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Search Results: 1 - 10 of 51405 matches for " James Thomas Butler "
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Localizing the Language Network with fMRI and Functional Connectivity: Implications for Pre-Surgical Planning  [PDF]
Victoria Lyn Ives-Deliperi, James Thomas Butler
Open Journal of Modern Neurosurgery (OJMN) , 2018, DOI: 10.4236/ojmn.2018.82015

Object: Functional MRI is frequently applied to lateralize language in pre-surgical planning, with potential to localize functionally important cortex too. Here we present BOLD signal activation maps and related functional connectivity, in response to three commonly administered fMRI language tasks. Methods: Datasets from 55 pre-surgical fMRI studies were analyzed. Verbal response naming, covert word generation and passive listening tasks were administered in all studies. Single-subject analyses, group analyses and region-of-interest analyses were conducted, and a multi-subject functional connectivity analysis was performed. Results: Single-subject analyses revealed that clinically important language regions were activated in all but three patients using the panel of tasks. Group analyses revealed significant bilateral BOLD signal increases in anterior and posterior language regions in response to verbal response naming and bilateral signal increase in posterior language regions only in response to passive listening. Covert word generation activated anterior language regions bilaterally and posterior language cortex in the dominant hemisphere. Functional

The EnzymeTracker: an open-source laboratory information management system for sample tracking
Thomas Triplet, Gregory Butler
BMC Bioinformatics , 2012, DOI: 10.1186/1471-2105-13-15
Abstract: In this paper, we propose the EnzymeTracker, a web-based laboratory information management system for sample tracking, as an open-source and flexible alternative that aims at facilitating entry, mining and sharing of experimental biological data. The EnzymeTracker features online spreadsheets and tools for monitoring numerous experiments conducted by several collaborators to identify and characterize samples. It also provides libraries of shared data such as protocols, and administration tools for data access control using OpenID and user/team management. Our system relies on a database management system for efficient data indexing and management and a user-friendly AJAX interface that can be accessed over the Internet. The EnzymeTracker facilitates data entry by dynamically suggesting entries and providing smart data-mining tools to effectively retrieve data. Our system features a number of tools to visualize and annotate experimental data, and export highly customizable reports. It also supports QR matrix barcoding to facilitate sample tracking.The EnzymeTracker was designed to be easy to use and offers many benefits over spreadsheets, thus presenting the characteristics required to facilitate acceptance by the scientific community. It has been successfully used for 20 months on a daily basis by over 50 scientists. The EnzymeTracker is freely available online at http://cubique.fungalgenomics.ca/enzymedb/index.html webcite under the GNU GPLv3 license.Spreadsheets are broadly used by the scientific community. Their intuitive and easily understandable user interface is a significant advantage. They are also visually appealing and feature a number of tools to visualize data using charts. Hence, spreadsheets are currently the primary means to store both experimental and manually curated genomic/proteomic data in most laboratories.Spreadsheets might be sufficient when one needs to organize simple data. However, this approach raises a number of problems as spreadsheets p
Fluctuation-driven Turing patterns
Thomas Butler,Nigel Goldenfeld
Physics , 2010, DOI: 10.1103/PhysRevE.84.011112
Abstract: Models of diffusion driven pattern formation that rely on the Turing mechanism are utilized in many areas of science. However, many such models suffer from the defect of requiring fine tuning of parameters or an unrealistic separation of scales in the diffusivities of the constituents of the system in order to predict the formation of spatial patterns. In the context of a very generic model of ecological pattern formation, we show that the inclusion of intrinsic noise in Turing models leads to the formation of "quasi-patterns" that form in generic regions of parameter space and are experimentally distinguishable from standard Turing patterns. The existence of quasi-patterns removes the need for unphysical fine tuning or separation of scales in the application of Turing models to real systems.
Robust ecological pattern formation induced by demographic noise
Thomas Butler,Nigel Goldenfeld
Quantitative Biology , 2009, DOI: 10.1103/PhysRevE.80.030902
Abstract: We demonstrate that demographic noise can induce persistent spatial pattern formation and temporal oscillations in the Levin-Segel predator-prey model for plankton-herbivore population dynamics. Although the model exhibits a Turing instability in mean field theory, demographic noise greatly enlarges the region of parameter space where pattern formation occurs. To distinguish between patterns generated by fluctuations and those present at the mean field level in real ecosystems, we calculate the power spectrum in the noise-driven case and predict the presence of fat tails not present in the mean field case. These results may account for the prevalence of large-scale ecological patterns, beyond that expected from traditional non-stochastic approaches.
Optimality Properties of a Proposed Precursor to the Genetic Code
Thomas Butler,Nigel Goldenfeld
Quantitative Biology , 2009, DOI: 10.1103/PhysRevE.80.032901
Abstract: We calculate the optimality of a doublet precursor to the canonical genetic code with respect to mitigating the effects of point mutations and compare our results to corresponding ones for the canonical genetic code. We find that the proposed precursor has much less optimality than that of the canonical code. Our results render unlikely the notion that the doublet precursor was an intermediate state in the evolution of the canonical genetic code. These findings support the notion that code optimality reflects evolutionary dynamics, and that if such a doublet code originally had a biochemical significance, it arose before the emergence of translation.
Predator-Prey Quasi-cycles from a Path Integral Formalism
Thomas Butler,David Reynolds
Quantitative Biology , 2008, DOI: 10.1103/PhysRevE.79.032901
Abstract: The existence of beyond mean field quasi-cycle oscillations in a simple spatial model of predator prey interactions is derived from a path integral formalism. The results agree substantially with those obtained from analysis of similar models using system size expansions of the master equation. In all of these analyses, the discrete nature of predator prey populations and finite size effects lead to persistent oscillations in time, but spatial patterns fail to form. The path integral formalism goes beyond mean field theory and provides a focus on individual realizations of the stochastic time evolution of population not captured in the standard master equation approach.
Diets of obese and non-obese older subjects  [PDF]
Yukoh Yaegashi, Atsuko Satoh, Hideaki Kudoh, Sangun Lee, Chiaki Kitamiy, James P. Butler, Hidetada Sasaki
Health (Health) , 2013, DOI: 10.4236/health.2013.53048

Aim: To compare diets between obese and non-obese in healthy older subjects. Methods: Forty-five obese and eighty-seven non-obese older subjects were recruited and their habitual factors that may contribute to obesity were assessed. Intakes of food by food-group in the obesity and non-obesity groups were checked using a visual type presentation of model nutriational balance chart (MNBC). Results: Average intake ratio of food relative to ideal food intake was significantly higher in the obesity group than the non-obesity group. The relationship of obesity and exercise or habitual activities was not significant. Conclusion: Food intake is a primary factor of obesity but regular exercise or habitual activities is not a key factor for obesity in older subjects. Since exercise habit is difficult to achieve in older subjects, particularly those who are obese, food control using the present visualtype MNBC would be one strategy forthe management of obesity.

Mechanism of Catch Force: Tethering of Thick and Thin Filaments by Twitchin
Thomas M. Butler,Marion J. Siegman
Journal of Biomedicine and Biotechnology , 2010, DOI: 10.1155/2010/725207
Abstract: Catch is a mechanical state occurring in some invertebrate smooth muscles characterized by high force maintenance and resistance to stretch during extremely slow relaxation. During catch, intracellular calcium is near basal concentration and myosin crossbridge cyctng rate is extremely slow. Catch force is relaxed by a protein kinase A-mediated phosphorylation of sites near the N- and C- temini of the minititin twitchin (~526 kDa). Some catch force maintenance car also occur together with cycling myosin crossbridges at submaximal calcium concentrations, but not when the muscle is maximally activated. Additionally, the link responsible for catch can adjust during shortening of submaximally activated muscles and maintain catch force at the new shorter length. Twitchin binds to both thick and thin filaments, and the thin filament binding shown by both the N- and Cterminal portions of twitchin is decreased by phosphorylation of the sites that regulate catch. The data suggest that the twitchin molecule itself is the catch force beanng tether between thick and thin filaments. We present a model for the regulation of catch in which the twitchin tether can be displaced from thin filaments by both (a) the phosphorylation of twitchin and (b) the attachment of high force myosin crossbridges.
Using Sports Wagering Markets to Evaluate and Compare Team Winning Streaks in Sports  [PDF]
R. Alan Bowman, Thomas Ashman, James Lambrinos
American Journal of Operations Research (AJOR) , 2015, DOI: 10.4236/ajor.2015.55029
Abstract: Point spreads and money lines from sports wagering markets are used to evaluate the impressiveness of team streaks. Sports wagering data have previously been useful in assessing competitive balance in sports. Our approach was motivated by the amount of media scrutiny that accompanied the winning streak of the NBA’s Miami Heat and the point streak of the NHL’s Chicago Blackhawks which occurred simultaneously for the most part in 2013. The topic came to the forefront again with the 2014-2015 winning streak of the Atlanta Hawks. Three streaks are highlighted in our paper. The length of the streaks, the quality of the competition, injuries, and a variety of other factors were mentioned in the media but the discussion was limited to subjective opinions as no way of properly weighing relative influence of the factors was identified. Wagering markets provide an excellent source of information for making these judgments. Several complementary measures are described and the most impressive team streaks within and across professional baseball, basketball, football, and ice hockey are identified.
Immortalized pathological human myoblasts: towards a universal tool for the study of neuromuscular disorders
Kamel Mamchaoui, Capucine Trollet, Anne Bigot, Elisa Negroni, Soraya Chaouch, Annie Wolff, Prashanth K Kandalla, Solenne Marie, James Di Santo, Jean St Guily, Francesco Muntoni, Jihee Kim, Susanne Philippi, Simone Spuler, Nicolas Levy, Sergiu C Blumen, Thomas Voit, Woodring E Wright, Ahmed Aamiri, Gillian Butler-Browne, Vincent Mouly
Skeletal Muscle , 2011, DOI: 10.1186/2044-5040-1-34
Abstract: Using transduction with both telomerase-expressing and cyclin-dependent kinase 4-expressing vectors, we were able to generate a battery of immortalized human muscle stem-cell lines from patients with various neuromuscular disorders.The immortalized human cell lines from patients with Duchenne muscular dystrophy, facioscapulohumeral muscular dystrophy, oculopharyngeal muscular dystrophy, congenital muscular dystrophy, and limb-girdle muscular dystrophy type 2B had greatly increased proliferative capacity, and maintained their potential to differentiate both in vitro and in vivo after transplantation into regenerating muscle of immunodeficient mice.Dystrophic cellular models are required as a supplement to animal models to assess cellular mechanisms, such as signaling defects, or to perform high-throughput screening for therapeutic molecules. These investigations have been conducted for many years on cells derived from animals, and would greatly benefit from having human cell models with prolonged proliferative capacity. Furthermore, the possibility to assess in vivo the regenerative capacity of these cells extends their potential use. The innovative cellular tools derived from several different neuromuscular diseases as described in this report will allow investigation of the pathophysiology of these disorders and assessment of new therapeutic strategies.Muscular dystrophies constitute a heterogeneous group of genetic muscle diseases characterized by progressive muscle weakness, wasting and degeneration, some of these features are common to muscle aging [1,2]. Over the past few years, the genetics and pathophysiology of some of these diseases has been deciphered, stimulating the development of novel gene-based (or mRNA-based) (for example, gene therapy, exon-skipping or codon read-through), cell-based and pharmacological therapies [3], which can either target the mutation directly, or target the consequences of that mutation, such as muscle wasting, atrophy or denerv
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