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Search Results: 1 - 10 of 144628 matches for " B. Skyler Buck "
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Improving Concrete Containment Structures Associated with Fixed-Cone Valves  [PDF]
B. Skyler Buck, Michael C. Johnson, Zachary B. Sharp
Engineering (ENG) , 2011, DOI: 10.4236/eng.2011.35051
Abstract: Fixed-Cone valves are often used to dissipate energy and regulate flow at the low level outlet works of dams. Fixed-Cone valves, also known as Howell-Bunger valves, create an expanding conical jet allowing the energy of the water to dissipate over a large area. However, in many applications constructing the large stilling basin necessary for these valves is either not possible or not feasible. In order to reduce the relative size of the stilling basin, hoods or concrete containment structures have been used in conjunction with Fixed-Cone valves. This paper discusses the use of baffles in concrete containment structures in order to dissipate energy in a considerably confined space. It was determined that using baffles, in place of a deflector ring and end sill (Used in traditional containment structures.), significantly improves the function of containment structures by reducing downstream flow velocities and improving flow patterns and stability. This information will be useful to engineers allowing them to minimize scour and erosion associated with concrete containment structures.
Probabilistic Foundations of Statistical Mechanics: A Bayesian Approach
B. Buck,A. C. Merchant
Physics , 2015,
Abstract: We examine the fundamental aspects of statistical mechanics, dividing the problem into a discussion purely about probability, which we analyse from a Bayesian standpoint. We argue that the existence of a unique maximising probability distribution $\{p(j\vert K)\}$ for states labelled by $j$ given data $K$ implies that the corresponding maximal value of the information entropy $\sigma(\{(p_j\vert K)\}) = -\sum_j (p_j \vert K)\ln{(p_j\vert K)}$ depends explicitly on the data at equilibrium and on the Hamiltonian of the system. As such, it is a direct measure of our uncertainty about the exact state of the body and can be identified with the traditional thermodynamic entropy. We consider the well known microcanonical, canonical and grand canonical methods and ensure that the fluctuations about mean values are generally minuscule for macroscopic systems before identifying these mean values with experimental observables and thereby connecting to many standard results from thermodynamics. Unexpectedly, we find that it is not generally possible for a quantum process to be both isentropic and reversibly adiabatic. This is in sharp contrast to traditional thermodynamics where it is assumed that isentropic, reversible adiabatic processes can be summoned up on demand and easily realised. By contrast, we find that linear relations between pressures $P_j$ and energies $E_j$ are necessary and sufficient conditions for a quasi-static and adiabatic change to be isentropic, but, of course, this relationship only holds for a few especially simple systems, such as the perfect gas, and is not generally true for more complicated systems. By considering the associated entropy increases up to second order in small volume changes we argue that the consequences are in practice negligible.
Aspen Increase Soil Moisture, Nutrients, Organic Matter and Respiration in Rocky Mountain Forest Communities
Joshua R. Buck, Samuel B. St. Clair
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0052369
Abstract: Development and change in forest communities are strongly influenced by plant-soil interactions. The primary objective of this paper was to identify how forest soil characteristics vary along gradients of forest community composition in aspen-conifer forests to better understand the relationship between forest vegetation characteristics and soil processes. The study was conducted on the Fishlake National Forest, Utah, USA. Soil measurements were collected in adjacent forest stands that were characterized as aspen dominated, mixed, conifer dominated or open meadow, which includes the range of vegetation conditions that exist in seral aspen forests. Soil chemistry, moisture content, respiration, and temperature were measured. There was a consistent trend in which aspen stands demonstrated higher mean soil nutrient concentrations than mixed and conifer dominated stands and meadows. Specifically, total N, NO3 and NH4 were nearly two-fold higher in soil underneath aspen dominated stands. Soil moisture was significantly higher in aspen stands and meadows in early summer but converged to similar levels as those found in mixed and conifer dominated stands in late summer. Soil respiration was significantly higher in aspen stands than conifer stands or meadows throughout the summer. These results suggest that changes in disturbance regimes or climate scenarios that favor conifer expansion or loss of aspen will decrease soil resource availability, which is likely to have important feedbacks on plant community development.
The Merkel Cell Polyomavirus Minor Capsid Protein
Rachel M. Schowalter,Christopher B. Buck
PLOS Pathogens , 2013, DOI: 10.1371/journal.ppat.1003558
Abstract: The surface of polyomavirus virions is composed of pentameric knobs of the major capsid protein, VP1. In previously studied polyomavirus species, such as SV40, two interior capsid proteins, VP2 and VP3, emerge from the virion to play important roles during the infectious entry process. Translation of the VP3 protein initiates at a highly conserved Met-Ala-Leu motif within the VP2 open reading frame. Phylogenetic analyses indicate that Merkel cell polyomavirus (MCV or MCPyV) is a member of a divergent clade of polyomaviruses that lack the conserved VP3 N-terminal motif. Consistent with this observation, we show that VP3 is not detectable in MCV-infected cells, VP3 is not found in native MCV virions, and mutation of possible alternative VP3-initiating methionine codons did not significantly affect MCV infectivity in culture. In contrast, VP2 knockout resulted in a >100-fold decrease in native MCV infectivity, despite normal virion assembly, viral DNA packaging, and cell attachment. Although pseudovirus-based experiments confirmed that VP2 plays an essential role for infection of some cell lines, other cell lines were readily transduced by pseudovirions lacking VP2. In cell lines where VP2 was needed for efficient infectious entry, the presence of a conserved myristoyl modification on the N-terminus of VP2 was important for its function. The results show that a single minor capsid protein, VP2, facilitates a post-attachment stage of MCV infectious entry into some, but not all, cell types.
Light propagation and fluorescence quantum yields in liquid scintillators
C. Buck,B. Gramlich,S. Wagner
Physics , 2015, DOI: 10.1088/1748-0221/10/09/P09007
Abstract: For the simulation of the scintillation and Cherenkov light propagation in large liquid scintillator detectors a detailed knowledge about the absorption and emission spectra of the scintillator molecules is mandatory. Furthermore reemission probabilities and quantum yields of the scintillator components influence the light propagation inside the liquid. Absorption and emission properties are presented for liquid scintillators using 2,5-Diphenyloxazole (PPO) and 4-bis-(2-Methylstyryl)benzene (bis-MSB) as primary and secondary wavelength shifter. New measurements of the quantum yields for various aromatic molecules are shown.
A Positive Feedback Synapse from Retinal Horizontal Cells to Cone Photoreceptors
Skyler L. Jackman,Norbert Babai,James J. Chambers,Wallace B. Thoreson,Richard H. Kramer
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.1001057
Abstract: Cone photoreceptors and horizontal cells (HCs) have a reciprocal synapse that underlies lateral inhibition and establishes the antagonistic center-surround organization of the visual system. Cones transmit to HCs through an excitatory synapse and HCs feed back to cones through an inhibitory synapse. Here we report that HCs also transmit to cone terminals a positive feedback signal that elevates intracellular Ca2+ and accelerates neurotransmitter release. Positive and negative feedback are both initiated by AMPA receptors on HCs, but positive feedback appears to be mediated by a change in HC Ca2+, whereas negative feedback is mediated by a change in HC membrane potential. Local uncaging of AMPA receptor agonists suggests that positive feedback is spatially constrained to active HC-cone synapses, whereas the negative feedback signal spreads through HCs to affect release from surrounding cones. By locally offsetting the effects of negative feedback, positive feedback may amplify photoreceptor synaptic release without sacrificing HC-mediated contrast enhancement.
A Positive Feedback Synapse from Retinal Horizontal Cells to Cone Photoreceptors
Skyler L. Jackman,Norbert Babai,James J. Chambers,Wallace B. Thoreson,Richard H. Kramer
PLOS Biology , 2011, DOI: 10.1371/journal.pbio.1001057
Abstract: Cone photoreceptors and horizontal cells (HCs) have a reciprocal synapse that underlies lateral inhibition and establishes the antagonistic center-surround organization of the visual system. Cones transmit to HCs through an excitatory synapse and HCs feed back to cones through an inhibitory synapse. Here we report that HCs also transmit to cone terminals a positive feedback signal that elevates intracellular Ca2+ and accelerates neurotransmitter release. Positive and negative feedback are both initiated by AMPA receptors on HCs, but positive feedback appears to be mediated by a change in HC Ca2+, whereas negative feedback is mediated by a change in HC membrane potential. Local uncaging of AMPA receptor agonists suggests that positive feedback is spatially constrained to active HC-cone synapses, whereas the negative feedback signal spreads through HCs to affect release from surrounding cones. By locally offsetting the effects of negative feedback, positive feedback may amplify photoreceptor synaptic release without sacrificing HC-mediated contrast enhancement.
The Potential of Photo-Talks to Reveal the Development of Scientific Discourses  [PDF]
Cassie Quigley, Gayle Buck
Creative Education (CE) , 2012, DOI: 10.4236/ce.2012.32033
Abstract: This study explores the potential of a photo-elicitation technique, photo-talks (Serriere, 2010), for understanding how young girls understand, employ and translate new scientific discourses. Over the course of a nine week period, 24 kindergarten girls in an urban girls’ academy were observed, videotaped, photographed and interviewed while they were immersed into scientific discourse. This paper explicitly describes how their emerging discursive patterns were made visible through this methodological tool. The findings are presented in vignettes in three themes uncovered during our analysis which are the following: Presented the recollection of the scientific Discourse, Described the understanding of scientific Discourse, and Created an opportunity for the translation into everyday discourse. Science educators can benefit from this methodological tool as a reflective tool with their participants, to validate and/or complicate data. Additionally, this methodological tool serves to make discourse patterns more visible by providing a visual backdrop to the conversations thus revealing the development as it is occurring in young children.
An Adjusted Model for Simple 1,2-Dyotropic Reactions. Ab Initio MO and VB Considerations  [PDF]
Henk M. Buck
Open Journal of Physical Chemistry (OJPC) , 2013, DOI: 10.4236/ojpc.2013.33015
Abstract:

With an adjusted model, we reconsider simple 1,2-dyotropic reactions with the introduction of a concept based on the intramolecular dynamics of a tetrahedron (van ’t Hoff modeling). In fact the dyotropic reactions are strongly related to conversions originated from neighbouring group participation or anchimeric assistance, defined as the interaction of a center with a lone pair of electrons in an atom and the electrons present in aδor π bond. The researchful 1,2-dyotropic reactions, based on the 1,2-interchange of halogens, methyl and hydrogen taking place in a concerted fashion, are in competition with the two-step reaction in which the neighbouring group participation or anchimeric assistance comes to full expression by ionic dissociation of the other exchangeable (halogen) atom. As to be expected there is an essential difference between halogen or methyl exchange regarding the number of electrons participating in the transition state. This aspect becomes evident in the geometries of the corresponding transition state geometries. In this paper we refer to ab initio MO calculations and VB considerations. We consider the 1,2-halogen exchange as a combination of two SN2 reactions each containing four electrons. The van ’t Hoff dynamics appears a useful model in order to illustrate the computations in a straightforward manner.

A conformational B-Z DNA study monitored with phosphatemethylated DNA as a model for epigenetic dynamics focused on 5-(hydroxy)methylcytosine  [PDF]
Henk M. Buck
Journal of Biophysical Chemistry (JBPC) , 2013, DOI: 10.4236/jbpc.2013.42005
Abstract:

This study was directed on the B- into Z-DNA isomerization with alternating CG sequences monitored with artificial DNA model-systems based on methylation of the phosphate backbone. The chemical concept for this transition wherein shielding of the oxygen anions of the backbone phosphates plays an essential role, resulted in the preparation of the phosphatemethylated d(CpG). Even on this primitive level of only two base pair long, the B-Z conformational aspects of this self-complementary duplex could be described in solution with nuclear magnetic resonance (NMR) and circular dichroism (CD) measurements. The exclusivity of this choice became clear after synthesizing phosphatemethylated DNA with longer alternating CG fragments. It could be shown that conflicting conformational effects of the CG and GC fragments resulted in an overall B structure of the phosphatemethylated tetramer d(CPGPCPG). From our model considerations, it is clear that the internal stress introduced by the alternating CG sequences will be promoted by a complete shielding of the phosphate backbone. Elimination of this effect may be realized by a site-specific phosphate shielding. The role of the anti-syn isomerization of G in the CG fragments is clarified by methylation of the phosphate group. This anti-syn transition is absent in corresponding methylphosphonates, suggesting an exclusive role for base-backbone coordination via hydrogen bonding. In addition, we propose that the B- into Z-DNA interconversion may offer a mechanistic view for differences in dynamics between cytosine and its epigenetic derivative 5-methylcytosine. This mechanism has been extended to the demethylation of 5-methylcytosine and the exchange of information between the new epigenetic base, 5-hydroxymethylcytosine and the DNA backbone via an intramolecular phosphorylation. The role of 5-hydroxymethylcytosine in Alzheimer disease has been briefly discussed. In our opinion, this study can be considered as a new dynamic concept for epigenetics based on the dynamics of the B-Z transition in natural and phosphatemethylated DNA.

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