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Adaptive dynamic networks as models for the immune system and autocatalytic sets

Description: A general class of network models is described that can be used to present complex adaptive systems. These models have two purposes: On a practical level they are closely based on real biological phenomena, and are intended to model detailed aspects of them. On a more general level, however, they provide a framework to address broader questions concerning evolution, pattern recognition, and other properties of living systems. This paper concentrates on the more general level, illustrating the basic concepts with two examples, a model of the immune system and a model for the spontaneous emergence of autocatalytic sets in a chemically reactive polymer soup. 10 refs., 3 figs.
Date: April 1, 1986
Creator: Farmer, J.D.; Kauffman, S.A.; Packard, N.H. & Perelson, A.S.
Partner: UNT Libraries Government Documents Department

Biosynthesis of metal-binding polypeptides and their precursors in response to cadmium in Datura innoxia

Description: Metal-tolerant Datura innoxia cells synthesize large amounts of a class of metal-binding polypeptides, poly({gamma}-glutamylcysteinyl) glycines (({gamma}-EC){sub n}G, n=2-5), when exposed to Cd. These polypeptides have a high affinity for Cd (2) and certain other metal ions and are thought to play a role in metal tolerance in higher plants. ({gamma}-EC){sub n}G is biosynthetically derived from glutathione. Therefore, the response of Datura cells to Cd must include an increase in production of glutathione and its precursors, since cells rapidly accumulate very high concentrations of these metal-binding polypeptides. The biosynthesis of ({gamma}-EC){sub n}Gs, glutathione, and cysteine in response to Cd exposure is described. The physiological significance of the synthesis of these polypeptides and their precursors and its relevance to Cd tolerance and metal homeostasis are discussed. 34 refs., 6 figs., 1 tab.
Date: January 1, 1991
Creator: Jackson, P.J.; Delhaize, E. & Kuske, C.R.
Partner: UNT Libraries Government Documents Department

Body shape differences in a pair of closely related Malawi cichlids and their hybrids: Effects of genetic variation, phenotypic plasticity, and transgressive segregation

Description: This article investigates the contributions of genetic and plastic components for differences in body shape in two species of Lake Malawi cichlids using wild-caught specimens and a common garden experiment.
Date: January 28, 2017
Creator: Husemann, Martin; Tobler, Michael; McCauley, Cagney; Ding, Baoqing & Danley, Patrick D.
Partner: UNT College of Arts and Sciences

A Case-Study for Life-Long Learning and Adaptation in Cooperative Robot Teams

Description: While considerable progress has been made in recent years toward the development of multi-robot teams, much work remains to be done before these teams are used widely in real-world applications. Two particular needs toward this end are the development of mechanisms that enable robot teams to generate cooperative behaviors on their own, and the development of techniques that allow these teams to autonomously adapt their behavior over time as the environment or the robot team changes. This paper proposes the use of the Cooperative Multi-Robot Observation of Multiple Moving Targets (CMOMMT) application as a rich domain for studying the issues of multi-robot learning and adaptation. After discussing the need for learning and adaptation in multi-robot teams, this paper describes the CMOMMT application and its relevance to multi-robot learning. We discuss the results of the previously- developed, hand-generated algorithm for CMOMMT and the potential for learning that was discovered from the hand-generated approach. We then describe the early work that has been done (by us and others) to generate multi- robot learning techniques for the CMOMMT application, as well as our ongoing research to develop approaches that give performance as good, or better, than the hand-generated approach. The ultimate goal of this research is to develop techniques for multi-robot learning and adaptation in the CMOMMT application domain that will generalize to cooperative robot applications in other domains, thus making the practical use of multi-robot teams in a wide variety of real-world applications much closer to reality.
Date: September 19, 1999
Creator: Parker, L.E.
Partner: UNT Libraries Government Documents Department

A comparison of global optimization algorithms with standard benchmark functions and real-world applications using Energy Plus

Description: There is an increasing interest in the use of computer algorithms to identify combinations of parameters which optimise the energy performance of buildings. For such problems, the objective function can be multi-modal and needs to be approximated numerically using building energy simulation programs. As these programs contain iterative solution algorithms, they introduce discontinuities in the numerical approximation to the objective function. Metaheuristics often work well for such problems, but their convergence to a global optimum cannot be established formally. Moreover, different algorithms tend to be suited to particular classes of optimization problems. To shed light on this issue we compared the performance of two metaheuristics, the hybrid CMA-ES/HDE and the hybrid PSO/HJ, in minimizing standard benchmark functions and real-world building energy optimization problems of varying complexity. From this we find that the CMA-ES/HDE performs well on more complex objective functions, but that the PSO/HJ more consistently identifies the global minimum for simpler objective functions. Both identified similar values in the objective functions arising from energy simulations, but with different combinations of model parameters. This may suggest that the objective function is multi-modal. The algorithms also correctly identified some non-intuitive parameter combinations that were caused by a simplified control sequence of the building energy system that does not represent actual practice, further reinforcing their utility.
Date: September 1, 2009
Creator: Kamph, Jerome Henri; Robinson, Darren & Wetter, Michael
Partner: UNT Libraries Government Documents Department

Diversity of macromycetes in Bandelier national monument 1991--1993, A survey

Description: Since the great La Mesa fire of 1977 in Bandelier, much attention has been given to the ensuing course of plant and animal life. This paper introduces the importance of fungi, the neglected third kingdom, and describes a field survey sponsored by Los Alamos National Laboratory and Bandelier. The survey sought macromycetes the fruits of large fungi, noting the position, habitat, type, host, date and other descriptive features. The emphasis was on diversity, as many species as we could find. The welfare of every species of vascular plants is intricately bound to an associated fungus, in a relationship which has evolved over time with the evolution of the plant species. The survey covered the three summer seasons of 1991--1993. We collected 836 specimens from a variety of habitats. These were identified, recorded in a computer database, dried, and stored, in an herbarium. We found members of 220 species in 111 genera. We were able to identify 97% of the specimens to genus, 83% to species. In Bandelier alone, we collected 145 specimens in 1991--1992 and 232 specimens in 1993. This involved 74 genera and 93 species in 1993. The three basic types were found: Parasitic Saprophytic, and Mycorrhizal. The latter type composes roughly three fourths of the collection. A variety of sites were studied, with special attention to sites at Bandelier that have, or will be, burned.
Date: April 1, 1994
Creator: Jarmie, N. & Rogers, F. J.
Partner: UNT Libraries Government Documents Department

Dysbaric gas bubble disease in dogs. IV. Acclimatization to diving

Description: Acclimatization to diving was documented to occur in dogs. An increase in the number of repetitive dives which could be tolerated, as well as a decrease in the total number of pulmonary artery venous gas emboli resulting from individual dives were observed. The results from the experimental subject ''Jason'' indicate that acclimatization involves a reduction in the number of bubbles, and not an increase in the ability of the body to tolerate bubbles. Acclimatization is principally a physical rather than a physiological event. Bubbles forming in vivo must grow from nuclei of some sort. If these nuclei are stable, discrete structure that are destroyed when they grow into gross bubbles, then repetitive diving might markedly reduce by attrition the number of such bubble micronuclei. This would result in fewer bubbles being formed during subsequent dives, thus leading to the observed acclimatization effect. 7 refs., 3 figs., 4 tabs.
Date: January 1, 1986
Creator: Kunkle, T. D.; Morita, A. & Beckman, E. L.
Partner: UNT Libraries Government Documents Department

Effects of electronic identification, temperature monitoring, and ELA on the meat industry. [Electronic monitoring of cattle herds and serological testing for diseases]

Description: Electronic identification of CaHl/sub e/ and temperature monitoring of tolerance to environmental changes are technically feasible for the management of breeder herds and dairy cattle. Some commercial organizations are already manfacturing simple forms of electronic identification. A nearly ideal system can become a reality if the various potential user groups work together with the developers, manufacturers, and regulatory agencies. Widespread use of electronic identification and temperature monitoring in the livestock industry would improve the cost/benefit ratios to all portions of the industry by enhancing efficiency of production and management of records. The enzyme-labeled antibody (ELA) serological test of cattle in the slaughter plant makes it possible to screen for many diseases in a simple, fast inexpensive way.
Date: January 1, 1977
Creator: Holm, D. M.
Partner: UNT Libraries Government Documents Department

Environmental genotoxicity: Probing the underlying mechanisms

Description: Environmental pollution is a complex issue because of the diversity of anthropogenic agents, both chemical and physical, that have been detected and catalogued. The consequences to biota from exposure to genotoxic agents present an additional problem because of the potential for these agents to produce adverse change at the cellular and organismal levels. Past studies in genetic toxicology at the Oak Ridge National Laboratory have focused on structural damage to the DNA of environmental species that may occur after exposure to genotoxic agents and the use of this information to document exposure and to monitor remediation. In an effort to predict effects at the population, community and ecosystem levels, current studies in genetic ecotoxicology are attempting to characterize the biological mechanisms at the gene level that regulate and limit the response of an individual organism to genotoxic factors in their environment.
Date: December 31, 1993
Creator: Shugart, L. & Theodorakis, C.
Partner: UNT Libraries Government Documents Department

Genetic manipulation of a cyanobacterium for heavy metal detoxivication

Description: Increasing heavy metal contamination of soil and water has produced a need for economical and effective methods to reduce toxic buildup of these materials. Biological systems use metallothionein proteins to sequester such metals as Cu, Cd, and Zn. Studies are underway to genetically engineer a cyanobacteria strain with increased ability for metallothionein production and increased sequestration capacity. Cyanobacteria require only sunlight and CO{sub 2}. Vector constructs are being developed in a naturally competent, unicellular cyanobacterium Anacystis nidulans R2. Closed copies of a yeast copper metallothionein gene have been inserted into a cyanobacterial shuttle vector as well as a vector designed for genomic integration. Transformation studies have produced recombinant cyanobacteria from both of these systems, and work is currently underway to assess the organism`s ability to withstand increasing Cu, Cd, and Zn concentrations.
Date: December 31, 1995
Creator: McCormick, P.; Cannon, G. & Heinhorst, S.
Partner: UNT Libraries Government Documents Department

Metagenomic Insights into Evolution of a Heavy Metal-Contaminated Groundwater Microbial Community

Description: Understanding adaptation of biological communities to environmental change is a central issue in ecology and evolution. Metagenomic analysis of a stressed groundwater microbial community reveals that prolonged exposure to high concentrations of heavy metals, nitric acid and organic solvents (~;;50 years) have resulted in a massive decrease in species and allelic diversity as well as a significant loss of metabolic diversity. Although the surviving microbial community possesses all metabolic pathways necessary for survival and growth in such an extreme environment, its structure is very simple, primarily composed of clonal denitrifying ?- and ?-proteobacterial populations. The resulting community is over-abundant in key genes conferring resistance to specific stresses including nitrate, heavy metals and acetone. Evolutionary analysis indicates that lateral gene transfer could be a key mechanism in rapidly responding and adapting to environmental contamination. The results presented in this study have important implications in understanding, assessing and predicting the impacts of human-induced activities on microbial communities ranging from human health to agriculture to environmental management, and their responses to environmental changes.
Date: February 15, 2010
Creator: Hemme, Christopher L.; Deng, Ye; Gentry, Terry J.; Fields, Matthew W.; Wu, Liyou; Barua, Soumitra et al.
Partner: UNT Libraries Government Documents Department

Molecular biology in studies of oceanic primary production

Description: Remote sensing and the use of moored in situ instrumentation has greatly improved our ability to measure phytoplankton chlorophyll and photosynthesis on global scales with high temporal resolution. However, the interpretation of these measurements and their significance with respect to the biogeochemical cycling of carbon relies on their relationship with physiological and biochemical processes in phytoplankton. For example, the use of satellite images of surface chlorophyll to estimate primary production is often based on the functional relationship between photosynthesis and irradiance. A variety of environmental factors such as light, temperature, nutrient availability affect the photosynthesis/irradiance (P vs I) relationship in phytoplankton. We present three examples showing how molecular biology can be used to provide basic insight into the factors controlling primary productivity at three different levels of complexity: 1. Studies of light intensity regulation in unicellular alga show how molecular biology can help understand the processing of environmental cues leading to the regulation of photosynthetic gene expression. 2. Probing of the photosynthetic apparatus using molecular techniques can be used to test existing mechanistic models derived from the interpretation of physiological and biophysical measurements. 3. Exploratory work on the expression of specific proteins during nutrient-limited growth of phytoplankton may lead to the identification and production of molecular probes for field studies.
Date: July 1, 1992
Creator: LaRoche, J.; Falkowski, P. G. & Geider, R.
Partner: UNT Libraries Government Documents Department

Molecular biology in studies of oceanic primary production

Description: Remote sensing and the use of moored in situ instrumentation has greatly improved our ability to measure phytoplankton chlorophyll and photosynthesis on global scales with high temporal resolution. However, the interpretation of these measurements and their significance with respect to the biogeochemical cycling of carbon relies on their relationship with physiological and biochemical processes in phytoplankton. For example, the use of satellite images of surface chlorophyll to estimate primary production is often based on the functional relationship between photosynthesis and irradiance. A variety of environmental factors such as light, temperature, nutrient availability affect the photosynthesis/irradiance (P vs I) relationship in phytoplankton. We present three examples showing how molecular biology can be used to provide basic insight into the factors controlling primary productivity at three different levels of complexity: 1. Studies of light intensity regulation in unicellular alga show how molecular biology can help understand the processing of environmental cues leading to the regulation of photosynthetic gene expression. 2. Probing of the photosynthetic apparatus using molecular techniques can be used to test existing mechanistic models derived from the interpretation of physiological and biophysical measurements. 3. Exploratory work on the expression of specific proteins during nutrient-limited growth of phytoplankton may lead to the identification and production of molecular probes for field studies.
Date: January 1, 1992
Creator: LaRoche, J.; Falkowski, P.G. (Brookhaven National Lab., Upton, NY (United States)) & Geider, R. (Delaware Univ., Lewes, DE (United States). Coll. of Marine Studies)
Partner: UNT Libraries Government Documents Department

Photosynthesis, environmental change, and plant adaptation: Research topics in plant molecular ecology. Summary report of a workshop

Description: As we approach the 21st Century, it is becoming increasingly clear that human activities, primarily related to energy extraction and use, will lead to marked environmental changes at the local, regional, and global levels. The realized and the potential photosynthetic performance of plants is determined by a combination of intrinsic genetic information and extrinsic environmental factors, especially climate. It is essential that the effects of environmental changes on the photosynthetic competence of individual species, communities, and ecosystems be accurately assessed. From October 24 to 26, 1993, a group of scientists specializing in various aspects of plant science met to discuss how our predictive capabilities could be improved by developing a more rational, mechanistic approach to relating photosynthetic processes to environmental factors. A consensus emerged that achieving this goal requires multidisciplinary research efforts that combine tools and techniques of genetics, molecular biology, biophysics, biochemistry, and physiology to understand the principles, mechanisms, and limitations of evolutional adaptation and physiological acclimation of photosynthetic processes. Many of these basic tools and techniques, often developed in other fields of science, already are available but have not been applied in a coherent, coordinated fashion to ecological research. The efforts of this research program are related to the broader efforts to develop more realistic prognostic models to forecast climate change that include photosynthetic responses and feedbacks at the regional and ecosystem levels.
Date: July 1, 1995
Partner: UNT Libraries Government Documents Department

The potential effects of concurrent increases in temperature, CO{sub 2} and O{sub 3} on net photosynthesis, as mediated by rubisCO

Description: At the leaf level, under light saturating and light limiting conditions, it is shown that elevated atmospheric CO{sub 2} concentration not only alters the scale of the response of carbon gain to rising temperature, but can alter the direction of response. These points bring into serious question the value of any predictions of plant production which ignore not only the direct effect Of C0{sub 2} on carbon gain, but also the basic interactions of temperature, C0{sub 2} and 0{sub 3}. Whilst many factors may potentially diminish the enhancement of lightsaturated leaf photosynthetic rates with increase in atmospheric CO{sub 2} concentrations, no mechanism has so far been identified which could remove the parallel stimulation of light-limited photosynthesis.
Date: July 1, 1992
Creator: Long, S.
Partner: UNT Libraries Government Documents Department

The potential effects of concurrent increases in temperature, CO sub 2 and O sub 3 on net photosynthesis, as mediated by rubisCO

Description: At the leaf level, under light saturating and light limiting conditions, it is shown that elevated atmospheric CO{sub 2} concentration not only alters the scale of the response of carbon gain to rising temperature, but can alter the direction of response. These points bring into serious question the value of any predictions of plant production which ignore not only the direct effect Of C0{sub 2} on carbon gain, but also the basic interactions of temperature, C0{sub 2} and 0{sub 3}. Whilst many factors may potentially diminish the enhancement of lightsaturated leaf photosynthetic rates with increase in atmospheric CO{sub 2} concentrations, no mechanism has so far been identified which could remove the parallel stimulation of light-limited photosynthesis.
Date: July 1, 1992
Creator: Long, S. (Brookhaven National Lab., Upton, NY (United States) Essex Univ., Colchester (United Kingdom). Dept. of Biology)
Partner: UNT Libraries Government Documents Department

Recent developments in ecological theory: hierarchy and scale

Description: Over the past decade, hierarchy and scale have been adopted as an ecological paradigm. Beyond this new awareness, however, a number of studies have attempted to test the underlying hierarchy theory and developed new analytical applications. The purpose of the present paper is to review these recent developments. Tests of the theory have focused on the prediction that ecological systems should not be uniformly distributed across scale, but grouped or lumped into discrete levels. The predicted breaks in spatial distribution have been found in vegetation transects. Vertebrate weight distributions are also distinctly aggregated, corresponding to the spatial scale at which each species operates. An important development of hierarchy theory has considered extrapolating information upscale. Simply stated, the dynamics of the higher level cannot be represented by the same functional form as its components. One cannot insert the mean parameter value for the components and predict higher level effects. Analytical methods, derived from hierarchy theory, have been developed deal with the problem.
Date: December 31, 1995
Creator: O`Neill, R.V.
Partner: UNT Libraries Government Documents Department

Resilient Plant Monitoring System: Design, Analysis, and Performance Evaluation

Description: Resilient monitoring systems are sensor networks that degrade gracefully under malicious attacks on their sensors, causing them to project misleading information. The goal of this paper is to design, analyze, and evaluate the performance of a resilient monitoring system intended to monitor plant conditions (normal or anomalous). The architecture developed consists of four layers: data quality assessment, process variable assessment, plant condition assessment, and sensor network adaptation. Each of these layers is analyzed by either analytical or numerical tools, and the performance of the overall system is evaluated using simulations. The measure of resiliency of the resulting system is evaluated using Kullback Leibler divergence, and is shown to be sufficiently high in all scenarios considered.
Date: December 1, 2013
Creator: Garcia, Humberto E.; Lin, Wen-Chiao; Meerkov, Semyon M. & Ravichandran, Maruthi T.
Partner: UNT Libraries Government Documents Department

Root adaptations at stress levels of nitrate, phosphate, or both simultaneously

Description: Sunflowers in flowing hydroponic culture show reduced growth rates at nitrate levels below 10 ..mu..M nitrate or phosphate levels below 0.3 ..mu..F. At least for phosphate, this level is a very small fraction (0.003) of the K/sub m/ for the uptake systems. We have quantified four major adaptations that enable high growth rates under incipient stress: increased root:shoot ratio; increased uptake capacity (V/sub max/) per unit root mass; nocturnal uptake of nutrients; and (only partially adaptive) reduced tissue concentrations of nutrients. We show that capital energy costs (in root growth) for acquiring nutrients can exceed direct or operational costs of internal metabolism (nitrate reduction, e.g.,); this has implications for the plant-controlled trade-off of NO/sub 3//sup -/-NH/sub 4//sup +/ - N/sub 2/ as N sources for legumes and other plant types. We outline needed further research and suggest guidelines for breeding plants for tolerating nutritional stresses; we also suggest that some measures of nutrient-use efficiency may be misleading. 6 references, 2 figures, 2 tables.
Date: August 1, 1984
Creator: Gutschick, V.P. & Kay, L.E.
Partner: UNT Libraries Government Documents Department

The Slow:Fast substitution ratio reveals changing patterns of natural selection in gamma-proteobacterial genomes

Description: Different microbial species are thought to occupy distinct ecological niches, subjecting each species to unique selective constraints, which may leave a recognizable signal in their genomes. Thus, it may be possible to extract insight into the genetic basis of ecological differences among lineages by identifying unusual patterns of substitutions in orthologous gene or protein sequences. We use the ratio of substitutions in slow versus fast-evolving sites (nucleotides in DNA, or amino acids in protein sequence) to quantify deviations from the typical pattern of selective constraint observed across bacterial lineages. We propose that elevated S:F in one branch (an excess of slow-site substitutions) can indicate a functionally-relevant change, due to either positive selection or relaxed evolutionary constraint. In a genome-wide comparative study of gamma-proteobacterial proteins, we find that cell-surface proteins involved with motility and secretion functions often have high S:F ratios, while information-processing genes do not. Change in evolutionary constraints in some species is evidenced by increased S:F ratios within functionally-related sets of genes (e.g., energy production in Pseudomonas fluorescens), while other species apparently evolve mostly by drift (e.g., uniformly elevated S:F across most genes in Buchnera spp.). Overall, S:F reveals several species-specific, protein-level changes with potential functional/ecological importance. As microbial genome projects yield more species-rich gene-trees, the S:F ratio will become an increasingly powerful tool for uncovering functional genetic differences among species.
Date: April 15, 2009
Creator: Alm, Eric & Shapiro, B. Jesse
Partner: UNT Libraries Government Documents Department

Stress Variances Among Informal Hospice Caregivers

Description: Article on stress variances among informal hospice caregivers.
Date: August 2012
Creator: Wittenberg-Lyles, Elaine; Demiris, George; Oliver, Debra Parker; Washington, Karla T.; Burt, Stephanie & Shaunfield, Sara
Partner: UNT College of Arts and Sciences

Transmutations across hierarchical levels. [Development of large-scale ecological models]

Description: The development of large-scale ecological models depends implicitly on a concept known as hierarchy theory which views biological systems in a series of hierarchical levels (i.e., organism, population, trophic level, ecosystem). The theory states that an explanation of a biological phenomenon is provided when it is shown to be the consequence of the activities of the system's components, which are themselves systems in the next lower level of the hierarchy. Thus, the behavior of a population is explained by the behavior of the organisms in the population. The initial step in any modeling project is, therefore, to identify the system components and the interactions between them. A series of examples of transmutations in aquatic and terrestrial ecosystems are presented to show how and why changes occur. The types of changes are summarized and possible implications of transmutation for hierarchy theory, for the modeler, and for the ecological theoretician are discussed.
Date: January 1, 1977
Creator: O'Neill, R. V.
Partner: UNT Libraries Government Documents Department