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Search Results: 1 - 10 of 475442 matches for " Mark A. Robbins "
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Alterations in Caspase-3 in Juvenile Rats Treated Neonatally with Domoic Acid  [PDF]
Mark A. Robbins, Catherine L. Ryan, Tracy A. Doucette
Journal of Behavioral and Brain Science (JBBS) , 2016, DOI: 10.4236/jbbs.2016.69034
Abstract: The clinical presentation of schizophrenia involves a variety of symptoms, which in many cases include hallucinations and delusions. Experimentally revealed alterations in both pre-pulse inhibition (PPI) and latent inhibition (LI) are also apparent in individuals afflicted with this disorder. Many have speculated that altered synaptic connections are, in part, responsible for this subset of behavioral abnormalities. We have previously reported that neonatal chronic low-dose injections of domoic acid (DOM) produce adult rats with deficits in PPI and LI. The current study was conducted to determine whether this toxin-treatment would alter the degree of apoptosis occurring in the developing brain. Results revealed significant decreases in caspase-3 within the right prelimbic cortex (PrL) in both male and female DOM-treated rats suggesting that even modest alterations in glutamate (Glu) signaling during critical periods of central nervous system (CNS) maturation will modify ontogenetic processes in the prefrontal cortex (PFC) of the juvenile rat.
Temporal Memory Dysfunction and Alterations in Tyrosine Hydroxylase Immunoreactivity in Adult Rats Following Neonatal Exposure to Domoic Acid  [PDF]
Mark A. Robbins, Catherine L. Ryan, Amber L. Marriott, Tracy Ann Doucette
Neuroscience & Medicine (NM) , 2013, DOI: 10.4236/nm.2013.41005

The purpose of the present study was to determine whether early alterations in glutamate signaling, via daily injections of the glutamate agonist, domoic acid (DOM; 20 μg/kg), during a critical period of CNS development (PND 8 - 14), would result in temporal memory deficits and/or alterations in tyrosine hydroxylase (TH) immunoreactivity. As adults, subjects were assessed for temporal memory ability using a recency discrimination paradigm. Both number and duration of exploratory contacts directed at familiar objects, differing by one hour in recall delay, were measured. Analyses revealed that DOM-treated females demonstrated temporal memory dysfunction, as evidenced in a significantly lower proportion of total exploratory behaviour directed toward the remote object. Integrity of the dopamine system was assessed using immunohistochemistry to examine TH immunoreactivity in the prefrontal cortex (PFC) and nucleus accumbens (NAcc). Sections obtained from DOM-treated males had significantly less TH immunoreactivity in the right mPFC, while DOM-treated females had significantly greater TH immunoreactivity in the left core and right shell of the NAcc. These findings are discussed in context of early alterations to glutamate signaling in the development of human neuropsychiatric disorders.

SIDECACHE: Information access, management and dissemination framework for web services
Mark S Doderer, Cory Burkhardt, Kay A Robbins
BMC Research Notes , 2011, DOI: 10.1186/1756-0500-4-182
Abstract: SideCache provides a framework for deploying web services that integrate information extracted from other databases and from web sources that are periodically updated. This situation occurs frequently in biotechnology where new information is being continuously generated and the latest information is important. SideCache provides several types of services including proxy access and rate control, local caching, and automatic web service updating.We have used the SideCache framework to automate the deployment and updating of a number of bioinformatics web services and tools that extract information from remote primary sources such as NCBI, NCIBI, and Ensembl. The SideCache framework also has been used to share research results through the use of a SideCache derived web service.Often bioinformatics researchers deploy new methods as web services to make them easily accessible in client browser applications or from other tools. For example, BioCatalogue [1] currently curates more than 1,700 life science web services and the number is rapidly growing. A typical bioinformatics web service performs a calculation or directly returns pre-computed information based on a user request. Many such services rely on or include information consolidated from other sites.A difficulty with this distribution strategy is that many major sources of bioinformatics information such as NCBI are regularly updated. Developers are then faced with the task of periodically re-downloading the data and rerunning computations in order to keep their results up-to-date. Users may find that the results based on the new information are not the same as the results obtained from earlier requests, but usually they have no way of knowing what information was used nor do they have the option of rolling back to a previous data state.The origin of data or provenance has received much attention in both the database community and in the scientific workflow community [2,3]. Detailed provenance information can be r
SIDEKICK: Genomic data driven analysis and decision-making framework
Mark S Doderer, Kihoon Yoon, Kay A Robbins
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-611
Abstract: Sidekick, a genomic data driven analysis and decision making framework, is a web-based tool that provides a user-friendly intuitive solution to the problem of information inaccessibility. Sidekick enables scientists without training in computation and data management to pursue answers to research questions like "What are the mechanisms for disease X" or "Does the set of genes associated with disease X also influence other diseases." Sidekick enables the process of combining heterogeneous data, finding and maintaining the most up-to-date data, evaluating data sources, quantifying confidence in results based on evidence, and managing the multi-step research tasks needed to answer these questions. We demonstrate Sidekick's effectiveness by showing how to accomplish a complex published analysis in a fraction of the original time with no computational effort using Sidekick.Sidekick is an easy-to-use web-based tool that organizes and facilitates complex genomic research, allowing scientists to explore genomic relationships and formulate hypotheses without computational effort. Possible analysis steps include gene list discovery, gene-pair list discovery, various enrichments for both types of lists, and convenient list manipulation. Further, Sidekick's ability to characterize pairs of genes offers new ways to approach genomic analysis that traditional single gene lists do not, particularly in areas such as interaction discovery.Increasingly, the search for mechanisms and biological processes in complex diseases begins with exploration of data from many sources to incorporate clinical, molecular, and high-throughput genomic data. A scientist might search literature and other databases for candidate interactions, pathways, etc. to hone in on likely candidates for study in the wet lab. The discovery process requires downloading data from several data sources, matching identifiers between data lists, and manipulating lists to match elements from one list with elements from oth
Letting Penguins Lead: Dynamic Modeling of Penguin Locations Guides Autonomous Robotic Sampling
Matthew J. Oliver,Mark A. Moline,Ian Robbins,William Fraser
Oceanography , 2012,
Abstract: The southwest coast of Anvers Island harbors one of five major populations of Adélie penguins in the West Antarctic Peninsula (WAP; Fraser and Trivelpiece, 1996). This "hotspot" is colocated with a submarine canyon that provides a conduit for warm, nutrient-rich Upper Circumpolar Deep Water to stimulate primary production and support a productive ecosystem (Prézelin et al., 2004). Paleoecological evidence shows Adélie penguins (Pygoscelis adeliae) have used this location for hundreds of years (Emslie et al., 1998). Since the mid- to late twentieth century, the Southern Ocean near the WAP has warmed significantly (Gille, 2002) and has lost significant sea ice (Stammerjohn et al., 2008). The maritime climate of the northern WAP has shifted poleward, replacing the cold continental Antarctic climate in the Anvers Island region. During this time period, there has been an 80% decrease in the sea ice dependent Adélie penguin populations and an introduction and increase of Gentoo penguins (P. papua; Ducklow et al., 2007). Sympatry of Adélie and Gentoo penguins during the breeding season is new to this coast, and it not known if these species will continue to coexist or if the Gentoos will supplant the Adélies. The stability of this new species interaction depends on how well each species is able to exploit the coastal ecosystem. It may be that while submarine canyons offer predictable prey populations, different foraging strategies may allow Gentoos better access to existing prey (krill and fish) populations relative to Adélies. This situation is difficult to assess because penguins are dynamic predators that rapidly forage for krill and fish across a heterogeneous and complex coastal ocean.
Structure and shear response in nanometer thick films
Peter A. Thompson,Mark O. Robbins,Gary S. Grest
Physics , 1995,
Abstract: Simulations of the structure and dynamics of fluid films confined to a thickness of a few molecular diameters are described. Confining walls introduce layering and in-plane order in the adjacent fluid. The latter is essential to transfer of shear stress. As the film thickness is decreased, by increasing pressure or decreasing the number of molecular layers, the entire film may undergo a phase transition. Spherical molecules tend to crystallize, while short chain molecules enter a glassy state with strong local orientational and translational order. These phase transitions lead to dramatic changes in the response of the film to imposed shear velocities $v$. Spherical molecules show an abrupt transition from Newtonian response to a yield stress as they crystallize. Chain molecules exhibit a continuously growing regime of non-Newtonian behavior where the shear viscosity drops as $v^{-2/3}$ at constant normal load. The same power law is found for a wide range of parameters, and extends to lower and lower velocities as a glass transition is approached. Once in the glassy state, chain molecules exhibit a finite yield stress. Shear may occur either within the film or at the film/wall interface. Interfacial shear dominates when films become glassy and when the film viscosity is increased by increasing the chain length.
Jamming, Friction and Unsteady Rheology
Mark O. Robbins
Physics , 1999,
Abstract: The connection between friction and jamming in granular media, molecular glasses, and complex fluids is explored. The paper first reviews the way friction is measured, the types of results that are observed, and what is known about the geometry of contacts between macroscopic surfaces. Then simple models for the origin of static friction are described. These are unable to explain the universal observation of static friction between macroscopic objects. The effects of surface roughness and chemical heterogeneity are discussed, and shown to yield exponentially weak static friction in our three dimensional world. In contrast, jamming of the "third bodies" that are present between most surfaces is shown to produce static friction that is consistent with macroscopic measurements. Experimental and simulation studies of jamming of molecularly thin fluid films are described and compared to studies of bulk glass transitions. The paper concludes by considering the unsteady stick-slip motion that often arises when systems become unjammed by sufficiently large stress. Different types of stick-slip motion are identified, and some of its origins are explored.
Nanoindentation of 35 Virus Capsids in a Molecular Model: Relating Mechanical Properties to Structure
Marek Cieplak, Mark O. Robbins
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0063640
Abstract: A coarse-grained model is used to study the mechanical response of 35 virus capsids of symmetries T = 1, T = 2, T = 3, pseudo T = 3, T = 4, and T = 7. The model is based on the native structure of the proteins that constitute the capsids and is described in terms of the C atoms associated with each amino acid. The number of these atoms ranges between 8 460 (for SPMV – satellite panicum mosaic virus) and 135 780 (for NBV – nudaureli virus). Nanoindentation by a broad AFM tip is modeled as compression between two planes: either both flat or one flat and one curved. Plots of the compressive force versus plate separation show a variety of behaviors, but in each case there is an elastic region which extends to a characteristic force . Crossing results in a drop in the force and irreversible damage. Across the 35 capsids studied, both and the elastic stiffness are observed to vary by a factor of 20. The changes in mechanical properties do not correlate simply with virus size or symmetry. There is a strong connection to the mean coordination number , defined as the mean number of interactions to neighboring amino acids. The Young's modulus for thin shell capsids rises roughly quadratically with , where 6 is the minimum coordination for elastic stability in three dimensions.
Defining Contact at the Atomic Scale
Shengfeng Cheng,Mark O. Robbins
Physics , 2010, DOI: 10.1007/s11249-010-9682-5
Abstract: Molecular dynamics simulations are used to study different definitions of contact at the atomic scale. The roles of temperature, adhesive interactions and atomic structure are studied for simple geometries. An elastic, crystalline substrate contacts a rigid, atomically flat surface or a spherical tip. The rigid surface is formed from a commensurate or incommensurate crystal or an amorphous solid. Spherical tips are made by bending crystalline planes or removing material outside a sphere. In continuum theory the fraction of atomically flat surfaces that is in contact rises sharply from zero to unity when a load is applied. This simple behavior is surprisingly difficult to reproduce with atomic scale definitions of contact. Due to thermal fluctuations, the number of atoms making contact at any instant rises linearly with load over a wide range of loads. Pressures comparable to the ideal hardness are needed to achieve full contact at typical temperatures. A simple harmonic mean-field theory provides a quantitative description of this behavior and explains why the instantaneous forces on atoms have a universal exponential form. Contact areas are also obtained by counting the number of atoms with a time-averaged repulsive force. For adhesive interactions, the resulting area is nearly independent of temperature and averaging interval, but usually rises from zero to unity over a range of pressures that is comparable to the ideal hardness. The only exception is the case of two identical commensurate surfaces. For nonadhesive surfaces, the mean pressure is repulsive if there is any contact during the averaging interval $\Delta t$. The associated area is very sensitive to $\Delta t$ and grows monotonically. Similar complications are encountered in defining contact areas for spherical tips.
Contact of Single Asperities with Varying Adhesion: Comparing Continuum Mechanics to Atomistic Simulations
Binquan Luan,Mark O. Robbins
Physics , 2006, DOI: 10.1103/PhysRevE.74.026111
Abstract: Atomistic simulations are used to test the equations of continuum contact mechanics in nanometer scale contacts. Nominally spherical tips, made by bending crystals or cutting crystalline or amorphous solids, are pressed into a flat, elastic substrate. The normal displacement, contact radius, stress distribution, friction and lateral stiffness are examined as a function of load and adhesion. The atomic scale roughness present on any tip made of discrete atoms is shown to have profound effects on the results. Contact areas, local stresses, and the work of adhesion change by factors of two to four, and the friction and lateral stiffness vary by orders of magnitude. The microscopic factors responsible for these changes are discussed. The results are also used to test methods for analyzing experimental data with continuum theory to determine information, such as contact area, that can not be measured directly in nanometer scale contacts. Even when the data appear to be fit by continuum theory, extracted quantities can differ substantially from their true values.
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