History of chemical and biological warfare agents.

PubMed

Szinicz, L

2005-10-30

Chemical and biological warfare agents constitute a low-probability, but high-impact risk both to the military and to the civilian population. The use of hazardous materials of chemical or biological origin as weapons and for homicide has been documented since ancient times. The first use of chemicals in terms of weapons of mass destruction goes back to World War I, when on April 22, 1915 large amounts of chlorine were released by German military forces at Ypres, Belgium. Until around the 1970s of the 20th century, the awareness of the threat by chemical and biological agents had been mainly confined to the military sector. In the following time, the development of increasing range delivery systems by chemical and biological agents possessors sensitised public attention to the threat emanating from these agents. Their proliferation to the terrorists field during the 1990s with the expanding scale and globalisation of terrorist attacks suggested that these agents are becoming an increasing threat to the whole world community. The following article gives a condensed overview on the history of use and development of the more prominent chemical and biological warfare agents.

Effects of lactoferrin derived peptides on simulants of biological warfare agents.

PubMed

Sijbrandij, Tjitske; Ligtenberg, Antoon J; Nazmi, Kamran; Veerman, Enno C I; Bolscher, Jan G M; Bikker, Floris J

2017-01-01

Lactoferrin (LF) is an important immune protein in neutrophils and secretory fluids of mammals. Bovine LF (bLF) harbours two antimicrobial stretches, lactoferricin and lactoferampin, situated in close proximity in the N1 domain. To mimic these antimicrobial domain parts a chimeric peptide (LFchimera) has been constructed comprising parts of both stretches (LFcin17-30 and LFampin265-284). To investigate the potency of this construct to combat a set of Gram positive and Gram negative bacteria which are regarded as simulants for biological warfare agents, the effect on bacterial killing, membrane permeability and membrane polarity were determined in comparison to the constituent peptides and the native bLF. Furthermore we aimed to increase the antimicrobial potency of the bLF derived peptides by cationic amino acid substitutions. Overall, the bactericidal activity of the peptides could be related to membrane disturbing effects, i.e. membrane permeabilization and depolarization. Those effects were most prominent for the LFchimera. Arginine residues were found to be crucial for displaying antimicrobial activity, as lysine to arginine substitutions resulted in an increased antimicrobial activity, affecting mostly LFampin265-284 whereas arginine to lysine substitutions resulted in a decreased bactericidal activity, predominantly in case of LFcin17-30.

Biomaterials for mediation of chemical and biological warfare agents.

PubMed

Russell, Alan J; Berberich, Jason A; Drevon, Geraldine F; Koepsel, Richard R

2003-01-01

Recent events have emphasized the threat from chemical and biological warfare agents. Within the efforts to counter this threat, the biocatalytic destruction and sensing of chemical and biological weapons has become an important area of focus. The specificity and high catalytic rates of biological catalysts make them appropriate for decommissioning nerve agent stockpiles, counteracting nerve agent attacks, and remediation of organophosphate spills. A number of materials have been prepared containing enzymes for the destruction of and protection against organophosphate nerve agents and biological warfare agents. This review discusses the major chemical and biological warfare agents, decontamination methods, and biomaterials that have potential for the preparation of decontamination wipes, gas filters, column packings, protective wear, and self-decontaminating paints and coatings.

Simulations of population dynamics of hemlock woolly adelgid and potential impact of biological control agents

Treesearch

Joseph S. Elkinton; Robert T. Trotter; Ann F. Paradis

2011-01-01

The hemlock woolly adelgid (Adelges tsugae) is a small invasive Hemipteran herbivore that threatens the continued presence and abundance of hemlock in eastern North America. Efforts to control the adelgid have focused on the introduction of classical biological control agents. These biological controls include six different species of predatory...

Babybot: a biologically inspired developing robotic agent

NASA Astrophysics Data System (ADS)

Metta, Giorgio; Panerai, Francesco M.; Sandini, Giulio

2000-10-01

The study of development, either artificial or biological, can highlight the mechanisms underlying learning and adaptive behavior. We shall argue whether developmental studies might provide a different and potentially interesting perspective either on how to build an artificial adaptive agent, or on understanding how the brain solves sensory, motor, and cognitive tasks. It is our opinion that the acquisition of the proper behavior might indeed be facilitated because within an ecological context, the agent, its adaptive structure and the environment dynamically interact thus constraining the otherwise difficult learning problem. In very general terms we shall describe the proposed approach and supporting biological related facts. In order to further analyze these aspects from the modeling point of view, we shall demonstrate how a twelve degrees of freedom baby humanoid robot acquires orienting and reaching behaviors, and what advantages the proposed framework might offer. In particular, the experimental setup consists of five degrees-of-freedom (dof) robot head, and an off-the-shelf six dof robot manipulator, both mounted on a rotating base: i.e. the torso. From the sensory point of view, the robot is equipped with two space-variant cameras, an inertial sensor simulating the vestibular system, and proprioceptive information through motor encoders. The biological parallel is exploited at many implementation levels. It is worth mentioning, for example, the space- variant eyes, exploiting foveal and peripheral vision in a single arrangement, the inertial sensor providing efficient image stabilization (vestibulo-ocular reflex).

Indirect effects of host-specific biological control agents

Treesearch

Dean E. Pearson; Ragan M. Callaway

2003-01-01

Biological control is a crucial tool in the battle against biological invasions, but biocontrol agents can have a deleterious impact on native species. Recognition of risks associated with host shifting has increased the emphasis on host specificity of biocontrol agents for invasive weeds. However, recent studies indicate host-specific biocontrol agents can...

Biological agents for controlling excessive scarring.

PubMed

Berman, Brian

2010-01-01

The potential of various biological agents to reduce or prevent excessive scar formation has now been evaluated in numerous in-vitro studies, experimental animal models and preliminary clinical trials, in some cases with particularly promising results. Perhaps prominent among this group of biological agents, and, to some degree, possibly representing marketed compounds already being used 'off label' to manage excessive scarring, are the tumor necrosis factor alpha antagonist etanercept, and immune-response modifiers such as IFNalpha2b and imiquimod. Additional assessment of these novel agents is now justified with a view to reducing or preventing hypertrophic scars, keloid scars and the recurrence of post-excision keloid lesions.

Agent-based model of angiogenesis simulates capillary sprout initiation in multicellular networks

PubMed Central

Walpole, J.; Chappell, J.C.; Cluceru, J.G.; Mac Gabhann, F.; Bautch, V.L.; Peirce, S. M.

2015-01-01

Many biological processes are controlled by both deterministic and stochastic influences. However, efforts to model these systems often rely on either purely stochastic or purely rule-based methods. To better understand the balance between stochasticity and determinism in biological processes a computational approach that incorporates both influences may afford additional insight into underlying biological mechanisms that give rise to emergent system properties. We apply a combined approach to the simulation and study of angiogenesis, the growth of new blood vessels from existing networks. This complex multicellular process begins with selection of an initiating endothelial cell, or tip cell, which sprouts from the parent vessels in response to stimulation by exogenous cues. We have constructed an agent-based model of sprouting angiogenesis to evaluate endothelial cell sprout initiation frequency and location, and we have experimentally validated it using high-resolution time-lapse confocal microscopy. ABM simulations were then compared to a Monte Carlo model, revealing that purely stochastic simulations could not generate sprout locations as accurately as the rule-informed agent-based model. These findings support the use of rule-based approaches for modeling the complex mechanisms underlying sprouting angiogenesis over purely stochastic methods. PMID:26158406

Agent-based model of angiogenesis simulates capillary sprout initiation in multicellular networks.

PubMed

Walpole, J; Chappell, J C; Cluceru, J G; Mac Gabhann, F; Bautch, V L; Peirce, S M

2015-09-01

Many biological processes are controlled by both deterministic and stochastic influences. However, efforts to model these systems often rely on either purely stochastic or purely rule-based methods. To better understand the balance between stochasticity and determinism in biological processes a computational approach that incorporates both influences may afford additional insight into underlying biological mechanisms that give rise to emergent system properties. We apply a combined approach to the simulation and study of angiogenesis, the growth of new blood vessels from existing networks. This complex multicellular process begins with selection of an initiating endothelial cell, or tip cell, which sprouts from the parent vessels in response to stimulation by exogenous cues. We have constructed an agent-based model of sprouting angiogenesis to evaluate endothelial cell sprout initiation frequency and location, and we have experimentally validated it using high-resolution time-lapse confocal microscopy. ABM simulations were then compared to a Monte Carlo model, revealing that purely stochastic simulations could not generate sprout locations as accurately as the rule-informed agent-based model. These findings support the use of rule-based approaches for modeling the complex mechanisms underlying sprouting angiogenesis over purely stochastic methods.

Indirect nontarget effects of host-specific biological control agents: Implications for biological control

Treesearch

Dean E. Pearson; Ragan M. Callaway

2005-01-01

Classical biological control of weeds currently operates under the assumption that biological control agents are safe (i.e., low risk) if they do not directly attack nontarget species. However, recent studies indicate that even highly host-specific biological control agents can impact nontarget species through indirect effects. This finding has profound...

Multi-agent-based bio-network for systems biology: protein-protein interaction network as an example.

PubMed

Ren, Li-Hong; Ding, Yong-Sheng; Shen, Yi-Zhen; Zhang, Xiang-Feng

2008-10-01

Recently, a collective effort from multiple research areas has been made to understand biological systems at the system level. This research requires the ability to simulate particular biological systems as cells, organs, organisms, and communities. In this paper, a novel bio-network simulation platform is proposed for system biology studies by combining agent approaches. We consider a biological system as a set of active computational components interacting with each other and with an external environment. Then, we propose a bio-network platform for simulating the behaviors of biological systems and modelling them in terms of bio-entities and society-entities. As a demonstration, we discuss how a protein-protein interaction (PPI) network can be seen as a society of autonomous interactive components. From interactions among small PPI networks, a large PPI network can emerge that has a remarkable ability to accomplish a complex function or task. We also simulate the evolution of the PPI networks by using the bio-operators of the bio-entities. Based on the proposed approach, various simulators with different functions can be embedded in the simulation platform, and further research can be done from design to development, including complexity validation of the biological system.

Solid-water detoxifying reagents for chemical and biological agents

DOEpatents

Hoffman, Dennis M [Livermore, CA; Chiu, Ing Lap [Castro Valley, CA

2006-04-18

Formation of solid-water detoxifying reagents for chemical and biological agents. Solutions of detoxifying reagent for chemical and biological agents are coated using small quantities of hydrophobic nanoparticles by vigorous agitation or by aerosolization of the solution in the presence of the hydrophobic nanoparticles to form a solid powder. For example, when hydrophobic fumed silica particles are shaken in the presence of IN oxone solution in approximately a 95:5-weight ratio, a dry powder results. The hydrophobic silica forms a porous coating of insoluble fine particles around the solution. Since the chemical or biological agent tends to be hydrophobic on contact with the weakly encapsulated detoxifying solution, the porous coating breaks down and the detoxifying reagent is delivered directly to the chemical or biological agent for maximum concentration at the point of need. The solid-water (coated) detoxifying solutions can be blown into contaminated ventilation ducting or other difficult to reach sites for detoxification of pools of chemical or biological agent. Once the agent has been detoxified, it can be removed by flushing the area with air or other techniques.

Transport behavior of surrogate biological warfare agents in a simulated landfill: effect of leachate recirculation and water infiltration.

PubMed

Saikaly, Pascal E; Hicks, Kristin; Barlaz, Morton A; de Los Reyes, Francis L

2010-11-15

An understanding of the transport behavior of biological warfare (BW) agents in landfills is required to evaluate the suitability of landfills for the disposal of building decontamination residue (BDR) following a bioterrorist attack on a building. Surrogate BW agents, Bacillus atrophaeus spores and Serratia marcescens, were spiked into simulated landfill reactors that were filled with synthetic building debris (SBD) and operated for 4 months with leachate recirculation or water infiltration. Quantitative polymerase chain reaction (Q-PCR) was used to monitor surrogate transport. In the leachate recirculation reactors, <10% of spiked surrogates were eluted in leachate over 4 months. In contrast, 45% and 31% of spiked S. marcescens and B. atrophaeus spores were eluted in leachate in the water infiltration reactors. At the termination of the experiment, the number of retained cells and spores in SBD was measured over the depth of the reactor. Less than 3% of the total spiked S. marcescens cells and no B. atrophaeus spores were detected in SBD. These results suggest that significant fractions of the spiked surrogates were strongly attached to SBD.

Preapproval and postapproval availability of published comparative efficacy research on biological agents.

PubMed

Thomas, Rachel Hutchins; Freeman, Maisha Kelly; Hughes, Peter J

2013-07-15

Preapproval and postapproval availability of published comparative efficacy studies on biological agents approved between 2000 and 2010 was investigated. Approval packages published on the Food and Drug Administration (FDA) website were examined for all biological agents approved between 2000 and 2010 to determine if comparative efficacy studies were available at the time of FDA approval. The availability of comparative efficacy studies published subsequent to approval was determined by searching PubMed for randomized, active-controlled experimental or observational study designs that measured efficacy as the primary endpoint and were relevant to the original FDA-approved indication. From 2000 to 2010, 107 biological agents were approved by FDA. Of the biological agents with alternative treatments, 54.6% had comparative efficacy data available at the time of approval. Although standard-reviewed biological agents were more likely to have comparative efficacy trials included in the FDA approval packages than priority-reviewed biological agents, statistically significant differences are unlikely. Subsequent to approval, 58.1% of biological agents had at least one published comparative efficacy trial, representing a 3.5% absolute increase in the availability of comparative efficacy studies since the time of approval. Vaccines and biological agents in the hematologic diseases, oncology, and miscellaneous diseases classes had fewer published postapproval comparative efficacy studies per agent compared with the overall group of biological agents. Nearly half of all biological agents approved for marketing between 2000 and 2010 lacked publicly accessible, active-controlled efficacy studies at the time of drug approval; a slightly greater proportion of biological agents had comparative efficacy data published subsequent to their approval.

Simulating cancer growth with multiscale agent-based modeling.

PubMed

Wang, Zhihui; Butner, Joseph D; Kerketta, Romica; Cristini, Vittorio; Deisboeck, Thomas S

2015-02-01

There have been many techniques developed in recent years to in silico model a variety of cancer behaviors. Agent-based modeling is a specific discrete-based hybrid modeling approach that allows simulating the role of diversity in cell populations as well as within each individual cell; it has therefore become a powerful modeling method widely used by computational cancer researchers. Many aspects of tumor morphology including phenotype-changing mutations, the adaptation to microenvironment, the process of angiogenesis, the influence of extracellular matrix, reactions to chemotherapy or surgical intervention, the effects of oxygen and nutrient availability, and metastasis and invasion of healthy tissues have been incorporated and investigated in agent-based models. In this review, we introduce some of the most recent agent-based models that have provided insight into the understanding of cancer growth and invasion, spanning multiple biological scales in time and space, and we further describe several experimentally testable hypotheses generated by those models. We also discuss some of the current challenges of multiscale agent-based cancer models. Copyright © 2014 Elsevier Ltd. All rights reserved.

Simulating Cancer Growth with Multiscale Agent-Based Modeling

PubMed Central

Wang, Zhihui; Butner, Joseph D.; Kerketta, Romica; Cristini, Vittorio; Deisboeck, Thomas S.

2014-01-01

There have been many techniques developed in recent years to in silico model a variety of cancer behaviors. Agent-based modeling is a specific discrete-based hybrid modeling approach that allows simulating the role of diversity in cell populations as well as within each individual cell; it has therefore become a powerful modeling method widely used by computational cancer researchers. Many aspects of tumor morphology including phenotype-changing mutations, the adaptation to microenvironment, the process of angiogenesis, the influence of extracellular matrix, reactions to chemotherapy or surgical intervention, the effects of oxygen and nutrient availability, and metastasis and invasion of healthy tissues have been incorporated and investigated in agent-based models. In this review, we introduce some of the most recent agent-based models that have provided insight into the understanding of cancer growth and invasion, spanning multiple biological scales in time and space, and we further describe several experimentally testable hypotheses generated by those models. We also discuss some of the current challenges of multiscale agent-based cancer models. PMID:24793698

[Occupational exposure to biological agents intentionally used in Polish enterprises].

PubMed

Kozajda, Anna; Szadkowska-Stańczyk, Irena

2015-01-01

The paper presents the intentional use of biological agents for industrial, diagnostic and research purposes in Polish enterprises. The National Register of Biological Agents (Krajowy Rejestr Czynników Biologicznych - KRCB) is an online database that collects the data on the intentional use of biological agents at work in Poland. As of December 2013 there were 533 notifications in KRCB, mainly for diagnostic (73%), research (20%) and industrial purposes (7%). Mostly there were hospital diagnostic laboratories (37%), and other laboratories (35%), as well as higher education and research institutions (11%). In total, 4015 workers (91.7% of women, 8.3% of men) were exposed tobiological agents. Agents classified in risk group 2 were used in 518 enterprises, and in risk group 3 in 107 enterprises. Of those agents the following bacteria were the most frequently used: Escherichia coli except for non-pathogenic strains (455 enterprises and 3314 exposed workers); Staphylococcus aureus (445 and 3270); and Pseudomonas aeruginosa (406 and 2969, respectively). In 66 enterprises there were used biological agents recognized by the International Agency for Research on Cancer (IARC) as carcinogens. They are viruses: Epstein-Barr (7 enterprises, 181 exposed workers); hepatitis B (16 and 257); hepatitis C virus (15 and 243); human immunodefi- ciency virus (8 and 107); human papillomaviruses (2 and 4); parasites: Clonorchis viverrini (1 and 2 ); Clonorchos sinensis (1 and 2); Schistosoma haematobium (1 and 2) and bacteria Helicobacter pylori; (15 and 230, respectively). The National Register of Biological Agents at Work permits to evaluate the situation of occupational exposure to biological agents used intentionally in enterprises in Poland.

Formalizing Knowledge in Multi-Scale Agent-Based Simulations

PubMed Central

Somogyi, Endre; Sluka, James P.; Glazier, James A.

2017-01-01

Multi-scale, agent-based simulations of cellular and tissue biology are increasingly common. These simulations combine and integrate a range of components from different domains. Simulations continuously create, destroy and reorganize constituent elements causing their interactions to dynamically change. For example, the multi-cellular tissue development process coordinates molecular, cellular and tissue scale objects with biochemical, biomechanical, spatial and behavioral processes to form a dynamic network. Different domain specific languages can describe these components in isolation, but cannot describe their interactions. No current programming language is designed to represent in human readable and reusable form the domain specific knowledge contained in these components and interactions. We present a new hybrid programming language paradigm that naturally expresses the complex multi-scale objects and dynamic interactions in a unified way and allows domain knowledge to be captured, searched, formalized, extracted and reused. PMID:29338063

Formalizing Knowledge in Multi-Scale Agent-Based Simulations.

PubMed

Somogyi, Endre; Sluka, James P; Glazier, James A

2016-10-01

Multi-scale, agent-based simulations of cellular and tissue biology are increasingly common. These simulations combine and integrate a range of components from different domains. Simulations continuously create, destroy and reorganize constituent elements causing their interactions to dynamically change. For example, the multi-cellular tissue development process coordinates molecular, cellular and tissue scale objects with biochemical, biomechanical, spatial and behavioral processes to form a dynamic network. Different domain specific languages can describe these components in isolation, but cannot describe their interactions. No current programming language is designed to represent in human readable and reusable form the domain specific knowledge contained in these components and interactions. We present a new hybrid programming language paradigm that naturally expresses the complex multi-scale objects and dynamic interactions in a unified way and allows domain knowledge to be captured, searched, formalized, extracted and reused.

Towards the implementation of a spectral database for the detection of biological warfare agents

NASA Astrophysics Data System (ADS)

Carestia, M.; Pizzoferrato, R.; Gelfusa, M.; Cenciarelli, O.; D'Amico, F.; Malizia, A.; Scarpellini, D.; Murari, A.; Vega, J.; Gaudio, P.

2014-10-01

The deliberate use of biological warfare agents (BWA) and other pathogens can jeopardize the safety of population, fauna and flora, and represents a concrete concern from the military and civil perspective. At present, the only commercially available tools for fast warning of a biological attack can perform point detection and require active or passive sampling collection. The development of a stand-off detection system would be extremely valuable to minimize the risk and the possible consequences of the release of biological aerosols in the atmosphere. Biological samples can be analyzed by means of several optical techniques, covering a broad region of the electromagnetic spectrum. Strong evidence proved that the informative content of fluorescence spectra could provide good preliminary discrimination among those agents and it can also be obtained through stand-off measurements. Such a system necessitates a database and a mathematical method for the discrimination of the spectral signatures. In this work, we collected fluorescence emission spectra of the main BWA simulants, to implement a spectral signature database and apply the Universal Multi Event Locator (UMEL) statistical method. Our preliminary analysis, conducted in laboratory conditions with a standard UV lamp source, considers the main experimental setups influencing the fluorescence signature of some of the most commonly used BWA simulants. Our work represents a first step towards the implementation of a spectral database and a laser-based biological stand-off detection and identification technique.

Biological agents and respiratory infections: Causative mechanisms and practice management.

PubMed

Takayanagi, Noboru

2015-09-01

Biological agents are increasingly being used to treat patients with immune-mediated inflammatory disease. In Japan, currently approved biological agents for patients with rheumatoid arthritis (RA) include tumor necrosis factor inhibitors, interleukin-6 receptor-blocking monoclonal antibody, and T-cell costimulation inhibitor. Rheumatologists have recognized that safety issues are critical aspects of treatment decisions in RA. Therefore, a wealth of safety data has been gathered from a number of sources, including randomized clinical trials and postmarketing data from large national registries. These data revealed that the most serious adverse events from these drugs are respiratory infections, especially pneumonia, tuberculosis, nontuberculous mycobacteriosis, and Pneumocystis jirovecii pneumonia, and that the most common risk factors associated with these respiratory infections are older age, concomitant corticosteroid use, and underlying respiratory comorbidities. Because of this background, in 2014, the Japanese Respiratory Society published their consensus statement of biological agents and respiratory disorders. This review summarizes this statement and adds recent evidence, especially concerning respiratory infections in RA patients, biological agents and respiratory infections, and practice management of respiratory infections in patients treated with biological agents. To decrease the incidence of infections and reduce mortality, we should know the epidemiology, risk factors, management, and methods of prevention of respiratory infections in patients receiving biological agents. Copyright © 2015 The Japanese Respiratory Society. Published by Elsevier B.V. All rights reserved.

An agent-based method for simulating porous fluid-saturated structures with indistinguishable components

NASA Astrophysics Data System (ADS)

Kashani, Jamal; Pettet, Graeme John; Gu, YuanTong; Zhang, Lihai; Oloyede, Adekunle

2017-10-01

Single-phase porous materials contain multiple components that intermingle up to the ultramicroscopic level. Although the structures of the porous materials have been simulated with agent-based methods, the results of the available methods continue to provide patterns of distinguishable solid and fluid agents which do not represent materials with indistinguishable phases. This paper introduces a new agent (hybrid agent) and category of rules (intra-agent rule) that can be used to create emergent structures that would more accurately represent single-phase structures and materials. The novel hybrid agent carries the characteristics of system's elements and it is capable of changing within itself, while also responding to its neighbours as they also change. As an example, the hybrid agent under one-dimensional cellular automata formalism in a two-dimensional domain is used to generate patterns that demonstrate the striking morphological and characteristic similarities with the porous saturated single-phase structures where each agent of the ;structure; carries semi-permeability property and consists of both fluid and solid in space and at all times. We conclude that the ability of the hybrid agent to change locally provides an enhanced protocol to simulate complex porous structures such as biological tissues which could facilitate models for agent-based techniques and numerical methods.

Biological control agents elevate hantavirus by subsidizing deer mouse populations

Treesearch

Dean E. Pearson; Ragan M. Callaway

2006-01-01

Biological control of exotic invasive plants using exotic insects is practiced under the assumption that biological control agents are safe if they do not directly attack non-target species. We tested this assumption by evaluating the potential for two host-specific biological control agents (Urophora spp.), widely established in North America for spotted...

Biocellion: accelerating computer simulation of multicellular biological system models

PubMed Central

Kang, Seunghwa; Kahan, Simon; McDermott, Jason; Flann, Nicholas; Shmulevich, Ilya

2014-01-01

Motivation: Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming. Results: We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies. Availability and implementation: Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information. Contact: seunghwa.kang@pnnl.gov PMID:25064572

Simulating Biological and Non-Biological Motion

ERIC Educational Resources Information Center

Bruzzo, Angela; Gesierich, Benno; Wohlschlager, Andreas

2008-01-01

It is widely accepted that the brain processes biological and non-biological movements in distinct neural circuits. Biological motion, in contrast to non-biological motion, refers to active movements of living beings. Aim of our experiment was to investigate the mechanisms underlying mental simulation of these two movement types. Subjects had to…

[Decontamination of chemical and biological warfare agents].

PubMed

Seto, Yasuo

2009-01-01

Chemical and biological warfare agents (CBWA's) are diverse in nature; volatile acute low-molecular-weight toxic compounds, chemical warfare agents (CWA's, gaseous choking and blood agents, volatile nerve gases and blister agents, nonvolatile vomit agents and lacrymators), biological toxins (nonvolatile low-molecular-weight toxins, proteinous toxins) and microbes (bacteria, viruses, rickettsiae). In the consequence management against chemical and biological terrorism, speedy decontamination of victims, facilities and equipment is required for the minimization of the damage. In the present situation, washing victims and contaminated materials with large volumes of water is the basic way, and additionally hypochlorite salt solution is used for decomposition of CWA's. However, it still remains unsolved how to dispose large volumes of waste water, and the decontamination reagents have serious limitation of high toxicity, despoiling nature against the environments, long finishing time and non-durability in effective decontamination. Namely, the existing decontamination system is not effective, nonspecifically affecting the surrounding non-target materials. Therefore, it is the urgent matter to build up the usable decontamination system surpassing the present technologies. The symposiast presents the on-going joint project of research and development of the novel decontamination system against CBWA's, in the purpose of realizing nontoxic, fast, specific, effective and economical terrorism on-site decontamination. The projects consists of (1) establishment of the decontamination evaluation methods and verification of the existing technologies and adaptation of bacterial organophosphorus hydrolase, (2) development of adsorptive elimination technologies using molecular recognition tools, and (4) development of deactivation technologies using photocatalysis.

High performance cellular level agent-based simulation with FLAME for the GPU.

PubMed

Richmond, Paul; Walker, Dawn; Coakley, Simon; Romano, Daniela

2010-05-01

Driven by the availability of experimental data and ability to simulate a biological scale which is of immediate interest, the cellular scale is fast emerging as an ideal candidate for middle-out modelling. As with 'bottom-up' simulation approaches, cellular level simulations demand a high degree of computational power, which in large-scale simulations can only be achieved through parallel computing. The flexible large-scale agent modelling environment (FLAME) is a template driven framework for agent-based modelling (ABM) on parallel architectures ideally suited to the simulation of cellular systems. It is available for both high performance computing clusters (www.flame.ac.uk) and GPU hardware (www.flamegpu.com) and uses a formal specification technique that acts as a universal modelling format. This not only creates an abstraction from the underlying hardware architectures, but avoids the steep learning curve associated with programming them. In benchmarking tests and simulations of advanced cellular systems, FLAME GPU has reported massive improvement in performance over more traditional ABM frameworks. This allows the time spent in the development and testing stages of modelling to be drastically reduced and creates the possibility of real-time visualisation for simple visual face-validation.

Biocellion: accelerating computer simulation of multicellular biological system models.

PubMed

Kang, Seunghwa; Kahan, Simon; McDermott, Jason; Flann, Nicholas; Shmulevich, Ilya

2014-11-01

Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming. We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies. Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Virtual agents in a simulated virtual training environment

NASA Technical Reports Server (NTRS)

Achorn, Brett; Badler, Norman L.

1993-01-01

A drawback to live-action training simulations is the need to gather a large group of participants in order to train a few individuals. One solution to this difficulty is the use of computer-controlled agents in a virtual training environment. This allows a human participant to be replaced by a virtual, or simulated, agent when only limited responses are needed. Each agent possesses a specified set of behaviors and is capable of limited autonomous action in response to its environment or the direction of a human trainee. The paper describes these agents in the context of a simulated hostage rescue training session, involving two human rescuers assisted by three virtual (computer-controlled) agents and opposed by three other virtual agents.

Biologic agents therapy for Saudi children with rheumatic diseases: indications and safety.

PubMed

Al-Mayouf, Sulaiman M; Alenazi, Abdullatif; AlJasser, Hind

2016-06-01

To report the indications and safety of biologic agents in childhood rheumatic diseases at a tertiary hospital. Children with rheumatic diseases treated with biologic agents at King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia, from January 2001 to December 2011 were included. All patients were reviewed for: demographic characteristics, diagnosis, concomitant treatment and indications of using biologic agents, age at start of therapy and side effects during the treatment period. In all, 134 children (89 female) with various rheumatic diseases were treated with biologic agents. Mean age at starting biologic treatment was 9.3 (4.25-14) years and mean therapy duration was 14.7 (3-88) months. Juvenile idiopathic arthritis (JIA) was the most frequent diagnosis (70.1%) followed by systemic lupus erythematosus (12.7%) and vasculitis (4.5%). All patients received concomitant therapy (corticosteroids and disease-modifying antirheumatic drugs). In total, 273 treatments with biologic agents were used, (95 etanercept, 52 rituximab, 47 adalimumab, 37 infliximab, 23 anakinra, 10 tocilizumab and nine abatacept). Therapy was switched to another agent in 57 (42.5%) patients, mainly because of inefficacy (89.4%) or adverse event (10.6%). A total of 95 (34.8%) adverse events were notified; of these, the most frequent were infusion-related reactions (33.7%) followed by infections (24.2%) and autoantibody positivity (10.6%). One patient developed macrophage activation syndrome. Biologic agents were used in children with a range of rheumatic diseases. Of these, the most frequent was JIA. Off-label use of biologic agents in our cohort is common. These agents seem safe. However, they may associated with various adverse events. Sequential therapy seems well tolerated. However, this should be carefully balanced and considered on an individual basis. © 2014 Asia Pacific League of Associations for Rheumatology and Wiley Publishing Asia Pty Ltd.

Biological control agents elevate hantavirus by subsidizing deer mouse populations.

PubMed

Pearson, Dean E; Callaway, Ragan M

2006-04-01

Biological control of exotic invasive plants using exotic insects is practiced under the assumption that biological control agents are safe if they do not directly attack non-target species. We tested this assumption by evaluating the potential for two host-specific biological control agents (Urophora spp.), widely established in North America for spotted knapweed (Centaurea maculosa) control, to indirectly elevate Sin Nombre hantavirus by providing food subsidies to populations of deer mice (Peromyscus maniculatus), the primary reservoir for the virus. We show that seropositive deer mice (mice testing positive for hantavirus) were over three times more abundant in the presence of the biocontrol food subsidy. Elevating densities of seropositive mice may increase risk of hantavirus infection in humans and significantly alter hantavirus ecology. Host specificity alone does not ensure safe biological control. To minimize indirect risks to non-target species, biological control agents must suppress pest populations enough to reduce their own numbers.

Oxidative decontamination of chemical and biological warfare agents using L-Gel.

PubMed

Raber, Ellen; McGuire, Raymond

2002-08-05

A decontamination method has been developed using a single reagent that is effective both against chemical warfare (CW) and biological warfare (BW) agents. The new reagent, "L-Gel", consists of an aqueous solution of a mild commercial oxidizer, Oxone, together with a commercial fumed silica gelling agent, Cab-O-Sil EH-5. L-Gel is non-toxic, environmentally friendly, relatively non-corrosive, maximizes contact time because of its thixotropic nature, clings to walls and ceilings, and does not harm carpets or painted surfaces. The new reagent also addresses the most demanding requirements for decontamination in the civilian sector, including availability, low maintenance, ease of application and deployment by a variety of dispersal mechanisms, minimal training and acceptable expense. Experiments to test the effectiveness of L-Gel were conducted at Lawrence Livermore National Laboratory and independently at four other locations. L-Gel was tested against all classes of chemical warfare agents and against various biological warfare agent surrogates, including spore-forming bacteria and non-virulent strains of real biological agents. Testing showed that L-Gel is as effective against chemical agents and biological materials, including spores, as the best military decontaminants.

Non-target effects of an introduced biological control agent on deer mouse ecology

Treesearch

Dean E. Pearson; Kevin S. McKelvey; Leonard F. Ruggiero

2000-01-01

Release of exotic insects as biological control agents is a common approach to controlling exotic plants. Though controversy has ensued regarding the deleterious direct effects of biological control agents to non-target species, few have examined the indirect effects of a "well-behaved" biological control agent on native fauna. We studied a grassland in west-...

Development of a persistent chemical agent simulation system

NASA Technical Reports Server (NTRS)

1983-01-01

A Persistent Chemical Agent Simulation System was developed (PCASS) to simulate, for force-on-force training exercises, the field environment produced by the presence of persistent chemical agents. Such a simulant system must satisfy several requirements to be of value as a training aid. Specifically, it must provide for realistic training which will generate competency in at least the following areas: (1) detection of the persistent agent presence; (2) proper use of protective equipment and procedures; (3) determination of the extent of contamination; and (4) decontamination of equipment and personnel.

Analysis of the Precursors, Simulants and Degradation Products of Chemical Warfare Agents.

PubMed

Witkiewicz, Zygfryd; Neffe, Slawomir; Sliwka, Ewa; Quagliano, Javier

2018-09-03

Recent advances in analysis of precursors, simulants and degradation products of chemical warfare agents (CWA) are reviewed. Fast and reliable analysis of precursors, simulants and CWA degradation products is extremely important at a time, when more and more terrorist groups and radical non-state organizations use or plan to use chemical weapons to achieve their own psychological, political and military goals. The review covers the open source literature analysis after the time, when the chemical weapons convention had come into force (1997). The authors stated that during last 15 years increased number of laboratories are focused not only on trace analysis of CWA (mostly nerve and blister agents) in environmental and biological samples, but the growing number of research are devoted to instrumental analysis of precursors and degradation products of these substances. The identification of low-level concentration of CWA degradation products is often more important and difficult than the original CWA, because of lower level of concentration and a very large number of compounds present in environmental and biological samples. Many of them are hydrolysis products and are present in samples in the ionic form. For this reason, two or three instrumental methods are used to perform a reliable analysis of these substances.

Validation techniques of agent based modelling for geospatial simulations

NASA Astrophysics Data System (ADS)

Darvishi, M.; Ahmadi, G.

2014-10-01

One of the most interesting aspects of modelling and simulation study is to describe the real world phenomena that have specific properties; especially those that are in large scales and have dynamic and complex behaviours. Studying these phenomena in the laboratory is costly and in most cases it is impossible. Therefore, Miniaturization of world phenomena in the framework of a model in order to simulate the real phenomena is a reasonable and scientific approach to understand the world. Agent-based modelling and simulation (ABMS) is a new modelling method comprising of multiple interacting agent. They have been used in the different areas; for instance, geographic information system (GIS), biology, economics, social science and computer science. The emergence of ABM toolkits in GIS software libraries (e.g. ESRI's ArcGIS, OpenMap, GeoTools, etc) for geospatial modelling is an indication of the growing interest of users to use of special capabilities of ABMS. Since ABMS is inherently similar to human cognition, therefore it could be built easily and applicable to wide range applications than a traditional simulation. But a key challenge about ABMS is difficulty in their validation and verification. Because of frequent emergence patterns, strong dynamics in the system and the complex nature of ABMS, it is hard to validate and verify ABMS by conventional validation methods. Therefore, attempt to find appropriate validation techniques for ABM seems to be necessary. In this paper, after reviewing on Principles and Concepts of ABM for and its applications, the validation techniques and challenges of ABM validation are discussed.

Technological advancements for the detection of and protection against biological and chemical warfare agents.

PubMed

Eubanks, Lisa M; Dickerson, Tobin J; Janda, Kim D

2007-03-01

There is a growing need for technological advancements to combat agents of chemical and biological warfare, particularly in the context of the deliberate use of a chemical and/or biological warfare agent by a terrorist organization. In this tutorial review, we describe methods that have been developed both for the specific detection of biological and chemical warfare agents in a field setting, as well as potential therapeutic approaches for treating exposure to these toxic species. In particular, nerve agents are described as a typical chemical warfare agent, and the two potent biothreat agents, anthrax and botulinum neurotoxin, are used as illustrative examples of potent weapons for which countermeasures are urgently needed.

Impact of Release Rates on the Effectiveness of Augmentative Biological Control Agents

PubMed Central

Crowder, David W.

2007-01-01

To access the effect of augmentative biological control agents, 31 articles were reviewed that investigated the impact of release rates of 35 augmentative biological control agents on the control of 42 arthropod pests. In 64% of the cases, the release rate of the biological control agent did not significantly affect the density or mortality of the pest insect. Results where similar when parasitoidsor predators were utilized as the natural enemy. Within any order of natural enemy, there were more cases where release rates did not affect augmentative biological control than cases where release rates were significant. There were more cases in which release rates did not affect augmentative biological control when pests were from the orders Hemiptera, Acari, or Diptera, but not with pests from the order Lepidoptera. In most cases, there was an optimal release rate that produced effective control of a pest species. This was especially true when predators were used as a biological control agent. Increasing the release rate above the optimal rate did not improve control of the pest and thus would be economically detrimental. Lower release rates were of ten optimal when biological control was used in conjunction with insecticides. In many cases, the timing and method of biological control applications were more significant factors impacting the effectiveness of biological control than the release rate. Additional factors that may limit the relative impact of release rates include natural enemy fecundity, establishment rates, prey availability, dispersal, and cannibalism. PMID:20307240

Exploration of Force Transition in Stability Operations Using Multi-Agent Simulation

DTIC Science & Technology

2006-09-01

risk, mission failure risk, and time in the context of the operational threat environment. The Pythagoras Multi-Agent Simulation and Data Farming...NUMBER OF PAGES 173 14. SUBJECT TERMS Stability Operations, Peace Operations, Data Farming, Pythagoras , Agent- Based Model, Multi-Agent Simulation...the operational threat environment. The Pythagoras Multi-Agent Simulation and Data Farming techniques are used to investigate force-level

Fiber-optic microsphere-based arrays for multiplexed biological warfare agent detection.

PubMed

Song, Linan; Ahn, Soohyoun; Walt, David R

2006-02-15

We report a multiplexed high-density DNA array capable of rapid, sensitive, and reliable identification of potential biological warfare agents. An optical fiber bundle containing 6000 individual 3.1-mum-diameter fibers was chemically etched to yield microwells and used as the substrate for the array. Eighteen different 50-mer single-stranded DNA probes were covalently attached to 3.1-mum microspheres. Probe sequences were designed for Bacillus anthracis, Yersinia pestis, Francisella tularensis, Brucella melitensis, Clostridium botulinum, Vaccinia virus, and one biological warfare agent (BWA) simulant, Bacillus thuringiensis kurstaki. The microspheres were distributed into the microwells to form a randomized multiplexed high-density DNA array. A detection limit of 10 fM in a 50-microL sample volume was achieved within 30 min of hybridization for B. anthracis, Y. pestis, Vaccinia virus, and B. thuringiensis kurstaki. We used both specific responses of probes upon hybridization to complementary targets as well as response patterns of the multiplexed array to identify BWAs with high accuracy. We demonstrated the application of this multiplexed high-density DNA array for parallel identification of target BWAs in spiked sewage samples after PCR amplification. The array's miniaturized feature size, fabrication flexibility, reusability, and high reproducibility may enable this array platform to be integrated into a highly sensitive, specific, and reliable portable instrument for in situ BWA detection.

Biological Select Agents and Toxins: Risk-Based Assessment Management and Oversight.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burnett, LouAnn Crawford; Brodsky, Benjamin H.

Sandia National Laboratories' International Biological and Chemical Threat Reduction (SNL/IBCTR) conducted, on behalf of the Federal Select Agent Program (FSAP), a review of risk assessment in modern select agent laboratories. This review and analysis consisted of literature review, interviews of FSAP staff, entities regulated by FSAP, and deliberations of an expert panel. Additionally, SNL/IBCTR reviewed oversight mechanisms used by industries, US agencies, and other countries for high-consequence risks (e.g, nuclear, chemical, or biological materials, aviation, off-shore drilling, etc.) to determine if alternate oversight mechanisms existed that might be applicable to FSAP oversight of biological select agents and toxins. This reportmore » contains five findings, based on these reviews and analyses, with recommendations and suggested actions for FSAP to consider.« less

Agent-Based Crowd Simulation Considering Emotion Contagion for Emergency Evacuation Problem

NASA Astrophysics Data System (ADS)

Faroqi, H.; Mesgari, M.-S.

2015-12-01

During emergencies, emotions greatly affect human behaviour. For more realistic multi-agent systems in simulations of emergency evacuations, it is important to incorporate emotions and their effects on the agents. In few words, emotional contagion is a process in which a person or group influences the emotions or behavior of another person or group through the conscious or unconscious induction of emotion states and behavioral attitudes. In this study, we simulate an emergency situation in an open square area with three exits considering Adults and Children agents with different behavior. Also, Security agents are considered in order to guide Adults and Children for finding the exits and be calm. Six levels of emotion levels are considered for each agent in different scenarios and situations. The agent-based simulated model initialize with the random scattering of agent populations and then when an alarm occurs, each agent react to the situation based on its and neighbors current circumstances. The main goal of each agent is firstly to find the exit, and then help other agents to find their ways. Numbers of exited agents along with their emotion levels and damaged agents are compared in different scenarios with different initialization in order to evaluate the achieved results of the simulated model. NetLogo 5.2 is used as the multi-agent simulation framework with R language as the developing language.

Physics-based agent to simulant correlations for vapor phase mass transport.

PubMed

Willis, Matthew P; Varady, Mark J; Pearl, Thomas P; Fouse, Janet C; Riley, Patrick C; Mantooth, Brent A; Lalain, Teri A

2013-12-15

Chemical warfare agent simulants are often used as an agent surrogate to perform environmental testing, mitigating exposure hazards. This work specifically addresses the assessment of downwind agent vapor concentration resulting from an evaporating simulant droplet. A previously developed methodology was used to estimate the mass diffusivities of the chemical warfare agent simulants methyl salicylate, 2-chloroethyl ethyl sulfide, di-ethyl malonate, and chloroethyl phenyl sulfide. Along with the diffusivity of the chemical warfare agent bis(2-chloroethyl) sulfide, the simulant diffusivities were used in an advection-diffusion model to predict the vapor concentrations downwind from an evaporating droplet of each chemical at various wind velocities and temperatures. The results demonstrate that the simulant-to-agent concentration ratio and the corresponding vapor pressure ratio are equivalent under certain conditions. Specifically, the relationship is valid within ranges of measurement locations relative to the evaporating droplet and observation times. The valid ranges depend on the relative transport properties of the agent and simulant, and whether vapor transport is diffusion or advection dominant. Published by Elsevier B.V.

Vaccines against biologic agents: uses and developments.

PubMed

Ales, Noel C; Katial, Rohit K

2004-03-01

Although the Geneva protocol that prohibits the use of chemical and biologic weapons was ratified in 1925, many countries failed to accept this protocol: others stipulated retaliation, and some, like the United States, did not ratify the protocol for decades. This delay allowed the continued development of chemical and biologic agents. Members of the health care community are responsible for determining the best way to protect society from the potentially devastating effects of these biologic agents. Ideally,these diseases would be prevented from ever developing into systemic illnesses. In the past, vaccination has been a successful means of eradicating disease. Vaccines remain a hopeful therapy for the future, but time is short,and there are many obstacles.Information regarding bioterrorism agents and their treatments comes mainly from dated data or from in vitro or animal studies that may not apply to human treatment and disease. Additionally, the current threat of bioterrorism does not allow enough time for accurate, well-designed,controlled studies in humans before the release of investigational vaccines. Furthermore, some human studies would not be safe or ethical. Finally,many members of society suffer from illnesses that would put them at high risk to receive prophylactic vaccination. It is therefore naive to believe that vaccines would be the ultimate protection from these agents. In addition to vaccine development, there must be concurrent investigations into disease management and treatment. Even in instances in which vaccination is known to be an effective means of disease protection. biologic agents may be presented in a manner that renders vaccines ineffective. Virulent strains of organisms may be used, more than one organism may be used in tandem to increase virulence, and strains may be selected for antibiotic and vaccine resistance. Genetically engineered strains may use virulence factors other than those targeted in vaccines, and high

Oxidizer gels for detoxification of chemical and biological agents

DOEpatents

Hoffman, Dennis M.; McGuire, Raymond R.

2002-01-01

A gel composition containing oxidizing agents and thickening or gelling agents is used to detoxify chemical and biological agents by application directly to a contaminated area. The gelling agent is a colloidal material, such as silica, alumina, or alumino-silicate clays, which forms a viscous gel that does not flow when applied to tilted or contoured surfaces. Aqueous or organic solutions of oxidizing agents can be readily gelled with less than about 30% colloidal material. Gel preparation is simple and suitable for field implementation, as the gels can be prepared at the site of decontamination and applied quickly and uniformly over an area by a sprayer. After decontamination, the residue can be washed away or vacuumed up for disposal.

Biological agents with potential for misuse: a historical perspective and defensive measures.

PubMed

Bhalla, Deepak K; Warheit, David B

2004-08-15

Biological and chemical agents capable of producing serious illness or mortality have been used in biowarfare from ancient times. Use of these agents has progressed from crude forms in early and middle ages, when snakes and infected cadavers were used as weapons in battles, to sophisticated preparations for use during and after the second World War. Cults and terrorist organizations have attempted the use of biological agents with an aim to immobilize populations or cause serious harm. The reasons for interest in these agents by individuals and organizations include relative ease of acquisition, potential for causing mass casualty or panic, modest financing requirement, availability of technology, and relative ease of delivery. The Centers for Disease Control and Prevention has classified Critical Biological Agents into three major categories. This classification was based on several criteria, which include severity of impact on human health, potential for delivery in a weapon, capacity to cause panic and special needs for development, and stockpiling of medication. Agents that could cause the greatest harm following deliberate use were placed in category A. Category B included agents capable of producing serious harm and significant mortality but of lower magnitude than category A agents. Category C included emerging pathogens that could be developed for mass dispersion in future and their potential as a major health threat. A brief description of the category A bioagents is included and the pathophysiology of two particularly prominent agents, namely anthrax and smallpox, is discussed in detail. The potential danger from biological agents and their ever increasing threat to human populations have created a need for developing technologies for their early detection, for developing treatment strategies, and for refinement of procedures to ensure survival of affected individuals so as to attain the ultimate goal of eliminating the threat from intentional use of

Biology of Leptoypha hospita (Hemiptera: Tingidae), a Potential Biological Control Agent of Chinese Privet

Treesearch

Yanzhuo Zhang; James L. Hanula; Scott Horn; Kristine Braman; Jianghua Sun

2011-01-01

The biology of Leptoypha hospita Drake et Poor (Hemiptera: Tingidae), a potential biological control agent from China for Chinese privet, Ligustrum sinense Lour., was studied in quarantine in the United States. Both nymphs and adults feed on Chinese privet mesophyll cells that lead to a bleached appearance of leaves and dieback of branch tips. L. hospita has five...

Detecting agency from the biological motion of veridical vs animated agents

PubMed Central

Kelley, William M.; Heatherton, Todd F.; Macrae, C. Neil

2007-01-01

The ability to detect agency is fundamental for understanding the social world. Underlying this capacity are neural circuits that respond to patterns of intentional biological motion in the superior temporal sulcus and temporoparietal junction. Here we show that the brain's blood oxygenation level dependent (BOLD) response to such motion is modulated by the representation of the actor. Dynamic social interactions were portrayed by either live-action agents or computer-animated agents, enacting the exact same patterns of biological motion. Using an event-related design, we found that the BOLD response associated with the perception and interpretation of agency was greater when identical physical movements were performed by real rather than animated agents. This finding has important implications for previous work on biological motion that has relied upon computer-animated stimuli and demonstrates that the neural substrates of social perception are finely tuned toward real-world agents. In addition, the response in lateral temporal areas was observed in the absence of instructions to make mental inferences, thus demonstrating the spontaneous implementation of the intentional stance. PMID:18985141

Agent-based modeling: Methods and techniques for simulating human systems

PubMed Central

Bonabeau, Eric

2002-01-01

Agent-based modeling is a powerful simulation modeling technique that has seen a number of applications in the last few years, including applications to real-world business problems. After the basic principles of agent-based simulation are briefly introduced, its four areas of application are discussed by using real-world applications: flow simulation, organizational simulation, market simulation, and diffusion simulation. For each category, one or several business applications are described and analyzed. PMID:12011407

iCrowd: agent-based behavior modeling and crowd simulator

NASA Astrophysics Data System (ADS)

Kountouriotis, Vassilios I.; Paterakis, Manolis; Thomopoulos, Stelios C. A.

2016-05-01

Initially designed in the context of the TASS (Total Airport Security System) FP-7 project, the Crowd Simulation platform developed by the Integrated Systems Lab of the Institute of Informatics and Telecommunications at N.C.S.R. Demokritos, has evolved into a complete domain-independent agent-based behavior simulator with an emphasis on crowd behavior and building evacuation simulation. Under continuous development, it reflects an effort to implement a modern, multithreaded, data-oriented simulation engine employing latest state-of-the-art programming technologies and paradigms. It is based on an extensible architecture that separates core services from the individual layers of agent behavior, offering a concrete simulation kernel designed for high-performance and stability. Its primary goal is to deliver an abstract platform to facilitate implementation of several Agent-Based Simulation solutions with applicability in several domains of knowledge, such as: (i) Crowd behavior simulation during [in/out] door evacuation. (ii) Non-Player Character AI for Game-oriented applications and Gamification activities. (iii) Vessel traffic modeling and simulation for Maritime Security and Surveillance applications. (iv) Urban and Highway Traffic and Transportation Simulations. (v) Social Behavior Simulation and Modeling.

Stable-isotope fingerprints of biological agents as forensic tools.

PubMed

Horita, Juske; Vass, Arpad A

2003-01-01

Naturally occurring stable isotopes of light elements in chemical and biological agents may possess unique "stable-isotope fingerprints" depending on their sources and manufacturing processes. To test this hypothesis, two strains of bacteria (Bacillus globigii and Erwinia agglomerans) were grown under controlled laboratory conditions. We observed that cultured bacteria cells faithfully inherited the isotopic composition (hydrogen, carbon, and nitrogen) of media waters and substrates in predictable manners in terms of bacterial metabolism and that even bacterial cells of the same strain, which grew in media water and substrates of different isotopic compositions, have readily distinguishable isotopic signatures. These "stable-isotopic fingerprints" of chemical and biological agents can be used as forensic tools in the event of biochemical terrorist attacks.

Agent 2003 Conference on Challenges in Social Simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Margaret Clemmons, ed.

Welcome to the Proceedings of the fourth in a series of agent simulation conferences cosponsored by Argonne National Laboratory and The University of Chicago. Agent 2003 is the second conference in which three Special Interest Groups from the North American Association for Computational Social and Organizational Science (NAACSOS) have been involved in planning the program--Computational Social Theory; Simulation Applications; and Methods, Toolkits and Techniques. The theme of Agent 2003, Challenges in Social Simulation, is especially relevant, as there seems to be no shortage of such challenges. Agent simulation has been applied with increasing frequency to social domains for several decades,more » and its promise is clear and increasingly visible. Like any nascent scientific methodology, however, it faces a number of problems or issues that must be addressed in order to progress. These challenges include: (1) Validating models relative to the social settings they are designed to represent; (2) Developing agents and interactions simple enough to understand but sufficiently complex to do justice to the social processes of interest; (3) Bridging the gap between empirically spare artificial societies and naturally occurring social phenomena; (4) Building multi-level models that span processes across domains; (5) Promoting a dialog among theoretical, qualitative, and empirical social scientists and area experts, on the one hand, and mathematical and computational modelers and engineers, on the other; (6) Using that dialog to facilitate substantive progress in the social sciences; and (7) Fulfilling the aspirations of users in business, government, and other application areas, while recognizing and addressing the preceding challenges. Although this list hardly exhausts the challenges the field faces, it does identify topics addressed throughout the presentations of Agent 2003. Agent 2003 is part of a much larger process in which new methods and techniques are applied

The pharmacology and toxicology of three new biologic agents used in pulmonary medicine.

PubMed

Albertson, T E; Walby, W F; Allen, R P; Tharratt, R S

1995-01-01

Biological agents have played an important role in the evolution of modern medical therapeutics. Recent advances in biologicals have in part been stimulated by the biotechnology revolution seen over the last several years. Toxicologists need to be aware of the proposed mechanisms and approved and experimental uses of these new biologic agents. Further, controversies about their use, efficacy, cost issues and potential toxicities should be known. Often these drugs are designed for small patient populations thus limiting the availability of human toxicological data bases. This paper reviews the pharmacology and toxicology of three new biologics (recombinant human DNase I, alpha 1-protease inhibitor, and nitric oxide). These agents appear to have important roles in treating specific diseases or disease states seen in pulmonary medicine.

Research on monocentric model of urbanization by agent-based simulation

NASA Astrophysics Data System (ADS)

Xue, Ling; Yang, Kaizhong

2008-10-01

Over the past years, GIS have been widely used for modeling urbanization from a variety of perspectives such as digital terrain representation and overlay analysis using cell-based data platform. Similarly, simulation of urban dynamics has been achieved with the use of Cellular Automata. In contrast to these approaches, agent-based simulation provides a much more powerful set of tools. This allows researchers to set up a counterpart for real environmental and urban systems in computer for experimentation and scenario analysis. This Paper basically reviews the research on the economic mechanism of urbanization and an agent-based monocentric model is setup for further understanding the urbanization process and mechanism in China. We build an endogenous growth model with dynamic interactions between spatial agglomeration and urban development by using agent-based simulation. It simulates the migration decisions of two main types of agents, namely rural and urban households between rural and urban area. The model contains multiple economic interactions that are crucial in understanding urbanization and industrial process in China. These adaptive agents can adjust their supply and demand according to the market situation by a learning algorithm. The simulation result shows this agent-based urban model is able to perform the regeneration and to produce likely-to-occur projections of reality.

Love-Wave Sensors Combined with Microfluidics for Fast Detection of Biological Warfare Agents

PubMed Central

Matatagui, Daniel; Fontecha, José Luis; Fernández, María Jesús; Gràcia, Isabel; Cané, Carles; Santos, José Pedro; Horrillo, María Carmen

2014-01-01

The following paper examines a time-efficient method for detecting biological warfare agents (BWAs). The method is based on a system of a Love-wave immunosensor combined with a microfluidic chip which detects BWA samples in a dynamic mode. In this way a continuous flow-through of the sample is created, promoting the reaction between antigen and antibody and allowing a fast detection of the BWAs. In order to prove this method, static and dynamic modes have been simulated and different concentrations of BWA simulants have been tested with two immunoreactions: phage M13 has been detected using the mouse monoclonal antibody anti-M13 (AM13), and the rabbit immunoglobulin (Rabbit IgG) has been detected using the polyclonal antibody goat anti-rabbit (GAR). Finally, different concentrations of each BWA simulants have been detected with a fast response time and a desirable level of discrimination among them has been achieved. PMID:25029282

Biology and preliminary host range assessment of two potential kudzu biological control agents

Treesearch

Matthew J. Fyre; Judith Hough-Goldstein; Jiang-Hua Sun

2007-01-01

Two insect species from China, Gonioctena tredecimmaclliata (Jacoby) (Coleoptera: Chrysomelidae) and Ornatalcides (Mesalcidodes) trifidus (Pascoe) (Coleoptera: Curculionidae), were studied in quarantine in the United States as potential biological control agents for kudzu, Pueraria nwntana variety Zobata (Willd.) Maesen and S. Almeida...

Modeling and simulating human teamwork behaviors using intelligent agents

NASA Astrophysics Data System (ADS)

Fan, Xiaocong; Yen, John

2004-12-01

Among researchers in multi-agent systems there has been growing interest in using intelligent agents to model and simulate human teamwork behaviors. Teamwork modeling is important for training humans in gaining collaborative skills, for supporting humans in making critical decisions by proactively gathering, fusing, and sharing information, and for building coherent teams with both humans and agents working effectively on intelligence-intensive problems. Teamwork modeling is also challenging because the research has spanned diverse disciplines from business management to cognitive science, human discourse, and distributed artificial intelligence. This article presents an extensive, but not exhaustive, list of work in the field, where the taxonomy is organized along two main dimensions: team social structure and social behaviors. Along the dimension of social structure, we consider agent-only teams and mixed human-agent teams. Along the dimension of social behaviors, we consider collaborative behaviors, communicative behaviors, helping behaviors, and the underpinning of effective teamwork-shared mental models. The contribution of this article is that it presents an organizational framework for analyzing a variety of teamwork simulation systems and for further studying simulated teamwork behaviors.

Development of a rapid method for the automatic classification of biological agents' fluorescence spectral signatures

NASA Astrophysics Data System (ADS)

Carestia, Mariachiara; Pizzoferrato, Roberto; Gelfusa, Michela; Cenciarelli, Orlando; Ludovici, Gian Marco; Gabriele, Jessica; Malizia, Andrea; Murari, Andrea; Vega, Jesus; Gaudio, Pasquale

2015-11-01

Biosecurity and biosafety are key concerns of modern society. Although nanomaterials are improving the capacities of point detectors, standoff detection still appears to be an open issue. Laser-induced fluorescence of biological agents (BAs) has proved to be one of the most promising optical techniques to achieve early standoff detection, but its strengths and weaknesses are still to be fully investigated. In particular, different BAs tend to have similar fluorescence spectra due to the ubiquity of biological endogenous fluorophores producing a signal in the UV range, making data analysis extremely challenging. The Universal Multi Event Locator (UMEL), a general method based on support vector regression, is commonly used to identify characteristic structures in arrays of data. In the first part of this work, we investigate fluorescence emission spectra of different simulants of BAs and apply UMEL for their automatic classification. In the second part of this work, we elaborate a strategy for the application of UMEL to the discrimination of different BAs' simulants spectra. Through this strategy, it has been possible to discriminate between these BAs' simulants despite the high similarity of their fluorescence spectra. These preliminary results support the use of SVR methods to classify BAs' spectral signatures.

Biological warfare agents as threats to potable water.

PubMed Central

Burrows, W D; Renner, S E

1999-01-01

Nearly all known biological warfare agents are intended for aerosol application. Although less effective as potable water threats, many are potentially capable of inflicting heavy casualties when ingested. Significant loss of mission capability can be anticipated even when complete recovery is possible. Properly maintained field army water purification equipment can counter this threat, but personnel responsible for the operation and maintenance of the equipment may be most at risk of exposure. Municipal water treatment facilities would be measurably less effective. Some replicating (infectious) agents and a few biotoxins are inactivated by chlorine disinfection; for others chlorine is ineffective or of unknown efficacy. This report assesses the state of our knowledge of agents as potable water threats and contemplates the consequences of intentional or collateral contamination of potable water supplies by 18 replicating agents and 9 biotoxins known or likely to be weaponized or otherwise used as threats. PMID:10585901

Functional Agents to Biologically Control Deoxynivalenol Contamination in Cereal Grains

PubMed Central

Tian, Ye; Tan, Yanglan; Liu, Na; Liao, Yucai; Sun, Changpo; Wang, Shuangxia; Wu, Aibo

2016-01-01

Mycotoxins, as microbial secondary metabolites, frequently contaminate cereal grains and pose a serious threat to human and animal health around the globe. Deoxynivalenol (DON), a commonly detected Fusarium mycotoxin, has drawn utmost attention due to high exposure levels and contamination frequency in the food chain. Biological control is emerging as a promising technology for the management of DON contamination. Functional biological control agents (BCAs), which include antagonistic microbes, natural fungicides derived from plants and detoxification enzymes, can be used to control DON contamination at different stages of grain production. In this review, studies regarding different biological agents for DON control in recent years are summarized for the first time. Furthermore, this article highlights the significance of BCAs for controlling DON contamination, as well as the need for more practical and efficient BCAs concerning food safety. PMID:27064760

Disinfection of biological agents in the field using a mobile ...

EPA Pesticide Factsheets

Report The Army’s Net Zero Initiative is an energy-conservation program that focuses on energy as well as water and waste usage procedures. All Net Zero projects are geared toward helping the military installation or community become more sustainable and resilient, with an emphasis on taking a systems approach. Net Zero projects must advance the state of the science and are focused on three general topic areas: water, energy, and waste, and the nexuses among them. This project examined the inactivation and/or removal of biological contaminants in dirty wash water using a portable ozone-UV AOP process. The strain of E. coli used in these experiments is not a biological warfare agent, but acts as a surrogate for certain of the vegetative biological agents such as the enterohemorrhagic strain designated E. coli 0157:H7.

Pythium species and isolate diversity influence inhibition by the biological control agent Streptomyces lydicus

USDA-ARS?s Scientific Manuscript database

Disease control of soilborne pathogens by biological control agents has often been inconsistent under field conditions. One factor that may contribute to this inconsistency is the variability in response among pathogen populations and/or communities to the selected biological control agent. One hund...

Airborne exposure limits for chemical and biological warfare agents: is everything set and clear?

PubMed

Sabelnikov, Alex; Zhukov, Vladimir; Kempf, C Ruth

2006-08-01

Emergency response strategies (guidelines) for biological, chemical, nuclear, or radiological terrorist events should be based on scientifically established exposure limits for all the agents or materials involved. In the case of a radiological terrorist event, emergency response guidelines (ERG) have been worked out. In the case of a terrorist event with the use of chemical warfare (CW) agents the situation is not that clear, though the new guidelines and clean-up values are being generated based on re-evaluation of toxicological and risk data. For biological warfare (BW) agents, such guidelines do not yet exist. In this paper the current status of airborne exposure limits (AELs) for chemical and biological warfare (CBW) agents are reviewed. Particular emphasis is put on BW agents that lack such data. An efficient, temporary solution to bridge the gap in experimental infectious data and to set provisional AELs for BW agents is suggested. It is based on mathematically generated risks of infection for BW agents grouped by their alleged ID50 values in three categories: with low, intermediate and high ID50 values.

Response of an invasive liana to simulated herbivory: implications for its biological control

NASA Astrophysics Data System (ADS)

Raghu, S.; Dhileepan, K.; Treviño, M.

2006-05-01

Pre-release evaluation of the efficacy of biological control agents is often not possible in the case of many invasive species targeted for biocontrol. In such circumstances simulating herbivory could yield significant insights into plant response to damage, thereby improving the efficiency of agent prioritisation, increasing the chances of regulating the performance of invasive plants through herbivory and minimising potential risks posed by release of multiple herbivores. We adopted this approach to understand the weaknesses herbivores could exploit, to manage the invasive liana, Macfadyena unguis-cati. We simulated herbivory by damaging the leaves, stem, root and tuber of the plant, in isolation and in combination. We also applied these treatments at multiple frequencies. Plant response in terms of biomass allocation showed that at least two severe defoliation treatments were required to diminish this liana's climbing habit and reduce its allocation to belowground tuber reserves. Belowground damage appears to have negligible effect on the plant's biomass production and tuber damage appears to trigger a compensatory response. Plant response to combinations of different types of damage did not differ significantly to that from leaf damage. This suggests that specialist herbivores in the leaf-feeding guild capable of removing over 50% of the leaf tissue may be desirable in the biological control of this invasive species.

Biological agents for moderately to severely active ulcerative colitis: a systematic review and network meta-analysis.

PubMed

Danese, Silvio; Fiorino, Gionata; Peyrin-Biroulet, Laurent; Lucenteforte, Ersilia; Virgili, Gianni; Moja, Lorenzo; Bonovas, Stefanos

2014-05-20

Biological agents are emerging treatment options for the management of ulcerative colitis (UC). To assess the comparative efficacy and harm of biological agents in adult patients with moderately to severely active UC who are naive to biological agents. MEDLINE, EMBASE, and Cochrane Library from inception through December 2013, without language restrictions, and ClinicalTrials.gov, European Medicines Agency, and U.S. Food and Drug Administration Web sites. Randomized, placebo-controlled or head-to-head trials assessing biological agents as induction or maintenance therapy for moderately to severely active UC. Two reviewers independently abstracted study data and outcomes and rated each trial's risk of bias. There were no head-to-head trials. There were 7 double-blind, placebo-controlled trials that were rated as low risk of bias and showed that all biological agents (adalimumab, golimumab, infliximab, and vedolizumab) resulted in more clinical responses, clinical remissions, and mucosal healings than placebo for induction therapy. The results of network meta-analysis suggested that infliximab is more effective to induce clinical response (odds ratio, 2.36 [95% credible interval, 1.22 to 4.63]) and mucosal healing (odds ratio, 2.02 [95% credible interval, 1.13 to 3.59]) than adalimumab. No other indirect comparison reached statistical significance. For maintenance, 6 double-blind, placebo-controlled trials that were rated high risk of bias showed that all biological agents have greater clinical efficacy than placebo. The occurrence of adverse events was not different between biological agents and placebo. Few trials, no head-to-head comparisons, and inadequate follow-up in maintenance trials. Biological agents are effective treatments for UC, but head-to-head trials are warranted to establish the best therapeutic option.

Applying GIS and high performance agent-based simulation for managing an Old World Screwworm fly invasion of Australia.

PubMed

Welch, M C; Kwan, P W; Sajeev, A S M

2014-10-01

Agent-based modelling has proven to be a promising approach for developing rich simulations for complex phenomena that provide decision support functions across a broad range of areas including biological, social and agricultural sciences. This paper demonstrates how high performance computing technologies, namely General-Purpose Computing on Graphics Processing Units (GPGPU), and commercial Geographic Information Systems (GIS) can be applied to develop a national scale, agent-based simulation of an incursion of Old World Screwworm fly (OWS fly) into the Australian mainland. The development of this simulation model leverages the combination of massively data-parallel processing capabilities supported by NVidia's Compute Unified Device Architecture (CUDA) and the advanced spatial visualisation capabilities of GIS. These technologies have enabled the implementation of an individual-based, stochastic lifecycle and dispersal algorithm for the OWS fly invasion. The simulation model draws upon a wide range of biological data as input to stochastically determine the reproduction and survival of the OWS fly through the different stages of its lifecycle and dispersal of gravid females. Through this model, a highly efficient computational platform has been developed for studying the effectiveness of control and mitigation strategies and their associated economic impact on livestock industries can be materialised. Copyright © 2014 International Atomic Energy Agency 2014. Published by Elsevier B.V. All rights reserved.

INSTAR: simulating the biological cycle of a forest pest in Mediterranean pine stands

NASA Astrophysics Data System (ADS)

Suárez-Muñoz, María; Bonet García, Francisco J.; Hódar, José A.

2017-04-01

The pine processionary moth (Thaumetopoea pityocampa) is a typically Mediterranean forest pest feeding on pine needles during its larval stages. The outbreaks of this pest cause important landscape impacts and public health problems (i.e. larvae are very urticant). Larvae feed during winter months and cold temperature is the main limiting factor in their development. Therefore, rising temperatures are thought to benefit this species. Indeed, observations suggest that outbreaks are becoming more frequent and populations are shifting uphill. The objective of this work is to simulate the biological cycle of T. pityocampa to make predictions about where and when outbreaks will occur. Thus, we have created a model called INSTAR that will help to identify hotspots and foresee massive defoliation episodes. This will enhance the information available for the control of this pest. INSTAR is an Agent-Based Model, which allows the inclusion of important characteristics of the system: emergence, feedback (i.e. interaction between agents and their environment), adaptation (i.e. decision based on the mentioned interactions) and path dependence (i.e. possibilities at one time point are determined by past conditions). These characteristics arise from a set of functions simulating pine growth, processionary development, mortality and movement. These functions are easily extrapolable to other similar biological processes and therefore INSTAR aims at serving of example for other forest pest models. INSTAR is the first comprehensive approach to simulate the biological cycle of T pityocampa. It simulates the pest development in a given area, from which elevation and pine trees are considered. Moreover, it is also a good example of integrating environmental information into a population dynamic model: meteorological variables and soil moisture are obtained from a hydrological model (WiMMed, Herrero et al. 2009) executed for the area of interest. These variables are the inputs of the

Simulation-based intelligent robotic agent for Space Station Freedom

NASA Technical Reports Server (NTRS)

Biegl, Csaba A.; Springfield, James F.; Cook, George E.; Fernandez, Kenneth R.

1990-01-01

A robot control package is described which utilizes on-line structural simulation of robot manipulators and objects in their workspace. The model-based controller is interfaced with a high level agent-independent planner, which is responsible for the task-level planning of the robot's actions. Commands received from the agent-independent planner are refined and executed in the simulated workspace, and upon successful completion, they are transferred to the real manipulators.

New-onset vitiligo and progression of pre-existing vitiligo during treatment with biological agents in chronic inflammatory diseases.

PubMed

Méry-Bossard, L; Bagny, K; Chaby, G; Khemis, A; Maccari, F; Marotte, H; Perrot, J L; Reguiai, Z; Sigal, M L; Avenel-Audran, M; Boyé, T; Grasland, A; Gillard, J; Jullien, D; Toussirot, E

2017-01-01

The development of vitiligo during treatment with biological agents is an unusual event and only a few isolated cases have been reported. To describe the clinical characteristics and evolution of patients developing new-onset vitiligo following initiation of a biological agent for chronic inflammatory disease; and also to report the clinical course of pre-existing vitiligo under biological therapy. This nationwide multicentre, retrospective study, carried out between July 2013 and January 2015, describes the characteristics of a large series of 18 patients (psoriasis N = 8, inflammatory rheumatic diseases N = 8, ulcerative colitis N = 1, uveitis N = 1) who developed new-onset vitiligo while receiving a biological agent. TNFα inhibitors were the most common biological agent involved (13/18) while anti-IL-12/23 and anti-IL-17 agents or abatacept were less common (4/18 and 1/18 respectively). Mean duration of biological agent exposure before vitiligo onset was 13.9 ± 16.5 months. Outcome was favourable for most patients (15/17) while maintaining the biological agent. Data were also collected for 18 patients (psoriasis N = 5, inflammatory rheumatic diseases N = 10, inflammatory bowel diseases N = 2, SAPHO N = 1) who had pre-existing vitiligo when treatment with a biological agent started (TNFα inhibitors N = 15, ustekinumab N = 1, rituximab N = 1, tocilizumab N = 1). Vitiligo progressed in seven patients and was stable or improved in eight cases. Vitiligo may thus emerge and/or progress during treatment with various biological agents, mainly TNFα inhibitors and could be a new paradoxical skin reaction. De novo vitiligo displays a favourable outcome when maintaining the biological agent, whereas the prognosis seems worse in cases of pre-existing vitiligo. © 2016 European Academy of Dermatology and Venereology.

High-throughput assay for optimising microbial biological control agent production and delivery

USDA-ARS?s Scientific Manuscript database

Lack of technologies to produce and deliver effective biological control agents (BCAs) is a major barrier to their commercialization. A myriad of variables associated with BCA cultivation, formulation, drying, storage, and reconstitution processes complicates agent quality maximization. An efficie...

Agent-based re-engineering of ErbB signaling: a modeling pipeline for integrative systems biology.

PubMed

Das, Arya A; Ajayakumar Darsana, T; Jacob, Elizabeth

2017-03-01

Experiments in systems biology are generally supported by a computational model which quantitatively estimates the parameters of the system by finding the best fit to the experiment. Mathematical models have proved to be successful in reverse engineering the system. The data generated is interpreted to understand the dynamics of the underlying phenomena. The question we have sought to answer is that - is it possible to use an agent-based approach to re-engineer a biological process, making use of the available knowledge from experimental and modelling efforts? Can the bottom-up approach benefit from the top-down exercise so as to create an integrated modelling formalism for systems biology? We propose a modelling pipeline that learns from the data given by reverse engineering, and uses it for re-engineering the system, to carry out in-silico experiments. A mathematical model that quantitatively predicts co-expression of EGFR-HER2 receptors in activation and trafficking has been taken for this study. The pipeline architecture takes cues from the population model that gives the rates of biochemical reactions, to formulate knowledge-based rules for the particle model. Agent-based simulations using these rules, support the existing facts on EGFR-HER2 dynamics. We conclude that, re-engineering models, built using the results of reverse engineering, opens up the possibility of harnessing the power pack of data which now lies scattered in literature. Virtual experiments could then become more realistic when empowered with the findings of empirical cell biology and modelling studies. Implemented on the Agent Modelling Framework developed in-house. C ++ code templates available in Supplementary material . liz.csir@gmail.com. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Mission planning and simulation via intelligent agents

NASA Technical Reports Server (NTRS)

Gargan, Robert A., Jr.; Tilley, Randall W.

1987-01-01

A system that can operate from a flight manifest to plan and simulate payload preparation and transport via Shuttle flights is described. The design alternatives and the prototype implementation of the payload hardware and inventory tracking system are discussed. It is shown how intelligent agents can be used to generate mission schedules, and how, through the use of these intelligent agents, knowledge becomes separated into small manageable knowledge bases.

Real-Time Agent-Based Modeling Simulation with in-situ Visualization of Complex Biological Systems: A Case Study on Vocal Fold Inflammation and Healing.

PubMed

Seekhao, Nuttiiya; Shung, Caroline; JaJa, Joseph; Mongeau, Luc; Li-Jessen, Nicole Y K

2016-05-01

We present an efficient and scalable scheme for implementing agent-based modeling (ABM) simulation with In Situ visualization of large complex systems on heterogeneous computing platforms. The scheme is designed to make optimal use of the resources available on a heterogeneous platform consisting of a multicore CPU and a GPU, resulting in minimal to no resource idle time. Furthermore, the scheme was implemented under a client-server paradigm that enables remote users to visualize and analyze simulation data as it is being generated at each time step of the model. Performance of a simulation case study of vocal fold inflammation and wound healing with 3.8 million agents shows 35× and 7× speedup in execution time over single-core and multi-core CPU respectively. Each iteration of the model took less than 200 ms to simulate, visualize and send the results to the client. This enables users to monitor the simulation in real-time and modify its course as needed.

Automated numerical simulation of biological pattern formation based on visual feedback simulation framework.

PubMed

Sun, Mingzhu; Xu, Hui; Zeng, Xingjuan; Zhao, Xin

2017-01-01

There are various fantastic biological phenomena in biological pattern formation. Mathematical modeling using reaction-diffusion partial differential equation systems is employed to study the mechanism of pattern formation. However, model parameter selection is both difficult and time consuming. In this paper, a visual feedback simulation framework is proposed to calculate the parameters of a mathematical model automatically based on the basic principle of feedback control. In the simulation framework, the simulation results are visualized, and the image features are extracted as the system feedback. Then, the unknown model parameters are obtained by comparing the image features of the simulation image and the target biological pattern. Considering two typical applications, the visual feedback simulation framework is applied to fulfill pattern formation simulations for vascular mesenchymal cells and lung development. In the simulation framework, the spot, stripe, labyrinthine patterns of vascular mesenchymal cells, the normal branching pattern and the branching pattern lacking side branching for lung branching are obtained in a finite number of iterations. The simulation results indicate that it is easy to achieve the simulation targets, especially when the simulation patterns are sensitive to the model parameters. Moreover, this simulation framework can expand to other types of biological pattern formation.

Automated numerical simulation of biological pattern formation based on visual feedback simulation framework

PubMed Central

Sun, Mingzhu; Xu, Hui; Zeng, Xingjuan; Zhao, Xin

2017-01-01

There are various fantastic biological phenomena in biological pattern formation. Mathematical modeling using reaction-diffusion partial differential equation systems is employed to study the mechanism of pattern formation. However, model parameter selection is both difficult and time consuming. In this paper, a visual feedback simulation framework is proposed to calculate the parameters of a mathematical model automatically based on the basic principle of feedback control. In the simulation framework, the simulation results are visualized, and the image features are extracted as the system feedback. Then, the unknown model parameters are obtained by comparing the image features of the simulation image and the target biological pattern. Considering two typical applications, the visual feedback simulation framework is applied to fulfill pattern formation simulations for vascular mesenchymal cells and lung development. In the simulation framework, the spot, stripe, labyrinthine patterns of vascular mesenchymal cells, the normal branching pattern and the branching pattern lacking side branching for lung branching are obtained in a finite number of iterations. The simulation results indicate that it is easy to achieve the simulation targets, especially when the simulation patterns are sensitive to the model parameters. Moreover, this simulation framework can expand to other types of biological pattern formation. PMID:28225811

Establish an Agent-Simulant Technology Relationship (ASTR)

DTIC Science & Technology

2017-04-14

for quantitative measures that characterize simulant performance in testing , such as the ability to be removed from surfaces. Component-level ASTRs...Overall Test and Agent-Simulant Technology Relationship (ASTR) process. 1.2 Background. a. Historically, many tests did not develop quantitative ...methodology report14. Report provides a VX-TPP ASTR for post -decon contact hazard and off- gassing. In the Stryker production verification test (PVT

Implementation of Multi-Agent Object Attention System Based on Biologically Inspired Attractor Selection

NASA Astrophysics Data System (ADS)

Hashimoto, Ryoji; Matsumura, Tomoya; Nozato, Yoshihiro; Watanabe, Kenji; Onoye, Takao

A multi-agent object attention system is proposed, which is based on biologically inspired attractor selection model. Object attention is facilitated by using a video sequence and a depth map obtained through a compound-eye image sensor TOMBO. Robustness of the multi-agent system over environmental changes is enhanced by utilizing the biological model of adaptive response by attractor selection. To implement the proposed system, an efficient VLSI architecture is employed with reducing enormous computational costs and memory accesses required for depth map processing and multi-agent attractor selection process. According to the FPGA implementation result of the proposed object attention system, which is accomplished by using 7,063 slices, 640×512 pixel input images can be processed in real-time with three agents at a rate of 9fps in 48MHz operation.

Agent-based simulation of a financial market

NASA Astrophysics Data System (ADS)

Raberto, Marco; Cincotti, Silvano; Focardi, Sergio M.; Marchesi, Michele

2001-10-01

This paper introduces an agent-based artificial financial market in which heterogeneous agents trade one single asset through a realistic trading mechanism for price formation. Agents are initially endowed with a finite amount of cash and a given finite portfolio of assets. There is no money-creation process; the total available cash is conserved in time. In each period, agents make random buy and sell decisions that are constrained by available resources, subject to clustering, and dependent on the volatility of previous periods. The model proposed herein is able to reproduce the leptokurtic shape of the probability density of log price returns and the clustering of volatility. Implemented using extreme programming and object-oriented technology, the simulator is a flexible computational experimental facility that can find applications in both academic and industrial research projects.

Water-driven micromotors for rapid photocatalytic degradation of biological and chemical warfare agents.

PubMed

Li, Jinxing; Singh, Virendra V; Sattayasamitsathit, Sirilak; Orozco, Jahir; Kaufmann, Kevin; Dong, Renfeng; Gao, Wei; Jurado-Sanchez, Beatriz; Fedorak, Yuri; Wang, Joseph

2014-11-25

Threats of chemical and biological warfare agents (CBWA) represent a serious global concern and require rapid and efficient neutralization methods. We present a highly effective micromotor strategy for photocatalytic degradation of CBWA based on light-activated TiO2/Au/Mg microspheres that propel autonomously in natural water and obviate the need for external fuel, decontaminating reagent, or mechanical agitation. The activated TiO2/Au/Mg micromotors generate highly reactive oxygen species responsible for the efficient destruction of the cell membranes of the anthrax simulant Bacillus globigii spore, as well as rapid and complete in situ mineralization of the highly persistent organophosphate nerve agents into nonharmful products. The water-driven propulsion of the TiO2/Au/Mg micromotors facilitates efficient fluid transport and dispersion of the photogenerated reactive oxidative species and their interaction with the CBWA. Coupling of the photocatalytic surface of the micromotors and their autonomous water-driven propulsion thus leads to a reagent-free operation which holds a considerable promise for diverse "green" defense and environmental applications.

Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems

PubMed Central

Cilfone, Nicholas A.; Kirschner, Denise E.; Linderman, Jennifer J.

2015-01-01

Biologically related processes operate across multiple spatiotemporal scales. For computational modeling methodologies to mimic this biological complexity, individual scale models must be linked in ways that allow for dynamic exchange of information across scales. A powerful methodology is to combine a discrete modeling approach, agent-based models (ABMs), with continuum models to form hybrid models. Hybrid multi-scale ABMs have been used to simulate emergent responses of biological systems. Here, we review two aspects of hybrid multi-scale ABMs: linking individual scale models and efficiently solving the resulting model. We discuss the computational choices associated with aspects of linking individual scale models while simultaneously maintaining model tractability. We demonstrate implementations of existing numerical methods in the context of hybrid multi-scale ABMs. Using an example model describing Mycobacterium tuberculosis infection, we show relative computational speeds of various combinations of numerical methods. Efficient linking and solution of hybrid multi-scale ABMs is key to model portability, modularity, and their use in understanding biological phenomena at a systems level. PMID:26366228

Treatment with biologic agents improves the prognosis of patients with rheumatoid arthritis and amyloidosis.

PubMed

Kuroda, Takeshi; Tanabe, Naohito; Kobayashi, Daisuke; Sato, Hiroe; Wada, Yoko; Murakami, Shuichi; Saeki, Takako; Nakano, Masaaki; Narita, Ichiei

2012-07-01

Reactive amyloid A (AA) amyloidosis is a serious and life-threatening systemic complication of rheumatoid arthritis (RA). We evaluated the safety of therapy with anti-tumor necrosis factor and anti-interleukin 6 biologic agents in RA patients with reactive AA amyloidosis, together with prognosis and hemodialysis (HD)-free survival, in comparison with patients with AA amyloidosis without such therapy. One hundred thirty-three patients with an established diagnosis of reactive AA amyloidosis participated in the study. Clinical data were assessed from patient records at the time of amyloid detection and administration of biologics. Survival was calculated from the date when amyloid was first demonstrated histologically or the date when biologic therapy was started until the time of death or to the end of 2010 for surviving patients. Patients who had started HD were selected for inclusion only after the presence of amyloid was demonstrated. Fifty-three patients were treated with biologic agents (biologic group) and 80 were not (nonbiologic group). Survival rate was significantly higher in the biologic group than in the nonbiologic group. Nine patients in the biologics group and 33 in the nonbiologic group started HD. Biologic therapy had a tendency for reduced risk of initiation of HD without any statistical significance. Patients with amyloidosis have a higher mortality rate, but the use of biologic agents can reduce risk of death. The use of biologics may not significantly influence the HD-free survival rate.

Non-target effects of an introduced biological control agent on deer mouse ecology.

PubMed

Pearson, D E; McKelvey, K S; Ruggiero, L F

2000-01-01

Release of exotic insects as biological control agents is a common approach to controlling exotic plants. Though controversy has ensued regarding the deleterious direct effects of biological control agents to non-target species, few have examined the indirect effects of a "well-behaved" biological control agent on native fauna. We studied a grassland in west-central Montana infested with spotted knapweed (Centaurea maculosa) to examine the effects of knapweed invasion and two gall flybiological control agents (Urophora affinis and U. quadrifasciata) on the native deer mouse (Peromyscus maniculatus). Stomach-content analysis revealed that Urophora were the primary food item in Peromyscus diets for most of the year and made up 84-86% of the winter diet. Stomach contents indicated that wild-caught mice consumed on average up to 247 Urophora larvae mouse -1 day -1 , while feeding trials revealed that deer mice could depredate nearly 5 times as many larvae under laboratory conditions. In feeding trials, deer mice selected knapweed seedheads with greater numbers of galls while avoiding uninfested seedheads. When Urophora larvae were present in knapweed seedheads, deer mice selected microhabitats with moderately high (31-45% cover) and high knapweed infestation (≥46% cover). After Urophora emerged and larvae were unavailable to Peromyscus, mice reversed habitat selection to favor sites dominated by native-prairie with low knapweed infestation (0-15%). Establishment of the biological control agent, Urophora spp., has altered deer mouse diets and habitat selection by effecting changes in foraging strategies. Deer mice and other predators may reduce Urophora populations below a threshold necessary to effectively control spotted knapweed.

Biologic agents in rheumatology: unmet issues after 200 trials and $200 billion sales.

PubMed

Ioannidis, John P A; Karassa, Fotini B; Druyts, Eric; Thorlund, Kristian; Mills, Edward J

2013-11-01

Anti-TNF agents and other biologic therapies are widely prescribed for a variety of indications, with total sales that exceed $200 billion to date. In rheumatic diseases, biologic agents have now been studied in more than 200 randomized clinical trials and over 100 subsequent meta-analyses; however, the information obtained does not always meet the needs of patients and clinicians. In this Review, we discuss the current issues concerning the evidence derived from such studies: potential biases favouring positive results; a paucity of head-to-head comparisons between biologically active agents; overwhelming involvement of manufacturer sponsors in trials and in the synthesis of the evidence; the preference for trials with limited follow-up; and the potential for spurious findings on adverse events, leading to endless debates about malignancy risk. We debate the responsibilities of regulatory authorities, the pharmaceutical industry and academia in attempting to solve these shortcomings and challenges. We propose that improvements in the evidence regarding biologic treatments that are continually being added to the therapeutic armamentarium for rheumatic diseases might require revisiting the design and conduct of studies. For example, trials with long-term follow-up that are independent of the pharmaceutical industry, head-to-head comparisons of therapeutic agents and the use of rigorous clinical outcomes should be considered, and public availability of raw data endorsed.

BioNSi: A Discrete Biological Network Simulator Tool.

PubMed

Rubinstein, Amir; Bracha, Noga; Rudner, Liat; Zucker, Noga; Sloin, Hadas E; Chor, Benny

2016-08-05

Modeling and simulation of biological networks is an effective and widely used research methodology. The Biological Network Simulator (BioNSi) is a tool for modeling biological networks and simulating their discrete-time dynamics, implemented as a Cytoscape App. BioNSi includes a visual representation of the network that enables researchers to construct, set the parameters, and observe network behavior under various conditions. To construct a network instance in BioNSi, only partial, qualitative biological data suffices. The tool is aimed for use by experimental biologists and requires no prior computational or mathematical expertise. BioNSi is freely available at http://bionsi.wix.com/bionsi , where a complete user guide and a step-by-step manual can also be found.

Agent-Based Modeling in Molecular Systems Biology.

PubMed

Soheilypour, Mohammad; Mofrad, Mohammad R K

2018-07-01

Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding of the behavior of molecular systems by enabling us to test assumptions and hypotheses, explore the effect of different parameters on the outcome, and eventually guide experiments. While several different mathematical and computational methods are developed to study molecular systems at different spatiotemporal scales, there is still a need for methods that bridge the gap between spatially-detailed and computationally-efficient approaches. In this review, we summarize the capabilities of agent-based modeling (ABM) as an emerging molecular systems biology technique that provides researchers with a new tool in exploring the dynamics of molecular systems/pathways in health and disease. © 2018 WILEY Periodicals, Inc.

Simulations in Medicine and Biology: Insights and perspectives

NASA Astrophysics Data System (ADS)

Spyrou, George M.

2015-01-01

Modern medicine and biology have been transformed into quantitative sciences of high complexity, with challenging objectives. The aims of medicine are related to early diagnosis, effective therapy, accurate intervention, real time monitoring, procedures/systems/instruments optimization, error reduction, and knowledge extraction. Concurrently, following the explosive production of biological data concerning DNA, RNA, and protein biomolecules, a plethora of questions has been raised in relation to their structure and function, the interactions between them, their relationships and dependencies, their regulation and expression, their location, and their thermodynamic characteristics. Furthermore, the interplay between medicine and biology gives rise to fields like molecular medicine and systems biology which are further interconnected with physics, mathematics, informatics, and engineering. Modelling and simulation is a powerful tool in the fields of Medicine and Biology. Simulating the phenomena hidden inside a diagnostic or therapeutic medical procedure, we are able to obtain control on the whole system and perform multilevel optimization. Furthermore, modelling and simulation gives insights in the various scales of biological representation, facilitating the understanding of the huge amounts of derived data and the related mechanisms behind them. Several examples, as well as the insights and the perspectives of simulations in biomedicine will be presented.

Biology and life history of Argopistes tsekooni (Coleoptera: Chrysomelidae) in China, a promising biological control agent of Chinese privet.

Treesearch

Y-Z Zhang; J. Sun; J.L. Hanula

2009-01-01

The biology and life history of Argopistes tsekooni Chen (Coleoptera: Chrysomelidae), a potential biological control agent of Chinese privet, Ligustrum sinense Lour., was studied under laboratory and outdoor conditions in Huangshan City of Anhui Province, China, in 2006. A. tsekooni larvae are leafminers that...

Modeling the transport of chemical warfare agents and simulants in polymeric substrates for reactive decontamination

NASA Astrophysics Data System (ADS)

Pearl, Thomas; Mantooth, Brent; Varady, Mark; Willis, Matthew

2014-03-01

Chemical warfare agent simulants are often used for environmental testing in place of highly toxic agents. This work sets the foundation for modeling decontamination of absorbing polymeric materials with the focus on determining relationships between agents and simulants. The correlations of agents to simulants must consider the three way interactions in the chemical-material-decontaminant system where transport and reaction occur in polymer materials. To this end, diffusion modeling of the subsurface transport of simulants and live chemical warfare agents was conducted for various polymer systems (e.g., paint coatings) with and without reaction pathways with applied decontamination. The models utilized 1D and 2D finite difference diffusion and reaction models to simulate absorption and reaction in the polymers, and subsequent flux of the chemicals out of the polymers. Experimental data including vapor flux measurements and dynamic contact angle measurements were used to determine model input parameters. Through modeling, an understanding of the relationship of simulant to live chemical warfare agent was established, focusing on vapor emission of agents and simulants from materials.

Update on the use of systemic biologic agents in the treatment of noninfectious uveitis

PubMed Central

Pasadhika, Sirichai; Rosenbaum, James T

2014-01-01

Uveitis is one of the leading causes of blindness worldwide. Noninfectious uveitis may be associated with other systemic conditions, such as human leukocyte antigen B27-related spondyloarthropathies, inflammatory bowel disease, juvenile idiopathic arthritis, Behçet’s disease, and sarcoidosis. Conventional therapy with corticosteroids and immunosuppressive agents (such as methotrexate, azathioprine, mycophenolate mofetil, and cyclosporine) may not be sufficient to control ocular inflammation or prevent non-ophthalmic complications in refractory patients. Off-label use of biologic response modifiers has been studied as primary and secondary therapeutic agents. They are very useful when conventional immunosuppressive therapy has failed or has been poorly tolerated, or to treat concomitant ophthalmic and systemic inflammation that might benefit from these medications. Biologic therapy, primarily infliximab, and adalimumab, have been shown to be rapidly effective for the treatment of various subtypes of refractory uveitis and retinal vasculitis, especially Behçet’s disease-related eye conditions and the uveitis associated with juvenile idiopathic arthritis. Other agents such as golimumab, abatacept, canakinumab, gevokizumab, tocilizumab, and alemtuzumab may have great future promise for the treatment of uveitis. It has been shown that with proper monitoring, biologic therapy can significantly improve quality of life in patients with uveitis, particularly those with concurrent systemic symptoms. However, given high cost as well as the limited long-term safety data, we do not routinely recommend biologics as first-line therapy for noninfectious uveitis in most patients. These agents should be used with caution by experienced clinicians. The present work aims to provide a broad and updated review of the current and in-development systemic biologic agents for the treatment of noninfectious uveitis. PMID:24600203

PERMANENCE OF BIOLOGICAL AND CHEMICAL WARFARE AGENTS IN MUNICIPAL SOLID WASTE LANDFILL LEACHATES

EPA Science Inventory

The objective of this work is to permit EPA/ORD's National Homeland Security Research Center (NHSRC) and Edgewood Chemical Biological Center to collaborate together to test the permanence of biological and chemical warfare agents in municipal solid waste landfills. Research into ...

76 FR 3076 - Availability of an Environmental Assessment for a Biological Control Agent for Air Potato

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-19

...] Availability of an Environmental Assessment for a Biological Control Agent for Air Potato AGENCY: Animal and... environmental assessment (EA) relative to the control of air potato (Dioscorea bulbifera). The EA considers the... States for use as a biological control agent to reduce the severity of air potato infestations. We are...

Use of Magnetic Bead Resin and Automated Liquid Handler Extraction Methods to Robotically Isolate Nucleic Acids of Biological Agent Simulates

DTIC Science & Technology

2003-09-01

concentration, and Bacillus subtilis var. niger spores were detectable at 10,000 CFU/ml. When combined with bead beating, these spores were consistently...Bioloeical Aaent Simulants. Cell suspensions of Bacillus subtilis var. niger spores (BG spores ) and Erwinia herbicola vegetative cells were prepared for...use as biological simulants. BG spores were prepared by inoculating 1 g spores of Bacillus subtilis var. niger (Merck & Co., Inc., Whitehouse Station

Current levels of suppression of waterhyacinth in Florida by classical biological control agents

USDA-ARS?s Scientific Manuscript database

Waterhyacinth, Eichhornia crassipes, has been a global target for classical biological control efforts for decades. In Florida, herbicides are the primary tactic employed, usually without regard for the activities of the three biological control agents introduced intentionally during the 1970's, na...

Infliximab is superior to other biological agents for treatment of active ulcerative colitis: A meta-analysis.

PubMed

Mei, Wei-Qun; Hu, Hui-Zhen; Liu, Ying; Li, Zhi-Chen; Wang, Wei-Guo

2015-05-21

To compare the efficacy and safety of biological agents for the treatment of active ulcerative colitis (UC). PubMed, MEDLINE, EMBASE and the Cochrane library were searched to screen relevant articles from January 1996 to August 2014. The mixed treatment comparison meta-analysis within a Bayesian framework was performed using WinBUGS14 software. The proportions of patients reaching clinical response, clinical remission and mucosal healing in induction and maintenance phases were analyzed as efficacy indicators. Serious adverse events in maintenance phase were analyzed as safety indicators. The meta-analysis results showed that biological agents achieved better clinical response, clinical remission and mucosal healing than placebo. Indirect comparison indicated that in induction phase, infliximab was more effective than adalimumab in inducing clinical response (OR = 0.41, 95%CI: 0.29-0.57), clinical remission (OR = 0.33, 95%CI: 0.19-0.56) and mucosal healing (OR = 0.33, 95%CI: 0.19-0.56), and golimumab in inducing clinical response (OR = 0.66, 95%CI: 0.39-2.33) and mucosal healing (OR = 2.15, 95%CI: 1.18-4.22). No significant difference was found between placebo and biological agents regarding their safety. All biological agents were superior to placebo for UC treatment in both induction and maintenance phases with a similar safety profile, and infliximab had a better clinical effect than the other biological agents.

Mode of Infection of Metarhizium spp. Fungus and Their Potential as Biological Control Agents

PubMed Central

Aw, Kimberly Moon San; Hue, Seow Mun

2017-01-01

Chemical insecticides have been commonly used to control agricultural pests, termites, and biological vectors such as mosquitoes and ticks. However, the harmful impacts of toxic chemical insecticides on the environment, the development of resistance in pests and vectors towards chemical insecticides, and public concern have driven extensive research for alternatives, especially biological control agents such as fungus and bacteria. In this review, the mode of infection of Metarhizium fungus on both terrestrial and aquatic insect larvae and how these interactions have been widely employed will be outlined. The potential uses of Metarhizium anisopliae and Metarhizium acridum biological control agents and molecular approaches to increase their virulence will be discussed. PMID:29371548

Bioterrorism and Biocrimes: The Illicit Use of Biological Agents Since 1900

DTIC Science & Technology

2001-02-01

to white supremacist groups, including the Aryan Nation and the Christian Identity movement, he 5 involve allegations of covert state activities ...toxin to poison livestock in what is now Kenya. The full extent of these activities is not known. Polish Resistance: Multiple reports suggest that...thorough reporting of Aum’s biological warfare activities . See page 47 for additional details. Table 1: Confirmed cases of illicit biological agent activity

Platinum-based anticancer agents: innovative design strategies and biological perspectives.

PubMed

Ho, Yee-Ping; Au-Yeung, Steve C F; To, Kenneth K W

2003-09-01

The impact of cisplatin on cancer chemotherapy cannot be denied. Over the past 20 years, much effort has been dedicated to discover new platinum-based anticancer agents that are superior to cisplatin or its analogue, carboplatin. Most structural modifications are based on changing one or both of the ligand types coordinated to platinum. Altering the leaving group can influence tissue and intracellular distribution of the drug, whereas the carrier ligand usually determines the structure of adducts formed with DNA. DNA-Pt adducts produced by cisplatin and many of its classical analogues are almost identical, and would explain their similar patterns of tumor sensitivity and susceptibility to resistance. Recently some highly innovative design strategies have emerged, aimed at overcoming platinum resistance and/or to introduce novel mechanisms of antitumor action. Platinum compounds bearing the 1,2-diaminocyclohexane carrier ligand; and those of multinuclear Pt complexes giving rise to radically different DNA-Pt adducts, have resulted in novel anticancer agents capable of circumventing cisplatin resistance. Other strategies have focused on integrating biologically active ligands with platinum moieties intended to selectively localizing the anticancer properties. With the rapid advance in molecular biology, combined with innovation, it is possible new Pt-based anticancer agents will materialize in the near future. Copyright 2003 Wiley Periodicals, Inc.

Agent-based modeling of malaria vectors: the importance of spatial simulation.

PubMed

Bomblies, Arne

2014-07-03

The modeling of malaria vector mosquito populations yields great insight into drivers of malaria transmission at the village scale. Simulation of individual mosquitoes as "agents" in a distributed, dynamic model domain may be greatly beneficial for simulation of spatial relationships of vectors and hosts. In this study, an agent-based model is used to simulate the life cycle and movement of individual malaria vector mosquitoes in a Niger Sahel village, with individual simulated mosquitoes interacting with their physical environment as well as humans. Various processes that are known to be epidemiologically important, such as the dependence of parity on flight distance between developmental habitat and blood meal hosts and therefore spatial relationships of pools and houses, are readily simulated using this modeling paradigm. Impacts of perturbations can be evaluated on the basis of vectorial capacity, because the interactions between individuals that make up the population- scale metric vectorial capacity can be easily tracked for simulated mosquitoes and human blood meal hosts, without the need to estimate vectorial capacity parameters. As expected, model results show pronounced impacts of pool source reduction from larvicide application and draining, but with varying degrees of impact depending on the spatial relationship between pools and human habitation. Results highlight the importance of spatially-explicit simulation that can model individuals such as in an agent-based model. The impacts of perturbations on village scale malaria transmission depend on spatial locations of individual mosquitoes, as well as the tracking of relevant life cycle events and characteristics of individual mosquitoes. This study demonstrates advantages of using an agent-based approach for village-scale mosquito simulation to address questions in which spatial relationships are known to be important.

Axinellamines as Broad-Spectrum Antibacterial Agents: Scalable Synthesis and Biology

PubMed Central

2015-01-01

Antibiotic-resistant bacteria present an ongoing challenge to both chemists and biologists as they seek novel compounds and modes of action to out-maneuver continually evolving resistance pathways, especially against Gram-negative strains. The dimeric pyrrole–imidazole alkaloids represent a unique marine natural product class with diverse primary biological activity and chemical architecture. This full account traces the strategy used to develop a second-generation route to key spirocycle 9, culminating in a practical synthesis of the axinellamines and enabling their discovery as broad-spectrum antibacterial agents, with promising activity against both Gram-positive and Gram-negative bacteria. While their detailed mode of antibacterial action remains unclear, the axinellamines appear to cause secondary membrane destabilization and impart an aberrant cellular morphology consistent with the inhibition of normal septum formation. This study serves as a rare example of a natural product initially reported to be devoid of biological activity surfacing as an active antibacterial agent with an intriguing mode of action. PMID:25328977

A proposed CT contrast agent using carboxybetaine zwitterionic tantalum oxide nanoparticles: Imaging, biological, and physicochemical performance

PubMed Central

FitzGerald, Paul F.; Butts, Matthew D.; Roberts, Jeannette C.; Colborn, Robert E.; Torres, Andrew S.; Lee, Brian D.; Yeh, Benjamin M.; Bonitatibus, Peter J.

2016-01-01

Objectives To produce and evaluate a proposed computed tomography (CT) contrast agent based on carboxybetaine zwitterionic (CZ) coated soluble tantalum oxide nanoparticles (CZ-TaO NPs). We chose tantalum to provide superior imaging performance compared to current iodine-based clinical CT contrast agents. We developed the CZ coating to provide biological and physical performance similar to that of current iodinated contrast agents. The aim of this study was to evaluate the imaging, biological, and physicochemical performance of this proposed contrast agent compared to clinically-used iodinated agents. Materials and Methods We evaluated CT imaging performance of our CZ-TaO NPs compared to an iodinated agent in live rats, imaged centrally-located within a tissue-equivalent plastic phantom that simulated a large patient. To evaluate vascular contrast enhancement, we scanned the rats’ great vessels at high temporal resolution during and following contrast agent injection. We performed several in vivo CZ-TaO NP studies in healthy rats to evaluate tolerability. These studies included injecting the agent at the anticipated clinical dose (ACD) and at 3 times and 6 times the ACD, followed by longitudinal hematology to assess impact to blood cells and organ function (from 4 hours to 1 week). Kidney histological analysis was performed 48 hours after injection at 3 times the ACD. We measured the elimination half-life of CZ-TaO NPs from blood, and we monitored acute kidney injury biomarkers with a kidney injury assay using urine collected from 4 hours to 1 week. We measured tantalum retention in individual organs and in the whole carcass 48 hours after injection at ACD. CZ-TaO NPs were synthesized and analyzed in detail. We used multi-dimensional nuclear magnetic resonance (NMR) to determine surface functionality of the nanoparticles. We measured nanoparticle size and solution properties (osmolality and viscosity) of the agent over a range of tantalum concentrations, including

Enhancement of biological control agents for use against forest insect pests and diseases through biotechnology

NASA Technical Reports Server (NTRS)

Slavicek, James M.

1991-01-01

Research and development efforts in our research group are focused on the generation of more efficacious biological control agents through the techniques of biotechnology for use against forest insect pests and diseases. Effective biological controls for the gypsy moth and for tree fungal wilt pathogens are under development. The successful use of Gypchek, a formulation of the Lymantria dispar nuclear polyhedrosis virus (LdNPV), in gypsy moth control programs has generated considerable interest in that agent. As a consequence of its specificity, LdPNV has negligible adverse ecological impacts compared to most gypsy moth control agents. However, LdNPV is not competitive with other control agents in terms of cost and efficacy. We are investigating several parameters of LdNPV replication and polyhedra production in order to enhance viral potency and efficacy thus mitigating the current disadvantages of LdNPV for gypsy moth control, and have identified LdNPV variants that will facilitate these efforts. Tree endophytic bacteria that synthesize antifungal compounds were identified and an antibiotic compound from one of these bacteria was characterized. The feasibility of developing tree endophytes as biological control agents for tree vascular fungal pathogens is being investigated.

A Participatory Agent-Based Simulation for Indoor Evacuation Supported by Google Glass.

PubMed

Sánchez, Jesús M; Carrera, Álvaro; Iglesias, Carlos Á; Serrano, Emilio

2016-08-24

Indoor evacuation systems are needed for rescue and safety management. One of the challenges is to provide users with personalized evacuation routes in real time. To this end, this project aims at exploring the possibilities of Google Glass technology for participatory multiagent indoor evacuation simulations. Participatory multiagent simulation combines scenario-guided agents and humans equipped with Google Glass that coexist in a shared virtual space and jointly perform simulations. The paper proposes an architecture for participatory multiagent simulation in order to combine devices (Google Glass and/or smartphones) with an agent-based social simulator and indoor tracking services.

A Participatory Agent-Based Simulation for Indoor Evacuation Supported by Google Glass

PubMed Central

Sánchez, Jesús M.; Carrera, Álvaro; Iglesias, Carlos Á.; Serrano, Emilio

2016-01-01

Indoor evacuation systems are needed for rescue and safety management. One of the challenges is to provide users with personalized evacuation routes in real time. To this end, this project aims at exploring the possibilities of Google Glass technology for participatory multiagent indoor evacuation simulations. Participatory multiagent simulation combines scenario-guided agents and humans equipped with Google Glass that coexist in a shared virtual space and jointly perform simulations. The paper proposes an architecture for participatory multiagent simulation in order to combine devices (Google Glass and/or smartphones) with an agent-based social simulator and indoor tracking services. PMID:27563911

The acquisition of dangerous biological materials: Technical facts sheets to assist risk assessments of 46 potential BW agents

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aceto, Donato Gonzalo; Astuto-Gribble, Lisa M.; Gaudioso, Jennifer M.

Numerous terrorist organizations have openly expressed interest in producing and deploying biological weapons. However, a limiting factor for many terrorists has been the acquisition of dangerous biological agents, as evidenced by the very few successful instances of biological weapons use compared to the number of documented hoaxes. Biological agents vary greatly in their ability to cause loss of life and economic damage. Some agents, if released properly, can kill many people and cause an extensive number of secondary infections; other agents will sicken only a small number of people for a short period of time. Consequently, several biological agents canmore » potentially be used to perpetrate a bioterrorism attack but few are likely capable of causing a high consequence event. It is crucial, from a US national security perspective, to more deeply understand the likelihood that terrorist organizations can acquire the range of these agents. Few studies have attempted to comprehensively compile the technical information directly relevant to the acquisition of dangerous bacteria, viruses and toxins. In this report, technical fact sheets were assembled for 46 potentially dangerous biological agents. Much of the information was taken from various research sources which could ultimately and significantly expedite and improve bioterrorism threat assessments. By systematically examining a number of specific agent characteristics included in these fact sheets, it may be possible to detect, target, and implement measures to thwart future terrorist acquisition attempts. In addition, the information in these fact sheets may be used as a tool to help laboratories gain a rudimentary understanding of how attractive a method laboratory theft is relative to other potential acquisition modes.« less

Biologically-inspired hexapod robot design and simulation

NASA Technical Reports Server (NTRS)

Espenschied, Kenneth S.; Quinn, Roger D.

1994-01-01

The design and construction of a biologically-inspired hexapod robot is presented. A previously developed simulation is modified to include models of the DC drive motors, the motor driver circuits and their transmissions. The application of this simulation to the design and development of the robot is discussed. The mechanisms thought to be responsible for the leg coordination of the walking stick insect were previously applied to control the straight-line locomotion of a robot. We generalized these rules for a robot walking on a plane. This biologically-inspired control strategy is used to control the robot in simulation. Numerical results show that the general body motion and performance of the simulated robot is similar to that of the robot based on our preliminary experimental results.

Synthesis, biological evaluation, and molecular modeling of cinnamic acyl sulfonamide derivatives as novel antitubulin agents.

PubMed

Luo, Yin; Qiu, Ke-Ming; Lu, Xiang; Liu, Kai; Fu, Jie; Zhu, Hai-Liang

2011-08-15

A series of novel cinnamic acyl sulfonamide derivatives (9a-16e) have been designed and synthesized and their biological activities were also evaluated as potential tubulin polymerization inhibitors. Among all the compounds, 10c showed the most potent growth inhibitory activity against B16-F10 cancer cell line in vitro, with an IC(50) value of 0.8μg/mL. Docking simulation was performed to insert compound 10c into the crystal structure of tubulin at colchicine binding site to determine the probable binding model. Based on the preliminary results, compound 10c with potent inhibitory activity in tumor growth may be a potential anticancer agent. Copyright © 2011 Elsevier Ltd. All rights reserved.

Agent-based evacuation simulation for spatial allocation assessment of urban shelters

NASA Astrophysics Data System (ADS)

Yu, Jia; Wen, Jiahong; Jiang, Yong

2015-12-01

The construction of urban shelters is one of the most important work in urban planning and disaster prevention. The spatial allocation assessment is a fundamental pre-step for spatial location-allocation of urban shelters. This paper introduces a new method which makes use of agent-based technology to implement evacuation simulation so as to conduct dynamic spatial allocation assessment of urban shelters. The method can not only accomplish traditional geospatial evaluation for urban shelters, but also simulate the evacuation process of the residents to shelters. The advantage of utilizing this method lies into three aspects: (1) the evacuation time of each citizen from a residential building to the shelter can be estimated more reasonably; (2) the total evacuation time of all the residents in a region is able to be obtained; (3) the road congestions in evacuation in sheltering can be detected so as to take precautionary measures to prevent potential risks. In this study, three types of agents are designed: shelter agents, government agents and resident agents. Shelter agents select specified land uses as shelter candidates for different disasters. Government agents delimitate the service area of each shelter, in other words, regulate which shelter a person should take, in accordance with the administrative boundaries and road distance between the person's position and the location of the shelter. Resident agents have a series of attributes, such as ages, positions, walking speeds, and so on. They also have several behaviors, such as reducing speed when walking in the crowd, helping old people and children, and so on. Integrating these three types of agents which are correlated with each other, evacuation procedures can be simulated and dynamic allocation assessment of shelters will be achieved. A case study in Jing'an District, Shanghai, China, was conducted to demonstrate the feasibility of the method. A scenario of earthquake disaster which occurs in nighttime

Building occupancy simulation and data assimilation using a graph-based agent-oriented model

NASA Astrophysics Data System (ADS)

Rai, Sanish; Hu, Xiaolin

2018-07-01

Building occupancy simulation and estimation simulates the dynamics of occupants and estimates their real-time spatial distribution in a building. It requires a simulation model and an algorithm for data assimilation that assimilates real-time sensor data into the simulation model. Existing building occupancy simulation models include agent-based models and graph-based models. The agent-based models suffer high computation cost for simulating large numbers of occupants, and graph-based models overlook the heterogeneity and detailed behaviors of individuals. Recognizing the limitations of existing models, this paper presents a new graph-based agent-oriented model which can efficiently simulate large numbers of occupants in various kinds of building structures. To support real-time occupancy dynamics estimation, a data assimilation framework based on Sequential Monte Carlo Methods is also developed and applied to the graph-based agent-oriented model to assimilate real-time sensor data. Experimental results show the effectiveness of the developed model and the data assimilation framework. The major contributions of this work are to provide an efficient model for building occupancy simulation that can accommodate large numbers of occupants and an effective data assimilation framework that can provide real-time estimations of building occupancy from sensor data.

Specialty Tier-Level Cost Sharing and Biologic Agent Use in the Medicare Part D Initial Coverage Period Among Beneficiaries With Rheumatoid Arthritis.

PubMed

Doshi, Jalpa A; Hu, Tianyan; Li, Pengxiang; Pettit, Amy R; Yu, Xinyan; Blum, Marissa

2016-11-01

To examine associations between specialty tier-level cost sharing and use of biologic agents for rheumatoid arthritis (RA) during Medicare Part D's initial coverage period (ICP). This was a retrospective study using 2007-2010 5% sample Medicare files to examine RA patients with use of a Part D RA biologic agent in the prior year. Patients without low-income subsidies (non-LIS group), who faced specialty tier-level cost sharing, were compared to a control group of low-income subsidy patients (LIS group), who faced nominal out-of-pocket costs in the ICP. Outcomes included use of a Part D or Part B RA biologic agent during the ICP and presence of a ≥30-day continuous gap in treatment among Part D biologic agent users in the ICP. Risk-adjusted outcomes were estimated using logistic regressions, controlling for patient demographic, clinical, and Part D plan characteristics. On average, a 30-day Part D biologic agent supply cost the non-LIS group $484 out of pocket (29.9% cost sharing) versus $5 (0.3% cost sharing) for the LIS group. The non-LIS group was less likely to fill Part D biologic agents (61.2% versus 72.7%, odds ratio [OR] 0.58 [95% confidence interval (95% CI) 0.46-0.72]; P < 0.001), more than twice as likely to receive Part B biologic agents (9.9% versus 4.4%, OR 2.41 [95% CI 1.61-3.60]; P < 0.001), and less likely to use any biologic agent (70.1% versus 76.9%, OR 0.69 [95% CI 0.55-0.88]; P = 0.002). The non-LIS subgroup filling Part D biologic agents had approximately twice the odds of a gap in both Part D biologic agent and any biologic agent availability. Specialty tier-level cost sharing was associated with interruptions in RA biologic agent treatment among Medicare patients. © 2016, American College of Rheumatology.

Infliximab is superior to other biological agents for treatment of active ulcerative colitis: A meta-analysis

PubMed Central

Mei, Wei-Qun; Hu, Hui-Zhen; Liu, Ying; Li, Zhi-Chen; Wang, Wei-Guo

2015-01-01

AIM: To compare the efficacy and safety of biological agents for the treatment of active ulcerative colitis (UC). METHODS: PubMed, MEDLINE, EMBASE and the Cochrane library were searched to screen relevant articles from January 1996 to August 2014. The mixed treatment comparison meta-analysis within a Bayesian framework was performed using WinBUGS14 software. The proportions of patients reaching clinical response, clinical remission and mucosal healing in induction and maintenance phases were analyzed as efficacy indicators. Serious adverse events in maintenance phase were analyzed as safety indicators. RESULTS: The meta-analysis results showed that biological agents achieved better clinical response, clinical remission and mucosal healing than placebo. Indirect comparison indicated that in induction phase, infliximab was more effective than adalimumab in inducing clinical response (OR = 0.41, 95%CI: 0.29-0.57), clinical remission (OR = 0.33, 95%CI: 0.19-0.56) and mucosal healing (OR = 0.33, 95%CI: 0.19-0.56), and golimumab in inducing clinical response (OR = 0.66, 95%CI: 0.39-2.33) and mucosal healing (OR = 2.15, 95%CI: 1.18-4.22). No significant difference was found between placebo and biological agents regarding their safety. CONCLUSION: All biological agents were superior to placebo for UC treatment in both induction and maintenance phases with a similar safety profile, and infliximab had a better clinical effect than the other biological agents. PMID:26019471

An agent-based stochastic Occupancy Simulator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Yixing; Hong, Tianzhen; Luo, Xuan

Occupancy has significant impacts on building performance. However, in current building performance simulation programs, occupancy inputs are static and lack diversity, contributing to discrepancies between the simulated and actual building performance. This work presents an Occupancy Simulator that simulates the stochastic behavior of occupant presence and movement in buildings, capturing the spatial and temporal occupancy diversity. Each occupant and each space in the building are explicitly simulated as an agent with their profiles of stochastic behaviors. The occupancy behaviors are represented with three types of models: (1) the status transition events (e.g., first arrival in office) simulated with probability distributionmore » model, (2) the random moving events (e.g., from one office to another) simulated with a homogeneous Markov chain model, and (3) the meeting events simulated with a new stochastic model. A hierarchical data model was developed for the Occupancy Simulator, which reduces the amount of data input by using the concepts of occupant types and space types. Finally, a case study of a small office building is presented to demonstrate the use of the Simulator to generate detailed annual sub-hourly occupant schedules for individual spaces and the whole building. The Simulator is a web application freely available to the public and capable of performing a detailed stochastic simulation of occupant presence and movement in buildings. Future work includes enhancements in the meeting event model, consideration of personal absent days, verification and validation of the simulated occupancy results, and expansion for use with residential buildings.« less

An agent-based stochastic Occupancy Simulator

DOE PAGES

Chen, Yixing; Hong, Tianzhen; Luo, Xuan

2017-06-01

Occupancy has significant impacts on building performance. However, in current building performance simulation programs, occupancy inputs are static and lack diversity, contributing to discrepancies between the simulated and actual building performance. This work presents an Occupancy Simulator that simulates the stochastic behavior of occupant presence and movement in buildings, capturing the spatial and temporal occupancy diversity. Each occupant and each space in the building are explicitly simulated as an agent with their profiles of stochastic behaviors. The occupancy behaviors are represented with three types of models: (1) the status transition events (e.g., first arrival in office) simulated with probability distributionmore » model, (2) the random moving events (e.g., from one office to another) simulated with a homogeneous Markov chain model, and (3) the meeting events simulated with a new stochastic model. A hierarchical data model was developed for the Occupancy Simulator, which reduces the amount of data input by using the concepts of occupant types and space types. Finally, a case study of a small office building is presented to demonstrate the use of the Simulator to generate detailed annual sub-hourly occupant schedules for individual spaces and the whole building. The Simulator is a web application freely available to the public and capable of performing a detailed stochastic simulation of occupant presence and movement in buildings. Future work includes enhancements in the meeting event model, consideration of personal absent days, verification and validation of the simulated occupancy results, and expansion for use with residential buildings.« less

Modeling and simulation of biological systems using SPICE language

PubMed Central

Lallement, Christophe; Haiech, Jacques

2017-01-01

The article deals with BB-SPICE (SPICE for Biochemical and Biological Systems), an extension of the famous Simulation Program with Integrated Circuit Emphasis (SPICE). BB-SPICE environment is composed of three modules: a new textual and compact description formalism for biological systems, a converter that handles this description and generates the SPICE netlist of the equivalent electronic circuit and NGSPICE which is an open-source SPICE simulator. In addition, the environment provides back and forth interfaces with SBML (System Biology Markup Language), a very common description language used in systems biology. BB-SPICE has been developed in order to bridge the gap between the simulation of biological systems on the one hand and electronics circuits on the other hand. Thus, it is suitable for applications at the interface between both domains, such as development of design tools for synthetic biology and for the virtual prototyping of biosensors and lab-on-chip. Simulation results obtained with BB-SPICE and COPASI (an open-source software used for the simulation of biochemical systems) have been compared on a benchmark of models commonly used in systems biology. Results are in accordance from a quantitative viewpoint but BB-SPICE outclasses COPASI by 1 to 3 orders of magnitude regarding the computation time. Moreover, as our software is based on NGSPICE, it could take profit of incoming updates such as the GPU implementation, of the coupling with powerful analysis and verification tools or of the integration in design automation tools (synthetic biology). PMID:28787027

Fluctuation-Enhanced Sensing for Biological Agent Detection and Identification

DTIC Science & Technology

2009-01-01

method for bacterium detection published earlier; sensing and evaluating the odors of microbes ; and spectral and amplitude distribution analysis of noise...REPORT TYPE 3. DATES COVERED 00-00-2009 to 00-00-2009 4. TITLE AND SUBTITLE Fluctuation-Enhanced Sensing for Biological Agent Detection and...evaluating the odors of microbes ; and spectral and amplitude distribution analysis of noise in light scattering to identify spores based on their

SPARK: A Framework for Multi-Scale Agent-Based Biomedical Modeling.

PubMed

Solovyev, Alexey; Mikheev, Maxim; Zhou, Leming; Dutta-Moscato, Joyeeta; Ziraldo, Cordelia; An, Gary; Vodovotz, Yoram; Mi, Qi

2010-01-01

Multi-scale modeling of complex biological systems remains a central challenge in the systems biology community. A method of dynamic knowledge representation known as agent-based modeling enables the study of higher level behavior emerging from discrete events performed by individual components. With the advancement of computer technology, agent-based modeling has emerged as an innovative technique to model the complexities of systems biology. In this work, the authors describe SPARK (Simple Platform for Agent-based Representation of Knowledge), a framework for agent-based modeling specifically designed for systems-level biomedical model development. SPARK is a stand-alone application written in Java. It provides a user-friendly interface, and a simple programming language for developing Agent-Based Models (ABMs). SPARK has the following features specialized for modeling biomedical systems: 1) continuous space that can simulate real physical space; 2) flexible agent size and shape that can represent the relative proportions of various cell types; 3) multiple spaces that can concurrently simulate and visualize multiple scales in biomedical models; 4) a convenient graphical user interface. Existing ABMs of diabetic foot ulcers and acute inflammation were implemented in SPARK. Models of identical complexity were run in both NetLogo and SPARK; the SPARK-based models ran two to three times faster.

Dynamic Biological Functioning Important for Simulating and Stabilizing Ocean Biogeochemistry

NASA Astrophysics Data System (ADS)

Buchanan, P. J.; Matear, R. J.; Chase, Z.; Phipps, S. J.; Bindoff, N. L.

2018-04-01

The biogeochemistry of the ocean exerts a strong influence on the climate by modulating atmospheric greenhouse gases. In turn, ocean biogeochemistry depends on numerous physical and biological processes that change over space and time. Accurately simulating these processes is fundamental for accurately simulating the ocean's role within the climate. However, our simulation of these processes is often simplistic, despite a growing understanding of underlying biological dynamics. Here we explore how new parameterizations of biological processes affect simulated biogeochemical properties in a global ocean model. We combine 6 different physical realizations with 6 different biogeochemical parameterizations (36 unique ocean states). The biogeochemical parameterizations, all previously published, aim to more accurately represent the response of ocean biology to changing physical conditions. We make three major findings. First, oxygen, carbon, alkalinity, and phosphate fields are more sensitive to changes in the ocean's physical state. Only nitrate is more sensitive to changes in biological processes, and we suggest that assessment protocols for ocean biogeochemical models formally include the marine nitrogen cycle to assess their performance. Second, we show that dynamic variations in the production, remineralization, and stoichiometry of organic matter in response to changing environmental conditions benefit the simulation of ocean biogeochemistry. Third, dynamic biological functioning reduces the sensitivity of biogeochemical properties to physical change. Carbon and nitrogen inventories were 50% and 20% less sensitive to physical changes, respectively, in simulations that incorporated dynamic biological functioning. These results highlight the importance of a dynamic biology for ocean properties and climate.

Agent Based Modeling Applications for Geosciences

NASA Astrophysics Data System (ADS)

Stein, J. S.

2004-12-01

Agent-based modeling techniques have successfully been applied to systems in which complex behaviors or outcomes arise from varied interactions between individuals in the system. Each individual interacts with its environment, as well as with other individuals, by following a set of relatively simple rules. Traditionally this "bottom-up" modeling approach has been applied to problems in the fields of economics and sociology, but more recently has been introduced to various disciplines in the geosciences. This technique can help explain the origin of complex processes from a relatively simple set of rules, incorporate large and detailed datasets when they exist, and simulate the effects of extreme events on system-wide behavior. Some of the challenges associated with this modeling method include: significant computational requirements in order to keep track of thousands to millions of agents, methods and strategies of model validation are lacking, as is a formal methodology for evaluating model uncertainty. Challenges specific to the geosciences, include how to define agents that control water, contaminant fluxes, climate forcing and other physical processes and how to link these "geo-agents" into larger agent-based simulations that include social systems such as demographics economics and regulations. Effective management of limited natural resources (such as water, hydrocarbons, or land) requires an understanding of what factors influence the demand for these resources on a regional and temporal scale. Agent-based models can be used to simulate this demand across a variety of sectors under a range of conditions and determine effective and robust management policies and monitoring strategies. The recent focus on the role of biological processes in the geosciences is another example of an area that could benefit from agent-based applications. A typical approach to modeling the effect of biological processes in geologic media has been to represent these processes in

Evaluation of "shotgun" proteomics for identification of biological threat agents in complex environmental matrixes: experimental simulations.

PubMed

Verberkmoes, Nathan C; Hervey, W Judson; Shah, Manesh; Land, Miriam; Hauser, Loren; Larimer, Frank W; Van Berkel, Gary J; Goeringer, Douglas E

2005-02-01

There is currently a great need for rapid detection and positive identification of biological threat agents, as well as microbial species in general, directly from complex environmental samples. This need is most urgent in the area of homeland security, but also extends into medical, environmental, and agricultural sciences. Mass-spectrometry-based analysis is one of the leading technologies in the field with a diversity of different methodologies for biothreat detection. Over the past few years, "shotgun"proteomics has become one method of choice for the rapid analysis of complex protein mixtures by mass spectrometry. Recently, it was demonstrated that this methodology is capable of distinguishing a target species against a large database of background species from a single-component sample or dual-component mixtures with relatively the same concentration. Here, we examine the potential of shotgun proteomics to analyze a target species in a background of four contaminant species. We tested the capability of a common commercial mass-spectrometry-based shotgun proteomics platform for the detection of the target species (Escherichia coli) at four different concentrations and four different time points of analysis. We also tested the effect of database size on positive identification of the four microbes used in this study by testing a small (13-species) database and a large (261-species) database. The results clearly indicated that this technology could easily identify the target species at 20% in the background mixture at a 60, 120, 180, or 240 min analysis time with the small database. The results also indicated that the target species could easily be identified at 20% or 6% but could not be identified at 0.6% or 0.06% in either a 240 min analysis or a 30 h analysis with the small database. The effects of the large database were severe on the target species where detection above the background at any concentration used in this study was impossible, though the three

Method and apparatus for the gas phase decontamination of chemical and biological agents

DOEpatents

O'Neill, Hugh J.; Brubaker, Kenneth L.

2003-10-07

An apparatus and method for decontaminating chemical and biological agents using the reactive properties of both the single atomic oxygen and the hydroxyl radical for the decontamination of chemical and biological agents. The apparatus is self contained and portable and allows for the application of gas reactants directly at the required decontamination point. The system provides for the use of ultraviolet light of a specific spectral range to photolytically break down ozone into molecular oxygen and hydroxyl radicals where some of the molecular oxygen is in the first excited state. The excited molecular oxygen will combine with water vapor to produce two hydroxyl radicals.

New biological agents in the treatment of multiple sclerosis.

PubMed

Buc, M

2018-01-01

Multiple sclerosis (MS) is an inflammatory disease induced by autoimmune processes. Their understanding has resulted in an introduction of biological agents to its treatment. Interferon beta and glatiramer acetate have been in clinical practice for more than 20 years. Nowadays, novel biologics, which target molecules involved in immunopathological processes more specifically have entered the scene. They are represented by monoclonal antibodies binding to molecules VLA4 (natalizumab), CD20 (ocrelizumab), CD52 (alemtuzumab) or alpha subunit of IL-2 receptor (daclizumab) or by small molecules such as those modulating the receptors involved in regulation of lymphocyte migration (fingolimod, ozanimod) or in induction of lymphopenia by apoptosis (dimethyl fumarate, cladribine). In the article, we shortly describe their efficacies, adverse reactions and perspectives of a future development in MS biologics. A treatment of neuromyelitis optica by monoclonal antibodies (rituximab, aquaporumab) is given too (Tab. 1, Fig. 2, Ref. 71).

Pedestrian simulation and distribution in urban space based on visibility analysis and agent simulation

NASA Astrophysics Data System (ADS)

Ying, Shen; Li, Lin; Gao, Yurong

2009-10-01

Spatial visibility analysis is the important direction of pedestrian behaviors because our visual conception in space is the straight method to get environment information and navigate your actions. Based on the agent modeling and up-tobottom method, the paper develop the framework about the analysis of the pedestrian flow depended on visibility. We use viewshed in visibility analysis and impose the parameters on agent simulation to direct their motion in urban space. We analyze the pedestrian behaviors in micro-scale and macro-scale of urban open space. The individual agent use visual affordance to determine his direction of motion in micro-scale urban street on district. And we compare the distribution of pedestrian flow with configuration in macro-scale urban environment, and mine the relationship between the pedestrian flow and distribution of urban facilities and urban function. The paper first computes the visibility situations at the vantage point in urban open space, such as street network, quantify the visibility parameters. The multiple agents use visibility parameters to decide their direction of motion, and finally pedestrian flow reach to a stable state in urban environment through the simulation of multiple agent system. The paper compare the morphology of visibility parameters and pedestrian distribution with urban function and facilities layout to confirm the consistence between them, which can be used to make decision support in urban design.

Biologic agents for anterior cruciate ligament healing: A systematic review

PubMed Central

Di Matteo, Berardo; Loibl, Markus; Andriolo, Luca; Filardo, Giuseppe; Zellner, Johannes; Koch, Matthias; Angele, Peter

2016-01-01

AIM To systematically review the currently available literature concerning the application of biologic agents such as platelet-rich plasma (PRP) and stem cells to promote anterior cruciate ligament (ACL) healing. METHODS A systematic review of the literature was performed on the use of biologic agents (i.e., PRP or stem cells) to favor ACL healing during reconstruction or repair. The following inclusion criteria for relevant articles were used: Clinical reports of any level of evidence, written in English language, on the use of PRP or stem cells during ACL reconstruction/repair. Exclusion criteria were articles written in other languages, reviews, or studies analyzing other applications of PRP/stem cells in knee surgery not related to promoting ACL healing. RESULTS The database search identified 394 records that were screened. A total of 23 studies were included in the final analysis: In one paper stem cells were applied for ACL healing, in one paper there was a concomitant application of PRP and stem cells, whereas in the remaining 21 papers PRP was used. Based on the ACL injury pattern, two papers investigated biologic agents in ACL partial tears whereas 21 papers in ACL reconstruction. Looking at the quality of the available literature, 17 out of 21 studies dealing with ACL reconstruction were randomized controlled trials. Both studies on ACL repair were case series. CONCLUSION There is a paucity of clinical trials investigating the role of stem cells in promoting ACL healing both in case of partial and complete tears. The role of PRP is still controversial and the only advantage emerging from the literature is related to a better graft maturation over time, without documenting beneficial effects in terms of clinical outcome, bone-graft integration and prevention of bony tunnel enlargement. PMID:27672573

Multispectral analysis of biological agents to implement a quick tool for stand-off biological detection

NASA Astrophysics Data System (ADS)

Carestia, M.; Pizzoferrato, R.; Lungaroni, M.; Gabriele, J.; Ludovici, G. M.; Cenciarelli, O.; Gelfusa, M.; Murari, A.; Malizia, A.; Gaudio, P.

2015-10-01

With the aim of identifying an approach to exploit the differences in the fluorescence signatures of biological agents BAs, we have investigated the response of some BAs simulants to a set of different excitation wavelengths in the UV spectral range (i.e. 266, 273, 280, 300, 340, 355 nm). Our preliminary results on bacterial spores and vegetative forms, dispersed in water, showed that the differences in the fluorescence spectra can be enhanced, and more easily revealed, by using different excitation wavelengths. Specifically, the photo luminescence (PL) spectra coming from different species of Bacillus, in the form of spores (used as simulants of Bacillus anthracis), show significant differences under excitation at all the wavelengths, with slightly larger differences at 300, 340, 355 nm. On the other hand, the vegetative forms of two Bacillus species, did not show any appreciable difference, i.e. the PL spectra are virtually identical, for the excitation wavelengths of 266, 273, 280 nm. Conversely, small yet appreciable difference appear at 300, 340, 355 nm. Finally, large difference appear between the spore and the vegetative form of each species at all the wavelengths, with slightly larger variations at 300, 340, 355 nm. Together, these preliminary results support the hypothesis that a multi-wavelength approach could be used to improve the sensitivity and specificity of UV-LIF based BAs detection systems. The second step of this work concerns the application of a Support Vector Regression (SVR) method, as evaluated in our previous work to define a methodology for the setup of a multispectral database for the stand-off detection of BAs.

A Proposed Computed Tomography Contrast Agent Using Carboxybetaine Zwitterionic Tantalum Oxide Nanoparticles: Imaging, Biological, and Physicochemical Performance.

PubMed

FitzGerald, Paul F; Butts, Matthew D; Roberts, Jeannette C; Colborn, Robert E; Torres, Andrew S; Lee, Brian D; Yeh, Benjamin M; Bonitatibus, Peter J

2016-12-01

The aim of this study was to produce and evaluate a proposed computed tomography (CT) contrast agent based on carboxybetaine zwitterionic (CZ)-coated soluble tantalum oxide (TaO) nanoparticles (NPs). We chose tantalum to provide superior imaging performance compared with current iodine-based clinical CT contrast agents. We developed the CZ coating to provide biological and physical performance similar to that of current iodinated contrast agents. In addition, the aim of this study was to evaluate the imaging, biological, and physicochemical performance of this proposed contrast agent compared with clinically used iodinated agents. We evaluated CT imaging performance of our CZ-TaO NPs compared with that of an iodinated agent in live rats, imaged centrally located within a tissue-equivalent plastic phantom that simulated a large patient. To evaluate vascular contrast enhancement, we scanned the rats' great vessels at high temporal resolution during and after contrast agent injection. We performed several in vivo CZ-TaO NP studies in healthy rats to evaluate tolerability. These studies included injecting the agent at the anticipated clinical dose (ACD) and at 3 times and 6 times the ACD, followed by longitudinal hematology to assess impact to blood cells and organ function (from 4 hours to 1 week). Kidney histological analysis was performed 48 hours after injection at 3 times the ACD. We measured the elimination half-life of CZ-TaO NPs from blood, and we monitored acute kidney injury biomarkers with a kidney injury assay using urine collected from 4 hours to 1 week. We measured tantalum retention in individual organs and in the whole carcass 48 hours after injection at ACD. Carboxybetaine zwitterionic TaO NPs were synthesized and analyzed in detail. We used multidimensional nuclear magnetic resonance to determine surface functionality of the NPs. We measured NP size and solution properties (osmolality and viscosity) of the agent over a range of tantalum concentrations

Cognitive Modeling for Agent-Based Simulation of Child Maltreatment

NASA Astrophysics Data System (ADS)

Hu, Xiaolin; Puddy, Richard

This paper extends previous work to develop cognitive modeling for agent-based simulation of child maltreatment (CM). The developed model is inspired from parental efficacy, parenting stress, and the theory of planned behavior. It provides an explanatory, process-oriented model of CM and incorporates causality relationship and feedback loops from different factors in the social ecology in order for simulating the dynamics of CM. We describe the model and present simulation results to demonstrate the features of this model.

Biological Warfare Agents, Toxins, Vectors and Pests as Biological Terrorism Agents

DTIC Science & Technology

2003-07-01

number of positive answers. According to criterion, no effective prophylaxis or therapy, positive answer signifies the absence of effective ...likelihood that the agent will be used. There are not effective prophylaxis and therapy against for the bulk of enlisted agents and toxins if used as...difficult to imagine how it would be looked like mass- vaccination often maybe simultaneously against more than one disease. Toxins are effective and

Crowd Simulation Incorporating Agent Psychological Models, Roles and Communication

DTIC Science & Technology

2005-01-01

system (PMFserv) that implements human behavior models from a range of ability, stress, emotion , decision theoretic and motivation sources. An...autonomous agents, human behavior models, culture and emotions 1. Introduction There are many applications of computer animation and simulation where...We describe a new architecture to integrate a psychological model into a crowd simulation system in order to obtain believable emergent behaviors

Mobile Robot Enabled Detection of Explosives and Biological Agents

DTIC Science & Technology

2006-11-01

Detection of Explosives and Biological Agents 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR( S ) 5d. PROJECT NUMBER 5e...TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME( S ) AND ADDRESS(ES) Wayne State University, SSIM Program, Detroit, Michigan 48202 8...PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING/MONITORING AGENCY NAME( S ) AND ADDRESS(ES) 10. SPONSOR/MONITOR’S ACRONYM( S ) 11. SPONSOR

Design and Simulation of Material-Integrated Distributed Sensor Processing with a Code-Based Agent Platform and Mobile Multi-Agent Systems

PubMed Central

Bosse, Stefan

2015-01-01

Multi-agent systems (MAS) can be used for decentralized and self-organizing data processing in a distributed system, like a resource-constrained sensor network, enabling distributed information extraction, for example, based on pattern recognition and self-organization, by decomposing complex tasks in simpler cooperative agents. Reliable MAS-based data processing approaches can aid the material-integration of structural-monitoring applications, with agent processing platforms scaled to the microchip level. The agent behavior, based on a dynamic activity-transition graph (ATG) model, is implemented with program code storing the control and the data state of an agent, which is novel. The program code can be modified by the agent itself using code morphing techniques and is capable of migrating in the network between nodes. The program code is a self-contained unit (a container) and embeds the agent data, the initialization instructions and the ATG behavior implementation. The microchip agent processing platform used for the execution of the agent code is a standalone multi-core stack machine with a zero-operand instruction format, leading to a small-sized agent program code, low system complexity and high system performance. The agent processing is token-queue-based, similar to Petri-nets. The agent platform can be implemented in software, too, offering compatibility at the operational and code level, supporting agent processing in strong heterogeneous networks. In this work, the agent platform embedded in a large-scale distributed sensor network is simulated at the architectural level by using agent-based simulation techniques. PMID:25690550

Design and simulation of material-integrated distributed sensor processing with a code-based agent platform and mobile multi-agent systems.

PubMed

Bosse, Stefan

2015-02-16

Multi-agent systems (MAS) can be used for decentralized and self-organizing data processing in a distributed system, like a resource-constrained sensor network, enabling distributed information extraction, for example, based on pattern recognition and self-organization, by decomposing complex tasks in simpler cooperative agents. Reliable MAS-based data processing approaches can aid the material-integration of structural-monitoring applications, with agent processing platforms scaled to the microchip level. The agent behavior, based on a dynamic activity-transition graph (ATG) model, is implemented with program code storing the control and the data state of an agent, which is novel. The program code can be modified by the agent itself using code morphing techniques and is capable of migrating in the network between nodes. The program code is a self-contained unit (a container) and embeds the agent data, the initialization instructions and the ATG behavior implementation. The microchip agent processing platform used for the execution of the agent code is a standalone multi-core stack machine with a zero-operand instruction format, leading to a small-sized agent program code, low system complexity and high system performance. The agent processing is token-queue-based, similar to Petri-nets. The agent platform can be implemented in software, too, offering compatibility at the operational and code level, supporting agent processing in strong heterogeneous networks. In this work, the agent platform embedded in a large-scale distributed sensor network is simulated at the architectural level by using agent-based simulation techniques.

UAV Swarm Tactics: An Agent-Based Simulation and Markov Process Analysis

DTIC Science & Technology

2013-06-01

CRN Common Random Numbers CSV Comma Separated Values DoE Design of Experiment GLM Generalized Linear Model HVT High Value Target JAR Java ARchive JMF... Java Media Framework JRE Java runtime environment Mason Multi-Agent Simulator Of Networks MOE Measure Of Effectiveness MOP Measures Of Performance...with every set several times, and to write a CSV file with the results. Rather than scripting the agent behavior deterministically, the agents should

DNA capture elements for rapid detection and identification of biological agents

NASA Astrophysics Data System (ADS)

Kiel, Johnathan L.; Parker, Jill E.; Holwitt, Eric A.; Vivekananda, Jeeva

2004-08-01

DNA capture elements (DCEs; aptamers) are artificial DNA sequences, from a random pool of sequences, selected for their specific binding to potential biological warfare agents. These sequences were selected by an affinity method using filters to which the target agent was attached and the DNA isolated and amplified by polymerase chain reaction (PCR) in an iterative, increasingly stringent, process. Reporter molecules were attached to the finished sequences. To date, we have made DCEs to Bacillus anthracis spores, Shiga toxin, Venezuelan Equine Encephalitis (VEE) virus, and Francisella tularensis. These DCEs have demonstrated specificity and sensitivity equal to or better than antibody.

Development of biosensors for the detection of biological warfare agents: its issues and challenges.

PubMed

Kumar, Harish; Rani, Renu

2013-01-01

This review discusses current development in biosensors for the detection of biological warfare agents (BWAs). BWAs include bacteria, virus and toxins that are added deliberately into air water and food to spread terrorism and cause disease or death. The rapid and unambiguous detection and identification of BWAs with early warning signals for detecting possible biological attack is a major challenge for government agencies particularly military and health. The detection devices--biosensors--can be classified (according to their physicochemical transducers) into four types: electrochemical, nucleic acid, optical and piezoelectric. Advantages and limitations of biosensors are discussed in this review followed by an assessment of the current state of development of different types of biosensors. The research and development in biosensors for biological warfare agent detection is of great interest for the public as well as for governments.

Insect-gene-activity detection system for chemical and biological warfare agents and toxic industrial chemicals

NASA Astrophysics Data System (ADS)

Mackie, Ryan S.; Schilling, Amanda S.; Lopez, Arturo M.; Rayms-Keller, Alfredo

2002-02-01

Detection of multiple chemical and biological weapons (CBW) agents and/or complex mixtures of toxic industrial chemicals (TIC) is imperative for both the commercial and military sectors. In a military scenario, a multi-CBW attack would create confusion, thereby delaying decontamination and therapeutic efforts. In the commercial sector, polluted sites invariably contain a mixture of TIC. Novel detection systems capable of detecting CBW and TIC are sorely needed. While it may be impossible to build a detector capable of discriminating all the possible combinations of CBW, a detection system capable of statistically predicting the most likely composition of a given mixture is within the reach of current emerging technologies. Aquatic insect-gene activity may prove to be a sensitive, discriminating, and elegant paradigm for the detection of CBW and TIC. We propose to systematically establish the expression patterns of selected protein markers in insects exposed to specific mixtures of chemical and biological warfare agents to generate a library of biosignatures of exposure. The predicting capabilities of an operational library of biosignatures of exposures will allow the detection of emerging novel or genetically engineered agents, as well as complex mixtures of chemical and biological weapons agents. CBW and TIC are discussed in the context of war, terrorism, and pollution.

Multi-Agent Flight Simulation with Robust Situation Generation

NASA Technical Reports Server (NTRS)

Johnson, Eric N.; Hansman, R. John, Jr.

1994-01-01

A robust situation generation architecture has been developed that generates multi-agent situations for human subjects. An implementation of this architecture was developed to support flight simulation tests of air transport cockpit systems. This system maneuvers pseudo-aircraft relative to the human subject's aircraft, generating specific situations for the subject to respond to. These pseudo-aircraft maneuver within reasonable performance constraints, interact in a realistic manner, and make pre-recorded voice radio communications. Use of this system minimizes the need for human experimenters to control the pseudo-agents and provides consistent interactions between the subject and the pseudo-agents. The achieved robustness of this system to typical variations in the subject's flight path was explored. It was found to successfully generate specific situations within the performance limitations of the subject-aircraft, pseudo-aircraft, and the script used.

Introduction to economic modeling for clinical rheumatologists: application to biologic agents in rheumatoid arthritis.

PubMed

Marra, Carlo A; Bansback, Nick; Anis, Aslam H; Shojania, Kamran

2011-03-01

Rheumatoid arthritis (RA) is a chronic, debilitating inflammatory, progressive musculoskeletal disease that affects 0.5-1.0% of the adult population in Western countries. The joint destruction and progressive functional disability associated with uncontrolled RA result in tremendous impacts on health-related quality of life, ability to work, and mortality. In addition, the treatment of the disease and associated complications exact a substantial economic burden to the patients, their families, and society. In the last decade, several biological agents (biologics) have been approved for use in RA, revolutionizing treatment. These biologics, which target cytokines such as tumor necrosis factor or lymphocytes such as B or T cells, reduce functional disability and substantially slow the progression of joint damage. However, because these agents typically cost ten to 100 times more than existing available older drug therapies, there has been worldwide concern regarding their impact on healthcare budgets. As such, there has been increased attention towards economic evaluation as a means to determine whether, and in which subgroup of patients, these newer, more expensive agents confer appropriate value for their additional cost. Indeed, evaluations have guided coverage decisions for both private and public health insurance agencies such as the National Institute for Health and Clinical Excellence in the UK. The use of economic evaluations to determine value for money for these agents has attracted both debate and controversy. Some of the controversy is related to the appropriateness of the structure of, and assumptions underlying, the decision models employed to estimate the long-term costs and benefits of these agents over existing therapies. To fully appreciate the debate, one must first understand the basic principles of economic evaluation and the necessity for using decision models to evaluate cost effectiveness. To understand the basic principles of economic

Multi-agent simulation of the von Thunen model formation mechanism

NASA Astrophysics Data System (ADS)

Tao, Haiyan; Li, Xia; Chen, Xiaoxiang; Deng, Chengbin

2008-10-01

This research tries to explain the internal driving forces of circular structure formation in urban geography via the simulation of interaction between individual behavior and market. On the premise of single city center, unchanged scale merit and complete competition, enterprise migration theory as well, an R-D algorithm, that has agents searched the best behavior rules in some given locations, is introduced with agent-based modeling technique. The experiment conducts a simulation on Swarm platform, whose result reflects and replays the formation process of Von Thünen circular structure. Introducing and considering some heterogeneous factors, such as traffic roads, the research verifies several landuse models and discusses the self-adjustment function of price mechanism.

A water market simulator considering pair-wise trades between agents

NASA Astrophysics Data System (ADS)

Huskova, I.; Erfani, T.; Harou, J. J.

2012-04-01

In many basins in England no further water abstraction licences are available. Trading water between water rights holders has been recognized as a potentially effective and economically efficient strategy to mitigate increasing scarcity. A screening tool that could assess the potential for trade through realistic simulation of individual water rights holders would help assess the solution's potential contribution to local water management. We propose an optimisation-driven water market simulator that predicts pair-wise trade in a catchment and represents its interaction with natural hydrology and engineered infrastructure. A model is used to emulate licence-holders' willingness to engage in short-term trade transactions. In their simplest form agents are represented using an economic benefit function. The working hypothesis is that trading behaviour can be partially predicted based on differences in marginal values of water over space and time and estimates of transaction costs on pair-wise trades. We discuss the further possibility of embedding rules, norms and preferences of the different water user sectors to more realistically represent the behaviours, motives and constraints of individual licence holders. The potential benefits and limitations of such a social simulation (agent-based) approach is contrasted with our simulator where agents are driven by economic optimization. A case study based on the Dove River Basin (UK) demonstrates model inputs and outputs. The ability of the model to suggest impacts of water rights policy reforms on trading is discussed.

Personal protection during resuscitation of casualties contaminated with chemical or biological warfare agents--a survey of medical first responders.

PubMed

Brinker, Andrea; Prior, Kate; Schumacher, Jan

2009-01-01

The threat of mass casualties caused by an unconventional terrorist attack is a challenge for the public health system, with special implications for emergency medicine, anesthesia, and intensive care. Advanced life support of patients injured by chemical or biological warfare agents requires an adequate level of personal protection. The aim of this study was to evaluate the personal protection knowledge of emergency physicians and anesthetists who would be at the frontline of the initial health response to a chemical/biological warfare agent incident. After institutional review board approval, knowledge of personal protection measures among emergency medicine (n = 28) and anesthetics (n = 47) specialty registrars in the South Thames Region of the United Kingdom was surveyed using a standardized questionnaire. Participants were asked for the recommended level of personal protection if a chemical/biological warfare agent(s) casualty required advanced life support in the designated hospital resuscitation area. The best awareness within both groups was regarding severe acute respiratory syndrome, and fair knowledge was found regarding anthrax, plague, Ebola, and smallpox. In both groups, knowledge about personal protection requirements against chemical warfare agents was limited. Knowledge about personal protection measures for biological agents was acceptable, but was limited for chemical warfare agents. The results highlight the need to improve training and education regarding personal protection measures for medical first receivers.

A framework for service enterprise workflow simulation with multi-agents cooperation

NASA Astrophysics Data System (ADS)

Tan, Wenan; Xu, Wei; Yang, Fujun; Xu, Lida; Jiang, Chuanqun

2013-11-01

Process dynamic modelling for service business is the key technique for Service-Oriented information systems and service business management, and the workflow model of business processes is the core part of service systems. Service business workflow simulation is the prevalent approach to be used for analysis of service business process dynamically. Generic method for service business workflow simulation is based on the discrete event queuing theory, which is lack of flexibility and scalability. In this paper, we propose a service workflow-oriented framework for the process simulation of service businesses using multi-agent cooperation to address the above issues. Social rationality of agent is introduced into the proposed framework. Adopting rationality as one social factor for decision-making strategies, a flexible scheduling for activity instances has been implemented. A system prototype has been developed to validate the proposed simulation framework through a business case study.

Stochastic simulation in systems biology

PubMed Central

Székely, Tamás; Burrage, Kevin

2014-01-01

Natural systems are, almost by definition, heterogeneous: this can be either a boon or an obstacle to be overcome, depending on the situation. Traditionally, when constructing mathematical models of these systems, heterogeneity has typically been ignored, despite its critical role. However, in recent years, stochastic computational methods have become commonplace in science. They are able to appropriately account for heterogeneity; indeed, they are based around the premise that systems inherently contain at least one source of heterogeneity (namely, intrinsic heterogeneity). In this mini-review, we give a brief introduction to theoretical modelling and simulation in systems biology and discuss the three different sources of heterogeneity in natural systems. Our main topic is an overview of stochastic simulation methods in systems biology. There are many different types of stochastic methods. We focus on one group that has become especially popular in systems biology, biochemistry, chemistry and physics. These discrete-state stochastic methods do not follow individuals over time; rather they track only total populations. They also assume that the volume of interest is spatially homogeneous. We give an overview of these methods, with a discussion of the advantages and disadvantages of each, and suggest when each is more appropriate to use. We also include references to software implementations of them, so that beginners can quickly start using stochastic methods for practical problems of interest. PMID:25505503

Synthesis and biological activity of imidazopyridine anticoccidial agents: part I.

PubMed

Scribner, Andrew; Dennis, Richard; Hong, Jean; Lee, Shuliang; McIntyre, Donald; Perrey, David; Feng, Dennis; Fisher, Michael; Wyvratt, Matthew; Leavitt, Penny; Liberator, Paul; Gurnett, Anne; Brown, Chris; Mathew, John; Thompson, Donald; Schmatz, Dennis; Biftu, Tesfaye

2007-01-01

Coccidiosis is the major cause of morbidity and mortality in the poultry industry. Protozoan parasites of the genus Eimeria invade the intestinal lining of the avian host causing tissue pathology, poor weight gain, and in some cases mortality. Resistance to current anticoccidials has prompted the search for new therapeutic agents with potent in vitro and in vivo activity against Eimeria. Antiparasitic activity is due to inhibition of a parasite specific cGMP-dependent protein kinase (PKG). In this study, we present the synthesis and biological activity of imidazo[1,2-a]pyridine anticoccidial agents. From this series, several compounds showed subnanomolar in vitro activity and commercial levels of in vivo activity. However, the potential genotoxicity of these compounds precludes them from further development.

Canada thistle biological control agents on two South Dakota wildlife refuges

USGS Publications Warehouse

Reed, C.C.; Larson, D.L.; Larson, J.L.

2006-01-01

We monitored populations of Canada thistle biocontrol agents Cassida rubiginosa, Ceutorhynchus litura, Larinus (= Hadroplantus) planus, Urophora cardui, Orellia (= Terellia) ruficauda, and Rhinocyllus conicus on Canada thistle (Cirsium arvense) at two national wildlife refuges in South Dakota from 1999 through 2003. C. litura, U. cardui, O. ruficauda, and R. conicus were present on both refuges. Agent populations were low except for C. litura, which was present in up to 90% of stems in some plots. C. litura infestation did not reduce thistle flowering, stem length, or over-winter survival. There was no change in thistle stem numbers over the study period and no difference in stem numbers in areas of high C. litura populations compared to areas of low C. litura populations. Our results suggest that insect biological control agents are inadequate for reduction of Canada thistle in southern South Dakota.

Simulation of economic agents interaction in a trade chain

NASA Astrophysics Data System (ADS)

Gimanova, I. A.; Dulesov, A. S.; Litvin, N. V.

2017-01-01

The mathematical model of economic agents interaction is offered in the work. It allowsconsidering the change of price and sales volumesin dynamics according to the process of purchase and sale in the single-product market of the trade and intermediary network. The description of data-flow processes is based on the use of the continuous dynamic market model. The application of ordinary differential equations during the simulation allows one to define areas of coefficients - characteristics of agents - and to investigate their interaction in a chain on stability.

A hybrid agent-based approach for modeling microbiological systems.

PubMed

Guo, Zaiyi; Sloot, Peter M A; Tay, Joc Cing

2008-11-21

Models for systems biology commonly adopt Differential Equations or Agent-Based modeling approaches for simulating the processes as a whole. Models based on differential equations presuppose phenomenological intracellular behavioral mechanisms, while models based on Multi-Agent approach often use directly translated, and quantitatively less precise if-then logical rule constructs. We propose an extendible systems model based on a hybrid agent-based approach where biological cells are modeled as individuals (agents) while molecules are represented by quantities. This hybridization in entity representation entails a combined modeling strategy with agent-based behavioral rules and differential equations, thereby balancing the requirements of extendible model granularity with computational tractability. We demonstrate the efficacy of this approach with models of chemotaxis involving an assay of 10(3) cells and 1.2x10(6) molecules. The model produces cell migration patterns that are comparable to laboratory observations.

Bacteriophage lambda: The path from biology to theranostic agent.

PubMed

Catalano, Carlos E

2018-03-13

Viral particles provide an attractive platform for the engineering of semisynthetic therapeutic nanoparticles. They can be modified both genetically and chemically in a defined manner to alter their surface characteristics, for targeting specific cell types, to improve their pharmacokinetic features and to attenuate (or enhance) their antigenicity. These advantages derive from a detailed understanding of virus biology, gleaned from decades of fundamental genetic, biochemical, and structural studies that have provided mechanistic insight into virus assembly pathways. In particular, bacteriophages offer significant advantages as nanoparticle platforms and several have been adapted toward the design and engineering of "designer" nanoparticles for therapeutic and diagnostic (theranostic) applications. The present review focuses on one such virus, bacteriophage lambda; I discuss the biology of lambda, the tools developed to faithfully recapitulate the lambda assembly reactions in vitro and the observations that have led to cooptation of the lambda system for nanoparticle design. This discussion illustrates how a fundamental understanding of virus assembly has allowed the rational design and construction of semisynthetic nanoparticles as potential theranostic agents and illustrates the concept of benchtop to bedside translational research. This article is categorized under: Biology-Inspired Nanomaterials> Protein and Virus-Based Structures Biology-Inspired Nanomaterials> Nucleic Acid-Based Structures. © 2018 Wiley Periodicals, Inc.

Chemical Computer Man: Chemical Agent Response Simulation (CARS). Technical report, January 1983-September 1985

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davis, E.G.; Mioduszewski, R.J.

The Chemical Computer Man: Chemical Agent Response Simulation (CARS) is a computer model and simulation program for estimating the dynamic changes in human physiological dysfunction resulting from exposures to chemical-threat nerve agents. The newly developed CARS methodology simulates agent exposure effects on the following five indices of human physiological function: mental, vision, cardio-respiratory, visceral, and limbs. Mathematical models and the application of basic pharmacokinetic principles were incorporated into the simulation so that for each chemical exposure, the relationship between exposure dosage, absorbed dosage (agent blood plasma concentration), and level of physiological response are computed as a function of time. CARS,more » as a simulation tool, is designed for the users with little or no computer-related experience. The model combines maximum flexibility with a comprehensive user-friendly interactive menu-driven system. Users define an exposure problem and obtain immediate results displayed in tabular, graphical, and image formats. CARS has broad scientific and engineering applications, not only in technology for the soldier in the area of Chemical Defense, but also in minimizing animal testing in biomedical and toxicological research and the development of a modeling system for human exposure to hazardous-waste chemicals.« less

Deciphering endophyte behaviour: the link between endophyte biology and efficacious biological control agents.

PubMed

Card, Stuart; Johnson, Linda; Teasdale, Suliana; Caradus, John

2016-08-01

Endophytes associate with the majority of plant species found in natural and managed ecosystems. They are regarded as extremely important plant partners that provide improved stress tolerance to the host compared with plants that lack this symbiosis. Fossil records of endophytes date back more than 400 million years, implicating these microorganisms in host plant adaptation to habitat transitions. However, it is only recently that endophytes, and their bioactive products, have received meaningful attention from the scientific community. The benefits some endophytes can confer on their hosts include plant growth promotion and survival through the inhibition of pathogenic microorganisms and invertebrate pests, the removal of soil contaminants, improved tolerance of low fertility soils, and increased tolerance of extreme temperatures and low water availability. Endophytes are extremely diverse and can exhibit many different biological behaviours. Not all endophyte technologies have been successfully commercialised. Of interest in the development of the next generation of plant protection products is how much of this is due to the biology of the particular endophytic microorganism. In this review, we highlight selected case studies of endophytes and discuss their lifestyles and behavioural traits, and discuss how these factors contribute towards their effectiveness as biological control agents. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Modeling Co-evolution of Speech and Biology.

PubMed

de Boer, Bart

2016-04-01

Two computer simulations are investigated that model interaction of cultural evolution of language and biological evolution of adaptations to language. Both are agent-based models in which a population of agents imitates each other using realistic vowels. The agents evolve under selective pressure for good imitation. In one model, the evolution of the vocal tract is modeled; in the other, a cognitive mechanism for perceiving speech accurately is modeled. In both cases, biological adaptations to using and learning speech evolve, even though the system of speech sounds itself changes at a more rapid time scale than biological evolution. However, the fact that the available acoustic space is used maximally (a self-organized result of cultural evolution) is constant, and therefore biological evolution does have a stable target. This work shows that when cultural and biological traits are continuous, their co-evolution may lead to cognitive adaptations that are strong enough to detect empirically. Copyright © 2016 Cognitive Science Society, Inc.

Guidelines for Managing Suspected Chemical and Biological Agent Incidents in Rail Tunnel Systems

DOT National Transportation Integrated Search

2002-03-01

These emergency management guidelines are designed to help transit managers (1) prepare and implement standard operating procedures (SOPs) for handling potential and actual chemical or biological agent attacks in their rail tunnel system and (2) unde...

Understanding the Impact of Intelligent Tutoring Agents on Real-Time Training Simulations

DTIC Science & Technology

2011-01-01

environments has increased. Intelligent Tutoring Systems (ITS) technology may include reactive or proactive simulation agents that monitor and... environments . These reactive agents monitor the trainee’s progress and provide hints or other feedback only when there is sufficient variance from... agents have a higher computational cost in that they need to sense and understand more about the trainee, environment and training context, but are

Agent-Based Deterministic Modeling of the Bone Marrow Homeostasis.

PubMed

Kurhekar, Manish; Deshpande, Umesh

2016-01-01

Modeling of stem cells not only describes but also predicts how a stem cell's environment can control its fate. The first stem cell populations discovered were hematopoietic stem cells (HSCs). In this paper, we present a deterministic model of bone marrow (that hosts HSCs) that is consistent with several of the qualitative biological observations. This model incorporates stem cell death (apoptosis) after a certain number of cell divisions and also demonstrates that a single HSC can potentially populate the entire bone marrow. It also demonstrates that there is a production of sufficient number of differentiated cells (RBCs, WBCs, etc.). We prove that our model of bone marrow is biologically consistent and it overcomes the biological feasibility limitations of previously reported models. The major contribution of our model is the flexibility it allows in choosing model parameters which permits several different simulations to be carried out in silico without affecting the homeostatic properties of the model. We have also performed agent-based simulation of the model of bone marrow system proposed in this paper. We have also included parameter details and the results obtained from the simulation. The program of the agent-based simulation of the proposed model is made available on a publicly accessible website.

Pre-release biological control agent recommendations for swallow-wort (Vincetoxicum spp.) informed by demographic matrix models

USDA-ARS?s Scientific Manuscript database

Weed biological control workers have advocated for the advance assessment of agent efficacy in order to minimize the release of host-specific but ineffective agents. One method involves demographic matrix modeling of target weed populations in order to identify plant life stage transitions that cont...

Manipulating biological agents and cells in micro-scale volumes for applications in medicine

PubMed Central

Tasoglu, Savas; Gurkan, Umut Atakan; Wang, ShuQi

2013-01-01

Recent technological advances provide new tools to manipulate cells and biological agents in micro/nano-liter volumes. With precise control over small volumes, the cell microenvironment and other biological agents can be bioengineered; interactions between cells and external stimuli can be monitored; and the fundamental mechanisms such as cancer metastasis and stem cell differentiation can be elucidated. Technological advances based on the principles of electrical, magnetic, chemical, optical, acoustic, and mechanical forces lead to novel applications in point-of-care diagnostics, regenerative medicine, in vitro drug testing, cryopreservation, and cell isolation/purification. In this review, we first focus on the underlying mechanisms of emerging examples for cell manipulation in small volumes targeting applications such as tissue engineering. Then, we illustrate how these mechanisms impact the aforementioned biomedical applications, discuss the associated challenges, and provide perspectives for further development. PMID:23575660

Combination Antimicrobial Nanocomposite Materials for Neutralization of Biological Threat Agents (PREPRINT)

DTIC Science & Technology

2008-09-01

AFRL-RX-TY-TP-2008-4601 PREPRINT COMBINATION ANTIMICROBIAL NANOCOMPOSITE MATERIALS FOR NEUTRALIZATION OF BIOLOGICAL THREAT AGENTS...AIRBASE TECHNOLOGIES DIVISION MATERIALS AND MANUFACTURING DIRECTORATE AIR FORCE RESEARCH LABORATORY AIR FORCE MATERIEL COMMAND 139 BARNES DRIVE, SUITE 2...a composite material that combines the protein and inorganic components. The process can be mimicked in vitro to some degree, providing methods for

The Unified Behavior Framework for the Simulation of Autonomous Agents

DTIC Science & Technology

2015-03-01

1980s, researchers have designed a variety of robot control architectures intending to imbue robots with some degree of autonomy. A recently developed ...Identification Friend or Foe viii THE UNIFIED BEHAVIOR FRAMEWORK FOR THE SIMULATION OF AUTONOMOUS AGENTS I. Introduction The development of autonomy has...room for research by utilizing methods like simulation and modeling that consume less time and fewer monetary resources. A recently developed reactive

Validating agent oriented methodology (AOM) for netlogo modelling and simulation

NASA Astrophysics Data System (ADS)

WaiShiang, Cheah; Nissom, Shane; YeeWai, Sim; Sharbini, Hamizan

2017-10-01

AOM (Agent Oriented Modeling) is a comprehensive and unified agent methodology for agent oriented software development. AOM methodology was proposed to aid developers with the introduction of technique, terminology, notation and guideline during agent systems development. Although AOM methodology is claimed to be capable of developing a complex real world system, its potential is yet to be realized and recognized by the mainstream software community and the adoption of AOM is still at its infancy. Among the reason is that there are not much case studies or success story of AOM. This paper presents two case studies on the adoption of AOM for individual based modelling and simulation. It demonstrate how the AOM is useful for epidemiology study and ecological study. Hence, it further validate the AOM in a qualitative manner.

Biology, behavior, and larval morphology of Salbia lotanalis (Lepidoptera: Crambidae), a potential biological control agent of Miconia calvescens (Myrtales: Melastomataceae) from Costa Rica

Treesearch

Alexander Castillo; M. Tracy Johnson; Francisco R. Badenes-Pérez

2014-01-01

The leaf roller Salbia lotanalis Druce (Lepidoptera: Crambidae), a potential biological control agent of Miconia calvescens de Candolle (Melastomataceae), was studied in Costa Rica. Larvae were collected from a field site near San Jose and the insect was reared in the laboratory to study its biology and behavior. Chaetotaxy and...

A support vector machine approach to the automatic identification of fluorescence spectra emitted by biological agents

NASA Astrophysics Data System (ADS)

Gelfusa, M.; Murari, A.; Lungaroni, M.; Malizia, A.; Parracino, S.; Peluso, E.; Cenciarelli, O.; Carestia, M.; Pizzoferrato, R.; Vega, J.; Gaudio, P.

2016-10-01

Two of the major new concerns of modern societies are biosecurity and biosafety. Several biological agents (BAs) such as toxins, bacteria, viruses, fungi and parasites are able to cause damage to living systems either humans, animals or plants. Optical techniques, in particular LIght Detection And Ranging (LIDAR), based on the transmission of laser pulses and analysis of the return signals, can be successfully applied to monitoring the release of biological agents into the atmosphere. It is well known that most of biological agents tend to emit specific fluorescence spectra, which in principle allow their detection and identification, if excited by light of the appropriate wavelength. For these reasons, the detection of the UVLight Induced Fluorescence (UV-LIF) emitted by BAs is particularly promising. On the other hand, the stand-off detection of BAs poses a series of challenging issues; one of the most severe is the automatic discrimination between various agents which emit very similar fluorescence spectra. In this paper, a new data analysis method, based on a combination of advanced filtering techniques and Support Vector Machines, is described. The proposed approach covers all the aspects of the data analysis process, from filtering and denoising to automatic recognition of the agents. A systematic series of numerical tests has been performed to assess the potential and limits of the proposed methodology. The first investigations of experimental data have already given very encouraging results.

Survey of rheumatologists on the use of the Philippine Guidelines on the Screening for Tuberculosis prior to use of Biologic Agents.

PubMed

Aquino-Villamin, Melissa; Tankeh-Torres, Sandra; Lichauco, Juan Javier

2016-11-01

The use of biologic agents has become an important option in treating patients with rheumatoid arthritis. However, these drugs have been associated with an increased risk of tuberculosis (TB) reactivation. Local guidelines for TB screening prior to the use of biologic agents were developed to address this issue. This study is a survey describing the compliance of Filipino rheumatologists to these guidelines. Eighty-seven rheumatologists in the Philippines were given the questionnaire and responses from 61 rheumatologists were included in the analysis. All respondents agree that patients should be screened prior to giving the biologic agents. Local guidelines recommend screening with tuberculin skin test (TST) and chest radiograph. However, cut-off values considered for a positive TST and timing of initiation of biologic agents after starting TB prophylaxis and treatment varied among respondents. In addition, screening of close household contacts were only performed by 41 (69.5%) respondents. There were 11 respondents who reported 16 patients developing TB during or after receiving biologic agents, despite adherence to the guidelines. This survey describes the compliance rate of Filipino rheumatologists in applying current local recommendations for TB screening prior to initiating biologic agents. The incidence of new TB cases despite the current guidelines emphasizes the importance of compliance and the need to revise the guidelines based on updated existing literature. © 2015 Asia Pacific League of Associations for Rheumatology and Wiley Publishing Asia Pty Ltd.

Microarray Analysis and Mutagenesis of the Biological Control Agent Pseudomonas fluorescens Pf-5

USDA-ARS?s Scientific Manuscript database

The biological control agent Pseudomonas fluorescens Pf-5 suppresses seedling emergence diseases caused by soilborne fungi and Oomycetes. Pf-5 produces at least ten secondary metabolites. These include hydrogen cyanide, pyrrolnitrin, pyoluteorin and 2,4-diacetylphloroglucinol, which have known funct...

How Long Does the Benefit of Biologics Last? An Update on Time To Relapse and Potential for Rebound of Biologic Agents for Psoriasis.

PubMed

Kamaria, Monique; Liao, Wilson; Koo, J Y

2010-01-01

The biologic agents vary considerably in terms of their long-term duration of effect. Using the definitions provided by the National Psoriasis Foundation Medical Board, the objective of this review was to compare all biologic agents with respect to time to relapse and potential for rebound. Overall, alefacept had the longest off-treatment benefit (29.9 weeks in Psoriasis Area and Severity Index [PASI] 75 responders), followed by ustekinumab (22 weeks), infliximab (19.5 weeks), adalimumab (18 weeks), etanercept (12.1 weeks in PASI 50 responders), and, lastly, efalizumab (9.6 weeks). Rebound was reported commonly for efalizumab (14%) and, extremely rarely, for etanercept (0.002%).

Heuristic Identification of Biological Architectures for Simulating Complex Hierarchical Genetic Interactions

PubMed Central

Moore, Jason H; Amos, Ryan; Kiralis, Jeff; Andrews, Peter C

2015-01-01

Simulation plays an essential role in the development of new computational and statistical methods for the genetic analysis of complex traits. Most simulations start with a statistical model using methods such as linear or logistic regression that specify the relationship between genotype and phenotype. This is appealing due to its simplicity and because these statistical methods are commonly used in genetic analysis. It is our working hypothesis that simulations need to move beyond simple statistical models to more realistically represent the biological complexity of genetic architecture. The goal of the present study was to develop a prototype genotype–phenotype simulation method and software that are capable of simulating complex genetic effects within the context of a hierarchical biology-based framework. Specifically, our goal is to simulate multilocus epistasis or gene–gene interaction where the genetic variants are organized within the framework of one or more genes, their regulatory regions and other regulatory loci. We introduce here the Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions (HIBACHI) method and prototype software for simulating data in this manner. This approach combines a biological hierarchy, a flexible mathematical framework, a liability threshold model for defining disease endpoints, and a heuristic search strategy for identifying high-order epistatic models of disease susceptibility. We provide several simulation examples using genetic models exhibiting independent main effects and three-way epistatic effects. PMID:25395175

From Here to Autonomicity: Self-Managing Agents and the Biological Metaphors that Inspire Them

NASA Technical Reports Server (NTRS)

Sterritt, Roy; Hinchey, Mike

2005-01-01

We seek inspiration for self-managing systems from (obviously, pre-existing) biological mechanisms. Autonomic Computing (AC), a self-managing systems initiative based on the biological metaphor of the autonomic nervous system, is increasingly gaining momentum as the way forward for integrating and designing reliable systems, while agent technologies have been identified as a key enabler for engineering autonomicity in systems. This paper looks at other biological metaphors such as reflex and healing, heart- beat monitors, pulse monitors and apoptosis for assisting in the realization of autonomicity.

Spectrally-resolved fluorescence cross sections of aerosolized biological live agents and simulants using five excitation wavelengths in a BSL-3 laboratory.

PubMed

Pan, Yong-Le; Hill, Steven C; Santarpia, Joshua L; Brinkley, Kelly; Sickler, Todd; Coleman, Mark; Williamson, Chatt; Gurton, Kris; Felton, Melvin; Pinnick, Ronald G; Baker, Neal; Eshbaugh, Jonathan; Hahn, Jerry; Smith, Emily; Alvarez, Ben; Prugh, Amber; Gardner, Warren

2014-04-07

A system for measuring spectrally-resolved fluorescence cross sections of single bioaerosol particles has been developed and employed in a biological safety level 3 (BSL-3) facility at Edgewood Chemical and Biological Center (ECBC). It is used to aerosolize the slurry or solution of live agents and surrogates into dried micron-size particles, and to measure the fluorescence spectra and sizes of the particles one at a time. Spectrally-resolved fluorescence cross sections were measured for (1) bacterial spores: Bacillus anthracis Ames (BaA), B. atrophaeus var. globigii (BG) (formerly known as Bacillus globigii), B. thuringiensis israelensis (Bti), B. thuringiensis kurstaki (Btk), B. anthracis Sterne (BaS); (2) vegetative bacteria: Escherichia coli (E. coli), Pantoea agglomerans (Eh) (formerly known as Erwinia herbicola), Yersinia rohdei (Yr), Yersinia pestis CO92 (Yp); and (3) virus preparations: Venezuelan equine encephalitis TC83 (VEE) and the bacteriophage MS2. The excitation wavelengths were 266 nm, 273 nm, 280 nm, 365 nm and 405 nm.

A program code generator for multiphysics biological simulation using markup languages.

PubMed

Amano, Akira; Kawabata, Masanari; Yamashita, Yoshiharu; Rusty Punzalan, Florencio; Shimayoshi, Takao; Kuwabara, Hiroaki; Kunieda, Yoshitoshi

2012-01-01

To cope with the complexity of the biological function simulation models, model representation with description language is becoming popular. However, simulation software itself becomes complex in these environment, thus, it is difficult to modify the simulation conditions, target computation resources or calculation methods. In the complex biological function simulation software, there are 1) model equations, 2) boundary conditions and 3) calculation schemes. Use of description model file is useful for first point and partly second point, however, third point is difficult to handle for various calculation schemes which is required for simulation models constructed from two or more elementary models. We introduce a simulation software generation system which use description language based description of coupling calculation scheme together with cell model description file. By using this software, we can easily generate biological simulation code with variety of coupling calculation schemes. To show the efficiency of our system, example of coupling calculation scheme with three elementary models are shown.

Leveraging culture collections for the discovery and development of microbial biological control agents

USDA-ARS?s Scientific Manuscript database

The incorporation of living microbial biological control agents into integrated pest management programs is highly desirable because it reduces the use of chemical insecticides harmful to livestock, humans and the environment. In addition, it provides an alternative means to combat resistance to che...

Engineered plant biomass particles coated with biological agents

DOEpatents

Dooley, James H.; Lanning, David N.

2014-06-24

Plant biomass particles coated with a biological agent such as a bacterium or seed, characterized by a length dimension (L) aligned substantially parallel to a grain direction and defining a substantially uniform distance along the grain, a width dimension (W) normal to L and aligned cross grain, and a height dimension (H) normal to W and L. In particular, the L.times.H dimensions define a pair of substantially parallel side surfaces characterized by substantially intact longitudinally arrayed fibers, the W.times.H dimensions define a pair of substantially parallel end surfaces characterized by crosscut fibers and end checking between fibers, and the L.times.W dimensions define a pair of substantially parallel top and bottom surfaces.

Advanced nanoelectronic architectures for THz-based biological agent detection

NASA Astrophysics Data System (ADS)

Woolard, Dwight L.; Jensen, James O.

2009-02-01

The U.S. Army Research Office (ARO) and the U.S. Army Edgewood Chemical Biological Center (ECBC) jointly lead and support novel research programs that are advancing the state-of-the-art in nanoelectronic engineering in application areas that have relevance to national defense and security. One fundamental research area that is presently being emphasized by ARO and ECBC is the exploratory investigation of new bio-molecular architectural concepts that can be used to achieve rapid, reagent-less detection and discrimination of biological warfare (BW) agents, through the control of multi-photon and multi-wavelength processes at the nanoscale. This paper will overview an ARO/ECBC led multidisciplinary research program presently under the support of the U.S. Defense Threat Reduction Agency (DTRA) that seeks to develop new devices and nanoelectronic architectures that are effective for extracting THz signatures from target bio-molecules. Here, emphasis will be placed on the new nanosensor concepts and THz/Optical measurement methodologies for spectral-based sequencing/identification of genetic molecules.

75 FR 69396 - Availability of an Environmental Assessment for a Biological Control Agent for Arundo donax

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-12

... infestations. The proposed biological control agent, Arundo scale, is one of the most damaging insects to A... feeding on cells that carry out photosynthesis and cellular respiration, resulting over time in gradual... donacis (Hemiptera: Diaspididae), an Insect for Biological Control of Arundo donax (Poaceae) in the...

Comparing Effects of Biologic Agents in Treating Patients with Rheumatoid Arthritis: A Multiple Treatment Comparison Regression Analysis.

PubMed

Tvete, Ingunn Fride; Natvig, Bent; Gåsemyr, Jørund; Meland, Nils; Røine, Marianne; Klemp, Marianne

2015-01-01

Rheumatoid arthritis patients have been treated with disease modifying anti-rheumatic drugs (DMARDs) and the newer biologic drugs. We sought to compare and rank the biologics with respect to efficacy. We performed a literature search identifying 54 publications encompassing 9 biologics. We conducted a multiple treatment comparison regression analysis letting the number experiencing a 50% improvement on the ACR score be dependent upon dose level and disease duration for assessing the comparable relative effect between biologics and placebo or DMARD. The analysis embraced all treatment and comparator arms over all publications. Hence, all measured effects of any biologic agent contributed to the comparison of all biologic agents relative to each other either given alone or combined with DMARD. We found the drug effect to be dependent on dose level, but not on disease duration, and the impact of a high versus low dose level was the same for all drugs (higher doses indicated a higher frequency of ACR50 scores). The ranking of the drugs when given without DMARD was certolizumab (ranked highest), etanercept, tocilizumab/ abatacept and adalimumab. The ranking of the drugs when given with DMARD was certolizumab (ranked highest), tocilizumab, anakinra/rituximab, golimumab/ infliximab/ abatacept, adalimumab/ etanercept [corrected]. Still, all drugs were effective. All biologic agents were effective compared to placebo, with certolizumab the most effective and adalimumab (without DMARD treatment) and adalimumab/ etanercept (combined with DMARD treatment) the least effective. The drugs were in general more effective, except for etanercept, when given together with DMARDs.

Comparing Effects of Biologic Agents in Treating Patients with Rheumatoid Arthritis: A Multiple Treatment Comparison Regression Analysis

PubMed Central

Tvete, Ingunn Fride; Natvig, Bent; Gåsemyr, Jørund; Meland, Nils; Røine, Marianne; Klemp, Marianne

2015-01-01

Rheumatoid arthritis patients have been treated with disease modifying anti-rheumatic drugs (DMARDs) and the newer biologic drugs. We sought to compare and rank the biologics with respect to efficacy. We performed a literature search identifying 54 publications encompassing 9 biologics. We conducted a multiple treatment comparison regression analysis letting the number experiencing a 50% improvement on the ACR score be dependent upon dose level and disease duration for assessing the comparable relative effect between biologics and placebo or DMARD. The analysis embraced all treatment and comparator arms over all publications. Hence, all measured effects of any biologic agent contributed to the comparison of all biologic agents relative to each other either given alone or combined with DMARD. We found the drug effect to be dependent on dose level, but not on disease duration, and the impact of a high versus low dose level was the same for all drugs (higher doses indicated a higher frequency of ACR50 scores). The ranking of the drugs when given without DMARD was certolizumab (ranked highest), etanercept, tocilizumab/ abatacept and adalimumab. The ranking of the drugs when given with DMARD was certolizumab (ranked highest), tocilizumab, anakinra, rituximab, golimumab/ infliximab/ abatacept, adalimumab/ etanercept. Still, all drugs were effective. All biologic agents were effective compared to placebo, with certolizumab the most effective and adalimumab (without DMARD treatment) and adalimumab/ etanercept (combined with DMARD treatment) the least effective. The drugs were in general more effective, except for etanercept, when given together with DMARDs. PMID:26356639

Evaluation of Nipah Virus as a Human and Animal Biological Terrorism and Warfare Agent

DTIC Science & Technology

2001-09-01

UNCLASSIFIED Defense Technical Information Center Compilation Part Notice ADP013384 TITLE: Evaluation of Nipah Virus as a Human and Animal Biological...following component part numbers comprise the compilation report: ADP013371 thru ADP013468 UNCLASSIFIED 14. EVALUATION OF NIPAH VIRUS AS A HUMAN AND ANIMAL...of BTWC proposed including Nipah virus in the list of animal pathogens. This paper describes an evaluation of Nipah virus as a biological agent for

Performance of Traditional and Molecular Methods for Detecting Biological Agents in Drinking Water

EPA Science Inventory

USGS Report - To reduce the impact from a possible bioterrorist attack on drinking-water supplies, analytical methods are needed to rapidly detect the presence of biological agents in water. To this end, 13 drinking-water samples were collected at 9 water-treatment plants in Ohio...

Ecological host-range of Lilioceris cheni (Coleoptera: Chrysomelidae), a biological control agent of Dioscorea bulbifera L.

USDA-ARS?s Scientific Manuscript database

Open-field host-specificity testing assesses the host-range of a biological control agent in a setting that permits the agent to use its full complement of host-seeking behaviors. This form of testing, particularly when it includes a no-choice phase in which the target weed is killed, may provide th...

Effects of Immunomodulators and Biologic Agents on Sexual Health in Patients With Inflammatory Bowel Disease.

PubMed

Kanar, Ozdemir; Berry, Andrew C; Nakshabendi, Rahman; Lee, Ann Joo; Aldridge, Petra; Myers, Travis; Eid, Emely

2017-01-01

Although much knowledge has been gained regarding the medical and surgical management of inflammatory bowel disease (IBD), a paucity of information is available on the psychosexual issues related to IBD. The aim of this study was to evaluate the sexual health of patients with IBD who were taking immunomodulators and/or biologic agents vs patients with IBD who were not on that medication regimen. All study participants completed a validated sexual health questionnaire, the Female Sexual Function Index or the International Index of Erectile Function, to assess their subjective perception of the effect of IBD on the different domains of sexual function during the prior 1-month time period. No statistically significant differences in any baseline demographic variables were found for either sex between the group taking immunomodulators/biologic agents and the nontreatment group. Among females and males, individual question responses, domain scores, and total scores showed no statistically significant differences between the 2 treatment groups. Our data suggest that the use of immunomodulators or biologic agents does not affect female or male sexual health. However, treatment of patients with IBD must be individualized based on the aggressive nature of the disease, treatment goals, and the tolerability of various medications.

An Agent-Based Simulation for Investigating the Impact of Stereotypes on Task-Oriented Group Formation

NASA Astrophysics Data System (ADS)

Maghami, Mahsa; Sukthankar, Gita

In this paper, we introduce an agent-based simulation for investigating the impact of social factors on the formation and evolution of task-oriented groups. Task-oriented groups are created explicitly to perform a task, and all members derive benefits from task completion. However, even in cases when all group members act in a way that is locally optimal for task completion, social forces that have mild effects on choice of associates can have a measurable impact on task completion performance. In this paper, we show how our simulation can be used to model the impact of stereotypes on group formation. In our simulation, stereotypes are based on observable features, learned from prior experience, and only affect an agent's link formation preferences. Even without assuming stereotypes affect the agents' willingness or ability to complete tasks, the long-term modifications that stereotypes have on the agents' social network impair the agents' ability to form groups with sufficient diversity of skills, as compared to agents who form links randomly. An interesting finding is that this effect holds even in cases where stereotype preference and skill existence are completely uncorrelated.

Indirect ecological effects in invaded landscapes: Spillover and spillback from biological control agents to native analogues

USDA-ARS?s Scientific Manuscript database

Biological control remains an effective option for managing large-scale weed problems in natural areas. The predation or parasitism of biological control agents by other species present in the introduced range (biotic resistance) is well studied and is often cited as the cause for a lack of establis...

High performance computing in biology: multimillion atom simulations of nanoscale systems

PubMed Central

Sanbonmatsu, K. Y.; Tung, C.-S.

2007-01-01

Computational methods have been used in biology for sequence analysis (bioinformatics), all-atom simulation (molecular dynamics and quantum calculations), and more recently for modeling biological networks (systems biology). Of these three techniques, all-atom simulation is currently the most computationally demanding, in terms of compute load, communication speed, and memory load. Breakthroughs in electrostatic force calculation and dynamic load balancing have enabled molecular dynamics simulations of large biomolecular complexes. Here, we report simulation results for the ribosome, using approximately 2.64 million atoms, the largest all-atom biomolecular simulation published to date. Several other nanoscale systems with different numbers of atoms were studied to measure the performance of the NAMD molecular dynamics simulation program on the Los Alamos National Laboratory Q Machine. We demonstrate that multimillion atom systems represent a 'sweet spot' for the NAMD code on large supercomputers. NAMD displays an unprecedented 85% parallel scaling efficiency for the ribosome system on 1024 CPUs. We also review recent targeted molecular dynamics simulations of the ribosome that prove useful for studying conformational changes of this large biomolecular complex in atomic detail. PMID:17187988

Predicting spillover risk to non-target plants pre-release: Bikasha collaris a potential biological control agent of Chinese tallowtree (Triadica sebifera)

USDA-ARS?s Scientific Manuscript database

Quarantine host range tests accurately predict direct risk of biological control agents to non-target species. However, a well-known indirect effect of biological control of weeds releases is spillover damage to non-target species. Spillover damage may occur when the population of agents achieves ou...

Experimental examination of ultraviolet Raman cross sections of chemical warfare agent simulants

NASA Astrophysics Data System (ADS)

Kullander, F.; Landström, L.; Lundén, H.; Wästerby, Pär.

2015-05-01

Laser induced Raman scattering from the commonly used chemical warfare agent simulants dimethyl sulfoxide, tributyl phosphate, triethyl phosphonoacetate was measured at excitation wavelengths ranging from 210 to 410 nm using a pulsed laser based spectrometer system with a probing distance of 1.4 m and with a field of view on the target of less than 1mm. For the purpose of comparison with well explored reference liquids the Raman scattering from simulants was measured in the form of an extended liquid surface layer on top of a silicon wafer. This way of measuring enabled direct comparison to the Raman scattering strength from cyclohexane. The reference Raman spectra were used to validate the signal strength of the simulants and the calibration of the experimental set up. Measured UV absorbance functions were used to calculate Raman cross sections. Established Raman cross sections of the simulants make it possible to use them as reference samples when measuring on chemical warfare agents in droplet form.

Potential of Neoactinolaimus as a biological control agent of root-knot and reniform nematodes

USDA-ARS?s Scientific Manuscript database

The predatory nematode Neoactinolaimus spp. (family Actinolaimidae) was examined as a potential biological control agent against root-knot (Meloidogyne spp.) and reniform (Rotylenchulus reniformis) nematodes in laboratory conditions. Neoactinolaimus possesses a large odontostylet to puncture the cu...

Rates of, and risk factors for, severe infections in patients with systemic autoimmune diseases receiving biological agents off-label

PubMed Central

2011-01-01

Introduction The purpose of this observational study was to analyze the rates, characteristics and associated risk factors of severe infections in patients with systemic autoimmune diseases (SAD) who were treated off-label with biological agents in daily practice. Methods The BIOGEAS registry is an ongoing Spanish prospective cohort study investigating the long-term safety and efficacy of the off-label use of biological agents in adult patients with severe, refractory SAD. Severe infections were defined according to previous studies as those that required intravenous treatment or that led to hospitalization or death. Patients contributed person-years of follow-up for the period in which they were treated with biological agents. Results A total of 344 patients with SAD treated with biological agents off-label were included in the Registry until July 2010. The first biological therapies included rituximab in 264 (77%) patients, infliximab in 37 (11%), etanercept in 21 (6%), adalimumab in 19 (5%), and 'other' agents in 3 (1%). Forty-five severe infections occurred in 37 patients after a mean follow-up of 26.76 months. These infections resulted in four deaths. The crude rate of severe infections was 90.9 events/1000 person-years (112.5 for rituximab, 76.9 for infliximab, 66.9 for adalimumab and 30.5 for etanercept respectively). In patients treated with more than two courses of rituximab, the crude rate of severe infection was 226.4 events/1000 person-years. A pathogen was identified in 24 (53%) severe infections. The most common sites of severe infection were the lower respiratory tract (39%), bacteremia/sepsis (20%) and the urinary tract (16%). There were no significant differences relating to gender, SAD, agent, other previous therapies, number of previous immunosuppressive agents received or other therapies administered concomitantly. Cox regression analysis showed that age (P = 0.015) was independently associated with an increased risk of severe infection

Review of the systems biology of the immune system using agent-based models.

PubMed

Shinde, Snehal B; Kurhekar, Manish P

2018-06-01

The immune system is an inherent protection system in vertebrate animals including human beings that exhibit properties such as self-organisation, self-adaptation, learning, and recognition. It interacts with the other allied systems such as the gut and lymph nodes. There is a need for immune system modelling to know about its complex internal mechanism, to understand how it maintains the homoeostasis, and how it interacts with the other systems. There are two types of modelling techniques used for the simulation of features of the immune system: equation-based modelling (EBM) and agent-based modelling. Owing to certain shortcomings of the EBM, agent-based modelling techniques are being widely used. This technique provides various predictions for disease causes and treatments; it also helps in hypothesis verification. This study presents a review of agent-based modelling of the immune system and its interactions with the gut and lymph nodes. The authors also review the modelling of immune system interactions during tuberculosis and cancer. In addition, they also outline the future research directions for the immune system simulation through agent-based techniques such as the effects of stress on the immune system, evolution of the immune system, and identification of the parameters for a healthy immune system.

Comparison of traditional and molecular analytical methods for detecting biological agents in raw and drinking water following ultrafiltration

USGS Publications Warehouse

Francy, D.S.; Bushon, R.N.; Brady, A.M.G.; Bertke, E.E.; Kephart, C.M.; Likirdopulos, C.A.; Mailot, B.E.; Schaefer, F. W.; Lindquist, H.D. Alan

2009-01-01

Aims: To compare the performance of traditional methods to quantitative polymerase chain reaction (qPCR) for detecting five biological agents in large-volume drinking-water samples concentrated by ultrafiltration (UF). Methods and Results: Drinking-water samples (100 l) were seeded with Bacillus anthracis, Cryptospordium parvum, Francisella tularensis, Salmonella Typhi, and Vibrio cholerae and concentrated by UF. Recoveries by traditional methods were variable between samples and between some replicates; recoveries were not determined by qPCR. Francisella tularensis and V. cholerae were detected in all 14 samples after UF, B. anthracis was detected in 13, and C. parvum was detected in 9 out of 14 samples. Numbers found by qPCR after UF were significantly or nearly related to those found by traditional methods for all organisms except for C. parvum. A qPCR assay for S. Typhi was not available. Conclusions: qPCR can be used to rapidly detect biological agents after UF as well as traditional methods, but additional work is needed to improve qPCR assays for several biological agents, determine recoveries by qPCR, and expand the study to other areas. Significance and Impact of the Study: To our knowledge, this is the first study to compare the use of traditional and qPCR methods to detect biological agents in large-volume drinking-water samples. ?? 2009 The Society for Applied Microbiology.

The systems biology simulation core algorithm

PubMed Central

2013-01-01

Background With the increasing availability of high dimensional time course data for metabolites, genes, and fluxes, the mathematical description of dynamical systems has become an essential aspect of research in systems biology. Models are often encoded in formats such as SBML, whose structure is very complex and difficult to evaluate due to many special cases. Results This article describes an efficient algorithm to solve SBML models that are interpreted in terms of ordinary differential equations. We begin our consideration with a formal representation of the mathematical form of the models and explain all parts of the algorithm in detail, including several preprocessing steps. We provide a flexible reference implementation as part of the Systems Biology Simulation Core Library, a community-driven project providing a large collection of numerical solvers and a sophisticated interface hierarchy for the definition of custom differential equation systems. To demonstrate the capabilities of the new algorithm, it has been tested with the entire SBML Test Suite and all models of BioModels Database. Conclusions The formal description of the mathematics behind the SBML format facilitates the implementation of the algorithm within specifically tailored programs. The reference implementation can be used as a simulation backend for Java™-based programs. Source code, binaries, and documentation can be freely obtained under the terms of the LGPL version 3 from http://simulation-core.sourceforge.net. Feature requests, bug reports, contributions, or any further discussion can be directed to the mailing list simulation-core-development@lists.sourceforge.net. PMID:23826941

Surveys for Biological Control Agents of Hydrilla verticillata in the People’s Republic of China in 2013

DTIC Science & Technology

2017-03-01

Hydrilla was rare at this site and only male plants were collected at 0.5-1 m from shore and a depth of 0.5-1m. The lake/wetlands were explored by boat...ER D C/ EL T R- 17 -3 Aquatic Plant Control Research Program Surveys for Biological Control Agents of Hydrilla verticillata in the...acwc.sdp.sirsi.net/client/default. Aquatic Plant Control Research Program ERDC/EL TR-17-3 March 2017 Surveys for Biological Control Agents of

Portuguese guidelines for the use of biological agents in rheumatoid arthritis - March 2010 update.

PubMed

Fonseca, João Eurico; Canhão, Helena; Reis, Paulo; Santos, Maria José; Branco, Jaime; Quintal, Alberto; Malcata, Armando; Araújo, Domingos; Ventura, Francisco; Figueiredo, Guilherme; da Silva, José Canas; Patto, José Vaz; de Queiroz, Mário Viana; Santos, Rui André; Neto, Adriano José; de Matos, Alves de; Rodrigues, Ana; Mourão, Ana Filipa; Ribeiro, Ana Sofia; Cravo, Ana Rita; Barcelos, Anabela; Cardoso, Anabela; Vilar, António; Braña, Arecili; Faustino, Augusto; Silva, Candida; Godinho, Fátima; Cunha, Inês; Costa, José António; Gomes, José António Melo; Pinto, José António Araújo; da Silva, J A Pereira; Miranda, Luís Cunha; Inês, Luís; Santos, Luís Maurício; Cruz, Margarida; Salvador, Maria João; Ferreira, Maria Júlia; Rial, Maria; Bernardes, Miguel; Bogas, Mónica; Araújo, Paula; Machado, Pedro; Pinto, Patrícia; de Melo, Rui Gomes; Cortes, Sara; Alcino, Sérgio; Capela, Susana

2010-01-01

The authors present the revised version of the Portuguese Society of Rheumatology (SPR) guidelines for the treatment of rheumatoid arthritis (RA) with biological therapies. In these guidelines the criteria for introduction and maintenance of biological agents are discussed as well as the contraindications and procedures in the case of non-responders. Biological treatment should be considered in RA patients with a disease activity score 28 (DAS 28) superior to 3.2 despite treatment with 20mg/week of methotrexate (MTX) for at least 3 months or, if such treatment is not possible, after 6 months of other conventional disease modifying drug or combination therapy. A DAS 28 score between 2.6 and 3.2 with a significant functional or radiological deterioration under treatment with conventional regimens could also constitute an indication for biological treatment. The treatment goal should be remission or, if that is not achievable, at least a low disease activity, characterized by a DAS28 lower than 3.2, without significative functional or radiological worsening. The response criteria, at the end of the first 3 months of treatment, are a decrease of 0.6 in the DAS28 score. After 6 months of treatment response criteria is defined as a decrease of more than 1.2 in the DAS28 score. Non-responders, in accordance to the Rheumatologist's clinical opinion, should try a switch to another biological agent (tumour necrosis factor antagonist, abatacept, rituximab or tocilizumab).

Method for distributed agent-based non-expert simulation of manufacturing process behavior

DOEpatents

Ivezic, Nenad; Potok, Thomas E.

2004-11-30

A method for distributed agent based non-expert simulation of manufacturing process behavior on a single-processor computer comprises the steps of: object modeling a manufacturing technique having a plurality of processes; associating a distributed agent with each the process; and, programming each the agent to respond to discrete events corresponding to the manufacturing technique, wherein each discrete event triggers a programmed response. The method can further comprise the step of transmitting the discrete events to each agent in a message loop. In addition, the programming step comprises the step of conditioning each agent to respond to a discrete event selected from the group consisting of a clock tick message, a resources received message, and a request for output production message.

Development of a Persistent Chemical Agent Simulator System (PCASS)

NASA Technical Reports Server (NTRS)

Mcginness, W. G.

1983-01-01

The development of a persistent chemical agent simulation system (PCASS) is described. This PCASS is to be used for the military training of troops to simulate actual chemical warfare. The purpose of this system is to facilitate in the determination of chemical contamination and effectiveness of decontamination for training purposes. The fluorescent tracer employed has no daylight activation, but yet is easily removed with a decontaminate solution or water and surfactants. Also employed is a time delayed color developing system. When an individual is subjected to the PCASS and does not decontaminate adequately, red blotches or red coloration will develop as a function of time and temperature. The intent of this is to simulate the delayed chemical reaction of mustard contaminates.

Effects of biological control agents and exotic plant invasion on deer mouse populations

Treesearch

Yvette K. Ortega; Dean E. Pearson; Kevin S. McKelvey

2004-01-01

Exotic insects are commonly introduced as biological control agents to reduce densities of invasive exotic plants. Although current biocontrol programs for weeds take precautions to minimize ecological risks, little attention is paid to the potential nontarget effects of introduced food subsidies on native consumers. Previous research demonstrated that two gall flies (...

Method for photo-altering a biological system to improve biological effect

DOEpatents

Hill, Richard A.; Doiron, Daniel R.; Crean, David H.

2000-08-01

Photodynamic therapy is a new adjunctive therapy for filtration surgery that does not use chemotherapy agents or radiation, but uses pharmacologically-active sensitizing compounds to produce a titratable, localized, transient, post operative avascular conjunctiva. A photosensitizing agent in a biological system is selectively activated by delivering the photosensitive agent to the biological system and laser activating only a spatially selected portion of the delivered photosensitive agent. The activated portion of the photosensitive agent reacts with the biological system to obtain a predetermined biological effect. As a result, an improved spatial disposition and effectuation of the biological effect by the photosensitive agent in the biological system is achieved.

Interfacial Stacks of Polymeric Nanofilms on Soft Biological Surfaces that Release Multiple Agents.

PubMed

Herron, Maggie; Schurr, Michael J; Murphy, Christopher J; McAnulty, Jonathan F; Czuprynski, Charles J; Abbott, Nicholas L

2016-10-03

We report a general and facile method that permits the transfer (stacking) of multiple independently fabricated and nanoscopically thin polymeric films, each containing a distinct bioactive agent, onto soft biomedically relevant surfaces (e.g., collagen-based wound dressings). By using polyelectrolyte multilayer films (PEMs) formed from poly(allyl amine hydrochloride) and poly(acrylic acid) as representative polymeric nanofilms and micrometer-thick water-soluble poly(vinyl alcohol) sacrificial films to stack the PEMs, we demonstrate that it is possible to create stacked polymeric constructs containing multiple bioactive agents (e.g., antimicrobial and antibiofilm agents) on soft and chemically complex surfaces onto which PEMs cannot be routinely transferred by stamping. We illustrate the characteristics and merits of the approach by fabricating stacks of Ga 3+ (antibiofilm agent)- and Ag + (antimicrobial agent)-loaded PEMs as prototypical examples of agent-containing PEMs and demonstrate that the stacked PEMs incorporate precise loadings of the agents and provide flexibility in terms of tuning release rates. Specifically, we show that simultaneous release of Ga 3+ and Ag + from the stacked PEMs on collagen-based wound dressings can lead to synergistic effects on bacteria, killing and dispersing biofilms formed by Pseudomonas aeruginosa (two strains: ATCC 27853 and MPAO1) at sufficiently low loadings of agents such that cytotoxic effects on mammalian cells are avoided. The approach is general (a wide range of bioactive agents other than Ga 3+ and Ag + can be incorporated into PEMs), and the modular nature of the approach potentially allows end-user functionalization of soft biological surfaces for programmed release of multiple bioactive agents.

Simbios: an NIH national center for physics-based simulation of biological structures.

PubMed

Delp, Scott L; Ku, Joy P; Pande, Vijay S; Sherman, Michael A; Altman, Russ B

2012-01-01

Physics-based simulation provides a powerful framework for understanding biological form and function. Simulations can be used by biologists to study macromolecular assemblies and by clinicians to design treatments for diseases. Simulations help biomedical researchers understand the physical constraints on biological systems as they engineer novel drugs, synthetic tissues, medical devices, and surgical interventions. Although individual biomedical investigators make outstanding contributions to physics-based simulation, the field has been fragmented. Applications are typically limited to a single physical scale, and individual investigators usually must create their own software. These conditions created a major barrier to advancing simulation capabilities. In 2004, we established a National Center for Physics-Based Simulation of Biological Structures (Simbios) to help integrate the field and accelerate biomedical research. In 6 years, Simbios has become a vibrant national center, with collaborators in 16 states and eight countries. Simbios focuses on problems at both the molecular scale and the organismal level, with a long-term goal of uniting these in accurate multiscale simulations.

Perception Modelling of Visitors in Vargas Museum Using Agent-Based Simulation and Visibility Analysis

NASA Astrophysics Data System (ADS)

Carcellar, B. G., III

2017-10-01

Museum exhibit management is one of the usual undertakings of museum facilitators. Art works must be strategically placed to achieve maximum viewing from the visitors. The positioning of the artworks also highly influences the quality of experience of the visitors. One solution in such problems is to utilize GIS and Agent-Based Modelling (ABM). In ABM, persistent interacting objects are modelled as agents. These agents are given attributes and behaviors that describe their properties as well as their motion. In this study, ABM approach that incorporates GIS is utilized to perform analyticcal assessment on the placement of the artworks in the Vargas Museum. GIS serves as the backbone for the spatial aspect of the simulation such as the placement of the artwork exhibits, as well as possible obstructions to perception such as the columns, walls, and panel boards. Visibility Analysis is also done to the model in GIS to assess the overall visibility of the artworks. The ABM is done using the initial GIS outputs and GAMA, an open source ABM software. Visitors are modelled as agents, moving inside the museum following a specific decision tree. The simulation is done in three use cases: the 10 %, 20 %, and 30 % chance of having a visitor in the next minute. For the case of the said museum, the 10 % chance is determined to be the closest simulation case to the actual and the recommended minimum time to achieve a maximum artwork perception is 1 hour and 40 minutes. Initial assessment of the results shows that even after 3 hours of simulation, small parts of the exhibit show lack of viewers, due to its distance from the entrance. A more detailed decision tree for the visitor agents can be incorporated to have a more realistic simulation.

Surface-enhanced Raman as a water monitor for warfare agents

NASA Astrophysics Data System (ADS)

Spencer, Kevin M.; Sylvia, James M.; Clauson, Susan L.; Janni, James A.

2002-02-01

The threat of chemical warfare agents being released upon civilian and military personnel continues to escalate. One aspect of chemical preparedness is to analyze and protect the portable water supply for the military. Chemical nerve, blister, and choking agents, as well as biological threats must all be analyzed and low limits of detection must be verified. For chemical agents, this generally means detection down to the low ppb levels. Surface-Enhanced Raman Spectroscopy (SERS) is a spectroscopic technique that can detect trace levels of contaminants directly in the aqueous environment. In this paper, results are presented on the use of SERS to detect chemical and biological agent simulants with an end goal of creating a Joint Service Agent Water Monitor. Detection of cyanide, 2-chloroethyl ethyl sulfide, phosphonates, Gram-positive and Gram-negative bacteria using SERS has been performed and is discussed herein. Aspects of transferring laboratory results to an unattended field instrument are also discussed.

Synthesis and biological activity of imidazopyridine anticoccidial agents: Part II.

PubMed

Scribner, Andrew; Dennis, Richard; Lee, Shuliang; Ouvry, Gilles; Perrey, David; Fisher, Michael; Wyvratt, Matthew; Leavitt, Penny; Liberator, Paul; Gurnett, Anne; Brown, Chris; Mathew, John; Thompson, Donald; Schmatz, Dennis; Biftu, Tesfaye

2008-06-01

Coccidiosis is the major cause of morbidity and mortality in the poultry industry. Protozoan parasites of the genus Eimeria invade the intestinal lining of the avian host causing tissue pathology, poor weight gain, and in some cases mortality. Resistance to current anticoccidials has prompted the search for new therapeutic agents with potent in vitro and in vivo activity against Eimeria. Recently, we reported the synthesis and biological activity of potent imidazo[1,2-a]pyridine anticoccidial agents. Antiparasitic activity is due to inhibition of a parasite specific cGMP-dependent protein kinase (PKG). In this study, we report the synthesis and anticoccidial activity of a second set of such compounds, focusing on derivatization of the amine side chain at the imidazopyridine 7-position. From this series, several compounds showed subnanomolar in vitro activity and commercial levels of in vivo activity. However, the potential genotoxicity of these compounds precludes them from further development.

Establishment of the armored scale, Rhizaspidiotus donacis, a biological control agent of Arundo donax

USDA-ARS?s Scientific Manuscript database

The armored scale biological control agent, Rhizaspidiotus donacis (Leonardi) (Hemiptera; Diaspididae) has established populations on the invasive weed, Arundo donax L. (Poaceae; Arundinoideae) in Del Rio (Val Verde, Co.) and in field plots at the USDA-APHIS-PPQ-Moore Airbase, Edinburg (Hidalgo Co.)...

[Numerical simulation and operation optimization of biological filter].

PubMed

Zou, Zong-Sen; Shi, Han-Chang; Chen, Xiang-Qiang; Xie, Xiao-Qing

2014-12-01

BioWin software and two sensitivity analysis methods were used to simulate the Denitrification Biological Filter (DNBF) + Biological Aerated Filter (BAF) process in Yuandang Wastewater Treatment Plant. Based on the BioWin model of DNBF + BAF process, the operation data of September 2013 were used for sensitivity analysis and model calibration, and the operation data of October 2013 were used for model validation. The results indicated that the calibrated model could accurately simulate practical DNBF + BAF processes, and the most sensitive parameters were the parameters related to biofilm, OHOs and aeration. After the validation and calibration of model, it was used for process optimization with simulating operation results under different conditions. The results showed that, the best operation condition for discharge standard B was: reflux ratio = 50%, ceasing methanol addition, influent C/N = 4.43; while the best operation condition for discharge standard A was: reflux ratio = 50%, influent COD = 155 mg x L(-1) after methanol addition, influent C/N = 5.10.

A framework for the use of agent based modeling to simulate ...

EPA Pesticide Factsheets

Simulation of human behavior in exposure modeling is a complex task. Traditionally, inter-individual variation in human activity has been modeled by drawing from a pool of single day time-activity diaries such as the US EPA Consolidated Human Activity Database (CHAD). Here, an agent-based model (ABM) is used to simulate population distributions of longitudinal patterns of four macro activities (sleeping, eating, working, and commuting) in populations of adults over a period of one year. In this ABM, an individual is modeled as an agent whose movement through time and space is determined by a set of decision rules. The rules are based on the agent having time-varying “needs” that are satisfied by performing actions. Needs are modeled as increasing over time, and taking an action reduces the need. Need-satisfying actions include sleeping (meeting the need for rest), eating (meeting the need for food), and commuting/working (meeting the need for income). Every time an action is completed, the model determines the next action the agent will take based on the magnitude of each of the agent’s needs at that point in time. Different activities advertise their ability to satisfy various needs of the agent (such as food to eat or sleeping in a bed or on a couch). The model then chooses the activity that satisfies the greatest of the agent’s needs. When multiple actions could address a need, the model will choose the most effective of the actions (bed over the couc

[Biosafety provision on handling pathogenic biological agents on the concept of biorisk assessment and management].

PubMed

Dobrokhotskiĭ, O N; Kolombet, L V

2010-01-01

The paper shows it urgent to realize the concept of biological risk assessment and management on handling pathogenic biological agents (PBA). It gives a number of objective reasons that impede development of a methodology to assess laboratory biological risks. A concept of continuous improvement (a process approach) is proposed for use as a biorisk management tool for biosafety assurance when handling PBA. It is demonstrated that development of international cooperation urgently requires that national concepts and standards be harmonized with international regulatory documents on biosafety assurance on handling PBA.

CRITTERS! A Realistic Simulation for Teaching Evolutionary Biology

ERIC Educational Resources Information Center

Latham, Luke G., II; Scully, Erik P.

2008-01-01

Evolutionary processes can be studied in nature and in the laboratory, but time and financial constraints result in few opportunities for undergraduate and high school students to explore the agents of genetic change in populations. One alternative to time consuming and expensive teaching laboratories is the use of computer simulations. We…

Biology, host specificity tests, and risk assessment of the sawfly Heteroperreyia hubrichi, a potential biological control agent of Schinus terebinthifolius in Hawaii

USDA-ARS?s Scientific Manuscript database

Abstract. Heteroperreyia hubrichi Malaise (Hymenoptera: Pergidae), a foliage feeding sawfly of Schinus terebinthifolius Raddi (Sapindales: Anacardiaceae), was studied to assess its suitability as a classical biological control agent of this invasive weed in Hawaii. Nochoice host-specificity tests we...

Anti-IL-23 and Anti-IL-17 Biologic Agents for the Treatment of Immune-Mediated Inflammatory Conditions.

PubMed

Frieder, Jillian; Kivelevitch, Dario; Haugh, Isabel; Watson, Ian; Menter, Alan

2018-01-01

Advancements in the immunopathogenesis of psoriasis have identified interleukin (IL)-23 and IL-17 as fundamental contributors in the immune pathways of the disease. Leveraging these promising therapeutic targets has led to the emergence of a number of anti-IL-23 and -17 biologic agents with the potential to treat multiple conditions with common underlying pathology. The unprecedented clinical efficacy of these agents in the treatment of psoriasis has paved way for their evaluation in diseases such as psoriatic arthritis, Crohn's disease, rheumatoid arthritis, in addition to other immune-mediated conditions. Here we review the IL-23/IL-17 immune pathways and discuss the key clinical and safety data of the anti-IL-23 and anti-IL-17 biologic agents in psoriasis and other immune-mediated diseases. © 2017 American Society for Clinical Pharmacology and Therapeutics.

A Systematic Review of Agent-Based Modelling and Simulation Applications in the Higher Education Domain

ERIC Educational Resources Information Center

Gu, X.; Blackmore, K. L.

2015-01-01

This paper presents the results of a systematic review of agent-based modelling and simulation (ABMS) applications in the higher education (HE) domain. Agent-based modelling is a "bottom-up" modelling paradigm in which system-level behaviour (macro) is modelled through the behaviour of individual local-level agent interactions (micro).…

BioSim (trademark) BG Non-Biological Aerosol Simulant

DTIC Science & Technology

2004-11-17

39.5 1.36 1,1- difluoroethane HFA 152a – Not used for pharmaceutical inhalers , is used for personal products Boiling point (-13o F) 63 (psig... 1 BIOSIMTM BG NON-BIOLOGICAL AEROSOL SIMULANT David S. Alburty, Kelly L. Brown, Jennifer L. Dannehl and Andrew E. Page Midwest...BioSafey Level 1 regulations. All of these materials of biological origin pose challenging logistics problems including safety issues, cost

Potential biological control agents for management of cogongrass (Cyperales: Poaceae) in the southeastern USA

USDA-ARS?s Scientific Manuscript database

Cogongrass, Imperata cylindrica (L.) Palisot de Beauvois (Cyperales: Poaceae), is a noxious invasive weed in the southeastern USA. Surveys for potential biological control agents of cogongrass were conducted in Asia and East Africa from 2013 to 2016. Several insect herbivores were found that may hav...

Predicting the host range of Nystalea ebalea: secondary plant chemistry and host selection by a surrogate biological control agent of Schinus terebinthifolia

USDA-ARS?s Scientific Manuscript database

The safety of weed biological control depends upon the selection and utilization of the target weed by the agent while causing minimal harm to non-target species. Selection of weed species by biological control agents is determined by the presence of behavioral cues, generally host secondary plant c...

Portuguese guidelines for the use of biological agents in rheumatoid arthritis - October 2011 update.

PubMed

Fonseca, João Eurico; Bernardes, Miguel; Canhão, Helena; Santos, Maria José; Quintal, Alberto; Malcata, Armando; Neto, Adriano; Cordeiro, Ana; Rodrigues, Ana; Mourão, Ana Filipa; Ribeiro, Ana Sofia; Cravo, Ana Rita; Barcelos, Anabela; Cardoso, Anabela; Vilar, António; Braña, Arecili; Faustino, Augusto; Silva, Candida; Duarte, Cátia; Araújo, Domingos; Nour, Dolores; Sousa, Elsa; Simões, Eugénia; Godinho, Fátima; Brandão, Filipe; Ventura, Francisco; Sequeira, Graça; Figueiredo, Guilherme; Cunha, Inês; Matos, J Alves; Branco, Jaime; Ramos, João; Costa, José António; Gomes, José António; Pinto, José; Silva, José Canas; Silva, J A; Patto, José Vaz; Costa, Lúcia; Miranda, Luís Cunha; Inês, Luís; Santos, Luís Maurício; Cruz, Margarida; Salvador, Maria João; Ferreira, Maria Júlia; Rial, Maria; Queiroz, Mário Viana; Bogas, Mónica; Araújo, Paula; Reis, Paulo; Abreu, Pedro; Machado, Pedro; Pinto, Patrícia; André, Rui; Melo, Rui; Garcês, Sandra; Cortes, Sara; Alcino, Sérgio; Ramiro, Sofia; Capela, Susana

2011-01-01

The authors present the revised version of the Portuguese Society of Rheumatology (SPR) guidelines for the treatment of Rheumatoid Arthritis (RA) with biological therapies. In these guidelines the criteria for introduction and maintenance of biological agents are discussed as well as the contraindications and procedures in the case of nonresponders. Biological treatment (with a tumour necrosis factor antagonist, abatacept or tocilizumab) should be considered in RA patients with a disease activity score 28 (DAS 28) equal to or greater than 3.2 despite treatment with at least 20mg-weekly-dose of methotrexate (MTX) for at least 3 months or, if such treatment is not possible, after 3 months of other conventional disease modifying drug or combination therapy. A DAS 28 score between 2.6 and 3.2 with a significant functional or radiological deterioration under treatment with conventional regimens could also constitute an indication for biological treatment. The treatment goal should be remission or, if that is not achievable, at least a low disease activity, defined by a DAS28 lower than 3.2, without significative functional or radiological worsening. The response criteria, at the end of the first 3 months of treatment, are a decrease of at least 0.6 in the DAS28 score. After 6 months of treatment res­ponse criteria is defined as a decrease greater than 1.2 in the DAS28 score. Non-responders, in accordance to the Rheumatologist’s clinical opinion, should try a switch to another biological agent (tumour necrosis factor antagonist, abatacept, rituximab or tocilizumab).

Simulation of interaction of damage agents of different shape with shaped-charge munition

NASA Astrophysics Data System (ADS)

Radchenko, P. A.; Batuev, S. P.; Radchenko, A. V.; Tukaev, A. M.

2017-01-01

The present paper studies the influence of the shape of projectile (damage agent) on its penetration capability. Steel projectiles of different shape have been considered as damage agents: sphere, regular tetrahedron, cube, cylinder and plate. The weight of projectiles has been kept the same. Antitank grenade has been used as a target. The study has been conducted by means of numerical simulation using finite element analysis. The simulation is three-dimensional. Behavior of materials has been described by elasto-plastic model taking into consideration the fracture and fragmentation of interacting bodies. The speed of interaction has been considered within the range of 800 to 2000 m/s. Research results demonstrated significant influence of the projectile shape on its penetration capability. Projectile in the shape of elongated cylinder has shown better penetration capability. Considering the weight of damage agents (except for sphere and plate) their maximum penetration capability has been reached at the speed of 1400 m/s. Increase of the speed of interaction has been followed by intensive fracture of damage agents and their penetration capability thus has worsened.

Pathogenetic validation of the use of biological protective agents and early treatment in cases of radiation injury simulating radiation effects under space flight conditions

NASA Technical Reports Server (NTRS)

Rogozkin, V. D.; Varteres, V.; Sabo, L.; Groza, N.; Nikolov, I.

1974-01-01

In considering a radiation safety system for space flights, the various measures to protect man against radiation include drug prophylaxis. At the present time a great deal of experimental material has been accumulated on the prevention and treatment of radiation injuries. Antiradiation effectiveness has been established for sulfur- and nitrogen-containing substances, auxins, cyanides, polynucleotides, mucopolysaccharides, lipopolysaccharides, aminosaccharides, synthetic polymers, vitamins, hormones, amino acids and other compounds which can be divided into two basic groups - biological and chemical protective agents.

Chromatographic immunoassays: strategies and recent developments in the analysis of drugs and biological agents

PubMed Central

Matsuda, Ryan; Rodriguez, Elliott; Suresh, Doddavenkatanna; Hage, David S

2015-01-01

A chromatographic immunoassay is a technique in which an antibody or antibody-related agent is used as part of a chromatographic system for the isolation or measurement of a specific target. Various binding agents, detection methods, supports and assay formats have been developed for this group of methods, and applications have been reported that range from drugs, hormones and herbicides to peptides, proteins and bacteria. This review discusses the general principles and applications of chromatographic immunoassays, with an emphasis being given to methods and formats that have been developed for the analysis of drugs and biological agents. The relative advantages or limitations of each format are discussed. Recent developments and research in this field, as well as possible future directions, are also considered. PMID:26571109

Decontamination of biological agents from drinking water infrastructure: a literature review and summary.

PubMed

Szabo, Jeff; Minamyer, Scott

2014-11-01

This report summarizes the current state of knowledge on the persistence of biological agents on drinking water infrastructure (such as pipes) along with information on decontamination should persistence occur. Decontamination options for drinking water infrastructure have been explored for some biological agents, but data gaps remain. Data on bacterial spore persistence on common water infrastructure materials such as iron and cement-mortar lined iron show that spores can be persistent for weeks after contamination. Decontamination data show that common disinfectants such as free chlorine have limited effectiveness. Decontamination results with germinant and alternate disinfectants such as chlorine dioxide are more promising. Persistence and decontamination data were collected on vegetative bacteria, such as coliforms, Legionella and Salmonella. Vegetative bacteria are less persistent than spores and more susceptible to disinfection, but the surfaces and water quality conditions in many studies were only marginally related to drinking water systems. However, results of real-world case studies on accidental contamination of water systems with E. coli and Salmonella contamination show that flushing and chlorination can help return a water system to service. Some viral persistence data were found, but decontamination data were lacking. Future research suggestions focus on expanding the available biological persistence data to other common infrastructure materials. Further exploration of non-traditional drinking water disinfectants is recommended for future studies. Published by Elsevier Ltd.

A Primer for Agent-Based Simulation and Modeling in Transportation Applications

DOT National Transportation Integrated Search

2013-11-01

Agent-based modeling and simulation (ABMS) methods have been applied in a spectrum of research domains. This primer focuses on ABMS in the transportation interdisciplinary domain, describes the basic concepts of ABMS and the recent progress of ABMS i...

Performance evaluation of an agent-based occupancy simulation model

DOE PAGES

Luo, Xuan; Lam, Khee Poh; Chen, Yixing; ...

2017-01-17

Occupancy is an important factor driving building performance. Static and homogeneous occupant schedules, commonly used in building performance simulation, contribute to issues such as performance gaps between simulated and measured energy use in buildings. Stochastic occupancy models have been recently developed and applied to better represent spatial and temporal diversity of occupants in buildings. However, there is very limited evaluation of the usability and accuracy of these models. This study used measured occupancy data from a real office building to evaluate the performance of an agent-based occupancy simulation model: the Occupancy Simulator. The occupancy patterns of various occupant types weremore » first derived from the measured occupant schedule data using statistical analysis. Then the performance of the simulation model was evaluated and verified based on (1) whether the distribution of observed occupancy behavior patterns follows the theoretical ones included in the Occupancy Simulator, and (2) whether the simulator can reproduce a variety of occupancy patterns accurately. Results demonstrated the feasibility of applying the Occupancy Simulator to simulate a range of occupancy presence and movement behaviors for regular types of occupants in office buildings, and to generate stochastic occupant schedules at the room and individual occupant levels for building performance simulation. For future work, model validation is recommended, which includes collecting and using detailed interval occupancy data of all spaces in an office building to validate the simulated occupant schedules from the Occupancy Simulator.« less

Performance evaluation of an agent-based occupancy simulation model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luo, Xuan; Lam, Khee Poh; Chen, Yixing

Occupancy is an important factor driving building performance. Static and homogeneous occupant schedules, commonly used in building performance simulation, contribute to issues such as performance gaps between simulated and measured energy use in buildings. Stochastic occupancy models have been recently developed and applied to better represent spatial and temporal diversity of occupants in buildings. However, there is very limited evaluation of the usability and accuracy of these models. This study used measured occupancy data from a real office building to evaluate the performance of an agent-based occupancy simulation model: the Occupancy Simulator. The occupancy patterns of various occupant types weremore » first derived from the measured occupant schedule data using statistical analysis. Then the performance of the simulation model was evaluated and verified based on (1) whether the distribution of observed occupancy behavior patterns follows the theoretical ones included in the Occupancy Simulator, and (2) whether the simulator can reproduce a variety of occupancy patterns accurately. Results demonstrated the feasibility of applying the Occupancy Simulator to simulate a range of occupancy presence and movement behaviors for regular types of occupants in office buildings, and to generate stochastic occupant schedules at the room and individual occupant levels for building performance simulation. For future work, model validation is recommended, which includes collecting and using detailed interval occupancy data of all spaces in an office building to validate the simulated occupant schedules from the Occupancy Simulator.« less

Simbios: an NIH national center for physics-based simulation of biological structures

PubMed Central

Delp, Scott L; Ku, Joy P; Pande, Vijay S; Sherman, Michael A

2011-01-01

Physics-based simulation provides a powerful framework for understanding biological form and function. Simulations can be used by biologists to study macromolecular assemblies and by clinicians to design treatments for diseases. Simulations help biomedical researchers understand the physical constraints on biological systems as they engineer novel drugs, synthetic tissues, medical devices, and surgical interventions. Although individual biomedical investigators make outstanding contributions to physics-based simulation, the field has been fragmented. Applications are typically limited to a single physical scale, and individual investigators usually must create their own software. These conditions created a major barrier to advancing simulation capabilities. In 2004, we established a National Center for Physics-Based Simulation of Biological Structures (Simbios) to help integrate the field and accelerate biomedical research. In 6 years, Simbios has become a vibrant national center, with collaborators in 16 states and eight countries. Simbios focuses on problems at both the molecular scale and the organismal level, with a long-term goal of uniting these in accurate multiscale simulations. PMID:22081222

High performance hybrid functional Petri net simulations of biological pathway models on CUDA.

PubMed

Chalkidis, Georgios; Nagasaki, Masao; Miyano, Satoru

2011-01-01

Hybrid functional Petri nets are a wide-spread tool for representing and simulating biological models. Due to their potential of providing virtual drug testing environments, biological simulations have a growing impact on pharmaceutical research. Continuous research advancements in biology and medicine lead to exponentially increasing simulation times, thus raising the demand for performance accelerations by efficient and inexpensive parallel computation solutions. Recent developments in the field of general-purpose computation on graphics processing units (GPGPU) enabled the scientific community to port a variety of compute intensive algorithms onto the graphics processing unit (GPU). This work presents the first scheme for mapping biological hybrid functional Petri net models, which can handle both discrete and continuous entities, onto compute unified device architecture (CUDA) enabled GPUs. GPU accelerated simulations are observed to run up to 18 times faster than sequential implementations. Simulating the cell boundary formation by Delta-Notch signaling on a CUDA enabled GPU results in a speedup of approximately 7x for a model containing 1,600 cells.

Heterapoderopsis bicallosicollis (Coleoptera: Attelabidae): a potential biological control agent for Triadica sebifera.

PubMed

Wang, Yi; Ding, Jianqing; Wheeler, Gregory S; Purcell, Matthew F; Zhang, Guoan

2009-08-01

Native to China, Chinese tallow, Triadica sebifera L. Small (Euphorbiaceae), is an invasive plant in the southeastern United States. The leaf-rolling weevil, Heterapoderopsis bicallosicollis Voss, is a common herbivore attacking this plant in China. To evaluate its potential as a biological control agent of T. sebifera, biology and host specificity of this weevil were studied in China. H. bicallosicollis occurs over a wide, native, geographic range and its immatures successfully develop at 15-35 degrees C, indicating its physiological potential to establish and persist throughout the range of climatic conditions where the target plant grows in the United States. Adults make feeding holes on leaves. Before oviposition, the female makes a sealed leaf roll called a nidus and then lays one to two eggs inside. Eggs, larvae, and pupae develop within nidi, and larvae survive only when they develop inside the nidi. This requirement makes the weevil highly host specific to T. sebifera. In laboratory no-choice tests of 54 species from eight families, adults fed on only 3 plant species, T. sebifera, Sapium chihsinianum S. K. Lee, and Phyllanthus urinaria L. and only oviposited on T. sebifera. These results were confirmed where, in multiple-choice tests, adults only oviposited on T. sebifera. Given that T. sebifera is the only species in the genus Triadica in the United States, the results of this study suggest that H. bicallosicollis is a potential biological control agent of T. sebifera and should be considered to be imported into quarantine in the United States for further tests on native North American species.

Use of pupal parasitoids as biological control agents of filth flies on equine facilities

USDA-ARS?s Scientific Manuscript database

House flies, Musca domestica L., and stable flies, Stomoxys calcitrans (L.), (Diptera: Muscidae), are common pests on horse farms. The use of pupal parasitoids as biological control agents for filth flies is becoming more popular on equine facilities; however, there is a lack of information on the e...

Chemical warfare agent simulants for human volunteer trials of emergency decontamination: A systematic review

PubMed Central

Wyke, Stacey; Marczylo, Tim; Collins, Samuel; Gaulton, Tom; Foxall, Kerry; Amlôt, Richard; Duarte‐Davidson, Raquel

2017-01-01

Abstract Incidents involving the release of chemical agents can pose significant risks to public health. In such an event, emergency decontamination of affected casualties may need to be undertaken to reduce injury and possible loss of life. To ensure these methods are effective, human volunteer trials (HVTs) of decontamination protocols, using simulant contaminants, have been conducted. Simulants must be used to mimic the physicochemical properties of more harmful chemicals, while remaining non‐toxic at the dose applied. This review focuses on studies that employed chemical warfare agent simulants in decontamination contexts, to identify those simulants most suitable for use in HVTs of emergency decontamination. Twenty‐two simulants were identified, of which 17 were determined unsuitable for use in HVTs. The remaining simulants (n = 5) were further scrutinized for potential suitability according to toxicity, physicochemical properties and similarities to their equivalent toxic counterparts. Three suitable simulants, for use in HVTs were identified; methyl salicylate (simulant for sulphur mustard), diethyl malonate (simulant for soman) and malathion (simulant for VX or toxic industrial chemicals). All have been safely used in previous HVTs, and have a range of physicochemical properties that would allow useful inference to more toxic chemicals when employed in future studies of emergency decontamination systems. PMID:28990191

A theranostic dental pulp capping agent with improved MRI and CT contrast and biological properties.

PubMed

Mastrogiacomo, S; Güvener, N; Dou, W; Alghamdi, H S; Camargo, W A; Cremers, J G O; Borm, P J A; Heerschap, A; Oosterwijk, E; Jansen, J A; Walboomers, X F

2017-10-15

Different materials have been used for vital dental pulp treatment. Preferably a pulp capping agent should show appropriate biological performance, excellent handling properties, and a good imaging contrast. These features can be delivered into a single material through the combination of therapeutic and diagnostic agents (i.e. theranostic). Calcium phosphate based composites (CPCs) are potentially ideal candidate for pulp treatment, although poor imaging contrast and poor dentino-inductive properties are limiting their clinical use. In this study, a theranostic dental pulp capping agent was developed. First, imaging properties of the CPC were improved by using a core-shell structured dual contrast agent (csDCA) consisting of superparamagnetic iron oxide (SPIO) and colloidal gold, as MRI and CT contrast agent respectively. Second, biological properties were implemented by using a dentinogenic factor (i.e. bone morphogenetic protein 2, BMP-2). The obtained CPC/csDCA/BMP-2 composite was tested in vivo, as direct pulp capping agent, in a male Habsi goat incisor model. Our outcomes showed no relevant alteration of the handling and mechanical properties (e.g. setting time, injectability, and compressive strength) by the incorporation of csDCA particles. In vivo results proved MRI contrast enhancement up to 7weeks. Incisors treated with BMP-2 showed improved tertiary dentin deposition as well as faster cement degradation as measured by µCT assessment. In conclusion, the presented theranostic agent matches the imaging and regenerative requirements for pulp capping applications. In this study, we combined diagnostic and therapeutic agents in order to developed a theranostic pulp capping agent with enhanced MRI and CT contrast and improved dentin regeneration ability. In our study we cover all the steps from material preparation, mechanical and in vitro characterization, to in vivo study in a goat dental model. To the best of our knowledge, this is the first time that a

Simulated Environments with Animated Agents: Effects on Visual Attention, Emotion, Performance, and Perception

ERIC Educational Resources Information Center

Romero-Hall, E.; Watson, G. S.; Adcock, A.; Bliss, J.; Adams Tufts, K.

2016-01-01

This research assessed how emotive animated agents in a simulation-based training affect the performance outcomes and perceptions of the individuals interacting in real time with the training application. A total of 56 participants consented to complete the study. The material for this investigation included a nursing simulation in which…

Chemical agent simulant release from clothing following vapor exposure.

PubMed

Feldman, Robert J

2010-02-01

Most ambulatory victims of a terrorist chemical attack will have exposure to vapor only. The study objective was to measure the duration of chemical vapor release from various types of clothing. A chemical agent was simulated using methyl salicylate (MeS), which has similar physical properties to sulfur mustard and was the agent used in the U.S. Army's Man-In-Simulant Test (MIST). Vapor concentration was measured with a Smiths Detection Advanced Portable Detector (APD)-2000 unit. The clothing items were exposed to vapor for 1 hour in a sealed cabinet; vapor concentration was measured at the start and end of each exposure. Clothing was then removed and assessed every 5 minutes with the APD-2000, using a uniform sweep pattern, until readings remained 0. Concentration and duration of vapor release from clothing varied with clothing composition and construction. Lightweight cotton shirts and jeans had the least trapped vapor; down outerwear, the most. Vapor concentration near the clothing often increased for several minutes after the clothing was removed from the contaminated environment. Compression of thick outerwear released additional vapor. Mean times to reach 0 ranged from 7 minutes for jeans to 42 minutes for down jackets. This simulation model of chemical vapor release demonstrates persistent presence of simulant vapor over time. This implies that chemical vapor may be released from the victims' clothing after they are evacuated from the site of exposure, resulting in additional exposure of victims and emergency responders. Insulated outerwear can release additional vapor when handled. If a patient has just moved to a vapor screening point, immediate assessment before additional vapor can be released from the clothing can lead to a false-negative assessment of contamination.

Biological and environmental hazards associated with exposure to chemical warfare agents: arsenicals.

PubMed

Li, Changzhao; Srivastava, Ritesh K; Athar, Mohammad

2016-08-01

Arsenicals are highly reactive inorganic and organic derivatives of arsenic. These chemicals are very toxic and produce both acute and chronic tissue damage. On the basis of these observations, and considering the low cost and simple methods of their bulk syntheses, these agents were thought to be appropriate for chemical warfare. Among these, the best-known agent that was synthesized and weaponized during World War I (WWI) is Lewisite. Exposure to Lewisite causes painful inflammatory and blistering responses in the skin, lung, and eye. These chemicals also manifest systemic tissue injury following their cutaneous exposure. Although largely discontinued after WWI, stockpiles are still known to exist in the former Soviet Union, Germany, Italy, the United States, and Asia. Thus, access by terrorists or accidental exposure could be highly dangerous for humans and the environment. This review summarizes studies that describe the biological, pathophysiological, toxicological, and environmental effects of exposure to arsenicals, with a major focus on cutaneous injury. Studies related to the development of novel molecular pathobiology-based antidotes against these agents are also described. © 2016 New York Academy of Sciences.

Biological and environmental hazards associated with exposure to chemical warfare agents: arsenicals

PubMed Central

Li, Changzhao; Srivastava, Ritesh K.; Athar, Mohammad

2016-01-01

Arsenicals are highly reactive inorganic and organic derivatives of arsenic. These chemicals are very toxic and produce both acute and chronic tissue damage. Based on these observations, and considering the low cost and simple methods of their bulk syntheses, these agents were thought to be appropriate for chemical warfare. Among these, the most known agent synthesized and weaponized during World War I (WWI) is Lewisite. Exposure to Lewisite causes painful inflammatory and blistering responses in the skin, lung, and eye. These chemicals also manifest systemic tissue injury following their cutaneous exposure. Although largely discontinued after WWI, their stockpiles are still known to exist in the former Soviet Union, Germany, Italy, the United States, and Asia. Thus, their access by terrorists or accidental exposure could be highly dangerous for humans and the environment. This review summarizes studies which describe the biological, pathophysiological, toxicological, and environmental effects of exposure to arsenicals, with a major focus on cutaneous injury. Studies related to the development of novel molecular pathobiology–based antidotes against these agents are also described. PMID:27636894

Laboratory evaluation of two native fishes from tropical North Queensland as biological control agents of subterranean Aedes aegypti.

PubMed

Russell, B M; Wang, J; Williams, Y; Hearnden, M N; Kay, B H

2001-06-01

The ability of 2 freshwater fishes, eastern rainbow fish Melanotaenia splendida splendida and fly-specked hardyhead Craterocephalus stercusmuscarum stercusmuscarum, native to North Queensland to prey on immature Aedes aegypti was evaluated under laboratory conditions. The predation efficiency of the 2 species was compared to the exotic guppy, Poecilia reticulata, which is commonly used as a biological control agent of mosquito larvae. Of the 3 fish species tested, M. s. splendida was shown to be the most promising agent for the biological control of Ae. aegypti that breed in wells. Melanotaenia s. splendida consumed significantly greater numbers of immature Ae. aegypti than P. reticulata, irrespective of developmental stage or light conditions. Unlike C s. stercusmuscarum, M. s. splendida could be handled, transported, and kept in captivity for extended periods with negligible mortality. However, M. s. splendida was also an efficient predator of Litoria caerulea tadpoles, a species of native frog found in wells during the dry season. This result may limit the usefulness of M. s. splendida as a biological control agent of well-breeding Ae. aegypti and suggests that predacious copepods, Mesocyclops spp., are more suitable. However, the use of M. s. splendida as a mosquito control agent in containers that are unlikely to support frog populations (e.g., aquaculture tanks and drinking troughs) should be given serious consideration.

SpikingLab: modelling agents controlled by Spiking Neural Networks in Netlogo.

PubMed

Jimenez-Romero, Cristian; Johnson, Jeffrey

2017-01-01

The scientific interest attracted by Spiking Neural Networks (SNN) has lead to the development of tools for the simulation and study of neuronal dynamics ranging from phenomenological models to the more sophisticated and biologically accurate Hodgkin-and-Huxley-based and multi-compartmental models. However, despite the multiple features offered by neural modelling tools, their integration with environments for the simulation of robots and agents can be challenging and time consuming. The implementation of artificial neural circuits to control robots generally involves the following tasks: (1) understanding the simulation tools, (2) creating the neural circuit in the neural simulator, (3) linking the simulated neural circuit with the environment of the agent and (4) programming the appropriate interface in the robot or agent to use the neural controller. The accomplishment of the above-mentioned tasks can be challenging, especially for undergraduate students or novice researchers. This paper presents an alternative tool which facilitates the simulation of simple SNN circuits using the multi-agent simulation and the programming environment Netlogo (educational software that simplifies the study and experimentation of complex systems). The engine proposed and implemented in Netlogo for the simulation of a functional model of SNN is a simplification of integrate and fire (I&F) models. The characteristics of the engine (including neuronal dynamics, STDP learning and synaptic delay) are demonstrated through the implementation of an agent representing an artificial insect controlled by a simple neural circuit. The setup of the experiment and its outcomes are described in this work.

Biological conversion system

DOEpatents

Scott, C.D.

A system for bioconversion of organic material comprises a primary bioreactor column wherein a biological active agent (zymomonas mobilis) converts the organic material (sugar) to a product (alcohol), a rejuvenator column wherein the biological activity of said biological active agent is enhanced, and means for circulating said biological active agent between said primary bioreactor column and said rejuvenator column.

A Multi-Agent Approach to the Simulation of Robotized Manufacturing Systems

NASA Astrophysics Data System (ADS)

Foit, K.; Gwiazda, A.; Banaś, W.

2016-08-01

The recent years of eventful industry development, brought many competing products, addressed to the same market segment. The shortening of a development cycle became a necessity if the company would like to be competitive. Because of switching to the Intelligent Manufacturing model the industry search for new scheduling algorithms, while the traditional ones do not meet the current requirements. The agent-based approach has been considered by many researchers as an important way of evolution of modern manufacturing systems. Due to the properties of the multi-agent systems, this methodology is very helpful during creation of the model of production system, allowing depicting both processing and informational part. The complexity of such approach makes the analysis impossible without the computer assistance. Computer simulation still uses a mathematical model to recreate a real situation, but nowadays the 2D or 3D virtual environments or even virtual reality have been used for realistic illustration of the considered systems. This paper will focus on robotized manufacturing system and will present the one of possible approaches to the simulation of such systems. The selection of multi-agent approach is motivated by the flexibility of this solution that offers the modularity, robustness and autonomy.

On Designing Multicore-Aware Simulators for Systems Biology Endowed with OnLine Statistics

PubMed Central

Calcagno, Cristina; Coppo, Mario

2014-01-01

The paper arguments are on enabling methodologies for the design of a fully parallel, online, interactive tool aiming to support the bioinformatics scientists .In particular, the features of these methodologies, supported by the FastFlow parallel programming framework, are shown on a simulation tool to perform the modeling, the tuning, and the sensitivity analysis of stochastic biological models. A stochastic simulation needs thousands of independent simulation trajectories turning into big data that should be analysed by statistic and data mining tools. In the considered approach the two stages are pipelined in such a way that the simulation stage streams out the partial results of all simulation trajectories to the analysis stage that immediately produces a partial result. The simulation-analysis workflow is validated for performance and effectiveness of the online analysis in capturing biological systems behavior on a multicore platform and representative proof-of-concept biological systems. The exploited methodologies include pattern-based parallel programming and data streaming that provide key features to the software designers such as performance portability and efficient in-memory (big) data management and movement. Two paradigmatic classes of biological systems exhibiting multistable and oscillatory behavior are used as a testbed. PMID:25050327

On designing multicore-aware simulators for systems biology endowed with OnLine statistics.

PubMed

Aldinucci, Marco; Calcagno, Cristina; Coppo, Mario; Damiani, Ferruccio; Drocco, Maurizio; Sciacca, Eva; Spinella, Salvatore; Torquati, Massimo; Troina, Angelo

2014-01-01

The paper arguments are on enabling methodologies for the design of a fully parallel, online, interactive tool aiming to support the bioinformatics scientists .In particular, the features of these methodologies, supported by the FastFlow parallel programming framework, are shown on a simulation tool to perform the modeling, the tuning, and the sensitivity analysis of stochastic biological models. A stochastic simulation needs thousands of independent simulation trajectories turning into big data that should be analysed by statistic and data mining tools. In the considered approach the two stages are pipelined in such a way that the simulation stage streams out the partial results of all simulation trajectories to the analysis stage that immediately produces a partial result. The simulation-analysis workflow is validated for performance and effectiveness of the online analysis in capturing biological systems behavior on a multicore platform and representative proof-of-concept biological systems. The exploited methodologies include pattern-based parallel programming and data streaming that provide key features to the software designers such as performance portability and efficient in-memory (big) data management and movement. Two paradigmatic classes of biological systems exhibiting multistable and oscillatory behavior are used as a testbed.

Identification of biological agents using surface enhanced Raman scattering

NASA Astrophysics Data System (ADS)

Paxon, Tracy L.; Duthie, R. Scott; Renko, Casey; Burns, Andrew A.; Lesaicherre, Marie L.; Mondello, Frank J.

2011-05-01

GE Global Research Center, in collaboration with Morpho Detection, Inc. has developed an assay scheme for the identification of biological agents using Surface Enhanced Raman Scattering (SERS). Specifically, unique spectroscopic signatures are generated using SERS tags consisting of individual glass-encapsulated gold nanoparticles and surfacebound reporter molecules. These SERS tags are modified with a capture moiety specific to the antigen of interest, and serve as a spectroscopic label in a bead-based sandwich assay. Assays are being developed for a variety of pathogens and this paper will focus on aspects of assay development, optimization, stabilization and validation. Results on the development of an assay to detect Ricin toxin will be presented, and preliminary feasibility studies for the detection of additional pathogens will be discussed.

Functionalized gold nanoparticle supported sensory mechanisms applied in detection of chemical and biological threat agents: a review.

PubMed

Upadhyayula, Venkata K K

2012-02-17

There is a great necessity for development of novel sensory concepts supportive of smart sensing capabilities in defense and homeland security applications for detection of chemical and biological threat agents. A smart sensor is a detection device that can exhibit important features such as speed, sensitivity, selectivity, portability, and more importantly, simplicity in identifying a target analyte. Emerging nanomaterial based sensors, particularly those developed by utilizing functionalized gold nanoparticles (GNPs) as a sensing component potentially offer many desirable features needed for threat agent detection. The sensitiveness of physical properties expressed by GNPs, e.g. color, surface plasmon resonance, electrical conductivity and binding affinity are significantly enhanced when they are subjected to functionalization with an appropriate metal, organic or biomolecular functional groups. This sensitive nature of functionalized GNPs can be potentially exploited in the design of threat agent detection devices with smart sensing capabilities. In the presence of a target analyte (i.e., a chemical or biological threat agent) a change proportional to concentration of the analyte is observed, which can be measured either by colorimetric, fluorimetric, electrochemical or spectroscopic means. This article provides a review of how functionally modified gold colloids are applied in the detection of a broad range of threat agents, including radioactive substances, explosive compounds, chemical warfare agents, biotoxins, and biothreat pathogens through any of the four sensory means mentioned previously. Copyright © 2011 Elsevier B.V. All rights reserved.

Evolution of a multi-agent system in a cyclical environment.

PubMed

Baptista, Tiago; Costa, Ernesto

2008-06-01

The synchronisation phenomena in biological systems is a current and recurring subject of scientific study. This topic, namely that of circadian clocks, served as inspiration to develop an agent-based simulation that serves the main purpose of being a proof-of-concept of the model used in the BitBang framework, that implements a modern autonomous agent model. Despite having been extensively studied, circadian clocks still have much to be investigated. Rather than wanting to learn more about the internals of this biological process, we look to study the emergence of this kind of adaptation to a daily cycle. To that end we implemented a world with a day/night cycle, and analyse the ways the agents adapt to that cycle. The results show the evolution of the agents' ability to gather food. If we look at the total number of agents over the course of an experiment, we can pinpoint the time when reproductive technology emerges. We also show that the agents adapt to the daily cycle. This circadian rhythm can be shown by analysing the variation on the agents metabolic rate, which is affected by the variation of their movement patterns. In the experiments conducted we can observe that the metabolic rate of the agents varies according to the daily cycle.

Metal organic frameworks (MOFs) for degrdation of nerve agent simulant parathion

USDA-ARS?s Scientific Manuscript database

Parathion, a simulant of nerve agent VX, has been studied for degradation on Fe3+, Fe2+ and zerovalent iron supported on chitosan. Chitosan, a naturally occurring biopolymer derivative of chitin, is a very good adsorbent for many chemicals including metals. Chitosan is used as supporting biopolymer ...

Metal organic frameworks (MOFs) for degradation of nerve agent simulant parathion

USDA-ARS?s Scientific Manuscript database

Parathion, a simulant of nerve agent VX, has been studied for degradation on Fe3+, Fe2+ and zerovalent iron supported on chitosan. Chitosan, a naturally occurring biopolymer derivative of chitin, is a very good adsorbent for many chemicals including metals. Chitosan is used as supporting biopolymer ...

"Design characteristics of the CORRONA CERTAIN study: a comparative effectiveness study of biologic agents for rheumatoid arthritis patients".

PubMed

Pappas, Dimitrios A; Kremer, Joel M; Reed, George; Greenberg, Jeffrey D; Curtis, Jeffrey R

2014-04-01

Comparative effectiveness research has recently attracted considerable attention. The Comparative Effectiveness Registry to study Therapies for Arthritis and Inflammatory Conditions (CERTAIN) is an ongoing prospective cohort study of adult patients with Rheumatoid Arthritis (RA). CERTAIN uses the existing Consortium of Rheumatology Researchers of North America (CORRONA) network of participating private and academic sites in order to recruit patients fulfilling the 1987 ACR criteria that have at least moderate disease activity. Patients starting or switching biologic agents either anti-TNF therapy or a non anti-TNF biologic are eligible for enrollment, depending on the treatment selected by their physician. Enrollment is expected to be completed by March of 2014, and 2711 patients will participate in the study. As of October 7th 2013, 2234 patients have been enrolled. Patient visits and laboratory blood work are mandated every three months for one year. Safety data is collected through one year and beyond. The primary comparative effectiveness endpoint is attainment of low RA disease activity at one year among patients who have been exposed to at least one prior TNF-α inhibitor agent prior to enrollment. Multiple secondary effectiveness and safety endpoints will be addressed by investigating the entire population enrolled (naïve and biologic experienced). The unique design features of CERTAIN will inform comparative effectiveness and safety questions for choosing biologic agents for the management of RA.

A Coupled Simulation Architecture for Agent-Based/Geohydrological Modelling

NASA Astrophysics Data System (ADS)

Jaxa-Rozen, M.

2016-12-01

The quantitative modelling of social-ecological systems can provide useful insights into the interplay between social and environmental processes, and their impact on emergent system dynamics. However, such models should acknowledge the complexity and uncertainty of both of the underlying subsystems. For instance, the agent-based models which are increasingly popular for groundwater management studies can be made more useful by directly accounting for the hydrological processes which drive environmental outcomes. Conversely, conventional environmental models can benefit from an agent-based depiction of the feedbacks and heuristics which influence the decisions of groundwater users. From this perspective, this work describes a Python-based software architecture which couples the popular NetLogo agent-based platform with the MODFLOW/SEAWAT geohydrological modelling environment. This approach enables users to implement agent-based models in NetLogo's user-friendly platform, while benefiting from the full capabilities of MODFLOW/SEAWAT packages or reusing existing geohydrological models. The software architecture is based on the pyNetLogo connector, which provides an interface between the NetLogo agent-based modelling software and the Python programming language. This functionality is then extended and combined with Python's object-oriented features, to design a simulation architecture which couples NetLogo with MODFLOW/SEAWAT through the FloPy library (Bakker et al., 2016). The Python programming language also provides access to a range of external packages which can be used for testing and analysing the coupled models, which is illustrated for an application of Aquifer Thermal Energy Storage (ATES).

Principles of antidote pharmacology: an update on prophylaxis, post-exposure treatment recommendations and research initiatives for biological agents

PubMed Central

Ramasamy, S; Liu, CQ; Tran, H; Gubala, A; Gauci, P; McAllister, J; Vo, T

2010-01-01

The use of biological agents has generally been confined to military-led conflicts. However, there has been an increase in non-state-based terrorism, including the use of asymmetric warfare, such as biological agents in the past few decades. Thus, it is becoming increasingly important to consider strategies for preventing and preparing for attacks by insurgents, such as the development of pre- and post-exposure medical countermeasures. There are a wide range of prophylactics and treatments being investigated to combat the effects of biological agents. These include antibiotics (for both conventional and unconventional use), antibodies, anti-virals, immunomodulators, nucleic acids (analogues, antisense, ribozymes and DNAzymes), bacteriophage therapy and micro-encapsulation. While vaccines are commercially available for the prevention of anthrax, cholera, plague, Q fever and smallpox, there are no licensed vaccines available for use in the case of botulinum toxins, viral encephalitis, melioidosis or ricin. Antibiotics are still recommended as the mainstay treatment following exposure to anthrax, plague, Q fever and melioidosis. Anti-toxin therapy and anti-virals may be used in the case of botulinum toxins or smallpox respectively. However, supportive care is the only, or mainstay, post-exposure treatment for cholera, viral encephalitis and ricin – a recommendation that has not changed in decades. Indeed, with the difficulty that antibiotic resistance poses, the development and further evaluation of techniques and atypical pharmaceuticals are fundamental to the development of prophylaxis and post-exposure treatment options. The aim of this review is to present an update on prophylaxis and post-exposure treatment recommendations and research initiatives for biological agents in the open literature from 2007 to 2009. PMID:20860656

GridLAB-D: An Agent-Based Simulation Framework for Smart Grids

DOE PAGES

Chassin, David P.; Fuller, Jason C.; Djilali, Ned

2014-01-01

Simulation of smart grid technologies requires a fundamentally new approach to integrated modeling of power systems, energy markets, building technologies, and the plethora of other resources and assets that are becoming part of modern electricity production, delivery, and consumption systems. As a result, the US Department of Energy’s Office of Electricity commissioned the development of a new type of power system simulation tool called GridLAB-D that uses an agent-based approach to simulating smart grids. This paper presents the numerical methods and approach to time-series simulation used by GridLAB-D and reviews applications in power system studies, market design, building control systemmore » design, and integration of wind power in a smart grid.« less

GridLAB-D: An Agent-Based Simulation Framework for Smart Grids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chassin, David P.; Fuller, Jason C.; Djilali, Ned

2014-06-23

Simulation of smart grid technologies requires a fundamentally new approach to integrated modeling of power systems, energy markets, building technologies, and the plethora of other resources and assets that are becoming part of modern electricity production, delivery, and consumption systems. As a result, the US Department of Energy’s Office of Electricity commissioned the development of a new type of power system simulation tool called GridLAB-D that uses an agent-based approach to simulating smart grids. This paper presents the numerical methods and approach to time-series simulation used by GridLAB-D and reviews applications in power system studies, market design, building control systemmore » design, and integration of wind power in a smart grid.« less

Chemical warfare agent simulants for human volunteer trials of emergency decontamination: A systematic review.

PubMed

James, Thomas; Wyke, Stacey; Marczylo, Tim; Collins, Samuel; Gaulton, Tom; Foxall, Kerry; Amlôt, Richard; Duarte-Davidson, Raquel

2018-01-01

Incidents involving the release of chemical agents can pose significant risks to public health. In such an event, emergency decontamination of affected casualties may need to be undertaken to reduce injury and possible loss of life. To ensure these methods are effective, human volunteer trials (HVTs) of decontamination protocols, using simulant contaminants, have been conducted. Simulants must be used to mimic the physicochemical properties of more harmful chemicals, while remaining non-toxic at the dose applied. This review focuses on studies that employed chemical warfare agent simulants in decontamination contexts, to identify those simulants most suitable for use in HVTs of emergency decontamination. Twenty-two simulants were identified, of which 17 were determined unsuitable for use in HVTs. The remaining simulants (n = 5) were further scrutinized for potential suitability according to toxicity, physicochemical properties and similarities to their equivalent toxic counterparts. Three suitable simulants, for use in HVTs were identified; methyl salicylate (simulant for sulphur mustard), diethyl malonate (simulant for soman) and malathion (simulant for VX or toxic industrial chemicals). All have been safely used in previous HVTs, and have a range of physicochemical properties that would allow useful inference to more toxic chemicals when employed in future studies of emergency decontamination systems. © 2017 Crown Copyright. Journal of Applied Toxicology published by John Wiley & Sons, Ltd.

DAMS: A Model to Assess Domino Effects by Using Agent-Based Modeling and Simulation.

PubMed

Zhang, Laobing; Landucci, Gabriele; Reniers, Genserik; Khakzad, Nima; Zhou, Jianfeng

2017-12-19

Historical data analysis shows that escalation accidents, so-called domino effects, have an important role in disastrous accidents in the chemical and process industries. In this study, an agent-based modeling and simulation approach is proposed to study the propagation of domino effects in the chemical and process industries. Different from the analytical or Monte Carlo simulation approaches, which normally study the domino effect at probabilistic network levels, the agent-based modeling technique explains the domino effects from a bottom-up perspective. In this approach, the installations involved in a domino effect are modeled as agents whereas the interactions among the installations (e.g., by means of heat radiation) are modeled via the basic rules of the agents. Application of the developed model to several case studies demonstrates the ability of the model not only in modeling higher-level domino effects and synergistic effects but also in accounting for temporal dependencies. The model can readily be applied to large-scale complicated cases. © 2017 Society for Risk Analysis.

STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB.

PubMed

Klingbeil, Guido; Erban, Radek; Giles, Mike; Maini, Philip K

2011-04-15

The importance of stochasticity in biological systems is becoming increasingly recognized and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU that exploits graphics processing units (GPUs) for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB. The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM) and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user's models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2. The software is open source under the GPL v3 and available at http://www.maths.ox.ac.uk/cmb/STOCHSIMGPU. The web site also contains supplementary information. klingbeil@maths.ox.ac.uk Supplementary data are available at Bioinformatics online.

WE-H-BRA-04: Biological Geometries for the Monte Carlo Simulation Toolkit TOPASNBio

DOE Office of Scientific and Technical Information (OSTI.GOV)

McNamara, A; Held, K; Paganetti, H

2016-06-15

Purpose: New advances in radiation therapy are most likely to come from the complex interface of physics, chemistry and biology. Computational simulations offer a powerful tool for quantitatively investigating radiation interactions with biological tissue and can thus help bridge the gap between physics and biology. The aim of TOPAS-nBio is to provide a comprehensive tool to generate advanced radiobiology simulations. Methods: TOPAS wraps and extends the Geant4 Monte Carlo (MC) simulation toolkit. TOPAS-nBio is an extension to TOPAS which utilizes the physics processes in Geant4-DNA to model biological damage from very low energy secondary electrons. Specialized cell, organelle and molecularmore » geometries were designed for the toolkit. Results: TOPAS-nBio gives the user the capability of simulating biological geometries, ranging from the micron-scale (e.g. cells and organelles) to complex nano-scale geometries (e.g. DNA and proteins). The user interacts with TOPAS-nBio through easy-to-use input parameter files. For example, in a simple cell simulation the user can specify the cell type and size as well as the type, number and size of included organelles. For more detailed nuclear simulations, the user can specify chromosome territories containing chromatin fiber loops, the later comprised of nucleosomes on a double helix. The chromatin fibers can be arranged in simple rigid geometries or within factual globules, mimicking realistic chromosome territories. TOPAS-nBio also provides users with the capability of reading protein data bank 3D structural files to simulate radiation damage to proteins or nucleic acids e.g. histones or RNA. TOPAS-nBio has been validated by comparing results to other track structure simulation software and published experimental measurements. Conclusion: TOPAS-nBio provides users with a comprehensive MC simulation tool for radiobiological simulations, giving users without advanced programming skills the ability to design and run complex

The Effects of 3D Computer Simulation on Biology Students' Achievement and Memory Retention

ERIC Educational Resources Information Center

Elangovan, Tavasuria; Ismail, Zurida

2014-01-01

A quasi experimental study was conducted for six weeks to determine the effectiveness of two different 3D computer simulation based teaching methods, that is, realistic simulation and non-realistic simulation on Form Four Biology students' achievement and memory retention in Perak, Malaysia. A sample of 136 Form Four Biology students in Perak,…

Trichogramma spp. (Hymenoptera: Trichogrammatidae) as biological control agents in the Philippines: history and current practice

USDA-ARS?s Scientific Manuscript database

Trichogramma parasitoids have long been recognized as important and viable biological control agents against lepidopteran pests of rice, corn and sugarcane in the Philippines. We describe the history of research and use of Trichogramma spp. in the Philippines in three main areas: 1) field surveys – ...

Design of a Mobile Agent-Based Adaptive Communication Middleware for Federations of Critical Infrastructure Simulations

NASA Astrophysics Data System (ADS)

Görbil, Gökçe; Gelenbe, Erol

The simulation of critical infrastructures (CI) can involve the use of diverse domain specific simulators that run on geographically distant sites. These diverse simulators must then be coordinated to run concurrently in order to evaluate the performance of critical infrastructures which influence each other, especially in emergency or resource-critical situations. We therefore describe the design of an adaptive communication middleware that provides reliable and real-time one-to-one and group communications for federations of CI simulators over a wide-area network (WAN). The proposed middleware is composed of mobile agent-based peer-to-peer (P2P) overlays, called virtual networks (VNets), to enable resilient, adaptive and real-time communications over unreliable and dynamic physical networks (PNets). The autonomous software agents comprising the communication middleware monitor their performance and the underlying PNet, and dynamically adapt the P2P overlay and migrate over the PNet in order to optimize communications according to the requirements of the federation and the current conditions of the PNet. Reliable communications is provided via redundancy within the communication middleware and intelligent migration of agents over the PNet. The proposed middleware integrates security methods in order to protect the communication infrastructure against attacks and provide privacy and anonymity to the participants of the federation. Experiments with an initial version of the communication middleware over a real-life networking testbed show that promising improvements can be obtained for unicast and group communications via the agent migration capability of our middleware.

Multi-Agent simulation of generation capacity expansion decisions.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Botterud, A.; Mahalik, M.; Conzelmann, G.

2008-01-01

In this paper, we use a multi-agent simulation model, EMCAS, to analyze generation expansion in the Iberian electricity market. The expansion model simulates generation investment decisions of decentralized generating companies (GenCos) interacting in a complex, multidimensional environment. A probabilistic dispatch algorithm calculates prices and profits for new candidate units in different future states of the system. Uncertainties in future load, hydropower conditions, and competitorspsila actions are represented in a scenario tree, and decision analysis is used to identify the optimal expansion decision for each individual GenCo. We run the model using detailed data for the Iberian market. In a scenariomore » analysis, we look at the impact of market design variables, such as the energy price cap and carbon emission prices. We also analyze how market concentration and GenCospsila risk preferences influence the timing and choice of new generating capacity.« less

Agent-Based Modeling in Systems Pharmacology.

PubMed

Cosgrove, J; Butler, J; Alden, K; Read, M; Kumar, V; Cucurull-Sanchez, L; Timmis, J; Coles, M

2015-11-01

Modeling and simulation (M&S) techniques provide a platform for knowledge integration and hypothesis testing to gain insights into biological systems that would not be possible a priori. Agent-based modeling (ABM) is an M&S technique that focuses on describing individual components rather than homogenous populations. This tutorial introduces ABM to systems pharmacologists, using relevant case studies to highlight how ABM-specific strengths have yielded success in the area of preclinical mechanistic modeling.

Development of a matrix to evaluate the threat of biological agents used for bioterrorism.

PubMed

Tegnell, A; Van Loock, F; Baka, A; Wallyn, S; Hendriks, J; Werner, A; Gouvras, G

2006-10-01

Adequate public health preparedness for bioterrorism includes the elaboration of an agreed list of biological and chemical agents that might be used in an attack or as threats of deliberate release. In the absence of counterterrorism intelligence information, public health authorities can also base their preparedness on the agents for which the national health structures would be most vulnerable. This article aims to describe a logical method and the characteristics of the variables to be brought in a weighing process to reach a priority list for preparedness. The European Union, in the aftermath of the anthrax events of October 2001 in the United States, set up a task force of experts from multiple member states to elaborate and implement a health security programme. One of the first tasks of this task force was to come up with a list of priority threats. The model, presented here, allows Web-based updates for newly identified agents and for the changes occurring in preventive measures for agents already listed. The same model also allows the identification of priority protection action areas.

Large-Area Chemical and Biological Decontamination Using a High Energy Arc Lamp (HEAL) System.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duty, Chad E; Smith, Rob R; Vass, Arpad Alexander

2008-01-01

Methods for quickly decontaminating large areas exposed to chemical and biological (CB) warfare agents can present significant logistical, manpower, and waste management challenges. Oak Ridge National Laboratory (ORNL) is pursuing an alternate method to decompose CB agents without the use of toxic chemicals or other potentially harmful substances. This process uses a high energy arc lamp (HEAL) system to photochemically decompose CB agents over large areas (12 m2). Preliminary tests indicate that more than 5 decades (99.999%) of an Anthrax spore simulant (Bacillus globigii) were killed in less than 7 seconds of exposure to the HEAL system. When combined withmore » a catalyst material (TiO2) the HEAL system was also effective against a chemical agent simulant, diisopropyl methyl phosphonate (DIMP). These results demonstrate the feasibility of a rapid, large-area chemical and biological decontamination method that does not require toxic or corrosive reagents or generate hazardous wastes.« less

An agent-based simulation model to study accountable care organizations.

PubMed

Liu, Pai; Wu, Shinyi

2016-03-01

Creating accountable care organizations (ACOs) has been widely discussed as a strategy to control rapidly rising healthcare costs and improve quality of care; however, building an effective ACO is a complex process involving multiple stakeholders (payers, providers, patients) with their own interests. Also, implementation of an ACO is costly in terms of time and money. Immature design could cause safety hazards. Therefore, there is a need for analytical model-based decision-support tools that can predict the outcomes of different strategies to facilitate ACO design and implementation. In this study, an agent-based simulation model was developed to study ACOs that considers payers, healthcare providers, and patients as agents under the shared saving payment model of care for congestive heart failure (CHF), one of the most expensive causes of sometimes preventable hospitalizations. The agent-based simulation model has identified the critical determinants for the payment model design that can motivate provider behavior changes to achieve maximum financial and quality outcomes of an ACO. The results show nonlinear provider behavior change patterns corresponding to changes in payment model designs. The outcomes vary by providers with different quality or financial priorities, and are most sensitive to the cost-effectiveness of CHF interventions that an ACO implements. This study demonstrates an increasingly important method to construct a healthcare system analytics model that can help inform health policy and healthcare management decisions. The study also points out that the likely success of an ACO is interdependent with payment model design, provider characteristics, and cost and effectiveness of healthcare interventions.

Early indicators of exposure to biological threat agents using host gene profiles in peripheral blood mononuclear cells

PubMed Central

Das, Rina; Hammamieh, Rasha; Neill, Roger; Ludwig, George V; Eker, Steven; Lincoln, Patrick; Ramamoorthy, Preveen; Dhokalia, Apsara; Mani, Sachin; Mendis, Chanaka; Cummings, Christiano; Kearney, Brian; Royaee, Atabak; Huang, Xiao-Zhe; Paranavitana, Chrysanthi; Smith, Leonard; Peel, Sheila; Kanesa-Thasan, Niranjan; Hoover, David; Lindler, Luther E; Yang, David; Henchal, Erik; Jett, Marti

2008-01-01

Background Effective prophylaxis and treatment for infections caused by biological threat agents (BTA) rely upon early diagnosis and rapid initiation of therapy. Most methods for identifying pathogens in body fluids and tissues require that the pathogen proliferate to detectable and dangerous levels, thereby delaying diagnosis and treatment, especially during the prelatent stages when symptoms for most BTA are indistinguishable flu-like signs. Methods To detect exposures to the various pathogens more rapidly, especially during these early stages, we evaluated a suite of host responses to biological threat agents using global gene expression profiling on complementary DNA arrays. Results We found that certain gene expression patterns were unique to each pathogen and that other gene changes occurred in response to multiple agents, perhaps relating to the eventual course of illness. Nonhuman primates were exposed to some pathogens and the in vitro and in vivo findings were compared. We found major gene expression changes at the earliest times tested post exposure to aerosolized B. anthracis spores and 30 min post exposure to a bacterial toxin. Conclusion Host gene expression patterns have the potential to serve as diagnostic markers or predict the course of impending illness and may lead to new stage-appropriate therapeutic strategies to ameliorate the devastating effects of exposure to biothreat agents. PMID:18667072

Principles of antidote pharmacology: an update on prophylaxis, post-exposure treatment recommendations and research initiatives for biological agents.

PubMed

Ramasamy, S; Liu, C Q; Tran, H; Gubala, A; Gauci, P; McAllister, J; Vo, T

2010-10-01

The use of biological agents has generally been confined to military-led conflicts. However, there has been an increase in non-state-based terrorism, including the use of asymmetric warfare, such as biological agents in the past few decades. Thus, it is becoming increasingly important to consider strategies for preventing and preparing for attacks by insurgents, such as the development of pre- and post-exposure medical countermeasures. There are a wide range of prophylactics and treatments being investigated to combat the effects of biological agents. These include antibiotics (for both conventional and unconventional use), antibodies, anti-virals, immunomodulators, nucleic acids (analogues, antisense, ribozymes and DNAzymes), bacteriophage therapy and micro-encapsulation. While vaccines are commercially available for the prevention of anthrax, cholera, plague, Q fever and smallpox, there are no licensed vaccines available for use in the case of botulinum toxins, viral encephalitis, melioidosis or ricin. Antibiotics are still recommended as the mainstay treatment following exposure to anthrax, plague, Q fever and melioidosis. Anti-toxin therapy and anti-virals may be used in the case of botulinum toxins or smallpox respectively. However, supportive care is the only, or mainstay, post-exposure treatment for cholera, viral encephalitis and ricin - a recommendation that has not changed in decades. Indeed, with the difficulty that antibiotic resistance poses, the development and further evaluation of techniques and atypical pharmaceuticals are fundamental to the development of prophylaxis and post-exposure treatment options. The aim of this review is to present an update on prophylaxis and post-exposure treatment recommendations and research initiatives for biological agents in the open literature from 2007 to 2009. © 2010 The Commonwealth of Australia. British Journal of Pharmacology © 2010 The British Pharmacological Society.

75 FR 28232 - Availability of an Environmental Assessment for a Biological Control Agent for Hemlock Woolly...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-20

... conditions. Existing HWA management options include chemical control and silvicultural control, which, in...] Availability of an Environmental Assessment for a Biological Control Agent for Hemlock Woolly Adelgid AGENCY... environmental assessment relative to the control of hemlock woolly adelgid (Adelges tsugae). The environmental...

Virtual Transgenics: Using a Molecular Biology Simulation to Impact Student Academic Achievement and Attitudes

NASA Astrophysics Data System (ADS)

Shegog, Ross; Lazarus, Melanie M.; Murray, Nancy G.; Diamond, Pamela M.; Sessions, Nathalie; Zsigmond, Eva

2012-10-01

The transgenic mouse model is useful for studying the causes and potential cures for human genetic diseases. Exposing high school biology students to laboratory experience in developing transgenic animal models is logistically prohibitive. Computer-based simulation, however, offers this potential in addition to advantages of fidelity and reach. This study describes and evaluates a computer-based simulation to train advanced placement high school science students in laboratory protocols, a transgenic mouse model was produced. A simulation module on preparing a gene construct in the molecular biology lab was evaluated using a randomized clinical control design with advanced placement high school biology students in Mercedes, Texas ( n = 44). Pre-post tests assessed procedural and declarative knowledge, time on task, attitudes toward computers for learning and towards science careers. Students who used the simulation increased their procedural and declarative knowledge regarding molecular biology compared to those in the control condition (both p < 0.005). Significant increases continued to occur with additional use of the simulation ( p < 0.001). Students in the treatment group became more positive toward using computers for learning ( p < 0.001). The simulation did not significantly affect attitudes toward science in general. Computer simulation of complex transgenic protocols have potential to provide a "virtual" laboratory experience as an adjunct to conventional educational approaches.

Evolutionary Agent-Based Simulation of the Introduction of New Technologies in Air Traffic Management

NASA Technical Reports Server (NTRS)

Yliniemi, Logan; Agogino, Adrian K.; Tumer, Kagan

2014-01-01

Accurate simulation of the effects of integrating new technologies into a complex system is critical to the modernization of our antiquated air traffic system, where there exist many layers of interacting procedures, controls, and automation all designed to cooperate with human operators. Additions of even simple new technologies may result in unexpected emergent behavior due to complex human/ machine interactions. One approach is to create high-fidelity human models coming from the field of human factors that can simulate a rich set of behaviors. However, such models are difficult to produce, especially to show unexpected emergent behavior coming from many human operators interacting simultaneously within a complex system. Instead of engineering complex human models, we directly model the emergent behavior by evolving goal directed agents, representing human users. Using evolution we can predict how the agent representing the human user reacts given his/her goals. In this paradigm, each autonomous agent in a system pursues individual goals, and the behavior of the system emerges from the interactions, foreseen or unforeseen, between the agents/actors. We show that this method reflects the integration of new technologies in a historical case, and apply the same methodology for a possible future technology.

Evaluation of a contraction flow field on hydrodynamic damage to entomopathogenic nematodes-A biological pest control agent.

PubMed

Fife, Jane P; Derksen, Richard C; Ozkan, H Erdal; Grewal, Parwinder S; Chalmers, Jeffrey J; Krause, Charles R

2004-04-05

Mechanized production and delivery of biological pesticides presents challenges because the biological agents must remain viable during these processes. This study evaluates the effect of flow through an abrupt contraction, where flow characteristics similar to that found within bioprocesses and spray equipment are developed, on damage to a benchmark biological pest control agent, entomopathogenic nematodes (EPNs). An opposed-pistons, contraction flow device generated volumetric flow rates ranging between 8.26 cm(3)/s and 41.3 cm(3)/s. Four EPN species were evaluated: Heterorhabditis bacteriophora, Heterorhabditis megidis, Steinernema carpocapsae, and Steinernema glaseri. Damage was quantified by counting living and dead EPNs. Optical and cold field emission scanning electron microscope (CFE-SEM) images provided qualitative information to describe how the damage occurred. The experimental flow field was completely described using FLUENT, a computational fluid dynamics program. Local flow parameters computed in FLUENT were compared to EPN damage. The type and extent of damage varied between EPN species. Damaged Heterorhabditis spp. generally remained whole with an internal rupture located near the center of the body, while Steinernema spp. most often broke into several pieces. The fast-transient stress field generated at the entrance to the contraction caused a momentary tensile loading and then relaxation that damaged the EPNs. At high flow rates, the tensile stresses became large enough to cause failure of the EPN structural membrane. The relative elasticity of the EPN structural membrane may explain the differences in damage observed between the species. It is speculated that the internal rupture of the Heterorhabditis spp. occurred during the processes of stretching and relaxing at the contraction entrance. Appreciable damage was observed at lower average energy dissipation rates for H. bacteriophora (1.23E + 8 W/m(3)), H. megidis (1.72E + 8 W/m(3)), and S

Analysis of waste management issues arising from a field study evaluating decontamination of a biological agent from a building.

PubMed

Lemieux, P; Wood, J; Drake, J; Minamyer, S; Silvestri, E; Yund, C; Nichols, T; Ierardi, M; Amidan, B

2016-01-01

The Bio-response Operational Testing and Evaluation (BOTE) Project was a cross-government effort designed to operationally test and evaluate a response to a biological incident (release of Bacillus anthracis [Ba] spores, the causative agent for anthrax) from initial public health and law enforcement response through environmental remediation. The BOTE Project was designed to address site remediation after the release of a Ba simulant, Bacillus atrophaeus spp. globigii (Bg), within a facility, drawing upon recent advances in the biological sampling and decontamination areas. A key component of response to a biological contamination incident is the proper management of wastes and residues, which is woven throughout all response activities. Waste is generated throughout the response and includes items like sampling media packaging materials, discarded personal protective equipment, items removed from the facility either prior to or following decontamination, aqueous waste streams, and materials generated through the application of decontamination technologies. The amount of residual contaminating agent will impact the available disposal pathways and waste management costs. Waste management is an integral part of the decontamination process and should be included through "Pre-Incident" response planning. Overall, the pH-adjusted bleach decontamination process generated the most waste from the decontamination efforts, and fumigation with chlorine dioxide generated the least waste. A majority of the solid waste generated during pH-adjusted bleach decontamination was the nonporous surfaces that were removed, bagged, decontaminated ex situ, and treated as waste. The waste during the two fumigation rounds of the BOTE Project was associated mainly with sampling activities. Waste management activities may represent a significant contribution to the overall cost of the response/recovery operation. This paper addresses the waste management activities for the BOTE field test

Performance of Traditional and Molecular Methods for Detecting Biological Agents in Drinking Water

USGS Publications Warehouse

Francy, Donna S.; Bushon, Rebecca N.; Brady, Amie M.G.; Bertke, Erin E.; Kephart, Christopher M.; Likirdopulos, Christina A.; Mailot, Brian E.; Schaefer, Frank W.; Lindquist, H.D. Alan

2009-01-01

To reduce the impact from a possible bioterrorist attack on drinking-water supplies, analytical methods are needed to rapidly detect the presence of biological agents in water. To this end, 13 drinking-water samples were collected at 9 water-treatment plants in Ohio to assess the performance of a molecular method in comparison to traditional analytical methods that take longer to perform. Two 100-liter samples were collected at each site during each sampling event; one was seeded in the laboratory with six biological agents - Bacillus anthracis (B. anthracis), Burkholderia cepacia (as a surrogate for Bu. pseudomallei), Francisella tularensis (F. tularensis), Salmonella Typhi (S. Typhi), Vibrio cholerae (V. cholerae), and Cryptospordium parvum (C. parvum). The seeded and unseeded samples were processed by ultrafiltration and analyzed by use of quantiative polymerase chain reaction (qPCR), a molecular method, and culture methods for bacterial agents or the immunomagnetic separation/fluorescent antibody (IMS/FA) method for C. parvum as traditional methods. Six replicate seeded samples were also processed and analyzed. For traditional methods, recoveries were highly variable between samples and even between some replicate samples, ranging from below detection to greater than 100 percent. Recoveries were significantly related to water pH, specific conductance, and dissolved organic carbon (DOC) for all bacteria combined by culture methods, but none of the water-quality characteristics tested were related to recoveries of C. parvum by IMS/FA. Recoveries were not determined by qPCR because of problems in quantifying organisms by qPCR in the composite seed. Instead, qPCR results were reported as detected, not detected (no qPCR signal), or +/- detected (Cycle Threshold or 'Ct' values were greater than 40). Several sample results by qPCR were omitted from the dataset because of possible problems with qPCR reagents, primers, and probes. For the remaining 14 qPCR results

Some Fundamental Issues of Mathematical Simulation in Biology

NASA Astrophysics Data System (ADS)

Razzhevaikin, V. N.

2018-02-01

Some directions of simulation in biology leading to original formulations of mathematical problems are overviewed. Two of them are discussed in detail: the correct solvability of first-order linear equations with unbounded coefficients and the construction of a reaction-diffusion equation with nonlinear diffusion for a model of genetic wave propagation.

Host range of the inadvertent biological control agent Caloptilia triadicae: an invasive herbivore of Chinese tallowtree

USDA-ARS?s Scientific Manuscript database

An inadvertent biological control agent of the invasive weed Chinese tallowtree (Triadica sebifera) first appeared in North America in 2004. Identified as a Caloptilia triadicae, this leaf miner was found damaging T. sebifera saplings. In Gainesville, FL we exposed naturalized populations of C. tria...

Multiple year effects of a biological control agent (Diorhabda carinulata) on Tamarix (saltcedar) ecosystem exchanges of carbon dioxide and water

USDA-ARS?s Scientific Manuscript database

Biological control of Tamarix spp. (saltcedar) with Diorhabda carinulata (the northern tamarisk beetle) is currently underway in several western states U.S.A. through historical releases and the natural migration of this insect. Given the widespread dispersal of this biological control agent and its...

Host Specificity of Epiplema albida: A Potential Biological Control Agent for Sri Lankan Privet in the Mascarene Islands

PubMed Central

Shaw, Richard H.

2017-01-01

Epiplema albida (Hampson) (Lepidoptera: Uraniidae, Epipleminae) from Sri Lanka, was studied to assess its safety for use as a biological control agent for Sri Lankan privet, Ligustrum robustum subsp. walkeri (Oleaceae) in La Réunion and other Mascarene Islands. Larval no-choice feeding tests using newly hatched larvae, larval development tests, and multiple choice oviposition tests were used. Adult females of E. albida are shown to have highly selective oviposition behaviour and the species is physiologically restricted to very few hosts for feeding and development. The risk to key test plants in La Réunion is minimal, so this species can be considered for use as a biological control agent there, but would need further evaluation for potential use elsewhere. PMID:28788086

Chemiluminescence assay for the detection of biological warfare agents

DOE Office of Scientific and Technical Information (OSTI.GOV)

Langry, K; Horn, J

A chemiluminescent homogeneous immunoassay and a hand-size multiassay reader are described that could be used for detecting biological materials. The special feature of the assay is that it employs two different antibodies that each bind to a unique epitope on the same antigen. Each group of epitope-specific antibodies has linked to it an enzyme of a proximal-enzyme pair. One enzyme of the pair utilizes a substrate in high concentration to produce a second substrate required by the second enzyme. This new substrate enables the second enzyme to function. The reaction of the second enzyme is configured to produce light. Thismore » chemiluminescence is detected with a charge-coupled device (CCD) camera. The proximal pair enzymes must be in close proximity to one another to allow the second enzyme to react with the product of the first enzyme. This only occurs when the enzyme-linked antibodies are attached to the antigen, whether antigen is a single protein with multiple epitopes or the surface of a cell with a variety of different antigens. As a result of their juxtaposition, the enzymes produce light only in the presence of the biological material. A brief description is given as to how this assay could be utilized in a personal bio-agent detector system.« less

Risk assessment and stakeholder perceptions in novel biological control agent release: YST as a case study

USDA-ARS?s Scientific Manuscript database

The objectives of risk assessment are to learn about whether a candidate agent would be safe to use in the environment where release is planned, and to present such information in a clear, understandable format to regulators, stakeholders, and the public. Plant pathogens evaluated for biological co...

Modeling formalisms in Systems Biology

PubMed Central

2011-01-01

Systems Biology has taken advantage of computational tools and high-throughput experimental data to model several biological processes. These include signaling, gene regulatory, and metabolic networks. However, most of these models are specific to each kind of network. Their interconnection demands a whole-cell modeling framework for a complete understanding of cellular systems. We describe the features required by an integrated framework for modeling, analyzing and simulating biological processes, and review several modeling formalisms that have been used in Systems Biology including Boolean networks, Bayesian networks, Petri nets, process algebras, constraint-based models, differential equations, rule-based models, interacting state machines, cellular automata, and agent-based models. We compare the features provided by different formalisms, and discuss recent approaches in the integration of these formalisms, as well as possible directions for the future. PMID:22141422

Biological agents: investigation into leprosy and other infectious diseases before indication*

PubMed Central

Antônio, João Roberto; Soubhia, Rosa Maria Cordeiro; Paschoal, Vania Del Arco; Amarante, Carolina Forte; Travolo, Ana Regina Franchi

2013-01-01

Biological agents are widely used for various immune-mediated diseases, with remarkable effectiveness in the treatment of rheumatoid arthritis (RA), psoriasis, psoriatic arthritis, ankylosing spondylitis and Crohn's disease. However, attention needs to be drawn to the adverse effects of these therapies and the risk of reactivating underlying granulomatous infectious diseases such as tuberculosis, leprosy, syphilis, leishmaniasis, among others. The objective of this paper is to describe a case of leprosy in a patient with RA using anti-TNF alfa, demonstrating the need for systematic investigation of skin lesions suggestive of leprosy in patients who require rheumatoid arthritis therapeutic treatment, especially in endemic regions like Brazil. PMID:24346871

An investigation of the evolutionary origin of reciprocal communication using simulated autonomous agents.

PubMed

Tuci, Elio

2009-09-01

How does communication originates in a population of originally non-communicating individuals? Providing an answer to this question from a neo-Darwinian epistemological perspective is not a trivial task. The reason is that, for non-communicating agents, the capabilities of emitting signals and responding to them are both adaptively neutral traits if they are not simultaneously present. Research studies based on rather general and theoretically oriented evolutionary simulation models have, so far, demonstrated that at least two different processes can account for the origin of communication. On the one hand, communicative behaviour may first evolve in a non-communicative context and only subsequently acquire its adaptive function.On the other hand, communication may originate thanks to cognitive constraints; that is, communication may originate thanks to the existence of neural substrates that are common to the signalling and categorising capabilities. This article provides a proof-of-concept demonstration of the origin of communication in a novel-simulated scenario in which groups of two homogeneous (i.e. genetically identical) agents exploit reciprocal communication to develop common perceptual categories nd to perform a collective task. In particular, in circumstances in which communication is evolutionarily advantageous, simulated agents evolve from scratch social behaviour through acoustic interactions.We look into the phylogeny of successful communication protocol, and we describe the evolutionary phenomena that, in early evolutionary stages, paved the way for the subsequent development of reciprocal communication, categorisation capabilities and successful cooperative strategies.

Differences in seasonal variation between two biotypes of Megamelus scutellaris (Hemiptera: Delphacidae), a biological control agent for Eichhornia crassipes in Florida.

USDA-ARS?s Scientific Manuscript database

Climate matching between the native and adventive ranges of insects used for biological control is a generally accepted strategy for both increasing the likelihood of establishing an agent, as well as improving its overall performance, thereby maximizing the potential utility of an agent across the...

An Agent-Based Epidemic Simulation of Social Behaviors Affecting HIV Transmission among Taiwanese Homosexuals

PubMed Central

2015-01-01

Computational simulations are currently used to identify epidemic dynamics, to test potential prevention and intervention strategies, and to study the effects of social behaviors on HIV transmission. The author describes an agent-based epidemic simulation model of a network of individuals who participate in high-risk sexual practices, using number of partners, condom usage, and relationship length to distinguish between high- and low-risk populations. Two new concepts—free links and fixed links—are used to indicate tendencies among individuals who either have large numbers of short-term partners or stay in long-term monogamous relationships. An attempt was made to reproduce epidemic curves of reported HIV cases among male homosexuals in Taiwan prior to using the agent-based model to determine the effects of various policies on epidemic dynamics. Results suggest that when suitable adjustments are made based on available social survey statistics, the model accurately simulates real-world behaviors on a large scale. PMID:25815047

“Design characteristics of the CORRONA CERTAIN study: a comparative effectiveness study of biologic agents for rheumatoid arthritis patients”

PubMed Central

2014-01-01

Background Comparative effectiveness research has recently attracted considerable attention. The Comparative Effectiveness Registry to study Therapies for Arthritis and Inflammatory Conditions (CERTAIN) is an ongoing prospective cohort study of adult patients with Rheumatoid Arthritis (RA). Methods/Design CERTAIN uses the existing Consortium of Rheumatology Researchers of North America (CORRONA) network of participating private and academic sites in order to recruit patients fulfilling the 1987 ACR criteria that have at least moderate disease activity. Patients starting or switching biologic agents either anti-TNF therapy or a non anti-TNF biologic are eligible for enrollment, depending on the treatment selected by their physician. Enrollment is expected to be completed by March of 2014, and 2711 patients will participate in the study. As of October 7th 2013, 2234 patients have been enrolled. Patient visits and laboratory blood work are mandated every three months for one year. Safety data is collected through one year and beyond. The primary comparative effectiveness endpoint is attainment of low RA disease activity at one year among patients who have been exposed to at least one prior TNF-α inhibitor agent prior to enrollment. Multiple secondary effectiveness and safety endpoints will be addressed by investigating the entire population enrolled (naïve and biologic experienced). Discussion The unique design features of CERTAIN will inform comparative effectiveness and safety questions for choosing biologic agents for the management of RA. PMID:24690143

Dual-Function Metal-Organic Framework as a Versatile Catalyst for Detoxifying Chemical Warfare Agent Simulants.

PubMed

Liu, Yangyang; Moon, Su-Young; Hupp, Joseph T; Farha, Omar K

2015-12-22

The nanocrystals of a porphyrin-based zirconium(IV) metal-organic framework (MOF) are used as a dual-function catalyst for the simultaneous detoxification of two chemical warfare agent simulants at room temperature. Simulants of nerve agent (such as GD, VX) and mustard gas, dimethyl 4-nitrophenyl phosphate and 2-chloroethyl ethyl sulfide, have been hydrolyzed and oxidized, respectively, to nontoxic products via a pair of pathways catalyzed by the same MOF. Phosphotriesterase-like activity of the Zr6-containing node combined with photoactivity of the porphyrin linker gives rise to a versatile MOF catalyst. In addition, bringing the MOF crystals down to the nanoregime leads to acceleration of the catalysis.

Host plant oviposition preference of Ceratapion basicorne (Coleoptera:Apionidae), a potential biological control agent of yellow starthistle

USDA-ARS?s Scientific Manuscript database

Ceratapion basicorne (Coleoptera: Apionidae) is a weevil native to Europe and western Asia that is being evaluated as a prospective classical biological control agent of Centaurea solstitialis (yellow starthistle) in the United States. Choice oviposition experiments were conducted under laboratory ...

Phenology and temperature-dependent development of Ceutorhynchus assimilis, a potential biological control agent for Lepidium draba

USDA-ARS?s Scientific Manuscript database

Heart-podded hoary cress (Lepidium draba) is an alien weed that has invaded rangeland in the northwestern USA. A host race (i;e; host-specific biotype) of the weevil, Ceutorhynchus assimilis, is being evaluated as a prospective biological control agent. This biotype is only known from southern Eur...

Decontamination issues for chemical and biological warfare agents: how clean is clean enough?

PubMed

Raber, E; Jin, A; Noonan, K; McGuire, R; Kirvel, R D

2001-06-01

The objective of this assessment is to determine what level of cleanup will be required to meet regulatory and stakeholder needs in the case of a chemical and/or biological incident at a civilian facility. A literature review for selected, potential chemical and biological warfare agents shows that dose information is often lacking or controversial. Environmental regulatory limits or other industrial health guidelines that could be used to help establish cleanup concentration levels for such agents are generally unavailable or not applicable for a public setting. Although dose information, cleanup criteria, and decontamination protocols all present challenges to effective planning, several decontamination approaches are available. Such approaches should be combined with risk-informed decision making to establish reasonable cleanup goals for protecting health, property, and resources. Key issues during a risk assessment are to determine exactly what constitutes a safety hazard and whether decontamination is necessary or not for a particular scenario. An important conclusion is that cleanup criteria are site dependent and stakeholder specific. The results of a modeling exercise for two outdoor scenarios are presented to reinforce this conclusion. Public perception of risk to health, public acceptance of recommendations based on scientific criteria, political support, time constraints, and economic concerns must all be addressed in the context of a specific scenario to yield effective and acceptable decontamination.

Enhanced sampling techniques in molecular dynamics simulations of biological systems.

PubMed

Bernardi, Rafael C; Melo, Marcelo C R; Schulten, Klaus

2015-05-01

Molecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.

Chemical warfare agent and biological toxin-induced pulmonary toxicity: could stem cells provide potential therapies?

PubMed

Angelini, Daniel J; Dorsey, Russell M; Willis, Kristen L; Hong, Charles; Moyer, Robert A; Oyler, Jonathan; Jensen, Neil S; Salem, Harry

2013-01-01

Chemical warfare agents (CWAs) as well as biological toxins present a significant inhalation injury risk to both deployed warfighters and civilian targets of terrorist attacks. Inhalation of many CWAs and biological toxins can induce severe pulmonary toxicity leading to the development of acute lung injury (ALI) as well as acute respiratory distress syndrome (ARDS). The therapeutic options currently used to treat these conditions are very limited and mortality rates remain high. Recent evidence suggests that human stem cells may provide significant therapeutic options for ALI and ARDS in the near future. The threat posed by CWAs and biological toxins for both civilian populations and military personnel is growing, thus understanding the mechanisms of toxicity and potential therapies is critical. This review will outline the pulmonary toxic effects of some of the most common CWAs and biological toxins as well as the potential role of stem cells in treating these types of toxic lung injuries.

Parallel Agent-Based Simulations on Clusters of GPUs and Multi-Core Processors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aaby, Brandon G; Perumalla, Kalyan S; Seal, Sudip K

2010-01-01

An effective latency-hiding mechanism is presented in the parallelization of agent-based model simulations (ABMS) with millions of agents. The mechanism is designed to accommodate the hierarchical organization as well as heterogeneity of current state-of-the-art parallel computing platforms. We use it to explore the computation vs. communication trade-off continuum available with the deep computational and memory hierarchies of extant platforms and present a novel analytical model of the tradeoff. We describe our implementation and report preliminary performance results on two distinct parallel platforms suitable for ABMS: CUDA threads on multiple, networked graphical processing units (GPUs), and pthreads on multi-core processors. Messagemore » Passing Interface (MPI) is used for inter-GPU as well as inter-socket communication on a cluster of multiple GPUs and multi-core processors. Results indicate the benefits of our latency-hiding scheme, delivering as much as over 100-fold improvement in runtime for certain benchmark ABMS application scenarios with several million agents. This speed improvement is obtained on our system that is already two to three orders of magnitude faster on one GPU than an equivalent CPU-based execution in a popular simulator in Java. Thus, the overall execution of our current work is over four orders of magnitude faster when executed on multiple GPUs.« less

Patient-Centered Appointment Scheduling Using Agent-Based Simulation

PubMed Central

Turkcan, Ayten; Toscos, Tammy; Doebbeling, Brad N.

2014-01-01

Enhanced access and continuity are key components of patient-centered care. Existing studies show that several interventions such as providing same day appointments, walk-in services, after-hours care, and group appointments, have been used to redesign the healthcare systems for improved access to primary care. However, an intervention focusing on a single component of care delivery (i.e. improving access to acute care) might have a negative impact other components of the system (i.e. reduced continuity of care for chronic patients). Therefore, primary care clinics should consider implementing multiple interventions tailored for their patient population needs. We collected rapid ethnography and observations to better understand clinic workflow and key constraints. We then developed an agent-based simulation model that includes all access modalities (appointments, walk-ins, and after-hours access), incorporate resources and key constraints and determine the best appointment scheduling method that improves access and continuity of care. This paper demonstrates the value of simulation models to test a variety of alternative strategies to improve access to care through scheduling. PMID:25954423

An agent-based simulation model for Clostridium difficile infection control.

PubMed

Codella, James; Safdar, Nasia; Heffernan, Rick; Alagoz, Oguzhan

2015-02-01

Control of Clostridium difficile infection (CDI) is an increasingly difficult problem for health care institutions. There are commonly recommended strategies to combat CDI transmission, such as oral vancomycin for CDI treatment, increased hand hygiene with soap and water for health care workers, daily environmental disinfection of infected patient rooms, and contact isolation of diseased patients. However, the efficacy of these strategies, particularly for endemic CDI, has not been well studied. The objective of this research is to develop a valid, agent-based simulation model (ABM) to study C. difficile transmission and control in a midsized hospital. We develop an ABM of a midsized hospital with agents such as patients, health care workers, and visitors. We model the natural progression of CDI in a patient using a Markov chain and the transmission of CDI through agent and environmental interactions. We derive input parameters from aggregate patient data from the 2007-2010 Wisconsin Hospital Association and published medical literature. We define a calibration process, which we use to estimate transition probabilities of the Markov model by comparing simulation results to benchmark values found in published literature. In a comparison of CDI control strategies implemented individually, routine bleach disinfection of CDI-positive patient rooms provides the largest reduction in nosocomial asymptomatic colonization (21.8%) and nosocomial CDIs (42.8%). Additionally, vancomycin treatment provides the largest reduction in relapse CDIs (41.9%), CDI-related mortalities (68.5%), and total patient length of stay (21.6%). We develop a generalized ABM for CDI control that can be customized and further expanded to specific institutions and/or scenarios. Additionally, we estimate transition probabilities for a Markov model of natural CDI progression in a patient through calibration. © The Author(s) 2014.

Life history and host range of Oxydia vesulia transpeneus, an unsuitable biological control agent of Brazilian peppertree

USDA-ARS?s Scientific Manuscript database

The suitability of Oxydia vesulia (Cramer) (Lepidoptera: Geometridae) was assessed as a potential biological control agent of the invasive weed Brazilian Peppertree Schinus terebinthifolia. Larvae were collected in Brazil feeding on the plant in its native range and colonized in quarantine where lif...

Graceful Failure and Societal Resilience Analysis Via Agent-Based Modeling and Simulation

NASA Astrophysics Data System (ADS)

Schopf, P. S.; Cioffi-Revilla, C.; Rogers, J. D.; Bassett, J.; Hailegiorgis, A. B.

2014-12-01

Agent-based social modeling is opening up new methodologies for the study of societal response to weather and climate hazards, and providing measures of resiliency that can be studied in many contexts, particularly in coupled human and natural-technological systems (CHANTS). Since CHANTS are complex adaptive systems, societal resiliency may or may not occur, depending on dynamics that lack closed form solutions. Agent-based modeling has been shown to provide a viable theoretical and methodological approach for analyzing and understanding disasters and societal resiliency in CHANTS. Our approach advances the science of societal resilience through computational modeling and simulation methods that complement earlier statistical and mathematical approaches. We present three case studies of social dynamics modeling that demonstrate the use of these agent based models. In Central Asia, we exmaine mutltiple ensemble simulations with varying climate statistics to see how droughts and zuds affect populations, transmission of wealth across generations, and the overall structure of the social system. In Eastern Africa, we explore how successive episodes of drought events affect the adaptive capacity of rural households. Human displacement, mainly, rural to urban migration, and livelihood transition particularly from pastoral to farming are observed as rural households interacting dynamically with the biophysical environment and continually adjust their behavior to accommodate changes in climate. In the far north case we demonstrate one of the first successful attempts to model the complete climate-permafrost-infrastructure-societal interaction network as a complex adaptive system/CHANTS implemented as a ``federated'' agent-based model using evolutionary computation. Analysis of population changes resulting from extreme weather across these and other cases provides evidence for the emergence of new steady states and shifting patterns of resilience.

Control of downy mildew (Pseudoperonospora cubensis) of greenhouse grown cucumbers with alternative biological agents.

PubMed

Scherf, A; Schuster, C; Marx, P; Gärber, U; Konstantinidou-Doltsinis, S; Schmitt, A

2010-01-01

In organic cucumber production infection with downy mildew (Pseudoperonospora cubensis) is a major problem. Plant extracts from Glycyrrhiza glabra L. (licorice), a plant belonging to the family Fabaceae, and Salvia officinalis (sage) as well as cultures of the bacterium Aneurinibacillus migulanus were investigated for efficacy of disease control under commercial growing conditions. Contrary to bioassays, where sage extract and the microorganism showed highest activity, in the trials of 2008 G. glabra extract was more effective than sage extract or A. migulanus against P. cubensis. Parameters such as concentrations of the preparations or application intervals could have been the reason for this. In the following year's trial (2009) the concentration of these agents was therefore increased somewhat and plants were either treated in seven day application intervals or in ten day application intervals. In the semi-commercial trials of 2009 all alternative biological agents showed good efficacies up to around 80% against infection with downy mildew. The application interval seemed to have a marginal effect only. Again, the licorice extract tended to be the best agent.

External rostral characters for differentiation of sexes in the biological control agent Mecinus janthinus (Coleoptera: Curculionidae)

Treesearch

Marjolein Schat; Sharlene E. Sing; Robert K. D. Peterson

2007-01-01

The stem-boring weevil, Mecinus janthinus (Germar), is a promising, well established classical biological control agent for the exotic invasive weed Dalmatian toadflax (Linaria dalmatica (L.) Mill.) (Scrophulariaceae). In this paper we present readily apparent rostral characters that can be used for sex differentiation of live stem-boring weevils at low magnification....

Incorporating Social Oriented Agent and Interactive Simulation in E-learning: Impact on Learning, Perceptions, Experiences to Non-Native English Students

ERIC Educational Resources Information Center

Ballera, Melvin; Elssaedi, Mosbah Mohamed

2012-01-01

There is an unrealized potential in the use of socially-oriented pedagogical agent and interactive simulation in e-learning system. In this paper, we investigate the impact of having a socially oriented tutor agent and the incorporation of interactive simulation in e-learning into student performances, perceptions and experiences for non-native…

Single-particle aerosol mass spectrometry for the detection and identification of chemical warfare agent simulants.

PubMed

Martin, Audrey N; Farquar, George R; Frank, Matthias; Gard, Eric E; Fergenson, David P

2007-08-15

Single-particle aerosol mass spectrometry (SPAMS) was used for the real-time detection of liquid nerve agent simulants. A total of 1000 dual-polarity time-of-flight mass spectra were obtained for micrometer-sized single particles each of dimethyl methyl phosphonate, diethyl ethyl phosphonate, diethyl phosphoramidate, and diethyl phthalate using laser fluences between 0.58 and 7.83 nJ/microm2, and mass spectral variation with laser fluence was studied. The mass spectra obtained allowed identification of single particles of the chemical warfare agent (CWA) simulants at each laser fluence used although lower laser fluences allowed more facile identification. SPAMS is presented as a promising real-time detection system for the presence of CWAs.

Proposal of Classification Method of Time Series Data in International Emissions Trading Market Using Agent-based Simulation

NASA Astrophysics Data System (ADS)

Nakada, Tomohiro; Takadama, Keiki; Watanabe, Shigeyoshi

This paper proposes the classification method using Bayesian analytical method to classify the time series data in the international emissions trading market depend on the agent-based simulation and compares the case with Discrete Fourier transform analytical method. The purpose demonstrates the analytical methods mapping time series data such as market price. These analytical methods have revealed the following results: (1) the classification methods indicate the distance of mapping from the time series data, it is easier the understanding and inference than time series data; (2) these methods can analyze the uncertain time series data using the distance via agent-based simulation including stationary process and non-stationary process; and (3) Bayesian analytical method can show the 1% difference description of the emission reduction targets of agent.

A Multi-agent Simulation Tool for Micro-scale Contagion Spread Studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koch, Daniel B

2016-01-01

Within the disaster preparedness and emergency response community, there is interest in how contagions spread person-to-person at large gatherings and if mitigation strategies can be employed to reduce new infections. A contagion spread simulation module was developed for the Incident Management Preparedness and Coordination Toolkit that allows a user to see how a geographically accurate layout of the gathering space helps or hinders the spread of a contagion. The results can inform mitigation strategies based on changing the physical layout of an event space. A case study was conducted for a particular event to calibrate the underlying simulation model. Thismore » paper presents implementation details of the simulation code that incorporates agent movement and disease propagation. Elements of the case study are presented to show how the tool can be used.« less

Proceedings of the Agent 2002 Conference on Social Agents : Ecology, Exchange, and Evolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Macal, C., ed.; Sallach, D., ed.

2003-04-10

Welcome to the ''Proceedings'' of the third in a series of agent simulation conferences cosponsored by Argonne National Laboratory and The University of Chicago. The theme of this year's conference, ''Social Agents: Ecology, Exchange and Evolution'', was selected to foster the exchange of ideas on some of the most important social processes addressed by agent simulation models, namely: (1) The translation of ecology and ecological constraints into social dynamics; (2) The role of exchange processes, including the peer dependencies they create; and (3) The dynamics by which, and the attractor states toward which, social processes evolve. As stated in themore » ''Call for Papers'', throughout the social sciences, the simulation of social agents has emerged as an innovative and powerful research methodology. The promise of this approach, however, is accompanied by many challenges. First, modeling complexity in agents, environments, and interactions is non-trivial, and these representations must be explored and assessed systematically. Second, strategies used to represent complexities are differentially applicable to any particular problem space. Finally, to achieve sufficient generality, the design and experimentation inherent in agent simulation must be coupled with social and behavioral theory. Agent 2002 provides a forum for reviewing the current state of agent simulation scholarship, including research designed to address such outstanding issues. This year's conference introduces an extensive range of domains, models, and issues--from pre-literacy to future projections, from ecology to oligopolistic markets, and from design to validation. Four invited speakers highlighted major themes emerging from social agent simulation.« less

Saccharomyces cerevisiae: A novel and efficient biological control agent for Colletotrichum acutatum during pre-harvest.

PubMed

Lopes, Marcos Roberto; Klein, Mariana Nadjara; Ferraz, Luriany Pompeo; da Silva, Aline Caroline; Kupper, Katia Cristina

2015-06-01

In this study, we evaluated the efficiency of six isolates of Saccharomyces cerevisiae in controlling Colletotrichum acutatum, the causal agent of postbloom fruit drop that occur in pre-harvest citrus. We analyzed the mechanisms of action involved in biological control such as: production of antifungal compounds, nutrient competition, detection of killer activity, and production of hydrolytic enzymes of the isolates of S. cerevisiae on C. acutatum and their efficiency in controlling postbloom fruit drop on detached citrus flowers. Our results showed that all six S. cerevisiae isolates produced antifungal compounds, competed for nutrients, inhibited pathogen germination, and produced killer activity and hydrolytic enzymes when in contact with the fungus wall. The isolates were able to control the disease when detached flowers were artificially inoculated, both preventively and curatively. In this work we identified a novel potential biological control agent for C. acutatum during pre-harvest. This is the first report of yeast efficiency for the biocontrol of postbloom fruit drop, which represents an important contribution to the field of biocontrol of diseases affecting citrus populations worldwide. Copyright © 2015 Elsevier GmbH. All rights reserved.

Model reduction for agent-based social simulation: coarse-graining a civil violence model.

PubMed

Zou, Yu; Fonoberov, Vladimir A; Fonoberova, Maria; Mezic, Igor; Kevrekidis, Ioannis G

2012-06-01

Agent-based modeling (ABM) constitutes a powerful computational tool for the exploration of phenomena involving emergent dynamic behavior in the social sciences. This paper demonstrates a computer-assisted approach that bridges the significant gap between the single-agent microscopic level and the macroscopic (coarse-grained population) level, where fundamental questions must be rationally answered and policies guiding the emergent dynamics devised. Our approach will be illustrated through an agent-based model of civil violence. This spatiotemporally varying ABM incorporates interactions between a heterogeneous population of citizens [active (insurgent), inactive, or jailed] and a population of police officers. Detailed simulations exhibit an equilibrium punctuated by periods of social upheavals. We show how to effectively reduce the agent-based dynamics to a stochastic model with only two coarse-grained degrees of freedom: the number of jailed citizens and the number of active ones. The coarse-grained model captures the ABM dynamics while drastically reducing the computation time (by a factor of approximately 20).

Model reduction for agent-based social simulation: Coarse-graining a civil violence model

NASA Astrophysics Data System (ADS)

Zou, Yu; Fonoberov, Vladimir A.; Fonoberova, Maria; Mezic, Igor; Kevrekidis, Ioannis G.

2012-06-01

Agent-based modeling (ABM) constitutes a powerful computational tool for the exploration of phenomena involving emergent dynamic behavior in the social sciences. This paper demonstrates a computer-assisted approach that bridges the significant gap between the single-agent microscopic level and the macroscopic (coarse-grained population) level, where fundamental questions must be rationally answered and policies guiding the emergent dynamics devised. Our approach will be illustrated through an agent-based model of civil violence. This spatiotemporally varying ABM incorporates interactions between a heterogeneous population of citizens [active (insurgent), inactive, or jailed] and a population of police officers. Detailed simulations exhibit an equilibrium punctuated by periods of social upheavals. We show how to effectively reduce the agent-based dynamics to a stochastic model with only two coarse-grained degrees of freedom: the number of jailed citizens and the number of active ones. The coarse-grained model captures the ABM dynamics while drastically reducing the computation time (by a factor of approximately 20).

Agent-based modeling of the spread of influenza-like illness in an emergency department: a simulation study.

PubMed

Laskowski, Marek; Demianyk, Bryan C P; Witt, Julia; Mukhi, Shamir N; Friesen, Marcia R; McLeod, Robert D

2011-11-01

The objective of this paper was to develop an agent-based modeling framework in order to simulate the spread of influenza virus infection on a layout based on a representative hospital emergency department in Winnipeg, Canada. In doing so, the study complements mathematical modeling techniques for disease spread, as well as modeling applications focused on the spread of antibiotic-resistant nosocomial infections in hospitals. Twenty different emergency department scenarios were simulated, with further simulation of four infection control strategies. The agent-based modeling approach represents systems modeling, in which the emergency department was modeled as a collection of agents (patients and healthcare workers) and their individual characteristics, behaviors, and interactions. The framework was coded in C++ using Qt4 libraries running under the Linux operating system. A simple ordinary least squares (OLS) regression was used to analyze the data, in which the percentage of patients that became infected in one day within the simulation was the dependent variable. The results suggest that within the given instance context, patient-oriented infection control policies (alternate treatment streams, masking symptomatic patients) tend to have a larger effect than policies that target healthcare workers. The agent-based modeling framework is a flexible tool that can be made to reflect any given environment; it is also a decision support tool for practitioners and policymakers to assess the relative impact of infection control strategies. The framework illuminates scenarios worthy of further investigation, as well as counterintuitive findings.

Efficient Allocation of Resources for Defense of Spatially Distributed Networks Using Agent-Based Simulation.

PubMed

Kroshl, William M; Sarkani, Shahram; Mazzuchi, Thomas A

2015-09-01

This article presents ongoing research that focuses on efficient allocation of defense resources to minimize the damage inflicted on a spatially distributed physical network such as a pipeline, water system, or power distribution system from an attack by an active adversary, recognizing the fundamental difference between preparing for natural disasters such as hurricanes, earthquakes, or even accidental systems failures and the problem of allocating resources to defend against an opponent who is aware of, and anticipating, the defender's efforts to mitigate the threat. Our approach is to utilize a combination of integer programming and agent-based modeling to allocate the defensive resources. We conceptualize the problem as a Stackelberg "leader follower" game where the defender first places his assets to defend key areas of the network, and the attacker then seeks to inflict the maximum damage possible within the constraints of resources and network structure. The criticality of arcs in the network is estimated by a deterministic network interdiction formulation, which then informs an evolutionary agent-based simulation. The evolutionary agent-based simulation is used to determine the allocation of resources for attackers and defenders that results in evolutionary stable strategies, where actions by either side alone cannot increase its share of victories. We demonstrate these techniques on an example network, comparing the evolutionary agent-based results to a more traditional, probabilistic risk analysis (PRA) approach. Our results show that the agent-based approach results in a greater percentage of defender victories than does the PRA-based approach. © 2015 Society for Risk Analysis.

Nanoparticle-labeled DNA capture elements for detection and identification of biological agents

NASA Astrophysics Data System (ADS)

Kiel, Johnathan L.; Holwitt, Eric A.; Parker, Jill E.; Vivekananda, Jeevalatha; Franz, Veronica

2004-12-01

Aptamers, synthetic DNA capture elements (DCEs), can be made chemically or in genetically engineered bacteria. DNA capture elements are artificial DNA sequences, from a random pool of sequences, selected for their specific binding to potential biological warfare or terrorism agents. These sequences were selected by an affinity method using filters to which the target agent was attached and the DNA isolated and amplified by polymerase chain reaction (PCR) in an iterative, increasingly stringent, process. The probes can then be conjugated to Quantum Dots and super paramagnetic nanoparticles. The former provide intense, bleach-resistant fluorescent detection of bioagent and the latter provide a means to collect the bioagents with a magnet. The fluorescence can be detected in a flow cytometer, in a fluorescence plate reader, or with a fluorescence microscope. To date, we have made DCEs to Bacillus anthracis spores, Shiga toxin, Venezuelan Equine Encephalitis (VEE) virus, and Francisella tularensis. DCEs can easily distinguish Bacillus anthracis from its nearest relatives, Bacillus cereus and Bacillus thuringiensis. Development of a high through-put process is currently being investigated.

Biology Students Building Computer Simulations Using StarLogo TNG

ERIC Educational Resources Information Center

Smith, V. Anne; Duncan, Ishbel

2011-01-01

Confidence is an important issue for biology students in handling computational concepts. This paper describes a practical in which honours-level bioscience students simulate complex animal behaviour using StarLogo TNG, a freely-available graphical programming environment. The practical consists of two sessions, the first of which guides students…

Study of photo-oxidative reactivity of sunscreening agents based on photo-oxidation of uric acid by kinetic Monte Carlo simulation.

PubMed

Moradmand Jalali, Hamed; Bashiri, Hadis; Rasa, Hossein

2015-05-01

In the present study, the mechanism of free radical production by light-reflective agents in sunscreens (TiO2, ZnO and ZrO2) was obtained by applying kinetic Monte Carlo simulation. The values of the rate constants for each step of the suggested mechanism have been obtained by simulation. The effect of the initial concentration of mineral oxides and uric acid on the rate of uric acid photo-oxidation by irradiation of some sun care agents has been studied. The kinetic Monte Carlo simulation results agree qualitatively with the existing experimental data for the production of free radicals by sun care agents. Copyright © 2015 Elsevier B.V. All rights reserved.

A Biologically Inspired Cooperative Multi-Robot Control Architecture

NASA Technical Reports Server (NTRS)

Howsman, Tom; Craft, Mike; ONeil, Daniel; Howell, Joe T. (Technical Monitor)

2002-01-01

A prototype cooperative multi-robot control architecture suitable for the eventual construction of large space structures has been developed. In nature, there are numerous examples of complex architectures constructed by relatively simple insects, such as termites and wasps, which cooperatively assemble their nests. The prototype control architecture emulates this biological model. Actions of each of the autonomous robotic construction agents are only indirectly coordinated, thus mimicking the distributed construction processes of various social insects. The robotic construction agents perform their primary duties stigmergically i.e., without direct inter-agent communication and without a preprogrammed global blueprint of the final design. Communication and coordination between individual agents occurs indirectly through the sensed modifications that each agent makes to the structure. The global stigmergic building algorithm prototyped during the initial research assumes that the robotic builders only perceive the current state of the structure under construction. Simulation studies have established that an idealized form of the proposed architecture was indeed capable of producing representative large space structures with autonomous robots. This paper will explore the construction simulations in order to illustrate the multi-robot control architecture.

Biological Simulations in Distance Learning. CAL Research Group Technical Report No. 12.

ERIC Educational Resources Information Center

Murphy, P. J.

When two biological simulations on evolution and genetics (one originally developed for a conventional university undergraduate course) were introduced into Open University distance education classes, the difficulties encountered required a reappraisal of the concept of using computer simulation for distance learning and decisions on which…

Gryphon: A Hybrid Agent-Based Modeling and Simulation Platform for Infectious Diseases

NASA Astrophysics Data System (ADS)

Yu, Bin; Wang, Jijun; McGowan, Michael; Vaidyanathan, Ganesh; Younger, Kristofer

In this paper we present Gryphon, a hybrid agent-based stochastic modeling and simulation platform developed for characterizing the geographic spread of infectious diseases and the effects of interventions. We study both local and non-local transmission dynamics of stochastic simulations based on the published parameters and data for SARS. The results suggest that the expected numbers of infections and the timeline of control strategies predicted by our stochastic model are in reasonably good agreement with previous studies. These preliminary results indicate that Gryphon is able to characterize other future infectious diseases and identify endangered regions in advance.

Influence of Decontaminating Agents and Swipe Materials on Laboratory Simulated Working Surfaces Wet Spilled with Sodium Pertechnetate

PubMed Central

Akchata, Suman; Lavanya, K; Shivanand, Bhushan

2017-01-01

Context: Decontamination of various working surfaces with sodium pertechnetate minor spillage is essential for maintaining good radiation safety practices as well as for regulatory compliance. Aim: To observe the influences of decontaminating agents and swipe materials on different type of surfaces used in nuclear medicine laboratory work area wet spilled with 99m-technetium (99mTc) sodium pertechnetate. Settings and Design: Lab-simulated working surface materials. Experimental study design. Materials and Methods: Direct decontamination method on dust-free lab simulated new working surfaces [stainless steel, polyvinyl chloride (PVC), Perspex, resin] using four decontaminating agents [tap water, soap water (SW), Radiacwash, and spirit] with four different swipe material [cotton, tissue paper (TP), Whatman paper (WP), adsorbent sheet (AS)] was taken 10 samples (n = 10) for each group. Statistical Analysis: Parametric test two-way analysis of variance is used with significance level of 0.005, was used to evaluate statistical differences between different group of decontaminating agent and swipe material, and the results are expressed in mean ± SD. Results: Decontamination factor is calculated after five cleaning for each group. A total of 160 samples result calculated using four decontaminating agent (tap water, SW, Radiacwash, and spirit), four swipe material (cotton, TP, WP, and AS) for commonly used surface (stainless steel, PVC, Perspex, resin) using direct method by 10 samples (n = 10) for each group. Conclusions: Tap water is the best decontaminating agent compared with SW, Radiac wash and spirit for the laboratory simulated stainless steel, PVC, and Perspex surface material, whereas in case of resin surface material, SW decontaminating agent is showing better effectiveness. Cotton is the best swipe material compared to WP-1, AS and TP for the stainless steel, PVC, Perspex, and resin laboratory simulated surface materials. Perspex and stainless steel are the

Influence of Decontaminating Agents and Swipe Materials on Laboratory Simulated Working Surfaces Wet Spilled with Sodium Pertechnetate.

PubMed

Akchata, Suman; Lavanya, K; Shivanand, Bhushan

2017-01-01

Decontamination of various working surfaces with sodium pertechnetate minor spillage is essential for maintaining good radiation safety practices as well as for regulatory compliance. To observe the influences of decontaminating agents and swipe materials on different type of surfaces used in nuclear medicine laboratory work area wet spilled with 99m-technetium (99mTc) sodium pertechnetate. Lab-simulated working surface materials. Experimental study design. Direct decontamination method on dust-free lab simulated new working surfaces [stainless steel, polyvinyl chloride (PVC), Perspex, resin] using four decontaminating agents [tap water, soap water (SW), Radiacwash, and spirit] with four different swipe material [cotton, tissue paper (TP), Whatman paper (WP), adsorbent sheet (AS)] was taken 10 samples (n = 10) for each group. Parametric test two-way analysis of variance is used with significance level of 0.005, was used to evaluate statistical differences between different group of decontaminating agent and swipe material, and the results are expressed in mean ± SD. Decontamination factor is calculated after five cleaning for each group. A total of 160 samples result calculated using four decontaminating agent (tap water, SW, Radiacwash, and spirit), four swipe material (cotton, TP, WP, and AS) for commonly used surface (stainless steel, PVC, Perspex, resin) using direct method by 10 samples (n = 10) for each group. Tap water is the best decontaminating agent compared with SW, Radiac wash and spirit for the laboratory simulated stainless steel, PVC, and Perspex surface material, whereas in case of resin surface material, SW decontaminating agent is showing better effectiveness. Cotton is the best swipe material compared to WP-1, AS and TP for the stainless steel, PVC, Perspex, and resin laboratory simulated surface materials. Perspex and stainless steel are the most suitable and recommended laboratory surface material compared to PVC and resin in nuclear medicine

ModelforAnalyzing Human Communication Network Based onAgent-Based Simulation

NASA Astrophysics Data System (ADS)

Matsuyama, Shinako; Terano, Takao

This paper discusses dynamic properties of human communications networks, which appears as a result of informationexchanges among people. We propose agent-based simulation (ABS) to examine implicit mechanisms behind the dynamics. The ABS enables us to reveal the characteristics and the differences of the networks regarding the specific communicationgroups. We perform experiments on the ABS with activity data from questionnaires survey and with virtual data which isdifferent from the activity data. We compare the difference between them and show the effectiveness of the ABS through theexperiments.

An agent based simulation tool for scheduling emergency department physicians.

PubMed

Jones, Spencer S; Evans, R Scott

2008-11-06

Emergency department overcrowding is a problem that threatens the public health of communities and compromises the quality of care given to individual patients. The Institute of Medicine recommends that hospitals employ information technology and operations research methods to reduce overcrowding. This paper describes the development of an agent based simulation tool that has been designed to evaluate the impact of various physician staffing configurations on patient waiting times in the emergency department. We evaluate the feasibility of this tool at a single hospital emergency department.

A Parallel Sliding Region Algorithm to Make Agent-Based Modeling Possible for a Large-Scale Simulation: Modeling Hepatitis C Epidemics in Canada.

PubMed

Wong, William W L; Feng, Zeny Z; Thein, Hla-Hla

2016-11-01

Agent-based models (ABMs) are computer simulation models that define interactions among agents and simulate emergent behaviors that arise from the ensemble of local decisions. ABMs have been increasingly used to examine trends in infectious disease epidemiology. However, the main limitation of ABMs is the high computational cost for a large-scale simulation. To improve the computational efficiency for large-scale ABM simulations, we built a parallelizable sliding region algorithm (SRA) for ABM and compared it to a nonparallelizable ABM. We developed a complex agent network and performed two simulations to model hepatitis C epidemics based on the real demographic data from Saskatchewan, Canada. The first simulation used the SRA that processed on each postal code subregion subsequently. The second simulation processed the entire population simultaneously. It was concluded that the parallelizable SRA showed computational time saving with comparable results in a province-wide simulation. Using the same method, SRA can be generalized for performing a country-wide simulation. Thus, this parallel algorithm enables the possibility of using ABM for large-scale simulation with limited computational resources.

Visualization in simulation tools: requirements and a tool specification to support the teaching of dynamic biological processes.

PubMed

Jørgensen, Katarina M; Haddow, Pauline C

2011-08-01

Simulation tools are playing an increasingly important role behind advances in the field of systems biology. However, the current generation of biological science students has either little or no experience with such tools. As such, this educational glitch is limiting both the potential use of such tools as well as the potential for tighter cooperation between the designers and users. Although some simulation tool producers encourage their use in teaching, little attempt has hitherto been made to analyze and discuss their suitability as an educational tool for noncomputing science students. In general, today's simulation tools assume that the user has a stronger mathematical and computing background than that which is found in most biological science curricula, thus making the introduction of such tools a considerable pedagogical challenge. This paper provides an evaluation of the pedagogical attributes of existing simulation tools for cell signal transduction based on Cognitive Load theory. Further, design recommendations for an improved educational simulation tool are provided. The study is based on simulation tools for cell signal transduction. However, the discussions are relevant to a broader biological simulation tool set.

Comparable Efficacy of Abatacept Used as First-line or Second-line Biological Agent for Severe Juvenile Idiopathic Arthritis-related Uveitis.

PubMed

Birolo, Carolina; Zannin, Maria Elisabetta; Arsenyeva, Svetlana; Cimaz, Rolando; Miserocchi, Elisabetta; Dubko, Margarita; Deslandre, Chantal Job; Falcini, Fernanda; Alessio, Maria; La Torre, Francesco; Denisova, Ekaterina; Martini, Giorgia; Nikishina, Irina; Zulian, Francesco

2016-11-01

Abatacept (ABA) has recently been proposed as second-line treatment in patients with juvenile idiopathic arthritis (JIA)-associated uveitis refractory to anti-tumor necrosis factor-α (anti-TNF) agents, but little is known about its efficacy as a first-line approach. The aim of the present study was to compare the safety and efficacy of ABA as a first-line biological agent (ABA-1) with that of ABA as a second-line treatment after 1 or more anti-TNF agents (ABA-2), in patients with severe JIA-related uveitis. In this multicenter study, we collected data on patients with severe JIA-related uveitis treated with ABA as a first-line or second-line biological agent. Changes in frequency of uveitis flares/year and ocular complications before and after ABA treatment, clinical remission, and side effects were recorded. Thirty-five patients with a mean age of 10.8 years were treated with ABA for a mean period of 19.6 months. In 4 patients, ABA administration was discontinued, owing to inefficacy on arthritis in 3 cases and allergic reaction in 1. Thirty-one patients, 14 in the ABA-1 group and 17 in the ABA-2 group, completed the 12-month followup period; of these, 17 (54.8%) had clinical remission. The mean frequency of uveitis flares decreased from 4.1 to 1.2 in the ABA-1 group (p = 0.002) and from 3.7 to 1.2 in the ABA-2 group (p = 0.004). Preexisting ocular complications improved or remained stable in all but 5 patients, all in the ABA-2 group. No significant difference was found between the efficacy of the 2 treatment modalities. ABA confirmed its good safety profile. ABA, used as first-line biological treatment or after 1 or more anti-TNF agents, induces a comparable improvement in severe refractory JIA-related uveitis.

Effect of capping agents: Structural, optical and biological properties of ZnO nanoparticles

NASA Astrophysics Data System (ADS)

Javed, Rabia; Usman, Muhammad; Tabassum, Saira; Zia, Muhammad

2016-11-01

Different biological activities of capped and uncapped ZnO nanoparticles were investigated, and the effects of potential capping agents on these biological activities were studied. ZnO nanoparticles were synthesized and capped by polyethylene glycol (PEG) and polyvinyl pyrrolidone (PVP) using a simple chemical method of co-precipitation. Characterization by X-ray diffraction (XRD), Fourier transform Infrared spectroscopy (FTIR) and UV-vis spectroscopy confirmed the crystallinity, size, functional group, and band gap of synthesized nanoparticles. Reduction in size occurred from 34 nm to 26 nm due to surfactant. Results of all biological activities indicated significantly higher values in capped as compared to uncapped nanoparticles. Antibacterial activity against Staphylococcus aureus (ATCC 6538), Bacillus subtilis (ATCC 6633), Escherichia coli (ATCC15224), and Acetobacter was obtained. This activity was more prominent against Gram-positive bacteria, and ZnO-PVP nanoparticles elucidated highest antibacterial activity (zone of inhibition 17 mm) against Gram-positive, Bacillus subtilis species. Antioxidant activities including total flavonoid content, total phenolic content, total antioxidant capacity, total reducing power and %age inhibition of DPPH, and antidiabetic activity against α-amylase enzyme found to be exhibited highest by ZnO-PEG nanoparticles.

Improved identification of cranial nerves using paired-agent imaging: topical staining protocol optimization through experimentation and simulation

NASA Astrophysics Data System (ADS)

Torres, Veronica C.; Wilson, Todd; Staneviciute, Austeja; Byrne, Richard W.; Tichauer, Kenneth M.

2018-03-01

Skull base tumors are particularly difficult to visualize and access for surgeons because of the crowded environment and close proximity of vital structures, such as cranial nerves. As a result, accidental nerve damage is a significant concern and the likelihood of tumor recurrence is increased because of more conservative resections that attempt to avoid injuring these structures. In this study, a paired-agent imaging method with direct administration of fluorophores is applied to enhance cranial nerve identification. Here, a control imaging agent (ICG) accounts for non-specific uptake of the nerve-targeting agent (Oxazine 4), and ratiometric data analysis is employed to approximate binding potential (BP, a surrogate of targeted biomolecule concentration). For clinical relevance, animal experiments and simulations were conducted to identify parameters for an optimized stain and rinse protocol using the developed paired-agent method. Numerical methods were used to model the diffusive and kinetic behavior of the imaging agents in tissue, and simulation results revealed that there are various combinations of stain time and rinse number that provide improved contrast of cranial nerves, as suggested by optimal measures of BP and contrast-to-noise ratio.

Newer biological agents in rheumatoid arthritis: impact on health-related quality of life and productivity.

PubMed

Strand, Vibeke; Singh, Jasvinder A

2010-01-01

Health-related quality of life (HR-QOL) in patients with rheumatoid arthritis (RA) is significantly impaired as a result of pain, deficits in physical function and fatigue associated with this disease. Decrements in HR-QOL are also associated with an increased probability of no longer working, absence from work due to RA-associated sickness, and reduced productivity while at work or in the home, all of which have consequences for the patient as well as society. HR-QOL and productivity are thus important components in the assessment of outcomes in RA, and assessment of HR-QOL is now recommended in clinical trials that assess the efficacy of new treatments for RA. Measures to assess HR-QOL include the Medical Outcomes Study Short Form 36 (SF-36), EuroQol (EQ-5D) and the Health Utilities Index - Mark 3 (HUI3); these measures not only provide an indication of the clinical (i.e. statistical) efficacy of a treatment, but also provide information on whether this efficacy is truly 'meaningful' from a patient's perspective. These measures have been utilized in clinical trials of biological agents in patients with RA, including tumour necrosis factor inhibitors (etanercept, infliximab, adalimumab, certolizumab pegol and golimumab), the co-stimulatory inhibitor molecule abatacept, the B-cell depletion agent rituximab and the interleukin-6 receptor antagonist tocilizumab, and have demonstrated that these agents can significantly improve HR-QOL. Assessment of work productivity in patients with RA and the impact of treatment is a practical way to measure disability from RA from individual and societal perspectives. As RA affects women three times more frequently than men, there is also a critical need for productivity assessment within the home as well as participation in family/social/leisure activities. Data from recent trials of biological agents demonstrate that these agents can reverse disease-related decrements in productivity and limitations in participation in family

Simulation and virtual reality in medical education and therapy: a protocol.

PubMed

Roy, Michael J; Sticha, Deborah L; Kraus, Patricia L; Olsen, Dale E

2006-04-01

Continuing medical education has historically been provided primarily by didactic lectures, though adult learners prefer experiential or self-directed learning. Young physicians have extensive experience with computer-based or "video" games, priming them for medical education--and treating their patients--via new technologies. We report our use of standardized patients (SPs) to educate physicians on the diagnosis and treatment of biological and chemical warfare agent exposure. We trained professional actors to serve as SPs representing exposure to biological agents such as anthrax and smallpox. We rotated workshop participants through teaching stations to interview, examine, diagnose and treat SPs. We also trained SPs to simulate a chemical mass casualty (MASCAL) incident. Workshop participants worked together to treat MASCAL victims, followed by discussion of key teaching points. More recently, we developed computer-based simulation (CBS) modules of patients exposed to biological agents. We compare the strengths and weaknesses of CBS vs. live SPs. Finally, we detail plans for a randomized controlled trial to assess the efficacy of virtual reality (VR) exposure therapy compared to pharmacotherapy for post-traumatic stress disorder (PTSD). PTSD is associated with significant disability and healthcare costs, which may be ameliorated by the identification of more effective therapy.

Ground truth methods for optical cross-section modeling of biological aerosols

NASA Astrophysics Data System (ADS)

Kalter, J.; Thrush, E.; Santarpia, J.; Chaudhry, Z.; Gilberry, J.; Brown, D. M.; Brown, A.; Carter, C. C.

2011-05-01

Light detection and ranging (LIDAR) systems have demonstrated some capability to meet the needs of a fastresponse standoff biological detection method for simulants in open air conditions. These systems are designed to exploit various cloud signatures, such as differential elastic backscatter, fluorescence, and depolarization in order to detect biological warfare agents (BWAs). However, because the release of BWAs in open air is forbidden, methods must be developed to predict candidate system performance against real agents. In support of such efforts, the Johns Hopkins University Applied Physics Lab (JHU/APL) has developed a modeling approach to predict the optical properties of agent materials from relatively simple, Biosafety Level 3-compatible bench top measurements. JHU/APL has fielded new ground truth instruments (in addition to standard particle sizers, such as the Aerodynamic particle sizer (APS) or GRIMM aerosol monitor (GRIMM)) to more thoroughly characterize the simulant aerosols released in recent field tests at Dugway Proving Ground (DPG). These instruments include the Scanning Mobility Particle Sizer (SMPS), the Ultraviolet Aerodynamic Particle Sizer (UVAPS), and the Aspect Aerosol Size and Shape Analyser (Aspect). The SMPS was employed as a means of measuring smallparticle concentrations for more accurate Mie scattering simulations; the UVAPS, which measures size-resolved fluorescence intensity, was employed as a path toward fluorescence cross section modeling; and the Aspect, which measures particle shape, was employed as a path towards depolarization modeling.

Simulation of transmission electron microscope images of biological specimens.

PubMed

Rullgård, H; Ofverstedt, L-G; Masich, S; Daneholt, B; Oktem, O

2011-09-01

We present a new approach to simulate electron cryo-microscope images of biological specimens. The framework for simulation consists of two parts; the first is a phantom generator that generates a model of a specimen suitable for simulation, the second is a transmission electron microscope simulator. The phantom generator calculates the scattering potential of an atomic structure in aqueous buffer and allows the user to define the distribution of molecules in the simulated image. The simulator includes a well defined electron-specimen interaction model based on the scalar Schrödinger equation, the contrast transfer function for optics, and a noise model that includes shot noise as well as detector noise including detector blurring. To enable optimal performance, the simulation framework also includes a calibration protocol for setting simulation parameters. To test the accuracy of the new framework for simulation, we compare simulated images to experimental images recorded of the Tobacco Mosaic Virus (TMV) in vitreous ice. The simulated and experimental images show good agreement with respect to contrast variations depending on dose and defocus. Furthermore, random fluctuations present in experimental and simulated images exhibit similar statistical properties. The simulator has been designed to provide a platform for development of new instrumentation and image processing procedures in single particle electron microscopy, two-dimensional crystallography and electron tomography with well documented protocols and an open source code into which new improvements and extensions are easily incorporated. © 2011 The Authors Journal of Microscopy © 2011 Royal Microscopical Society.

Measurement of drug facilitated sexual assault agents in simulated sweat by ion mobility spectrometry.

PubMed

Demoranville, Leonard T; Verkouteren, Jennifer R

2013-03-15

Ion mobility spectrometry has found widespread use for the detection of explosives and illicit drugs. The technique offers rapid results with high sensitivity and little sample preparation. As such, it is well suited for field deployed screening settings. Here the response of ion mobility spectrometers for three drug-facilitated sexual assault (DFSA) agents - flunitrazepam, ketamine, and MDMA - and related metabolites has been studied in the presence of a simulated sweat. While all three DFSA agents present certain challenges for qualitative identification, IMS can provide useful information to guide the early treatment and investigation of sexual assault cases. Used as a presumptive test, the identification of DFSA agents would later require confirmatory analysis by other techniques. Published by Elsevier B.V.

Are three colonies of Neostromboceros albicomus, a candidate biological control agent for Lygodium microphyllum, the same host biotype?

USDA-ARS?s Scientific Manuscript database

Three colonies of Neostromboceros albicomus, a candidate biological control agent of Lygodium microphyllum, were barcoded using the D2 expansion domain, to determine which of two biotypes they represented. The first colony, collected in 2005 & 2007, was used for the initial host range testing. Colon...

Minimum threshold for establishment and dispersal of Lilioceris cheni (Coleoptera: Chrysomelide): a biological control agent of Dioscorea bulbifera

USDA-ARS?s Scientific Manuscript database

The successful establishment or failure of a new population is often attributed to propagule pressure, the combination of the number of independent introduction events, and the number of individuals released at each event. Design of optimal release strategies for biological control agents benefits f...

Opportunities for improving risk communication during the permitting process for entomophagous biological control agents: A review of current systems

USDA-ARS?s Scientific Manuscript database

Concerns about potentially irreversible non-target impacts from the importation and release of entomophagous biological control agents (BCAs) have resulted in increasingly stringent import requirements by National Plant Protection Organizations. Despite numerous scientific publications on the poten...

A Collective Case Study of Secondary Students' Model-Based Inquiry on Natural Selection through Programming in an Agent-Based Modeling Environment

ERIC Educational Resources Information Center

Xiang, Lin

2011-01-01

This is a collective case study seeking to develop detailed descriptions of how programming an agent-based simulation influences a group of 8th grade students' model-based inquiry (MBI) by examining students' agent-based programmable modeling (ABPM) processes and the learning outcomes. The context of the present study was a biology unit on…

CHARMM-GUI Membrane Builder toward realistic biological membrane simulations.

PubMed

Wu, Emilia L; Cheng, Xi; Jo, Sunhwan; Rui, Huan; Song, Kevin C; Dávila-Contreras, Eder M; Qi, Yifei; Lee, Jumin; Monje-Galvan, Viviana; Venable, Richard M; Klauda, Jeffery B; Im, Wonpil

2014-10-15

CHARMM-GUI Membrane Builder, http://www.charmm-gui.org/input/membrane, is a web-based user interface designed to interactively build all-atom protein/membrane or membrane-only systems for molecular dynamics simulations through an automated optimized process. In this work, we describe the new features and major improvements in Membrane Builder that allow users to robustly build realistic biological membrane systems, including (1) addition of new lipid types, such as phosphoinositides, cardiolipin (CL), sphingolipids, bacterial lipids, and ergosterol, yielding more than 180 lipid types, (2) enhanced building procedure for lipid packing around protein, (3) reliable algorithm to detect lipid tail penetration to ring structures and protein surface, (4) distance-based algorithm for faster initial ion displacement, (5) CHARMM inputs for P21 image transformation, and (6) NAMD equilibration and production inputs. The robustness of these new features is illustrated by building and simulating a membrane model of the polar and septal regions of E. coli membrane, which contains five lipid types: CL lipids with two types of acyl chains and phosphatidylethanolamine lipids with three types of acyl chains. It is our hope that CHARMM-GUI Membrane Builder becomes a useful tool for simulation studies to better understand the structure and dynamics of proteins and lipids in realistic biological membrane environments. Copyright © 2014 Wiley Periodicals, Inc.

Modelling and simulation techniques for membrane biology.

PubMed

Burrage, Kevin; Hancock, John; Leier, André; Nicolau, Dan V

2007-07-01

One of the most important aspects of Computational Cell Biology is the understanding of the complicated dynamical processes that take place on plasma membranes. These processes are often so complicated that purely temporal models cannot always adequately capture the dynamics. On the other hand, spatial models can have large computational overheads. In this article, we review some of these issues with respect to chemistry, membrane microdomains and anomalous diffusion and discuss how to select appropriate modelling and simulation paradigms based on some or all the following aspects: discrete, continuous, stochastic, delayed and complex spatial processes.

A Systematic Screen of FDA-Approved Drugs for Inhibitors of Biological Threat Agents

PubMed Central

Madrid, Peter B.; Chopra, Sidharth; Manger, Ian D.; Gilfillan, Lynne; Keepers, Tiffany R.; Shurtleff, Amy C.; Green, Carol E.; Iyer, Lalitha V.; Dilks, Holli Hutcheson; Davey, Robert A.; Kolokoltsov, Andrey A.; Carrion, Ricardo; Patterson, Jean L.; Bavari, Sina; Panchal, Rekha G.; Warren, Travis K.; Wells, Jay B.; Moos, Walter H.; Burke, RaeLyn L.; Tanga, Mary J.

2013-01-01

Background The rapid development of effective medical countermeasures against potential biological threat agents is vital. Repurposing existing drugs that may have unanticipated activities as potential countermeasures is one way to meet this important goal, since currently approved drugs already have well-established safety and pharmacokinetic profiles in patients, as well as manufacturing and distribution networks. Therefore, approved drugs could rapidly be made available for a new indication in an emergency. Methodology/Principal Findings A large systematic effort to determine whether existing drugs can be used against high containment bacterial and viral pathogens is described. We assembled and screened 1012 FDA-approved drugs for off-label broad-spectrum efficacy against Bacillus anthracis; Francisella tularensis; Coxiella burnetii; and Ebola, Marburg, and Lassa fever viruses using in vitro cell culture assays. We found a variety of hits against two or more of these biological threat pathogens, which were validated in secondary assays. As expected, antibiotic compounds were highly active against bacterial agents, but we did not identify any non-antibiotic compounds with broad-spectrum antibacterial activity. Lomefloxacin and erythromycin were found to be the most potent compounds in vivo protecting mice against Bacillus anthracis challenge. While multiple virus-specific inhibitors were identified, the most noteworthy antiviral compound identified was chloroquine, which disrupted entry and replication of two or more viruses in vitro and protected mice against Ebola virus challenge in vivo. Conclusions/Significance The feasibility of repurposing existing drugs to face novel threats is demonstrated and this represents the first effort to apply this approach to high containment bacteria and viruses. PMID:23577127

Potential of Biological Agents in Decontamination of Agricultural Soil

PubMed Central

Javaid, Muhammad Kashif; Ashiq, Mehrban; Tahir, Muhammad

2016-01-01

Pesticides are widely used for the control of weeds, diseases, and pests of cultivated plants all over the world, mainly since the period after the Second World War. The use of pesticides is very extensive to control harm of pests all over the globe. Persistent nature of most of the synthetic pesticides causes serious environmental concerns. Decontamination of these hazardous chemicals is very essential. This review paper elaborates the potential of various biological agents in decontamination of agricultural soils. The agricultural crop fields are contaminated by the periodic applications of pesticides. Biodegradation is an ecofriendly, cost-effective, highly efficient approach compared to the physical and chemical methods which are expensive as well as unfriendly towards environment. Biodegradation is sensitive to the concentration levels of hydrogen peroxide and nitrogen along with microbial community, temperature, and pH changes. Experimental work for optimum conditions at lab scale can provide very fruitful results about specific bacterial, fungal strains. This study revealed an upper hand of bioremediation over physicochemical approaches. Further studies should be carried out to understand mechanisms of biotransformation. PMID:27293964

Potential of Biological Agents in Decontamination of Agricultural Soil.

PubMed

Javaid, Muhammad Kashif; Ashiq, Mehrban; Tahir, Muhammad

2016-01-01

Pesticides are widely used for the control of weeds, diseases, and pests of cultivated plants all over the world, mainly since the period after the Second World War. The use of pesticides is very extensive to control harm of pests all over the globe. Persistent nature of most of the synthetic pesticides causes serious environmental concerns. Decontamination of these hazardous chemicals is very essential. This review paper elaborates the potential of various biological agents in decontamination of agricultural soils. The agricultural crop fields are contaminated by the periodic applications of pesticides. Biodegradation is an ecofriendly, cost-effective, highly efficient approach compared to the physical and chemical methods which are expensive as well as unfriendly towards environment. Biodegradation is sensitive to the concentration levels of hydrogen peroxide and nitrogen along with microbial community, temperature, and pH changes. Experimental work for optimum conditions at lab scale can provide very fruitful results about specific bacterial, fungal strains. This study revealed an upper hand of bioremediation over physicochemical approaches. Further studies should be carried out to understand mechanisms of biotransformation.

Chemical and biological threat-agent detection using electrophoresis-based lab-on-a-chip devices.

PubMed

Borowsky, Joseph; Collins, Greg E

2007-10-01

The ability to separate complex mixtures of analytes has made capillary electrophoresis (CE) a powerful analytical tool since its modern configuration was first introduced over 25 years ago. The technique found new utility with its application to the microfluidics based lab-on-a-chip platform (i.e., microchip), which resulted in ever smaller footprints, sample volumes, and analysis times. These features, coupled with the technique's potential for portability, have prompted recent interest in the development of novel analyzers for chemical and biological threat agents. This article will comment on three main areas of microchip CE as applied to the separation and detection of threat agents: detection techniques and their corresponding limits of detection, sampling protocol and preparation time, and system portability. These three areas typify the broad utility of lab-on-a-chip for meeting critical, present-day security, in addition to illustrating areas wherein advances are necessary.

Biology and host range of Tecmessa elegans (Lepidoptera:Notodontidae) a leaf-feeding moth evaluated as a potential biological control agent for Schinus terebinthifolius (Sapindales: Anacardiaceae) in the USA

USDA-ARS?s Scientific Manuscript database

During surveys for natural enemies that could potentially be used as classical biological control agents of Schinus terebinthifolius Raddi (Brazilian pepper) which is invasive in the USA, the caterpillar, Tecmessa elegans Schaus (Lepidoptera: Notodontidae), was recorded feeding on the leaves of the ...

A review of recent patents on macroorganisms as biological control agents.

PubMed

Sáenz-de-Cabezón, Francisco Javier; Zalom, Frank G; López-Olguín, Jesús Francisco

2010-01-01

The indiscriminate use of synthetic pesticides has brought undesired problems to human health, agriculture, and the environment. Integrated Pest Management (IPM) and Biological Control (BC) programs, which are based on minimum use of pesticides, are seen as alternative, more ecological solutions to the unintended problems associated with pesticide use. These programs combine the introduction, augmentation, and/or conservation of pest natural enemies, with other protection tools. Although patents and the process of commercialization of microorganisms has been the subject of various reviews, macroorganisms used for pest and disease control have stimulated less comprehensive analyses. From our review of patents, there has been an enormous increase in the number of macroorganism-related patents registered in the last two decades. Private companies own 65% of all these patents. Rearing methods and crop protection strategies are the main intellectual property patented, with parasitoid wasps and predatory mites being the primary Biological Control Agent (BCA) focus of patents. Among countries, Japan was the first country with these types of patents, followed by the United States, Canada and China. Increasing concern for pesticide risks by governments and the public is seen as the main impetus for change in "traditional" crop protection practices and for investment in other more ecological products like BCAs.

HIGHLY SELECTIVE SENSORS FOR CHEMICAL AND BIOLOGICAL WARFARE AGENTS, INSECTICIDES AND VOCS BASED ON A MOLECULAR SURFACE IMPRINTING TECHNIQUE

EPA Science Inventory

Abstract was given as an oral platform presentation at the Pittsburgh Conference, Orlando FL (March 5-9, 2006). Research described is the development of sensors based on molecular surface imprinting. Applications include the monitoring of chemical and biological agents and inse...

Prognostic factors of methotrexate-associated lymphoproliferative disorders associated with rheumatoid arthritis and plausible application of biological agents.

PubMed

Katsuyama, Takayuki; Sada, Ken-Ei; Yan, Minglu; Zeggar, Sonia; Hiramatsu, Sumie; Miyawaki, Yoshia; Ohashi, Keiji; Morishita, Michiko; Watanabe, Haruki; Katsuyama, Eri; Takano-Narazaki, Mariko; Toyota-Tatebe, Noriko; Sunahori-Watanabe, Katsue; Kawabata, Tomoko; Miyake, Kohei; Kiguchi, Toru; Wada, Jun

2017-09-01

To determine prognostic factors of methotrexate-associated lymphoproliferative disorder (MTX-LPD) and evaluate the efficacy and safety of biological therapy in rheumatoid arthritis (RA) complicated with MTX-LPD. Thirty RA patients who developed MTX-LPD were investigated in this study. We compared the clinical and laboratory parameters of patients who achieved regression of LPD by MTX withdrawal with those who required chemotherapy and evaluated the clinical course of RA after LPD development. Twenty-three patients (76.7%) achieved regression of LPD by MTX withdrawal. Chemotherapy-free patients had a tendency of shorter RA duration (13.1 vs. 22.0 years, p = 0.108) and higher doses of MTX at LPD diagnosis (8.0 vs. 5.3 mg/w, p = 0.067) than patients who required chemotherapy. A significantly higher positive rate of peripheral blood Epstein-Barr virus (EBV)-DNA was observed in the chemotherapy-free group (9/9 vs. 0/3, p = 0.0002). Of 15 patients that received biological agents after LPD development, 14 patients (93.3%) demonstrated an improved disease activity of RA and persistent remission of LPD, whereas only one patient experienced relapse of LPD during tocilizumab therapy. Peripheral blood EBV-DNA positivity is a potential prognostic marker of better outcome in MTX-LPD. Biological agents could be an option for the treatment of RA patients with MTX-LPD.

Electrostatic thin film chemical and biological sensor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prelas, Mark A.; Ghosh, Tushar K.; Tompson, Jr., Robert V.

A chemical and biological agent sensor includes an electrostatic thin film supported by a substrate. The film includes an electrostatic charged surface to attract predetermined biological and chemical agents of interest. A charge collector associated with said electrostatic thin film collects charge associated with surface defects in the electrostatic film induced by the predetermined biological and chemical agents of interest. A preferred sensing system includes a charge based deep level transient spectroscopy system to read out charges from the film and match responses to data sets regarding the agents of interest. A method for sensing biological and chemical agents includesmore » providing a thin sensing film having a predetermined electrostatic charge. The film is exposed to an environment suspected of containing the biological and chemical agents. Quantum surface effects on the film are measured. Biological and/or chemical agents can be detected, identified and quantified based on the measured quantum surface effects.« less

Ocular side effects of biological agents in oncology: what should the clinician be aware of?

PubMed Central

Hager, Tobias; Seitz, B

2014-01-01

During the last 20 years, biologicals have become increasingly relevant in oncologic therapy. Depending on the medication used, there are different profiles of ocular side effects. Although these can be present in up to 70% of patients, they are generally underreported in the literature. Therefore, the pathophysiological details of their development are often poorly understood. Herein we attempt to identify groups of biologicals to which a specific side effect profile can be assigned. We also tried to capture all relevant side effects and therefore conducted several database investigation including Medline, Cochrane library, and the drugs section of the US Food and Drug Administration (FDA), using the following search strings: “name of biological agent (both generic and commercial names)” AND “eye” OR “ocular”. If we found a side effect that has been associated with a drug, we researched Medline using the following search string: “name of biological agent” (both generic and commercial names) AND “term for the specific side effect”. Due to the wealth of material we report only the drugs that are approved by the FDA. PMID:24391443

Multi-agent simulation of generation expansion in electricity markets.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Botterud, A; Mahalik, M. R.; Veselka, T. D.

2007-06-01

We present a new multi-agent model of generation expansion in electricity markets. The model simulates generation investment decisions of decentralized generating companies (GenCos) interacting in a complex, multidimensional environment. A probabilistic dispatch algorithm calculates prices and profits for new candidate units in different future states of the system. Uncertainties in future load, hydropower conditions, and competitors actions are represented in a scenario tree, and decision analysis is used to identify the optimal expansion decision for each individual GenCo. We test the model using real data for the Korea power system under different assumptions about market design, market concentration, and GenCo'smore » assumed expectations about their competitors investment decisions.« less

Fractal propagation method enables realistic optical microscopy simulations in biological tissues

PubMed Central

Glaser, Adam K.; Chen, Ye; Liu, Jonathan T.C.

2017-01-01

Current simulation methods for light transport in biological media have limited efficiency and realism when applied to three-dimensional microscopic light transport in biological tissues with refractive heterogeneities. We describe here a technique which combines a beam propagation method valid for modeling light transport in media with weak variations in refractive index, with a fractal model of refractive index turbulence. In contrast to standard simulation methods, this fractal propagation method (FPM) is able to accurately and efficiently simulate the diffraction effects of focused beams, as well as the microscopic heterogeneities present in tissue that result in scattering, refractive beam steering, and the aberration of beam foci. We validate the technique and the relationship between the FPM model parameters and conventional optical parameters used to describe tissues, and also demonstrate the method’s flexibility and robustness by examining the steering and distortion of Gaussian and Bessel beams in tissue with comparison to experimental data. We show that the FPM has utility for the accurate investigation and optimization of optical microscopy methods such as light-sheet, confocal, and nonlinear microscopy. PMID:28983499

Modeling the Information Age Combat Model: An Agent-Based Simulation of Network Centric Operations

NASA Technical Reports Server (NTRS)

Deller, Sean; Rabadi, Ghaith A.; Bell, Michael I.; Bowling, Shannon R.; Tolk, Andreas

2010-01-01

The Information Age Combat Model (IACM) was introduced by Cares in 2005 to contribute to the development of an understanding of the influence of connectivity on force effectiveness that can eventually lead to quantitative prediction and guidelines for design and employment. The structure of the IACM makes it clear that the Perron-Frobenius Eigenvalue is a quantifiable metric with which to measure the organization of a networked force. The results of recent experiments presented in Deller, et aI., (2009) indicate that the value of the Perron-Frobenius Eigenvalue is a significant measurement of the performance of an Information Age combat force. This was accomplished through the innovative use of an agent-based simulation to model the IACM and represents an initial contribution towards a new generation of combat models that are net-centric instead of using the current platform-centric approach. This paper describes the intent, challenges, design, and initial results of this agent-based simulation model.

A Computational Systems Biology Software Platform for Multiscale Modeling and Simulation: Integrating Whole-Body Physiology, Disease Biology, and Molecular Reaction Networks

PubMed Central

Eissing, Thomas; Kuepfer, Lars; Becker, Corina; Block, Michael; Coboeken, Katrin; Gaub, Thomas; Goerlitz, Linus; Jaeger, Juergen; Loosen, Roland; Ludewig, Bernd; Meyer, Michaela; Niederalt, Christoph; Sevestre, Michael; Siegmund, Hans-Ulrich; Solodenko, Juri; Thelen, Kirstin; Telle, Ulrich; Weiss, Wolfgang; Wendl, Thomas; Willmann, Stefan; Lippert, Joerg

2011-01-01

Today, in silico studies and trial simulations already complement experimental approaches in pharmaceutical R&D and have become indispensable tools for decision making and communication with regulatory agencies. While biology is multiscale by nature, project work, and software tools usually focus on isolated aspects of drug action, such as pharmacokinetics at the organism scale or pharmacodynamic interaction on the molecular level. We present a modeling and simulation software platform consisting of PK-Sim® and MoBi® capable of building and simulating models that integrate across biological scales. A prototypical multiscale model for the progression of a pancreatic tumor and its response to pharmacotherapy is constructed and virtual patients are treated with a prodrug activated by hepatic metabolization. Tumor growth is driven by signal transduction leading to cell cycle transition and proliferation. Free tumor concentrations of the active metabolite inhibit Raf kinase in the signaling cascade and thereby cell cycle progression. In a virtual clinical study, the individual therapeutic outcome of the chemotherapeutic intervention is simulated for a large population with heterogeneous genomic background. Thereby, the platform allows efficient model building and integration of biological knowledge and prior data from all biological scales. Experimental in vitro model systems can be linked with observations in animal experiments and clinical trials. The interplay between patients, diseases, and drugs and topics with high clinical relevance such as the role of pharmacogenomics, drug–drug, or drug–metabolite interactions can be addressed using this mechanistic, insight driven multiscale modeling approach. PMID:21483730

Advanced UV Source for Biological Agent Destruction

DTIC Science & Technology

2006-01-01

protection against chemical agents. The AUVS can be inserted into HVAC air ducts to eliminate BW agents, used to purify water, and / or used to reduce...operating costs are very low. The technology has been shown to be very effective for destroying Bacillus pumilus endospores that are significantly more...resistant to UV than anthrax spores . Up to7 orders of magnitude (7 logs) kill of B. pumilus spores have been demonstrated with the AUVS technology

IMPROVEMENT OF BUSINESS EFFICIENCY USING A MULTI-AGENT SIMULATION FOR HIGHWAY PATROL ON URBAN EXPRESSWAY

NASA Astrophysics Data System (ADS)

Okamoto, Taro; Taniguchi, Eiichi; Yamada, Tadashi

In Japan, the network of urban expressway has been expanding with the development of urban areas. However, the patrol systems in the urban expressway has not been operated on the basis of scientific evidence, but of conformity and experience. It is therefore crucial to efficiently operate such systems, not only to facilitate the rapid recovery of decreased expressway functionality, but also to acquire the income that supports the operation of privatized expressway companies. Therefore, we develop a multiagent simulation model consisting of the decision-making of four agents, including expressway company, highway patol company, road network users and road authority. These agents determines their schemes depending on their profit obtained. Results of the simulation identyfies the schemes that could offer the profits to the expressway companies in terms of the convenience of the users and the improvement of their operation.

STSE: Spatio-Temporal Simulation Environment Dedicated to Biology.

PubMed

Stoma, Szymon; Fröhlich, Martina; Gerber, Susanne; Klipp, Edda

2011-04-28

Recently, the availability of high-resolution microscopy together with the advancements in the development of biomarkers as reporters of biomolecular interactions increased the importance of imaging methods in molecular cell biology. These techniques enable the investigation of cellular characteristics like volume, size and geometry as well as volume and geometry of intracellular compartments, and the amount of existing proteins in a spatially resolved manner. Such detailed investigations opened up many new areas of research in the study of spatial, complex and dynamic cellular systems. One of the crucial challenges for the study of such systems is the design of a well stuctured and optimized workflow to provide a systematic and efficient hypothesis verification. Computer Science can efficiently address this task by providing software that facilitates handling, analysis, and evaluation of biological data to the benefit of experimenters and modelers. The Spatio-Temporal Simulation Environment (STSE) is a set of open-source tools provided to conduct spatio-temporal simulations in discrete structures based on microscopy images. The framework contains modules to digitize, represent, analyze, and mathematically model spatial distributions of biochemical species. Graphical user interface (GUI) tools provided with the software enable meshing of the simulation space based on the Voronoi concept. In addition, it supports to automatically acquire spatial information to the mesh from the images based on pixel luminosity (e.g. corresponding to molecular levels from microscopy images). STSE is freely available either as a stand-alone version or included in the linux live distribution Systems Biology Operational Software (SB.OS) and can be downloaded from http://www.stse-software.org/. The Python source code as well as a comprehensive user manual and video tutorials are also offered to the research community. We discuss main concepts of the STSE design and workflow. We

Introduction, establishment and dispersal in Mexico of the wasp Tetramesa romana, biological control agent of the giant reed

USDA-ARS?s Scientific Manuscript database

The arundo wasp, Tetramesa romana, is a specialist, plant-feeding insect biological control agent for the invasive weed - Arundo donax, also known as giant reed, carrizo cane, and in Mexico, carrizo gigante and el ladron de agua. This weed, which is native to Spain, grows along the banks of rivers, ...

Rogue taxa phenomenon: a biological companion to simulation analysis

PubMed Central

Westover, Kristi M.; Rusinko, Joseph P.; Hoin, Jon; Neal, Matthew

2013-01-01

To provide a baseline biological comparison to simulation study predictions about the frequency of rogue taxa effects, we evaluated the frequency of a rogue taxa effect using viral data sets which differed in diversity. Using a quartet-tree framework, we measured the frequency of a rogue taxa effect in three data sets of increasing genetic variability (within viral serotype, between viral serotype, and between viral family) to test whether the rogue taxa was correlated with the mean sequence diversity of the respective data sets. We found a slight increase in the percentage of rogues as nucleotide diversity increased. Even though the number of rogues increased with diversity, the distribution of the types of rogues (friendly, crazy, or evil) did not depend on the diversity and in the case of the order-level data set the net rogue effect was slightly positive. This study, assessing frequency of the rogue taxa effect using biological data, indicated that simulation studies may over-predict the prevalence of the rogue taxa effect. Further investigations are necessary to understand which types of data sets are susceptible to a negative rogue effect and thus merit the removal of taxa from large phylogenetic reconstructions. PMID:23707704

An Agent-Based Model of New Venture Creation: Conceptual Design for Simulating Entrepreneurship

NASA Technical Reports Server (NTRS)

Provance, Mike; Collins, Andrew; Carayannis, Elias

2012-01-01

There is a growing debate over the means by which regions can foster the growth of entrepreneurial activity in order to stimulate recovery and growth of their economies. On one side, agglomeration theory suggests the regions grow because of strong clusters that foster knowledge spillover locally; on the other side, the entrepreneurial action camp argues that innovative business models are generated by entrepreneurs with unique market perspectives who draw on knowledge from more distant domains. We will show you the design for a novel agent-based model of new venture creation that will demonstrate the relationship between agglomeration and action. The primary focus of this model is information exchange as the medium for these agent interactions. Our modeling and simulation study proposes to reveal interesting relationships in these perspectives, offer a foundation on which these disparate theories from economics and sociology can find common ground, and expand the use of agent-based modeling into entrepreneurship research.

High-Performance Agent-Based Modeling Applied to Vocal Fold Inflammation and Repair.

PubMed

Seekhao, Nuttiiya; Shung, Caroline; JaJa, Joseph; Mongeau, Luc; Li-Jessen, Nicole Y K

2018-01-01

Fast and accurate computational biology models offer the prospect of accelerating the development of personalized medicine. A tool capable of estimating treatment success can help prevent unnecessary and costly treatments and potential harmful side effects. A novel high-performance Agent-Based Model (ABM) was adopted to simulate and visualize multi-scale complex biological processes arising in vocal fold inflammation and repair. The computational scheme was designed to organize the 3D ABM sub-tasks to fully utilize the resources available on current heterogeneous platforms consisting of multi-core CPUs and many-core GPUs. Subtasks are further parallelized and convolution-based diffusion is used to enhance the performance of the ABM simulation. The scheme was implemented using a client-server protocol allowing the results of each iteration to be analyzed and visualized on the server (i.e., in-situ ) while the simulation is running on the same server. The resulting simulation and visualization software enables users to interact with and steer the course of the simulation in real-time as needed. This high-resolution 3D ABM framework was used for a case study of surgical vocal fold injury and repair. The new framework is capable of completing the simulation, visualization and remote result delivery in under 7 s per iteration, where each iteration of the simulation represents 30 min in the real world. The case study model was simulated at the physiological scale of a human vocal fold. This simulation tracks 17 million biological cells as well as a total of 1.7 billion signaling chemical and structural protein data points. The visualization component processes and renders all simulated biological cells and 154 million signaling chemical data points. The proposed high-performance 3D ABM was verified through comparisons with empirical vocal fold data. Representative trends of biomarker predictions in surgically injured vocal folds were observed.

High-Performance Agent-Based Modeling Applied to Vocal Fold Inflammation and Repair

PubMed Central

Seekhao, Nuttiiya; Shung, Caroline; JaJa, Joseph; Mongeau, Luc; Li-Jessen, Nicole Y. K.

2018-01-01

Fast and accurate computational biology models offer the prospect of accelerating the development of personalized medicine. A tool capable of estimating treatment success can help prevent unnecessary and costly treatments and potential harmful side effects. A novel high-performance Agent-Based Model (ABM) was adopted to simulate and visualize multi-scale complex biological processes arising in vocal fold inflammation and repair. The computational scheme was designed to organize the 3D ABM sub-tasks to fully utilize the resources available on current heterogeneous platforms consisting of multi-core CPUs and many-core GPUs. Subtasks are further parallelized and convolution-based diffusion is used to enhance the performance of the ABM simulation. The scheme was implemented using a client-server protocol allowing the results of each iteration to be analyzed and visualized on the server (i.e., in-situ) while the simulation is running on the same server. The resulting simulation and visualization software enables users to interact with and steer the course of the simulation in real-time as needed. This high-resolution 3D ABM framework was used for a case study of surgical vocal fold injury and repair. The new framework is capable of completing the simulation, visualization and remote result delivery in under 7 s per iteration, where each iteration of the simulation represents 30 min in the real world. The case study model was simulated at the physiological scale of a human vocal fold. This simulation tracks 17 million biological cells as well as a total of 1.7 billion signaling chemical and structural protein data points. The visualization component processes and renders all simulated biological cells and 154 million signaling chemical data points. The proposed high-performance 3D ABM was verified through comparisons with empirical vocal fold data. Representative trends of biomarker predictions in surgically injured vocal folds were observed. PMID:29706894

Emulating a System Dynamics Model with Agent-Based Models: A Methodological Case Study in Simulation of Diabetes Progression

DOE PAGES

Schryver, Jack; Nutaro, James; Shankar, Mallikarjun

2015-10-30

An agent-based simulation model hierarchy emulating disease states and behaviors critical to progression of diabetes type 2 was designed and implemented in the DEVS framework. The models are translations of basic elements of an established system dynamics model of diabetes. In this model hierarchy, which mimics diabetes progression over an aggregated U.S. population, was dis-aggregated and reconstructed bottom-up at the individual (agent) level. Four levels of model complexity were defined in order to systematically evaluate which parameters are needed to mimic outputs of the system dynamics model. Moreover, the four estimated models attempted to replicate stock counts representing disease statesmore » in the system dynamics model, while estimating impacts of an elderliness factor, obesity factor and health-related behavioral parameters. Health-related behavior was modeled as a simple realization of the Theory of Planned Behavior, a joint function of individual attitude and diffusion of social norms that spread over each agent s social network. Although the most complex agent-based simulation model contained 31 adjustable parameters, all models were considerably less complex than the system dynamics model which required numerous time series inputs to make its predictions. In all three elaborations of the baseline model provided significantly improved fits to the output of the system dynamics model. The performances of the baseline agent-based model and its extensions illustrate a promising approach to translate complex system dynamics models into agent-based model alternatives that are both conceptually simpler and capable of capturing main effects of complex local agent-agent interactions.« less

Emulating a System Dynamics Model with Agent-Based Models: A Methodological Case Study in Simulation of Diabetes Progression

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schryver, Jack; Nutaro, James; Shankar, Mallikarjun

An agent-based simulation model hierarchy emulating disease states and behaviors critical to progression of diabetes type 2 was designed and implemented in the DEVS framework. The models are translations of basic elements of an established system dynamics model of diabetes. In this model hierarchy, which mimics diabetes progression over an aggregated U.S. population, was dis-aggregated and reconstructed bottom-up at the individual (agent) level. Four levels of model complexity were defined in order to systematically evaluate which parameters are needed to mimic outputs of the system dynamics model. Moreover, the four estimated models attempted to replicate stock counts representing disease statesmore » in the system dynamics model, while estimating impacts of an elderliness factor, obesity factor and health-related behavioral parameters. Health-related behavior was modeled as a simple realization of the Theory of Planned Behavior, a joint function of individual attitude and diffusion of social norms that spread over each agent s social network. Although the most complex agent-based simulation model contained 31 adjustable parameters, all models were considerably less complex than the system dynamics model which required numerous time series inputs to make its predictions. In all three elaborations of the baseline model provided significantly improved fits to the output of the system dynamics model. The performances of the baseline agent-based model and its extensions illustrate a promising approach to translate complex system dynamics models into agent-based model alternatives that are both conceptually simpler and capable of capturing main effects of complex local agent-agent interactions.« less

Methods for improving simulations of biological systems: systemic computation and fractal proteins

PubMed Central

Bentley, Peter J.

2009-01-01

Modelling and simulation are becoming essential for new fields such as synthetic biology. Perhaps the most important aspect of modelling is to follow a clear design methodology that will help to highlight unwanted deficiencies. The use of tools designed to aid the modelling process can be of benefit in many situations. In this paper, the modelling approach called systemic computation (SC) is introduced. SC is an interaction-based language, which enables individual-based expression and modelling of biological systems, and the interactions between them. SC permits a precise description of a hypothetical mechanism to be written using an intuitive graph-based or a calculus-based notation. The same description can then be directly run as a simulation, merging the hypothetical mechanism and the simulation into the same entity. However, even when using well-designed modelling tools to produce good models, the best model is not always the most accurate one. Frequently, computational constraints or lack of data make it infeasible to model an aspect of biology. Simplification may provide one way forward, but with inevitable consequences of decreased accuracy. Instead of attempting to replace an element with a simpler approximation, it is sometimes possible to substitute the element with a different but functionally similar component. In the second part of this paper, this modelling approach is described and its advantages are summarized using an exemplar: the fractal protein model. Finally, the paper ends with a discussion of good biological modelling practice by presenting lessons learned from the use of SC and the fractal protein model. PMID:19324681

Wealth distribution, Pareto law, and stretched exponential decay of money: Computer simulations analysis of agent-based models

NASA Astrophysics Data System (ADS)

Aydiner, Ekrem; Cherstvy, Andrey G.; Metzler, Ralf

2018-01-01

We study by Monte Carlo simulations a kinetic exchange trading model for both fixed and distributed saving propensities of the agents and rationalize the person and wealth distributions. We show that the newly introduced wealth distribution - that may be more amenable in certain situations - features a different power-law exponent, particularly for distributed saving propensities of the agents. For open agent-based systems, we analyze the person and wealth distributions and find that the presence of trap agents alters their amplitude, leaving however the scaling exponents nearly unaffected. For an open system, we show that the total wealth - for different trap agent densities and saving propensities of the agents - decreases in time according to the classical Kohlrausch-Williams-Watts stretched exponential law. Interestingly, this decay does not depend on the trap agent density, but rather on saving propensities. The system relaxation for fixed and distributed saving schemes are found to be different.

Properties and applications of antimicrobial peptides in biodefense against biological warfare threat agents.

PubMed

Dawson, Raymond Murray; Liu, Chun-Qiang

2008-01-01

Recent advances in knowledge of the properties of antimicrobial peptides (AMPs) are reviewed. AMPs are typically small, positively charged, amphipathic peptides that interact electrostatically and non-stereospecifically with the bacterial cell membrane, resulting in its permeabilization and cell death. Classes of AMPs, their mechanisms of action, hemolytic activity, and cytotoxicity towards host cells are discussed. A particular focus is AMPs with potential for use in defense against biological warfare agents. Some AMPs cytotoxic to Bacillus anthracis have been described. Synthesis of these peptides in multivalent form leads to a synergistic increase in antibacterial activity. Strategies to enhance the potency, stability, and selectivity of AMPs are discussed.

Applying the Nernst equation to simulate redox potential variations for biological nitrification and denitrification processes.

PubMed

Chang, Cheng-Nan; Cheng, Hong-Bang; Chao, Allen C

2004-03-15

In this paper, various forms of Nernst equations have been developed based on the real stoichiometric relationship of biological nitrification and denitrification reactions. Instead of using the Nernst equation based on a one-to-one stoichiometric relation for the oxidizing and the reducing species, the basic Nernst equation is modified into slightly different forms. Each is suitable for simulating the redox potential (ORP) variation of a specific biological nitrification or denitrification process. Using the data published in the literature, the validity of these developed Nernst equations has been verified by close fits of the measured ORP data with the calculated ORP curve. The simulation results also indicate that if the biological process is simulated using an incorrect form of Nernst equation, the calculated ORP curve will not fit the measured data. Using these Nernst equations, the ORP value that corresponds to a predetermined degree of completion for the biochemical reaction can be calculated. Thus, these Nernst equations will enable a more efficient on-line control of the biological process.

Decontamination of chemical and biological warfare agents with a single multi-functional material.

PubMed

Amitai, Gabi; Murata, Hironobu; Andersen, Jill D; Koepsel, Richard R; Russell, Alan J

2010-05-01

We report the synthesis of new polymers based on a dimethylacrylamide-methacrylate (DMAA-MA) co-polymer backbone that support both chemical and biological agent decontamination. Polyurethanes containing the redox enzymes glucose oxidase and horseradish peroxidase can convert halide ions into active halogens and exert striking bactericidal activity against gram positive and gram negative bacteria. New materials combining those biopolymers with a family of N-alkyl 4-pyridinium aldoxime (4-PAM) halide-acrylate co-polymers offer both nucleophilic activity for the detoxification of organophosphorus nerve agents and internal sources of halide ions for generation of biocidal activity. Generation of free bromine and iodine was observed in the combined material resulting in bactericidal activity of the enzymatically formed free halogens that caused complete kill of E. coli (>6 log units reduction) within 1 h at 37 degrees C. Detoxification of diisopropylfluorophosphate (DFP) by the polyDMAA MA-4-PAM iodide component was dose-dependent reaching 85% within 30 min. A subset of 4-PAM-halide co-polymers was designed to serve as a controlled release reservoir for N-hydroxyethyl 4-PAM (HE 4-PAM) molecules that reactivate nerve agent-inhibited acetylcholinesterase (AChE). Release rates for HE 4-PAM were consistent with hydrolysis of the HE 4-PAM from the polymer backbone. The HE 4-PAM that was released from the polymer reactivated DFP-inhibited AChE at a similar rate to the oxime antidote 4-PAM. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

[Non-biological 3D printed simulator for training in percutaneous nephro- lithotripsy].

PubMed

Alyaev, Yu G; Sirota, E S; Bezrukov, E A; Ali, S Kh; Bukatov, M D; Letunovskiy, A V; Byadretdinov, I Sh

2018-03-01

To develop a non-biological 3D printed simulator for training and preoperative planning in percutaneous nephrolithotripsy (PCNL), which allows doctors to master and perform all stages of the operation under ultrasound and fluoroscopy guidance. The 3D model was constructed using multislice spiral computed tomography (MSCT) images of a patient with staghorn urolithiasis. The MSCT data were processed and used to print the model. The simulator consisted of two parts: a non-biological 3D printed soft model of a kidney with reproduced intra-renal vascular and collecting systems and a printed 3D model of a human body. Using this 3D printed simulator, PCNL was performed in the interventional radiology operating room under ultrasound and fluoroscopy guidance. The designed 3D printed model of the kidney completely reproduces the individual features of the intra-renal structures of the particular patient. During the training, all the main stages of PCNL were performed successfully: the puncture, dilation of the nephrostomy tract, endoscopic examination, intra-renal lithotripsy. Our proprietary 3D-printed simulator is a promising development in the field of endourologic training and preoperative planning in the treatment of complicated forms of urolithiasis.

Radiobiological aspects of high altitude flight : relative biological effectiveness of fast neutrons in suppressing immune capacity to an infective agent.

DOT National Transportation Integrated Search

1978-02-01

We investigated the relative biological effectiveness (RBE) of fast neutrons compared with X-rays in impeding development of immunity to an infective agent, the intestinal cestode Hymenolepis nana. Mice were irradiated with neutrons or X-rays and 2 d...

Sensitive and Rapid Identification of Biological Threat Agents

DTIC Science & Technology

1999-12-01

plague, and Bruceila abortis , the etiologic agent of brucellosis, indicate that the Qiagen procedures will also be effective in preparing these agents for...procedure for two bacteria, Yersinia pestis and Bruceila abortis , and found that DNA isolated with this method yielded PCR detection limits at least

Agent-Based Simulation to Support the Effectiveness, Procurement, and Employment of Non-Lethal Weapon Systems

DTIC Science & Technology

2017-06-01

cases have the most significant impact on reducing the number of lethal shots fired in the simulation. Table 10 shows the reduction in the average...Figure ES-2 was developed to show the results of the focused study on maximum effective range. After analyzing the results of the 1,700 simulated...toward other agents based on whose side they are on at that time. This attribute is critical to this study as the sidedness of the local population is

Integrating the simulation of domestic water demand behaviour to an urban water model using agent based modelling

NASA Astrophysics Data System (ADS)

Koutiva, Ifigeneia; Makropoulos, Christos

2015-04-01

The urban water system's sustainable evolution requires tools that can analyse and simulate the complete cycle including both physical and cultural environments. One of the main challenges, in this regard, is the design and development of tools that are able to simulate the society's water demand behaviour and the way policy measures affect it. The effects of these policy measures are a function of personal opinions that subsequently lead to the formation of people's attitudes. These attitudes will eventually form behaviours. This work presents the design of an ABM tool for addressing the social dimension of the urban water system. The created tool, called Urban Water Agents' Behaviour (UWAB) model, was implemented, using the NetLogo agent programming language. The main aim of the UWAB model is to capture the effects of policies and environmental pressures to water conservation behaviour of urban households. The model consists of agents representing urban households that are linked to each other creating a social network that influences the water conservation behaviour of its members. Household agents are influenced as well by policies and environmental pressures, such as drought. The UWAB model simulates behaviour resulting in the evolution of water conservation within an urban population. The final outcome of the model is the evolution of the distribution of different conservation levels (no, low, high) to the selected urban population. In addition, UWAB is implemented in combination with an existing urban water management simulation tool, the Urban Water Optioneering Tool (UWOT) in order to create a modelling platform aiming to facilitate an adaptive approach of water resources management. For the purposes of this proposed modelling platform, UWOT is used in a twofold manner: (1) to simulate domestic water demand evolution and (2) to simulate the response of the water system to the domestic water demand evolution. The main advantage of the UWAB - UWOT model

Towards a conceptual multi-agent-based framework to simulate the spatial group decision-making process

NASA Astrophysics Data System (ADS)

Ghavami, Seyed Morsal; Taleai, Mohammad

2017-04-01

Most spatial problems are multi-actor, multi-issue and multi-phase in nature. In addition to their intrinsic complexity, spatial problems usually involve groups of actors from different organizational and cognitive backgrounds, all of whom participate in a social structure to resolve or reduce the complexity of a given problem. Hence, it is important to study and evaluate what different aspects influence the spatial problem resolution process. Recently, multi-agent systems consisting of groups of separate agent entities all interacting with each other have been put forward as appropriate tools to use to study and resolve such problems. In this study, then in order to generate a better level of understanding regarding the spatial problem group decision-making process, a conceptual multi-agent-based framework is used that represents and specifies all the necessary concepts and entities needed to aid group decision making, based on a simulation of the group decision-making process as well as the relationships that exist among the different concepts involved. The study uses five main influencing entities as concepts in the simulation process: spatial influence, individual-level influence, group-level influence, negotiation influence and group performance measures. Further, it explains the relationship among different concepts in a descriptive rather than explanatory manner. To illustrate the proposed framework, the approval process for an urban land use master plan in Zanjan—a provincial capital in Iran—is simulated using MAS, the results highlighting the effectiveness of applying an MAS-based framework when wishing to study the group decision-making process used to resolve spatial problems.

Design of a multi-agent hydroeconomic model to simulate a complex human-water system: Early insights from the Jordan Water Project

NASA Astrophysics Data System (ADS)

Yoon, J.; Klassert, C. J. A.; Lachaut, T.; Selby, P. D.; Knox, S.; Gorelick, S.; Rajsekhar, D.; Tilmant, A.; Avisse, N.; Harou, J. J.; Gawel, E.; Klauer, B.; Mustafa, D.; Talozi, S.; Sigel, K.

2015-12-01

Our work focuses on development of a multi-agent, hydroeconomic model for purposes of water policy evaluation in Jordan. The model adopts a modular approach, integrating biophysical modules that simulate natural and engineered phenomena with human modules that represent behavior at multiple levels of decision making. The hydrologic modules are developed using spatially-distributed groundwater and surface water models, which are translated into compact simulators for efficient integration into the multi-agent model. For the groundwater model, we adopt a response matrix method approach in which a 3-dimensional MODFLOW model of a complex regional groundwater system is converted into a linear simulator of groundwater response by pre-processing drawdown results from several hundred numerical simulation runs. Surface water models for each major surface water basin in the country are developed in SWAT and similarly translated into simple rainfall-runoff functions for integration with the multi-agent model. The approach balances physically-based, spatially-explicit representation of hydrologic systems with the efficiency required for integration into a complex multi-agent model that is computationally amenable to robust scenario analysis. For the multi-agent model, we explicitly represent human agency at multiple levels of decision making, with agents representing riparian, management, supplier, and water user groups. The agents' decision making models incorporate both rule-based heuristics as well as economic optimization. The model is programmed in Python using Pynsim, a generalizable, open-source object-oriented code framework for modeling network-based water resource systems. The Jordan model is one of the first applications of Pynsim to a real-world water management case study. Preliminary results from a tanker market scenario run through year 2050 are presented in which several salient features of the water system are investigated: competition between urban and

Effect of host-plant genotypes on the performance of three candidate biological control agents of Schinus terebinthifolius in Florida.

USDA-ARS?s Scientific Manuscript database

Brazilian pepper is a weed in Florida, California and Hawaii that originates from South America. In Florida we have found two distinct types of Brazilian pepper plant and a hybrid between these two types. To control this weed, three biological control agents are being evaluated from Brazil. These ar...

Selection of reference genes for RT-qPCR analysis in a predatory biological control agent, Coleomegilla maculata (Coleoptera: Coccinellidae).

PubMed

Yang, Chunxiao; Pan, Huipeng; Noland, Jeffrey Edward; Zhang, Deyong; Zhang, Zhanhong; Liu, Yong; Zhou, Xuguo

2015-12-10

Reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) is a reliable technique for quantifying gene expression across various biological processes, of which requires a set of suited reference genes to normalize the expression data. Coleomegilla maculata (Coleoptera: Coccinellidae), is one of the most extensively used biological control agents in the field to manage arthropod pest species. In this study, expression profiles of 16 housekeeping genes selected from C. maculata were cloned and investigated. The performance of these candidates as endogenous controls under specific experimental conditions was evaluated by dedicated algorithms, including geNorm, Normfinder, BestKeeper, and ΔCt method. In addition, RefFinder, a comprehensive platform integrating all the above-mentioned algorithms, ranked the overall stability of these candidate genes. As a result, various sets of suitable reference genes were recommended specifically for experiments involving different tissues, developmental stages, sex, and C. maculate larvae treated with dietary double stranded RNA. This study represents the critical first step to establish a standardized RT-qPCR protocol for the functional genomics research in a ladybeetle C. maculate. Furthermore, it lays the foundation for conducting ecological risk assessment of RNAi-based gene silencing biotechnologies on non-target organisms; in this case, a key predatory biological control agent.

REPORT ON THE HOMELAND SECURITY WORKSHOP ON TRANSPORT AND DISPOSAL OF WASTES FROM FACILITIES CONTAMINATED WITH CHEMICAL AND BIOLOGICAL AGENTS

EPA Science Inventory

This report summarizes discussions from the "Homeland Security Workshop on Transport and Disposal of Wastes From Facilities Contaminated With Chemical or Biological Agents." The workshop was held on May 28-30, 2003, in Cincinnati, Ohio, and its objectives were to:

.Documen...

Rogue taxa phenomenon: a biological companion to simulation analysis.

PubMed

Westover, Kristi M; Rusinko, Joseph P; Hoin, Jon; Neal, Matthew

2013-10-01

To provide a baseline biological comparison to simulation study predictions about the frequency of rogue taxa effects, we evaluated the frequency of a rogue taxa effect using viral data sets which differed in diversity. Using a quartet-tree framework, we measured the frequency of a rogue taxa effect in three data sets of increasing genetic variability (within viral serotype, between viral serotype, and between viral family) to test whether the rogue taxa was correlated with the mean sequence diversity of the respective data sets. We found a slight increase in the percentage of rogues as nucleotide diversity increased. Even though the number of rogues increased with diversity, the distribution of the types of rogues (friendly, crazy, or evil) did not depend on the diversity and in the case of the order-level data set the net rogue effect was slightly positive. This study, assessing frequency of the rogue taxa effect using biological data, indicated that simulation studies may over-predict the prevalence of the rogue taxa effect. Further investigations are necessary to understand which types of data sets are susceptible to a negative rogue effect and thus merit the removal of taxa from large phylogenetic reconstructions. Copyright © 2013 Elsevier Inc. All rights reserved.

An agent-based simulation combined with group decision-making technique for improving the performance of an emergency department.

PubMed

Yousefi, M; Ferreira, R P M

2017-03-30

This study presents an agent-based simulation modeling in an emergency department. In a traditional approach, a supervisor (or a manager) allocates the resources (receptionist, nurses, doctors, etc.) to different sections based on personal experience or by using decision-support tools. In this study, each staff agent took part in the process of allocating resources based on their observation in their respective sections, which gave the system the advantage of utilizing all the available human resources during the workday by being allocated to a different section. In this simulation, unlike previous studies, all staff agents took part in the decision-making process to re-allocate the resources in the emergency department. The simulation modeled the behavior of patients, receptionists, triage nurses, emergency room nurses and doctors. Patients were able to decide whether to stay in the system or leave the department at any stage of treatment. In order to evaluate the performance of this approach, 6 different scenarios were introduced. In each scenario, various key performance indicators were investigated before and after applying the group decision-making. The outputs of each simulation were number of deaths, number of patients who leave the emergency department without being attended, length of stay, waiting time and total number of discharged patients from the emergency department. Applying the self-organizing approach in the simulation showed an average of 12.7 and 14.4% decrease in total waiting time and number of patients who left without being seen, respectively. The results showed an average increase of 11.5% in total number of discharged patients from emergency department.

Stability of subsystem solutions in agent-based models

NASA Astrophysics Data System (ADS)

Perc, Matjaž

2018-01-01

The fact that relatively simple entities, such as particles or neurons, or even ants or bees or humans, give rise to fascinatingly complex behaviour when interacting in large numbers is the hallmark of complex systems science. Agent-based models are frequently employed for modelling and obtaining a predictive understanding of complex systems. Since the sheer number of equations that describe the behaviour of an entire agent-based model often makes it impossible to solve such models exactly, Monte Carlo simulation methods must be used for the analysis. However, unlike pairwise interactions among particles that typically govern solid-state physics systems, interactions among agents that describe systems in biology, sociology or the humanities often involve group interactions, and they also involve a larger number of possible states even for the most simplified description of reality. This begets the question: when can we be certain that an observed simulation outcome of an agent-based model is actually stable and valid in the large system-size limit? The latter is key for the correct determination of phase transitions between different stable solutions, and for the understanding of the underlying microscopic processes that led to these phase transitions. We show that a satisfactory answer can only be obtained by means of a complete stability analysis of subsystem solutions. A subsystem solution can be formed by any subset of all possible agent states. The winner between two subsystem solutions can be determined by the average moving direction of the invasion front that separates them, yet it is crucial that the competing subsystem solutions are characterised by a proper composition and spatiotemporal structure before the competition starts. We use the spatial public goods game with diverse tolerance as an example, but the approach has relevance for a wide variety of agent-based models.

A framework for stochastic simulations and visualization of biological electron-transfer dynamics

NASA Astrophysics Data System (ADS)

Nakano, C. Masato; Byun, Hye Suk; Ma, Heng; Wei, Tao; El-Naggar, Mohamed Y.

2015-08-01

Electron transfer (ET) dictates a wide variety of energy-conversion processes in biological systems. Visualizing ET dynamics could provide key insight into understanding and possibly controlling these processes. We present a computational framework named VizBET to visualize biological ET dynamics, using an outer-membrane Mtr-Omc cytochrome complex in Shewanella oneidensis MR-1 as an example. Starting from X-ray crystal structures of the constituent cytochromes, molecular dynamics simulations are combined with homology modeling, protein docking, and binding free energy computations to sample the configuration of the complex as well as the change of the free energy associated with ET. This information, along with quantum-mechanical calculations of the electronic coupling, provides inputs to kinetic Monte Carlo (KMC) simulations of ET dynamics in a network of heme groups within the complex. Visualization of the KMC simulation results has been implemented as a plugin to the Visual Molecular Dynamics (VMD) software. VizBET has been used to reveal the nature of ET dynamics associated with novel nonequilibrium phase transitions in a candidate configuration of the Mtr-Omc complex due to electron-electron interactions.

Antimicrobial Peptides As Biologic and Immunotherapeutic Agents against Cancer: A Comprehensive Overview.

PubMed

Roudi, Raheleh; Syn, Nicholas L; Roudbary, Maryam

2017-01-01

Antimicrobial peptides (AMPs) are a pervasive and evolutionarily ancient component of innate host defense which is present in virtually all classes of life. In recent years, evidence has accumulated that parallel or de novo mechanisms by which AMPs curb infectious pathologies are also effective at restraining cancer cell proliferation and dissemination, and have consequently stimulated significant interest in their deployment as novel biologic and immunotherapeutic agents against human malignancies. In this review, we explicate the biochemical underpinnings of their tumor-selectivity, and discuss results of recent clinical trials (outside of oncologic indications) which substantiate their safety and tolerability profiles. Next, we present evidence for their preclinical antitumor activity, systematically organized by the major and minor classes of natural AMPs. Finally, we discuss the barriers to their clinical implementation and envision directions for further development.

Effects of chemical and biological warfare remediation agents on the materials of museum objects

NASA Astrophysics Data System (ADS)

Solazzo, C.; Erhardt, D.; Marte, F.; von Endt, D.; Tumosa, C.

In the fall of 2001, anthrax-contaminated letters were sent to public figures in the United States. Chemical and radiation treatments were employed to decontaminate exposed buildings, objects, and materials. These treatments are effective, but potentially damaging to exposed objects and materials. The recommended surface chemical treatments include solutions, gels, and foams of oxidizing agents such as peroxides or chlorine bleaching agents. Such oxidizing agents are effective against a wide range of hazardous chemical and biological agents. Knowing how these reagents affect various substrates would help to anticipate and to minimize any potential damage. We are examining the effects on typical museum materials of reagents likely to be used, including hydrogen peroxide, sodium hypochlorite, and potassium peroxymonosulfate. Results so far show significant changes in a number of materials. Surface corrosion was observed on metals such as copper, silver, iron, and brass. Color changes occurred with at least one reagent in about one-fourth of the dyed fabric swatches tested, and about half of the inks. Samples of aged yellowed paper are bleached. Effects varied with both the substrate and the tested reagent. The observed changes were generally less drastic than might have been expected. Enough materials were affected, though, to preclude the use of these reagents on museum objects unless no less drastic alternative is available. It appears that many objects of lesser intrinsic value can be treated without severe loss of properties or usefulness. For example, most documents should remain legible if the appropriate reagent is used. This work will provide a basis for determining which treatment is most appropriate for a specific situation and what consequences are to be expected from other treatments.

Pre-release assessment of Gadirtha inexacta a proposed biological control agent of Chinese tallow (Triadica sebifera) in the United States

USDA-ARS?s Scientific Manuscript database

Native to China, Chinese tallow, Triadica sebifera (Euphorbiaceae) is an aggressive woody invader in the southeastern United States. The noctuid, Gadirtha inexacta, is a multivoltine herbivore attacking this plant in China. To evaluate its potential as a biological control agent in the United States...

In Situ Probes of Capture and Decomposition of Chemical Warfare Agent Simulants by Zr-Based Metal Organic Frameworks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Plonka, Anna M.; Wang, Qi; Gordon, Wesley O.

Recently, Zr-based metal organic frameworks (MOFs) were shown to be among the fastest catalysts of nerve-agent hydrolysis in solution. Here, we report a detailed study of the adsorption and decomposition of a nerve-agent simulant, dimethyl methylphosphonate (DMMP), on UiO-66, UiO-67, MOF-808, and NU-1000 using synchrotron-based X-ray powder diffraction, X-ray absorption, and infrared spectroscopy, which reveals key aspects of the reaction mechanism. The diffraction measurements indicate that all four MOFs adsorb DMMP (introduced at atmospheric pressures through a flow of helium or air) within the pore space. In addition, the combination of X-ray absorption and infrared spectra suggests direct coordination ofmore » DMMP to the Zr6 cores of all MOFs, which ultimately leads to decomposition to phosphonate products. Our experimental probes into the mechanism of adsorption and decomposition of chemical warfare agent simulants on Zr-based MOFs open new opportunities in rational design of new and superior decontamination materials.« less

In Situ Probes of Capture and Decomposition of Chemical Warfare Agent Simulants by Zr-Based Metal Organic Frameworks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Plonka, Anna M.; Wang, Qi; Gordon, Wesley O.

Zr-based metal organic frameworks (MOFs) have been recently shown to be among the fastest catalysts of nerve-agent hydrolysis in solution. We report a detailed study of the adsorption and decomposition of a nerve-agent simulant, dimethyl methylphosphonate (DMMP), on UiO-66, UiO-67, MOF-808, and NU-1000 using synchrotron-based X-ray powder diffraction, X-ray absorption, and infrared spectroscopy, which reveals key aspects of the reaction mechanism. The diffraction measurements indicate that all four MOFs adsorb DMMP (introduced at atmospheric pressures through a flow of helium or air) within the pore space. In addition, the combination of X-ray absorption and infrared spectra suggests direct coordination ofmore » DMMP to the Zr6 cores of all MOFs, which ultimately leads to decomposition to phosphonate products. These experimental probes into the mechanism of adsorption and decomposition of chemical warfare agent simulants on Zr-based MOFs open new opportunities in rational design of new and superior decontamination materials.« less

In Situ Probes of Capture and Decomposition of Chemical Warfare Agent Simulants by Zr-Based Metal Organic Frameworks

DOE PAGES

Plonka, Anna M.; Wang, Qi; Gordon, Wesley O.; ...

2016-12-30

Recently, Zr-based metal organic frameworks (MOFs) were shown to be among the fastest catalysts of nerve-agent hydrolysis in solution. Here, we report a detailed study of the adsorption and decomposition of a nerve-agent simulant, dimethyl methylphosphonate (DMMP), on UiO-66, UiO-67, MOF-808, and NU-1000 using synchrotron-based X-ray powder diffraction, X-ray absorption, and infrared spectroscopy, which reveals key aspects of the reaction mechanism. The diffraction measurements indicate that all four MOFs adsorb DMMP (introduced at atmospheric pressures through a flow of helium or air) within the pore space. In addition, the combination of X-ray absorption and infrared spectra suggests direct coordination ofmore » DMMP to the Zr6 cores of all MOFs, which ultimately leads to decomposition to phosphonate products. Our experimental probes into the mechanism of adsorption and decomposition of chemical warfare agent simulants on Zr-based MOFs open new opportunities in rational design of new and superior decontamination materials.« less

Simulating the elimination of sleeping sickness with an agent-based model.

PubMed

Grébaut, Pascal; Girardin, Killian; Fédérico, Valentine; Bousquet, François

2016-01-01

Although Human African Trypanosomiasis is largely considered to be in the process of extinction today, the persistence of human and animal reservoirs, as well as the vector, necessitates a laborious elimination process. In this context, modeling could be an effective tool to evaluate the ability of different public health interventions to control the disease. Using the Cormas ® system, we developed HATSim, an agent-based model capable of simulating the possible endemic evolutions of sleeping sickness and the ability of National Control Programs to eliminate the disease. This model takes into account the analysis of epidemiological, entomological, and ecological data from field studies conducted during the last decade, making it possible to predict the evolution of the disease within this area over a 5-year span. In this article, we first present HATSim according to the Overview, Design concepts, and Details (ODD) protocol that is classically used to describe agent-based models, then, in a second part, we present predictive results concerning the evolution of Human African Trypanosomiasis in the village of Lambi (Cameroon), in order to illustrate the interest of such a tool. Our results are consistent with what was observed in the field by the Cameroonian National Control Program (CNCP). Our simulations also revealed that regular screening can be sufficient, although vector control applied to all areas with human activities could be significantly more efficient. Our results indicate that the current model can already help decision-makers in planning the elimination of the disease in foci. © P. Grébaut et al., published by EDP Sciences, 2016.

Portable Sensor for Chemical Nerve Agents and Organophosphorus Compounds

DTIC Science & Technology

2015-08-18

as pesticides in crop, livestock, and poultry products and as chemical and biological warfare agents. As a result of the high toxicity and the...agents have been exploited for use as pesticides in crop, livestock, and poultry products and as chemical and biological warfare agents. As a result of

[Biological and toxin terrorism weapons].

PubMed

Bokan, Slavko

2003-03-01

The use of biological agents and toxins in warfare and terrorism has a long history. Human, animal and plant pathogens and toxins can cause disease and can be used as a threat to humans, animals and staple crops. The same is true for biological agents. Although the use of biological agents and toxins in military conflicts has been a concern of military communities for many years, several recent events have increased the awareness of terrorist use of these weapons against civilian population. A Mass Casualty Biological (Toxin) Weapon (MCBTW) is any biological and toxin weapon capable of causing death or disease on a large scale, such that the military or civilian infrastructure of the state or organization being attacked is overwhelmed. A militarily significant (or terrorist) weapon is any weapon capable of affecting, directly or indirectly, that is physically or psychologically, the outcome of a military operation. Although many biological agents such as toxins and bioregulators can be used to cause diseases, there are only a few that can truly threaten civilian populations on a large scale. Bioregulators or modulators are biochemical compounds, such as peptides, that occur naturally in organisms. They are new class of weapons that can damage nervous system, alter moods, trigger psychological changes and kill. The potential military or terrorist use of bioregulators is similar to that of toxins. Some of these compounds are several hundred times more potent than traditional chemical warfare agents. Important features and military advantages of new bioregulators are novel sites of toxic action; rapid and specific effects; penetration of protective filters and equipment, and militarily effective physical incapacitation. This overview of biological agents and toxins is largely intended to help healthcare providers on all levels to make decisions in protecting general population from these agents.

Combining SBR systems for chemical and biological treatment: the destruction of the nerve agent VX.

PubMed

Irvine, R L; Haraburda, S S; Galbis-Reig, C

2004-01-01

The US Army is pilot testing the neutralization of VX nerve agent stockpiled at Newport, Indiana using caustic hydrolysis in a Sequencing Batch Reactor (SBR). The resulting hydrolysate was tested at the bench-scale for treatment with activated sludge biodegradation in two distinct studies, one in the SBR and another, in the PACT process. The feed to both biological systems was pretreated to enhance the biodegradability of the hydrolysis products. Both biodegradation studies demonstrated that the hydrolysate could easily meet the Chemical Weapons Convention treaty and US environmental regulations following pretreatment.

Gold nanorods as contrast agents for biological imaging: optical properties, surface conjugation, and photothermal effects†

PubMed Central

Tong, Ling; Wei, Qingshan; Wei, Alexander; Cheng, Ji-Xin

2009-01-01

Gold nanorods (NRs) have plasmon-resonant absorption and scattering in the near-infrared (NIR) region, making them attractive probes for in vitro and in vivo imaging. In the cellular environment, NRs can provide scattering contrast for darkfield microscopy, or emit a strong two-photon luminescence (TPL) due to plasmon-enhanced two-photon absorption. NRs have also been employed in biomedical imaging modalities such as optical coherence tomography (OCT) or photoacoustic tomography (PAT). Careful control over surface chemistry enhances the capacity of NRs as biological imaging agents by enabling cell-specific targeting, and by increasing their dispersion stability and circulation lifetimes. NRs can also efficiently convert optical energy into heat, and inflict localized damage to tumor cells. Laser-induced heating of NRs can disrupt cell membrane integrity and homeostasis, resulting in Ca2+ influx and the depolymerization of the intracellular actin network. The combination of plasmon-resonant optical properties, intense local photothermal effects, and robust surface chemistry render gold NRs as promising theragnostic agents. PMID:19161395

Need for new technologies for detection of adventitious agents in vaccines and other biological products.

PubMed

Mallet, Laurent; Gisonni-Lex, Lucy

2014-01-01

From an industrial perspective, the conventional in vitro and in vivo assays used for detection of viral contaminants have shown their limitations, as illustrated by the unfortunate detection of porcine circovirus contamination in a licensed rotavirus vaccine. This contamination event illustrates the gaps within the existing adventitious agent strategy and the potential use of new broader molecular detection methods. This paper serves to summarize current testing approaches and challenges, along with opportunities for the use of these new technologies. Testing of biological products is required to ensure the safety of patients. Recently, a licensed vaccine was found to be contaminated with a virus. This contamination did not cause a safety concern to the patients; however, it highlights the need for using new testing methods to control our biological products. This paper introduces the benefits of these new tests and outlines the challenges with the current tests. © PDA, Inc. 2014.

Meta-analysis of studies on chemical, physical and biological agents in the control of Aedes aegypti.

PubMed

Lima, Estelita Pereira; Goulart, Marília Oliveira Fonseca; Rolim Neto, Modesto Leite

2015-09-04

Aedes aegypti is a vector of international concern because it can transmit to humans three important arboviral diseases: yellow fever, dengue and chikungunya. Epidemics that are repeated year after year in a variety of urban centers indicate that there are control failures, allowing the vector to continue expanding. To identify the most effective vector control strategies and the factors that contributed to the success or failure of each strategy, we carried out a systematic review with meta-analysis of articles published in 12 databases, from 1974 to the month of December 2013. We evaluated the association between the use of whatever chemical substance, mechanical agent, biological or integrated actions against A. aegypti and the control of the vector, as measured by 10 indicators. We found 2,791 articles, but after careful selection, only 26 studies remained for analysis related to control interventions implemented in 15 countries, with 5 biological, 5 chemical, 3 mechanical and 13 integrated strategies. The comparison among all of them, indicated that the control of A. aegypti is significantly associated with the type of strategy used, and that integrated interventions consist of the most effective method for controlling A. aegypti. The most effective control method was the integrated approach, considering the influence of eco-bio-social determinants in the virus-vector-man epidemiological chain, and community involvement, starting with community empowerment as active agents of vector control.

Issues in chemical and biological terrorism.

PubMed

Salem, Harry

2003-01-01

This manuscript describes the overview presented at the 23rd Annual Meeting of the American College of Toxicology in 2002. Although it is recognized that weapons of mass destruction that can be used against our military and civilian populations include chemical, biological, radiological, and nuclear (CBRN) agents, this overview is limited primarily to chemical and biological (CB) agents. The issues of CB terrorism are discussed in terms of When, What, How, and Who. The US Army has been providing chemical and biological solutions since 1917, and has since 1996 applied these solutions to homeland defense and domestic preparedness. The use of chemical and biological agents as terrorist weapons both in the United States and elsewhere in the world is reviewed. The CB threat spectrum is presented, as is the further categorization of biological threat agents by the Centers for Disease Control and Prevention (CDC). In addition, the CB agents considered to be a potential threat to our water supply are also presented. These are agents that are water soluble, stable, and resistant to water treatment and/or disinfection. The overview concludes with the chronological accomplishments of ECBC since 1917.

Cold tolerance of Trissolcus japonicus and T. cultratus, potential biological control agents of Halyomorpha halys, the brown marmorated stink bug

Treesearch

Erica Nystrom Santacruz; Robert C. Venette; Christine Dieckhoff; Kim Hoelmer; Robert L. Koch

2017-01-01

Halyomorpha halys (Stål) (Hemiptera: Pentatomidae) is native to Asia and has become a severe agricultural and nuisance pest in the U.S. Therefore, foreign exploration was conducted in Asia to identify potential classical biological control agents. Several Trissolcus spp. (Hymenoptera: Scelionidae) parasitize H. halys...

Enhancement of Population Size of a Biological Control Agent and Efficacy in Control of Bacterial Speck of Tomato through Salicylate and Ammonium Sulfate Amendments

PubMed Central

Ji, Pingsheng; Wilson, Mark

2003-01-01

Sodium salicylate and ammonium sulfate were applied to leaf surfaces along with suspensions of the biological control agents Pseudomonas syringae Cit7(pNAH7), which catabolizes salicylate, and Cit7, which does not catabolize salicylate, to determine whether enhanced biological control of bacterial speck of tomato could be achieved. Foliar amendment with salicylate alone significantly enhanced the population size and the efficacy of Cit7(pNAH7), but not of Cit7, on tomato leaves. Application of ammonium sulfate alone did not result in enhanced population size or biological control efficacy of either Cit7(pNAH7) or Cit7; however, when foliar amendments with both sodium salicylate and ammonium sulfate were applied, a trend toward further increases in population size and biological control efficacy of Cit7(pNAH7) was observed. This study demonstrates the potential of using a selective carbon source to improve the efficacy of a bacterial biological control agent in the control of a bacterial plant disease and supports previous conclusions that the growth of P. syringae in the phyllosphere is primarily carbon limited and secondarily nitrogen limited. PMID:12571060

Bioforensics: Characterization of biological weapons agents by NanoSIMS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weber, P K; Ghosal, S; Leighton, T J

2007-02-26

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 developedmore » 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.« less

Using an agent-based model to simulate children's active travel to school.

PubMed

Yang, Yong; Diez-Roux, Ana V

2013-05-26

Despite the multiple advantages of active travel to school, only a small percentage of US children and adolescents walk or bicycle to school. Intervention studies are in a relatively early stage and evidence of their effectiveness over long periods is limited. The purpose of this study was to illustrate the utility of agent-based models in exploring how various policies may influence children's active travel to school. An agent-based model was developed to simulate children's school travel behavior within a hypothetical city. The model was used to explore the plausible implications of policies targeting two established barriers to active school travel: long distance to school and traffic safety. The percent of children who walk to school was compared for various scenarios. To maximize the percent of children who walk to school the school locations should be evenly distributed over space and children should be assigned to the closest school. In the case of interventions to improve traffic safety, targeting a smaller area around the school with greater intensity may be more effective than targeting a larger area with less intensity. Despite the challenges they present, agent based models are a useful complement to other analytical strategies in studying the plausible impact of various policies on active travel to school.

Can we forecast the effects of climate change on entomophagous biological control agents?

PubMed

Aguilar-Fenollosa, Ernestina; Jacas, Josep A

2014-06-01

The worldwide climate has been changing rapidly over the past decades. Air temperatures have been increasing in most regions and will probably continue to rise for most of the present century, regardless of any mitigation policy put in place. Although increased herbivory from enhanced biomass production and changes in plant quality are generally accepted as a consequence of global warming, the eventual status of any pest species will mostly depend on the relative effects of climate change on its own versus its natural enemies' complex. Because a bottom-up amplification effect often occurs in trophic webs subjected to any kind of disturbance, natural enemies are expected to suffer the effects of climate change to a greater extent than their phytophagous hosts/preys. A deeper understanding of the genotypic diversity of the populations of natural enemies and their target pests will allow an informed reaction to climate change. New strategies for the selection of exotic natural enemies and their release and establishment will have to be adopted. Conservation biological control will probably become the keystone for the successful management of these biological control agents. © 2013 Society of Chemical Industry.

A versatile petri net based architecture for modeling and simulation of complex biological processes.

PubMed

Nagasaki, Masao; Doi, Atsushi; Matsuno, Hiroshi; Miyano, Satoru

2004-01-01

The research on modeling and simulation of complex biological systems is getting more important in Systems Biology. In this respect, we have developed Hybrid Function Petri net (HFPN) that was newly developed from existing Petri net because of their intuitive graphical representation and their capabilities for mathematical analyses. However, in the process of modeling metabolic, gene regulatory or signal transduction pathways with the architecture, we have realized three extensions of HFPN, (i) an entity should be extended to contain more than one value, (ii) an entity should be extended to handle other primitive types, e.g. boolean, string, (iii) an entity should be extended to handle more advanced type called object that consists of variables and methods, are necessary for modeling biological systems with Petri net based architecture. To deal with it, we define a new enhanced Petri net called hybrid functional Petri net with extension (HFPNe). To demonstrate the effectiveness of the enhancements, we model and simulate with HFPNe four biological processes that are diffcult to represent with the previous architecture HFPN.

An agent-based simulation combined with group decision-making technique for improving the performance of an emergency department

PubMed Central

Yousefi, M.; Ferreira, R.P.M.

2017-01-01

This study presents an agent-based simulation modeling in an emergency department. In a traditional approach, a supervisor (or a manager) allocates the resources (receptionist, nurses, doctors, etc.) to different sections based on personal experience or by using decision-support tools. In this study, each staff agent took part in the process of allocating resources based on their observation in their respective sections, which gave the system the advantage of utilizing all the available human resources during the workday by being allocated to a different section. In this simulation, unlike previous studies, all staff agents took part in the decision-making process to re-allocate the resources in the emergency department. The simulation modeled the behavior of patients, receptionists, triage nurses, emergency room nurses and doctors. Patients were able to decide whether to stay in the system or leave the department at any stage of treatment. In order to evaluate the performance of this approach, 6 different scenarios were introduced. In each scenario, various key performance indicators were investigated before and after applying the group decision-making. The outputs of each simulation were number of deaths, number of patients who leave the emergency department without being attended, length of stay, waiting time and total number of discharged patients from the emergency department. Applying the self-organizing approach in the simulation showed an average of 12.7 and 14.4% decrease in total waiting time and number of patients who left without being seen, respectively. The results showed an average increase of 11.5% in total number of discharged patients from emergency department. PMID:28380196

On-lattice agent-based simulation of populations of cells within the open-source Chaste framework.

PubMed

Figueredo, Grazziela P; Joshi, Tanvi V; Osborne, James M; Byrne, Helen M; Owen, Markus R

2013-04-06

Over the years, agent-based models have been developed that combine cell division and reinforced random walks of cells on a regular lattice, reaction-diffusion equations for nutrients and growth factors; and ordinary differential equations for the subcellular networks regulating the cell cycle. When linked to a vascular layer, this multiple scale model framework has been applied to tumour growth and therapy. Here, we report on the creation of an agent-based multi-scale environment amalgamating the characteristics of these models within a Virtual Physiological Human (VPH) Exemplar Project. This project enables reuse, integration, expansion and sharing of the model and relevant data. The agent-based and reaction-diffusion parts of the multi-scale model have been implemented and are available for download as part of the latest public release of Chaste (Cancer, Heart and Soft Tissue Environment; http://www.cs.ox.ac.uk/chaste/), part of the VPH Toolkit (http://toolkit.vph-noe.eu/). The environment functionalities are verified against the original models, in addition to extra validation of all aspects of the code. In this work, we present the details of the implementation of the agent-based environment, including the system description, the conceptual model, the development of the simulation model and the processes of verification and validation of the simulation results. We explore the potential use of the environment by presenting exemplar applications of the 'what if' scenarios that can easily be studied in the environment. These examples relate to tumour growth, cellular competition for resources and tumour responses to hypoxia (low oxygen levels). We conclude our work by summarizing the future steps for the expansion of the current system.

A Virtual Look at Epstein–Barr Virus Infection: Biological Interpretations

PubMed Central

Delgado-Eckert, Edgar; Hadinoto, Vey; Jarrah, Abdul S; Laubenbacher, Reinhard; Lee, Kichol; Luzuriaga, Katherine; Polys, Nicholas F; Thorley-Lawson, David A

2007-01-01

The possibility of using computer simulation and mathematical modeling to gain insight into biological and other complex systems is receiving increased attention. However, it is as yet unclear to what extent these techniques will provide useful biological insights or even what the best approach is. Epstein–Barr virus (EBV) provides a good candidate to address these issues. It persistently infects most humans and is associated with several important diseases. In addition, a detailed biological model has been developed that provides an intricate understanding of EBV infection in the naturally infected human host and accounts for most of the virus' diverse and peculiar properties. We have developed an agent-based computer model/simulation (PathSim, Pathogen Simulation) of this biological model. The simulation is performed on a virtual grid that represents the anatomy of the tonsils of the nasopharyngeal cavity (Waldeyer ring) and the peripheral circulation—the sites of EBV infection and persistence. The simulation is presented via a user friendly visual interface and reproduces quantitative and qualitative aspects of acute and persistent EBV infection. The simulation also had predictive power in validation experiments involving certain aspects of viral infection dynamics. Moreover, it allows us to identify switch points in the infection process that direct the disease course towards the end points of persistence, clearance, or death. Lastly, we were able to identify parameter sets that reproduced aspects of EBV-associated diseases. These investigations indicate that such simulations, combined with laboratory and clinical studies and animal models, will provide a powerful approach to investigating and controlling EBV infection, including the design of targeted anti-viral therapies. PMID:17953479

Simulating the conversion of rural settlements to town land based on multi-agent systems and cellular automata.

PubMed

Liu, Yaolin; Kong, Xuesong; Liu, Yanfang; Chen, Yiyun

2013-01-01

Rapid urbanization in China has triggered the conversion of land from rural to urban use, particularly the conversion of rural settlements to town land. This conversion is the result of the joint effects of the geographic environment and agents involving the government, investors, and farmers. To understand the dynamic interaction dominated by agents and to predict the future landscape of town expansion, a small town land-planning model is proposed based on the integration of multi-agent systems (MAS) and cellular automata (CA). The MAS-CA model links the decision-making behaviors of agents with the neighbor effect of CA. The interaction rules are projected by analyzing the preference conflicts among agents. To better illustrate the effects of the geographic environment, neighborhood, and agent behavior, a comparative analysis between the CA and MAS-CA models in three different towns is presented, revealing interesting patterns in terms of quantity, spatial characteristics, and the coordinating process. The simulation of rural settlements conversion to town land through modeling agent decision and human-environment interaction is very useful for understanding the mechanisms of rural-urban land-use change in developing countries. This process can assist town planners in formulating appropriate development plans.