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Search Results: 1 - 10 of 334123 matches for " Jonathan S. Dordick "
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Comparative void-volume analysis of psychrophilic and mesophilic enzymes: Structural bioinformatics of psychrophilic enzymes reveals sources of core flexibility
Diana I Paredes, Kyle Watters, Derek J Pitman, Christopher Bystroff, Jonathan S Dordick
BMC Structural Biology , 2011, DOI: 10.1186/1472-6807-11-42
Abstract: We examine twenty homologous enzyme pairs from psychrophiles and mesophiles to investigate flexibility as a key characteristic for cold adaptation. B-factors in protein X-ray structures are one way to measure flexibility. Comparing psychrophilic to mesophilic protein B-factors reveals that psychrophilic enzymes are more flexible in 5-turn and strand secondary structures. Enzyme cavities, identified using CASTp at various probe sizes, indicate that psychrophilic enzymes have larger average cavity sizes at probe radii of 1.4-1.5 ?, sufficient for water molecules. Furthermore, amino acid side chains lining these cavities show an increased frequency of acidic groups in psychrophilic enzymes.These findings suggest that embedded water molecules may play a significant role in cavity flexibility, and therefore, overall protein flexibility. Thus, our results point to the important role enzyme flexibility plays in adaptation to cold environments.Life exists over a wide temperature range, from as low as -15°C to as high as 122°C [1]. On the upper end of the temperature spectrum, thermophiles and hyperthermophiles have been studied extensively by the scientific community, particularly the molecular mechanisms that support protein structure and function at high temperatures. For example, compact and strong hydrophobic packing is typically found in most cores of thermophilic proteins, which increases the energy needed to unfold the protein, making it possible for thermophilic proteins to retain native structure at high temperatures [2]. Indeed, a strong correlation exists between high core packing density and thermostability [2-4]. We are also intrigued by the obverse - organisms that survive optimally at cold temperatures; harsh environments with restricted molecular mobility and reduced reaction kinetics that hinder myriad cellular and biomolecular processes [5-7].Psychrophiles, "cold-loving" microorganisms, have adapted to life at low temperatures by using a variety of mechani
Artificial Organelles: Digital Microfluidic Platform for Proteoglycan and Glycoprotein Biosynthesis
Jeffrey G. Martin,Julie M. Beaudet,Jonathan S. Dordick,Robert J. Linhardt
The Scientific World Journal , 2010, DOI: 10.1100/tsw.2010.95
Apocynin Derivatives Interrupt Intracellular Signaling Resulting in Decreased Migration in Breast Cancer Cells
Robert F. Klees,Paul C. De Marco,Roman M. Salasznyk,Disha Ahuja,Michael Hogg,Sylvain Antoniotti,Lakshmi Kamath,Jonathan S. Dordick,George E. Plopper
Journal of Biomedicine and Biotechnology , 2006, DOI: 10.1155/jbb/2006/87246
Abstract: Cancer cells are defined by their ability to divide uncontrollably and metastasize to secondary sites in the body. Consequently, tumor cell migration represents a promising target for anticancer drug development. Using our high-throughput cell migration assay, we have screened several classes of compounds for noncytotoxic tumor cell migration inhibiting activity. One such compound, apocynin (4-acetovanillone), is oxidized by peroxidases to yield a variety of oligophenolic and quinone-type compounds that are recognized inhibitors of NADPH oxidase and may be inhibitors of the small G protein Rac1 that controls cell migration. We report here that while apocynin itself is not effective, apocynin derivatives inhibit migration of the breast cancer cell line MDA-MB-435 at subtoxic concentrations; the migration of nonmalignant MCF10A breast cells is unaffected. These compounds also cause a significant rearrangement of the actin cytoskeleton, cell rounding, and decreased levels of active Rac1 and its related G protein Cdc42. These results may suggest a promising new route to the development of novel anticancer therapeutics.
Spaceflight Promotes Biofilm Formation by Pseudomonas aeruginosa
Wooseong Kim, Farah K. Tengra, Zachary Young, Jasmine Shong, Nicholas Marchand, Hon Kit Chan, Ravindra C. Pangule, Macarena Parra, Jonathan S. Dordick, Joel L. Plawsky, Cynthia H. Collins
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0062437
Abstract: Understanding the effects of spaceflight on microbial communities is crucial for the success of long-term, manned space missions. Surface-associated bacterial communities, known as biofilms, were abundant on the Mir space station and continue to be a challenge on the International Space Station. The health and safety hazards linked to the development of biofilms are of particular concern due to the suppression of immune function observed during spaceflight. While planktonic cultures of microbes have indicated that spaceflight can lead to increases in growth and virulence, the effects of spaceflight on biofilm development and physiology remain unclear. To address this issue, Pseudomonas aeruginosa was cultured during two Space Shuttle Atlantis missions: STS-132 and STS-135, and the biofilms formed during spaceflight were characterized. Spaceflight was observed to increase the number of viable cells, biofilm biomass, and thickness relative to normal gravity controls. Moreover, the biofilms formed during spaceflight exhibited a column-and-canopy structure that has not been observed on Earth. The increase in the amount of biofilms and the formation of the novel architecture during spaceflight were observed to be independent of carbon source and phosphate concentrations in the media. However, flagella-driven motility was shown to be essential for the formation of this biofilm architecture during spaceflight. These findings represent the first evidence that spaceflight affects community-level behaviors of bacteria and highlight the importance of understanding how both harmful and beneficial human-microbe interactions may be altered during spaceflight.
Sensori-Motor Lateral Preferences of Amateur Motorsport Drivers
Jonathan S. Pointer
Research Journal of Medical Sciences , 2012,
Abstract: Vision-related aspects of motorsport activity have been little reported. We consider here oculo-visual influence upon hand and foot action for the kart racing driver as investigated through an assessment of patterns of sensori-motor lateral preference. Functional lateral preferences for eye, hand and foot were determined by a self-administered questionnaire, initially amongst a population of kart racing drivers (N = 60, 90% males, aged 10-52 years) and subsequently for a matched control group of optometric patients. Further comparative laterality data were located in a published study of healthy male subjects in the general population (N = 2,756, 94% aged 8-55 years). For each modality the kart drivers recorded no statistically significant difference in degree of right preference compared to either the matched control group or the larger general population; 70% were right-eyed, 85% right-footed and 90% right-handed. Lateral congruency of sensori-motor combinations was statistically similar in motorsport and non-participating individuals, being only slightly more ipsilateral than chance would predict. Patterns of lateral association between the sighting eye and the preferred upper/lower limbs of kart drivers were no different to those recorded for a non-motorsport population. This outcome is considered in the context of the physical restrictions imposed on the driver by the race equipment and the specific motion dynamics of competitive kart racing.
An Alternative Vision Test Stimulus: Orientation-Performance Isotropy Confirmed in Central Fixation for an Angular Broken Ring Test Target
Jonathan S. Pointer
Research Journal of Medical Sciences , 2012,
Abstract: Ophthalmologists and optometrists use charts displaying the Landolt broken ring stimulus instead of letters when testing the vision of specific patient groups. However, a degree of performance inequality versus stimulus orientation has been claimed in association with the use of the classic circular broken ring design. In recent years an angular version of the stimulus has found application in several clinical and vision-related studies. The present investigation was undertaken to assess whether testing with this alternative angular optotype design has any influence on orientation-performance anisotropy in central fixation. Ten normally-sighted subjects undertook an automated four-alternative forced-choice visual discrimination task under monocular foveal viewing conditions. Their error (orientation misidentification) performance was recorded in response to a randomised sequence of high-contrast single, variously sized, four-alternative orientation angular broken ring stimuli. Having first weighted the grouped error scores to counter orientation heterogeneity in stimulus presentation, statistical analysis indicated equality of performance across the four orientations of presentation. Subsidiary analysis failed to reveal any evidence of a systematic error bias associated with stimulus angular subtense. The angular design of the broken ring optotype tested here appears to have promoted isotropic orientation performance in central fixation for this group of normally-sighted adult subjects.
Jonathan S. Russ
Essays in Economic & Business History , 2001,
Abstract: This paper examines Honda of America Manufacturing and its experiences recruiting personnel in the U.S. during the l970s and 1980s. Honda’s Japanese management faced significant challenges hiring a workforce it considered capable of upholding the firm’s quality standards. In order to meet manufacturing goals, company officials adapted management practices successfully used in Japan to suit American cultural and legal environments. The challenges the firm faced in transferring its management model to the U.S. were at times anticipated, and at other times were not. Nevertheless, as a result of shrewd planning, flexibility, and difficult lessons drawn from experience, the firm prevailed in an American environment.
Classification of intended phoneme production from chronic intracortical microelectrode recordings in speech motor cortex
Jonathan S. Brumberg
Frontiers in Neuroscience , 2011, DOI: 10.3389/fnins.2011.00065
Abstract: We conducted a neurophysiological study of attempted speech production in a paralyzed human volunteer using chronic microelectrode recordings. The volunteer suffers from locked-in syndrome leaving him in a state of near-total paralysis, though he maintains good cognition and sensation. In this study, we investigated the feasibility of supervised classification techniques for prediction of intended phoneme production in the absence of any overt movements including speech. Such classification or decoding ability has the potential to greatly improve the quality-of-life of many people who are otherwise unable to speak by providing a direct communicative link to the general community. We examined the performance of three classifiers on a multi-class discrimination problem in which the items were 38 American English phonemes including monophthong and diphthong vowels and consonants. The three classifiers differed in performance, but averaged between 16 and 21% overall accuracy (chance-level is 1/38 or 2.6%). Further, the distribution of phonemes classified statistically above chance was non-uniform though 20 of 38 phonemes were classified with statistical significance for all three classifiers. These preliminary results suggest supervised classification techniques are capable of performing large scale multi-class discrimination for attempted speech production and may provide the basis for future communication prostheses.
piecewiseSEM: Piecewise structural equation modeling in R for ecology, evolution, and systematics
Jonathan S. Lefcheck
Quantitative Biology , 2015,
Abstract: Ecologists and evolutionary biologists are relying on an increasingly sophisticated set of statistical tools to describe complex natural systems. One such tool that has gained increasing traction in the life sciences is structural equation modeling (SEM), a variant of path analysis that resolves complex multivariate relationships among a suite of interrelated variables. SEM has historically relied on covariances among variables, rather than the values of the data points themselves. While this approach permits a wide variety of model forms, it limits the incorporation of detailed specifications. Here, I present a fully-documented, open-source R package piecewiseSEM that builds on the base R syntax for all current generalized linear, least-square, and mixed effects models. I also provide two worked examples: one involving a hierarchical dataset with non-normally distributed variables, and a second involving phylogenetically-independent contrasts. My goal is to provide a user-friendly and tractable implementation of SEM that also reflects the ecological and methodological processes generating data.
Methodology for Comparing Coupling Algorithms for Fluid-Structure Interaction Problems  [PDF]
Jason P. Sheldon, Scott T. Miller, Jonathan S. Pitt
World Journal of Mechanics (WJM) , 2014, DOI: 10.4236/wjm.2014.42007

The multi-physics simulation of coupled fluid-structure interaction problems, with disjoint fluid and solid domains, requires one to choose a method for enforcing the fluid-structure coupling at the interface between solid and fluid. While it is common knowledge that the choice of coupling technique can be very problem dependent, there exists no satisfactory coupling comparison methodology that allows for conclusions to be drawn with respect to the comparison of computational cost and solution accuracy for a given scenario. In this work, we develop a computational framework where all aspects of the computation can be held constant, save for the method in which the coupled nature of the fluid-structure equations is enforced. To enable a fair comparison of coupling methods, all simulations presented in this work are implemented within a single numerical framework within the deal.ii [1] finite element library. We have chosen the two-dimensional benchmark test problem of Turek and Hron [2] as an example to examine the relative accuracy of the coupling methods studied; however, the comparison technique is equally applicable to more complex problems. We show that for the specific case considered herein the monolithic approach outperforms partitioned and quasi-direct methods; however, this result is problem dependent and we discuss computational and modeling aspects which may affect other comparison studies.

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