Readiness Potentials: LRP) modulations in a positional blocked and a conditional mixed design in twelve university students. Results revealed that the performance was less accurate and the RTs, as well as the LRP onset, were delayed under the mixed conditional design. A greater compatibility effect was also noted on accuracy, RTs and LRP onset latency in the mixed design. Consistent with these findings, smaller peak activation at fronto-central areas suggests that more selective inhibition is needed in a mixed design context. Despite a smaller activation, the topographical distribution is similar in both designs. These results indicate that the translation time between stimulus- and response codes are greater under the mixed instruction, while the similar LRP topography suggests that common neural structures underlie LRPs in response to both type of designs.
Weight of preterm newborns during the first twelve weeks of life
Anchieta, L.M.;Xavier, C.C.;Colosimo, E.A.;Souza, M.F.;
Brazilian Journal of Medical and Biological Research , 2003, DOI: 10.1590/S0100-879X2003000600012
Abstract: a longitudinal and prospective study was carried out at two state-operated maternity hospitals in belo horizonte during 1996 in order to assess the weight of preterm appropriate-for-gestational-age newborns during the first twelve weeks of life. two hundred and sixty appropriate-for-gestational-age preterm infants with birth weight <2500 g were evaluated weekly. the infants were divided into groups based on birth weight at 250-g intervals. using weight means, somatic growth curves were constructed and adjusted to count's model. absolute (g/day) and relative (g kg-1 day-1) velocity curves were obtained from a derivative of this model. the growth curve was characterized by weight loss during the 1st week (4-6 days) ranging from 5.9 to 13.3% (the greater the percentage, the lower the birth weight), recovery of birth weight within 17 and 21 days, and increasingly higher rates of weight gain after the 3rd week. these rates were proportional to birth weight when expressed as g/day (the lowest and the highest birth weight neonates gained 15.9 and 30.1 g/day, respectively). however, if expressed as g kg-1 day-1, the rates were inversely proportional to birth weight (during the 3rd week, the lowest and the highest weight newborns gained 18.0 and 11.5 g kg-1 day-1, respectively). during the 12th week the rates were similar for all groups (7.5 to 10.2 g kg-1 day-1). the relative velocity accurately reflects weight gain of preterm infants who are appropriate for gestational age and, in the present study, it was inversely proportional to birth weight, with a peak during the 3rd week of life, and a homogeneous behavior during the 12th week for all weight groups.
Weight of preterm newborns during the first twelve weeks of life
Anchieta L.M.,Xavier C.C.,Colosimo E.A.,Souza M.F.
Brazilian Journal of Medical and Biological Research , 2003,
Abstract: A longitudinal and prospective study was carried out at two state-operated maternity hospitals in Belo Horizonte during 1996 in order to assess the weight of preterm appropriate-for-gestational-age newborns during the first twelve weeks of life. Two hundred and sixty appropriate-for-gestational-age preterm infants with birth weight <2500 g were evaluated weekly. The infants were divided into groups based on birth weight at 250-g intervals. Using weight means, somatic growth curves were constructed and adjusted to Count's model. Absolute (g/day) and relative (g kg-1 day-1) velocity curves were obtained from a derivative of this model. The growth curve was characterized by weight loss during the 1st week (4-6 days) ranging from 5.9 to 13.3% (the greater the percentage, the lower the birth weight), recovery of birth weight within 17 and 21 days, and increasingly higher rates of weight gain after the 3rd week. These rates were proportional to birth weight when expressed as g/day (the lowest and the highest birth weight neonates gained 15.9 and 30.1 g/day, respectively). However, if expressed as g kg-1 day-1, the rates were inversely proportional to birth weight (during the 3rd week, the lowest and the highest weight newborns gained 18.0 and 11.5 g kg-1 day-1, respectively). During the 12th week the rates were similar for all groups (7.5 to 10.2 g kg-1 day-1). The relative velocity accurately reflects weight gain of preterm infants who are appropriate for gestational age and, in the present study, it was inversely proportional to birth weight, with a peak during the 3rd week of life, and a homogeneous behavior during the 12th week for all weight groups.
Effect of emotional valence on episodic memory stages as indexed by event-related potentials  [PDF]
Marc E. Lavoie, Kieron P. O’Connor
World Journal of Neuroscience (WJNS) , 2013, DOI: 10.4236/wjns.2013.34034
Abstract:

Several investigations have shown that emotional events show superior recall than non-emotional ones. However, the cortical mechanisms underlying the episodic recall of emotional scenes are still poorly understood. Our main aim was to compare the magnitude of the Event-Related brain Potentials (ERP) old-new effect related to emotionally unpleasant, pleasant and neutral photographic images. As expected, correct recognition of all types of images elicited three topographically distinct ERP components sensitive to the classical old-new recognition effect. The results revealed that the behavioral performances were mainly sensitive to arousal, while the ERP old/new effect over posterior regions (300 - 1000 ms) was exclusively affected by unpleasantness. A later component (1000 - 1400 ms) showed an inverted old/ new effect at parietal sites, which was also sensitive to unpleasantness. These results imply that ERP reflecting episodic conscious recollection and post-retrieval monitoring are clearly affected both by valence and arousal.

Teaching, Designing, and Organizing: Concept Mapping for Librarians
April Colosimo,Megan Fitzgibbons
Partnership : the Canadian Journal of Library and Information Practice and Research , 2012,
Abstract: Concept maps are graphical representations of relationships among concepts that can be an effective tool for teaching, designing, and organizing information in a variety of library settings. First, concept mapping can be used wherever training or formal teaching occurs as a visual aid to explain complex ideas. They can also help learners articulate their understanding of a subject area when they create their own concept maps. When using concept mapping as a teaching tool, students may have a more meaningful learning experience when they add information to a concept map that is based on their current knowledge. Next, concept maps are an effective design tool for librarians who are planning projects. They can also serve as a reference point for project implementation and evaluation. The same is true for the design of courses, presentations, and library workshops. A concept map based on the content of a course, for example, is valuable when selecting learning outcomes and strategies for teaching and assessment. Finally, concept mapping can used as a method for capturing tacit or institutional knowledge through the creation and organization of ideas and resources. Librarians can collaborate on concept maps with each other or with non-librarian colleagues to facilitate communication. Resulting maps can be published online and link to documentation and relevant resources. This paper provides an overview of the literature related to concept mapping in libraries. Concrete applications and examples of concept mapping for teaching and learning, designing, and organizing in library settings are then elaborated. The authors draw from their own success and experience with different concept mapping methods and software programs.
Dynamical Friction in Stellar Systems: an introduction
Hector Aceves,Maria Colosimo
Physics , 2006,
Abstract: An introductory exposition of Chandrasekhar's gravitational dynamical friction, appropriate for an undergraduate class in mec hanics, is presented. This friction results when a massive particle moving through a ``sea'' of much lighter star particles experiences a retarding force du to an exchange of energy and momentum. General features of dynamical friction are presented, both in an elementary and in a more elaborate way using hyperbolic two-body interactions. The orbital decay of a massive particle in an homogeneous gravitational system is solved analytically, that leads to an underdamped harmonic oscillator type of motion. A numerical integration of the equation of motion in a more realistic c ase is done. These results are compared to those of an N-body computer simulation. Several problems and projects are suggested to students for further st udy.
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