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God and the God-Image: An Extended Reflection

Description: Abstract: This paper examines the parallels between my anesthetic-related near-death experience and Rudolph Otto's description of numinous states. I discuss Otto's arguments about such perceptions and their implications, and explore internal numinous processes such as they might be seen through Carl Jung's psychology.
Date: Summer 1991
Creator: Leighton, Sally M.
Partner: UNT Libraries

Multi-level mass store implementation

Description: The National Magnetic Fusion Energy Center is currently installing a very large mass data storage system. The storage system will comprise three distinct levels: magnetic disk, a CDC 38500 Mass Storage Facility, and high density 10/sup 1///sub 2/-inch reel magnetic tape. The resulting storage facility will emphasize the best characteristics of each level while masking the weaker characteristics. The goal is to give the overall system the performance and reliability of a magnetic disk system, the capacity of the CDC 38500 system, and the off-line archival storage characteristic of magnetic tape. 2 figures.
Date: December 1, 1977
Creator: Leighton, J.F.
Partner: UNT Libraries Government Documents Department

Unified parallel C and the computing needs of Sandia National Laboratories.

Description: As Sandia looks toward petaflops computing and other advanced architectures, it is necessary to provide a programming environment that can exploit this additional computing power while supporting reasonable development time for applications. Thus, they evaluate the Partitioned Global Address Space (PGAS) programming model as implemented in Unified Parallel C (UPC) for its applicability. They report on their experiences in implementing sorting and minimum spanning tree algorithms on a test system, a Cray T3e, with UPC support. They describe several macros that could serve as language extensions and several building-block operations that could serve as a foundation for a PGAS programming library. They analyze the limitations of the UPC implementation available on the test system, and suggest improvements necessary before UPC can be used in a production environment.
Date: September 1, 2004
Creator: Brown, Jonathan Leighton & Wen, Zhaofang
Partner: UNT Libraries Government Documents Department

PRAM C:a new programming environment for fine-grain and coarse-grain parallelism.

Description: In the search for ''good'' parallel programming environments for Sandia's current and future parallel architectures, they revisit a long-standing open question. Can the PRAM parallel algorithms designed by theoretical computer scientists over the last two decades be implemented efficiently? This open question has co-existed with ongoing efforts in the HPC community to develop practical parallel programming models that can simultaneously provide ease of use, expressiveness, performance, and scalability. Unfortunately, no single model has met all these competing requirements. Here they propose a parallel programming environment, PRAM C, to bridge the gap between theory and practice. This is an attempt to provide an affirmative answer to the PRAM question, and to satisfy these competing practical requirements. This environment consists of a new thin runtime layer and an ANSI C extension. The C extension has two control constructs and one additional data type concept, ''shared''. This C extension should enable easy translation from PRAM algorithms to real parallel programs, much like the translation from sequential algorithms to C programs. The thin runtime layer bundles fine-grained communication requests into coarse-grained communication to be served by message-passing. Although the PRAM represents SIMD-style fine-grained parallelism, a stand-alone PRAM C environment can support both fine-grained and coarse-grained parallel programming in either a MIMD or SPMD style, interoperate with existing MPI libraries, and use existing hardware. The PRAM C model can also be integrated easily with existing models. Unlike related efforts proposing innovative hardware with the goal to realize the PRAM, ours can be a pure software solution with the purpose to provide a practical programming environment for existing parallel machines; it also has the potential to perform well on future parallel architectures.
Date: November 1, 2004
Creator: Brown, Jonathan Leighton & Wen, Zhaofang.
Partner: UNT Libraries Government Documents Department

The Published Writings of Ernest McClain Through Spring, 1976

Description: This thesis considers all of Ernest McClain's published writings, from March, 1970, to September, 1976, from the standpoint of their present-day acoustical significance. Although much of the material comes from McClain's writings, some is drawn from other related musical, mathematical, and philosophical works. The four chapters begin with a biographical sketch of McClain, presenting his background which aided him in becoming a theoretical musicologist. The second chapter contains a chronological itemization of his writings and provides a synopsis of them in layman's terms. The following chapter offers an examination of some salient points of McClain's work. The final chapter briefly summarizes the findings and contains conclusions as to their germaneness to current music theory, thereby giving needed exposure to McClain's ideas.
Date: August 1977
Creator: Wingate, F. Leighton
Partner: UNT Libraries

Neutrons for Catalysis: A Workshop on Neutron Scattering Techniques for Studies in Catalysis

Description: This report summarizes the Workshop on Neutron Scattering Techniques for Studies in Catalysis, held at the Spallation Neutron Source (SNS) at Oak Ridge National Laboratory (ORNL) on September 16 and 17, 2010. The goal of the Workshop was to bring experts in heterogeneous catalysis and biocatalysis together with neutron scattering experimenters to identify ways to attack new problems, especially Grand Challenge problems in catalysis, using neutron scattering. The Workshop locale was motivated by the neutron capabilities at ORNL, including the High Flux Isotope Reactor (HFIR) and the new and developing instrumentation at the SNS. Approximately 90 researchers met for 1 1/2 days with oral presentations and breakout sessions. Oral presentations were divided into five topical sessions aimed at a discussion of Grand Challenge problems in catalysis, dynamics studies, structure characterization, biocatalysis, and computational methods. Eleven internationally known invited experts spoke in these sessions. The Workshop was intended both to educate catalyst experts about the methods and possibilities of neutron methods and to educate the neutron community about the methods and scientific challenges in catalysis. Above all, it was intended to inspire new research ideas among the attendees. All attendees were asked to participate in one or more of three breakout sessions to share ideas and propose new experiments that could be performed using the ORNL neutron facilities. The Workshop was expected to lead to proposals for beam time at either the HFIR or the SNS; therefore, it was expected that each breakout session would identify a few experiments or proof-of-principle experiments and a leader who would pursue a proposal after the Workshop. Also, a refereed review article will be submitted to a prominent journal to present research and ideas illustrating the benefits and possibilities of neutron methods for catalysis research.
Date: October 1, 2011
Creator: Overbury, Steven H.; Coates, Leighton; Herwig, Kenneth W. & Kidder, Michelle
Partner: UNT Libraries Government Documents Department

Analysis of bacterial spore permeability to water and ions using Nano-Secondary Ion Mass Spectrometry (NanoSIMS)

Description: Regulation of bacterial spore solvent and solute permeability is a fundamental feature of dormancy but is poorly understood. Here we present a new technique, nano-scale secondary ion mass spectrometry (NanoSIMS) that allows the direct visualization and quantification of chemical gradients within spores. Using NanoSIMS, we demonstrate the penetration of water and a simple ionic salt, LiF, into the core of Bacillus thuringiensis israelensis (Bti) spores. The results demonstrate chemical gradients spanning the outer coat to the inner spore core that are driven by concentration-dependent ionic fluxes. Using deuterated water (D{sub 2}O), we have shown that external water is either retained or exchanged with water contained within the spore. Hydration and exchange are rapid, on a timescale of < 1 minute. Our results suggest a permeation mechanism by which short-time scale diffusion into and out of the spore can occur along hydration pathways. Additional studies are in progress to define the flux rates and mechanisms controlling these processes.
Date: November 17, 2005
Creator: Ghosal, S; Fallon, S; Leighton, T; Wheeler, K; Hutcheon, I & Weber, P K
Partner: UNT Libraries Government Documents Department

Characterization and Detection of Biological Weapons with Atomic Force Microscopy

Description: Critical gaps exist in our capabilities to rapidly characterize threat agents which could be used in attacks on facilities and military forces. DNA-based PCR and immunoassay-based techniques provide unique identification of species, strains and protein signatures of pathogens. However, differentiation between naturally occurring and weaponized bioagents and the identification of formulation signatures are beyond current technologies. One of the most effective and often the only definitive means to identify a threat agent is by its direct visualization. Atomic force microscopy (AFM) is a rapid imaging technique that covers the size range of most biothreat agents (several nanometers to tens of microns), is capable of resolving pathogen morphology and structure, and could be developed into a portable device for biological weapons (BW) field characterization. AFM can detect pathogens in aerosol, liquid, surface and soil samples while concomitantly acquiring their weaponization and threat agent digital signatures. BW morphological and structural signatures, including modifications to pathogen microstructural architecture and topology that occur during formulation and weaponization, provide the means for their differentiation from crude or purified unformulated agent, processing signatures, as well as assessment of their potential for dispersion, inhalation and environmental persistence. AFM visualization of pathogen morphology and architecture often provides valuable digital signatures and allows direct detection and identification of threat agents. We have demonstrated that pathogens, spanning the size range from several nanometers for small agricultural satellite viruses to almost half micron for pox viruses, and to several microns for bacteria and bacterial spores, can be visualized by AFM under physiological conditions to a resolution of {approx}20-30 {angstrom}. We have also demonstrated that viruses from closely related families could be differentiated by AFM on the basis of their structural attributes. Similarly, we have shown3-5 that bacterial spore coat structures are phylogenetically and growth medium determined. These findings validate that AFM ...
Date: September 25, 2006
Creator: Malkin, A J; Plomp, M; Leighton, T J & McPherson, A
Partner: UNT Libraries Government Documents Department

Multi-Probe Investigation of Proteomic Structure of Pathogens

Description: Complete genome sequences are available for understanding biotransformation, environmental resistance and pathogenesis of microbial, cellular and pathogen systems. The present technological and scientific challenges are to unravel the relationships between the organization and function of protein complexes at cell, microbial and pathogens surfaces, to understand how these complexes evolve during the bacterial, cellular and pathogen life cycles, and how they respond to environmental changes, chemical stimulants and therapeutics. In particular, elucidating the molecular structure and architecture of human pathogen surfaces is essential to understanding mechanisms of pathogenesis, immune response, physicochemical interactions, environmental resistance and development of countermeasures against bioterrorist agents. The objective of this project was to investigate the architecture, proteomic structure, and function of bacterial spores through a combination of high-resolution in vitro atomic force microscopy (AFM) and AFM-based immunolabeling with threat-specific antibodies. Particular attention in this project was focused on spore forming Bacillus species including the Sterne vaccine strain of Bacillus anthracis and the spore forming near-neighbor of Clostridium botulinum, C. novyi-NT. Bacillus species, including B. anthracis, the causative agent of inhalation anthrax are laboratory models for elucidating spore structure/function. Even though the complete genome sequence is available for B. subtilis, cereus, anthracis and other species, the determination and composition of spore structure/function is not understood. Prof. B. Vogelstein and colleagues at the John Hopkins University have recently developed a breakthrough bacteriolytic therapy for cancer treatment (1). They discovered that intravenously injected Clostridium novyi-NT spores germinate exclusively within the avascular regions of tumors in mice and destroy advanced cancerous lesions. The bacteria were also found to significantly improve the efficacy of chemotherapeutic drugs and radiotherapy (2,3). Currently, there is no understanding of the structure-function relationships of Clostridium novyi-NT spores. As well as their therapeutic interest, studies of Clostridium noyii spores could provide a model for further studies of ...
Date: January 24, 2008
Creator: Malkin, A J; Plomp, M; Leighton, T J; Vogelstein, B & Wheeler, K E
Partner: UNT Libraries Government Documents Department

In vitro high-resolution structural dynamics of single germinating bacterial spores

Description: Although significant progress has been achieved in understanding the genetic and biochemical bases of the spore germination process, the structural basis for breaking the dormant spore state remains poorly understood. We have used atomic force microscopy (AFM) to probe the high-resolution structural dynamics of single Bacillus atrophaeus spores germinating under native conditions. Here we show that AFM can reveal previously unrecognized germination-induced alterations in spore coat architecture and topology as well as the disassembly of outer spore coat rodlet structures. These results and previous studies in other microorganisms suggest that the spore coat rodlets are structurally similar to amyloid fibrils. AFM analysis of the nascent surface of the emerging germ cell revealed a porous network of peptidoglycan fibers. The results are consistent with a honeycomb model structure for synthetic peptidoglycan oligomers determined by nuclear magnetic resonance. AFM is a promising experimental tool for investigating the morphogenesis of spore germination and cell wall peptidoglycan structure.
Date: November 14, 2006
Creator: Plomp, M; Leighton, T; Wheeler, K & Malkin, A
Partner: UNT Libraries Government Documents Department

Bioforensics: Characterization of biological weapons agents by NanoSIMS

Description: The anthrax attacks of Fall 2001 highlight the need to develop forensic methods based on multiple identifiers to determine the origin of biological weapons agents. Genetic typing methods (i.e., DNA and RNA-based) provide one attribution technology, but genetic information alone is not usually sufficient to determine the provenance of the material. Non-genetic identifiers, including elemental and isotopic signatures, provide complementary information that can be used to identify the means, geographic location and date of production. Under LDRD funding, we have successfully developed the techniques necessary to perform bioforensic characterization with the NanoSIMS at the individual spore level. We have developed methods for elemental and isotopic characterization at the single spore scale. We have developed methods for analyzing spore sections to map elemental abundance within spores. We have developed rapid focused ion beam (FIB) sectioning techniques for spores to preserve elemental and structural integrity. And we have developed a high-resolution depth profiling method to characterize the elemental distribution in individual spores without sectioning. We used these newly developed methods to study the controls on elemental abundances in spores, characterize the elemental distribution of in spores, and to study elemental uptake by spores. Our work under this LDRD project attracted FBI and DHS funding for applied purposes.
Date: February 26, 2007
Creator: Weber, P K; Ghosal, S; Leighton, T J; Wheeler, K E & Hutcheon, I D
Partner: UNT Libraries Government Documents Department

Probing the Structure-Function Relationships of Microbial Systems

Description: The elucidation of microbial surface architecture and function is critical to determining mechanisms of pathogenesis, immune response, physicochemical properties, environmental resistance and development of countermeasures against bioterrorist agents. We have utilized high-resolution in vitro AFM for studies of structure, assembly, function and environmental dynamics of several microbial systems including bacteria and bacterial spores. Lateral resolutions of {approx}2.0 nm were achieved on pathogens, in vitro. We have demonstrated, using various species of Bacillus and Clostridium bacterial spores, that in vitro AFM can address spatially explicit spore coat protein interactions, structural dynamics in response to environmental changes, and the life cycle of pathogens at near-molecular resolution under physiological conditions. We found that strikingly different species-dependent crystalline structures of the spore coat appear to be a consequence of nucleation and crystallization mechanisms that regulate the assembly of the outer spore coat, and we proposed a unifying mechanism for outer spore coat self-assembly. Furthermore, we revealed molecular-scale transformations of the spore coat during the germination process, which include profound, previously unrecognized changes of the spore coat. We will present data on the direct visualization of stress-induced environmental response of metal-resistant Arthrobacter oxydans bacteria to Cr (VI) exposure, resulting in the formation of a supramolecular crystalline hexagonal structure on the cell surface. At higher Cr (VI) concentrations the formation of microbial extracellular polymers, which cover microbial colony was observed. High-resolution visualization of stress-induced structures on bacterial surfaces builds a foundation for real time in vitro molecular scale studies of structural dynamics of metal-resistant bacteria in response to environmental stimuli. In the case of the bacterium Chlamedia trachomatis, we were able to identify surface exposed proteins versus proteins embedded in the outer membrane. These studies establish in vitro AFM as a powerful new tool capable of revealing pathogen architecture, structural dynamics and variability at nanometer-to-micrometer scales.
Date: November 3, 2005
Creator: Plomp, M; Leighton, T J; Holman, H & Malkin, A J
Partner: UNT Libraries Government Documents Department

A doubly logarithmic communication algorithm for the Completely Connected Optical Communication Parallel Computer

Description: In this paper we consider the problem of interprocessor communication on a Completely Connected Optical Communication Parallel Computer (OCPC). The particular problem we study is that of realizing an h-relation. In this problem, each processor has at most h messages to send and at most h messages to receive. It is clear that any 1-relation can be realized in one communication step on an OCPC. However, the best known p-processor OCPC algorithm for realizing an arbitrary h-relation for h > 1 requires {Theta}(h + log p) expected communication steps. (This algorithm is due to Valiant and is based on earlier work of Anderson and Miller.) Valiant`s algorithm is optimal only for h = {Omega}(log p) and it is an open question of Gereb-Graus and Tsantilas whether there is a faster algorithm for h = o(log p). In this paper we answer this question in the affirmative by presenting a {Theta} (h + log log p) communication step algorithm that realizes an arbitrary h-relation on a p-processor OCPC. We show that if h {le} log p then the failure probability can be made as small as p{sup -{alpha}} for any positive constant {alpha}.
Date: January 20, 1993
Creator: Goldberg, L. A.; Jerrum, M.; Leighton, T. & Rao, S.
Partner: UNT Libraries Government Documents Department

Bacterial chromate reduction and product characterization

Description: Bacillus subtilis reduced hexavalent chromate to trivalent chromium under either aerobic or anaerobic conditions. Reduction of CR(VI) and appearance of extracellular Cr(III) were demonstrated by electron spin resonance and spectrophotometry. Chromate reduction was stimulated more than five-fold by freeze-thawing, indicating that intracellular reductases or chemical reductants reduce chromate more rapidly than do intact cells. Moderately concentrated cells (10% pellet volume after centrifugation) reduced approximately 40 {mu}M chromate/min (2 mg Cr/1-min) when exposed to 100 {mu}M chromate (5 mg Cr/1). Highly concentrated cells (70% pellet volume) reduced more than 99.8% of 2 mM chromate (100 mg Cr/1) within 15 min. This rate of chromate reduction was of the same order of magnitude as the rate of respiration in aerobic cells. A substantial fraction of the reduction product (ca. 75%) was extracellular Cr(M), which could readily be separated from the cells by centrifugation. At high chromate concentrations, some fraction of reduced CR(VI) appeared to be taken up by cells, consistent with a detection of intracellular paramagnetic products. At low chromate concentrations, undefined growth medium alone reduced Cr(VI), but at a slow rate, relative to cells. Under appropriate conditions, B. subtilis appears to be an organism of choice for detoxifying chromate-contaminated soil and water.
Date: November 1, 1992
Creator: Mehlhorn, R. J.; Buchanan, B. B. & Leighton, T.
Partner: UNT Libraries Government Documents Department

Architecture and High-Resolution Structure of Bacillus thuringiensis and Bacillus cereus Spore Coat Surfaces

Description: We have utilized atomic force microscopy (AFM) to visualize the native surface topology and ultrastructure of Bacillus thuringiensis and Bacillus cereus spores in water and in air. AFM was able to resolve the nanostructure of the exosporium and three distinctive classes of appendages. Removal of the exosporium exposed either a hexagonal honeycomb layer (B. thuringiensis) or a rodlet outer spore coat layer (B. cereus). Removal of the rodlet structure from B. cereus spores revealed an underlying honeycomb layer similar to that observed with B. thuringiensis spores. The periodicity of the rodlet structure on the outer spore coat of B. cereus was {approx}8 nm, and the length of the rodlets was limited to the cross-patched domain structure of this layer to {approx}200 nm. The lattice constant of the honeycomb structures was {approx}9 nm for both B. cereus and B. thuringiensis spores. Both honeycomb structures were composed of multiple, disoriented domains with distinct boundaries. Our results demonstrate that variations in storage and preparation procedures result in architectural changes in individual spore surfaces, which establish AFM as a useful tool for evaluation of preparation and processing ''fingerprints'' of bacterial spores. These results establish that high-resolution AFM has the capacity to reveal species-specific assembly and nanometer scale structure of spore surfaces. These species-specific spore surface structural variations are correlated with sequence divergences in a spore core structural protein SspE.
Date: February 18, 2005
Creator: Plomp, M; Leighton, T; Wheeler, K & Malkin, A
Partner: UNT Libraries Government Documents Department

The high-resolution architecture and structural dynamics of Bacillus spores

Description: The capability to image single microbial cell surfaces at nanometer scale under native conditions would profoundly impact mechanistic and structural studies of pathogenesis, immunobiology, environmental resistance and biotransformation. We report here that advances in atomic force microscopy (AFM) have allowed us to directly visualize high-resolution native structures of bacterial endospores, including the exosporium and spore coats of four Bacillus species in air and water environments. The dimensions of individual Bacillus atrophaeus spores were found to decrease reversibly by 12% in response to a change in the environment from aqueous to aerial phase. Intraspecies spore size distribution analyses revealed that spore length could vary by a factor of 2 while the absolute deviation is 7 - 13% in length and 4 - 6 % in width. AFM analysis also demonstrated that the mechanisms of spore coat self-assembly are similar to those described for inorganic and macromolecular crystallization. These results establish AFM as a powerful new tool for the analysis of molecular architecture and variability as a function of spatial, temporal and developmental organizational scales.
Date: May 6, 2004
Creator: Plomp, M; Leighton, T J; Wheeler, K E & Malkin, A J
Partner: UNT Libraries Government Documents Department

Unraveling the Architecture and Structural Dynamics of Pathogens by High-Resolution in vitro Atomic Force Microscopy

Description: Progress in structural biology very much depends upon the development of new high-resolution techniques and tools. Despite decades of study of viruses, bacteria and bacterial spores and their pressing importance in human medicine and biodefense, many of their structural properties are poorly understood. Thus, characterization and understanding of the architecture of protein surface and internal structures of pathogens is critical to elucidating mechanisms of disease, immune response, physicochemical properties, environmental resistance and development of countermeasures against bioterrorist agents. Furthermore, even though complete genome sequences are available for various pathogens, the structure-function relationships are not understood. Because of their lack of symmetry and heterogeneity, large human pathogens are often refractory to X-ray crystallographic analysis or reconstruction by cryo-electron microscopy (cryo-EM). An alternative high-resolution method to examine native structure of pathogens is atomic force microscopy (AFM), which allows direct visualization of macromolecular assemblies at near-molecular resolution. The capability to image single pathogen surfaces at nanometer scale in vitro would profoundly impact mechanistic and structural studies of pathogenesis, immunobiology, specific cellular processes, environmental dynamics and biotransformation.
Date: April 12, 2005
Creator: Malkin, A J; Plomp, M; Leighton, T J; McPherson, A & Wheeler, K E
Partner: UNT Libraries Government Documents Department

Bacillus atrophaeus Outer Spore Coat Assembly and Ultrastructure

Description: Our previous atomic force microscopy (AFM) studies successfully visualized native Bacillus atrophaeus spore coat ultrastructure and surface morphology. We have shown that the outer spore coat surface is formed by a crystalline array of {approx}11 nm thick rodlets, having a periodicity of {approx}8 nm. We present here further AFM ultrastructural investigations of air-dried and fully hydrated spore surface architecture. In the rodlet layer, planar and point defects, as well as domain boundaries, similar to those described for inorganic and macromolecular crystals, were identified. For several Bacillus species, rodlet structure assembly and architectural variation appear to be a consequence of species-specific nucleation and crystallization mechanisms that regulate the formation of the outer spore coat. We propose a unifying mechanism for nucleation and self-assembly of this crystalline layer on the outer spore coat surface.
Date: November 21, 2005
Creator: Plomp, M; Leighton, T J; Wheeler, K E; Pitesky, M E & Malkin, A J
Partner: UNT Libraries Government Documents Department