A Virtual Research Environment for a Secondary Ion Mass Spectrometer (SIMS)

NASA Astrophysics Data System (ADS)

Wiedenbeck, M.; Schäfer, L.; Klump, J.; Galkin, A.

2013-12-01

Overview: This poster describes the development of a Virtual Research Environment for the Secondary Ion Mass Spectrometer (SIMS) at GFZ Potsdam. Background: Secondary Ion Mass Spectrometers (SIMS) are extremely sensitive instruments for analyzing the surfaces of solid and thin film samples. These instruments are rare, expensive and experienced operators are very highly sought after. As such, measurement time is a precious commodity, until now only accessible to small numbers of researchers. The challenge: The Virtual SIMS Project aims to set up a Virtual Research Environment for the operation of the CAMECA IMS 1280-HR instrument at the GFZ Potsdam. The objective of the VRE is to provide SIMS access not only to researchers locally present in Potsdam but also to scientists working with SIMS cooperation partners in e.g., South Africa, Brazil or India. The requirements: The system should address the complete spectrum of laboratory procedures - from online application for measurement time, to remote access for data acquisition to data archiving for the subsequent publication and for future reuse. The approach: The targeted Virtual SIMS Environment will consist of a: 1. Web Server running the Virtual SIMS website providing general information about the project, lab access proposal forms and calendar for the timing of project related tasks. 2. LIMS Server, responsible for scheduling procedures, data management and, if applicable, accounting and billing. 3. Remote SIMS Tool, devoted to the operation of the experiment within a remote control environment. 4. Publishing System, which supports the publication of results in cooperation with the GFZ Library services. 5. Training Simulator, which offers the opportunity to rehearse experiments and to prepare for possible events such as a power outages or interruptions to broadband services. First results: The SIMS Virtual Research Environment will be mainly based on open source software, the only exception being the CAMECA IMS 1280-HR SIMS operating under LabView. The Publishing System will be based on eSciDoc, which is already successfully used by the GFZ scientific library. For the LIMS Server we are currently testing various options. The challenge, however, is the successful integration of all the various components and, where necessary, the definition of useful interfaces between the modules.

SIMS Studies of Allende Projectiles Fired into Stardust-type Aluminum Foils at 6 km/s

NASA Technical Reports Server (NTRS)

Hoppe, Peter; Stadermann, Frank J.; Stephan, Thomas; Floss, Christine; Leitner, Jan; Marhas, Kuljeet; Horz, Friedrich

2006-01-01

We have explored the feasibility of C-, N-, and O-isotopic measurements by NanoSIMS and of elemental abundance determinations by TOF-SIMS on residues of Allende projectiles that impacted Stardust-type aluminum foils in the laboratory at 6 km/s. These investigations are part of a consortium study aimed at providing the foundation for the characterization of matter associated with micro-craters that were produced during the encounter of the Stardust space probe with comet 81P/Wild 2. Eleven experimental impact craters were studied by NanoSIMS and eighteen by TOF-SIMS. Crater sizes were between 3 and 190 microns. The NanoSIMS measurements have shown that the crater morphology has only a minor effect on spatial resolution and on instrumental mass fractionation. The achievable spatial resolution is always better than 200 nm, and C- and O-isotopic ratios can be measured with a precision of several percent at a scale of several 100 nm, the typical size of presolar grains. This clearly demonstrates that presolar matter, provided it survives the impact into the aluminum foil partly intact, is recognizable even if embedded in material of Solar System origin. TOF-SIMS studies are restricted to materials from the crater rim. The element ratios of the major rockforming elements in the Allende projectiles are well characterized by the TOF-SIMS measurements, indicating that fractionation of those elements during impact can be expected to be negligible. This permits information on the type of impactor material to be obtained. For any more detailed assignments to specific chondrite groups, however, information on the abundances of the light elements, especially C, is crucial.

Combination of structured illumination and single molecule localization microscopy in one setup

NASA Astrophysics Data System (ADS)

Rossberger, Sabrina; Best, Gerrit; Baddeley, David; Heintzmann, Rainer; Birk, Udo; Dithmar, Stefan; Cremer, Christoph

2013-09-01

Understanding the positional and structural aspects of biological nanostructures simultaneously is as much a challenge as a desideratum. In recent years, highly accurate (20 nm) positional information of optically isolated targets down to the nanometer range has been obtained using single molecule localization microscopy (SMLM), while highly resolved (100 nm) spatial information has been achieved using structured illumination microscopy (SIM). In this paper, we present a high-resolution fluorescence microscope setup which combines the advantages of SMLM with SIM in order to provide high-precision localization and structural information in a single setup. Furthermore, the combination of the wide-field SIM image with the SMLM data allows us to identify artifacts produced during the visualization process of SMLM data, and potentially also during the reconstruction process of SIM images. We describe the SMLM-SIM combo and software, and apply the instrument in a first proof-of-principle to the same region of H3K293 cells to achieve SIM images with high structural resolution (in the 100 nm range) in overlay with the highly accurate position information of localized single fluorophores. Thus, with its robust control software, efficient switching between the SMLM and SIM mode, fully automated and user-friendly acquisition and evaluation software, the SMLM-SIM combo is superior over existing solutions.

MODELING MULTI-WAVELENGTH STELLAR ASTROMETRY. I. SIM LITE OBSERVATIONS OF INTERACTING BINARIES

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

Coughlin, Jeffrey L.; Harrison, Thomas E.; Gelino, Dawn M.

Interacting binaries (IBs) consist of a secondary star that fills or is very close to filling its Roche lobe, resulting in accretion onto the primary star, which is often, but not always, a compact object. In many cases, the primary star, secondary star, and the accretion disk can all be significant sources of luminosity. SIM Lite will only measure the photocenter of an astrometric target, and thus determining the true astrometric orbits of such systems will be difficult. We have modified the Eclipsing Light Curve code to allow us to model the flux-weighted reflex motions of IBs, in a codemore » we call REFLUX. This code gives us sufficient flexibility to investigate nearly every configuration of IB. We find that SIM Lite will be able to determine astrometric orbits for all sufficiently bright IBs where the primary or secondary star dominates the luminosity. For systems where there are multiple components that comprise the spectrum in the optical bandpass accessible to SIM Lite, we find it is possible to obtain absolute masses for both components, although multi-wavelength photometry will be required to disentangle the multiple components. In all cases, SIM Lite will at least yield accurate inclinations and provide valuable information that will allow us to begin to understand the complex evolution of mass-transferring binaries. It is critical that SIM Lite maintains a multi-wavelength capability to allow for the proper deconvolution of the astrometric orbits in multi-component systems.« less

IntNetLncSim: an integrative network analysis method to infer human lncRNA functional similarity

PubMed Central

Hu, Yang; Yang, Haixiu; Zhou, Chen; Sun, Jie; Zhou, Meng

2016-01-01

Increasing evidence indicated that long non-coding RNAs (lncRNAs) were involved in various biological processes and complex diseases by communicating with mRNAs/miRNAs each other. Exploiting interactions between lncRNAs and mRNA/miRNAs to lncRNA functional similarity (LFS) is an effective method to explore function of lncRNAs and predict novel lncRNA-disease associations. In this article, we proposed an integrative framework, IntNetLncSim, to infer LFS by modeling the information flow in an integrated network that comprises both lncRNA-related transcriptional and post-transcriptional information. The performance of IntNetLncSim was evaluated by investigating the relationship of LFS with the similarity of lncRNA-related mRNA sets (LmRSets) and miRNA sets (LmiRSets). As a result, LFS by IntNetLncSim was significant positively correlated with the LmRSet (Pearson correlation γ2=0.8424) and LmiRSet (Pearson correlation γ2=0.2601). Particularly, the performance of IntNetLncSim is superior to several previous methods. In the case of applying the LFS to identify novel lncRNA-disease relationships, we achieved an area under the ROC curve (0.7300) in experimentally verified lncRNA-disease associations based on leave-one-out cross-validation. Furthermore, highly-ranked lncRNA-disease associations confirmed by literature mining demonstrated the excellent performance of IntNetLncSim. Finally, a web-accessible system was provided for querying LFS and potential lncRNA-disease relationships: http://www.bio-bigdata.com/IntNetLncSim. PMID:27323856

IntNetLncSim: an integrative network analysis method to infer human lncRNA functional similarity.

PubMed

Cheng, Liang; Shi, Hongbo; Wang, Zhenzhen; Hu, Yang; Yang, Haixiu; Zhou, Chen; Sun, Jie; Zhou, Meng

2016-07-26

Increasing evidence indicated that long non-coding RNAs (lncRNAs) were involved in various biological processes and complex diseases by communicating with mRNAs/miRNAs each other. Exploiting interactions between lncRNAs and mRNA/miRNAs to lncRNA functional similarity (LFS) is an effective method to explore function of lncRNAs and predict novel lncRNA-disease associations. In this article, we proposed an integrative framework, IntNetLncSim, to infer LFS by modeling the information flow in an integrated network that comprises both lncRNA-related transcriptional and post-transcriptional information. The performance of IntNetLncSim was evaluated by investigating the relationship of LFS with the similarity of lncRNA-related mRNA sets (LmRSets) and miRNA sets (LmiRSets). As a result, LFS by IntNetLncSim was significant positively correlated with the LmRSet (Pearson correlation γ2=0.8424) and LmiRSet (Pearson correlation γ2=0.2601). Particularly, the performance of IntNetLncSim is superior to several previous methods. In the case of applying the LFS to identify novel lncRNA-disease relationships, we achieved an area under the ROC curve (0.7300) in experimentally verified lncRNA-disease associations based on leave-one-out cross-validation. Furthermore, highly-ranked lncRNA-disease associations confirmed by literature mining demonstrated the excellent performance of IntNetLncSim. Finally, a web-accessible system was provided for querying LFS and potential lncRNA-disease relationships: http://www.bio-bigdata.com/IntNetLncSim.

Health information systems and pesticide poisoning at Pernambuco.

PubMed

de Albuquerque, Pedro Costa Cavalcanti; Gurgel, Idê Gomes Dantas; Gurgel, Aline do Monte; Augusto, Lia Giraldo da Silva; de Siqueira, Marília Teixeira

2015-01-01

Understanding the epidemiologic profile of a particular disease is key to undertake health actions. To that end, information systems that present quality data help in the decision-making process and demonstrate the impact of the problems. To analyze the contribution of health information systems for the characterization of pesticide poisoning through SINAN, CEATOX and SIM in the State of Pernambuco. In this study, the completeness and consistency of the data were assessed, as well as the epidemiological profile of pesticide poisoning in Pernambuco in the period from 2008 to 2012, based on the following Health Information Systems: Center for Toxicological Assistance of Pernambuco (CEATOX), Notifiable Diseases Information System (SINAN) and Mortality Information System (SIM). The data revealed incompleteness and inconsistencies in information. Regarding the profile, females are more affected in the morbidity profile, and men have a higher mortality rate. Poisoning was more frequent in young adults with low educational level. With regard to the circumstances, most of the cases were suicide attempts, unique acute cases and not related to work. Despite suggesting underreporting, the data showed that persons engaged in agriculture are most commonly affected. The strengthening of these systems is necessary for the generation of consistent information that support health policies for the population groups involved.

Application of a PExSim for modeling a POLVAD artificial heart and the human circulatory system with left ventricle assistance

NASA Astrophysics Data System (ADS)

Siewnicka, Alicja; Fajdek, Bartlomiej; Janiszowski, Krzysztof

2010-01-01

This paper presents a model of the human circulatory system with the possible addition of a parallel assist device, which was developed for the purpose of artificial heart monitoring. Information about an identification experiment of an extracorporeal ventricle assist device POLVAD is included. The modelling methods applied and the corresponding functional blocks in a PExSim package are presented. The results of the simulation for physiological conditions, left ventricle failure and pathological conditions with parallel assistance are included.

Design of a framework for modeling, integration and simulation of physiological models.

PubMed

Erson, E Zeynep; Cavuşoğlu, M Cenk

2012-09-01

Multiscale modeling and integration of physiological models carry challenges due to the complex nature of physiological processes. High coupling within and among scales present a significant challenge in constructing and integrating multiscale physiological models. In order to deal with such challenges in a systematic way, there is a significant need for an information technology framework together with related analytical and computational tools that will facilitate integration of models and simulations of complex biological systems. Physiological Model Simulation, Integration and Modeling Framework (Phy-SIM) is an information technology framework providing the tools to facilitate development, integration and simulation of integrated models of human physiology. Phy-SIM brings software level solutions to the challenges raised by the complex nature of physiological systems. The aim of Phy-SIM, and this paper is to lay some foundation with the new approaches such as information flow and modular representation of the physiological models. The ultimate goal is to enhance the development of both the models and the integration approaches of multiscale physiological processes and thus this paper focuses on the design approaches that would achieve such a goal. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Study and optimisation of SIMS performed with He+ and Ne+ bombardment

NASA Astrophysics Data System (ADS)

Pillatsch, L.; Vanhove, N.; Dowsett, D.; Sijbrandij, S.; Notte, J.; Wirtz, T.

2013-10-01

The combination of the high-brightness He+/Ne+ atomic level ion source with the detection capabilities of secondary ion mass spectrometry (SIMS) opens up the prospect of obtaining chemical information with high lateral resolution and high sensitivity on the Zeiss ORION helium ion microscope (HIM). A feasibility study with He+ and Ne+ ion bombardment is presented in order to determine the performance of SIMS analyses using the HIM. Therefore, the sputtering yields, useful yields and detection limits obtained for metallic (Al, Ni and W) as well as semiconductor samples (Si, Ge, GaAs and InP) were investigated. All the experiments were performed on a Cameca IMS4f SIMS instrument which was equipped with a caesium evaporator and oxygen flooding system. For most of the elements, useful yields in the range of 10-4 to 3 × 10-2 were measured with either O2 or Cs flooding. SIMS experiments performed directly on the ORION with a prototype secondary ion extraction and detection system lead to results that are consistent with those obtained on the IMS4f. Taking into account the obtained useful yields and the analytical conditions, such as the ion current and typical dwell time on the ORION HIM, detection limits in the at% range and better can be obtained during SIMS imaging at 10 nm lateral resolution with Ne+ bombardment and down to the ppm level when a lateral resolution of 100 nm is chosen. Performing SIMS on the HIM with a good detection limit while maintaining an excellent lateral resolution (<50 nm) is therefore very promising.

Proceedings of the first U.S. Geological Survey scientific information management workshop, March 21-23, 2006

USGS Publications Warehouse

Henkel, Heather S.

2007-01-01

In March 2006, the U.S. Geological Survey (USGS) held the first Scientific Information Management (SIM) Workshop in Reston, Virginia. The workshop brought together more than 150 SIM professionals from across the organization to discuss the range and importance of SIM problems, identify common challenges and solutions, and investigate the use and value of “communities of practice” (CoP) as mechanisms to address these issues. The 3-day workshop began with presentations of SIM challenges faced by the Long Term Ecological Research (LTER) network and two USGS programs from geology and hydrology. These presentations were followed by a keynote address and discussion of CoP by Dr. Etienne Wenger, a pioneer and leading expert in CoP, who defined them as "groups of people who share a passion for something that they know how to do and who interact regularly to learn how to do it better." Wenger addressed the roles and characteristics of CoP, how they complement formal organizational structures, and how they can be fostered. Following this motivating overview, five panelists (including Dr. Wenger) with CoP experience in different institutional settings provided their perspectives and lessons learned. The first day closed with an open discussion on the potential intersection of SIM at the USGS with SIM challenges and the potential for CoP. The second session began the process of developing a common vocabulary for both scientific data management and CoP, and a list of eight guiding principles for information management were proposed for discussion and constructive criticism. Following this discussion, 20 live demonstrations and posters of SIM tools developed by various USGS programs and projects were presented. Two community-building sessions were held to explore the next steps in 12 specific areas: Archiving of Scientific Data and Information; Database Networks; Digital Libraries; Emerging Workforce; Field Data for Small Research Projects; Knowledge Capture; Knowledge Organization Systems and Controlled Vocabularies; Large Time Series Data Sets; Metadata; Portals and Frameworks; Preservation of Physical Collections; and Scientific Data from Monitoring Programs. In about two-thirds of these areas, initial steps to forming CoP are now underway. The final afternoon included a panel in which information professionals, managers, program coordinators, and associate directors shared their perspectives on the workshop, on ways in which the USGS could better manage its scientific information, and on the use of CoP as informal mechanisms to complement formal organizational structures. The final session focused on developing the next steps, an action plan, and a communication strategy to ensure continued development.

Surface Contamination Monitor and Survey Information Management System

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

NONE

1998-02-01

Shonka Research Associates, Inc.`s (SRA) Surface Contamination Monitor and Survey Information management System (SCM/SIMS) is designed to perform alpha and beta radiation surveys of floors and surfaces and document the measured data. The SRA-SCM/SIMS technology can be applied to routine operational surveys, characterization surveys, and free release and site closure surveys. Any large nuclear site can make use of this technology. This report describes a demonstration of the SRA-SCM/SIMS technology. This demonstration is part of the chicago Pile-5 (CP-5) Large-Scale Demonstration Project (LSDP) sponsored by the US Department of Energy (DOE), Office of Science and Technology (ST), Deactivation and Decommissioningmore » Focus Area (DDFA). The objective of the LSDP is to select and demonstrate potentially beneficial technologies at the Argonne National Laboratory-East`s (ANL) CP-5 Research Reactor Facility. The purpose of the LSDP is to demonstrate that by using innovative and improved deactivation and decommissioning (D and D) technologies from various sources, significant benefits can be achieved when compared to baseline D and D technologies.« less

Study of the Au-Cr bilayer system using X-ray reflectivity, GDOES, and ToF-SIMS

DOE PAGES

Jonnard, Philippe; Modi, Mohammed H.; Le Guen, Karine; ...

2018-04-17

Here, we study a Au (25 nm)/Cr (10 nm) bilayer system as a model of mirror for the soft X–ray energy range. The Au and Cr thin films are a few nanometer thick and are deposited on a float glass substrate. The sample is characterized by using 3 complementary techniques: soft X–ray reflectivity, glow discharge optical emission spectrometry (GDOES), and time–of–flight secondary ion mass spectroscopy (ToF–SIMS). Soft X–ray reflectivity provides information about the thickness and roughness of the different layers, while GDOES is used to obtain the elemental depth profile of the stack and ToF–SIMS to obtain the elemental andmore » chemical depth profiles. GDOES and ToF–SIMS have both a nanometer depth resolution. A coherent description of the bilayer stack is obtained through the combination of these techniques. It consists in 5 layers namely a surface contamination layer, a principal gold layer, a Au–Cr mixed layer, a Cr layer, and another contamination layer at the top of the substrate.« less

Recent advances in secondary ion mass spectrometry of solid acid catalysts: large zeolite crystals under bombardment.

PubMed

Hofmann, Jan P; Rohnke, Marcus; Weckhuysen, Bert M

2014-03-28

This Perspective aims to inform the heterogeneous catalysis and materials science community about the recent advances in Time-of-Flight-Secondary Ion Mass Spectrometry (ToF-SIMS) to characterize catalytic solids by taking large model H-ZSM-5 zeolite crystals as a showcase system. SIMS-based techniques have been explored in the 1980-1990's to study porous catalyst materials but, due to their limited spectral and spatiotemporal resolution, there was no real major breakthrough at that time. The technical advancements in SIMS instruments, namely improved ion gun design and new mass analyser concepts, nowadays allow for a much more detailed analysis of surface species relevant to catalytic action. Imaging with high mass and lateral resolution, determination of fragment ion patterns, novel sputter ion concepts as well as new mass analysers (e.g. ToF, FTICR) are just a few novelties, which will lead to new fundamental insight from SIMS analysis of heterogeneous catalysts. The Perspective article ends with an outlook on instrumental innovations and their potential use for catalytic systems other than zeolite crystals.

Study of the Au-Cr bilayer system using X-ray reflectivity, GDOES, and ToF-SIMS

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

Jonnard, Philippe; Modi, Mohammed H.; Le Guen, Karine

Here, we study a Au (25 nm)/Cr (10 nm) bilayer system as a model of mirror for the soft X–ray energy range. The Au and Cr thin films are a few nanometer thick and are deposited on a float glass substrate. The sample is characterized by using 3 complementary techniques: soft X–ray reflectivity, glow discharge optical emission spectrometry (GDOES), and time–of–flight secondary ion mass spectroscopy (ToF–SIMS). Soft X–ray reflectivity provides information about the thickness and roughness of the different layers, while GDOES is used to obtain the elemental depth profile of the stack and ToF–SIMS to obtain the elemental andmore » chemical depth profiles. GDOES and ToF–SIMS have both a nanometer depth resolution. A coherent description of the bilayer stack is obtained through the combination of these techniques. It consists in 5 layers namely a surface contamination layer, a principal gold layer, a Au–Cr mixed layer, a Cr layer, and another contamination layer at the top of the substrate.« less

The QuakeSim Project: Web Services for Managing Geophysical Data and Applications

NASA Astrophysics Data System (ADS)

Pierce, Marlon E.; Fox, Geoffrey C.; Aktas, Mehmet S.; Aydin, Galip; Gadgil, Harshawardhan; Qi, Zhigang; Sayar, Ahmet

2008-04-01

We describe our distributed systems research efforts to build the “cyberinfrastructure” components that constitute a geophysical Grid, or more accurately, a Grid of Grids. Service-oriented computing principles are used to build a distributed infrastructure of Web accessible components for accessing data and scientific applications. Our data services fall into two major categories: Archival, database-backed services based around Geographical Information System (GIS) standards from the Open Geospatial Consortium, and streaming services that can be used to filter and route real-time data sources such as Global Positioning System data streams. Execution support services include application execution management services and services for transferring remote files. These data and execution service families are bound together through metadata information and workflow services for service orchestration. Users may access the system through the QuakeSim scientific Web portal, which is built using a portlet component approach.

System design package for SIMS prototype system 2, solar hot water

NASA Technical Reports Server (NTRS)

1977-01-01

Information necessary to evaluate the design and assembly of a solar hot water system is presented. A prototype system designed for use in a single family dwelling is investigated in terms of the following subsystems: collector, storage, energy transport, and control.

SimPackJ/S: a web-oriented toolkit for discrete event simulation

NASA Astrophysics Data System (ADS)

Park, Minho; Fishwick, Paul A.

2002-07-01

SimPackJ/S is the JavaScript and Java version of SimPack, which means SimPackJ/S is a collection of JavaScript and Java libraries and executable programs for computer simulations. The main purpose of creating SimPackJ/S is that we allow existing SimPack users to expand simulation areas and provide future users with a freeware simulation toolkit to simulate and model a system in web environments. One of the goals for this paper is to introduce SimPackJ/S. The other goal is to propose translation rules for converting C to JavaScript and Java. Most parts demonstrate the translation rules with examples. In addition, we discuss a 3D dynamic system model and overview an approach to 3D dynamic systems using SimPackJ/S. We explain an interface between SimPackJ/S and the 3D language--Virtual Reality Modeling Language (VRML). This paper documents how to translate C to JavaScript and Java and how to utilize SimPackJ/S within a 3D web environment.

System importance measures: A new approach to resilient systems-of-systems

NASA Astrophysics Data System (ADS)

Uday, Payuna

Resilience is the ability to withstand and recover rapidly from disruptions. While this attribute has been the focus of research in several fields, in the case of system-of-systems (SoSs), addressing resilience is particularly interesting and challenging. As infrastructure SoSs, such as power, transportation, and communication networks, grow in complexity and interconnectivity, measuring and improving the resilience of these SoSs is vital in terms of safety and providing uninterrupted services. The characteristics of systems-of-systems make analysis and design of resilience challenging. However, these features also offer opportunities to make SoSs resilient using unconventional methods. In this research, we present a new approach to the process of resilience design. The core idea behind the proposed design process is a set of system importance measures (SIMs) that identify systems crucial to overall resilience. Using the results from the SIMs, we determine appropriate strategies from a list of design principles to improve SoS resilience. The main contribution of this research is the development of an aid to design that provides specific guidance on where and how resources need to be targeted. Based on the needs of an SoS, decision-makers can iterate through the design process to identify a set of practical and effective design improvements. We use two case studies to demonstrate how the SIM-based design process can inform decision-making in the context of SoS resilience. The first case study focuses on a naval warfare SoS and describes how the resilience framework can leverage existing simulation models to support end-to-end design. We proceed through stages of the design approach using an agent-based model (ABM) that enables us to demonstrate how simulation tools and analytical models help determine the necessary inputs for the design process and, subsequently, inform decision-making regarding SoS resilience. The second case study considers the urban transportation network in Boston. This case study focuses on interpreting the results of the resilience framework and on describing how they can be used to guide design choices in large infrastructure networks. We use different resilience maps to highlight the range of design-related information that can be obtained from the framework. Specific advantages of the SIM-based resilience design include: (1) incorporates SoS- specific features within existing risk-based design processes - the SIMs determine the relative importance of different systems based on their impacts on SoS-level performance, and suggestions for resilience improvement draw from design options that leverage SoS- specific characteristics, such as the ability to adapt quickly (such as add new systems or re-task existing ones) and to provide partial recovery of performance in the aftermath of a disruption; (2) allows rapid understanding of different areas of concern within the SoS - the visual nature of the resilience map (a key outcome of the SIM analysis) provides a useful way to summarize the current resilience of the SoS as well as point to key systems of concern; and (3) provides a platform for multiple analysts and decision- makers to study, modify, discuss and document options for SoS.

Pilot Test and Evaluation of a System of Computer-Managed Instruction.

ERIC Educational Resources Information Center

Spuck, Dennis W.; Bozeman, William C.

1978-01-01

The Wisconsin System for Instructional Management (WIS SIM) was evaluated on three dimensions (functioning, utilization, and effects) and the information gathered was classified into three types--actual, perceptual, and judgmental. The test demonstrates that a system supportive of an individualized system of education can be designed, developed,…

Topochemical Analysis of Cell Wall Components by TOF-SIMS.

PubMed

Aoki, Dan; Fukushima, Kazuhiko

2017-01-01

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is a recently developing analytical tool and a type of imaging mass spectrometry. TOF-SIMS provides mass spectral information with a lateral resolution on the order of submicrons, with widespread applicability. Sometimes, it is described as a surface analysis method without the requirement for sample pretreatment; however, several points need to be taken into account for the complete utilization of the capabilities of TOF-SIMS. In this chapter, we introduce methods for TOF-SIMS sample treatments, as well as basic knowledge of wood samples TOF-SIMS spectral and image data analysis.

Quality of the record of data on fatal workplace injuries in Brazil

PubMed Central

Galdino, Adriana; Santana, Vilma Sousa; Ferrite, Silvia

2017-01-01

ABSTRACT OBJECTIVE To evaluate the quality of the data on fatal workplace injuries in Brazil, in the Mortality Information System (SIM) and the Information System of Notifiable Diseases (SINAN-AT), analyzing the spatial and temporal distribution between 2007 and 2012. METHODS We identified fields related to fatal workplace injuries, which were examined for completeness and the use of the “ignored” option. From the SIM, we extracted the records of deaths from external causes, which require the completing of the field about their relation with work. From the SINAN, we analyzed the field, which allows us to identify fatal cases among s severe workplace injuries. RESULTS In the SIM, from 469,121 records, the field was left unfilled or filled as ignored in 84.2% of them; the Brazilian region with the highest proportion was the Northeast (79.1%), from which the state of Alagoas (94.4%) had the highest amount. There was a 5.5% decreasing trend between 2007 (86.6%) and 2012 (81.8%). Among the 251,681 records found in the SINAN-AT, 28.3% had unfilled or ignored responses for , varying from 39.7% in 2007 to 23.2% in 2012, a 41.6% decrease. CONCLUSIONS The quality of the records on the fields of interest needed to identify fatal workplace injuries is poor in the SIM, but gradually improving. Recording quality was better for SINAN-AT, which has also been strongly getting better lately. PMID:29236875

Quality of the record of data on fatal workplace injuries in Brazil.

PubMed

Galdino, Adriana; Santana, Vilma Sousa; Ferrite, Silvia

2017-12-11

To evaluate the quality of the data on fatal workplace injuries in Brazil, in the Mortality Information System (SIM) and the Information System of Notifiable Diseases (SINAN-AT), analyzing the spatial and temporal distribution between 2007 and 2012. We identified fields related to fatal workplace injuries, which were examined for completeness and the use of the "ignored" option. From the SIM, we extracted the records of deaths from external causes, which require the completing of the field about their relation with work. From the SINAN, we analyzed the field, which allows us to identify fatal cases among s severe workplace injuries. In the SIM, from 469,121 records, the field was left unfilled or filled as ignored in 84.2% of them; the Brazilian region with the highest proportion was the Northeast (79.1%), from which the state of Alagoas (94.4%) had the highest amount. There was a 5.5% decreasing trend between 2007 (86.6%) and 2012 (81.8%). Among the 251,681 records found in the SINAN-AT, 28.3% had unfilled or ignored responses for , varying from 39.7% in 2007 to 23.2% in 2012, a 41.6% decrease. The quality of the records on the fields of interest needed to identify fatal workplace injuries is poor in the SIM, but gradually improving. Recording quality was better for SINAN-AT, which has also been strongly getting better lately.

Systems Engineering and Application of System Performance Modeling in SIM Lite Mission

NASA Technical Reports Server (NTRS)

Moshir, Mehrdad; Murphy, David W.; Milman, Mark H.; Meier, David L.

2010-01-01

The SIM Lite Astrometric Observatory will be the first space-based Michelson interferometer operating in the visible wavelength, with the ability to perform ultra-high precision astrometric measurements on distant celestial objects. SIM Lite data will address in a fundamental way questions such as characterization of Earth-mass planets around nearby stars. To accomplish these goals it is necessary to rely on a model-based systems engineering approach - much more so than most other space missions. This paper will describe in further detail the components of this end-to-end performance model, called "SIM-sim", and show how it has helped the systems engineering process.

Visualizing Microbial Biogeochemistry: NanoSIMS and Stable Isotope Probing (Invited)

NASA Astrophysics Data System (ADS)

Pett-Ridge, J.; Weber, P. K.

2009-12-01

Linking phylogenetic information to function in microbial communities is a key challenge for microbial ecology. Isotope-labeling experiments provide a useful means to investigate the ecophysiology of microbial populations and cells in the environment and allow measurement of nutrient transfers between cell types, symbionts and consortia. The combination of Nano-Secondary Ion Mass Spectrometry (NanoSIMS) analysis, in situ labeling and high resolution microscopy allows isotopic analysis to be linked to phylogeny and morphology and holds great promise for fine-scale studies of microbial systems. In NanoSIMS analysis, samples are sputtered with an energetic primary beam (Cs+, O-) liberating secondary ions that are separated by the mass spectrometer and detected in a suite of electron multipliers. Five isotopic species may be analyzed concurrently with spatial resolution as fine as 50nm. A high sensitivity isotope ratio ‘map’ can then be generated for the analyzed area. NanoSIMS images of 13C, 15N and Mo (a nitrogenase co-factor) localization in diazotrophic cyanobacteria show how cells differentially allocate resources within filaments and allow calculation of nutrient uptake rates on a cell by cell basis. Images of AM fungal hyphae-root and cyanobacteria-rhizobia associations indicate the mobilization and sharing (stealing?) of newly fixed C and N. In a related technique, “El-FISH”, stable isotope labeled biomass is probed with oligonucleotide-elemental labels and then imaged by NanoSIMS. In microbial consortia and cyanobacterial mats, this technique helps link microbial structure and function simultaneously even in systems with unknown and uncultivated microbes. Finally, the combination of re-engineered universal 16S oligonucleotide microarrays with NanoSIMS analyses may allow microbial identity to be linked to functional roles in complex systems such as mats and cellulose degrading hindgut communities. These newly developed methods provide correlated oligonucleotide, functional enzyme and metabolic image data and should help unravel the metabolic processes of complex microbial communities in soils, biofilms and aquatic systems.

Improving the Molecular Ion Signal Intensity for In Situ Liquid SIMS Analysis

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

Zhou, Yufan; Yao, Juan; Ding, Yuanzhao

In situ liquid secondary ion mass spectrometry (SIMS) enabled by system for analysis at the liquid vacuum interface (SALVI) has proven to be a promising new tool to provide molecular information at solid–liquid and liquid–vacuum interfaces. However, the initial data showed that useful signals in positive ion spectra are too weak to be meaningful in most cases. In addition, it is difficult to obtain strong negative molecular ion signals when m/z>200. These two drawbacks have been the biggest obstacle towards practical use of this new analytical approach. In this study, we report that strong and reliable positive and negative molecularmore » signals are achievable after optimizing the SIMS experimental conditions. Four model systems, including a 1,8-diazabicycloundec-7-ene (DBU)-base switchable ionic liquid, a live Shewanella oneidensis biofilm, a hydrated mammalian epithelia cell, and an electrolyte popularly used in Li ion batteries were studied. A signal enhancement of about two orders of magnitude was obtained in comparison with non-optimized conditions. Therefore, molecular ion signal intensity has become very acceptable to use for in situ liquid SIMS to study solid–liquid and liquid–vacuum interfaces.« less

Improving the Molecular Ion Signal Intensity for In Situ Liquid SIMS Analysis.

PubMed

Zhou, Yufan; Yao, Juan; Ding, Yuanzhao; Yu, Jiachao; Hua, Xin; Evans, James E; Yu, Xiaofei; Lao, David B; Heldebrant, David J; Nune, Satish K; Cao, Bin; Bowden, Mark E; Yu, Xiao-Ying; Wang, Xue-Lin; Zhu, Zihua

2016-12-01

In situ liquid secondary ion mass spectrometry (SIMS) enabled by system for analysis at the liquid vacuum interface (SALVI) has proven to be a promising new tool to provide molecular information at solid-liquid and liquid-vacuum interfaces. However, the initial data showed that useful signals in positive ion spectra are too weak to be meaningful in most cases. In addition, it is difficult to obtain strong negative molecular ion signals when m/z>200. These two drawbacks have been the biggest obstacle towards practical use of this new analytical approach. In this study, we report that strong and reliable positive and negative molecular signals are achievable after optimizing the SIMS experimental conditions. Four model systems, including a 1,8-diazabicycloundec-7-ene (DBU)-base switchable ionic liquid, a live Shewanella oneidensis biofilm, a hydrated mammalian epithelia cell, and an electrolyte popularly used in Li ion batteries were studied. A signal enhancement of about two orders of magnitude was obtained in comparison with non-optimized conditions. Therefore, molecular ion signal intensity has become very acceptable for use of in situ liquid SIMS to study solid-liquid and liquid-vacuum interfaces. Graphical Abstract ᅟ.

Documents Similarity Measurement Using Field Association Terms.

ERIC Educational Resources Information Center

Atlam, El-Sayed; Fuketa, M.; Morita, K.; Aoe, Jun-ichi

2003-01-01

Discussion of text analysis and information retrieval and measurement of document similarity focuses on a new text manipulation system called FA (field association)-Sim that is useful for retrieving information in large heterogeneous texts and for recognizing content similarity in text excerpts. Discusses recall and precision, automatic indexing…

Biochemical imaging of tissues by SIMS for biomedical applications

NASA Astrophysics Data System (ADS)

Lee, Tae Geol; Park, Ji-Won; Shon, Hyun Kyong; Moon, Dae Won; Choi, Won Woo; Li, Kapsok; Chung, Jin Ho

2008-12-01

With the development of optimal surface cleaning techniques by cluster ion beam sputtering, certain applications of SIMS for analyzing cells and tissues have been actively investigated. For this report, we collaborated with bio-medical scientists to study bio-SIMS analyses of skin and cancer tissues for biomedical diagnostics. We pay close attention to the setting up of a routine procedure for preparing tissue specimens and treating the surface before obtaining the bio-SIMS data. Bio-SIMS was used to study two biosystems, skin tissues for understanding the effects of photoaging and colon cancer tissues for insight into the development of new cancer diagnostics for cancer. Time-of-flight SIMS imaging measurements were taken after surface cleaning with cluster ion bombardment by Bi n or C 60 under varying conditions. The imaging capability of bio-SIMS with a spatial resolution of a few microns combined with principal component analysis reveal biologically meaningful information, but the lack of high molecular weight peaks even with cluster ion bombardment was a problem. This, among other problems, shows that discourse with biologists and medical doctors are critical to glean any meaningful information from SIMS mass spectrometric and imaging data. For SIMS to be accepted as a routine, daily analysis tool in biomedical laboratories, various practical sample handling methodology such as surface matrix treatment, including nano-metal particles and metal coating, in addition to cluster sputtering, should be studied.

SIM PlanetQuest: Science with the Space Interferometry Mission

NASA Technical Reports Server (NTRS)

Unwin, Stephen (Editor); Turyshev, Slava (Editor)

2004-01-01

SIM - the Space Interferometry Mission - will perform precision optical astrometry on objects as faint as R magnitude 20. It will be the first space-based astrometric interferometer, operating in the optical band with a 10-m baseline. The Project is managed by the Jet Propulsion Laboratory, California Institute of Technology, in close collaboration with two industry partners, Lockheed Martin Missiles and Space, and TRW Inc., Space and Electronics Group. Launch of SIM is currently planned for 2009. In its wide-angle astrometric mode, SIM will yield 4 microarcsecond absolute position and parallax measurements. Astrometric planet searches will be done in a narrow-angle mode, with an accuracy of 4 microarcseconds or better in a single measurement. As a pointed rather than a survey instrument, SIM will maintain.its astrometric accuracy down to the faintest, magnitudes, opening up the opportunity for astrometry of active galactic nuclei to better than 10 pas. SIM will define a new astrometric reference frame, using a grid of approximately 1500 stars with positions accurate to 4 microarcseconds. The SIM Science Team comprises the Principal Investigators of ten Key Projects, and five Mission Scientists contributing their expertise to specific areas of the mission. Their science programs cover a wide range of topics in Galactic and extragalactic astronomy. They include: searches for low-mass planets - including analogs to our own solar system - tlie formation and dynamics of our Galaxy, calibration of the cosmic distance scale, and fundamental stellar astrophysics. All of the science observing on SIM is competitively awarded; the Science Team programs total about 40% of the total available, and the remainder will be assigned via future NASA competitions. This report is a compilation of science summaries by members of the Science Team, and it illustrates the wealth of scientific problems that microarcsecond-precision astrometry can contribute to. More information on SIM, including copies of this report, may be obtained from the project web site, at http://sim. jpl.nasa.gov.

NanoSIMS for biological applications: Current practices and analyses

DOE PAGES

Nunez, Jamie R.; Renslow, Ryan S.; Cliff, III, John B.; ...

2017-09-27

Secondary ion mass spectrometry (SIMS) has become an increasingly utilized tool in biologically-relevant studies. Of these, high lateral resolution methodologies using the NanoSIMS 50/50L have been especially powerful within many biological fields over the past decade. Here, we provide a review of this technology, sample preparation and analysis considerations, examples of recent biological studies, data analysis, and current outlooks. Specifically, we offer an overview of SIMS and development of the NanoSIMS. We describe the major experimental factors that should be considered prior to NanoSIMS analysis and then provide information on best practices for data analysis and image generation, which includesmore » an in-depth discussion of appropriate colormaps. Additionally, we provide an open-source method for data representation that allows simultaneous visualization of secondary electron and ion information within a single image. Lastly, we present a perspective on the future of this technology and where we think it will have the greatest impact in near future.« less

NanoSIMS for biological applications: Current practices and analyses

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

Nunez, Jamie R.; Renslow, Ryan S.; Cliff, III, John B.

Secondary ion mass spectrometry (SIMS) has become an increasingly utilized tool in biologically-relevant studies. Of these, high lateral resolution methodologies using the NanoSIMS 50/50L have been especially powerful within many biological fields over the past decade. Here, we provide a review of this technology, sample preparation and analysis considerations, examples of recent biological studies, data analysis, and current outlooks. Specifically, we offer an overview of SIMS and development of the NanoSIMS. We describe the major experimental factors that should be considered prior to NanoSIMS analysis and then provide information on best practices for data analysis and image generation, which includesmore » an in-depth discussion of appropriate colormaps. Additionally, we provide an open-source method for data representation that allows simultaneous visualization of secondary electron and ion information within a single image. Lastly, we present a perspective on the future of this technology and where we think it will have the greatest impact in near future.« less

CalSimHydro Tool - A Web-based interactive tool for the CalSim 3.0 Hydrology Prepropessor

NASA Astrophysics Data System (ADS)

Li, P.; Stough, T.; Vu, Q.; Granger, S. L.; Jones, D. J.; Ferreira, I.; Chen, Z.

2011-12-01

CalSimHydro, the CalSim 3.0 Hydrology Preprocessor, is an application designed to automate the various steps in the computation of hydrologic inputs for CalSim 3.0, a water resources planning model developed jointly by California State Department of Water Resources and United States Bureau of Reclamation, Mid-Pacific Region. CalSimHydro consists of a five-step FORTRAN based program that runs the individual models in succession passing information from one model to the next and aggregating data as required by each model. The final product of CalSimHydro is an updated CalSim 3.0 state variable (SV) DSS input file. CalSimHydro consists of (1) a Rainfall-Runoff Model to compute monthly infiltration, (2) a Soil moisture and demand calculator (IDC) that estimates surface runoff, deep percolation, and water demands for natural vegetation cover and various crops other than rice, (3) a Rice Water Use Model to compute the water demands, deep percolation, irrigation return flow, and runoff from precipitation for the rice fields, (4) a Refuge Water Use Model that simulates the ponding operations for managed wetlands, and (5) a Data Aggregation and Transfer Module to aggregate the outputs from the above modules and transfer them to the CalSim SV input file. In this presentation, we describe a web-based user interface for CalSimHydro using Google Earth Plug-In. The CalSimHydro tool allows users to - interact with geo-referenced layers of the Water Budget Areas (WBA) and Demand Units (DU) displayed over the Sacramento Valley, - view the input parameters of the hydrology preprocessor for a selected WBA or DU in a time series plot or a tabular form, - edit the values of the input parameters in the table or by downloading a spreadsheet of the selected parameter in a selected time range, - run the CalSimHydro modules in the backend server and notify the user when the job is done, - visualize the model output and compare it with a base run result, - download the output SV file to be used to run CalSim 3.0. The CalSimHydro tool streamlines the complicated steps to configure and run the hydrology preprocessor by providing a user-friendly visual interface and back-end services to validate user inputs and manage the model execution. It is a powerful addition to the new CalSim 3.0 system.

Why don't biologists use SIMS?. A critical evaluation of imaging MS

NASA Astrophysics Data System (ADS)

Heeren, R. M. A.; McDonnell, L. A.; Amstalden, E.; Luxembourg, S. L.; Altelaar, A. F. M.; Piersma, S. R.

2006-07-01

Secondary ion mass spectrometry is commonly used to study many different types of complex surfaces. Yet, compared with MALDI and ESI-MS, SIMS has not made a significant impact in biological or biomedical research. The key features of the technique, namely high spatial resolution, high detection efficiency of ions spanning a wide m/ z range, surface sensitivity and the high scan rates seem to match ideally with several questions posed at the cellular level. To this date, SIMS has had only limited success in the biological arena. Why is this and what is needed to change this? This discussion paper will critically review the advances and the usefulness of SIMS in biomedical research and compare it to other approaches that offer spatially resolved molecular information available to a researcher with a biological interest. We will demonstrate that the type of information generated by the various incarnations of SIMS is strongly dependent on sample preparation and surface condition and these phenomena are only poorly understood. Modern approaches such as the cluster gun developments, ME-SIMS, gold coating and MALDI stigmatic imaging on a SIMS instrument might change the perception of SIMS being a tool for semiconductor manufacturers and physicists, and might persuade biologists to use these innovative mass spectrometric imaging tools.

Stroboscopic Image Modulation to Reduce the Visual Blur of an Object Being Viewed by an Observer Experiencing Vibration

NASA Technical Reports Server (NTRS)

Kaiser, Mary K. (Inventor); Adelstein, Bernard D. (Inventor); Anderson, Mark R. (Inventor); Beutter, Brent R. (Inventor); Ahumada, Albert J., Jr. (Inventor); McCann, Robert S. (Inventor)

2014-01-01

A method and apparatus for reducing the visual blur of an object being viewed by an observer experiencing vibration. In various embodiments of the present invention, the visual blur is reduced through stroboscopic image modulation (SIM). A SIM device is operated in an alternating "on/off" temporal pattern according to a SIM drive signal (SDS) derived from the vibration being experienced by the observer. A SIM device (controlled by a SIM control system) operates according to the SDS serves to reduce visual blur by "freezing" (or reducing an image's motion to a slow drift) the visual image of the viewed object. In various embodiments, the SIM device is selected from the group consisting of illuminator(s), shutter(s), display control system(s), and combinations of the foregoing (including the use of multiple illuminators, shutters, and display control systems).

Automated Interpretation and Extraction of Topographic Information from Time of Flight Secondary Ion Mass Spectrometry Data

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

Ievlev, Anton V.; Belianinov, Alexei; Jesse, Stephen

Time of flight secondary ion mass spectrometry (ToF SIMS) is one of the most powerful characterization tools allowing imaging of the chemical properties of various systems and materials. It allows precise studies of the chemical composition with sub-100-nm lateral and nanometer depth spatial resolution. However, comprehensive interpretation of ToF SIMS results is challengeable, because of the data volume and its multidimensionality. Furthermore, investigation of the samples with pronounced topographical features are complicated by the spectral shift. In this work we developed approach for the comprehensive ToF SIMS data interpretation based on the data analytics and automated extraction of the samplemore » topography based on time of flight shift. We further applied this approach to investigate correlation between biological function and chemical composition in Arabidopsis roots.« less

Automated Interpretation and Extraction of Topographic Information from Time of Flight Secondary Ion Mass Spectrometry Data

DOE PAGES

Ievlev, Anton V.; Belianinov, Alexei; Jesse, Stephen; ...

2017-12-06

Time of flight secondary ion mass spectrometry (ToF SIMS) is one of the most powerful characterization tools allowing imaging of the chemical properties of various systems and materials. It allows precise studies of the chemical composition with sub-100-nm lateral and nanometer depth spatial resolution. However, comprehensive interpretation of ToF SIMS results is challengeable, because of the data volume and its multidimensionality. Furthermore, investigation of the samples with pronounced topographical features are complicated by the spectral shift. In this work we developed approach for the comprehensive ToF SIMS data interpretation based on the data analytics and automated extraction of the samplemore » topography based on time of flight shift. We further applied this approach to investigate correlation between biological function and chemical composition in Arabidopsis roots.« less

Evaluation of biomolecular distributions in rat brain tissues by means of ToF-SIMS using a continuous beam of Ar clusters.

PubMed

Nakano, Shusuke; Yokoyama, Yuta; Aoyagi, Satoka; Himi, Naoyuki; Fletcher, John S; Lockyer, Nicholas P; Henderson, Alex; Vickerman, John C

2016-06-08

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) provides detailed chemical structure information and high spatial resolution images. Therefore, ToF-SIMS is useful for studying biological phenomena such as ischemia. In this study, in order to evaluate cerebral microinfarction, the distribution of biomolecules generated by ischemia was measured with ToF-SIMS. ToF-SIMS data sets were analyzed by means of multivariate analysis for interpreting complex samples containing unknown information and to obtain biomolecular mapping indicated by fragment ions from the target biomolecules. Using conventional ToF-SIMS (primary ion source: Bi cluster ion), it is difficult to detect secondary ions beyond approximately 1000 u. Moreover, the intensity of secondary ions related to biomolecules is not always high enough for imaging because of low concentration even if the masses are lower than 1000 u. However, for the observation of biomolecular distributions in tissues, it is important to detect low amounts of biological molecules from a particular area of tissue. Rat brain tissue samples were measured with ToF-SIMS (J105, Ionoptika, Ltd., Chandlers Ford, UK), using a continuous beam of Ar clusters as a primary ion source. ToF-SIMS with Ar clusters efficiently detects secondary ions related to biomolecules and larger molecules. Molecules detected by ToF-SIMS were examined by analyzing ToF-SIMS data using multivariate analysis. Microspheres (45 μm diameter) were injected into the rat unilateral internal carotid artery (MS rat) to cause cerebral microinfarction. The rat brain was sliced and then measured with ToF-SIMS. The brain samples of a normal rat and the MS rat were examined to find specific secondary ions related to important biomolecules, and then the difference between them was investigated. Finally, specific secondary ions were found around vessels incorporating microspheres in the MS rat. The results suggest that important biomolecules related to cerebral microinfarction can be detected by ToF-SIMS.

QuakeSim 2.0

NASA Technical Reports Server (NTRS)

Donnellan, Andrea; Parker, Jay W.; Lyzenga, Gregory A.; Granat, Robert A.; Norton, Charles D.; Rundle, John B.; Pierce, Marlon E.; Fox, Geoffrey C.; McLeod, Dennis; Ludwig, Lisa Grant

2012-01-01

QuakeSim 2.0 improves understanding of earthquake processes by providing modeling tools and integrating model applications and various heterogeneous data sources within a Web services environment. QuakeSim is a multisource, synergistic, data-intensive environment for modeling the behavior of earthquake faults individually, and as part of complex interacting systems. Remotely sensed geodetic data products may be explored, compared with faults and landscape features, mined by pattern analysis applications, and integrated with models and pattern analysis applications in a rich Web-based and visualization environment. Integration of heterogeneous data products with pattern informatics tools enables efficient development of models. Federated database components and visualization tools allow rapid exploration of large datasets, while pattern informatics enables identification of subtle, but important, features in large data sets. QuakeSim is valuable for earthquake investigations and modeling in its current state, and also serves as a prototype and nucleus for broader systems under development. The framework provides access to physics-based simulation tools that model the earthquake cycle and related crustal deformation. Spaceborne GPS and Inter ferometric Synthetic Aperture (InSAR) data provide information on near-term crustal deformation, while paleoseismic geologic data provide longerterm information on earthquake fault processes. These data sources are integrated into QuakeSim's QuakeTables database system, and are accessible by users or various model applications. UAVSAR repeat pass interferometry data products are added to the QuakeTables database, and are available through a browseable map interface or Representational State Transfer (REST) interfaces. Model applications can retrieve data from Quake Tables, or from third-party GPS velocity data services; alternatively, users can manually input parameters into the models. Pattern analysis of GPS and seismicity data has proved useful for mid-term forecasting of earthquakes, and for detecting subtle changes in crustal deformation. The GPS time series analysis has also proved useful as a data-quality tool, enabling the discovery of station anomalies and data processing and distribution errors. Improved visualization tools enable more efficient data exploration and understanding. Tools provide flexibility to science users for exploring data in new ways through download links, but also facilitate standard, intuitive, and routine uses for science users and end users such as emergency responders.

The SIM Time Network

PubMed Central

Lombardi, Michael A.; Novick, Andrew N.; Lopez R, J. Mauricio; Jimenez, Francisco; de Carlos Lopez, Eduardo; Boulanger, Jean-Simon; Pelletier, Raymond; de Carvalho, Ricardo J.; Solis, Raul; Sanchez, Harold; Quevedo, Carlos Andres; Pascoe, Gregory; Perez, Daniel; Bances, Eduardo; Trigo, Leonardo; Masi, Victor; Postigo, Henry; Questelles, Anthony; Gittens, Anselm

2011-01-01

The Sistema Interamericano de Metrologia (SIM) is a regional metrology organization (RMO) whose members are the national metrology institutes (NMIs) located in the 34 nations of the Organization of American States (OAS). The SIM/OAS region extends throughout North, Central, and South America and the Caribbean Islands. About half of the SIM NMIs maintain national standards of time and frequency and must participate in international comparisons in order to establish metrological traceability to the International System (SI) of units. The SIM time network (SIMTN) was developed as a practical, cost effective, and technically sound way to automate these comparisons. The SIMTN continuously compares the time standards of SIM NMIs and produces measurement results in near real-time by utilizing the Internet and the Global Positioning System (GPS). Fifteen SIM NMIs have joined the network as of December 2010. This paper provides a brief overview of SIM and a technical description of the SIMTN. It presents international comparison results and examines the measurement uncertainties. It also discusses the metrological benefits that the network provides to its participants. PMID:26989584

The SIM Time Network.

PubMed

Lombardi, Michael A; Novick, Andrew N; Lopez R, J Mauricio; Jimenez, Francisco; de Carlos Lopez, Eduardo; Boulanger, Jean-Simon; Pelletier, Raymond; de Carvalho, Ricardo J; Solis, Raul; Sanchez, Harold; Quevedo, Carlos Andres; Pascoe, Gregory; Perez, Daniel; Bances, Eduardo; Trigo, Leonardo; Masi, Victor; Postigo, Henry; Questelles, Anthony; Gittens, Anselm

2011-01-01

The Sistema Interamericano de Metrologia (SIM) is a regional metrology organization (RMO) whose members are the national metrology institutes (NMIs) located in the 34 nations of the Organization of American States (OAS). The SIM/OAS region extends throughout North, Central, and South America and the Caribbean Islands. About half of the SIM NMIs maintain national standards of time and frequency and must participate in international comparisons in order to establish metrological traceability to the International System (SI) of units. The SIM time network (SIMTN) was developed as a practical, cost effective, and technically sound way to automate these comparisons. The SIMTN continuously compares the time standards of SIM NMIs and produces measurement results in near real-time by utilizing the Internet and the Global Positioning System (GPS). Fifteen SIM NMIs have joined the network as of December 2010. This paper provides a brief overview of SIM and a technical description of the SIMTN. It presents international comparison results and examines the measurement uncertainties. It also discusses the metrological benefits that the network provides to its participants.

Rock art at the 'Mini-Yengo' site near Kulnura, New South Wales

NASA Astrophysics Data System (ADS)

Hamacher, Duane W.; Clegg, John K.; Pankhurst, Robert S.

2012-11-01

The "Mini-Yengo" rock art site is located in Mangrove Creek Dam Park on Kyola Road, near the corner of Kyola Road and George Downes Drive, approximately 1.8 km to the northwest of Kulnura, New South Wales, Australia. No records of this site were identified in the published literature (Sim 1966; Needham 1981; McCarthy 1983; Gordon 1993; McDonald 1993) but it was included in site card 45-3-0528 from the Aboriginal Heritage Information Management System (AHIMS). The site card contained unpublished surveys by V. Attenbrow in 1980 and I.M. Sim in 1976.

Overview of SIMS-Based Experimental Studies of Tracer Diffusion in Solids and Application to Mg Self-Diffusion

DOE PAGES

Kulkarni, Nagraj S.; Bruce Warmack, Robert J.; Radhakrishnan, Bala; ...

2014-09-23

Tracer diffusivities provide the most fundamental information on diffusion in materials and are the foundation of robust diffusion databases. Compared to traditional radiotracer techniques that utilize radioactive isotopes, the secondary ion mass spectrometry (SIMS) based thin-film technique for tracer diffusion is based on the use of enriched stable isotopes that can be accurately profiled using SIMS. Experimental procedures & techniques that are utilized for the measurement of tracer diffusion coefficients are presented for pure magnesium, which presents some unique challenges due to the ease of oxidation. The development of a modified Shewmon-Rhines diffusion capsule for annealing Mg and an ultra-highmore » vacuum (UHV) system for sputter deposition of Mg isotopes are discussed. Optimized conditions for accurate SIMS depth profiling in polycrystalline Mg are provided. An automated procedure for the correction of heat-up and cool-down times during tracer diffusion annealing is discussed. The non-linear fitting of a SIMS depth profile data using the thin film Gaussian solution to obtain the tracer diffusivity along with the background tracer concentration and tracer film thickness is discussed. An Arrhenius fit of the Mg self-diffusion data obtained using the low-temperature SIMS measurements from this study and the high-temperature radiotracer measurements of Shewmon and Rhines (1954) was found to be a good representation of both types of diffusion data that cover a broad range of temperatures between 250 - 627° C (523 900 K).« less

Space Interferometry Mission: Dynamical Observations of Galaxies (SIMDOG)

NASA Technical Reports Server (NTRS)

Shaya, Edward J.; Borne, Kirk D.; Nusser, Adi; Peebles, P. J. E.; Tonry, John; Tully, Brent R.; Vogel, Stuart; Zaritsky, Dennis

2004-01-01

Space Interferometry Mission (SIM) will be used to obtain proper motions for a sample of 27 galaxies; the first proper motion measurements of galaxies beyond the satellite system of the Milky Way. SIM measurements lead to knowledge of the full 6-dimensional position and velocity vector of each galaxy. In conjunction with new gravitational flow models, the result will be the first total mass measurements of individual galaxies. The project, includes developnient of powerful theoretical methods for orbital calculations. This SIM study will lead to vastly improved determinations of individual galaxy masses, halo sizes, and the fractional contribution of dark matter. Astronomers have struggled to calculate the orbits of galaxies with only position and redshift information. Traditional N-body techniques are unsuitable for an analysis backward in time from a present distribution if any components of velocity or position are not very precisely known.

Photo ion spectrometer

DOEpatents

Gruen, Dieter M.; Young, Charles E.; Pellin, Michael J.

1989-01-01

A charged particle spectrometer for performing ultrasensitive quantitative analysis of selected atomic components removed from a sample. Significant improvements in performing energy and angular refocusing spectroscopy are accomplished by means of a two dimensional structure for generating predetermined electromagnetic field boundary conditions. Both resonance and non-resonance ionization of selected neutral atomic components allow accumulation of increased chemical information. A multiplexed operation between a SIMS mode and a neutral atomic component ionization mode with EARTOF analysis enables comparison of chemical information from secondary ions and neutral atomic components removed from the sample. An electronic system is described for switching high level signals, such as SIMS signals, directly to a transient recorder and through a charge amplifier to the transient recorder for a low level signal pulse counting mode, such as for a neutral atomic component ionization mode.

SIMS prototype system 1 test results: Engineering analysis

NASA Technical Reports Server (NTRS)

1978-01-01

The space and domestic water solar heating system designated SIMS Prototype Systems 1 was evaluated. The test system used 720 ft (gross) of Solar Energy Products Air Collectors, a Solar Control Corporation SAM 20 Air Handler with Model 75-175 control unit, a Jackson Solar Storage tank with Rho Sigma Mod 106 controller, and 20 tons of rack storage. The test data analysis performed evaluates the system performance and documents the suitability of SIMS Prototype System 1 hardware for field installation.

Automated Knowledge Discovery From Simulators

NASA Technical Reports Server (NTRS)

Burl, Michael; DeCoste, Dennis; Mazzoni, Dominic; Scharenbroich, Lucas; Enke, Brian; Merline, William

2007-01-01

A computational method, SimLearn, has been devised to facilitate efficient knowledge discovery from simulators. Simulators are complex computer programs used in science and engineering to model diverse phenomena such as fluid flow, gravitational interactions, coupled mechanical systems, and nuclear, chemical, and biological processes. SimLearn uses active-learning techniques to efficiently address the "landscape characterization problem." In particular, SimLearn tries to determine which regions in "input space" lead to a given output from the simulator, where "input space" refers to an abstraction of all the variables going into the simulator, e.g., initial conditions, parameters, and interaction equations. Landscape characterization can be viewed as an attempt to invert the forward mapping of the simulator and recover the inputs that produce a particular output. Given that a single simulation run can take days or weeks to complete even on a large computing cluster, SimLearn attempts to reduce costs by reducing the number of simulations needed to effect discoveries. Unlike conventional data-mining methods that are applied to static predefined datasets, SimLearn involves an iterative process in which a most informative dataset is constructed dynamically by using the simulator as an oracle. On each iteration, the algorithm models the knowledge it has gained through previous simulation trials and then chooses which simulation trials to run next. Running these trials through the simulator produces new data in the form of input-output pairs. The overall process is embodied in an algorithm that combines support vector machines (SVMs) with active learning. SVMs use learning from examples (the examples are the input-output pairs generated by running the simulator) and a principle called maximum margin to derive predictors that generalize well to new inputs. In SimLearn, the SVM plays the role of modeling the knowledge that has been gained through previous simulation trials. Active learning is used to determine which new input points would be most informative if their output were known. The selected input points are run through the simulator to generate new information that can be used to refine the SVM. The process is then repeated. SimLearn carefully balances exploration (semi-randomly searching around the input space) versus exploitation (using the current state of knowledge to conduct a tightly focused search). During each iteration, SimLearn uses not one, but an ensemble of SVMs. Each SVM in the ensemble is characterized by different hyper-parameters that control various aspects of the learned predictor - for example, whether the predictor is constrained to be very smooth (nearby points in input space lead to similar output predictions) or whether the predictor is allowed to be "bumpy." The various SVMs will have different preferences about which input points they would like to run through the simulator next. SimLearn includes a formal mechanism for balancing the ensemble SVM preferences so that a single choice can be made for the next set of trials.

An Investigation of Psychological Typology as an Intervening Variable in the Implementation of a Computer Managed Instruction System. Technical Report No. 454.

ERIC Educational Resources Information Center

Bozeman, William C.

This study explores the relationships between psychological types of users as identified by the Myers-Briggs Type Indicator and factors associated with the implementation and utilization of the Wisconsin System for Instructional Management (WIS-SIM), a computer management information system designed to support management processes in…

[Infant mortality according to color or race based on the 2010 Population Census and national health information systems in Brazil].

PubMed

Caldas, Aline Diniz Rodrigues; Santos, Ricardo Ventura; Borges, Gabriel Mendes; Valente, Joaquim Gonçalves; Portela, Margareth Crisóstomo; Marinho, Gerson Luiz

2017-08-07

The aim of this study was to investigate infant mortality data according to color or race in Brazil with a focus on indigenous individuals, based on data from the 2010 Population Census and the Brazilian Mortality Information System (SIM) and Brazilian Information System on Live Births (SINASC). In both sources, the infant mortality rate (IMR) for indigenous individuals was the highest of all the various population segments. Although the census data indicate inequalities by color or race, the infant mortality rates for indigenous and black individuals were lower than those based on data from SIM/SINASC. Methodological specificities in the data collection in the two sources should be considered. The reduction in IMR in Brazil in recent decades is largely attributed to the priority of infant health on the policy agenda. The study's findings indicate that the impact of public policies failed to reach indigenous peoples on the same scale as in the rest of the population. New sources of nationwide data on deaths in households, as in the case of the 2010 Census, can contribute to a better understanding of inequalities by color or race in Brazil.

Ontology- and graph-based similarity assessment in biological networks.

PubMed

Wang, Haiying; Zheng, Huiru; Azuaje, Francisco

2010-10-15

A standard systems-based approach to biomarker and drug target discovery consists of placing putative biomarkers in the context of a network of biological interactions, followed by different 'guilt-by-association' analyses. The latter is typically done based on network structural features. Here, an alternative analysis approach in which the networks are analyzed on a 'semantic similarity' space is reported. Such information is extracted from ontology-based functional annotations. We present SimTrek, a Cytoscape plugin for ontology-based similarity assessment in biological networks. http://rosalind.infj.ulst.ac.uk/SimTrek.html francisco.azuaje@crp-sante.lu Supplementary data are available at Bioinformatics online.

The Future of Architecture Collaborative Information Sharing: DoDAF Version 2.03 Updates

DTIC Science & Technology

2012-04-30

Salamander x Select Solution Factory Select Business Solutions BPMN , UML x SimonTool Simon Labs x SimProcess CACI BPMN x System Architecture Management...for DoDAF Mega UML x Metastorm ProVision Metastorm BPMN x Naval Simulation System - 4 Aces METRON x NetViz CA x OPNET OPNET x Tool Name Vendor Primary

ToF-SIMS cluster ion imaging of hippocampal CA1 pyramidal rat neurons

NASA Astrophysics Data System (ADS)

Francis, J. T.; Nie, H.-Y.; Taylor, A. R.; Walzak, M. J.; Chang, W. H.; MacFabe, D. F.; Lau, W. M.

2008-12-01

Recent studies have demonstrated the power of time-of-flight secondary ion mass spectrometry (ToF-SIMS) cluster ion imaging to characterize biological structures, such as that of the rat central nervous system. A large number of the studies to date have been carried out on the "structural scale" imaging several mm 2 using mounted thin sections. In this work, we present our ToF-SIMS cluster ion imaging results on hippocampal rat brain neurons, at the cellular and sub-cellular levels. As a part of an ongoing investigation to examine gut linked metabolic factors in autism spectrum disorders using a novel rat model, we have observed a possible variation in hippocampal Cornu ammonis 1 (CA1) pyramidal neuron geometry in thin, paraformaldehyde fixed brain sections. However, the fixation process alters the tissue matrix such that much biochemical information appears to be lost. In an effort to preserve as much as possible this original information, we have established a protocol using unfixed thin brain sections, along with low dose, 500 eV Cs + pre-sputtering that allows imaging down to the sub-cellular scale with minimal sample preparation.

Renewable Energy Power System Modular SIMulators: RPM-Sim User's Guide (Supersedes October 1999 edition)

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

Bialasiewicz, J.T.; Muljadi, E.; Nix, G.R.

This version of the RPM-SIM User's Guide supersedes the October 1999 edition. Using the VisSimTM visual environment, researchers developed a modular simulation system to facilitate an application-specific, low-cost study of the system dynamics for wind-diesel hybrid power systems. This manual presents the principal modules of the simulator and, using case studies of a hybrid system, demonstrates some of the benefits that can be gained from understanding the effects of the designer's modifications to these complex dynamic systems.

Photo ion spectrometer

DOEpatents

Gruen, D.M.; Young, C.E.; Pellin, M.J.

1989-12-26

A charged particle spectrometer is described for performing ultrasensitive quantitative analysis of selected atomic components removed from a sample. Significant improvements in performing energy and angular refocusing spectroscopy are accomplished by means of a two dimensional structure for generating predetermined electromagnetic field boundary conditions. Both resonance and non-resonance ionization of selected neutral atomic components allow accumulation of increased chemical information. A multiplexed operation between a SIMS mode and a neutral atomic component ionization mode with EARTOF analysis enables comparison of chemical information from secondary ions and neutral atomic components removed from the sample. An electronic system is described for switching high level signals, such as SIMS signals, directly to a transient recorder and through a charge amplifier to the transient recorder for a low level signal pulse counting mode, such as for a neutral atomic component ionization mode. 12 figs.

Astrometric Planet Searches with SIM PlanetQuest

NASA Technical Reports Server (NTRS)

Beichman, Charles A.; Unwin, Stephen C.; Shao, Michael; Tanner, Angelle M.; Catanzarite, Joseph H.; March, Geoffrey W.

2007-01-01

SIM will search for planets with masses as small as the Earth's orbiting in the habitable zones' around more than 100 of the stars and could discover many dozen if Earth-like planets are common. With a planned 'Deep Survey' of 100-450 stars (depending on desired mass sensitivity) SIM will search for terrestrial planets around all of the candidate target stars for future direct detection missions such as Terrestrial Planet Finder and Darwin, SIM's 'Broad Survey' of 2010 stars will characterize single and multiple-planet systems around a wide variety of stellar types, including many now inaccessible with the radial velocity technique. In particular, SIM will search for planets around young stars providing insights into how planetary systems are born and evolve with time.

A holistic approach to SIM platform and its application to early-warning satellite system

NASA Astrophysics Data System (ADS)

Sun, Fuyu; Zhou, Jianping; Xu, Zheyao

2018-01-01

This study proposes a new simulation platform named Simulation Integrated Management (SIM) for the analysis of parallel and distributed systems. The platform eases the process of designing and testing both applications and architectures. The main characteristics of SIM are flexibility, scalability, and expandability. To improve the efficiency of project development, new models of early-warning satellite system were designed based on the SIM platform. Finally, through a series of experiments, the correctness of SIM platform and the aforementioned early-warning satellite models was validated, and the systematical analyses for the orbital determination precision of the ballistic missile during its entire flight process were presented, as well as the deviation of the launch/landing point. Furthermore, the causes of deviation and prevention methods will be fully explained. The simulation platform and the models will lay the foundations for further validations of autonomy technology in space attack-defense architecture research.

Visualization of metallodrugs in single cells by secondary ion mass spectrometry imaging.

PubMed

Wu, Kui; Jia, Feifei; Zheng, Wei; Luo, Qun; Zhao, Yao; Wang, Fuyi

2017-07-01

Secondary ion mass spectrometry, including nanoscale secondary ion mass spectrometry (NanoSIMS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS), has emerged as a powerful tool for biological imaging, especially for single cell imaging. SIMS imaging can provide information on subcellular distribution of endogenous and exogenous chemicals, including metallodrugs, from membrane through to cytoplasm and nucleus without labeling, and with high spatial resolution and chemical specificity. In this mini-review, we summarize recent progress in the field of SIMS imaging, particularly in the characterization of the subcellular distribution of metallodrugs. We anticipate that the SIMS imaging method will be widely applied to visualize subcellular distributions of drugs and drug candidates in single cells, exerting significant influence on early drug evaluation and metabolism in medicinal and pharmaceutical chemistry. Recent progress of SIMS applications in characterizing the subcellular distributions of metallodrugs was summarized.

Nitric oxide assisted C60 secondary ion mass spectrometry for molecular depth profiling of polyelectrolyte multilayers.

PubMed

Zappalà, G; Motta, V; Tuccitto, N; Vitale, S; Torrisi, A; Licciardello, A

2015-12-15

Secondary ion mass spectrometry (SIMS) with polyatomic primary ions provides a successful tool for molecular depth profiling of polymer systems, relevant in many technological applications. Widespread C60 sources, however, cause in some polymers extensive damage with loss of molecular information along depth. We study a method, based on the use of a radical scavenger, for inhibiting ion-beam-induced reactions causing sample damage. Layered polystyrene sulfonate and polyacrylic acid based polyelectrolyte films, behaving differently towards C60 beam-induced damage, were selected and prepared as model systems. They were depth profiled by means of time-of-flight (TOF)-SIMS in dual beam mode, using fullerene ions for sputtering. Nitric oxide was introduced into the analysis chamber as a radical scavenger. The effect of sample cooling combined with NO-dosing on the quality of depth profiles was explored. NO-dosing during C60-SIMS depth profiling of >1 micrometer-thick multilayered polyelectrolytes allows detection, along depth, of characteristic fragments from systems otherwise damaged by C60 bombardment, and increases sputtering yield by more than one order of magnitude. By contrast, NO has little influence on those layers that are well profiled with C60 alone. Such leveling effect, more pronounced at low temperature, leads to a dramatic improvement of profile quality, with a clear definition of interfaces. NO-dosing provides a tool for extending the applicability, in SIMS depth profiling, of the widely spread fullerene ion sources. In view of the acceptable erosion rates on inorganics, obtainable with C60, the method could be of relevance also in connection with the 3D-imaging of hybrid polymer/inorganic systems. Copyright © 2015 John Wiley & Sons, Ltd.

Integrating Satellite and Surface Sensor Networks for Irrigation Management Applications in California

NASA Astrophysics Data System (ADS)

Melton, F. S.; Johnson, L.; Post, K. M.; Guzman, A.; Zaragoza, I.; Spellenberg, R.; Rosevelt, C.; Michaelis, A.; Nemani, R. R.; Cahn, M.; Frame, K.; Temesgen, B.; Eching, S.

2016-12-01

Satellite mapping of evapotranspiration (ET) from irrigated agricultural lands can provide agricultural producers and water managers with information that can be used to optimize agricultural water use, especially in regions with limited water supplies. The timely delivery of information on agricultural crop water requirements has the potential to make irrigation scheduling more practical, convenient, and accurate. We present a system for irrigation scheduling and management support in California and describe lessons learned from the development and implementation of the system. The Satellite Irrigation Management Support (SIMS) framework integrates satellite data with information from agricultural weather networks to map crop canopy development, basal crop coefficients (Kcb), and basal crop evapotranspiration (ETcb) at the scale of individual fields. Information is distributed to agricultural producers and water managers via a web-based irrigation management decision support system and web data services. SIMS also provides an application programming interface (API) that facilitates integration with other irrigation decision support tools, estimation of total crop evapotranspiration (ETc) and calculation of on-farm water use efficiency metrics. Accuracy assessments conducted in commercial fields for more than a dozen crop types to date have shown that SIMS seasonal ETcb estimates are within 10% mean absolute error (MAE) for well-watered crops and within 15% across all crop types studied, and closely track daily ETc and running totals of ETc measured in each field. Use of a soil water balance model to correct for soil evaporation and crop water stress reduces this error to less than 8% MAE across all crop types studied to date relative to field measurements of ETc. Results from irrigation trials conducted by the project for four vegetable crops have also demonstrated the potential for use of ET-based irrigation management strategies to reduce total applied water by 20-40% relative to grower standard practices while maintaining crop yields and quality.

TOF-SIMS investigation of metallic material surface after culturing cells

NASA Astrophysics Data System (ADS)

Aoyagi, Satoka; Hiromoto, Sachiko; Hanawa, Takao; Kudo, Masahiro

2004-06-01

Biomolecules such as extracellular matrix and adhesive proteins generated by adhered cells on metallic specimens were characterized by means of time-of-flight secondary ion mass spectrometry (TOF-SIMS) in order to clarify the interaction between cells and metal surfaces. Since composition and structure of the extracellular matrix depends on conditions of cells, characterization of the interaction between cells and metallic specimens is important in order to evaluate the biocompatibility and the degradation behavior of metallic biomaterials and artificial organs. Moreover, the obtained data can contribute to the development of new metallic biomaterials. TOF-SIMS spectra were analyzed by means of mutual information described by information theory and principal components analysis (PCA). The results show that cells have great influence on adsorption of biomolecules on metallic materials because they change surface conditions of the materials. Thus TOF-SIMS is a useful technique to investigate the interaction between metallic biomaterials and cells.

Development and Validation of High Precision Thermal, Mechanical, and Optical Models for the Space Interferometry Mission

NASA Technical Reports Server (NTRS)

Lindensmith, Chris A.; Briggs, H. Clark; Beregovski, Yuri; Feria, V. Alfonso; Goullioud, Renaud; Gursel, Yekta; Hahn, Inseob; Kinsella, Gary; Orzewalla, Matthew; Phillips, Charles

2006-01-01

SIM Planetquest (SIM) is a large optical interferometer for making microarcsecond measurements of the positions of stars, and to detect Earth-sized planets around nearby stars. To achieve this precision, SIM requires stability of optical components to tens of picometers per hour. The combination of SIM s large size (9 meter baseline) and the high stability requirement makes it difficult and costly to measure all aspects of system performance on the ground. To reduce risks, costs and to allow for a design with fewer intermediate testing stages, the SIM project is developing an integrated thermal, mechanical and optical modeling process that will allow predictions of the system performance to be made at the required high precision. This modeling process uses commercial, off-the-shelf tools and has been validated against experimental results at the precision of the SIM performance requirements. This paper presents the description of the model development, some of the models, and their validation in the Thermo-Opto-Mechanical (TOM3) testbed which includes full scale brassboard optical components and the metrology to test them at the SIM performance requirement levels.

System Design Package for SIMS Prototype System 3, Solar Heating and Domestic Hot Water

NASA Technical Reports Server (NTRS)

1978-01-01

A collation of documents and drawings are presented that describe a prototype solar heating and hot water system using liquid flat plate collectors and a gas or electric furnace energy subsystem. The system was designed for installation into a single-family dwelling. The description, performance specification, subsystem drawings, verification plan/procedure, and hazard analysis of the system are packaged for evaluation of the system with information sufficient to assemble a similar system.

Error Modeling of Multibaseline Optical Truss: Part 1: Modeling of System Level Performance

NASA Technical Reports Server (NTRS)

Milman, Mark H.; Korechoff, R. E.; Zhang, L. D.

2004-01-01

Global astrometry is the measurement of stellar positions and motions. These are typically characterized by five parameters, including two position parameters, two proper motion parameters, and parallax. The Space Interferometry Mission (SIM) will derive these parameters for a grid of approximately 1300 stars covering the celestial sphere to an accuracy of approximately 4uas, representing a two orders of magnitude improvement over the most precise current star catalogues. Narrow angle astrometry will be performed to a 1uas accuracy. A wealth of scientific information will be obtained from these accurate measurements encompassing many aspects of both galactic (and extragalactic science. SIM will be subject to a number of instrument errors that can potentially degrade performance. Many of these errors are systematic in that they are relatively static and repeatable with respect to the time frame and direction of the observation. This paper and its companion define the modeling of the, contributing factors to these errors and the analysis of how they impact SIM's ability to perform astrometric science.

Reversible solvatomagnetic switching in a single-ion magnet from an entatic state.

PubMed

Vallejo, J; Pardo, E; Viciano-Chumillas, M; Castro, I; Amorós, P; Déniz, M; Ruiz-Pérez, C; Yuste-Vivas, C; Krzystek, J; Julve, M; Lloret, F; Cano, J

2017-05-01

A vast impact on molecular nanoscience can be achieved using simple transition metal complexes as dynamic chemical systems to perform specific and selective tasks under the control of an external stimulus that switches "ON" and "OFF" their electronic properties. While the interest in single-ion magnets (SIMs) lies in their potential applications in information storage and quantum computing, the switching of their slow magnetic relaxation associated with host-guest processes is insufficiently explored. Herein, we report a unique example of a mononuclear cobalt(ii) complex in which geometrical constraints are the cause of easy and reversible water coordination and its release. As a result, a reversible and selective colour and SIM behaviour switch occurs between a "slow-relaxing" deep red anhydrous material (compound 1 ) and its "fast-relaxing" orange hydrated form (compound 2 ). The combination of this optical and magnetic switching in this new class of vapochromic and thermochromic SIMs offers fascinating possibilities for designing multifunctional molecular materials.

Open-source image reconstruction of super-resolution structured illumination microscopy data in ImageJ

PubMed Central

Müller, Marcel; Mönkemöller, Viola; Hennig, Simon; Hübner, Wolfgang; Huser, Thomas

2016-01-01

Super-resolved structured illumination microscopy (SR-SIM) is an important tool for fluorescence microscopy. SR-SIM microscopes perform multiple image acquisitions with varying illumination patterns, and reconstruct them to a super-resolved image. In its most frequent, linear implementation, SR-SIM doubles the spatial resolution. The reconstruction is performed numerically on the acquired wide-field image data, and thus relies on a software implementation of specific SR-SIM image reconstruction algorithms. We present fairSIM, an easy-to-use plugin that provides SR-SIM reconstructions for a wide range of SR-SIM platforms directly within ImageJ. For research groups developing their own implementations of super-resolution structured illumination microscopy, fairSIM takes away the hurdle of generating yet another implementation of the reconstruction algorithm. For users of commercial microscopes, it offers an additional, in-depth analysis option for their data independent of specific operating systems. As a modular, open-source solution, fairSIM can easily be adapted, automated and extended as the field of SR-SIM progresses. PMID:26996201

Elemental and isotopic imaging of biological samples using NanoSIMS.

PubMed

Kilburn, Matt R; Clode, Peta L

2014-01-01

With its low detection limits and the ability to analyze most of the elements in the periodic table, secondary ion mass spectrometry (SIMS) represents one of the most versatile in situ analytical techniques available, and recent developments have resulted in significant advantages for the use of imaging mass spectrometry in biological and biomedical research. Increases in spatial resolution and sensitivity allow detailed interrogation of samples at relevant scales and chemical concentrations. Advances in dynamic SIMS, specifically with the advent of NanoSIMS, now allow the tracking of stable isotopes within biological systems at subcellular length scales, while static SIMS combines subcellular imaging with molecular identification. In this chapter, we present an introduction to the SIMS technique, with particular reference to NanoSIMS, and discuss its application in biological and biomedical research.

A platform for dynamic simulation and control of movement based on OpenSim and MATLAB.

PubMed

Mansouri, Misagh; Reinbolt, Jeffrey A

2012-05-11

Numerical simulations play an important role in solving complex engineering problems and have the potential to revolutionize medical decision making and treatment strategies. In this paper, we combine the rapid model-based design, control systems and powerful numerical method strengths of MATLAB/Simulink with the simulation and human movement dynamics strengths of OpenSim by developing a new interface between the two software tools. OpenSim is integrated with Simulink using the MATLAB S-function mechanism, and the interface is demonstrated using both open-loop and closed-loop control systems. While the open-loop system uses MATLAB/Simulink to separately reproduce the OpenSim Forward Dynamics Tool, the closed-loop system adds the unique feature of feedback control to OpenSim, which is necessary for most human movement simulations. An arm model example was successfully used in both open-loop and closed-loop cases. For the open-loop case, the simulation reproduced results from the OpenSim Forward Dynamics Tool with root mean square (RMS) differences of 0.03° for the shoulder elevation angle and 0.06° for the elbow flexion angle. MATLAB's variable step-size integrator reduced the time required to generate the forward dynamic simulation from 7.1s (OpenSim) to 2.9s (MATLAB). For the closed-loop case, a proportional-integral-derivative controller was used to successfully balance a pole on model's hand despite random force disturbances on the pole. The new interface presented here not only integrates the OpenSim and MATLAB/Simulink software tools, but also will allow neuroscientists, physiologists, biomechanists, and physical therapists to adapt and generate new solutions as treatments for musculoskeletal conditions. Copyright © 2012 Elsevier Ltd. All rights reserved.

A platform for dynamic simulation and control of movement based on OpenSim and MATLAB

PubMed Central

Mansouri, Misagh; Reinbolt, Jeffrey A.

2013-01-01

Numerical simulations play an important role in solving complex engineering problems and have the potential to revolutionize medical decision making and treatment strategies. In this paper, we combine the rapid model-based design, control systems and powerful numerical method strengths of MATLAB/Simulink with the simulation and human movement dynamics strengths of OpenSim by developing a new interface between the two software tools. OpenSim is integrated with Simulink using the MATLAB S-function mechanism, and the interface is demonstrated using both open-loop and closed-loop control systems. While the open-loop system uses MATLAB/Simulink to separately reproduce the OpenSim Forward Dynamics Tool, the closed-loop system adds the unique feature of feedback control to OpenSim, which is necessary for most human movement simulations. An arm model example was successfully used in both open-loop and closed-loop cases. For the open-loop case, the simulation reproduced results from the OpenSim Forward Dynamics Tool with root mean square (RMS) differences of 0.03° for the shoulder elevation angle and 0.06° for the elbow flexion angle. MATLAB’s variable step-size integrator reduced the time required to generate the forward dynamic simulation from 7.1 s (OpenSim) to 2.9 s (MATLAB). For the closed-loop case, a proportional–integral–derivative controller was used to successfully balance a pole on model’s hand despite random force disturbances on the pole. The new interface presented here not only integrates the OpenSim and MATLAB/Simulink software tools, but also will allow neuroscientists, physiologists, biomechanists, and physical therapists to adapt and generate new solutions as treatments for musculoskeletal conditions. PMID:22464351

SIMS prototype system 3 test results: Engineering analysis

NASA Technical Reports Server (NTRS)

1978-01-01

The results obtained during testing of a closed hydronic drain down solar system designed for space and hot water heating is presented. Data analysis is included which documents the system performance and verifies the suitability of SIMS Prototype System 3 for field installation.

Determination of oligomeric chain length distributions at surfaces using ToF-SIMS: segregation effects and polymer properties

NASA Astrophysics Data System (ADS)

Gardella, Joseph A.; Mahoney, Christine M.

2004-06-01

While many XPS and SIMS studies of polymers have detected and quantified segregation of low surface energy blocks or components in copolymers and polymer blends [D. Briggs, in: D.R. Clarke, S. Suresh, I.M. Ward (Eds.), Surface Analysis of Polymers by XPS and Static SIMS, Cambridge University Press, Cambridge, 1998 (Chapter 5).], this paper reports ToF-SIMS studies of direct measurement of the segment length distribution at the surface of siloxane copolymers. These data allow insight into the segregation of particular portions of the oligomeric distribution; specifically, in this study, longer PDMS oligomers segregated at the expense of shorter PDMS chains. We have reported XPS analysis of competitive segregation effects for short PDMS chains [Macromolecules 35 (13) (2002) 5256]. In this study, a series of poly(ureaurethane)-poly(dimethylsiloxane) (PUU-PDMS) copolymers have been synthesized containing varying ratios of G-3 and G-9 (G- X describes the average segment length of the PDMS added), while maintaining a constant overall siloxane weight percentage (10, 30, and 60%). These copolymers were utilized as model systems to study the preferential segregation of certain siloxane segment lengths to the surface over others. ToF-SIMS analysis of PUU-PDMS copolymers has yielded high-mass range copolymer fragmentation patterns containing intact PDMS segments. For the first time, this information is utilized to determine PDMS segment length distributions at the copolymer surface as compared to the bulk. The results show that longer siloxane segment lengths are preferentially segregating to the surface over shorter chain lengths. These results also show the importance of ToF-SIMS and mass spectrometry in the development of new materials containing low molecular weight amino-propyl-terminated siloxanes.

Review of Forensic Tools for Smartphones

NASA Astrophysics Data System (ADS)

Jahankhani, Hamid; Azam, Amir

The technological capability of mobile devices in particular Smartphones makes their use of value to the criminal community as a data terminal in the facilitation of organised crime or terrorism. The effective targeting of these devices from criminal and security intelligence perspectives and subsequent detailed forensic examination of the targeted device will significantly enhance the evidence available to the law enforcement community. When phone devices are involved in crimes, forensic examiners require tools that allow the proper retrieval and prompt examination of information present on these devices. Smartphones that are compliant to Global System for Mobile Communication (GSM) standards, will maintains their identity and user's personal information on Subscriber Identity Module (SIM). Beside SIM cards, substantial amount of information is stored on device's internal memory and external memory modules. The aim of this paper is to give an overview of the currently available forensic software tools that are developed to carry out forensic investigation of mobile devices and point to current weaknesses within this process.

Kite: Status of the External Metrology Testbed for SIM

NASA Technical Reports Server (NTRS)

Dekens, Frank G.; Alvarez-Salazar, Oscar; Azizi, Alireza; Moser, Steven; Nemati, Bijan; Negron, John; Neville, Timothy; Ryan, Daniel

2004-01-01

Kite is a system level testbed for the External Metrology system of the Space Interferometry Mission (SIM). The External Metrology System is used to track the fiducial that are located at the centers of the interferometer's siderostats. The relative changes in their positions needs to be tracked to tens of picometers in order to correct for thermal measurements, the Kite testbed was build to test both the metrology gauges and out ability to optically model the system at these levels. The Kite testbed is an over-constraint system where 6 lengths are measured, but only 5 are needed to determine the system. The agreement in the over-constrained length needs to be on the order of 140 pm for the SIM Wide-Angle observing scenario and 8 pm for the Narrow-Angle observing scenario. We demonstrate that we have met the Wide-Angle goal with our current setup. For the Narrow-Angle case, we have only reached the goal for on-axis observations. We describe the testbed improvements that have been made since our initial results, and outline the future Kite changes that will add further effects that SIM faces in order to make the testbed more SIM like.

High-resolution high-sensitivity elemental imaging by secondary ion mass spectrometry: from traditional 2D and 3D imaging to correlative microscopy

NASA Astrophysics Data System (ADS)

Wirtz, T.; Philipp, P.; Audinot, J.-N.; Dowsett, D.; Eswara, S.

2015-10-01

Secondary ion mass spectrometry (SIMS) constitutes an extremely sensitive technique for imaging surfaces in 2D and 3D. Apart from its excellent sensitivity and high lateral resolution (50 nm on state-of-the-art SIMS instruments), advantages of SIMS include high dynamic range and the ability to differentiate between isotopes. This paper first reviews the underlying principles of SIMS as well as the performance and applications of 2D and 3D SIMS elemental imaging. The prospects for further improving the capabilities of SIMS imaging are discussed. The lateral resolution in SIMS imaging when using the microprobe mode is limited by (i) the ion probe size, which is dependent on the brightness of the primary ion source, the quality of the optics of the primary ion column and the electric fields in the near sample region used to extract secondary ions; (ii) the sensitivity of the analysis as a reasonable secondary ion signal, which must be detected from very tiny voxel sizes and thus from a very limited number of sputtered atoms; and (iii) the physical dimensions of the collision cascade determining the origin of the sputtered ions with respect to the impact site of the incident primary ion probe. One interesting prospect is the use of SIMS-based correlative microscopy. In this approach SIMS is combined with various high-resolution microscopy techniques, so that elemental/chemical information at the highest sensitivity can be obtained with SIMS, while excellent spatial resolution is provided by overlaying the SIMS images with high-resolution images obtained by these microscopy techniques. Examples of this approach are given by presenting in situ combinations of SIMS with transmission electron microscopy (TEM), helium ion microscopy (HIM) and scanning probe microscopy (SPM).

Space Interferometry Mission: Measuring the Universe

NASA Technical Reports Server (NTRS)

Marr, James; Dallas, Saterios; Laskin, Robert; Unwin, Stephen; Yu, Jeffrey

1991-01-01

The Space Interferometry Mission (SIM) will be the NASA Origins Program's first space based long baseline interferometric observatory. SIM will use a 10 m Michelson stellar interferometer to provide 4 microarcsecond precision absolute position measurements of stars down to 20th magnitude over its 5 yr. mission lifetime. SIM will also provide technology demonstrations of synthesis imaging and interferometric nulling. This paper describes the what, why and how of the SIM mission, including an overall mission and system description, science objectives, general description of how SIM makes its measurements, description of the design concepts now under consideration, operations concept, and supporting technology program.

Subcellular boron and fluorine distributions with SIMS ion microscopy in BNCT and cancer research

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

Subhash Chandra

2008-05-30

The development of a secondary ion mass spectrometry (SIMS) based technique of Ion Microscopy in boron neutron capture therapy (BNCT) was the main goal of this project, so that one can study the subcellular location of boron-10 atoms and their partitioning between the normal and cancerous tissue. This information is fundamental for the screening of boronated drugs appropriate for neutron capture therapy of cancer. Our studies at Cornell concentrated mainly on studies of glioblastoma multiforme (GBM). The early years of the grant were dedicated to the development of cryogenic methods and correlative microscopic approaches so that a reliable subcellular analysismore » of boron-10 atoms can be made with SIMS. In later years SIMS was applied to animal models and human tissues of GBM for studying the efficacy of potential boronated agents in BNCT. Under this grant the SIMS program at Cornell attained a new level of excellence and collaborative SIMS studies were published with leading BNCT researchers in the U.S.« less

Secondary ion mass spectrometry: The application in the analysis of atmospheric particulate matter

DOE PAGES

Huang, Di; Hua, Xin; Xiu, Guang-Li; ...

2017-07-24

Currently, considerable attention has been paid to atmospheric particulate matter (PM) investigation due to its importance in human health and global climate change. Surface characterization, single particle analysis and depth profiling of PM is important for a better understanding of its formation processes and predicting its impact on the environment and human being. Secondary ion mass spectrometry (SIMS) is a surface technique with high surface sensitivity, high spatial resolution chemical imaging and unique depth profiling capabilities. Recent research shows that SIMS has great potential in analyzing both surface and bulk chemical information of PM. In this review, we give amore » brief introduction of SIMS working principle and survey recent applications of SIMS in PM characterization. In particular, analyses from different types of PM sources by various SIMS techniques were discussed concerning their advantages and limitations. Finally, we propose, the future development and needs of SIMS in atmospheric aerosol measurement with a perspective in broader environmental sciences.« less

Secondary ion mass spectrometry: The application in the analysis of atmospheric particulate matter

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

Huang, Di; Hua, Xin; Xiu, Guang-Li

Currently, considerable attention has been paid to atmospheric particulate matter (PM) investigation due to its importance in human health and global climate change. Surface characterization, single particle analysis and depth profiling of PM is important for a better understanding of its formation processes and predicting its impact on the environment and human being. Secondary ion mass spectrometry (SIMS) is a surface technique with high surface sensitivity, high spatial resolution chemical imaging and unique depth profiling capabilities. Recent research shows that SIMS has great potential in analyzing both surface and bulk chemical information of PM. In this review, we give amore » brief introduction of SIMS working principle and survey recent applications of SIMS in PM characterization. In particular, analyses from different types of PM sources by various SIMS techniques were discussed concerning their advantages and limitations. Finally, we propose, the future development and needs of SIMS in atmospheric aerosol measurement with a perspective in broader environmental sciences.« less

TOF-SIMS Analysis of Red Color Inks of Writing and Printing Tools on Questioned Documents.

PubMed

Lee, Jihye; Nam, Yun Sik; Min, Jisook; Lee, Kang-Bong; Lee, Yeonhee

2016-05-01

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is a well-established surface technique that provides both elemental and molecular information from several monolayers of a sample surface while also allowing depth profiling or image mapping to be performed. Static TOF-SIMS with improved performances has expanded the application of TOF-SIMS to the study of a variety of organic, polymeric, biological, archaeological, and forensic materials. In forensic investigation, the use of a minimal sample for the analysis is preferable. Although the TOF-SIMS technique is destructive, the probing beams have microsized diameters so that only small portion of the questioned sample is necessary for the analysis, leaving the rest available for other analyses. In this study, TOF-SIMS and attenuated total reflectance Fourier transform infrared (ATR-FTIR) were applied to the analysis of several different pen inks, red sealing inks, and printed patterns on paper. The overlapping areas of ballpoint pen writing, red seal stamping, and laser printing in a document were investigated to identify the sequence of recording. The sequence relations for various cases were determined from the TOF-SIMS mapping image and the depth profile. TOF-SIMS images were also used to investigate numbers or characters altered with two different red pens. TOF-SIMS was successfully used to determine the sequence of intersecting lines and the forged numbers on the paper. © 2016 American Academy of Forensic Sciences.

Binding properties of SUMO-interacting motifs (SIMs) in yeast.

PubMed

Jardin, Christophe; Horn, Anselm H C; Sticht, Heinrich

2015-03-01

Small ubiquitin-like modifier (SUMO) conjugation and interaction play an essential role in many cellular processes. A large number of yeast proteins is known to interact non-covalently with SUMO via short SUMO-interacting motifs (SIMs), but the structural details of this interaction are yet poorly characterized. In the present work, sequence analysis of a large dataset of 148 yeast SIMs revealed the existence of a hydrophobic core binding motif and a preference for acidic residues either within or adjacent to the core motif. Thus the sequence properties of yeast SIMs are highly similar to those described for human. Molecular dynamics simulations were performed to investigate the binding preferences for four representative SIM peptides differing in the number and distribution of acidic residues. Furthermore, the relative stability of two previously observed alternative binding orientations (parallel, antiparallel) was assessed. For all SIMs investigated, the antiparallel binding mode remained stable in the simulations and the SIMs were tightly bound via their hydrophobic core residues supplemented by polar interactions of the acidic residues. In contrary, the stability of the parallel binding mode is more dependent on the sequence features of the SIM motif like the number and position of acidic residues or the presence of additional adjacent interaction motifs. This information should be helpful to enhance the prediction of SIMs and their binding properties in different organisms to facilitate the reconstruction of the SUMO interactome.

In Situ SIMS and IR Spectroscopy of Well-defined Surfaces Prepared by Soft Landing of Mass-selected Ions

PubMed Central

Johnson, Grant E.; Gunaratne, K. Don Dasitha; Laskin, Julia

2014-01-01

Soft landing of mass-selected ions onto surfaces is a powerful approach for the highly-controlled preparation of materials that are inaccessible using conventional synthesis techniques. Coupling soft landing with in situ characterization using secondary ion mass spectrometry (SIMS) and infrared reflection absorption spectroscopy (IRRAS) enables analysis of well-defined surfaces under clean vacuum conditions. The capabilities of three soft-landing instruments constructed in our laboratory are illustrated for the representative system of surface-bound organometallics prepared by soft landing of mass-selected ruthenium tris(bipyridine) dications, [Ru(bpy)3]2+ (bpy = bipyridine), onto carboxylic acid terminated self-assembled monolayer surfaces on gold (COOH-SAMs). In situ time-of-flight (TOF)-SIMS provides insight into the reactivity of the soft-landed ions. In addition, the kinetics of charge reduction, neutralization and desorption occurring on the COOH-SAM both during and after ion soft landing are studied using in situ Fourier transform ion cyclotron resonance (FT-ICR)-SIMS measurements. In situ IRRAS experiments provide insight into how the structure of organic ligands surrounding metal centers is perturbed through immobilization of organometallic ions on COOH-SAM surfaces by soft landing. Collectively, the three instruments provide complementary information about the chemical composition, reactivity and structure of well-defined species supported on surfaces. PMID:24961913

In Situ SIMS and IR Spectroscopy of Well-Defined Surfaces Prepared by Soft Landing of Mass-Selected Ions

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

Johnson, Grant E.; Gunaratne, Kalupathirannehelage Don D.; Laskin, Julia

2014-06-16

Soft landing of mass-selected ions onto surfaces is a powerful approach for the highly-controlled preparation of materials that are inaccessible using conventional synthesis techniques. Coupling soft landing with in situ characterization using secondary ion mass spectrometry (SIMS) and infrared reflection absorption spectroscopy (IRRAS) enables analysis of well-defined surfaces under clean vacuum conditions. The capabilities of three soft-landing instruments constructed in our laboratory are illustrated for the representative system of surface-bound organometallics prepared by soft landing of mass-selected ruthenium tris(bipyridine) dications, [Ru(bpy)3]2+, onto carboxylic acid terminated self-assembled monolayer surfaces on gold (COOH-SAMs). In situ time-of-flight (TOF)-SIMS provides insight into the reactivitymore » of the soft-landed ions. In addition, the kinetics of charge reduction, neutralization and desorption occurring on the COOH-SAM both during and after ion soft landing are studied using in situ Fourier transform ion cyclotron resonance (FT-ICR)-SIMS measurements. In situ IRRAS experiments provide insight into how the structure of organic ligands surrounding metal centers is perturbed through immobilization of organometallic ions on COOH-SAM surfaces by soft landing. Collectively, the three instruments provide complementary information about the chemical composition, reactivity and structure of well-defined species supported on surfaces.« less

S-SIMS and MetA-SIMS study of organic additives in thin polymer coatings

NASA Astrophysics Data System (ADS)

Adriaensen, L.; Vangaever, F.; Lenaerts, J.; Gijbels, R.

2006-07-01

In the present study a methodology for TOF-S-SIMS measurements is developed to gain information on the distribution of molecules on and in polymer coatings (thickness ˜100 μm). Experiments were carried out on model systems consisting of one or more additive-containing polyvinylbutyral coatings. Several organic additives were selected: carbocyanine dyes, basonyl blue and the pharmaceutical risperidone. The additives have been measured as pure compounds on a Si substrate to obtain good reference spectra. After optimisation of the sample preparation method, the coatings were embedded in epoxy resin and stored in an oven (60 °C) for 24 h. Cross-sections were made by means of a microtome. S-SIMS spectra were taken on the prepared cross-sections before and after Au was deposited on the sample surface. Compared to the untreated samples, the Au covered samples give rise to more intense secondary ion signals. Generally, signals of the intact cations were more intense than those of the fragment ions. Apart from mass spectra, images of the additive distribution in the coatings could also be acquired by recording structural ion signals. It was possible to make secondary ion images of the additive molecule ions with a (sub)-micrometer lateral resolution.

Imaging of Al/Fe ratios in synthetic Al-goethite revealed by nanoscale secondary ion mass spectrometry.

PubMed

Pohl, Lydia; Kölbl, Angelika; Werner, Florian; Mueller, Carsten W; Höschen, Carmen; Häusler, Werner; Kögel-Knabner, Ingrid

2018-04-30

Aluminium (Al)-substituted goethite is ubiquitous in soils and sediments. The extent of Al-substitution affects the physicochemical properties of the mineral and influences its macroscale properties. Bulk analysis only provides total Al/Fe ratios without providing information with respect to the Al-substitution of single minerals. Here, we demonstrate that nanoscale secondary ion mass spectrometry (NanoSIMS) enables the precise determination of Al-content in single minerals, while simultaneously visualising the variation of the Al/Fe ratio. Al-substituted goethite samples were synthesized with increasing Al concentrations of 0.1, 3, and 7 % and analysed by NanoSIMS in combination with established bulk spectroscopic methods (XRD, FTIR, Mössbauer spectroscopy). The high spatial resolution (50-150 nm) of NanoSIMS is accompanied by a high number of single-point measurements. We statistically evaluated the Al/Fe ratios derived from NanoSIMS, while maintaining the spatial information and reassigning it to its original localization. XRD analyses confirmed increasing concentration of incorporated Al within the goethite structure. Mössbauer spectroscopy revealed 11 % of the goethite samples generated at high Al concentrations consisted of hematite. The NanoSIMS data show that the Al/Fe ratios are in agreement with bulk data derived from total digestion and demonstrated small spatial variability between single-point measurements. More advantageously, statistical analysis and reassignment of single-point measurements allowed us to identify distinct spots with significantly higher or lower Al/Fe ratios. NanoSIMS measurements confirmed the capacity to produce images, which indicated the uniform increase in Al-concentrations in goethite. Using a combination of statistical analysis with information from complementary spectroscopic techniques (XRD, FTIR and Mössbauer spectroscopy) we were further able to reveal spots with lower Al/Fe ratios as hematite. Copyright © 2018 John Wiley & Sons, Ltd.

Advantages to Geoscience and Disaster Response from QuakeSim Implementation of Interferometric Radar Maps in a GIS Database System

NASA Astrophysics Data System (ADS)

Parker, Jay; Donnellan, Andrea; Glasscoe, Margaret; Fox, Geoffrey; Wang, Jun; Pierce, Marlon; Ma, Yu

2015-08-01

High-resolution maps of earth surface deformation are available in public archives for scientific interpretation, but are primarily available as bulky downloads on the internet. The NASA uninhabited aerial vehicle synthetic aperture radar (UAVSAR) archive of airborne radar interferograms delivers very high resolution images (approximately seven meter pixels) making remote handling of the files that much more pressing. Data exploration requiring data selection and exploratory analysis has been tedious. QuakeSim has implemented an archive of UAVSAR data in a web service and browser system based on GeoServer (http://geoserver.org). This supports a variety of services that supply consistent maps, raster image data and geographic information systems (GIS) objects including standard earthquake faults. Browsing the database is supported by initially displaying GIS-referenced thumbnail images of the radar displacement maps. Access is also provided to image metadata and links for full file downloads. One of the most widely used features is the QuakeSim line-of-sight profile tool, which calculates the radar-observed displacement (from an unwrapped interferogram product) along a line specified through a web browser. Displacement values along a profile are updated to a plot on the screen as the user interactively redefines the endpoints of the line and the sampling density. The profile and also a plot of the ground height are available as CSV (text) files for further examination, without any need to download the full radar file. Additional tools allow the user to select a polygon overlapping the radar displacement image, specify a downsampling rate and extract a modest sized grid of observations for display or for inversion, for example, the QuakeSim simplex inversion tool which estimates a consistent fault geometry and slip model.

Rapid characterisation of surface modifications and treatments using a benchtop SIMS instrument

NASA Astrophysics Data System (ADS)

McPhail, D. S.; Sokhan, M.; Rees, E. E.; Cliff, B.; Eccles, A. J.; Chater, R. J.

2004-06-01

The development of a novel benchtop SIMS instrument (Millbrook MiniSIMS) [Appl. Surf. Sci. 144 (1999) 106] has brought routine SIMS analysis to many new users, for example museum conservators. This is a result of the simple operation and the relatively low capital cost of the instrument. We report here on the continued development of the system in terms of increasing performance and functionality and its use in museum conservation based applications where a mobile instrument for high throughput, rapid SIMS analysis has proven to be of great benefit to the user. The example we describe here is the application of the MiniSIMS to the analysis of silver thread woven into a silk dress before and after laser cleaning.

PRUNE—SIM users guide.

Treesearch

R.D. Fight; J.M. Cahill; T.A. Snellgrove; T.D. Fahey

1987-01-01

PRUNE-SIM is a spreadsheet template (program) that allows users to simulate a financial analysis of pruning coast Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco var. menziesii). The program estimates the increase in product value resulting from pruning the butt 17-foot log. Product recovery information is based on actual...

TOF-SIMS imaging of protein adsorption on dialysis membrane

NASA Astrophysics Data System (ADS)

Aoyagi, Satoka; Hayama, Msayo; Hasegawa, Urara; Sakai, Kiyotaka; Hoshi, Takahiro; Kudo, Masahiro

2004-06-01

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is capable of chemical imaging of proteins on insulated samples such as hollow-fiber dialysis membranes. Albumin loss and a lowering of diffusive permeability caused by protein adsorption on dialysis membranes should be reduced in order to enhance dialysis adequacy of the patients. Bovine serum albumin (BSA)-adsorbed hollow-fiber dialysis membranes were tested in the present study. TOF-SIMS images and spectra of both native membranes and BSA-adsorbed membranes were compared in order to identify secondary ions related to BSA and membranes. Peaks of secondary ions related to BSA and each membrane were selected by means of information theory, and they are characterized by principal component analysis (PCA). Chemical images of BSA adsorption on both native and treated membranes were obtained to find that BSA permeability and interaction between the membranes and BSA definitely depend on the properties of a membrane. TOF-SIMS imaging obtained with information theory is a powerful tool to estimate protein adsorption on the dialysis membranes.

Exploratory analysis of TOF-SIMS data from biological surfaces

NASA Astrophysics Data System (ADS)

Vaidyanathan, Seetharaman; Fletcher, John S.; Henderson, Alex; Lockyer, Nicholas P.; Vickerman, John C.

2008-12-01

The application of multivariate analytical tools enables simplification of TOF-SIMS datasets so that useful information can be extracted from complex spectra and images, especially those that do not give readily interpretable results. There is however a challenge in understanding the outputs from such analyses. The problem is complicated when analysing images, given the additional dimensions in the dataset. Here we demonstrate how the application of simple pre-processing routines can enable the interpretation of TOF-SIMS spectra and images. For the spectral data, TOF-SIMS spectra used to discriminate bacterial isolates associated with urinary tract infection were studied. Using different criteria for picking peaks before carrying out PC-DFA enabled identification of the discriminatory information with greater certainty. For the image data, an air-dried salt stressed bacterial sample, discussed in another paper by us in this issue, was studied. Exploration of the image datasets with and without normalisation prior to multivariate analysis by PCA or MAF resulted in different regions of the image being highlighted by the techniques.

Co-clustering directed graphs to discover asymmetries and directional communities

PubMed Central

Rohe, Karl; Qin, Tai; Yu, Bin

2016-01-01

In directed graphs, relationships are asymmetric and these asymmetries contain essential structural information about the graph. Directed relationships lead to a new type of clustering that is not feasible in undirected graphs. We propose a spectral co-clustering algorithm called di-sim for asymmetry discovery and directional clustering. A Stochastic co-Blockmodel is introduced to show favorable properties of di-sim. To account for the sparse and highly heterogeneous nature of directed networks, di-sim uses the regularized graph Laplacian and projects the rows of the eigenvector matrix onto the sphere. A nodewise asymmetry score and di-sim are used to analyze the clustering asymmetries in the networks of Enron emails, political blogs, and the Caenorhabditis elegans chemical connectome. In each example, a subset of nodes have clustering asymmetries; these nodes send edges to one cluster, but receive edges from another cluster. Such nodes yield insightful information (e.g., communication bottlenecks) about directed networks, but are missed if the analysis ignores edge direction. PMID:27791058

Co-clustering directed graphs to discover asymmetries and directional communities.

PubMed

Rohe, Karl; Qin, Tai; Yu, Bin

2016-10-21

In directed graphs, relationships are asymmetric and these asymmetries contain essential structural information about the graph. Directed relationships lead to a new type of clustering that is not feasible in undirected graphs. We propose a spectral co-clustering algorithm called di-sim for asymmetry discovery and directional clustering. A Stochastic co-Blockmodel is introduced to show favorable properties of di-sim To account for the sparse and highly heterogeneous nature of directed networks, di-sim uses the regularized graph Laplacian and projects the rows of the eigenvector matrix onto the sphere. A nodewise asymmetry score and di-sim are used to analyze the clustering asymmetries in the networks of Enron emails, political blogs, and the Caenorhabditis elegans chemical connectome. In each example, a subset of nodes have clustering asymmetries; these nodes send edges to one cluster, but receive edges from another cluster. Such nodes yield insightful information (e.g., communication bottlenecks) about directed networks, but are missed if the analysis ignores edge direction.

Probing nanoparticles and nanoparticle-conjugated biomolecules using time-of-flight secondary ion mass spectrometry.

PubMed

Kim, Young-Pil; Shon, Hyun Kyong; Shin, Seung Koo; Lee, Tae Geol

2015-01-01

Bio-conjugated nanoparticles have emerged as novel molecular probes in nano-biotechnology and nanomedicine and chemical analyses of their surfaces have become challenges. The time-of-flight (TOF) secondary ion mass spectrometry (SIMS) has been one of the most powerful surface characterization techniques for both nanoparticles and biomolecules. When combined with various nanoparticle-based signal enhancing strategies, TOF-SIMS can probe the functionalization of nanoparticles as well as their locations and interactions in biological systems. Especially, nanoparticle-based SIMS is an attractive approach for label-free drug screening because signal-enhancing nanoparticles can be designed to directly measure the enzyme activity. The chemical-specific imaging analysis using SIMS is also well suited to screen nanoparticles and nanoparticle-biomolecule conjugates in complex environments. This review presents some recent applications of nanoparticle-based TOF-SIMS to the chemical analysis of complex biological systems. © 2014 Wiley Periodicals, Inc.

Subcarrier intensity modulation for MIMO visible light communications

NASA Astrophysics Data System (ADS)

Celik, Yasin; Akan, Aydin

2018-04-01

In this paper, subcarrier intensity modulation (SIM) is investigated for multiple-input multiple-output (MIMO) visible light communication (VLC) systems. A new modulation scheme called DC-aid SIM (DCA-SIM) is proposed for the spatial modulation (SM) transmission plan. Then, DCA-SIM is extended for multiple subcarrier case which is called DC-aid Multiple Subcarrier Modulation (DCA-MSM). Bit error rate (BER) performances of the considered system are analyzed for different MIMO schemes. The power efficiencies of DCA-SIM and DCA-MSM are shown in correlated MIMO VLC channels. The upper bound BER performances of the proposed models are obtained analytically for PSK and QAM modulation types in order to validate the simulation results. Additionally, the effect of power imbalance method on the performance of SIM is studied and remarkable power gains are obtained compared to the non-power imbalanced cases. In this work, Pulse amplitude modulation (PAM) and MSM-Index are used as benchmarks for single carrier and multiple carrier cases, respectively. And the results show that the proposed schemes outperform PAM and MSM-Index for considered single carrier and multiple carrier communication scenarios.

Social Cues as Information Sources. Extensions and Refinements.

DTIC Science & Technology

1983-09-01

measured by the Job Characteristic Inventory (Sims, Szilagyi , and Keller, 1976). Intrinsic, ex- trinsic, and overall satisfaction were measured with the MSO...Communications Re- search, 1975, 1, 333-344. Sims, H.P., Szilagyi , A.D. & Keller, R.T. The measurement of job character- istics. Academy of Management

Mask Design for the Space Interferometry Mission Internal Metrology

NASA Technical Reports Server (NTRS)

Marx, David; Zhao, Feng; Korechoff, Robert

2005-01-01

This slide presentation reviews the mask design used for the internal metrology of the Space Interferometry Mission (SIM). Included is information about the project, the method of measurements with SIM, the internal metrology, numerical model of internal metrology, wavefront examples, performance metrics, and mask design

Understanding the Changes to Biomass Surface Characteristics after Ammonia and Organosolv Pretreatments by Using Time-of-Flight Secondary-Ion Mass Spectrometry (TOF-SIMS)

DOE PAGES

Tolbert, Allison K.; Yoo, Chang Geun; Ragauskas, Arthur J.

2017-03-20

Surface characteristic changes to poplar after ammonia and organosolv pretreatments were investigated by means of time-of-flight secondary-ion mass spectrometry (TOF-SIMS) analysis. Whereas normalized total polysaccharides and lignin contents on the surface differed from bulk chemical compositions, the surface cellulose ions detected by TOF-SIMS showed the same value trend as the cellulose content in the biomass. In addition, the lignin syringyl/guaiacyl ratio according to TOF-SIMS results showed the same trend as the ratio measured by means of NMR spectroscopic analysis, even though the ratio scales for each method were different. A similar correlation was determined between the surface cellulose and glucosemore » release after enzymatic hydrolysis. Lastly, these results demonstrate that surface characterization using TOF-SIMS can provide important information about the effects of pretreatment on biomass properties and its hydrolysis.« less

Understanding the Changes to Biomass Surface Characteristics after Ammonia and Organosolv Pretreatments by Using Time-of-Flight Secondary-Ion Mass Spectrometry (TOF-SIMS)

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

Tolbert, Allison K.; Yoo, Chang Geun; Ragauskas, Arthur J.

Surface characteristic changes to poplar after ammonia and organosolv pretreatments were investigated by means of time-of-flight secondary-ion mass spectrometry (TOF-SIMS) analysis. Whereas normalized total polysaccharides and lignin contents on the surface differed from bulk chemical compositions, the surface cellulose ions detected by TOF-SIMS showed the same value trend as the cellulose content in the biomass. In addition, the lignin syringyl/guaiacyl ratio according to TOF-SIMS results showed the same trend as the ratio measured by means of NMR spectroscopic analysis, even though the ratio scales for each method were different. A similar correlation was determined between the surface cellulose and glucosemore » release after enzymatic hydrolysis. Lastly, these results demonstrate that surface characterization using TOF-SIMS can provide important information about the effects of pretreatment on biomass properties and its hydrolysis.« less

ToF-SIMS analysis of a polymer microarray composed of poly(meth)acrylates with C6 derivative pendant groups.

PubMed

Hook, Andrew L; Scurr, David J

2016-04-01

Surface analysis plays a key role in understanding the function of materials, particularly in biological environments. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) provides highly surface sensitive chemical information that can readily be acquired over large areas and has, thus, become an important surface analysis tool. However, the information-rich nature of ToF-SIMS complicates the interpretation and comparison of spectra, particularly in cases where multicomponent samples are being assessed. In this study, a method is presented to assess the chemical variance across 16 poly(meth)acrylates. Materials are selected to contain C 6 pendant groups, and ten replicates of each are printed as a polymer microarray. SIMS spectra are acquired for each material with the most intense and unique ions assessed for each material to identify the predominant and distinctive fragmentation pathways within the materials studied. Differentiating acrylate/methacrylate pairs is readily achieved using secondary ions derived from both the polymer backbone and pendant groups. Principal component analysis (PCA) is performed on the SIMS spectra of the 16 polymers, whereby the resulting principal components are able to distinguish phenyl from benzyl groups, mono-functional from multi-functional monomers and acrylates from methacrylates. The principal components are applied to copolymer series to assess the predictive capabilities of the PCA. Beyond being able to predict the copolymer ratio, in some cases, the SIMS analysis is able to provide insight into the molecular sequence of a copolymer. The insight gained in this study will be beneficial for developing structure-function relationships based upon ToF-SIMS data of polymer libraries. © 2016 The Authors Surface and Interface Analysis Published by John Wiley & Sons Ltd.

Secondary Ion Mass Spectrometers (SIMS) for calcium isotope measurements as an application to biological samples

NASA Astrophysics Data System (ADS)

Craven, S. M.; Hoenigman, J. R.; Moddeman, W. E.

1981-11-01

The potential use of secondary ion mass spectroscopy (SIMS) to analyze biological samples for calcium isotopes is discussed. Comparison of UTI and Extranuclear based quadrupole systems is made on the basis of the analysis of CaO and calcium metal. The Extranuclear quadrupole based system is superior in resolution and sensitivity to the UTI system and is recommended. For determination of calcium isotopes to within an accuracy of a few percent a high resolution quadrupole, such as the Extranuclear, and signal averaging capability are required. Charge neutralization will be mandated for calcium oxide, calcium nitrate, or calcium oxalate. SIMS is not capable of the high precision and high accuracy results possible by thermal ionization methods, but where faster analysis is desirable with an accuracy of a few percent, SIMS is a viable alternative.

Integrating Training Simulations and e-Learning Systems: The SimSCORM Platform (Integratie van Training Simulaties en e-Learning Systemen: Het SimSCORM Platform)

DTIC Science & Technology

2008-07-01

SimSCORM Opdrachtnummer Trainingsconcepten voor Defensie Datum Programmanummer Projectnummer juli 2008 V406 032.13224 Auteur (s) ir H.L.H. de Penning...simulators can provide learners with powerful and realistic learning environments: whereas e-learning systems provide them with interactive, mostly theory ...practice and theory , in both learning and evaluation, is becoming increasingly important. From a learner’s point of view, a powerful learning environment

Hybrid Simulator

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

Trujillo, David J.; Sridharan, Srikesh; Weinstock, Irvin

HybSim (short for Hybrid Simulator) is a flexible, easy to use screening tool that allows the user to quanti the technical and economic benefits of installing a village hybrid generating system and simulates systems with any combination of —Diesel generator sets —Photovoltaic arrays -Wind Turbines and -Battery energy storage systems Most village systems (or small population sites such as villages, remote military bases, small communities, independent or isolated buildings or centers) depend on diesel generation systems for their source of energy. HybSim allows the user to determine other "sources" of energy that can greatly reduce the dollar to kilo-watt hourmore » ratio. Supported by the DOE, Energy Storage Program, HybSim was initially developed to help analyze the benefits of energy storage systems in Alaskan villages. Soon after its development, other sources of energy were added providing the user with a greater range of analysis opportunities and providing the village with potentially added savings. In addition to village systems, HybSim has generated interest for use from military institutions in energy provisions and USAID for international village analysis.« less

A simplified interventional mapping system (SIMS) for the selection of combinations of targeted treatments in non-small cell lung cancer

PubMed Central

Lazar, Vladimir; Martini, Jean-François; Gomez-Navarro, Jesus; Yver, Antoine; Kan, Zhengyin; Dry, Jonathan R.; Kehren, Jeanne; Validire, Pierre; Rodon, Jordi; Vielh, Philippe; Ducreux, Michel; Galbraith, Susan; Lehnert, Manfred; Onn, Amir; Berger, Raanan; Pierotti, Marco A.; Porgador, Angel; Pramesh, CS; Ye, Ding-wei; Carvalho, Andre L.; Batist, Gerald; Le Chevalier, Thierry; Morice, Philippe; Besse, Benjamin; Vassal, Gilles; Mortlock, Andrew; Hansson, Johan; Berindan-Neagoe, Ioana; Dann, Robert; Haspel, Joel; Irimie, Alexandru; Laderman, Steve; Nechushtan, Hovav; Al Omari, Amal S.; Haywood, Trent; Bresson, Catherine; Soo, Khee Chee; Osman, Iman; Mata, Hilario; Lee, Jack J.; Jhaveri, Komal; Meurice, Guillaume; Palmer, Gary; Lacroix, Ludovic; Koscielny, Serge; Eterovic, Karina Agda; Blay, Jean-Yves; Buller, Richard; Eggermont, Alexander; Schilsky, Richard L.; Mendelsohn, John; Soria, Jean-Charles; Rothenberg, Mace

2015-01-01

Non-small cell lung cancer (NSCLC) is a leading cause of death worldwide. Targeted monotherapies produce high regression rates, albeit for limited patient subgroups, who inevitably succumb. We present a novel strategy for identifying customized combinations of triplets of targeted agents, utilizing a simplified interventional mapping system (SIMS) that merges knowledge about existent drugs and their impact on the hallmarks of cancer. Based on interrogation of matched lung tumor and normal tissue using targeted genomic sequencing, copy number variation, transcriptomics, and miRNA expression, the activation status of 24 interventional nodes was elucidated. An algorithm was developed to create a scoring system that enables ranking of the activated interventional nodes for each patient. Based on the trends of co-activation at interventional points, combinations of drug triplets were defined in order to overcome resistance. This methodology will inform a prospective trial to be conducted by the WIN consortium, aiming to significantly impact survival in metastatic NSCLC and other malignancies. PMID:25944621

Towards a SIM-Less Existence: The Evolution of Smart Learning Networks

ERIC Educational Resources Information Center

Al-Khouri, Ali M.

2015-01-01

This article proposes that the widespread availability of wireless networks creates a case in which there is no real need for SIM cards. Recent technological developments offer the capability to outperform SIM cards and provide more innovative dimensions to current systems of mobility. In this context of changing realities in the domain of…

The Determination of Remaining Satellite Propellant Using Measured Moments of Inertia

DTIC Science & Technology

2006-06-01

Simulated Satellite (SimSat) were developed. These models were created using dynamic response analysis techniques on the reaction wheel and SimSat systems...Flowchart ......................................................... 5 Figure 2. Air Force Institute of Technology’s Simulated Satellite (SimSat...Determining Change in Satellite Fuel ............................... 88 xiv List of Symbols and Abbreviations ai Acceleration of a particle

Avoidable deaths until 48 [corrected] months of age among children from the 2004 Pelotas birth cohort.

PubMed

Gorgot, Luis Ramon Marques da Rocha; Santos, Iná; Valle, Neiva; Matijasevich, Alicia; Matisajevich, Alicia; Barros, Aluisio J D; Albernaz, Elaine

2011-04-01

To describe avoidable deaths of children from the 2004 Pelotas Birth Cohort. The death of 92 children between 2004/2008 from Pelotas Birth Cohort were identified and classified according to the Brazilian List of Avoidable Causes of Mortality of Brazilian Unified Healthcare System. The Mortality Information System (SIM) for the State of Rio Grande do Sul (Southern Brazil) and the city of Pelotas were screened to search for deaths that occurred outside the city, as well as causes of deaths after the 1st year. Causes of infant deaths (<1 year of age) were compared between information from a sub-study and SIM. Mortality coefficients per 1,000 LB and proportional mortality for avoidable causes, including by type of health facility (traditional or Family Health Strategy) were calculated. The mortality coefficient was 22.2/ 1,000 LB, 82 the deaths occurred in the first year of life (19.4/1,000LB), and these included 37 (45%) in the first week. More than ¾ of the deaths (70/92) were avoidable. In infancy, according to the sub-study, the majority (42/82) could be prevented through adequate care of the woman during pregnancy; according to SIM, the majority could have been prevented through adequate newborn care (32/82). There was no difference in the proportion of avoidable deaths by type of health facility. The proportion of avoidable deaths is high. The quality of death certificate registries needs improvement so that avoidable deaths can be employed as an indicator to monitor maternal and child health care.

Secondary ion mass spectrometers (SIMS) for calcium isotope measurements as an application to biological samples

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

Craven, S.M.; Hoenigman, J.R.; Moddeman, W.E.

1981-11-20

The potential use of secondary ion mass spectroscopy (SIMS) to analyze biological samples for calcium isotopes is discussed. Comparison of UTI and Extranuclear based quadrupole systems is made on the basis of the analysis of CaO and calcium metal. The Extranuclear quadrupole based system is superior in resolution and sensitivity to the UTI system and is recommended. For determination of calcium isotopes to within an accuracy of a few percent a high resolution quadrupole, such as the Extranuclear, and signal averaging capability are required. Charge neutralization will be mandated for calcium oxide, calcium nitrate, or calcium oxalate. SIMS is notmore » capable of the high precision and high accuracy results possible by thermal ionization methods, but where faster analysis is desirable with an accuracy of a few percent, SIMS is a viable alternative.« less

Integrating Metagenomics and NanoSIMS to Investigate the Evolution and Ecophysiology of Magnetotactic Bacteria

NASA Astrophysics Data System (ADS)

Lin, W.; Zhang, W.; He, M.; Pan, Y.

2017-12-01

Magnetotactic bacteria (MTB) synthesize intracellular nano-sized magnetite (Fe3O4) and/or greigite (Fe3S4) crystals, called magnetosomes, which impart a permanent magnetic dipole moment to the cell causing it to align along the geomagnetic field lines as it swims. MTB play essential roles in global cycling of Fe, S, N and C, and represent an excellent model system not just for the investigation of the mechanisms of microbial engines that drive Earth's biogeochemical cycles but also for magnetotaxis and microbial biomineralization. Most of the previous studies on MTB were based on 16S rRNA gene-targeting analyses, which are powerful approaches to characterize the diversity, ecology and biogeography of MTB in nature. However, these approaches are somewhat limited in the physiological detail they can provide. In the present study, we have combined the genome-resolved metagenomics and nanoscale secondary ion mass spectrometry (NanoSIMS) analyses to study the genomic information, biomineralization mechanism and metabolic potential of environmental MTB. Two nearly complete genomes from uncultivated MTB belonging to the Nitrospirae phylum were reconstructed and their proposed metabolisms were further investigated and confirmed through NanoSIMS analyses. These results improve our understanding about the ecophysiology and evolution of MTB and their environmental function. The development of metagenomics-NanoSIMS integrated approach will provide a powerful tool for the research of geomicrobiology and environmental microbiology.

Spatial and temporal localization during embryonic and fetal human development of the transcription factor SIM2 in brain regions altered in Down syndrome.

PubMed

Rachidi, Mohammed; Lopes, Carmela; Charron, Giselle; Delezoide, Anne-Lise; Paly, Evelyne; Bloch, Bernard; Delabar, Jean-Maurice

2005-08-01

Human SIM2 is the ortholog of Drosophila single-minded (sim), a master regulator of neurogenesis and transcriptional factor controlling midline cell fate determination. We previously localized SIM2 in a chromosome 21 critical region for Down syndrome (DS). Here, we studied SIM2 gene using a new approach to provide insights in understanding of its potential role in human development. For the first time, we showed SIM2 spatial and temporal expression pattern during human central nervous system (CNS) development, from embryonic to fetal stages. Additional investigations were performed using a new optic microscopy technology to compare signal intensity and cell density [M. Rachidi, C. Lopes, S. Gassanova, P.M. Sinet, M. Vekemans, T. Attie, A.L. Delezoide, J.M. Delabar, Regional and cellular specificity of the expression of TPRD, the tetratricopeptide Down syndrome gene, during human embryonic development, Mech. Dev. 93 (2000) 189--193]. In embryonic stages, SIM2 was identified predominantly in restricted regions of CNS, in ventral part of D1/D2 diencephalic neuroepithelium, along the neural tube and in a few cell subsets of dorsal root ganglia. In fetal stages, SIM2 showed differential expression in pyramidal and granular cell layers of hippocampal formation, in cortical cells and in cerebellar external granular and Purkinje cell layers. SIM2 expression in embryonic and fetal brain could suggest a potential role in human CNS development, in agreement with Drosophila and mouse Sim mutant phenotypes and with the conservation of the Sim function in CNS development from Drosophila to Human. SIM2 expression in human fetal brain regions, which correspond to key structures for cognitive processes, correlates well with the behavioral phenotypes of Drosophila Sim mutants and transgenic mice overexpressing Sim2. In addition, SIM2-expressing brain regions correspond to the altered structures in DS patients. All together, these findings suggest a potential role of SIM2 in CNS development and indicate that SIM2 overexpression could participate to the pathogenesis of mental retardation in Down syndrome patients.

Reversible solvatomagnetic switching in a single-ion magnet from an entatic state† †Electronic supplementary information (ESI) available: Preparation methods and physical characterization data. Crystallographic refinement and computational details. Additional figures (Fig. S1–S12) and tables (Tables S1–S5). CCDC 952077 and 938463. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c6sc05188j Click here for additional data file. Click here for additional data file.

PubMed Central

Vallejo, J.; Viciano-Chumillas, M.; Castro, I.; Amorós, P.; Déniz, M.; Ruiz-Pérez, C.; Yuste-Vivas, C.; Krzystek, J.; Julve, M.; Lloret, F.

2017-01-01

A vast impact on molecular nanoscience can be achieved using simple transition metal complexes as dynamic chemical systems to perform specific and selective tasks under the control of an external stimulus that switches “ON” and “OFF” their electronic properties. While the interest in single-ion magnets (SIMs) lies in their potential applications in information storage and quantum computing, the switching of their slow magnetic relaxation associated with host–guest processes is insufficiently explored. Herein, we report a unique example of a mononuclear cobalt(ii) complex in which geometrical constraints are the cause of easy and reversible water coordination and its release. As a result, a reversible and selective colour and SIM behaviour switch occurs between a “slow-relaxing” deep red anhydrous material (compound 1) and its “fast-relaxing” orange hydrated form (compound 2). The combination of this optical and magnetic switching in this new class of vapochromic and thermochromic SIMs offers fascinating possibilities for designing multifunctional molecular materials. PMID:28580105

Simvastatin Prodrug Micelles Target Fracture and Improve Healing

PubMed Central

Dusad, Anand; Yuan, Hongjiang; Ren, Ke; Li, Fei; Fehringer, Edward V.; Purdue, P. Edward; Goldring, Steven R.; Daluiski, Aaron; Wang, Dong

2014-01-01

Simvastatin (SIM), a widely used anti-lipidaemic drug, has been identified as a bone anabolic agent. Its poor water solubility and the lack of distribution to the skeleton, however, have limited its application in the treatment of bone metabolic diseases. In this study, an amphiphilic macromolecular prodrug of SIM was designed and synthesized to overcome these limitations. The polyethylene glycol (PEG)-based prodrug can spontaneously self-assemble to form micelles. The use of SIM trimer as the prodrug’s hydrophobic segment allows easy encapsulation of additional free SIM. The in vitro studies showed that SIM/SIM-mPEG micelles were internalized by MC3T3 cells via lysosomal trafficking and consistently induced expression of both BMP2 and DKK1 mRNA, suggesting that the prodrug micelle retains the biological functions of SIM. After systemic administration, optical imaging suggests that the micelles would passively target to bone fracture sites associated with hematoma and inflammation. Furthermore, flow cytometry study revealed that SIM/SIM-mPEG micelles had preferred cellular uptake by inflammatory and resident cells within the fracture callus tissue. The treatment study using a mouse osteotomy model validated the micelles’ therapeutic efficacy in promoting bone fracture healing as demonstrated by micro-CT and histological analyses. Collectively, these data suggest that the macromolecular prodrug-based micelle formulation of SIM may have great potential for clinical management of impaired fracture healing. PMID:25542644

Preparation of Emulsifying Wax/GMO Nanoparticles and Evaluation as a Delivery System for Repurposing Simvastatin in Bone Regeneration.

PubMed

Eskinazi-Budge, Aaron; Manickavasagam, Dharani; Czech, Tori; Novak, Kimberly; Kunzler, James; Oyewumi, Moses O

2018-05-30

Simvastatin (Sim) is a widely known drug in the treatment of hyperlipidemia that has attracted so much attention in bone regeneration based on its potential osteoanabolic effect. However, repurposing of Sim in bone regeneration will require suitable delivery systems that can negate undesirable off-target/side effects. In this study, we have investigated a new lipid nanoparticle (NP) platform that was fabricated using a binary blend of emulsifying wax (Ewax) and glyceryl monooleate (GMO). Using the binary matrix materials, NPs loaded with Sim (0-500 µg/mL) were prepared and showed an average particle size of about 150 nm. NP size stability was dependent on Sim concentration loaded in NPs. The suitability of NPs prepared with the binary matrix materials in Sim delivery for potential application in bone regeneration was supported by biocompatibility in pre-osteoclastic and pre-osteoblastic cells. Additional data demonstrated that biofunctional Sim was released from NPs that facilitated differentiation of osteoblasts (cells that form bones) while inhibiting differentiation of osteoclasts (cells that resorb bones). The overall work demonstrated the preparation of NPs from Ewax/GMO blends and characterization to ascertain potential suitability in Sim delivery for bone regeneration. Additional studies on osteoblast and osteoclast functions are warranted to fully evaluate the efficacy simvastatin-loaded Ewax/GMO NPs using in-vitro and in-vivo approaches.

Design and Build of Reactor Simulator for Fission Surface Power Technology Demonstrator Unit

NASA Technical Reports Server (NTRS)

Godfroy, Thomas; Dickens, Ricky; Houts, Michael; Pearson, Boise; Webster, Kenny; Gibson, Marc; Qualls, Lou; Poston, Dave; Werner, Jim; Radel, Ross

2011-01-01

The Nuclear Systems Team at NASA Marshall Space Flight Center (MSFC) focuses on technology development for state of the art capability in non-nuclear testing of nuclear system and Space Nuclear Power for fission reactor systems for lunar and Mars surface power generation as well as radioisotope power systems for both spacecraft and surface applications. Currently being designed and developed is a reactor simulator (RxSim) for incorporation into the Technology Demonstrator Unit (TDU) for the Fission Surface Power System (FSPS) Program, which is supported by multiple national laboratories and NASA centers. The ultimate purpose of the RxSim is to provide heated NaK to a pair of Stirling engines in the TDU. The RxSim includes many different systems, components, and instrumentation that have been developed at MSFC while working with pumped NaK systems and in partnership with the national laboratories and NASA centers. The main components of the RxSim are a core, a pump, a heat exchanger (to mimic the thermal load of the Stirling engines), and a flow meter for tests at MSFC. When tested at NASA Glenn Research Center (GRC) the heat exchanger will be replaced with a Stirling power conversion engine. Additional components include storage reservoirs, expansion volumes, overflow catch tanks, safety and support hardware, instrumentation (temperature, pressure, flow) for data collection, and power supplies. This paper will discuss the design and current build status of the RxSim for delivery to GRC in early 2012.

Design and Build of Reactor Simulator for Fission Surface Power Technology Demonstrator Unit

NASA Astrophysics Data System (ADS)

Godfroy, T.; Dickens, R.; Houts, M.; Pearson, B.; Webster, K.; Gibson, M.; Qualls, L.; Poston, D.; Werner, J.; Radel, R.

The Nuclear Systems Team at Marshall Space Flight Center (MSFC) focuses on technology development for state of the art capability in non-nuclear testing of nuclear system and Space Nuclear Power for fission reactor systems for lunar and mars surface power generation as well as radioisotope power systems for both spacecraft and surface applications. Currently being designed and developed is a reactor simulator (RxSim) for incorporation into the Technology Demonstrator Unit (TDU) for the Fission Surface Power System (FSPS) Program which is supported by multiple national laboratories and NASA centers. The ultimate purpose of the RxSim is to provide heated NaK to a pair of Stirling engines in the TDU. The RxSim includes many different systems, components, and instrumentation that have been developed at MSFC while working with pumped NaK systems and in partnership with the national laboratories and NASA centers. The main components of the RxSim are a core, a pump, a heat exchanger (to mimic the thermal load of the Stirling engines), and a flow meter when being tested at MSFC. When tested at GRC the heat exchanger will be replaced with a Stirling power conversion engine. Additional components include storage reservoirs, expansion volumes, overflow catch tanks, safety and support hardware, instrumenta- tion (temperature, pressure, flow) data collection, and power supplies. This paper will discuss the design and current build status of the RxSim for delivery to GRC in early 2012.

Securely Partitioning Spacecraft Computing Resources: Validation of a Separation Kernel

NASA Astrophysics Data System (ADS)

Bremer, Leon; Schreutelkamp, Erwin

2011-08-01

The F-35 Lightning II, also known as the Joint Strike Fighter, will be the first operational fighter aircraft equipped with an operational MultiShip Embedded Training capability. This onboard training system allows teams of fighter pilots to jointly operate their F-35 in flight against virtual threats, avoiding the need for real adversary air threats and surface threat systems in their training. The European Real-time Operations Simulator (EuroSim) framework is well known in the space domain, particularly in support of engineering and test phases of space system development. In the MultiShip Embedded Training project, EuroSim is not only the essential tool for development and verification throughout the project but is also the engine of the final embedded simulator on board of the F-35 aircraft. The novel ways in which EuroSim is applied in the project in relation to distributed simulation problems, team collaboration, tool chains and embedded systems can benefit many projects and applications. The paper describes the application of EuroSim as the simulation engine of the F-35 Embedded Training solution, the extensions to the EuroSim product that enable this application, and its usage in development and verification of the whole project as carried out at the sites of Dutch Space and the National Aerospace Laboratory (NLR).

Kite: status of the external metrology testbed for SIM

NASA Astrophysics Data System (ADS)

Dekens, Frank G.; Alvarez-Salazar, Oscar S.; Azizi, Alireza; Moser, Steven J.; Nemati, Bijan; Negron, John; Neville, Timothy; Ryan, Daniel

2004-10-01

Kite is a system level testbed for the External Metrology System of the Space Interferometry Mission (SIM). The External Metrology System is used to track the fiducials that are located at the centers of the interferometer's siderostats. The relative changes in their positions needs to be tracked to an accuracy of tens of picometers in order to correct for thermal deformations and attitude changes of the spacecraft. Because of the need for such high precision measurements, the Kite testbed was build to test both the metrology gauges and our ability to optically model the system at these levels. The Kite testbed is a redundant metrology truss, in which 6 lengths are measured, but only 5 are needed to define the system. The RMS error between the redundant measurements needs to be less than 140pm for the SIM Wide-Angle observing scenario and less than 8 pm for the Narrow-Angle observing scenario. With our current testbed layout, we have achieved an RMS of 85 pm in the Wide-Angle case, meeting the goal. For the Narrow-Angle case, we have reached 5.8 pm, but only for on-axis observations. We describe the testbed improvements that have been made since our initial results, and outline the future Kite changes that will add further effects that SIM faces in order to make the testbed more representative of SIM.

Taking the Measure of the Universe : Precision Astrometry with SIM PlanetQuest

NASA Technical Reports Server (NTRS)

Unwin, Stephen C.; Shao, Michael; Tanner, Angelle M.; Allen, Ronald J.; Beichman, Charles A.; Boboltz, David; Catanzarite, Joseph H.; Chaboyer, Brian C.; Ciardi, David R.; Edberg, Stephen J.;

Storage Information Management System (SIMS) Spaceflight Hardware Warehousing at Goddard Space Flight Center

NASA Technical Reports Server (NTRS)

Kubicko, Richard M.; Bingham, Lindy

1995-01-01

Goddard Space Flight Center (GSFC) on site and leased warehouses contain thousands of items of ground support equipment (GSE) and flight hardware including spacecraft, scaffolding, computer racks, stands, holding fixtures, test equipment, spares, etc. The control of these warehouses, and the management, accountability, and control of the items within them, is accomplished by the Logistics Management Division. To facilitate this management and tracking effort, the Logistics and Transportation Management Branch, is developing a system to provide warehouse personnel, property owners, and managers with storage and inventory information. This paper will describe that PC-based system and address how it will improve GSFC warehouse and storage management.

ToF-SIMS PCA analysis of Myrtus communis L.

NASA Astrophysics Data System (ADS)

Piras, F. M.; Dettori, M. F.; Magnani, A.

2009-06-01

Nowadays there is a growing interest of researchers for the application of sophisticated analytical techniques in conjunction with statistical data analysis methods to the characterization of natural products to assure their authenticity and quality, and for the possibility of direct analysis of food to obtain maximum information. In this work, time-of-flight secondary ion mass spectrometry (ToF-SIMS) in conjunction with principal components analysis (PCA) are applied to study the chemical composition and variability of Sardinian myrtle ( Myrtus communis L.) through the analysis of both berries alcoholic extracts and berries epicarp. ToF-SIMS spectra of berries epicarp show that the epicuticular waxes consist mainly of carboxylic acids with chain length ranging from C20 to C30, or identical species formed from fragmentation of long-chain esters. PCA of ToF-SIMS data from myrtle berries epicarp distinguishes two groups characterized by a different surface concentration of triacontanoic acid. Variability in antocyanins, flavonols, α-tocopherol, and myrtucommulone contents is showed by ToF-SIMS PCA analysis of myrtle berries alcoholic extracts.

Time and Frequency Transfer Activities at NIST

DTIC Science & Technology

2008-12-01

differences. The graph shows data from MJD 54466 to MJD 54763 (January 1, 2008 to October 24, 2008). II.E. The Sistema Interamericano de...Metrologia (SIM) Time Network The Sistema Interamericano de Metrologia (SIM) consists of national metrology institutes (NMIs) located in the 34...designed to mitigate multipath signals. All SIM systems are connected to the Internet and upload their measurement results to Internet Web servers

Systematics of Ni, Co, Cr and V in Olivine from Planetary Melt Systems: Martian Basalts

NASA Technical Reports Server (NTRS)

Herd, C. D. K.; Jones, J. H.; Shearer, C. K.; Papike, J. J.

2001-01-01

Secondary Ion Mass Spectrometry (SIMS) data for Ni, Co, Cr, and V in olivine in martian basalts is compared to data from lunar and terrestrial basalts. We use experimentally-derived and published D values to calculate as-yet unsampled, olivine-bearing, non-cumulus melt compositions. Additional information is contained in the original extended abstract.

ToF-SIMS Investigation of the Effectiveness of Acid-Cleaning procedures for Genesis Solar Wind Collectors

NASA Technical Reports Server (NTRS)

Goreva, Y. S.; Humanyun, M.; Burnett, D. S.; Jurewicz, A. J.; Gonzalez, C. P.

2014-01-01

ToF-SIMS images of Genesis sample surfaces contain an incredible amount of important information, but they also show that the crash-derived surface contamination has many components, presenting a challenge to cleaning. Within the variability, we have shown that there are some samples which appear to be clean to begin with, e.g. 60471, and some are more contaminated. Samples 60493 and 60500 are a part of a focused study of the effectiveness of aqua regia and/or sulfuric acid cleaning of small flight Si implanted with Li-6 using ToF-SIMS.

Fusing literature and full network data improves disease similarity computation.

PubMed

Li, Ping; Nie, Yaling; Yu, Jingkai

2016-08-30

Identifying relatedness among diseases could help deepen understanding for the underlying pathogenic mechanisms of diseases, and facilitate drug repositioning projects. A number of methods for computing disease similarity had been developed; however, none of them were designed to utilize information of the entire protein interaction network, using instead only those interactions involving disease causing genes. Most of previously published methods required gene-disease association data, unfortunately, many diseases still have very few or no associated genes, which impeded broad adoption of those methods. In this study, we propose a new method (MedNetSim) for computing disease similarity by integrating medical literature and protein interaction network. MedNetSim consists of a network-based method (NetSim), which employs the entire protein interaction network, and a MEDLINE-based method (MedSim), which computes disease similarity by mining the biomedical literature. Among function-based methods, NetSim achieved the best performance. Its average AUC (area under the receiver operating characteristic curve) reached 95.2 %. MedSim, whose performance was even comparable to some function-based methods, acquired the highest average AUC in all semantic-based methods. Integration of MedSim and NetSim (MedNetSim) further improved the average AUC to 96.4 %. We further studied the effectiveness of different data sources. It was found that quality of protein interaction data was more important than its volume. On the contrary, higher volume of gene-disease association data was more beneficial, even with a lower reliability. Utilizing higher volume of disease-related gene data further improved the average AUC of MedNetSim and NetSim to 97.5 % and 96.7 %, respectively. Integrating biomedical literature and protein interaction network can be an effective way to compute disease similarity. Lacking sufficient disease-related gene data, literature-based methods such as MedSim can be a great addition to function-based algorithms. It may be beneficial to steer more resources torward studying gene-disease associations and improving the quality of protein interaction data. Disease similarities can be computed using the proposed methods at http:// www.digintelli.com:8000/ .

Shuttle Inventory Management

NASA Technical Reports Server (NTRS)

1983-01-01

Inventory Management System (SIMS) consists of series of integrated support programs providing supply support for both Shuttle program and Kennedy Space Center base opeations SIMS controls all supply activities and requirements from single point. Programs written in COBOL.

Integration of SimSET photon history generator in GATE for efficient Monte Carlo simulations of pinhole SPECT.

PubMed

Chen, Chia-Lin; Wang, Yuchuan; Lee, Jason J S; Tsui, Benjamin M W

2008-07-01

The authors developed and validated an efficient Monte Carlo simulation (MCS) workflow to facilitate small animal pinhole SPECT imaging research. This workflow seamlessly integrates two existing MCS tools: simulation system for emission tomography (SimSET) and GEANT4 application for emission tomography (GATE). Specifically, we retained the strength of GATE in describing complex collimator/detector configurations to meet the anticipated needs for studying advanced pinhole collimation (e.g., multipinhole) geometry, while inserting the fast SimSET photon history generator (PHG) to circumvent the relatively slow GEANT4 MCS code used by GATE in simulating photon interactions inside voxelized phantoms. For validation, data generated from this new SimSET-GATE workflow were compared with those from GATE-only simulations as well as experimental measurements obtained using a commercial small animal pinhole SPECT system. Our results showed excellent agreement (e.g., in system point response functions and energy spectra) between SimSET-GATE and GATE-only simulations, and, more importantly, a significant computational speedup (up to approximately 10-fold) provided by the new workflow. Satisfactory agreement between MCS results and experimental data were also observed. In conclusion, the authors have successfully integrated SimSET photon history generator in GATE for fast and realistic pinhole SPECT simulations, which can facilitate research in, for example, the development and application of quantitative pinhole and multipinhole SPECT for small animal imaging. This integrated simulation tool can also be adapted for studying other preclinical and clinical SPECT techniques.

SIMS(DAIRY): a modelling framework to identify sustainable dairy farms in the UK. Framework description and test for organic systems and N fertiliser optimisation.

PubMed

Del Prado, A; Misselbrook, T; Chadwick, D; Hopkins, A; Dewhurst, R J; Davison, P; Butler, A; Schröder, J; Scholefield, D

2011-09-01

Multiple demands are placed on farming systems today. Society, national legislation and market forces seek what could be seen as conflicting outcomes from our agricultural systems, e.g. food quality, affordable prices, a healthy environmental, consideration of animal welfare, biodiversity etc., Many of these demands, or desirable outcomes, are interrelated, so reaching one goal may often compromise another and, importantly, pose a risk to the economic viability of the farm. SIMS(DAIRY), a farm-scale model, was used to explore this complexity for dairy farm systems. SIMS(DAIRY) integrates existing approaches to simulate the effect of interactions between farm management, climate and soil characteristics on losses of nitrogen, phosphorus and carbon. The effects on farm profitability and attributes of biodiversity, milk quality, soil quality and animal welfare are also included. SIMS(DAIRY) can also be used to optimise fertiliser N. In this paper we discuss some limitations and strengths of using SIMS(DAIRY) compared to other modelling approaches and propose some potential improvements. Using the model we evaluated the sustainability of organic dairy systems compared with conventional dairy farms under non-optimised and optimised fertiliser N use. Model outputs showed for example, that organic dairy systems based on grass-clover swards and maize silage resulted in much smaller total GHG emissions per l of milk and slightly smaller losses of NO(3) leaching and NO(x) emissions per l of milk compared with the grassland/maize-based conventional systems. These differences were essentially because the conventional systems rely on indirect energy use for 'fixing' N compared with biological N fixation for the organic systems. SIMS(DAIRY) runs also showed some other potential benefits from the organic systems compared with conventional systems in terms of financial performance and soil quality and biodiversity scores. Optimisation of fertiliser N timings and rates showed a considerable scope to reduce the (GHG emissions per l milk too). Copyright © 2011 Elsevier B.V. All rights reserved.

ToF-SIMS measurements with topographic information in combined images.

PubMed

Koch, Sabrina; Ziegler, Georg; Hutter, Herbert

2013-09-01

In 2D and 3D time-of-flight secondary ion mass spectrometric (ToF-SIMS) analysis, accentuated structures on the sample surface induce distorted element distributions in the measurement. The origin of this effect is the 45° incidence angle of the analysis beam, recording planar images with distortion of the sample surface. For the generation of correct element distributions, these artifacts associated with the sample surface need to be eliminated by measuring the sample surface topography and applying suitable algorithms. For this purpose, the next generation of ToF-SIMS instruments will feature a scanning probe microscope directly implemented in the sample chamber which allows the performance of topography measurements in situ. This work presents the combination of 2D and 3D ToF-SIMS analysis with topographic measurements by ex situ techniques such as atomic force microscopy (AFM), confocal microscopy (CM), and digital holographic microscopy (DHM). The concept of the combination of topographic and ToF-SIMS measurements in a single representation was applied to organic and inorganic samples featuring surface structures in the nanometer and micrometer ranges. The correct representation of planar and distorted ToF-SIMS images was achieved by the combination of topographic data with images of 2D as well as 3D ToF-SIMS measurements, using either AFM, CM, or DHM for the recording of topographic data.

Chemical imaging of molecular changes in a hydrated single cell by dynamic secondary ion mass spectrometry and super-resolution microscopy

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

Hua, Xin; Szymanski, Craig; Wang, Zhaoying

2016-01-01

Chemical imaging of single cells is important in capturing biological dynamics. Single cell correlative imaging is realized between structured illumination microscopy (SIM) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) using System for Analysis at the Liquid Vacuum Interface (SALVI), a multimodal microreactor. SIM characterized cells and guided subsequent ToF-SIMS analysis. Dynamic ToF-SIMS provided time- and space-resolved cell molecular mapping. Lipid fragments were identified in the hydrated cell membrane. Principal component analysis was used to elucidate chemical component differences among mouse lung cells that uptake zinc oxide nanoparticles. Our results provided submicron chemical spatial mapping for investigations of cell dynamics atmore » the molecular level.« less

NREL's Water Power Software Makes a Splash; NREL Highlights, Research & Development, NREL (National Renewable Energy Laboratory)

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

None

2015-06-01

WEC-Sim is a DOE-funded software tool being jointly developed by NREL and SNL. WEC-Sim computationally models wave energy converters (WEC), devices that generate electricity using movement of water systems such as oceans, rivers, etc. There is great potential for WECs to generate electricity, but as of yet, the industry has yet to establish a commercially viable concept. Modeling, design, and simulations tools are essential to the successful development of WECs. Commercial WEC modeling software tools can't be modified by the user. In contrast, WEC-Sim is a free, open-source, and flexible enough to be modified to meet the rapidly evolving needsmore » of the WEC industry. By modeling the power generation performance and dynamic loads of WEC designs, WEC-Sim can help support the development of new WEC devices by optimizing designs for cost of energy and competitiveness. By being easily accessible, WEC-Sim promises to help level the playing field in the WEC industry. Importantly, WEC-Sim is also excellent at its job! In 2014, WEC-Sim was used in conjunction with NREL’s FAST modeling software to win a hydrodynamic modeling competition. WEC-Sim and FAST performed very well at predicting the motion of a test device in comparison to other modeling tools. The most recent version of WEC-Sim (v1.1) was released in April 2015.« less

Validation of the SimSET simulation package for modeling the Siemens Biograph mCT PET scanner

NASA Astrophysics Data System (ADS)

Poon, Jonathan K.; Dahlbom, Magnus L.; Casey, Michael E.; Qi, Jinyi; Cherry, Simon R.; Badawi, Ramsey D.

2015-02-01

Monte Carlo simulation provides a valuable tool in performance assessment and optimization of system design parameters for PET scanners. SimSET is a popular Monte Carlo simulation toolkit that features fast simulation time, as well as variance reduction tools to further enhance computational efficiency. However, SimSET has lacked the ability to simulate block detectors until its most recent release. Our goal is to validate new features of SimSET by developing a simulation model of the Siemens Biograph mCT PET scanner and comparing the results to a simulation model developed in the GATE simulation suite and to experimental results. We used the NEMA NU-2 2007 scatter fraction, count rates, and spatial resolution protocols to validate the SimSET simulation model and its new features. The SimSET model overestimated the experimental results of the count rate tests by 11-23% and the spatial resolution test by 13-28%, which is comparable to previous validation studies of other PET scanners in the literature. The difference between the SimSET and GATE simulation was approximately 4-8% for the count rate test and approximately 3-11% for the spatial resolution test. In terms of computational time, SimSET performed simulations approximately 11 times faster than GATE simulations. The new block detector model in SimSET offers a fast and reasonably accurate simulation toolkit for PET imaging applications.

Alteration of the RANKL/RANK/OPG System in Periprosthetic Osteolysis with Septic Loosening.

PubMed

Wang, Long; Dai, Zixun; Xie, Jie; Liao, Hao; Lv, Cheng; Hu, Yihe

2016-02-01

The pathogenesis of periprosthetic osteolysis with septic loosening remains incompletely understood. The purpose of this study was to investigate whether expression of the RANKL/RANK/OPG system is altered in septic interface membranes (SIMs). Seventeen cases with a SIM, 26 cases with an aseptic interface membrane (AIM), and 12 cases with a normal synovium (NS) were assessed. Scanning and transmission electron microscopy (SEM and TEM, respectively) were used to observe the microscopic morphology of three tissue conditions. Differences in RANKL, RANK, and OPG expression at the mRNA level were assessed by real-time quantitative PCR, and differences at the protein level were assessed by immunohistochemical staining and Western blotting. SEM showed wear debris widely distributed on the AIM surface, and TEM showed Bacillus activity in the SIM. RANKL expression and the RANKL/OPG ratio were significantly increased in SIMs. Imbalance in the RANKL/RANK/OPG system is related to periprosthetic osteolysis with septic loosening but is not the only possible pathogenic mechanism.

MI-Sim: A MATLAB package for the numerical analysis of microbial ecological interactions.

PubMed

Wade, Matthew J; Oakley, Jordan; Harbisher, Sophie; Parker, Nicholas G; Dolfing, Jan

2017-01-01

Food-webs and other classes of ecological network motifs, are a means of describing feeding relationships between consumers and producers in an ecosystem. They have application across scales where they differ only in the underlying characteristics of the organisms and substrates describing the system. Mathematical modelling, using mechanistic approaches to describe the dynamic behaviour and properties of the system through sets of ordinary differential equations, has been used extensively in ecology. Models allow simulation of the dynamics of the various motifs and their numerical analysis provides a greater understanding of the interplay between the system components and their intrinsic properties. We have developed the MI-Sim software for use with MATLAB to allow a rigorous and rapid numerical analysis of several common ecological motifs. MI-Sim contains a series of the most commonly used motifs such as cooperation, competition and predation. It does not require detailed knowledge of mathematical analytical techniques and is offered as a single graphical user interface containing all input and output options. The tools available in the current version of MI-Sim include model simulation, steady-state existence and stability analysis, and basin of attraction analysis. The software includes seven ecological interaction motifs and seven growth function models. Unlike other system analysis tools, MI-Sim is designed as a simple and user-friendly tool specific to ecological population type models, allowing for rapid assessment of their dynamical and behavioural properties.

NanoSIMS Reveals New Structural and Elemental Signatures of Early Life

NASA Technical Reports Server (NTRS)

Oehler, Dorothy Z.; Mostefaoui, Smail; Meibom, Anders; Selo, Madeleine; Robert, Francois; McKay, David S.

2006-01-01

The young technology of NanoSIMS is unlocking new information from organic matter in ancient sediments. We have used this technique to characterize sub-micron scale element composition of Proterozoic organics that are clearly biogenic as a guide for interpreting problematic structures in terrestrial or extraterrestrial samples. We used the NanoSIMS 50 of the National Museum of Natural History in Paris to map carbon, nitrogen (as CN), and sulfur in organic structures from the approximately 0.8 Ga Bitter Springs Formation. We analyzed spheroidal and filamentous microfossils as well as organic laminae that appeared amorphous by optical and scanning electron microscopy. In clear-cut microfossils, a coincidence between optical images and NanoSIMS element maps suggests a biological origin for the mapped carbon, sulfur, and nitrogen; this conclusion is supported by high resolution NanoSIMS maps showing identical spatial distributions of C, CN and S. High resolution images also demonstrate distinctive nano structure of the filaments and spheroids. In the amorphous laminae, NanoSIMS reveals morphologies reminiscent of compressed microfossils. Distinct CN/C ratios of the spheroids, filaments, and laminae may reflect their biological precursors (cell walls, cyanobacterial sheaths, and microbial communities/biofilms, respectively). Similar amorphous laminae comprise a preponderance of the organic matter in many Precambrian deposits. Thus it is possible that NanoSIMS will provide fresh insight into a large body of previously uninterpretable material. Additionally, NanoSIMS analysis may establish new biosignatures that will be helpful for assessing the origin and biogenicity of controversial Archean structures and any organic materials that may occur in Martian or other extraterrestrial samples.

OpenSim: a musculoskeletal modeling and simulation framework for in silico investigations and exchange.

PubMed

Seth, Ajay; Sherman, Michael; Reinbolt, Jeffrey A; Delp, Scott L

Movement science is driven by observation, but observation alone cannot elucidate principles of human and animal movement. Biomechanical modeling and computer simulation complement observations and inform experimental design. Biological models are complex and specialized software is required for building, validating, and studying them. Furthermore, common access is needed so that investigators can contribute models to a broader community and leverage past work. We are developing OpenSim, a freely available musculoskeletal modeling and simulation application and libraries specialized for these purposes, by providing: musculoskeletal modeling elements, such as biomechanical joints, muscle actuators, ligament forces, compliant contact, and controllers; and tools for fitting generic models to subject-specific data, performing inverse kinematics and forward dynamic simulations. OpenSim performs an array of physics-based analyses to delve into the behavior of musculoskeletal models by employing Simbody, an efficient and accurate multibody system dynamics code. Models are publicly available and are often reused for multiple investigations because they provide a rich set of behaviors that enables different lines of inquiry. This report will discuss one model developed to study walking and applied to gain deeper insights into muscle function in pathological gait and during running. We then illustrate how simulations can test fundamental hypotheses and focus the aims of in vivo experiments, with a postural stability platform and human model that provide a research environment for performing human posture experiments in silico . We encourage wide adoption of OpenSim for community exchange of biomechanical models and methods and welcome new contributors.

A perspective on two chemometrics tools: PCA and MCR, and introduction of a new one: Pattern recognition entropy (PRE), as applied to XPS and ToF-SIMS depth profiles of organic and inorganic materials

NASA Astrophysics Data System (ADS)

Chatterjee, Shiladitya; Singh, Bhupinder; Diwan, Anubhav; Lee, Zheng Rong; Engelhard, Mark H.; Terry, Jeff; Tolley, H. Dennis; Gallagher, Neal B.; Linford, Matthew R.

2018-03-01

X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) are much used analytical techniques that provide information about the outermost atomic and molecular layers of materials. In this work, we discuss the application of multivariate spectral techniques, including principal component analysis (PCA) and multivariate curve resolution (MCR), to the analysis of XPS and ToF-SIMS depth profiles. Multivariate analyses often provide insight into data sets that is not easily obtained in a univariate fashion. Pattern recognition entropy (PRE), which has its roots in Shannon's information theory, is also introduced. This approach is not the same as the mutual information/entropy approaches sometimes used in data processing. A discussion of the theory of each technique is presented. PCA, MCR, and PRE are applied to four different data sets obtained from: a ToF-SIMS depth profile through ca. 100 nm of plasma polymerized C3F6 on Si, a ToF-SIMS depth profile through ca. 100 nm of plasma polymerized PNIPAM (poly (N-isopropylacrylamide)) on Si, an XPS depth profile through a film of SiO2 on Si, and an XPS depth profile through a film of Ta2O5 on Ta. PCA, MCR, and PRE reveal the presence of interfaces in the films, and often indicate that the first few scans in the depth profiles are different from those that follow. PRE and backward difference PRE provide this information in a straightforward fashion. Rises in the PRE signals at interfaces suggest greater complexity to the corresponding spectra. Results from PCA, especially for the higher principal components, were sometimes difficult to understand. MCR analyses were generally more interpretable.

Semiquantitative analysis of atherosclerotic plaque using optical coherence tomography and time-of-flight secondary ion mass spectrometry

NASA Astrophysics Data System (ADS)

Korol, Renee M.; Togonu-Bickersteth, Babajide; Yang, Victor X.; Dimov, Stamen; Vatsya, Pracha; Gordon, Maggie; Vitkin, Alex; Liu, Liying; Canham, Peter; Clarke, Sharon; Lucas, Alexandra

2003-10-01

Atherosclerosis is the underlying vascular pathology that initiates arterial thromboembolic occlusions (myocardial infarctions, strokes and peripheral vessel blockage). Two imaging modalities, Optical Coherence Tomography (OCT) and Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS), were investigated for detection and compositional analysis of unstable plaque associated with plaque erosion and sudden occlusion. OCT produces high resolution images whereas mass spectrometry images provide information on the spatial distribution of chemical elements. Diseased carotid arteries taken from patients with high-risk lesions were imaged with OCT and ToF-SIMS to give molecular and metabolic information, and matched with histopathology. OCT results show clear indications of vascular remodeling by the presence of fatty acid deposits, fibrous tissue and calcifications. ToF-SIMS further characterized changes based on secondary ion topography analysis where a high 23Na/39K ratio was indicative of arterial tissue degradation and the amount of 40Ca corresponded with late stage atherosclerosis. This pilot experiment has demonstrated that in vitro OCT imaging and ToF-SIMS of diseased carotid arteries have scientific merit for targeting clinically relevant morphology and metabolic changes to compare stable and unstable plaque. These optical techniques provide complimentary metabolic and molecular information on unstable plaque, specifically cell break-down with altered ion ratios of 23Na, 39K and 40Ca.

SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.

PubMed

Boniecki, Michal J; Lach, Grzegorz; Dawson, Wayne K; Tomala, Konrad; Lukasz, Pawel; Soltysinski, Tomasz; Rother, Kristian M; Bujnicki, Janusz M

2016-04-20

RNA molecules play fundamental roles in cellular processes. Their function and interactions with other biomolecules are dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is laborious and challenging, and therefore, the majority of known RNAs remain structurally uncharacterized. Here, we present SimRNA: a new method for computational RNA 3D structure prediction, which uses a coarse-grained representation, relies on the Monte Carlo method for sampling the conformational space, and employs a statistical potential to approximate the energy and identify conformations that correspond to biologically relevant structures. SimRNA can fold RNA molecules using only sequence information, and, on established test sequences, it recapitulates secondary structure with high accuracy, including correct prediction of pseudoknots. For modeling of complex 3D structures, it can use additional restraints, derived from experimental or computational analyses, including information about secondary structure and/or long-range contacts. SimRNA also can be used to analyze conformational landscapes and identify potential alternative structures. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

The Latest SORCE Solar Spectral Irradiance Data Release: Inter-Comparison and a First Look at TSIS SIM Measurement.

NASA Astrophysics Data System (ADS)

Beland, S.; Sandoval, L.; Vanier, B.; Elliott, J.; Harder, J. W.; Snow, M. A.; Woods, T. N.; Richard, E. C.; Pilewskie, P.

2017-12-01

The Spectral Irradiance Monitor (SIM), the SOLar STellar Irradiance Comparison Experiment (SOLSTICE), and the XUV Photometer System (XPS) instruments on board the Solar Radiation and Climate Experiment (SORCE) mission have been taking daily Solar spectral irradiance (SSI) measurements since April 2003. We present the latest data releases from these instruments, describing the improvements in the new datasets and the trends measured during Solar cycles 23 and 24. An inter-comparison of the SSI over the overlapping wavelengths for SIM and SOLSTICE is presented as well as, if the data is available, a comparison with the first light measurements from TSIS-SIM.

Sub-100 nm resolution microscopy based on proximity projection grating scheme

PubMed Central

Hu, Feng; Somekh, Michael G.; Albutt, Darren J.; Webb, Kevin; Moradi, Emilia; See, Chung W.

2015-01-01

Structured illumination microscopy (SIM) has been widely used in life science imaging applications. The maximum resolution improvement of SIM, compared to conventional bright field system is a factor of 2. Here we present an approach to structured illumination microscopy using the proximity projection grating scheme (PPGS), which has the ability to further enhance the SIM resolution without invoking any nonlinearity response from the sample. With the PPGS-based SIM, sub-100 nm resolution has been obtained experimentally, and results corresponding to 2.4 times resolution improvement are presented. Furthermore, it will be shown that an improvement of greater than 3 times can be achieved. PMID:25715953

An earth imaging camera simulation using wide-scale construction of reflectance surfaces

NASA Astrophysics Data System (ADS)

Murthy, Kiran; Chau, Alexandra H.; Amin, Minesh B.; Robinson, M. Dirk

2013-10-01

Developing and testing advanced ground-based image processing systems for earth-observing remote sensing applications presents a unique challenge that requires advanced imagery simulation capabilities. This paper presents an earth-imaging multispectral framing camera simulation system called PayloadSim (PaySim) capable of generating terabytes of photorealistic simulated imagery. PaySim leverages previous work in 3-D scene-based image simulation, adding a novel method for automatically and efficiently constructing 3-D reflectance scenes by draping tiled orthorectified imagery over a geo-registered Digital Elevation Map (DEM). PaySim's modeling chain is presented in detail, with emphasis given to the techniques used to achieve computational efficiency. These techniques as well as cluster deployment of the simulator have enabled tuning and robust testing of image processing algorithms, and production of realistic sample data for customer-driven image product development. Examples of simulated imagery of Skybox's first imaging satellite are shown.

Kaiser Permanente-Sandia National Health Care Model: Phase 1 prototype final report. Part 2 -- Domain analysis

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

Edwards, D.; Yoshimura, A.; Butler, D.

This report describes the results of a Cooperative Research and Development Agreement between Sandia National Laboratories and Kaiser Permanente Southern California to develop a prototype computer model of Kaiser Permanente`s health care delivery system. As a discrete event simulation, SimHCO models for each of 100,000 patients the progression of disease, individual resource usage, and patient choices in a competitive environment. SimHCO is implemented in the object-oriented programming language C{sup 2}, stressing reusable knowledge and reusable software components. The versioned implementation of SimHCO showed that the object-oriented framework allows the program to grow in complexity in an incremental way. Furthermore, timingmore » calculations showed that SimHCO runs in a reasonable time on typical workstations, and that a second phase model will scale proportionally and run within the system constraints of contemporary computer technology.« less

Design of transnational mobile e-payment application based on SIM card

NASA Astrophysics Data System (ADS)

Qian, Tang; Zhen, Li

2018-05-01

Facing the stronger demands of transnational mobile communications and internet-based mobile wireless value-added services, the interconnection and interworking of multiple communication operators and their win-win cooperations become a crucial target in the new round of mobile economic development. Previous researches showed that mobile communications and value-add services are not only technical problems, but also more economic problems.we design a general oncard operating system based on SIM card that could be responsible for coordinating and distributing card hardware and software resources. These applications such as transnational mobile payment, consumption management and many other supplemented functions share the API interfaces, hardware and software resources provided by the operation system, although they are independent of each other. The layer structure of SIM card design not only greatly reduces the complexity of COS development, but also saves the most tense card resources and extends SIM cards applications.

Towards nanometric resolution in multilayer depth profiling: a comparative study of RBS, SIMS, XPS and GDOES.

PubMed

Escobar Galindo, Ramón; Gago, Raul; Duday, David; Palacio, Carlos

2010-04-01

An increasing amount of effort is currently being directed towards the development of new functionalized nanostructured materials (i.e., multilayers and nanocomposites). Using an appropriate combination of composition and microstructure, it is possible to optimize and tailor the final properties of the material to its final application. The analytical characterization of these new complex nanostructures requires high-resolution analytical techniques that are able to provide information about surface and depth composition at the nanometric level. In this work, we comparatively review the state of the art in four different depth-profiling characterization techniques: Rutherford backscattering spectroscopy (RBS), secondary ion mass spectrometry (SIMS), X-ray photoelectron spectroscopy (XPS) and glow discharge optical emission spectroscopy (GDOES). In addition, we predict future trends in these techniques regarding improvements in their depth resolutions. Subnanometric resolution can now be achieved in RBS using magnetic spectrometry systems. In SIMS, the use of rotating sample holders and oxygen flooding during analysis as well as the optimization of floating low-energy ion guns to lower the impact energy of the primary ions improves the depth resolution of the technique. Angle-resolved XPS provides a very powerful and nondestructive technique for obtaining depth profiling and chemical information within the range of a few monolayers. Finally, the application of mathematical tools (deconvolution algorithms and a depth-profiling model), pulsed sources and surface plasma cleaning procedures is expected to greatly improve GDOES depth resolution.

[Determination of acetanilide herbicide residues in tea by gas chromatography-mass spectrometry with two different ionization techniques].

PubMed

Shen, Weijian; Xu, Jinzhong; Yang, Wenquan; Shen, Chongyu; Zhao, Zengyun; Ding, Tao; Wu, Bin

2007-09-01

An analytical method of solid phase extraction-gas chromatography-mass spectrometry with two different ionization techniques was established for simultaneous determination of 12 acetanilide herbicide residues in tea-leaves. Herbicides were extracted from tea-leaf samples with ethyl acetate. The extract was cleaned-up on an active carbon SPE column connected to a Florisil SPE column. Analytical screening was determined by the technique of gas chromatography (GC)-mass spectrometry (MS) in the selected ion monitoring (SIM) mode with either electron impact ionization (EI) or negative chemical ionization (NCI). It is reliable and stable that the recoveries of all herbicides were in the range from 50% to 110% at three spiked levels, 10 microg/kg, 20 microg/kg and 40 microg/kg, and the relative standard deviations (RSDs) were no more than 10.9%. The two different ionization techniques are complementary as more ion fragmentation information can be obtained from the EI mode while more molecular ion information from the NCI mode. By comparison of the two techniques, the selectivity of NCI-SIM was much better than that of EI-SIM method. The sensitivities of the both techniques were high, the limit of quantitative (LOQ) for each herbicide was no more than 2.0 microg/kg, and the limit of detection (LOD) with NCI-SIM technique was much lower than that of EI-SIM when analyzing herbicides with several halogen atoms in the molecule.

Characterization of Natural Dyes and Traditional Korean Silk Fabric by Surface Analytical Techniques.

PubMed

Lee, Jihye; Kang, Min Hwa; Lee, Kang-Bong; Lee, Yeonhee

2013-05-15

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) and X-ray photoelectron spectroscopy (XPS) are well established surface techniques that provide both elemental and organic information from several monolayers of a sample surface, while also allowing depth profiling or image mapping to be carried out. The static TOF-SIMS with improved performances has expanded the application of TOF-SIMS to the study of a variety of organic, polymeric and biological materials. In this work, TOF-SIMS, XPS and Fourier Transform Infrared (FTIR) measurements were used to characterize commercial natural dyes and traditional silk fabric dyed with plant extracts dyes avoiding the time-consuming and destructive extraction procedures necessary for the spectrophotometric and chromatographic methods previously used. Silk textiles dyed with plant extracts were then analyzed for chemical and functional group identification of their dye components and mordants. TOF-SIMS spectra for the dyed silk fabric showed element ions from metallic mordants, specific fragment ions and molecular ions from plant-extracted dyes. The results of TOF-SIMS, XPS and FTIR are very useful as a reference database for comparison with data about traditional Korean silk fabric and to provide an understanding of traditional dyeing materials. Therefore, this study shows that surface techniques are useful for micro-destructive analysis of plant-extracted dyes and Korean dyed silk fabric.

Microstructural development inside the stress induced martensite variant in a Ti-Ni-Nb shape memory alloy

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

Zheng, Y.F.; Cai, W.; Zhang, J.X.

2000-04-03

The microstructural development inside the stress induced martensite (SIM) variants in Ti-Ni-Nb alloy with various degrees of deformation have been revealed by electron microscopic observations. The orientation relationship between the SIM and the parent phase has been found: [1{bar 1}0]{sub M}{parallel}[11{bar 1}]{sub B2}, (001){sub M} 5{degree} away from (101){sub B2}. The lattice invariant shear of the SIM variants at the slightly deformed stage is dominantly (11{bar 1}) Type I twin. Besides the ordinary slip, the adjustment and development of the internal secondary twinning from (11{bar 1}) Type I twin to {l_angle}011{r_angle} Type II/ or (011) Type I twin, (001)compound twinmore » and (111) Type I twin happen concurrently or in combination inside the SIM variants with the further deformation. The corresponding deformation mechanisms include stress induced reorientation of SIM substructural bands by the most favorably oriented twin system, stress induced migration of the SIM substructural boundary through internal twinning and stress induced injection of foreign SIM variant to the preexisting substructural bands.« less

[Calmette Hospital, Phnom Penh, Cambodia. Assessment of the implementation of the Medical Information System (SIM). Global analysis of the 1998 results].

PubMed

Fabre-Teste, B; Sokha, O

1999-01-01

Calmette is a national university hospital with 220 adult beds. It has emergency, surgical, medical and gynecology and obstetrics departments, along with a radiology unit, a laboratory for medical analyses, a central pharmacy and an outpatient clinic. This hospital has an unusual statute, with managerial autonomy and a system of cost recovery that currently provides 64% of the hospital's income. Since 1994, it has benefited from a French cooperation program. The French NGO, Médecins du Monde, has been present at Calmette since 1990, providing support for , the indigent sector of the medical department. The aim of the Medical Information System (SIM) is to develop a simple, reliable and reproducible system so that, for every action undertaken at the hospital (hospitalization, day hospital and outpatient clinic) the following pieces of information are recorded: 1) the disease; 2) the type of patient; 3) the type of management; 4) the means used to treat the patient; 5) the cost. Data are collected and analyzed using programs created with EPIINFO software (CDC, WHO), using the EPIGLUE module. In 1998, 10,814 admissions were recorded at Calmette Hospital, 7,811 (72.2%) of which were to the Emergency Department and 3,003 (27.2%) of which were direct admissions to other wards. We analyzed 10,603 (95%) computerized medical summaries (RMI). About 50% of beds were occupied in the maternity and gynecology ward whereas almost 90% of beds were occupied in the surgical and emergency wards. AIDS and tuberculosis were the conditions most frequently treated by the medical department, despite a marked increase in more specialized areas of medicine such as cardiology and diabetology. The surgical department reflected the concentration on emergency services of the hospital, with cranial traumatism the primary reason for admission for the hospital as a whole. The mean age of patients was 27 years for the maternity ward and 49 years for the medicine A ward. The mortality rate was about 5% for the medical wards (mainly due to AIDS) and almost 50% in the emergency department (cerebrovascular neurologic disease, cranial traumatism). The proportion of nonpaying patients was high (about 40% in terms of stays in hospital and about 50% of all days spent in hospital). The training of a Cambodian manager for the SIM is a key priority. The point of the SIM is to use the treated data it produces to improve management and decision-making. The data it produces should be used to define the profile of the patients treated, both from a medical point of view and in terms of their ability to pay. This is a fundamental step towards identifying activities that should receive priority as part of a development strategy for a structure evolving in a highly competitive environment. The SIM data are also invaluable for the short-term management of the hospital through the contribution they make to the development of effective analytical accounting, making it possible to evaluate costs and to adjust charges appropriately. Finally, the involvement of the SIM in the setting up and functioning of the Comité de Lutte Contre les Infections Nosocomiales (CLIN; the Hospital-Acquired Infections Committee) in 1999 to 2000 is not utopia, it is the logical continuation of improvements in the overall quality of care It involves, in particular, the training of nurses and head nurses, initiated by nurses acting as technical assistants in the French cooperation program. The definition of the role of the hygiene nurse and the selection of such a nurse from the trained head nurses are also part of this process.

ToF-SIMS and Laser-SNMS Imaging of Heterogeneous Topographically Complex Polymer Systems.

PubMed

Pelster, Andreas; Körsgen, Martin; Kurosawa, Takako; Morita, Hiromi; Arlinghaus, Heinrich F

2016-10-04

Heterogeneous polymer coatings, such as those used in organic electronics and medical devices, are of increasing industrial importance. In order to advance the development of these types of systems, analytical techniques are required which are able to determine the elemental and molecular spatial distributions, on a nanometer scale, with very high detection efficiency and sensitivity. The goal of this study was to investigate the suitability of laser postionization secondary neutral mass spectrometry (Laser-SNMS) with a 157 nm postionization laser beam to image structured polymer mixtures and compare the results with time-of-flight secondary ion mass spectrometry (ToF-SIMS) measurements using Bi 3 + primary ions. The results showed that Laser-SNMS is better suited than ToF-SIMS for unambiguous detection and submicrometer imaging of the wide range of polymers investigated. The data also showed that Laser-SNMS has the advantage of being much more sensitive (in general higher by more than an order of magnitude and peaking at up to 3 orders of magnitude) than ToF-SIMS while also showing superior performance on topographically complex structured insulating surfaces, due to significantly reduced field effects and a higher dynamic range as compared to ToF-SIMS. It is concluded that Laser-SNMS is a powerful complementary technique to ToF-SIMS for the analysis of heterogeneous polymers and other complex structured organic mixtures, providing submicrometer resolution and high sensitivity.

Mobile Element Reservoir Mass Balance on Mars: New SIMS and EMP Data from Lonar and Mistastin Craters

NASA Technical Reports Server (NTRS)

Newsom, H. E.; Hagerty, J. J.; Shearer, C. W.

2002-01-01

New SIMS data for mobile elements in Lonar Crater clay minerals are remarkably similar to data for alteration material in the Lafayette Mars meteorite. This work strongly supports the use of terrestrial analogues for Mars, including a new mass balance model for mobile elements through time. Additional information is contained in the original extended abstract.

Parachute Drag Model

NASA Technical Reports Server (NTRS)

Cuthbert, Peter

2010-01-01

DTV-SIM is a computer program that implements a mathematical model of the flight dynamics of a missile-shaped drop test vehicle (DTV) equipped with a multistage parachute system that includes two simultaneously deployed drogue parachutes and three main parachutes deployed subsequently and simultaneously by use of pilot parachutes. DTV-SIM was written to support air-drop tests of the DTV/parachute system, which serves a simplified prototype of a proposed crew capsule/parachute landing system.

Quantitative analysis of the Ge concentration in a SiGe quantum well: comparison of low-energy RBS and SIMS measurements.

PubMed

Krecar, D; Rosner, M; Draxler, M; Bauer, P; Hutter, H

2006-01-01

The germanium concentration and the position and thickness of the quantum well in molecular beam epitaxy (MBE)-grown SiGe were quantitatively analyzed via low-energy Rutherford backscattering (RBS) and secondary ion mass spectrometry (SIMS). In these samples, the concentrations of Si and Ge were assumed to be constant, except for the quantum well, where the germanium concentration was lower. The thickness of the analyzed quantum well was about 12 nm and it was situated at a depth of about 60 nm below the surface. A dip showed up in the RBS spectra due to the lower germanium concentration in the quantum well, and this was evaluated. Good depth resolution was required in order to obtain quantitative results, and this was obtained by choosing a primary energy of 500 keV and a tilt angle of 51 degrees with respect to the surface normal. Quantitative information was deduced from the raw data by comparing it with SIMNRA simulated spectra. The SIMS measurements were performed with oxygen primary ions. Given the response function of the SIMS instrument (the SIMS depth profile of the germanium delta (delta) layer), and using the forward convolution (point-to-point convolution) model, it is possible to determine the germanium concentration and the thickness of the analyzed quantum well from the raw SIMS data. The aim of this work was to compare the results obtained via RBS and SIMS and to show their potential for use in the semiconductor and microelectronics industry. The detection of trace elements (here the doping element antimony) that could not be evaluated with RBS in low-energy mode is also demonstrated using SIMS instead.

From Information to Simulation: Improving Competency in ECT Training Using High-Fidelity Simulation.

PubMed

Raysin, Anetta; Gillett, Brian; Carmody, Joseph; Goel, Nidhi; McAfee, Scot; Jacob, Theresa

2017-12-18

This study was intended to develop a new educational model that supplements ECT didactics with simulation-based procedural training and to evaluate the learning gains conferred by such a curriculum. Two types of curricula were evaluated for educational efficacy in this prospective randomized controlled trial. Psychiatry residents (n = 35) completed surveys to ascertain their baseline experience, knowledge, and proficiency with the ECT procedure. They were then block-randomized to receive either a didactic ECT curriculum (non-SIM) or one augmented by simulation training (SIM). Three months post-completion of the two types of instruction, all residents were re-administered the surveys and a procedural post-assessment. The median number of ECTs performed prior to the study was similar between the two groups (SIM group = 3, non-SIM group = 4.) The SIM group showed significant improvement on pre- and post- survey theoretical knowledge scores: 51% (95% CI = 41 to 61%) and 69% (95% CI = 64 to 74%), respectively, p = .02; this difference was not significant in the non-SIM group, p = .2. Improvement between pre- and post- proficiency scores were seen in the SIM group: 22% (95% CI = 13 to 32%) and 51% (95% CI = 53 to 59%), p < .001 while the effect was less pronounced in the non-SIM group. Inter-rater agreement for the proficiency assessment was excellent: k, = .9. Residents showed significant improvement in knowledge, comfort, and skills following ECT simulation training. With the proposed curriculum, residents would receive comprehensive education not only in the theory behind ECT but also in procedural skills. This curriculum can be modeled in other programs that do not have extensive ECT facilities.

Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma.

PubMed

Caldas, José; Gehlenborg, Nils; Kettunen, Eeva; Faisal, Ali; Rönty, Mikko; Nicholson, Andrew G; Knuutila, Sakari; Brazma, Alvis; Kaski, Samuel

2012-01-15

Genome-wide measurement of transcript levels is an ubiquitous tool in biomedical research. As experimental data continues to be deposited in public databases, it is becoming important to develop search engines that enable the retrieval of relevant studies given a query study. While retrieval systems based on meta-data already exist, data-driven approaches that retrieve studies based on similarities in the expression data itself have a greater potential of uncovering novel biological insights. We propose an information retrieval method based on differential expression. Our method deals with arbitrary experimental designs and performs competitively with alternative approaches, while making the search results interpretable in terms of differential expression patterns. We show that our model yields meaningful connections between biological conditions from different studies. Finally, we validate a previously unknown connection between malignant pleural mesothelioma and SIM2s suggested by our method, via real-time polymerase chain reaction in an independent set of mesothelioma samples. Supplementary data and source code are available from http://www.ebi.ac.uk/fg/research/rex.

Comparison of two structured illumination techniques based on different 3D illumination patterns

NASA Astrophysics Data System (ADS)

Shabani, H.; Patwary, N.; Doblas, A.; Saavedra, G.; Preza, C.

2017-02-01

Manipulating the excitation pattern in optical microscopy has led to several super-resolution techniques. Among different patterns, the lateral sinusoidal excitation was used for the first demonstration of structured illumination microscopy (SIM), which provides the fastest SIM acquisition system (based on the number of raw images required) compared to the multi-spot illumination approach. Moreover, 3D patterns that include lateral and axial variations in the illumination have attracted more attention recently as they address resolution enhancement in three dimensions. A threewave (3W) interference technique based on coherent illumination has already been shown to provide super-resolution and optical sectioning in 3D-SIM. In this paper, we investigate a novel tunable technique that creates a 3D pattern from a set of multiple incoherently illuminated parallel slits that act as light sources for a Fresnel biprism. This setup is able to modulate the illumination pattern in the object space both axially and laterally with adjustable modulation frequencies. The 3D forward model for the new system is developed here to consider the effect of the axial modulation due to the 3D patterned illumination. The performance of 3D-SIM based on 3W interference and the tunable system are investigated in simulation and compared based on two different criteria. First, restored images obtained for both 3D-SIM systems using a generalized Wiener filter are compared to determine the effect of the illumination pattern on the reconstruction. Second, the effective frequency response of both systems is studied to determine the axial and lateral resolution enhancement that is obtained in each case.

Local delivery of controlled-release simvastatin to improve the biocompatibility of polyethylene terephthalate artificial ligaments for reconstruction of the anterior cruciate ligament.

PubMed

Zhang, Peng; Han, Fei; Li, Yunxia; Chen, Jiwu; Chen, Tianwu; Zhi, Yunlong; Jiang, Jia; Lin, Chao; Chen, Shiyi; Zhao, Peng

2016-01-01

The Ligament Advanced Reinforcement System has recently been widely used as the primary graft of choice in anterior cruciate ligament (ACL) reconstruction. But the biological graft-bone healing still remains a problem. Previous studies have shown that simvastatin (SIM) stimulates bone formation. The objective of this study was to investigate whether surface coating with collagen containing low-dose SIM microsphere could enhance the surface biocompatibility of polyethylene terephthalate (PET) artificial ligaments to accelerate graft-to-bone healing. The in vitro studies demonstrated that bone marrow stromal cells on the collagen-coated PET scaffolds (COL/PET) and simvastatin/collagen-coated PET scaffolds (SIM/COL/PET) proliferated vigorously. Compared with the PET group and the COL/PET group, SIM could induce bone marrow stromal cells' osteoblastic differentiation, high alkaline phosphatase activity, more mineralization deposition, and more expression of osteoblast-related genes, such as osteocalcin, runt-related transcription factor 2, bone morphogenetic protein-2, and vascular endothelial growth factor, in the SIM/COL/PET group. In vivo, rabbits received ACL reconstruction with different scaffolds. Histological analysis demonstrated that graft-bone healing was significantly greater with angiogenesis and osteogenesis in the SIM/COL/PET group than the other groups. In addition, biomechanical testing at the eighth week demonstrated a significant increase in the ultimate failure load and stiffness in the SIM/COL/PET group. The low dose of SIM-sustained release from SIM/COL/PET promoted the graft-bone healing via its effect on both angiogenesis and osteogenesis. This study suggested that collagen containing low-dose SIM microsphere coating on the surface of PET artificial ligaments could be potentially applied for ACL reconstruction.

Research on the SIM card implementing functions of transport card

NASA Astrophysics Data System (ADS)

Li, Yi; Wang, Lin

2015-12-01

This paper is based on the analysis for theory and key technologies of contact communication, contactless communication card and STK menu, and proposes complete software and hardware solution for achieving convenience and secure mobile payment system on SIM card.

Hybrid-coded 3D structured illumination imaging with Bayesian estimation (Conference Presentation)

NASA Astrophysics Data System (ADS)

Chen, Hsi-Hsun; Luo, Yuan; Singh, Vijay R.

2016-03-01

Light induced fluorescent microscopy has long been developed to observe and understand the object at microscale, such as cellular sample. However, the transfer function of lense-based imaging system limits the resolution so that the fine and detailed structure of sample cannot be identified clearly. The techniques of resolution enhancement are fascinated to break the limit of resolution for objective given. In the past decades, the resolution enhancement imaging has been investigated through variety of strategies, including photoactivated localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM), stimulated emission depletion (STED), and structure illuminated microscopy (SIM). In those methods, only SIM can intrinsically improve the resolution limit for a system without taking the structure properties of object into account. In this paper, we develop a SIM associated with Bayesian estimation, furthermore, with optical sectioning capability rendered from HiLo processing, resulting the high resolution through 3D volume. This 3D SIM can provide the optical sectioning and resolution enhancement performance, and be robust to noise owing to the Data driven Bayesian estimation reconstruction proposed. For validating the 3D SIM, we show our simulation result of algorithm, and the experimental result demonstrating the 3D resolution enhancement.

Visualization of water transport into soybean nodules by Tof-SIMS cryo system.

PubMed

Iijima, Morio; Watanabe, Toshimasa; Yoshida, Tomoharu; Kawasaki, Michio; Kato, Toshiyuki; Yamane, Koji

2015-04-15

This paper examined the route of water supply into soybean nodules through the new visualization technique of time of flight secondary ion mass spectrometry (Tof-SIMS) cryo system, and obtained circumstantial evidence for the water inflow route. The maximum resolution of the Tof-SIMS imaging used by this study was 1.8 μm (defined as the three pixel step length), which allowed us to detect water movement at the cellular level. Deuterium-labeled water was supplied to soybean plants for 4h and the presence of deuterium in soybean nodules was analyzed by the Tof-SIMS cryo system. Deuterium ions were found only in the endodermis tissue surrounding the central cylinder in soybean nodules. Neither xylem vessels nor phloem complex itself did not indicate any deuterium accumulation. Deuterium-ion counts in the endodermis tissue were not changed by girdling treatment, which restricted water movement through the phloem complex. The results strongly indicated that nodule tissues did not receive water directly from the phloem complex, but received water through root cortex apoplastic pathway from the root axis. Copyright © 2015 Elsevier GmbH. All rights reserved.

Apollo guidance, navigation, and control: Candidate configuration trade study, Stellar-Inertial Measurement System (SIMS) for an Earth Observation Satellite (EOS)

NASA Technical Reports Server (NTRS)

Ogletree, G.; Coccoli, J.; Mckern, R.; Smith, M.; White, R.

1972-01-01

The ten candidate SIMS configurations were reduced to three in preparation for the final trade comparison. The report emphasizes subsystem design trades, star availability studies, data processing (smoothing) methods, and the analytical and simulation studies at subsystem and system levels from which candidate accuracy estimates will be presented.

Human Interoperability: Experimentation to Understand & Improve the Human Component of Complex Systems

DTIC Science & Technology

2008-09-30

and Accountability Act of 1996 ) prohibit health care providers from sharing certain information about patients, and the Posse Comitatus Act (1878...Publishers, pp. 333-380. Carley, K.M., and Svoboda, D.M. ( 1996 ). Modeling Organizational Adaptation as a Simulated Annealing Process. Sociological...Privacy: Interdisciplinary Frameworks and Solution. Hershey , PA: IGI Global. Salas, E., Sims, D.E., & Burke, C.S. (2005). Is there a big five in

Community as client: environmental issues in the real world. A SimCity computer simulation.

PubMed

Bareford, C G

2001-01-01

The ability to think critically has become a crucial part of professional practice and education. SimCity, a popular computer simulation game, provides an opportunity to practice community assessment and interventions using a systems approach. SimCity is an interactive computer simulation game in which the player takes an active part in community planning. SimCity is supported on either a Windows 95/98 or a Macintosh platform and is available on CD-ROM at retail stores or at www.simcity.com. Students complete a tutorial and then apply a selected scenario in SimCity. Scenarios consist of hypothetical communities that have varying types and degrees of environmental problems, e.g., traffic, crime, nuclear meltdown, flooding, fire, and earthquakes. In problem solving with the simulated scenarios, students (a) identify systems and subsystems within the community that are critical factors impacting the environmental health of the community, (b) create changes in the systems and subsystems in an effort to solve the environmental health problem, and (c) evaluate the effectiveness of interventions based on the game score, demographic and fiscal data, and amount of community support. Because the consequences of planned intervention are part of the simulation, nursing students are able to develop critical-thinking skills. The simulation provides essential content in community planning in an interesting and interactive format.

Chromium localization in plant tissues of Lycopersicum esculentum Mill using ICP-MS and ion microscopy (SIMS)

NASA Astrophysics Data System (ADS)

Mangabeira, Pedro Antonio; Gavrilov, Konstantin L.; Almeida, Alex-Alan Furtado de; Oliveira, Arno Heeren; Severo, Maria Isabel; Rosa, Tiago Santana; Silva, Delmira da Costa; Labejof, Lise; Escaig, Françoise; Levi-Setti, Riccardo; Mielke, Marcelo Schramm; Loustalot, Florence Grenier; Galle, Pierre

2006-03-01

High-resolution imaging secondary ion mass spectrometry (HRI-SIMS) in combination with inductively coupled plasma mass spectrometry (ICP-MS) were utilised to determine specific sites of chromium concentration in tomato plant tissues (roots, stems and leaves). The tissues were obtained from plants grown for 2 months in hydroponic conditions with Cr added in a form chromium salt (CrCl 3·6H 2O) to concentrations of 25 and 50 mg/L. The chemical fixation procedure used permit to localize only insoluble or strongly bound Cr components in tomato plant tissue. In this work no quantitative SIMS analysis was made. HRI-SIMS analysis revealed that the transport of chromium is restricted to the vascular system of roots, stems and leaves. No Cr was detected in epidermis, palisade parenchyma and spongy parenchyma cells of the leaves. The SIMS-300 spectra obtained from the tissues confirm the HRI-SIMS observations. The roots, and especially walls of xylem vessels, were determined as the principal site of chromium accumulation in tomato plants.

Biological Analysis of Simvastatin-releasing Chitosan Scaffold as a Cell-free System for Pulp-dentin Regeneration.

PubMed

Soares, Diana G; Anovazzi, Giovanna; Bordini, Ester Alves F; Zuta, Uxua O; Silva Leite, Maria Luísa A; Basso, Fernanda G; Hebling, Josimeri; de Souza Costa, Carlos A

2018-06-01

The improvement of biomaterials capable of driving the regeneration of the pulp-dentin complex mediated by resident cells is the goal of regenerative dentistry. In the present investigation, a chitosan scaffold (CHSC) that released bioactive concentrations of simvastatin (SIM) was tested, aimed at the development of a cell-free tissue engineering system. First, we performed a dose-response assay to select the bioactive dose of SIM capable of inducing an odontoblastic phenotype in dental pulp cells (DPCs); after which we evaluated the synergistic effect of this dosage with the CHSC/DPC construct. SIM at 1.0 μmol/L (CHSC-SIM1.0) and 0.5 μmol/L were incorporated into the CHSC, and cell viability, adhesion, and calcium deposition were evaluated. Finally, we assessed the biomaterials in an artificial pulp chamber/3-dimensional culture model to simulate the cell-free approach in vitro. SIM at 0.1 μmol/L was selected as the bioactive dose. This drug was capable of strongly inducing an odontoblastic phenotype on the DPC/CHSC construct. The incorporation of SIM into CHSC had no deleterious effect on cell viability and adhesion to the scaffold structure. CHSC-SIM1.0 led to significantly higher calcium-rich matrix deposition on scaffold/dentin disc assay compared with the control (CHSC). This biomaterial induced the migration of DPCs from a 3-dimensional culture to its surface as well as stimulated significantly higher expressions of alkaline phosphatase, collagen type 1 alpha 1, dentin matrix acidic phosphoprotein 1, and dentin sialophosphoprotein on 3-dimensional-cultured DPCs than on those in contact with CHSC. CHSC-SIM1.0 scaffold was capable of increasing the chemotaxis and regenerative potential of DPCs. Copyright © 2018 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Project Status Update and SIM Science Breadth Discussion for the Origins Subcommittee (OS)

NASA Technical Reports Server (NTRS)

Marr, James C., IV; Shao, Mike

2003-01-01

This viewgraph presentation is composed of two sections The first reviews the features and the science goals of the Space Interferometry Mission (SIM). The goals are: (1) Perform a search for other planetary systems by surveying 2000 nearby stars for astrometric signatures of planetary companion, (2) Survey a sample of 200 nearby stars for orbiting planets down to terrestrial-type masses (3) Improve best current catalog of star positions by >lOOx and extend to fainter stars to allow extension of stellar knowledge to include our entire galaxy (4) Study dynamics and evolution of stars and star clusters in our galaxy to understand how our galaxy was formed and how it will evolve. (5) Calibrate luminosities of important stars and cosmological distance indicators to improve our understanding of stellar processes and to measure precise distance in the distant universe. The presentation also reviews the accomplishments since 2002, the plans for the subsequent 6 months. The second entitled "The Breadth of SIM Science," reviews SIM science goals in a larger context. SIM will serve to complement and pave the way for the Terrestrial Planet Finder (TPF). SIM observations of the motions of stars will tell us about the distribution of all gravitating mass (light plus dark matter) in the Galaxy. SIM observations of the motions of dwarf galaxies around our own will determine the mass distribution (light plus dark matter in the Halo. SIM will greatly extend these observations to test the theories of accretion disks around super massive black holes. SIM has advantages for studying AGN and other very compact objects.

Tank System Integrated Model: A Cryogenic Tank Performance Prediction Program

NASA Technical Reports Server (NTRS)

Bolshinskiy, L. G.; Hedayat, A.; Hastings, L. J.; Sutherlin, S. G.; Schnell, A. R.; Moder, J. P.

2017-01-01

Accurate predictions of the thermodynamic state of the cryogenic propellants, pressurization rate, and performance of pressure control techniques in cryogenic tanks are required for development of cryogenic fluid long-duration storage technology and planning for future space exploration missions. This Technical Memorandum (TM) presents the analytical tool, Tank System Integrated Model (TankSIM), which can be used for modeling pressure control and predicting the behavior of cryogenic propellant for long-term storage for future space missions. Utilizing TankSIM, the following processes can be modeled: tank self-pressurization, boiloff, ullage venting, mixing, and condensation on the tank wall. This TM also includes comparisons of TankSIM program predictions with the test data andexamples of multiphase mission calculations.

Comparison of Confocal and Super-Resolution Reflectance Imaging of Metal Oxide Nanoparticles

PubMed Central

Guggenheim, Emily J.; Khan, Abdullah; Pike, Jeremy; Chang, Lynne; Lynch, Iseult; Rappoport, Joshua Z.

2016-01-01

The potential for human exposure to manufactured nanoparticles (NPs) has increased in recent years, in part through the incorporation of engineered particles into a wide range of commercial goods and medical applications. NP are ideal candidates for use as therapeutic and diagnostic tools within biomedicine, however concern exists regarding their efficacy and safety. Thus, developing techniques for the investigation of NP uptake into cells is critically important. Current intracellular NP investigations rely on the use of either Transmission Electron Microscopy (TEM), which provides ultrahigh resolution, but involves cumbersome sample preparation rendering the technique incompatible with live cell imaging, or fluorescent labelling, which suffers from photobleaching, poor bioconjugation and, often, alteration of NP surface properties. Reflected light imaging provides an alternative non-destructive label free technique well suited, but not limited to, the visualisation of NP uptake within model systems, such as cells. Confocal reflectance microscopy provides optical sectioning and live imaging capabilities, with little sample preparation. However confocal microscopy is diffraction limited, thus the X-Y resolution is restricted to ~250 nm, substantially larger than the <100 nm size of NPs. Techniques such as super-resolution light microscopy overcome this fundamental limitation, providing increased X-Y resolution. The use of Reflectance SIM (R-SIM) for NP imaging has previously only been demonstrated on custom built microscopes, restricting the widespread use and limiting NP investigations. This paper demonstrates the use of a commercial SIM microscope for the acquisition of super-resolution reflectance data with X-Y resolution of 115 nm, a greater than two-fold increase compared to that attainable with RCM. This increase in resolution is advantageous for visualising small closely spaced structures, such as NP clusters, previously unresolvable by RCM. This is advantageous when investigating the subcellular trafficking of NP within fluorescently labelled cellular compartments. NP signal can be observed using RCM, R-SIM and TEM and a direct comparison is presented. Each of these techniques has its own benefits and limitations; RCM and R-SIM provide novel complementary information while the combination of modalities provides a unique opportunity to gain additional information regarding NP uptake. The use of multiple imaging methods therefore greatly enhances the range of NPs that can be studied under label-free conditions. PMID:27695038

Extrasolar Planet Inferometric Survey (EPIcS)

NASA Technical Reports Server (NTRS)

Shao, Michael; Baliunas, Sallie; Boden, Andrew; Kulkarni, Shrinivas; Lin, Douglas N. C.; Loredo, Tom; Queloz, Didier; Shaklan, Stuart; Tremaine, Scott; Wolszczan, Alexander

2004-01-01

The discovery of the nature of the solar system was a crowning achievement of Renaissance science. The quest to evaluate the properties of extrasolar planetary systems is central to both the intellectual understanding of our origins and the cultural understanding of humanity's place in the Universe; thus it is appropriate that the goals and objectives of NASA's breakthrough Origins program emphasize the study of planetary systems, with a focus on the search for habitable planets. We propose an ambitious research program that will use SIM - the first major mission of the Origins program - to explore planetary systems in our Galactic neighborhood. Our program is a novel two-tiered SIM survey of nearby stars that exploits the capabilities of SIM to achieve two scientific objectives: (i) to identify Earth-like planets in habitable regions around nearby Sunlike stars: and (ii) to explore the nature and evolution of planetary systems in their full variety. The first of these objectives was recently recommended by the Astronomy and Astrophysics Survey Committee (the McKee-Taylor Committee) as a prerequisite for the development of the Terrestrial Planet Finder mission later in the decade. Our program combines this two-part survey with preparatory and contemporaneous research designed to maximize the scientific return from the limited and thus precious observing resources of SIM.

OpenSim: a musculoskeletal modeling and simulation framework for in silico investigations and exchange

PubMed Central

Seth, Ajay; Sherman, Michael; Reinbolt, Jeffrey A.; Delp, Scott L.

2015-01-01

Movement science is driven by observation, but observation alone cannot elucidate principles of human and animal movement. Biomechanical modeling and computer simulation complement observations and inform experimental design. Biological models are complex and specialized software is required for building, validating, and studying them. Furthermore, common access is needed so that investigators can contribute models to a broader community and leverage past work. We are developing OpenSim, a freely available musculoskeletal modeling and simulation application and libraries specialized for these purposes, by providing: musculoskeletal modeling elements, such as biomechanical joints, muscle actuators, ligament forces, compliant contact, and controllers; and tools for fitting generic models to subject-specific data, performing inverse kinematics and forward dynamic simulations. OpenSim performs an array of physics-based analyses to delve into the behavior of musculoskeletal models by employing Simbody, an efficient and accurate multibody system dynamics code. Models are publicly available and are often reused for multiple investigations because they provide a rich set of behaviors that enables different lines of inquiry. This report will discuss one model developed to study walking and applied to gain deeper insights into muscle function in pathological gait and during running. We then illustrate how simulations can test fundamental hypotheses and focus the aims of in vivo experiments, with a postural stability platform and human model that provide a research environment for performing human posture experiments in silico. We encourage wide adoption of OpenSim for community exchange of biomechanical models and methods and welcome new contributors. PMID:25893160

Structured illumination microscopy as a diagnostic tool for nephrotic disease

NASA Astrophysics Data System (ADS)

Nylk, Jonathan; Pullman, James M.; Campbell, Elaine C.; Gunn-Moore, Frank J.; Prystowsky, Michael B.; Dholakia, Kishan

2017-02-01

Nephrotic disease is a group of debilitating and sometimes lethal diseases affecting kidney function, specifically the loss of ability to retain vital proteins in the blood while smaller molecules are removed through filtration into the urine. Treatment routes are often dictated by microscopic analysis of kidney biopsies. Podocytes within the glomeruli of the kidney have many interdigitating projections (foot processes), which form the main filtration system. Nephrotic disease is characterised by the loss of this tightly interdigitating substructure and its observation by electron microscopy (EM) is necessitated as these structures are typically 250 500nm wide, with 40nm spacing. Diagnosis by EM is both expensive and time consuming; it can take up to one week to complete the preparation, imaging, and analysis of a single sample. We propose structured illumination microscopy (SIM) as an alternative, optical diagnostic tool. Our results show that SIM can resolve the structure of fluorescent probes tagged to podocin, a protein localised to the periphery of the podocyte foot processes. Three-dimensional podocin maps were acquired in healthy tissue and tissue from patients diagnosed with two different nephrotic disease states; minimal change disease and membranous nephropathy. These structures correlated well with EM images of the same structure. Preparation, imaging, and analysis could be achieved in several hours. Additionally, the volumetric information of the SIM images revealed morphological changes in disease states not observed by EM. This evidence supports the use of SIM as a diagnostic tool for nephrotic disease and can potentially reduce the time and cost per diagnosis.

XCluSim: a visual analytics tool for interactively comparing multiple clustering results of bioinformatics data

PubMed Central

2015-01-01

Background Though cluster analysis has become a routine analytic task for bioinformatics research, it is still arduous for researchers to assess the quality of a clustering result. To select the best clustering method and its parameters for a dataset, researchers have to run multiple clustering algorithms and compare them. However, such a comparison task with multiple clustering results is cognitively demanding and laborious. Results In this paper, we present XCluSim, a visual analytics tool that enables users to interactively compare multiple clustering results based on the Visual Information Seeking Mantra. We build a taxonomy for categorizing existing techniques of clustering results visualization in terms of the Gestalt principles of grouping. Using the taxonomy, we choose the most appropriate interactive visualizations for presenting individual clustering results from different types of clustering algorithms. The efficacy of XCluSim is shown through case studies with a bioinformatician. Conclusions Compared to other relevant tools, XCluSim enables users to compare multiple clustering results in a more scalable manner. Moreover, XCluSim supports diverse clustering algorithms and dedicated visualizations and interactions for different types of clustering results, allowing more effective exploration of details on demand. Through case studies with a bioinformatics researcher, we received positive feedback on the functionalities of XCluSim, including its ability to help identify stably clustered items across multiple clustering results. PMID:26328893

Look@NanoSIMS--a tool for the analysis of nanoSIMS data in environmental microbiology.

PubMed

Polerecky, Lubos; Adam, Birgit; Milucka, Jana; Musat, Niculina; Vagner, Tomas; Kuypers, Marcel M M

2012-04-01

We describe an open-source freeware programme for high throughput analysis of nanoSIMS (nanometre-scale secondary ion mass spectrometry) data. The programme implements basic data processing and analytical functions, including display and drift-corrected accumulation of scanned planes, interactive and semi-automated definition of regions of interest (ROIs), and export of the ROIs' elemental and isotopic composition in graphical and text-based formats. Additionally, the programme offers new functions that were custom-designed to address the needs of environmental microbiologists. Specifically, it allows manual and automated classification of ROIs based on the information that is derived either from the nanoSIMS dataset itself (e.g. from labelling achieved by halogen in situ hybridization) or is provided externally (e.g. as a fluorescence in situ hybridization image). Moreover, by implementing post-processing routines coupled to built-in statistical tools, the programme allows rapid synthesis and comparative analysis of results from many different datasets. After validation of the programme, we illustrate how these new processing and analytical functions increase flexibility, efficiency and depth of the nanoSIMS data analysis. Through its custom-made and open-source design, the programme provides an efficient, reliable and easily expandable tool that can help a growing community of environmental microbiologists and researchers from other disciplines process and analyse their nanoSIMS data. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Characterization of Natural Dyes and Traditional Korean Silk Fabric by Surface Analytical Techniques

PubMed Central

Lee, Jihye; Kang, Min Hwa; Lee, Kang-Bong; Lee, Yeonhee

2013-01-01

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) and X-ray photoelectron spectroscopy (XPS) are well established surface techniques that provide both elemental and organic information from several monolayers of a sample surface, while also allowing depth profiling or image mapping to be carried out. The static TOF-SIMS with improved performances has expanded the application of TOF-SIMS to the study of a variety of organic, polymeric and biological materials. In this work, TOF-SIMS, XPS and Fourier Transform Infrared (FTIR) measurements were used to characterize commercial natural dyes and traditional silk fabric dyed with plant extracts dyes avoiding the time-consuming and destructive extraction procedures necessary for the spectrophotometric and chromatographic methods previously used. Silk textiles dyed with plant extracts were then analyzed for chemical and functional group identification of their dye components and mordants. TOF-SIMS spectra for the dyed silk fabric showed element ions from metallic mordants, specific fragment ions and molecular ions from plant-extracted dyes. The results of TOF-SIMS, XPS and FTIR are very useful as a reference database for comparison with data about traditional Korean silk fabric and to provide an understanding of traditional dyeing materials. Therefore, this study shows that surface techniques are useful for micro-destructive analysis of plant-extracted dyes and Korean dyed silk fabric. PMID:28809257

Challenges of biological sample preparation for SIMS imaging of elements and molecules at subcellular resolution

NASA Astrophysics Data System (ADS)

Chandra, Subhash

2008-12-01

Secondary ion mass spectrometry (SIMS) based imaging techniques capable of subcellular resolution characterization of elements and molecules are becoming valuable tools in many areas of biology and medicine. Due to high vacuum requirements of SIMS, the live cells cannot be analyzed directly in the instrument. The sample preparation, therefore, plays a critical role in preserving the native chemical composition for SIMS analysis. This work focuses on the evaluation of frozen-hydrated and frozen freeze-dried sample preparations for SIMS studies of cultured cells with a CAMECA IMS-3f dynamic SIMS ion microscope instrument capable of producing SIMS images with a spatial resolution of 500 nm. The sandwich freeze-fracture method was used for fracturing the cells. The complimentary fracture planes in the plasma membrane were characterized by field-emission secondary electron microscopy (FESEM) in the frozen-hydrated state. The cells fractured at the dorsal surface were used for SIMS analysis. The frozen-hydrated SIMS analysis of individual cells under dynamic primary ion beam (O 2+) revealed local secondary ion signal enhancements correlated with the water image signals of 19(H 3O) +. A preferential removal of water from the frozen cell matrix in the Z-axis was also observed. These complications render the frozen-hydrated sample type less desirable for subcellular dynamic SIMS studies. The freeze-drying of frozen-hydrated cells, either inside the instrument or externally in a freeze-drier, allowed SIMS imaging of subcellular chemical composition. Morphological evaluations of fractured freeze-dried cells with SEM and confocal laser scanning microscopy (CLSM) revealed well-preserved mitochondria, Golgi apparatus, and stress fibers. SIMS analysis of fractured freeze-dried cells revealed well-preserved chemical composition of even the most highly diffusible ions like K + and Na + in physiologically relevant concentrations. The high K-low Na signature in individual cells provided a rule-of-thumb criterion for the validation of sample preparation. The fractured freeze-dried cells allowed 3-D SIMS imaging and localization of 13C 15N labeled molecules and therapeutic drugs containing an elemental tag. Examples are shown to demonstrate that both diffusible elements and molecules are prone to artifact-induced relocation at subcellular scale if the sample preparation is compromised. The sample preparation is problem dependent and may vary widely between the diverse sample types of biological systems and the type of instrument used for SIMS analysis. The sample preparation, however, must be validated so that SIMS can be applied with confidence in biology and medicine.

The Technologies of EXPER SIM.

ERIC Educational Resources Information Center

Hedberg, John G.

EXPER SIM has been translated into two basic software systems: the Michigan Experimental Simulation Supervisor (MESS) and Louisville Experiment Simulation Supervisor (LESS). MESS and LESS have been programed to facilitate student interaction with the computer for research purposes. The programs contain models for several statistical analyses, and…

The Parallel System for Integrating Impact Models and Sectors (pSIMS)

NASA Technical Reports Server (NTRS)

Elliott, Joshua; Kelly, David; Chryssanthacopoulos, James; Glotter, Michael; Jhunjhnuwala, Kanika; Best, Neil; Wilde, Michael; Foster, Ian

2014-01-01

We present a framework for massively parallel climate impact simulations: the parallel System for Integrating Impact Models and Sectors (pSIMS). This framework comprises a) tools for ingesting and converting large amounts of data to a versatile datatype based on a common geospatial grid; b) tools for translating this datatype into custom formats for site-based models; c) a scalable parallel framework for performing large ensemble simulations, using any one of a number of different impacts models, on clusters, supercomputers, distributed grids, or clouds; d) tools and data standards for reformatting outputs to common datatypes for analysis and visualization; and e) methodologies for aggregating these datatypes to arbitrary spatial scales such as administrative and environmental demarcations. By automating many time-consuming and error-prone aspects of large-scale climate impacts studies, pSIMS accelerates computational research, encourages model intercomparison, and enhances reproducibility of simulation results. We present the pSIMS design and use example assessments to demonstrate its multi-model, multi-scale, and multi-sector versatility.

Analysis of corneal topography in patients with pure microphthalmia in Eastern China.

PubMed

Hu, Pei-Hong; Gao, Gui-Ping; Yu, Yao; Pei, Chong-Gang; Zhou, Qiong; Huang, Xin; Zhang, Ying; Shao, Yi

2015-12-01

To determine the typical corneal changes in pure microphthalmia using a corneal topography system and identify characteristics that may assist in early diagnosis. Patients with pure microphthalmia and healthy control subjects underwent corneal topography analysis (Orbscan IIZ® Corneal Topography System; Bausch and Lomb, Bridgewater, NJ, USA) to determine degree of corneal astigmatism (mean A), simulation of corneal astigmatism (sim A), mean keratometry (mean K), simulated keratometry (sim K), irregularities in the 3 - and 5-mm zone, and mean thickness of nine distinct corneal regions. Patients with pure microphthalmia (n = 12) had significantly higher mean K, sim K, mean A, sim A, 3.0 mm irregularity and 5.0 mm irregularity, and exhibited significantly more false keratoconus than controls (n = 12). There was a significant between-group difference in the morphology of the anterior corneal surface and the central curvature of the cornea. Changes in corneal morphology observed in this study could be useful in borderline situations to confirm the diagnosis of pure microphthalmia. © The Author(s) 2015.

Understanding Earthquake Fault Systems Using QuakeSim Analysis and Data Assimilation Tools

NASA Technical Reports Server (NTRS)

Donnellan, Andrea; Parker, Jay; Glasscoe, Margaret; Granat, Robert; Rundle, John; McLeod, Dennis; Al-Ghanmi, Rami; Grant, Lisa

2008-01-01

We are using the QuakeSim environment to model interacting fault systems. One goal of QuakeSim is to prepare for the large volumes of data that spaceborne missions such as DESDynI will produce. QuakeSim has the ability to ingest distributed heterogenous data in the form of InSAR, GPS, seismicity, and fault data into various earthquake modeling applications, automating the analysis when possible. Virtual California simulates interacting faults in California. We can compare output from long time history Virtual California runs with the current state of strain and the strain history in California. In addition to spaceborne data we will begin assimilating data from UAVSAR airborne flights over the San Francisco Bay Area, the Transverse Ranges, and the Salton Trough. Results of the models are important for understanding future earthquake risk and for providing decision support following earthquakes. Improved models require this sensor web of different data sources, and a modeling environment for understanding the combined data.

Overview of Single-Molecule Speckle (SiMS) Microscopy and Its Electroporation-Based Version with Efficient Labeling and Improved Spatiotemporal Resolution.

PubMed

Yamashiro, Sawako; Watanabe, Naoki

2017-07-06

Live-cell single-molecule imaging was introduced more than a decade ago, and has provided critical information on remodeling of the actin cytoskeleton, the motion of plasma membrane proteins, and dynamics of molecular motor proteins. Actin remodeling has been the best target for this approach because actin and its associated proteins stop diffusing when assembled, allowing visualization of single-molecules of fluorescently-labeled proteins in a state specific manner. The approach based on this simple principle is called Single-Molecule Speckle (SiMS) microscopy. For instance, spatiotemporal regulation of actin polymerization and lifetime distribution of actin filaments can be monitored directly by tracking actin SiMS. In combination with fluorescently labeled probes of various actin regulators, SiMS microscopy has contributed to clarifying the processes underlying recycling, motion and remodeling of the live-cell actin network. Recently, we introduced an electroporation-based method called eSiMS microscopy, with high efficiency, easiness and improved spatiotemporal precision. In this review, we describe the application of live-cell single-molecule imaging to cellular actin dynamics and discuss the advantages of eSiMS microscopy over previous SiMS microscopy.

'Nano' Morphology and Element Signatures of Early Life on Earth: A New Tool for Assessing Biogenicity

NASA Technical Reports Server (NTRS)

Oehler, D. Z.; Mostefaoui, S.; Meibom, A.; Selo, M.; McKay, D. S.; Robert, F.

2006-01-01

The relatively young technology of NanoSIMS is unlocking an exciting new level of information from organic matter in ancient sediments. We are using this technique to characterize Proterozoic organic material that is clearly biogenic as a guide for interpreting controversial organic structures in either terrestrial or extraterrestrial samples. NanoSIMS is secondary ion mass spectrometry for trace element and isotope analysis at sub-micron resolution. In 2005, Robert et al. [1] combined NanoSIMS element maps with optical microscopic imagery in an effort to develop a new method for assessing biogenicity of Precambrian structures. The ability of NanoSIMS to map simultaneously the distribution of organic elements with a 50 nm spatial resolution provides new biologic markers that could help define the timing of life s development on Earth. The current study corroborates the work of Robert et al. and builds on their study by using NanoSIMS to map C, N (as CN), S, Si and O of both excellently preserved microfossils and less well preserved, non-descript organics in Proterozoic chert from the ca. 0.8 Ga Bitter Springs Formation of Australia.

Phase 1 Validation Testing and Simulation for the WEC-Sim Open Source Code

NASA Astrophysics Data System (ADS)

Ruehl, K.; Michelen, C.; Gunawan, B.; Bosma, B.; Simmons, A.; Lomonaco, P.

2015-12-01

WEC-Sim is an open source code to model wave energy converters performance in operational waves, developed by Sandia and NREL and funded by the US DOE. The code is a time-domain modeling tool developed in MATLAB/SIMULINK using the multibody dynamics solver SimMechanics, and solves the WEC's governing equations of motion using the Cummins time-domain impulse response formulation in 6 degrees of freedom. The WEC-Sim code has undergone verification through code-to-code comparisons; however validation of the code has been limited to publicly available experimental data sets. While these data sets provide preliminary code validation, the experimental tests were not explicitly designed for code validation, and as a result are limited in their ability to validate the full functionality of the WEC-Sim code. Therefore, dedicated physical model tests for WEC-Sim validation have been performed. This presentation provides an overview of the WEC-Sim validation experimental wave tank tests performed at the Oregon State University's Directional Wave Basin at Hinsdale Wave Research Laboratory. Phase 1 of experimental testing was focused on device characterization and completed in Fall 2015. Phase 2 is focused on WEC performance and scheduled for Winter 2015/2016. These experimental tests were designed explicitly to validate the performance of WEC-Sim code, and its new feature additions. Upon completion, the WEC-Sim validation data set will be made publicly available to the wave energy community. For the physical model test, a controllable model of a floating wave energy converter has been designed and constructed. The instrumentation includes state-of-the-art devices to measure pressure fields, motions in 6 DOF, multi-axial load cells, torque transducers, position transducers, and encoders. The model also incorporates a fully programmable Power-Take-Off system which can be used to generate or absorb wave energy. Numerical simulations of the experiments using WEC-Sim will be presented. These simulations highlight the code features included in the latest release of WEC-Sim (v1.2), including: wave directionality, nonlinear hydrostatics and hydrodynamics, user-defined wave elevation time-series, state space radiation, and WEC-Sim compatibility with BEMIO (open source AQWA/WAMI/NEMOH coefficient parser).

A Symbolic and Graphical Computer Representation of Dynamical Systems

NASA Astrophysics Data System (ADS)

Gould, Laurence I.

2005-04-01

AUTONO is a Macsyma/Maxima program, designed at the University of Hartford, for solving autonomous systems of differential equations as well as for relating Lagrangians and Hamiltonians to their associated dynamical equations. AUTONO can be used in a number of fields to decipher a variety of complex dynamical systems with ease, producing their Lagrangian and Hamiltonian equations in seconds. These equations can then be incorporated into VisSim, a modeling and simulation program, which yields graphical representations of motion in a given system through easily chosen input parameters. The program, along with the VisSim differential-equations graphical package, allows for resolution and easy understanding of complex problems in a relatively short time; thus enabling quicker and more advanced computing of dynamical systems on any number of platforms---from a network of sensors on a space probe, to the behavior of neural networks, to the effects of an electromagnetic field on components in a dynamical system. A flowchart of AUTONO, along with some simple applications and VisSim output, will be shown.

A Guide to Structured Illumination TIRF Microscopy at High Speed with Multiple Colors

PubMed Central

Young, Laurence J.; Ströhl, Florian; Kaminski, Clemens F.

2016-01-01

Optical super-resolution imaging with structured illumination microscopy (SIM) is a key technology for the visualization of processes at the molecular level in the chemical and biomedical sciences. Although commercial SIM systems are available, systems that are custom designed in the laboratory can outperform commercial systems, the latter typically designed for ease of use and general purpose applications, both in terms of imaging fidelity and speed. This article presents an in-depth guide to building a SIM system that uses total internal reflection (TIR) illumination and is capable of imaging at up to 10 Hz in three colors at a resolution reaching 100 nm. Due to the combination of SIM and TIRF, the system provides better image contrast than rival technologies. To achieve these specifications, several optical elements are used to enable automated control over the polarization state and spatial structure of the illumination light for all available excitation wavelengths. Full details on hardware implementation and control are given to achieve synchronization between excitation light pattern generation, wavelength, polarization state, and camera control with an emphasis on achieving maximum acquisition frame rate. A step-by-step protocol for system alignment and calibration is presented and the achievable resolution improvement is validated on ideal test samples. The capability for video-rate super-resolution imaging is demonstrated with living cells. PMID:27285848

Synchrotron based mass spectrometry to investigate the molecular properties of mineral-organic associations

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

Liu, Suet Yi; Kleber, Markus; Takahashi, Lynelle K.

2013-04-01

Soil organic matter (OM) is important because its decay drives life processes in the biosphere. Analysis of organic compounds in geological systems is difficult because of their intimate association with mineral surfaces. To date there is no procedure capable of quantitatively separating organic from mineral phases without creating artifacts or mass loss. Therefore, analytical techniques that can (a) generate information about both organic and mineral phases simultaneously and (b) allow the examination of predetermined high-interest regions of the sample as opposed to conventional bulk analytical techniques are valuable. Laser Desorption Synchrotron Postionization (synchrotron-LDPI) mass spectrometry is introduced as a novelmore » analytical tool to characterize the molecular properties of organic compounds in mineral-organic samples from terrestrial systems, and it is demonstrated that when combined with Secondary Ion Mass Spectrometry (SIMS), can provide complementary information on mineral composition. Mass spectrometry along a decomposition gradient in density fractions, verifies the consistency of our results with bulk analytical techniques. We further demonstrate that by changing laser and photoionization energies, variations in molecular stability of organic compounds associated with mineral surfaces can be determined. The combination of synchrotron-LDPI and SIMS shows that the energetic conditions involved in desorption and ionization of organic matter may be a greater determinant of mass spectral signatures than the inherent molecular structure of the organic compounds investigated. The latter has implications for molecular models of natural organic matter that are based on mass spectrometric information.« less

Are You Getting the Message? The Effects of SimCom on the Message Received by Deaf, Hard of Hearing, and Hearing Students

ERIC Educational Resources Information Center

Tevenal, Stephanie; Villanueva, Miako

2009-01-01

When hearing speakers address a mixed audience of hearing and deaf participants,[1] they have a choice of three methods by which to convey the information in their presentation. They may choose to use English and provide an English-to-ASL interpreter, use ASL and provide an ASL-to-English interpreter, or use simultaneous communication (SimCom).…

SimCoach: An Intelligent Virtual Human System for Proving Healthcare Information and Support

DTIC Science & Technology

2010-08-01

classrooms , offices, markets, etc.), the next important challenge will involve populating these environments with Virtual Human (VH) representations...in a virtual classroom (Parsons et al., 2007; Rizzo et al., 2006). Additionally, VHs have been used effectively for the conduct of social psychology...T Bowerly, J G Buckwalter and A A Rizzo (2007), A controlled clinical comparison of attention performance in children with ADHD in a virtual reality

Characterization of high explosive particles using cluster secondary ion mass spectrometry.

PubMed

Gillen, Greg; Mahoney, Christine; Wight, Scott; Lareau, Richard

2006-01-01

The use of secondary ion mass spectrometry (SIMS) for the detection and spatially resolved analysis of individual high explosive particles is described. A C(8) (-) carbon cluster primary ion beam was used in a commercial SIMS instrument to analyze samples of high explosives dispersed as particles on silicon substrates. In comparison with monatomic primary ion bombardment, the carbon cluster primary ion beam was found to greatly enhance characteristic secondary ion signals from the explosive compounds while causing minimal beam-induced degradation. The resistance of these compounds to degradation under ion bombardment allows explosive particles to be analyzed under high primary ion dose bombardment (dynamic SIMS) conditions, facilitating the rapid acquisition of spatially resolved molecular information. The use of cluster SIMS combined with computer control of the sample stage position allows for the automated identification and counting of explosive particle distributions on silicon surfaces. This will be useful for characterizing the efficiency of transfer of particulates in trace explosive detection portal collectors and/or swipes utilized for ion mobility spectrometry applications.

Artificial Intelligence (Al) Center of Excellence at the University of Pennsylvania

DTIC Science & Technology

1995-07-01

Approach and repel behaviors were implemented in order to study higher level behavioral simulation . Parallel algorithms for motion planning (as a...of decision-making accuracy can be specified for this graph-reduction process. We have also developed a mixed qualitative/quantitative simulation ...system, called QobiSIM. QobiSIM has been used to develop a cardiovascular simulation to be incorporated into the TraumAID system. This cardiovascular

In Situ Characterization of Hydrated Proteins in Water by SALVI and ToF-SIMS

PubMed Central

Yu, Jiachao; Zhu, Zihua; Yu, Xiao-Ying

2016-01-01

This work demonstrates in situ characterization of protein biomolecules in the aqueous solution using the System for Analysis at the Liquid Vacuum Interface (SALVI) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). The fibronectin protein film was immobilized on the silicon nitride (SiN) membrane that forms the SALVI detection area. During ToF-SIMS analysis, three modes of analysis were conducted including high spatial resolution mass spectrometry, two-dimensional (2D) imaging, and depth profiling. Mass spectra were acquired in both positive and negative modes. Deionized water was also analyzed as a reference sample. Our results show that the fibronectin film in water has more distinct and stronger water cluster peaks compared to water alone. Characteristic peaks of amino acid fragments are also observable in the hydrated protein ToF-SIMS spectra. These results illustrate that protein molecule adsorption on a surface can be studied dynamically using SALVI and ToF-SIMS in the liquid environment for the first time. PMID:26966995

A TOF-SIMS Investigation of the Volatile Inventory of Lithic and Mineral Clasts in Lunar Regolith Samples

NASA Astrophysics Data System (ADS)

Tartèse, R.; Lyon, I. C.

2017-07-01

The lunar regolith offers a key record to characterise the transfer of volatiles across the solar system for the past 4.5 billion years. We tackle this issue by investigating the volatile inventory of lunar regolith samples using TOF-SIMS.

Extension of the SIM Hydrometeorological Reanalysis Over the Entire 20th Century by Combination of Observations and Statistical Downscaling

NASA Astrophysics Data System (ADS)

Minvielle, M.; Céron, J.; Page, C.

2013-12-01

The SAFRAN-ISBA-MODCOU (SIM) system is a combination of three different components: an atmospheric analysis system (SAFRAN) providing the atmospheric forcing for a land surface model (ISBA) that computes surface water and energy budgets and a hydrological model (MODCOU) that provides river flows and level of several aquifers. The variables generated by the SIM chain constitute the SIM reanalysis and the current version only covers the 1958-2012 period. However, long climate datasets are required for evaluation and verification of climate hindcasts/forecasts and to isolate the contribution of natural decadal variability from that of anthropogenic forcing to climate variations. The aim of this work is to extend of the fine-mesh SIM reanalysis to the entire 20th century, especially focusing on temperature and rainfall over France, but also soil wetness and river flows. This extension will first allow a detailed investigation of the influence of decadal variability on France at very fine spatial scales and will provide crucial information for climate model evaluation. Before 1958, the density of available observations from Météo-France necessary to force SAFRAN (rainfall, snow, wind, temperature, humidity, cloudiness) is much lower than today, and not sufficient to produce a correct SIM reanalysis. That's why is has been decided to use the available atmospheric observations over the past decades combined to a statistical downscaling algorithm to overcome the lack of observations. The DSCLIM software package implemented by the CERFACS and using a weather typing based statistical methodology will be used as statistical downscaling method to reconstruct the atmospheric variables necessary to force the ISBA-MODCOU hydrological component. The first stage of this work was to estimate and compare the bias and strengths of the two approaches in their ability to reconstruct the past decades. In this sense, SIM hydro-meteorological experiments were performed for some recent years, with a number of observations artificially reduced to a number similar to years 1910, 1930 and 1950. Concurrently, the same recent years have been downscaled by DSCLIM and used to force ISBA-MODCOU. Afterwards, some additional experiments with some modified parameters in the DSCLIM algorithm have been performed in order to adapt the methodology to the study case, and thus trying to improve its performances. Several configurations of the DSCLIM algorithm were applied to the entire century, using the NOAA20CR reanalysis as large-scale predictor. The reconstructed atmospheric variables are compared to the available observations over the entire century to estimate the ability of the statistical downscaling method to reproduce a correct interannual to multidecadal variability. Finally, a novel method is tested: available observations over past decades are introduced in the DSCLIM algorithm, in order to obtain a reconstructed dataset as realistic as possible.

Nonlinear Structured Illumination Using a Fluorescent Protein Activating at the Readout Wavelength

PubMed Central

Hou, Wenya; Kielhorn, Martin; Arai, Yoshiyuki; Nagai, Takeharu; Kessels, Michael M.; Qualmann, Britta; Heintzmann, Rainer

2016-01-01

Structured illumination microscopy (SIM) is a wide-field technique in fluorescence microscopy that provides fast data acquisition and two-fold resolution improvement beyond the Abbe limit. We observed a further resolution improvement using the nonlinear emission response of a fluorescent protein. We demonstrated a two-beam nonlinear structured illumination microscope by introducing only a minor change into the system used for linear SIM (LSIM). To achieve the required nonlinear dependence in nonlinear SIM (NL-SIM) we exploited the photoswitching of the recently introduced fluorophore Kohinoor. It is particularly suitable due to its positive contrast photoswitching characteristics. Contrary to other reversibly photoswitchable fluorescent proteins which only have high photostability in living cells, Kohinoor additionally showed little degradation in fixed cells over many switching cycles. PMID:27783656

Epidemilogical Simulation System, Version 2.4

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

2004-01-30

EpiSims uses a detailed simulation of disease spread to evaluate demographically and geographically targeted biological threat reduction strategies. Abstract: EpiSims simulates the spread of disease and analyzes the consequences of intervention strategies in a large urban area at the level of individuals. The simulation combines models of three dynamical systems: urban social networks, disease transmission, and within-host progression of a disease. Validated population mobility and activity generation technology provides the social network models, Disease models are based on fusion of expert opinion and available data. EpiSims provides a previously unavailable detailed representation of the course of an outbreak in urbanmore » area. A letter of August 16, 2002 from the Office of Homeland Security states: "Ability of EpiSims to provide comprehensive data on daily activity patterns of individuals makes it far superior to traditional SIR models — clearly had an impact on pre-attack smallpox vaccination policy." EpiSims leverages a unique Los Alamos National Laboratory resource — the population mobility and activity data developed by TRANSIMS (Transportation Analysis and SiMulation System) — to create epidemiological analyses at an unprecedented level of detail. We create models of microscopic (individual-level) physical and biological processes from which, through simulation, emerge the macroscopic (urban regional level) quantities that are the inputs to alternative models. For example, the contact patterns of individuals in different demographic groups determine the overall mixing rates those groups. The characteristics of a person-to-person transmission together with their contact patterns determine the reproductive numbers — how many people will be infected on average by each case. Mixing rates and reproductive numbers are the basic parameters of other epidemiological models. Because interventions — and people’s reactions to them — are ultimately applied at the individual level, EpiSims is uniquely suited to evaluate their macroscopic consequences. For example, the debate over the logistics of targeted vaccination for smallpox, and thus the magnitude of the threat it poses, can best be resolved through an individual- based approach. EpiSims is the only available analytical tool using the individual-based approach that can scale to populations of a million or more without introducing ad-hoc assumptions about the nature of the social network. Impact: The first study commissioned for the EpiSims project was to analyze the effectiveness of targeted vaccination and isolation strategies in the aftermath of a covert release of smallpox at a crowded urban location. In particular we compared casualties and resources required for targeted strategies with those in the case of large-scale quarantine and/or mass vaccination campaigns. We produced this analysis in a sixty-day effort, while prototype software was still under development and delivered it to the Office of Homeland Security in June 2002. More recently, EpiSims provided casualty estimates and cost/benefit analyses for various proposed responses to an attack with pneumonic plague during the TOPOFF-2 exercise. Capabilities: EpiSims is designed to simulate human-human transmissible disease, but it is part of a suite of tools that naturally allow it to estimate individual exposures to air-borne or water-borne spread. Combined with data on animal density and mobility, EpiSims could simulate diseases spread by non-human vectors. EpiSims incorporates reactions of individuals, and is particularly powerful if those reactions are correlated with demographics. It provides a standard for modeling scenarios that cuts across agencies.« less

Discovery of two neighbouring satellites in the Carina constellation with MagLiteS

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

Torrealba, G.; Belokurov, V.; Koposov, S. E.

Here, we report the discovery of two ultra-faint satellites in the vicinity of the Large Magellanic Cloud (LMC) in data from the Magellanic Satellites Survey (MagLiteS). Situated 18more » $$^{\\circ}$$ ($$\\sim 20$$ kpc) from the LMC and separated from each other by only $$18^\\prime$$, Carina~II and III form an intriguing pair. By simultaneously modeling the spatial and the color-magnitude stellar distributions, we find that both Carina~II and Carina~III are likely dwarf galaxies, although this is less clear for Carina~III. There are in fact several obvious differences between the two satellites. While both are well described by an old and metal poor population, Carina~II is located at $$\\sim 36$$ kpc from the Sun, with $$M_V\\sim-4.5$$ and $$r_h\\sim 90$$ pc, and it is further confirmed by the discovery of 3 RR Lyrae at the right distance. In contrast, Carina~III is much more elongated, measured to be fainter ($$M_V\\sim-2.4$$), significantly more compact ($$r_h\\sim30$$ pc), and closer to the Sun, at $$\\sim 28$$ kpc, placing it only 8 kpc away from Car~II. Together with several other systems detected by the Dark Energy Camera, Carina~II and III form a strongly anisotropic cloud of satellites in the vicinity of the Magellanic Clouds.« less

Discovery of two neighbouring satellites in the Carina constellation with MagLiteS

DOE PAGES

Torrealba, G.; Belokurov, V.; Koposov, S. E.; ...

2018-01-23

Here, we report the discovery of two ultra-faint satellites in the vicinity of the Large Magellanic Cloud (LMC) in data from the Magellanic Satellites Survey (MagLiteS). Situated 18more » $$^{\\circ}$$ ($$\\sim 20$$ kpc) from the LMC and separated from each other by only $$18^\\prime$$, Carina~II and III form an intriguing pair. By simultaneously modeling the spatial and the color-magnitude stellar distributions, we find that both Carina~II and Carina~III are likely dwarf galaxies, although this is less clear for Carina~III. There are in fact several obvious differences between the two satellites. While both are well described by an old and metal poor population, Carina~II is located at $$\\sim 36$$ kpc from the Sun, with $$M_V\\sim-4.5$$ and $$r_h\\sim 90$$ pc, and it is further confirmed by the discovery of 3 RR Lyrae at the right distance. In contrast, Carina~III is much more elongated, measured to be fainter ($$M_V\\sim-2.4$$), significantly more compact ($$r_h\\sim30$$ pc), and closer to the Sun, at $$\\sim 28$$ kpc, placing it only 8 kpc away from Car~II. Together with several other systems detected by the Dark Energy Camera, Carina~II and III form a strongly anisotropic cloud of satellites in the vicinity of the Magellanic Clouds.« less

Underreporting of Congenital Syphilis as a Cause of Fetal and Infant Deaths in Northeastern Brazil.

PubMed

Cardoso, Ana Rita Paulo; Araújo, Maria Alix Leite; Andrade, Roumayne Fernandes Vieira; Saraceni, Valéria; Miranda, Angelica E; Dourado, Maria Inês Costa

2016-01-01

Of all syphilis-related pregnancy outcomes, fetal death is certainly the most common one, being directly related to the availability, accessibility and quality of prenatal care. The present study aimed to analyze the underreporting of fetal and infant deaths and other maternal factors associated with congenital syphilis (CS) death. This cross-sectional study integrated data of infants that were diagnosed and/or died of CS from the Sistema de Informação de Agravos de Notificação-Sinan (Notifiable Diseases Information System) and the Sistema de Informação de Mortalidade-SIM (Mortality Information System) in Fortaleza, Northeastern Brasil to identify unreported cases of congenital syphilis. We assessed data during the period from 2007 to 2013. The underreporting of CS as a cause of fetal or infant death increased from 41 to 415 cases (90.1%) during 2007-2013. Exactly 3,209 cases of CS were identified in Sinan and 6,578 deaths in SIM. After database linkage, we identified 382 cases that were reported in the SIM and SINAN databases consisting of 309 fetal deaths and 73 infant deaths related to CS. From the children notified at Sinan that born alive, 3.0% (78/2,542) died; Out of these, 39 (50.0%) were early and 25 (32.1%) were late neonatal deaths. The proportion of death by CS increased from 0.62 to 5.8 from 2007 to 2013. At logistic regression, the variable that maintained statistical significance with fetal and infant death outcomes was the presence of CS signs and/or symptoms at birth (OR = 3.20; IC 95% 1.54-6.62; p = 0.002). Neonatal and Infant deaths following CS-associated live births are underreported in Northeastern Brazil. Data base linkage identified unreported fetal and neonatal deaths due to CS leading to an increased awareness of fetal/infant mortality due to this infection.

Underreporting of Congenital Syphilis as a Cause of Fetal and Infant Deaths in Northeastern Brazil

PubMed Central

Cardoso, Ana Rita Paulo; Araújo, Maria Alix Leite; Andrade, Roumayne Fernandes Vieira; Saraceni, Valéria; Miranda, Angelica E.; Dourado, Maria Inês Costa

2016-01-01

Introduction Of all syphilis-related pregnancy outcomes, fetal death is certainly the most common one, being directly related to the availability, accessibility and quality of prenatal care. The present study aimed to analyze the underreporting of fetal and infant deaths and other maternal factors associated with congenital syphilis (CS) death. Methods This cross-sectional study integrated data of infants that were diagnosed and/or died of CS from the Sistema de Informação de Agravos de Notificação–Sinan (Notifiable Diseases Information System) and the Sistema de Informação de Mortalidade–SIM (Mortality Information System) in Fortaleza, Northeastern Brasil to identify unreported cases of congenital syphilis. We assessed data during the period from 2007 to 2013. Results The underreporting of CS as a cause of fetal or infant death increased from 41 to 415 cases (90.1%) during 2007–2013. Exactly 3,209 cases of CS were identified in Sinan and 6,578 deaths in SIM. After database linkage, we identified 382 cases that were reported in the SIM and SINAN databases consisting of 309 fetal deaths and 73 infant deaths related to CS. From the children notified at Sinan that born alive, 3.0% (78/2,542) died; Out of these, 39 (50.0%) were early and 25 (32.1%) were late neonatal deaths. The proportion of death by CS increased from 0.62 to 5.8 from 2007 to 2013. At logistic regression, the variable that maintained statistical significance with fetal and infant death outcomes was the presence of CS signs and/or symptoms at birth (OR = 3.20; IC 95% 1.54–6.62; p = 0.002). Conclusions Neonatal and Infant deaths following CS-associated live births are underreported in Northeastern Brazil. Data base linkage identified unreported fetal and neonatal deaths due to CS leading to an increased awareness of fetal/infant mortality due to this infection. PMID:27941983

Pediatric siMS score: A new, simple and accurate continuous metabolic syndrome score for everyday use in pediatrics.

PubMed

Vukovic, Rade; Milenkovic, Tatjana; Stojan, George; Vukovic, Ana; Mitrovic, Katarina; Todorovic, Sladjana; Soldatovic, Ivan

2017-01-01

The dichotomous nature of the current definition of metabolic syndrome (MS) in youth results in loss of information. On the other hand, the calculation of continuous MS scores using standardized residuals in linear regression (Z scores) or factor scores of principal component analysis (PCA) is highly impractical for clinical use. Recently, a novel, easily calculated continuous MS score called siMS score was developed based on the IDF MS criteria for the adult population. To develop a Pediatric siMS score (PsiMS), a modified continuous MS score for use in the obese youth, based on the original siMS score, while keeping the score as simple as possible and retaining high correlation with more complex scores. The database consisted of clinical data on 153 obese (BMI ≥95th percentile) children and adolescents. Continuous MS scores were calculated using Z scores and PCA, as well as the original siMS score. Four variants of PsiMS score were developed in accordance with IDF criteria for MS in youth and correlation of these scores with PCA and Z score derived MS continuous scores was assessed. PsiMS score calculated using formula: (2xWaist/Height) + (Glucose(mmol/l)/5.6) + (triglycerides(mmol/l)/1.7) + (Systolic BP/130)-(HDL(mmol/l)/1.02) showed the highest correlation with most of the complex continuous scores (0.792-0.901). The original siMS score also showed high correlation with continuous MS scores. PsiMS score represents a practical and accurate score for the evaluation of MS in the obese youth. The original siMS score should be used when evaluating large cohorts consisting of both adults and children.

Detection of SiO2 nanoparticles in lung tissue by ToF-SIMS imaging and fluorescence microscopy.

PubMed

Veith, Lothar; Vennemann, Antje; Breitenstein, Daniel; Engelhard, Carsten; Wiemann, Martin; Hagenhoff, Birgit

2017-07-10

The direct detection of nanoparticles in tissues at high spatial resolution is a current goal in nanotoxicology. Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) is widely used for the direct detection of inorganic and organic substances with high spatial resolution but its capability to detect nanoparticles in tissue sections is still insufficiently explored. To estimate the applicability of this technique for nanotoxicological questions, comparative studies with established techniques on the detection of nanoparticles can offer additional insights. Here, we compare ToF-SIMS imaging data with sub-micrometer spatial resolution to fluorescence microscopy imaging data to explore the usefulness of ToF-SIMS for the detection of nanoparticles in tissues. SiO 2 nanoparticles with a mean diameter of 25 nm, core-labelled with fluorescein isothiocyanate, were intratracheally instilled into rat lungs. Subsequently, imaging of lung cryosections was performed with ToF-SIMS and fluorescence microscopy. Nanoparticles were successfully detected with ToF-SIMS in 3D microanalysis mode based on the lateral distribution of SiO 3 - (m/z 75.96), which was co-localized with the distribution pattern that was obtained from nanoparticle fluorescence. In addition, the lateral distribution of protein (CN - , m/z 26.00) and phosphate based signals (PO 3 - , m/z 78.96) originating from the tissue material could be related to the SiO 3 - lateral distribution. In conclusion, ToF-SIMS is suitable to directly detect and laterally resolve SiO 2 nanomaterials in biological tissue at sufficient intensity levels. At the same time, information about the chemical environment of the nanoparticles in the lung tissue sections is obtained.

The OncoSim model: development and use for better decision-making in Canadian cancer control.

PubMed

Gauvreau, C L; Fitzgerald, N R; Memon, S; Flanagan, W M; Nadeau, C; Asakawa, K; Garner, R; Miller, A B; Evans, W K; Popadiuk, C M; Wolfson, M; Coldman, A J

2017-12-01

The Canadian Partnership Against Cancer was created in 2007 by the federal government to accelerate cancer control across Canada. Its OncoSim microsimulation model platform, which consists of a suite of specific cancer models, was conceived as a tool to augment conventional resources for population-level policy- and decision-making. The Canadian Partnership Against Cancer manages the OncoSim program, with funding from Health Canada and model development by Statistics Canada. Microsimulation modelling allows for the detailed capture of population heterogeneity and health and demographic history over time. Extensive data from multiple Canadian sources were used as inputs or to validate the model. OncoSim has been validated through expert consultation; assessments of face validity, internal validity, and external validity; and model fit against observed data. The platform comprises three in-depth cancer models (lung, colorectal, cervical), with another in-depth model (breast) and a generalized model (25 cancers) being in development. Unique among models of its class, OncoSim is available online for public sector use free of charge. Users can customize input values and output display, and extensive user support is provided. OncoSim has been used to support decision-making at the national and jurisdictional levels. Although simulation studies are generally not included in hierarchies of evidence, they are integral to informing cancer control policy when clinical studies are not feasible. OncoSim can evaluate complex intervention scenarios for multiple cancers. Canadian decision-makers thus have a powerful tool to assess the costs, benefits, cost-effectiveness, and budgetary effects of cancer control interventions when faced with difficult choices for improvements in population health and resource allocation.

Development practices and lessons learned in developing SimPEG

NASA Astrophysics Data System (ADS)

Cockett, R.; Heagy, L. J.; Kang, S.; Rosenkjaer, G. K.

2015-12-01

Inverse modelling provides a mathematical framework for constructing a model of physical property distributions in the subsurface that are consistent with the data collected in geophysical surveys. The geosciences are increasingly moving towards the integration of geological, geophysical, and hydrological information to better characterize the subsurface. This integration must span disciplines and is not only challenging scientifically, but additionally the inconsistencies between conventions often makes implementations complicated, non­ reproducible, or inefficient. SimPEG is an open-source, multi-university effort aimed at providing a generalized framework for solving forward and inverse problems. SimPEG includes finite volume discretizations on structured and unstructured meshes, interfaces to standard numerical solver packages, convex optimization algorithms, model parameterizations, and visualization routines. The SimPEG package (http://simpeg.xyz) supports an ecosystem of forward and inverse modelling applications, including electromagnetics, vadose zone flow, seismic, and potential­ fields, that are all written with a common interface and toolbox. The goal of SimPEG is to support a community of researchers with well-tested, extensible tools, and encourage transparency and reproducibility both of the SimPEG software and the geoscientific research it is applied to. In this presentation, we will share some of the lessons we have learned in designing the modular infrastructure, testing and development practices of SimPEG. We will discuss our use of version control, extensive unit-testing, continuous integration, documentation, issue tracking, and resources that facilitate communication between existing team members and allows new researchers to get involved. These practices have enabled the use of SimPEG in research, industry, and education as well as the ability to support a growing number of dependent repositories and applications. We hope that sharing our practices and experiences will help other researchers who are creating communities around their own scientific software. As this session suggests, "software is critical to the success of science," but, it is the *communities* of researchers that must be supported as we strive to create top quality research tools.

SealSim Version 1.1

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

SealSim 1.1 is a state-of-the-art, Microsoft Windows based computer program developed for the U.S. Department of Energy by Aspen Research Corporation with Contracted support from TNO TPD. It is intended to be used by manufacturers, engineers, educators, students, architects, and others to help determine the relative durability of Insulating Glass Units (IGU). As a function of time, SealSim 1.1 simulates the behaviour of an Insulating Glass Unit, exposed to realistic or user-defined weather climates. Stresses and strains in the IGU are calculated as a function of time, together with temperature distributions, gas permeation effects (gas loss, desiccant loading), dew pointmore » temperature, U-factor, etc. The current version of SealSim 1.1 supports double-glazing Units. where the spacer system is either a Thermo Plastic Spacer (TPS) or Box type spacer. For the determination of solar properties of glazing systems, SealSim 1.1 uses the Tntemational Glazing Database of LBNL, which is also used by OPTICS and WINDOW. The goal of the SealSim 1.1 simulations is to predict the IGU's average lifetime, expressed in terms of the "Durability Index", together with the associated failure mechanisms. The Durability Index of a particular IGU and its most probable failure mechanism can be compared with other IGU's. How the predicted Durability Index relates to the actual durability of an IGU is not known, simply because sufficient experimental data is lacking for describing the behaviour of IG Units over extended periods of time together with a lack of knowledge of the conditions it is subjected to and initial state of the CU at the time of manufacturing. In order to simulate the IGU behaviour in time, the conditions of the IGU must be defined; together with the weather and or climate that the IGU is subjected to. Using physical models of the IGU, SealSim 1.1 calculates tte response of the CU in time. These physical models are described in more detail in separate documents provided with the SealSim 1.1 program. Though much care was taken to test the correct implementation of physical sub models in SealSim 1.1, make the graphical user interface intuitive, making it robust, and to check all options that are available in SealSim 1.1, it will certainly suffer from the deficiencies of a first release. Aspen Research Corporation 1700 Buerkle Road St Paul, Minnesota 55110« less

Design and validation of the eyesafe ladar testbed (ELT) using the LadarSIM system simulator

NASA Astrophysics Data System (ADS)

Neilsen, Kevin D.; Budge, Scott E.; Pack, Robert T.; Fullmer, R. Rees; Cook, T. Dean

2009-05-01

The development of an experimental full-waveform LADAR system has been enhanced with the assistance of the LadarSIM system simulation software. The Eyesafe LADAR Test-bed (ELT) was designed as a raster scanning, single-beam, energy-detection LADAR with the capability of digitizing and recording the return pulse waveform at up to 2 GHz for 3D off-line image formation research in the laboratory. To assist in the design phase, the full-waveform LADAR simulation in LadarSIM was used to simulate the expected return waveforms for various system design parameters, target characteristics, and target ranges. Once the design was finalized and the ELT constructed, the measured specifications of the system and experimental data captured from the operational sensor were used to validate the behavior of the system as predicted during the design phase. This paper presents the methodology used, and lessons learned from this "design, build, validate" process. Simulated results from the design phase are presented, and these are compared to simulated results using measured system parameters and operational sensor data. The advantages of this simulation-based process are also presented.

Long-Baseline Comparisons of the Brazilian National Time Scale to UTC (NIST) Using Near Real-Time and Postprocessed Solutions

DTIC Science & Technology

2007-11-01

long baseline of ~8600 km. The comparisons were made with measurement systems developed for the Sistema Interamericano de Metrologia (SIM) comparison...measurements are compared and summarized. I. INTRODUCTION The Sistema Interamericano de Metrologia (SIM) is a regional metrology organization...Brazil. The two time scales are separated by a long baseline of ~8600 km. The comparisons were made with measurement systems developed for the Sistema

Student Perceptions of SocialSim for Simulation-Based Interprofessional Education in Healthcare

ERIC Educational Resources Information Center

Smith, Mary Kathryn

2016-01-01

This descriptive qualitative study investigates perceptions of students regarding the use of SocialSim, a tool designed to deliver simulation in a virtual environment using social media as a platform to facilitate inteprofessional education. There have been exponential changes in U.S. healthcare system in recent years, prompting the need for…

Agriculture Education SimFarm(TM). Technology Learning Activity. Teacher Edition.

ERIC Educational Resources Information Center

Oklahoma State Dept. of Vocational and Technical Education, Stillwater. Curriculum and Instructional Materials Center.

This Technology Learning Activity (TLA) for agriculture education in grades 6-10 is designed to help students learn the basic terminology of a farm system while they experience the responsibility of keeping a profitable farm in operation through use of the interactive SimFarm software. Introductory materials provide an overview of technology…

Conventional box model training improves laparoscopic skills during salpingectomy on LapSim: a randomized trial.

PubMed

Akdemir, Ali; Ergenoğlu, Ahmet Mete; Yeniel, Ahmet Özgür; Sendağ, Fatih

2013-01-01

Box model trainers have been used for many years to facilitate the improvement of laparoscopic skills. However, there are limited data available on box trainers and their impact on skill acquisition, assessed by virtual reality systems. Twenty-two Postgraduate Year 1 gynecology residents with no laparoscopic experience were randomly divided into one group that received structured box model training and a control group. All residents performed a salpingectomy on LapSim before and after the training. Performances before and after the training were assessed using LapSim and were recorded using objective parameters, registered by a computer system (time, damage, and economy of motion scores). There were initially no differences between the two groups. The box trainer group showed significantly greater improvement in time (p=0.01) and economy of motion scores (p=0.001) compared with the control group post-training. The present study confirmed the positive effect of low cost box model training on laparoscopic skill acquisition as assessed using LapSim. Novice surgeons should obtain practice on box trainers and teaching centers should make efforts to establish training laboratories.

Kaiser Permanente/Sandia National health care model. Phase I prototype final report. Part 1 - model overview

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

Edwards, D.; Yoshimura, A.; Butler, D.

1996-11-01

This report describes the results of a Cooperative Research and Development Agreement between Sandia National Laboratories and Kaiser Permanente Southern California to develop a prototype computer model of Kaiser Permanente`s health care delivery system. As a discrete event simulation, SimHCO models for each of 100,000 patients the progression of disease, individual resource usage, and patient choices in a competitive environment. SimHCO is implemented in the object-oriented programming language C++, stressing reusable knowledge and reusable software components. The versioned implementation of SimHCO showed that the object-oriented framework allows the program to grow in complexity in an incremental way. Furthermore, timing calculationsmore » showed that SimHCO runs in a reasonable time on typical workstations, and that a second phase model will scale proportionally and run within the system constraints of contemporary computer technology. This report is published as two documents: Model Overview and Domain Analysis. A separate Kaiser-proprietary report contains the Disease and Health Care Organization Selection Models.« less

Use of QuakeSim and UAVSAR for Earthquake Damage Mitigation and Response

NASA Technical Reports Server (NTRS)

Donnellan, A.; Parker, J. W.; Bawden, G.; Hensley, S.

2009-01-01

Spaceborne, airborne, and modeling and simulation techniques are being applied to earthquake risk assessment and response for mitigation from this natural disaster. QuakeSim is a web-based portal for modeling interseismic strain accumulation using paleoseismic and crustal deformation data. The models are used for understanding strain accumulation and release from earthquakes as well as stress transfer to neighboring faults. Simulations of the fault system can be used for understanding the likelihood and patterns of earthquakes as well as the likelihood of large aftershocks from events. UAVSAR is an airborne L-band InSAR system for collecting crustal deformation data. QuakeSim, UAVSAR, and DESDynI (following launch) can be used for monitoring earthquakes, the associated rupture and damage, and postseismic motions for prediction of aftershock locations.

MALDI-TOF and cluster-TOF-SIMS imaging of Fabry disease biomarkers

NASA Astrophysics Data System (ADS)

Touboul, David; Roy, Sandrine; Germain, Dominique P.; Chaminade, Pierre; Brunelle, Alain; Laprevote, Olivier

2007-02-01

Fabry disease is an X-linked disorder of glycosphingolipid metabolism, in which a partial or total deficiency of [alpha]-galactosidase A, a lysosomal enzyme, results in the progressive accumulation of neutral glycosphingolipids (globotriaosylceramide and digalactosylceramide) in most fluids and tissues of the body. Few information is available about the composition and distribution in tissues of the accumulated glycosphingolipids species. Mass spectrometry imaging is an innovative technique, which can provide pieces of information about the distribution of numerous biological compounds, such as lipids, directly on the tissue sections. MALDI-TOF and cluster-TOF-SIMS imaging approaches were used to study the localization of lipids (cholesterol, cholesterol sulfate, vitamin E, glycosphingolipids ...) on skin and kidney sections of patients affected by the Fabry disease. Numerous information on pathophysiology were enlightened by both techniques.

SIM Lite Detection of Habitable Planets in P-Type Binary-Planetary Systems

NASA Technical Reports Server (NTRS)

Pan, Xiaopei; Shao, Michael; Shaklan, Stuart; Goullioud, Renaud

2010-01-01

Close binary stars like spectroscopic binaries create a completely different environment than single stars for the evolution of a protoplanetary disk. Dynamical interactions between one star and protoplanets in such systems provide more challenges for theorists to model giant planet migration and formation of multiple planets. For habitable planets the majority of host stars are in binary star systems. So far only a small amount of Jupiter-size planets have been discovered in binary stars, whose minimum separations are 20 AU and the median value is about 1000 AU (because of difficulties in radial velocity measurements). The SIM Lite mission, a space-based astrometric observatory, has a unique capability to detect habitable planets in binary star systems. This work analyzed responses of the optical system to the field stop for companion stars and demonstrated that SIM Lite can observe exoplanets in visual binaries with small angular separations. In particular we investigated the issues for the search for terrestrial planets in P-type binary-planetary systems, where the planets move around both stars in a relatively distant orbit.

Construction of an instant structured illumination microscope

PubMed Central

Curd, Alistair; Cleasby, Alexa; Makowska, Katarzyna; York, Andrew; Shroff, Hari; Peckham, Michelle

2015-01-01

A challenge in biological imaging is to capture high-resolution images at fast frame rates in live cells. The “instant structured illumination microscope” (iSIM) is a system designed for this purpose. Similarly to standard structured illumination microscopy (SIM), an iSIM provides a twofold improvement over widefield microscopy, in x, y and z, but also allows much faster image acquisition, with real-time display of super-resolution images. The assembly of an iSIM is reasonably complex, involving the combination and alignment of many optical components, including three micro-optics arrays (two lenslet arrays and an array of pinholes, all with a pitch of 222 μm) and a double-sided scanning mirror. In addition, a number of electronic components must be correctly controlled. Construction of the system is therefore not trivial, but is highly desirable, particularly for live-cell imaging. We report, and provide instructions for, the construction of an iSIM, including minor modifications to a previous design in both hardware and software. The final instrument allows us to rapidly acquire fluorescence images at rates faster than 100 fps, with approximately twofold improvement in resolution in both x–y and z; sub-diffractive biological features have an apparent size (full width at half maximum) of 145 nm (lateral) and 320 nm (axial), using a 1.49 NA objective and 488 nm excitation. PMID:26210400

Facilitating CCS Business Planning by Extending the Functionality of the SimCCS Integrated System Model

DOE PAGES

Ellett, Kevin M.; Middleton, Richard S.; Stauffer, Philip H.; ...

2017-08-18

The application of integrated system models for evaluating carbon capture and storage technology has expanded steadily over the past few years. To date, such models have focused largely on hypothetical scenarios of complex source-sink matching involving numerous large-scale CO 2 emitters, and high-volume, continuous reservoirs such as deep saline formations to function as geologic sinks for carbon storage. Though these models have provided unique insight on the potential costs and feasibility of deploying complex networks of integrated infrastructure, there remains a pressing need to translate such insight to the business community if this technology is to ever achieve a trulymore » meaningful impact in greenhouse gas mitigation. Here, we present a new integrated system modelling tool termed SimCCUS aimed at providing crucial decision support for businesses by extending the functionality of a previously developed model called SimCCS. The primary innovation of the SimCCUS tool development is the incorporation of stacked geological reservoir systems with explicit consideration of processes and costs associated with the operation of multiple CO 2 utilization and storage targets from a single geographic location. In such locations provide significant efficiencies through economies of scale, effectively minimizing CO 2 storage costs while simultaneously maximizing revenue streams via the utilization of CO 2 as a commodity for enhanced hydrocarbon recovery.« less

Facilitating CCS Business Planning by Extending the Functionality of the SimCCS Integrated System Model

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

Ellett, Kevin M.; Middleton, Richard S.; Stauffer, Philip H.

The application of integrated system models for evaluating carbon capture and storage technology has expanded steadily over the past few years. To date, such models have focused largely on hypothetical scenarios of complex source-sink matching involving numerous large-scale CO 2 emitters, and high-volume, continuous reservoirs such as deep saline formations to function as geologic sinks for carbon storage. Though these models have provided unique insight on the potential costs and feasibility of deploying complex networks of integrated infrastructure, there remains a pressing need to translate such insight to the business community if this technology is to ever achieve a trulymore » meaningful impact in greenhouse gas mitigation. Here, we present a new integrated system modelling tool termed SimCCUS aimed at providing crucial decision support for businesses by extending the functionality of a previously developed model called SimCCS. The primary innovation of the SimCCUS tool development is the incorporation of stacked geological reservoir systems with explicit consideration of processes and costs associated with the operation of multiple CO 2 utilization and storage targets from a single geographic location. In such locations provide significant efficiencies through economies of scale, effectively minimizing CO 2 storage costs while simultaneously maximizing revenue streams via the utilization of CO 2 as a commodity for enhanced hydrocarbon recovery.« less

The sim Operon Facilitates the Transport and Metabolism of Sucrose Isomers in Lactobacillus casei ATCC 334▿

PubMed Central

Thompson, John; Jakubovics, Nicholas; Abraham, Bindu; Hess, Sonja; Pikis, Andreas

2008-01-01

Inspection of the genome sequence of Lactobacillus casei ATCC 334 revealed two operons that might dissimilate the five isomers of sucrose. To test this hypothesis, cells of L. casei ATCC 334 were grown in a defined medium supplemented with various sugars, including each of the five isomeric disaccharides. Extracts prepared from cells grown on the sucrose isomers contained high levels of two polypeptides with Mrs of ∼50,000 and ∼17,500. Neither protein was present in cells grown on glucose, maltose or sucrose. Proteomic, enzymatic, and Western blot analyses identified the ∼50-kDa protein as an NAD+- and metal ion-dependent phospho-α-glucosidase. The oligomeric enzyme was purified, and a catalytic mechanism is proposed. The smaller polypeptide represented an EIIA component of the phosphoenolpyruvate-dependent sugar phosphotransferase system. Phospho-α-glucosidase and EIIA are encoded by genes at the LSEI_0369 (simA) and LSEI_0374 (simF) loci, respectively, in a block of seven genes comprising the sucrose isomer metabolism (sim) operon. Northern blot analyses provided evidence that three mRNA transcripts were up-regulated during logarithmic growth of L. casei ATCC 334 on sucrose isomers. Internal simA and simF gene probes hybridized to ∼1.5- and ∼1.3-kb transcripts, respectively. A 6.8-kb mRNA transcript was detected by both probes, which was indicative of cotranscription of the entire sim operon. PMID:18310337

Surface immobilized antibody orientation determined using ToF-SIMS and multivariate analysis.

PubMed

Welch, Nicholas G; Madiona, Robert M T; Payten, Thomas B; Easton, Christopher D; Pontes-Braz, Luisa; Brack, Narelle; Scoble, Judith A; Muir, Benjamin W; Pigram, Paul J

2017-06-01

Antibody orientation at solid phase interfaces plays a critical role in the sensitive detection of biomolecules during immunoassays. Correctly oriented antibodies with solution-facing antigen binding regions have improved antigen capture as compared to their randomly oriented counterparts. Direct characterization of oriented proteins with surface analysis methods still remains a challenge however surface sensitive techniques such as Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) provide information-rich data that can be used to probe antibody orientation. Diethylene glycol dimethyl ether plasma polymers (DGpp) functionalized with chromium (DGpp+Cr) have improved immunoassay performance that is indicative of preferential antibody orientation. Herein, ToF-SIMS data from proteolytic fragments of anti-EGFR antibody bound to DGpp and DGpp+Cr are used to construct artificial neural network (ANN) and principal component analysis (PCA) models indicative of correctly oriented systems. Whole antibody samples (IgG) test against each of the models indicated preferential antibody orientation on DGpp+Cr. Cross-reference between ANN and PCA models yield 20 mass fragments associated with F(ab') 2 region representing correct orientation, and 23 mass fragments associated with the Fc region representing incorrect orientation. Mass fragments were then compared to amino acid fragments and amino acid composition in F(ab') 2 and Fc regions. A ratio of the sum of the ToF-SIMS ion intensities from the F(ab') 2 fragments to the Fc fragments demonstrated a 50% increase in intensity for IgG on DGpp+Cr as compared to DGpp. The systematic data analysis methodology employed herein offers a new approach for the investigation of antibody orientation applicable to a range of substrates. Controlled orientation of antibodies at solid phases is critical for maximizing antigen detection in biosensors and immunoassays. Surface-sensitive techniques (such as ToF-SIMS), capable of direct characterization of surface immobilized and oriented antibodies, are under-utilized in current practice. Selection of a small number of mass fragments for analysis, typically pertaining to amino acids, is commonplace in literature, leaving the majority of the information-rich spectra unanalyzed. The novelty of this work is the utilization of a comprehensive, unbiased mass fragment list and the employment of principal component analysis (PCA) and artificial neural network (ANN) models in a unique methodology to prove antibody orientation. This methodology is of significant and broad interest to the scientific community as it is applicable to a range of substrates and allows for direct, label-free characterization of surface bound proteins. Copyright © 2017 Acta Materialia Inc. All rights reserved.

Testing of a Methane Cryogenic Heat Pipe with a Liquid Trap Turn-Off Feature for use on Space Interferometer Mission (SIM)

NASA Technical Reports Server (NTRS)

Cepeda-Rizo, Juan; Krylo, Robert; Fisher, Melanie; Bugby, David C.

2011-01-01

Camera cooling for SIM presents three thermal control challenges; stable operation at 163K (110 C), decontamination heating to +20 C, and a long span from the cameras to the radiator. A novel cryogenic cooling system based on a methane heat pipe meets these challenges. The SIM thermal team, with the help of heat pipe vendor ATK, designed and tested a complete, low temperature, cooling system. The system accommodates the two SIM cameras with a double-ended conduction bar, a single methane heat pipe, independent turn-off devices, and a flight-like radiator. The turn ]off devices consist of a liquid trap, for removing the methane from the pipe, and an electrical heater to raise the methane temperature above the critical point thus preventing two-phase operation. This is the first time a cryogenic heat pipe has been tested at JPL and is also the first heat pipe to incorporate the turn-off features. Operation at 163K with a methane heat pipe is an important new thermal control capability for the lab. In addition, the two turn-off technologies enhance the "bag of tricks" available to the JPL thermal community. The successful test program brings this heat pipe to a high level of technology readiness.

Candidate configuration trade study, Stellar-inertial Measurement Systems (SIMS) for an Earth Observation Satellite (EOS)

NASA Technical Reports Server (NTRS)

Ogletree, G.; Coccoli, J.; Mckern, R.; Smith, M.; White, R.

1972-01-01

The results of analytical and simulation studies of the stellar-inertial measurement system (SIMS) for an earth observation satellite are presented. Subsystem design analyses and sensor design trades are reported. Three candidate systems are considered: (1) structure-mounted gyros with structure-mounted star mapper, (2) structure-mounted gyros with gimbaled star tracker, and (3) gimbaled gyros with structure-mounted star mapper. The purpose of the study is to facilitate the decisions pertaining to gimbaled versus structure-mounted gyros and star sensors, and combinations of systems suitable for the EOS satellite.

120nm resolution in thick samples with structured illumination and adaptive optics

NASA Astrophysics Data System (ADS)

Thomas, Benjamin; Sloan, Megan; Wolstenholme, Adrian J.; Kner, Peter

2014-03-01

μLinear Structured Illumination Microscopy (SIM) provides a two-fold increase over the diffraction limited resolution. SIM produces excellent images with 120nm resolution in tissue culture cells in two and three dimensions. For SIM to work correctly, the point spread function (PSF) and optical transfer function (OTF) must be known, and, ideally, should be unaberrated. When imaging through thick samples, aberrations will be introduced into the optical system which will reduce the peak intensity and increase the width of the PSF. This will lead to reduced resolution and artifacts in SIM images. Adaptive optics can be used to correct the optical wavefront restoring the PSF to its unaberrated state, and AO has been used in several types of fluorescence microscopy. We demonstrate that AO can be used with SIM to achieve 120nm resolution through 25m of tissue by imaging through the full thickness of an adult C. elegans roundworm. The aberrations can be corrected over a 25μm × 45μm field of view with one wavefront correction setting, demonstrating that AO can be used effectively with widefield superresolution techniques.

SIM_ADJUST -- A computer code that adjusts simulated equivalents for observations or predictions

USGS Publications Warehouse

Poeter, Eileen P.; Hill, Mary C.

2008-01-01

This report documents the SIM_ADJUST computer code. SIM_ADJUST surmounts an obstacle that is sometimes encountered when using universal model analysis computer codes such as UCODE_2005 (Poeter and others, 2005), PEST (Doherty, 2004), and OSTRICH (Matott, 2005; Fredrick and others (2007). These codes often read simulated equivalents from a list in a file produced by a process model such as MODFLOW that represents a system of interest. At times values needed by the universal code are missing or assigned default values because the process model could not produce a useful solution. SIM_ADJUST can be used to (1) read a file that lists expected observation or prediction names and possible alternatives for the simulated values; (2) read a file produced by a process model that contains space or tab delimited columns, including a column of simulated values and a column of related observation or prediction names; (3) identify observations or predictions that have been omitted or assigned a default value by the process model; and (4) produce an adjusted file that contains a column of simulated values and a column of associated observation or prediction names. The user may provide alternatives that are constant values or that are alternative simulated values. The user may also provide a sequence of alternatives. For example, the heads from a series of cells may be specified to ensure that a meaningful value is available to compare with an observation located in a cell that may become dry. SIM_ADJUST is constructed using modules from the JUPITER API, and is intended for use on any computer operating system. SIM_ADJUST consists of algorithms programmed in Fortran90, which efficiently performs numerical calculations.

Quasar Astrophysics with the Space Interferometry Mission

NASA Technical Reports Server (NTRS)

Unwin, Stephen; Wehrle, Ann; Meier, David; Jones, Dayton; Piner, Glenn

2007-01-01

Optical astrometry of quasars and active galaxies can provide key information on the spatial distribution and variability of emission in compact nuclei. The Space Interferometry Mission (SIM PlanetQuest) will have the sensitivity to measure a significant number of quasar positions at the microarcsecond level. SIM will be very sensitive to astrometric shifts for objects as faint as V = 19. A variety of AGN phenomena are expected to be visible to SIM on these scales, including time and spectral dependence in position offsets between accretion disk and jet emission. These represent unique data on the spatial distribution and time dependence of quasar emission. It will also probe the use of quasar nuclei as fundamental astrometric references. Comparisons between the time-dependent optical photocenter position and VLBI radio images will provide further insight into the jet emission mechanism. Observations will be tailored to each specific target and science question. SIM will be able to distinguish spatially between jet and accretion disk emission; and it can observe the cores of galaxies potentially harboring binary supermassive black holes resulting from mergers.

Search for the direct production of charginos and neutralinos in final states with tau leptons in $$\\sqrt{s}$$ =13 TeV pp collisions with the ATLAS detector

DOE PAGES

Aaboud, M.; Aad, G.; Abbott, B.; ...

2018-02-22

Here, a search for the direct production of charginos and neutralinos in final states with at least two hadronically decaying tau leptons is presented. The analysis uses a dataset of pp collisions corresponding to an integrated luminosity of 36.1fb -1, recorded with the ATLAS detector at the Large Hadron Collider at a centre-of-mass energy of 13 TeV. No significant deviation from the expected Standard Model background is observed. Limits are derived in scenarios ofmore » $$\\sim\\atop{\\chi}$$ $$+\\atop{1}$$ $$\\sim\\atop{\\chi}$$ $$\\bar{1}$$ pair production and of $$\\sim\\atop{\\chi}$$ $$±\\atop{1}$$ $$\\sim\\atop{\\chi}$$ $$0\\atop{2}$$ and $$\\sim\\atop{\\chi}$$ $$+\\atop{1}$$ $$\\sim\\atop{\\chi}$$ $$\\bar{1}$$ production in simplified models where the neutralinos and charginos decay solely via intermediate left-handed staus and tau sneutrinos, and the mass of the $$\\sim\\atop{\\tau}_L$$ state is set to be halfway between the masses of the $$\\sim\\atop{\\chi}$$ $$±\\atop{1}$$ and the $$\\sim\\atop{\\chi}$$ $$0\\atop{1}$$. Chargino masses up to 630 GeV are excluded at 95% confidence level in the scenario of direct production of $$\\sim\\atop{\\chi}$$ $$+\\atop{1}$$ $$\\sim\\atop{\\chi}$$ $$\\bar{1}$$ for a massless $$\\sim\\atop{\\chi}$$ $$0\\atop{1}$$. Common $$\\sim\\atop{\\chi}$$ $$±\\atop{1}$$ and $$\\sim\\atop{\\chi}$$ $$0\\atop{2}$$ masses up to 760 GeV are excluded in the case of production of $$\\sim\\atop{\\chi}$$ $$±\\atop{1}$$ $$\\sim\\atop{\\chi}$$ $$0\\atop{2}$$ and $$\\sim\\atop{\\chi}$$ $$+\\atop{1}$$ $$\\sim\\atop{\\chi}$$ $$-\\atop{1}$$ assuming a massless $$\\sim\\atop{\\chi}$$ $$0\\atop{1}$$. Exclusion limits for additional benchmark scenarios with large and small mass-splitting between the Open image in new window $$\\sim\\atop{\\chi}$$ $$±\\atop{1}$$ and the $$\\sim\\atop{\\chi}$$ $$0\\atop{1}$$ are also studied by varying the $$\\sim\\atop{\\tau}_L$$ mass between the masses of the $$\\sim\\atop{\\chi}$$ $$±\\atop{1}$$ and the $$\\sim\\atop{\\chi}$$ $$0\\atop{1}$$.« less

Search for the direct production of charginos and neutralinos in final states with tau leptons in $$\\sqrt{s}$$ =13 TeV pp collisions with the ATLAS detector

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

Aaboud, M.; Aad, G.; Abbott, B.

Here, a search for the direct production of charginos and neutralinos in final states with at least two hadronically decaying tau leptons is presented. The analysis uses a dataset of pp collisions corresponding to an integrated luminosity of 36.1fb -1, recorded with the ATLAS detector at the Large Hadron Collider at a centre-of-mass energy of 13 TeV. No significant deviation from the expected Standard Model background is observed. Limits are derived in scenarios ofmore » $$\\sim\\atop{\\chi}$$ $$+\\atop{1}$$ $$\\sim\\atop{\\chi}$$ $$\\bar{1}$$ pair production and of $$\\sim\\atop{\\chi}$$ $$±\\atop{1}$$ $$\\sim\\atop{\\chi}$$ $$0\\atop{2}$$ and $$\\sim\\atop{\\chi}$$ $$+\\atop{1}$$ $$\\sim\\atop{\\chi}$$ $$\\bar{1}$$ production in simplified models where the neutralinos and charginos decay solely via intermediate left-handed staus and tau sneutrinos, and the mass of the $$\\sim\\atop{\\tau}_L$$ state is set to be halfway between the masses of the $$\\sim\\atop{\\chi}$$ $$±\\atop{1}$$ and the $$\\sim\\atop{\\chi}$$ $$0\\atop{1}$$. Chargino masses up to 630 GeV are excluded at 95% confidence level in the scenario of direct production of $$\\sim\\atop{\\chi}$$ $$+\\atop{1}$$ $$\\sim\\atop{\\chi}$$ $$\\bar{1}$$ for a massless $$\\sim\\atop{\\chi}$$ $$0\\atop{1}$$. Common $$\\sim\\atop{\\chi}$$ $$±\\atop{1}$$ and $$\\sim\\atop{\\chi}$$ $$0\\atop{2}$$ masses up to 760 GeV are excluded in the case of production of $$\\sim\\atop{\\chi}$$ $$±\\atop{1}$$ $$\\sim\\atop{\\chi}$$ $$0\\atop{2}$$ and $$\\sim\\atop{\\chi}$$ $$+\\atop{1}$$ $$\\sim\\atop{\\chi}$$ $$-\\atop{1}$$ assuming a massless $$\\sim\\atop{\\chi}$$ $$0\\atop{1}$$. Exclusion limits for additional benchmark scenarios with large and small mass-splitting between the Open image in new window $$\\sim\\atop{\\chi}$$ $$±\\atop{1}$$ and the $$\\sim\\atop{\\chi}$$ $$0\\atop{1}$$ are also studied by varying the $$\\sim\\atop{\\tau}_L$$ mass between the masses of the $$\\sim\\atop{\\chi}$$ $$±\\atop{1}$$ and the $$\\sim\\atop{\\chi}$$ $$0\\atop{1}$$.« less

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

Yu, Jiachao; Zhou, Yufan; Hua, Xin

We demonstrate in situ chemical imaging of protein biomolecules in the aqueous solution using System for Analysis at the Liquid Vacuum Interface (SALVI) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). The fibronectin protein film was immobilized on the silicon nitride (SiN) membrane forming the SALVI detection area. During ToF-SIMS analysis, three modes of analysis were conducted including high spatial resolution mass spectra, two-dimensional (2D) imaging, and depth profiling. Mass spectra were acquired in both positive and negative modes. Deionized water was also analyzed as a reference sample. Our results show that fibronectin film in water has more distinct and strongermore » water cluster peaks compared to water alone. Characteristic peaks of amino acid fragments are also observable in the hydrated protein ToF-SIMS spectra. These results illustrate that protein molecule adsorption on a surface can be studied dynamically using SALVI and ToF-SIMS in the liquid environment.« less

PowderSim: Lagrangian Discrete and Mesh-Free Continuum Simulation Code for Cohesive Soils

NASA Technical Reports Server (NTRS)

Johnson, Scott; Walton, Otis; Settgast, Randolph

2013-01-01

PowderSim is a calculation tool that combines a discrete-element method (DEM) module, including calibrated interparticle-interaction relationships, with a mesh-free, continuum, SPH (smoothed-particle hydrodynamics) based module that utilizes enhanced, calibrated, constitutive models capable of mimicking both large deformations and the flow behavior of regolith simulants and lunar regolith under conditions anticipated during in situ resource utilization (ISRU) operations. The major innovation introduced in PowderSim is to use a mesh-free method (SPH-based) with a calibrated and slightly modified critical-state soil mechanics constitutive model to extend the ability of the simulation tool to also address full-scale engineering systems in the continuum sense. The PowderSim software maintains the ability to address particle-scale problems, like size segregation, in selected regions with a traditional DEM module, which has improved contact physics and electrostatic interaction models.

SIMS studies of oxide growth on beta-NiAl

NASA Technical Reports Server (NTRS)

Mitchell, D. F.; Prescott, R.; Graham, M. J.; Doychak, J.

1992-01-01

This paper reports on a study of the growth of aluminum oxide on beta-NiAl at temperatures up to 1200 C. The scales have been formed in two-stage experiments using O2-16 and O2-18 gases, and the various isotopic species have been located by direct imaging using SIMS. Supplementary information on oxide morphologies and structures has been obtained by SEM. SIMS images and depth profiles indicate where oxidation has taken place predominantly by cation or anion diffusion at different stages of the growth process. The way in which the presence of small amounts of reactive elements can affect scale growth is also considered. These results help to provide an improved understanding of the mechanism of alumina scale formation, which is of benefit in the development of oxidation-resistant alloys and intermetallics for service at high temperatures.

Secondary ion mass spectrometry: The application in the analysis of atmospheric particulate matter

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

Huang, Di; Hua, Xin; Xiu, Guang-Li

Currently, considerable attention has been paid to atmospheric particulate matter (PM) investigation due to its importance in human health and global climate change. Surface characterization of PM is important since the chemical heterogeneity between the surface and bulk may vary its impact on the environment and human being. Secondary ion mass spectrometry (SIMS) is a surface technique with high surface sensitivity, capable of high spatial chemical imaging and depth profiling. Recent research shows that SIMS holds great potential in analyzing both surface and bulk chemical information of PM. In this review, we presented the working principal of SIMS in PMmore » characterization, summarized recent applications in PM analysis from different sources, discussed its advantages and limitations, and proposed the future development of this technique with a perspective in environmental sciences.« less

Astrophysics with Microarcsecond Accuracy Astrometry

NASA Technical Reports Server (NTRS)

Unwin, Stephen C.

2008-01-01

Space-based astrometry promises to provide a powerful new tool for astrophysics. At a precision level of a few microarcsonds, a wide range of phenomena are opened up for study. In this paper we discuss the capabilities of the SIM Lite mission, the first space-based long-baseline optical interferometer, which will deliver parallaxes to 4 microarcsec. A companion paper in this volume will cover the development and operation of this instrument. At the level that SIM Lite will reach, better than 1 microarcsec in a single measurement, planets as small as one Earth can be detected around many dozen of the nearest stars. Not only can planet masses be definitely measured, but also the full orbital parameters determined, allowing study of system stability in multiple planet systems. This capability to survey our nearby stellar neighbors for terrestrial planets will be a unique contribution to our understanding of the local universe. SIM Lite will be able to tackle a wide range of interesting problems in stellar and Galactic astrophysics. By tracing the motions of stars in dwarf spheroidal galaxies orbiting our Milky Way, SIM Lite will probe the shape of the galactic potential history of the formation of the galaxy, and the nature of dark matter. Because it is flexibly scheduled, the instrument can dwell on faint targets, maintaining its full accuracy on objects as faint as V=19. This paper is a brief survey of the diverse problems in modern astrophysics that SIM Lite will be able to address.

A possible mechanism to detect super-earth formation in protoplanetary disks

NASA Astrophysics Data System (ADS)

Dong, Ruobing; Chiang, Eugene; Li, Hui; Li, Shengtai

2017-06-01

Using combined gas+dust global hydrodynamics and radiative transfer simulations, we calculate the distribution of gas and sub-mm-sized dust in protoplanetary disks with a super-Earth at tens of AU, and examine observational signatures of such systems in resolved observations. We confirm previous results that in a typical disk with a low viscosity ($\\alpha\\lesssim10^{-4}$), a super-Earth is able to open two gaps at $\\sim$scale-height away around its orbit in $\\sim$mm-sized dust (St$\\sim$0.01), due to differential dust drift in a perturbed gas background. Additional rings and gaps may also be produced under certain conditions. These features, particularly a signature ``double-gap'' feature, can be detected in a Taurus target by ALMA in dust continuum under an angular resolution of $\\sim0\\arcsec.025$ with two hours of integration. The features are robust --- it can survive in a variety of background disk profiles, withstand modest planetary radial migration ($|r/\\dot{r}|\\sim$ a few Myr), and last for thousands of orbits. Multiple ring/gap systems observed by ALMA were typically modeled using multiple (Saturn-to-Jupiter sized) planets. Here, we argue that a single super-Earth in a low viscosity disk could produce multiple rings and gaps as well. By examining the prevalence of such features in nearby disks, upcoming high angular resolution ALMA surveys may infer how common super-Earth formation events are at tens of au.

simBio: a Java package for the development of detailed cell models.

PubMed

Sarai, Nobuaki; Matsuoka, Satoshi; Noma, Akinori

2006-01-01

Quantitative dynamic computer models, which integrate a variety of molecular functions into a cell model, provide a powerful tool to create and test working hypotheses. We have developed a new modeling tool, the simBio package (freely available from ), which can be used for constructing cell models, such as cardiac cells (the Kyoto model from Matsuoka et al., 2003, 2004 a, b, the LRd model from Faber and Rudy, 2000, and the Noble 98 model from Noble et al., 1998), epithelial cells (Strieter et al., 1990) and pancreatic beta cells (Magnus and Keizer, 1998). The simBio package is written in Java, uses XML and can solve ordinary differential equations. In an attempt to mimic biological functional structures, a cell model is, in simBio, composed of independent functional modules called Reactors, such as ion channels and the sarcoplasmic reticulum, and dynamic variables called Nodes, such as ion concentrations. The interactions between Reactors and Nodes are described by the graph theory and the resulting graph represents a blueprint of an intricate cellular system. Reactors are prepared in a hierarchical order, in analogy to the biological classification. Each Reactor can be composed or improved independently, and can easily be reused for different models. This way of building models, through the combination of various modules, is enabled through the use of object-oriented programming concepts. Thus, simBio is a straightforward system for the creation of a variety of cell models on a common database of functional modules.

Predicting cancer risk knowledge and information seeking: the role of social and cognitive factors.

PubMed

Hovick, Shelly R; Liang, Ming-Ching; Kahlor, Leeann

2014-01-01

This study tests an expanded Structural Influence Model (SIM) to gain a greater understanding of the social and cognitive factors that contribute to disparities in cancer risk knowledge and information seeking. At the core of this expansion is the planned risk information seeking model (PRISM). This study employed an online sample (N = 1,007) of African American, Hispanic, and non-Hispanic White adults. The addition of four cognitive predictors to the SIM substantially increased variance explained in cancer risk knowledge (R(2) = .29) and information seeking (R(2) = .56). Health literacy mediated the effects of social determinants (socioeconomic status [SES] and race/ethnicity) on cancer risk knowledge, while subjective norms mediated their effects on cancer risk information seeking. Social capital and perceived seeking control were also shown to be important mediators of the relationships between SES and cancer communication outcomes. Our results illustrate the social and cognitive mechanisms by which social determinants impact cancer communication outcomes, as well as several points of intervention to reduce communication disparities.

OpenSim: open-source software to create and analyze dynamic simulations of movement.

PubMed

Delp, Scott L; Anderson, Frank C; Arnold, Allison S; Loan, Peter; Habib, Ayman; John, Chand T; Guendelman, Eran; Thelen, Darryl G

2007-11-01

Dynamic simulations of movement allow one to study neuromuscular coordination, analyze athletic performance, and estimate internal loading of the musculoskeletal system. Simulations can also be used to identify the sources of pathological movement and establish a scientific basis for treatment planning. We have developed a freely available, open-source software system (OpenSim) that lets users develop models of musculoskeletal structures and create dynamic simulations of a wide variety of movements. We are using this system to simulate the dynamics of individuals with pathological gait and to explore the biomechanical effects of treatments. OpenSim provides a platform on which the biomechanics community can build a library of simulations that can be exchanged, tested, analyzed, and improved through a multi-institutional collaboration. Developing software that enables a concerted effort from many investigators poses technical and sociological challenges. Meeting those challenges will accelerate the discovery of principles that govern movement control and improve treatments for individuals with movement pathologies.

Optically sectioned wide-field fluorescence lifetime imaging endoscopy enabled by structured illumination (Conference Presentation)

NASA Astrophysics Data System (ADS)

Hinsdale, Taylor; Malik, Bilal H.; Rico-Jimenez, Jose J.; Jo, Javier A.; Maitland, Kristen C.

2016-03-01

We present a wide-field fluorescence lifetime imaging (FLIM) system with optical sectioning by structured illumination microscopy (SIM). FLIM measurements were made using a time gated ICCD camera in conjunction with a pulsed nitrogen dye laser operating at 450 nm. Intensity images were acquired at multiple time delays from a trigger initiated by a laser pulse to create a wide-field FLIM image, which was then combined with three phase SIM to provide optical sectioning. Such a mechanism has the potential to increase the reliability and accuracy of the FLIM measurements by rejecting background intensity. SIM also provides the opportunity to create volumetric FLIM images with the incorporation of scanning mechanisms for the sample plane. We present multiple embodiments of such a system: one as a free space endoscope and the other as a fiber microendoscope enabled by the introduction of a fiber bundle. Finally, we demonstrate the efficacy of such an imaging system by imaging dyes embedded in a tissue phantom.

ToF-SIMS analysis of poly(L-lysine)-graft-poly(2-methyl-2-oxazoline) ultrathin adlayers.

PubMed

Pidhatika, Bidhari; Chen, Yin; Coullerez, Geraldine; Al-Bataineh, Sameer; Textor, Marcus

2014-02-01

Understanding of the interfacial chemistry of ultrathin polymeric adlayers is fundamentally important in the context of establishing quantitative design rules for the fabrication of nonfouling surfaces in various applications such as biomaterials and medical devices. In this study, seven poly(L-lysine)-graft-poly(2-methyl-2-oxazoline) (PLL-PMOXA) copolymers with grafting density (number of PMOXA chains per lysine residue) 0.09, 0.14, 0.19, 0.33, 0.43, 0.56, and 0.77, respectively, were synthesized and characterized by means of nuclear magnetic resonance spectroscopy (NMR). The copolymers were then adsorbed on Nb2O5 surfaces. Optical waveguide lightmode spectroscopy method was used to monitor the surface adsorption in situ of these copolymers and provide information on adlayer masses that were then converted into PLL and PMOXA surface densities. To investigate the relationship between copolymer bulk architecture (as shown by NMR data) and surface coverage as well as surface architecture, time-of-flight secondary ion mass spectrometry (ToF-SIMS) analysis was performed. Furthermore, ToF-SIMS method combined with principal component analysis (PCA) was used to verify the protein resistant properties of PLL-PMOXA adlayers, by thorough characterization before and after adlayer exposure to human serum. ToF-SIMS analysis revealed that the chemical composition as well as the architecture of the different PLL-PMOXA adlayers indeed reflects the copolymer bulk composition. ToF-SIMS results also indicated a heterogeneous surface coverage of PLL-PMOXA adlayers with high grafting densities higher than 0.33. In the case of protein resistant surface, PCA results showed clear differences between protein resistant and nonprotein-resistant surfaces. Therefore, ToF-SIMS results combined with PCA confirmed that the PLL-PMOXA adlayer with brush architecture resists protein adsorption. However, low increases of some amino acid signals in ToF-SIMS spectra were detected after the adlayer has been exposed to human serum.

ToF-SIMS imaging of molecular-level alteration mechanisms in Le Bonheur de vivre by Henri Matisse.

PubMed

Voras, Zachary E; deGhetaldi, Kristin; Wiggins, Marcie B; Buckley, Barbara; Baade, Brian; Mass, Jennifer L; Beebe, Thomas P

2015-11-01

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) has recently been shown to be a valuable tool for cultural heritage studies, especially when used in conjunction with established analytical techniques in the field. The ability of ToF-SIMS to simultaneously image inorganic and organic species within a paint cross section at micrometer-level spatial resolution makes it a uniquely qualified analytical technique to aid in further understanding the processes of pigment and binder alteration, as well as pigment-binder interactions. In this study, ToF-SIMS was used to detect and image both molecular and elemental species related to CdS pigment and binding medium alteration on the painting Le Bonheur de vivre (1905-1906, The Barnes Foundation) by Henri Matisse. Three categories of inorganic and organic components were found throughout Le Bonheur de vivre and co-localized in cross-sectional samples using high spatial resolution ToF-SIMS analysis: (1) species relating to the preparation and photo-induced oxidation of CdS yellow pigments (2) varying amounts of long-chain fatty acids present in both the paint and primary ground layer and (3) specific amino acid fragments, possibly relating to the painting's complex restoration history. ToF-SIMS's ability to discern both organic and inorganic species via cross-sectional imaging was used to compare samples collected from Le Bonheur de vivre to artificially aged reference paints in an effort to gather mechanistic information relating to alteration processes that have been previously explored using μXANES, SR-μXRF, SEM-EDX, and SR-FTIR. The relatively high sensitivity offered by ToF-SIMS imaging coupled to the high spatial resolution allowed for the positive identification of degradation products (such as cadmium oxalate) in specific paint regions that have before been unobserved. The imaging of organic materials has provided an insight into the extent of destruction of the original binding medium, as well as identifying unexpected organic materials in specific paint layers.

ToF-SIMS imaging of molecular-level alteration mechanisms in Le Bonheur de vivre by Henri Matisse

NASA Astrophysics Data System (ADS)

Voras, Zachary E.; deGhetaldi, Kristin; Wiggins, Marcie B.; Buckley, Barbara; Baade, Brian; Mass, Jennifer L.; Beebe, Thomas P.

2015-11-01

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) has recently been shown to be a valuable tool for cultural heritage studies, especially when used in conjunction with established analytical techniques in the field. The ability of ToF-SIMS to simultaneously image inorganic and organic species within a paint cross section at micrometer-level spatial resolution makes it a uniquely qualified analytical technique to aid in further understanding the processes of pigment and binder alteration, as well as pigment-binder interactions. In this study, ToF-SIMS was used to detect and image both molecular and elemental species related to CdS pigment and binding medium alteration on the painting Le Bonheur de vivre (1905-1906, The Barnes Foundation) by Henri Matisse. Three categories of inorganic and organic components were found throughout Le Bonheur de vivre and co-localized in cross-sectional samples using high spatial resolution ToF-SIMS analysis: (1) species relating to the preparation and photo-induced oxidation of CdS yellow pigments (2) varying amounts of long-chain fatty acids present in both the paint and primary ground layer and (3) specific amino acid fragments, possibly relating to the painting's complex restoration history. ToF-SIMS's ability to discern both organic and inorganic species via cross-sectional imaging was used to compare samples collected from Le Bonheur de vivre to artificially aged reference paints in an effort to gather mechanistic information relating to alteration processes that have been previously explored using μXANES, SR-μXRF, SEM-EDX, and SR-FTIR. The relatively high sensitivity offered by ToF-SIMS imaging coupled to the high spatial resolution allowed for the positive identification of degradation products (such as cadmium oxalate) in specific paint regions that have before been unobserved. The imaging of organic materials has provided an insight into the extent of destruction of the original binding medium, as well as identifying unexpected organic materials in specific paint layers.

siMS Score: Simple Method for Quantifying Metabolic Syndrome.

PubMed

Soldatovic, Ivan; Vukovic, Rade; Culafic, Djordje; Gajic, Milan; Dimitrijevic-Sreckovic, Vesna

2016-01-01

To evaluate siMS score and siMS risk score, novel continuous metabolic syndrome scores as methods for quantification of metabolic status and risk. Developed siMS score was calculated using formula: siMS score = 2*Waist/Height + Gly/5.6 + Tg/1.7 + TAsystolic/130-HDL/1.02 or 1.28 (for male or female subjects, respectively). siMS risk score was calculated using formula: siMS risk score = siMS score * age/45 or 50 (for male or female subjects, respectively) * family history of cardio/cerebro-vascular events (event = 1.2, no event = 1). A sample of 528 obese and non-obese participants was used to validate siMS score and siMS risk score. Scores calculated as sum of z-scores (each component of metabolic syndrome regressed with age and gender) and sum of scores derived from principal component analysis (PCA) were used for evaluation of siMS score. Variants were made by replacing glucose with HOMA in calculations. Framingham score was used for evaluation of siMS risk score. Correlation between siMS score with sum of z-scores and weighted sum of factors of PCA was high (r = 0.866 and r = 0.822, respectively). Correlation between siMS risk score and log transformed Framingham score was medium to high for age groups 18+,30+ and 35+ (0.835, 0.707 and 0.667, respectively). siMS score and siMS risk score showed high correlation with more complex scores. Demonstrated accuracy together with superior simplicity and the ability to evaluate and follow-up individual patients makes siMS and siMS risk scores very convenient for use in clinical practice and research as well.

Doppler lidar power, aperture diameter, and FFT size trade-off study

NASA Astrophysics Data System (ADS)

Chester, David B.; Budge, Scott E.

2017-05-01

In the design or selection of a Doppler lidar instrument for a spacecraft landing system, it is important to evaluate the balance between performance requirements and cost, weight, and power consumption. Leveraging the capability of LadarSIM, a trade-off study was performed to evaluate the interaction between the laser transmission power, aperture diameter, and FFT size in a Doppler lidar system. For this study the probabilities of detection and false alarm were calculated using LadarSIM to simulate FMCW lidar systems with varying power, aperture diameter, and FFT size. This paper reports the results of this trade-off study.

SIM_EXPLORE: Software for Directed Exploration of Complex Systems

NASA Technical Reports Server (NTRS)

Burl, Michael; Wang, Esther; Enke, Brian; Merline, William J.

2013-01-01

Physics-based numerical simulation codes are widely used in science and engineering to model complex systems that would be infeasible to study otherwise. While such codes may provide the highest- fidelity representation of system behavior, they are often so slow to run that insight into the system is limited. Trying to understand the effects of inputs on outputs by conducting an exhaustive grid-based sweep over the input parameter space is simply too time-consuming. An alternative approach called "directed exploration" has been developed to harvest information from numerical simulators more efficiently. The basic idea is to employ active learning and supervised machine learning to choose cleverly at each step which simulation trials to run next based on the results of previous trials. SIM_EXPLORE is a new computer program that uses directed exploration to explore efficiently complex systems represented by numerical simulations. The software sequentially identifies and runs simulation trials that it believes will be most informative given the results of previous trials. The results of new trials are incorporated into the software's model of the system behavior. The updated model is then used to pick the next round of new trials. This process, implemented as a closed-loop system wrapped around existing simulation code, provides a means to improve the speed and efficiency with which a set of simulations can yield scientifically useful results. The software focuses on the case in which the feedback from the simulation trials is binary-valued, i.e., the learner is only informed of the success or failure of the simulation trial to produce a desired output. The software offers a number of choices for the supervised learning algorithm (the method used to model the system behavior given the results so far) and a number of choices for the active learning strategy (the method used to choose which new simulation trials to run given the current behavior model). The software also makes use of the LEGION distributed computing framework to leverage the power of a set of compute nodes. The approach has been demonstrated on a planetary science application in which numerical simulations are used to study the formation of asteroid families.

Cross-Compiler for Modeling Space-Flight Systems

NASA Technical Reports Server (NTRS)

James, Mark

2007-01-01

Ripples is a computer program that makes it possible to specify arbitrarily complex space-flight systems in an easy-to-learn, high-level programming language and to have the specification automatically translated into LibSim, which is a text-based computing language in which such simulations are implemented. LibSim is a very powerful simulation language, but learning it takes considerable time, and it requires that models of systems and their components be described at a very low level of abstraction. To construct a model in LibSim, it is necessary to go through a time-consuming process that includes modeling each subsystem, including defining its fault-injection states, input and output conditions, and the topology of its connections to other subsystems. Ripples makes it possible to describe the same models at a much higher level of abstraction, thereby enabling the user to build models faster and with fewer errors. Ripples can be executed in a variety of computers and operating systems, and can be supplied in either source code or binary form. It must be run in conjunction with a Lisp compiler.

Improvement of the Correlative AFM and ToF-SIMS Approach Using an Empirical Sputter Model for 3D Chemical Characterization.

PubMed

Terlier, T; Lee, J; Lee, K; Lee, Y

2018-02-06

Technological progress has spurred the development of increasingly sophisticated analytical devices. The full characterization of structures in terms of sample volume and composition is now highly complex. Here, a highly improved solution for 3D characterization of samples, based on an advanced method for 3D data correction, is proposed. Traditionally, secondary ion mass spectrometry (SIMS) provides the chemical distribution of sample surfaces. Combining successive sputtering with 2D surface projections enables a 3D volume rendering to be generated. However, surface topography can distort the volume rendering by necessitating the projection of a nonflat surface onto a planar image. Moreover, the sputtering is highly dependent on the probed material. Local variation of composition affects the sputter yield and the beam-induced roughness, which in turn alters the 3D render. To circumvent these drawbacks, the correlation of atomic force microscopy (AFM) with SIMS has been proposed in previous studies as a solution for the 3D chemical characterization. To extend the applicability of this approach, we have developed a methodology using AFM-time-of-flight (ToF)-SIMS combined with an empirical sputter model, "dynamic-model-based volume correction", to universally correct 3D structures. First, the simulation of 3D structures highlighted the great advantages of this new approach compared with classical methods. Then, we explored the applicability of this new correction to two types of samples, a patterned metallic multilayer and a diblock copolymer film presenting surface asperities. In both cases, the dynamic-model-based volume correction produced an accurate 3D reconstruction of the sample volume and composition. The combination of AFM-SIMS with the dynamic-model-based volume correction improves the understanding of the surface characteristics. Beyond the useful 3D chemical information provided by dynamic-model-based volume correction, the approach permits us to enhance the correlation of chemical information from spectroscopic techniques with the physical properties obtained by AFM.

Reactor Simulator Testing

NASA Technical Reports Server (NTRS)

Schoenfeld, Michael P.; Webster, Kenny L.; Pearson, Boise J.

2013-01-01

As part of the Nuclear Systems Office Fission Surface Power Technology Demonstration Unit (TDU) project, a reactor simulator test loop (RxSim) was design & built to perform integrated testing of the TDU components. In particular, the objectives of RxSim testing was to verify the operation of the core simulator, the instrumentation and control system, and the ground support gas and vacuum test equipment. In addition, it was decided to include a thermal test of a cold trap purification design and a pump performance test at pump voltages up to 150 V since the targeted mass flow rate of 1.75 kg/s was not obtained in the RxSim at the originally constrained voltage of 120 V. This paper summarizes RxSim testing. The gas and vacuum ground support test equipment performed effectively in NaK fill, loop pressurization, and NaK drain operations. The instrumentation and control system effectively controlled loop temperature and flow rates or pump voltage to targeted settings. The cold trap design was able to obtain the targeted cold temperature of 480 K. An outlet temperature of 636 K was obtained which was lower than the predicted 750 K but 156 K higher than the cold temperature indicating the design provided some heat regeneration. The annular linear induction pump (ALIP) tested was able to produce a maximum flow rate of 1.53 kg/s at 800 K when operated at 150 V and 53 Hz.

Reactor Simulator Integration and Testing

NASA Technical Reports Server (NTRS)

Schoenfield, M. P.; Webster, K. L.; Pearson, J. B.

2013-01-01

As part of the Nuclear Systems Office Fission Surface Power Technology Demonstration Unit (TDU) project, a reactor simulator (RxSim) test loop was designed and built to perform integrated testing of the TDU components. In particular, the objectives of RxSim testing were to verify the operation of the core simulator, the instrumentation and control system, and the ground support gas and vacuum test equipment. In addition, it was decided to include a thermal test of a cold trap purification design and a pump performance test at pump voltages up to 150 V because the targeted mass flow rate of 1.75 kg/s was not obtained in the RxSim at the originally constrained voltage of 120 V. This Technical Memorandum summarizes RxSim testing. The gas and vacuum ground support test equipment performed effectively in NaK fill, loop pressurization, and NaK drain operations. The instrumentation and control system effectively controlled loop temperature and flow rates or pump voltage to targeted settings. The cold trap design was able to obtain the targeted cold temperature of 480 K. An outlet temperature of 636 K was obtained, which was lower than the predicted 750 K but 156 K higher than the cold temperature, indicating the design provided some heat regeneration. The annular linear induction pump tested was able to produce a maximum flow rate of 1.53 kg/s at 800 K when operated at 150 V and 53 Hz.

A simple and low-cost structured illumination microscopy using a pico-projector

NASA Astrophysics Data System (ADS)

Özgürün, Baturay

2018-02-01

Here, development of a low-cost structured illumination microscopy (SIM) based on a pico-projector is presented. The pico-projector consists of independent red, green and blue LEDs that remove need for an external illumination source. Moreover, display element of the pico-projector serves as a pattern generating spatial light modulator. A simple lens group is employed to couple light from the projector to an epi-illumination port of a commercial microscope system. 2D sub SIM images are acquired and synthesized to surpass the diffraction limit using 40x (0.75 NA) objective. Resolution of the reconstructed SIM images is verified with a dye-and-object object and a fixed cell sample.

Specimen preparation for NanoSIMS analysis of biological materials

NASA Astrophysics Data System (ADS)

Grovenor, C. R. M.; Smart, K. E.; Kilburn, M. R.; Shore, B.; Dilworth, J. R.; Martin, B.; Hawes, C.; Rickaby, R. E. M.

2006-07-01

In order to achieve reliable and reproducible analysis of biological materials by SIMS, it is critical both that the chosen specimen preparation method does not modify substantially the in vivo chemistry that is the focus of the study and that any chemical information obtained can be calibrated accurately by selection of appropriate standards. In Oxford, we have been working with our new Cameca NanoSIMS50 on two very distinct classes of biological materials; the first where the sample preparation problems are relatively undemanding - human hair - but calibration for trace metal analysis is a critical issue and, the second, marine coccoliths and hyperaccumulator plants where reliable specimen preparation by rapid freezing and controlled drying to preserve the distribution of diffusible species is the first and most demanding requirement, but worthwhile experiments on tracking key elements can still be undertaken even when it is clear that some redistribution of the most diffusible ions has occurred.

Characterization of individual complex particles in urban atmospheric environment

NASA Astrophysics Data System (ADS)

Suzuki, K.; Takii, T.; Tomiyasu, B.; Nihei, Y.

2006-07-01

The origins of carrier particles of complex particles (iron-rich particles) collected from the urban atmospheric environment near to road traffic and a railroad were investigated from the detailed surface information using FE-SEM/EDS and TOF-SIMS analyses. From the FE-SEM/EDS analyses, the iron-rich particles were classified into two typical types (spherical type and non-spherical type). From the TOF-SIMS measurements, the characteristic secondary ions of spherical type of iron-rich particles were 23Na + and 39K +. The minor components of non-spherical type were Al, Ca and Ba. On the other hand, we carried out TOF-SIMS measurement to materials of rail origin and brake origin. From the comparison of these spectra pattern, it seemed that the spherical type of iron-rich particles was emitted from the rail origin. We concluded that the origin of non-spherical type of iron-rich particles were brake pad of vehicles.

New Constraints on the Abundance of 60Fe in the Early Solar System

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

Trappitsch, Reto; Boehnke, Patrick; Stephan, Thomas

Establishing the abundance of the extinct radionuclide 60Fe (half-life 2.62 Ma) in the early solar system is important for understanding the astrophysical context of solar system formation. While bulk measurements of early solar system phases show a low abundance consistent with galactic background, some in situ measurements by secondary ion mass spectrometry (SIMS) imply a higher abundance, which would require injection from a nearby supernova (SN). In this paper, we present in situ nickel isotopic analyses by resonance ionization mass spectrometry (RIMS) in a chondrule from the primitive meteorite Semarkona (LL3.00). The same chondrule had been previously analyzed by SIMS.more » Despite improved precision compared to SIMS, the RIMS nickel isotopic data do not reveal any resolved excesses of 60Ni that could be unambiguously ascribed to in situ 60Fe decay. Linear regression of 60Ni/ 58Ni versus 56Fe/ 58Ni yields an initial 60Fe/ 56Fe ratio for this chondrule of (3.8 ± 6.9) × 10 -8, which is consistent with both the low initial value found by bulk measurements and the low end of the range of initial ratios inferred from some in situ work. The same regression also gives a solar initial 60Ni/ 58Ni ratio, which shows that this sample was not disturbed by nickel mobilization, thus agreeing with a low initial 60Fe/ 56Fe ratio. These findings agree with a re-evaluation of previous SIMS measurements of the same sample. Finally, supernova injection of 60Fe into the solar system or its parental cloud material is therefore not necessary to account for the measured solar system's initial amount of 60Fe.« less

New Constraints on the Abundance of 60Fe in the Early Solar System

DOE PAGES

Trappitsch, Reto; Boehnke, Patrick; Stephan, Thomas; ...

2018-04-19

Establishing the abundance of the extinct radionuclide 60Fe (half-life 2.62 Ma) in the early solar system is important for understanding the astrophysical context of solar system formation. While bulk measurements of early solar system phases show a low abundance consistent with galactic background, some in situ measurements by secondary ion mass spectrometry (SIMS) imply a higher abundance, which would require injection from a nearby supernova (SN). In this paper, we present in situ nickel isotopic analyses by resonance ionization mass spectrometry (RIMS) in a chondrule from the primitive meteorite Semarkona (LL3.00). The same chondrule had been previously analyzed by SIMS.more » Despite improved precision compared to SIMS, the RIMS nickel isotopic data do not reveal any resolved excesses of 60Ni that could be unambiguously ascribed to in situ 60Fe decay. Linear regression of 60Ni/ 58Ni versus 56Fe/ 58Ni yields an initial 60Fe/ 56Fe ratio for this chondrule of (3.8 ± 6.9) × 10 -8, which is consistent with both the low initial value found by bulk measurements and the low end of the range of initial ratios inferred from some in situ work. The same regression also gives a solar initial 60Ni/ 58Ni ratio, which shows that this sample was not disturbed by nickel mobilization, thus agreeing with a low initial 60Fe/ 56Fe ratio. These findings agree with a re-evaluation of previous SIMS measurements of the same sample. Finally, supernova injection of 60Fe into the solar system or its parental cloud material is therefore not necessary to account for the measured solar system's initial amount of 60Fe.« less

Assessment of photoselective vaporization of prostate skills during Urology Objective Structured Clinical Examinations (OSCE)

PubMed Central

Noureldin, Yasser A.; Elkoushy, Mohamed A.; Fahmy, Nader; Carrier, Serge; Elhilali, Mostafa M.; Andonian, Sero

2015-01-01

Introduction: We evaluated the use of the GreenLight Simulator (GL-SIM) (American Medical Systems, Guelph, ON) in the skill assessment of postgraduate trainees (PGTs) in photoselective vaporization of the prostate (PVP). We also sought to determine whether previous PVP experience or GL-SIM practice improved performance. Methods: PGTs in postgraduate years (PGY-3 to PGY-5) from all 4 Quebec urology training programs were recruited during 2 annual Objective Structured Clinical Examinations (OSCEs). During a 20-minute OSCE station, PGTs were asked to perform 2 exercises: (1) identification of endoscopic landmarks and (2) a PVP of a 30-g normal prostate. Grams vaporized, global scores, and number of correct anatomical landmarks were recorded and correlated with PGY level, practice on the GL-SIM, and previous PVP experience. Results: In total, 25 PGTs were recruited at each OSCE, with 13 PGTs participating in both OSCEs. When comparing scores from the first and second OSCEs, there was a significant improvement in the number of grams vaporized (2.9 vs. 4.3 g; p = 0.003) and global score (100 vs. 165; p = 0.03). There was good correlation between the number of previously performed PVPs and the global score (r = 0.4, p = 0.04). Similarly, PGTs with previous practice on the GL-SIM had significantly higher global score (100.6 vs. 162.6; p = 0.04) and grams vaporized (3.1 vs. 4.1 g; p = 0.04) when compared with those who did not practice on GL-SIM. Furthermore, there were significantly more competent PGTs among those who had previously practiced on the GL-SIM (32.7% vs. 10.2%; p = 0.009). PGY level did not significantly affect grams vaporized or global score (p > 0.05). Conclusion: Performance on the GL-SIM at OSCEs significantly correlated with previous practice on the GL-SIM and previous PVP experience rather than PGY level. Furthermore, there were significantly more competent PGTs among those who had previously practiced on the GL-SIM. PMID:25737763

A novel field search and rescue system based on SIM card location

NASA Astrophysics Data System (ADS)

Zhang, Huihui; Guo, Shutao; Cui, Dejing

2017-06-01

Nowadays, the rapid development of outdoor sports and adventure leads to the increase of the frequency of missing accidents. On the other hand, it becomes much more convenient and efficient for the criminals to escape with the help of new technologies. So we have developed a long-distance raids targeted field search and rescue system which utilizes RSSI ranging and Kalman filtering algorithm to realize remote positioning and dynamic supervision management only by a mobile phone with a SIM card, without any additional terminal equipment.

CBP PHASE I CODE INTEGRATION

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

Smith, F.; Brown, K.; Flach, G.

The goal of the Cementitious Barriers Partnership (CBP) is to develop a reasonable and credible set of software tools to predict the structural, hydraulic, and chemical performance of cement barriers used in nuclear applications over extended time frames (greater than 100 years for operating facilities and greater than 1000 years for waste management). The simulation tools will be used to evaluate and predict the behavior of cementitious barriers used in near surface engineered waste disposal systems including waste forms, containment structures, entombments, and environmental remediation. These cementitious materials are exposed to dynamic environmental conditions that cause changes in material propertiesmore » via (i) aging, (ii) chloride attack, (iii) sulfate attack, (iv) carbonation, (v) oxidation, and (vi) primary constituent leaching. A set of state-of-the-art software tools has been selected as a starting point to capture these important aging and degradation phenomena. Integration of existing software developed by the CBP partner organizations was determined to be the quickest method of meeting the CBP goal of providing a computational tool that improves the prediction of the long-term behavior of cementitious materials. These partner codes were selected based on their maturity and ability to address the problems outlined above. The GoldSim Monte Carlo simulation program (GTG 2010a, GTG 2010b) was chosen as the code integration platform (Brown & Flach 2009b). GoldSim (current Version 10.5) is a Windows based graphical object-oriented computer program that provides a flexible environment for model development (Brown & Flach 2009b). The linking of GoldSim to external codes has previously been successfully demonstrated (Eary 2007, Mattie et al. 2007). GoldSim is capable of performing deterministic and probabilistic simulations and of modeling radioactive decay and constituent transport. As part of the CBP project, a general Dynamic Link Library (DLL) interface was developed to link GoldSim with external codes (Smith III et al. 2010). The DLL uses a list of code inputs provided by GoldSim to create an input file for the external application, runs the external code, and returns a list of outputs (read from files created by the external application) back to GoldSim. In this way GoldSim provides: (1) a unified user interface to the applications, (2) the capability of coupling selected codes in a synergistic manner, and (3) the capability of performing probabilistic uncertainty analysis with the codes. GoldSim is made available by the GoldSim Technology Group as a free 'Player' version that allows running but not editing GoldSim models. The player version makes the software readily available to a wider community of users that would wish to use the CBP application but do not have a license for GoldSim.« less

Advanced emergency braking controller design for pedestrian protection oriented automotive collision avoidance system.

PubMed

Lie, Guo; Zejian, Ren; Pingshu, Ge; Jing, Chang

2014-01-01

Automotive collision avoidance system, which aims to enhance the active safety of the vehicle, has become a hot research topic in recent years. However, most of the current systems ignore the active protection of pedestrian and other vulnerable groups in the transportation system. An advanced emergency braking control system is studied by taking into account the pedestrians and the vehicles. Three typical braking scenarios are defined and the safety situations are assessed by comparing the current distance between the host vehicle and the obstacle with the critical braking distance. To reflect the nonlinear time-varying characteristics and control effect of the longitudinal dynamics, the vehicle longitudinal dynamics model is established in CarSim. Then the braking controller with the structure of upper and lower layers is designed based on sliding mode control and the single neuron PID control when confronting deceleration or emergency braking conditions. Cosimulations utilizing CarSim and Simulink are finally carried out on a CarSim intelligent vehicle model to explore the effectiveness of the proposed controller. Results display that the designed controller has a good response in preventing colliding with the front vehicle or pedestrian.

Advanced Emergency Braking Controller Design for Pedestrian Protection Oriented Automotive Collision Avoidance System

PubMed Central

Lie, Guo; Zejian, Ren; Pingshu, Ge; Jing, Chang

2014-01-01

Automotive collision avoidance system, which aims to enhance the active safety of the vehicle, has become a hot research topic in recent years. However, most of the current systems ignore the active protection of pedestrian and other vulnerable groups in the transportation system. An advanced emergency braking control system is studied by taking into account the pedestrians and the vehicles. Three typical braking scenarios are defined and the safety situations are assessed by comparing the current distance between the host vehicle and the obstacle with the critical braking distance. To reflect the nonlinear time-varying characteristics and control effect of the longitudinal dynamics, the vehicle longitudinal dynamics model is established in CarSim. Then the braking controller with the structure of upper and lower layers is designed based on sliding mode control and the single neuron PID control when confronting deceleration or emergency braking conditions. Cosimulations utilizing CarSim and Simulink are finally carried out on a CarSim intelligent vehicle model to explore the effectiveness of the proposed controller. Results display that the designed controller has a good response in preventing colliding with the front vehicle or pedestrian. PMID:25097870

Multi-dimensional TOF-SIMS analysis for effective profiling of disease-related ions from the tissue surface.

PubMed

Park, Ji-Won; Jeong, Hyobin; Kang, Byeongsoo; Kim, Su Jin; Park, Sang Yoon; Kang, Sokbom; Kim, Hark Kyun; Choi, Joon Sig; Hwang, Daehee; Lee, Tae Geol

2015-06-05

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) emerges as a promising tool to identify the ions (small molecules) indicative of disease states from the surface of patient tissues. In TOF-SIMS analysis, an enhanced ionization of surface molecules is critical to increase the number of detected ions. Several methods have been developed to enhance ionization capability. However, how these methods improve identification of disease-related ions has not been systematically explored. Here, we present a multi-dimensional SIMS (MD-SIMS) that combines conventional TOF-SIMS and metal-assisted SIMS (MetA-SIMS). Using this approach, we analyzed cancer and adjacent normal tissues first by TOF-SIMS and subsequently by MetA-SIMS. In total, TOF- and MetA-SIMS detected 632 and 959 ions, respectively. Among them, 426 were commonly detected by both methods, while 206 and 533 were detected uniquely by TOF- and MetA-SIMS, respectively. Of the 426 commonly detected ions, 250 increased in their intensities by MetA-SIMS, whereas 176 decreased. The integrated analysis of the ions detected by the two methods resulted in an increased number of discriminatory ions leading to an enhanced separation between cancer and normal tissues. Therefore, the results show that MD-SIMS can be a useful approach to provide a comprehensive list of discriminatory ions indicative of disease states.

Multi-dimensional TOF-SIMS analysis for effective profiling of disease-related ions from the tissue surface

PubMed Central

Park, Ji-Won; Jeong, Hyobin; Kang, Byeongsoo; Kim, Su Jin; Park, Sang Yoon; Kang, Sokbom; Kim, Hark Kyun; Choi, Joon Sig; Hwang, Daehee; Lee, Tae Geol

2015-01-01

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) emerges as a promising tool to identify the ions (small molecules) indicative of disease states from the surface of patient tissues. In TOF-SIMS analysis, an enhanced ionization of surface molecules is critical to increase the number of detected ions. Several methods have been developed to enhance ionization capability. However, how these methods improve identification of disease-related ions has not been systematically explored. Here, we present a multi-dimensional SIMS (MD-SIMS) that combines conventional TOF-SIMS and metal-assisted SIMS (MetA-SIMS). Using this approach, we analyzed cancer and adjacent normal tissues first by TOF-SIMS and subsequently by MetA-SIMS. In total, TOF- and MetA-SIMS detected 632 and 959 ions, respectively. Among them, 426 were commonly detected by both methods, while 206 and 533 were detected uniquely by TOF- and MetA-SIMS, respectively. Of the 426 commonly detected ions, 250 increased in their intensities by MetA-SIMS, whereas 176 decreased. The integrated analysis of the ions detected by the two methods resulted in an increased number of discriminatory ions leading to an enhanced separation between cancer and normal tissues. Therefore, the results show that MD-SIMS can be a useful approach to provide a comprehensive list of discriminatory ions indicative of disease states. PMID:26046669

Improving Memory after Interruption: Exploiting Soft Constraints and Manipulating Information Access Cost

ERIC Educational Resources Information Center

Morgan, Phillip L.; Patrick, John; Waldron, Samuel M.; King, Sophia L.; Patrick, Tanya

2009-01-01

Forgetting what one was doing prior to interruption is an everyday problem. The recent soft constraints hypothesis (Gray, Sims, Fu, & Schoelles, 2006) emphasizes the strategic adaptation of information processing strategy to the task environment. It predicts that increasing information access cost (IAC: the time, and physical and mental effort…

Automated innovative diagnostic, data management and communication tool, for improving malaria vector control in endemic settings.

PubMed

Vontas, John; Mitsakakis, Konstantinos; Zengerle, Roland; Yewhalaw, Delenasaw; Sikaala, Chadwick Haadezu; Etang, Josiane; Fallani, Matteo; Carman, Bill; Müller, Pie; Chouaïbou, Mouhamadou; Coleman, Marlize; Coleman, Michael

2016-01-01

Malaria is a life-threatening disease that caused more than 400,000 deaths in sub-Saharan Africa in 2015. Mass prevention of the disease is best achieved by vector control which heavily relies on the use of insecticides. Monitoring mosquito vector populations is an integral component of control programs and a prerequisite for effective interventions. Several individual methods are used for this task; however, there are obstacles to their uptake, as well as challenges in organizing, interpreting and communicating vector population data. The Horizon 2020 project "DMC-MALVEC" consortium will develop a fully integrated and automated multiplex vector-diagnostic platform (LabDisk) for characterizing mosquito populations in terms of species composition, Plasmodium infections and biochemical insecticide resistance markers. The LabDisk will be interfaced with a Disease Data Management System (DDMS), a custom made data management software which will collate and manage data from routine entomological monitoring activities providing information in a timely fashion based on user needs and in a standardized way. The ResistanceSim, a serious game, a modern ICT platform that uses interactive ways of communicating guidelines and exemplifying good practices of optimal use of interventions in the health sector will also be a key element. The use of the tool will teach operational end users the value of quality data (relevant, timely and accurate) to make informed decisions. The integrated system (LabDisk, DDMS & ResistanceSim) will be evaluated in four malaria endemic countries, representative of the vector control challenges in sub-Saharan Africa, (Cameroon, Ivory Coast, Ethiopia and Zambia), highly representative of malaria settings with different levels of endemicity and vector control challenges, to support informed decision-making in vector control and disease management.

SimGen: A General Simulation Method for Large Systems.

PubMed

Taylor, William R

2017-02-03

SimGen is a stand-alone computer program that reads a script of commands to represent complex macromolecules, including proteins and nucleic acids, in a structural hierarchy that can then be viewed using an integral graphical viewer or animated through a high-level application programming interface in C++. Structural levels in the hierarchy range from α-carbon or phosphate backbones through secondary structure to domains, molecules, and multimers with each level represented in an identical data structure that can be manipulated using the application programming interface. Unlike most coarse-grained simulation approaches, the higher-level objects represented in SimGen can be soft, allowing the lower-level objects that they contain to interact directly. The default motion simulated by SimGen is a Brownian-like diffusion that can be set to occur across all levels of representation in the hierarchy. Links can also be defined between objects, which, when combined with large high-level random movements, result in an effective search strategy for constraint satisfaction, including structure prediction from predicted pairwise distances. The implementation of SimGen makes use of the hierarchic data structure to avoid unnecessary calculation, especially for collision detection, allowing it to be simultaneously run and viewed on a laptop computer while simulating large systems of over 20,000 objects. It has been used previously to model complex molecular interactions including the motion of a myosin-V dimer "walking" on an actin fibre, RNA stem-loop packing, and the simulation of cell motion and aggregation. Several extensions to this original functionality are described. Copyright © 2016 The Francis Crick Institute. Published by Elsevier Ltd.. All rights reserved.

SmartSIM - a virtual reality simulator for laparoscopy training using a generic physics engine.

PubMed

Khan, Zohaib Amjad; Kamal, Nabeel; Hameed, Asad; Mahmood, Amama; Zainab, Rida; Sadia, Bushra; Mansoor, Shamyl Bin; Hasan, Osman

2017-09-01

Virtual reality (VR) training simulators have started playing a vital role in enhancing surgical skills, such as hand-eye coordination in laparoscopy, and practicing surgical scenarios that cannot be easily created using physical models. We describe a new VR simulator for basic training in laparoscopy, i.e. SmartSIM, which has been developed using a generic open-source physics engine called the simulation open framework architecture (SOFA). This paper describes the systems perspective of SmartSIM including design details of both hardware and software components, while highlighting the critical design decisions. Some of the distinguishing features of SmartSIM include: (i) an easy-to-fabricate custom-built hardware interface; (ii) use of a generic physics engine to facilitate wider accessibility of our work and flexibility in terms of using various graphical modelling algorithms and their implementations; and (iii) an intelligent and smart evaluation mechanism that facilitates unsupervised and independent learning. Copyright © 2016 John Wiley & Sons, Ltd.

DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation

PubMed Central

Sherfey, Jason S.; Soplata, Austin E.; Ardid, Salva; Roberts, Erik A.; Stanley, David A.; Pittman-Polletta, Benjamin R.; Kopell, Nancy J.

2018-01-01

DynaSim is an open-source MATLAB/GNU Octave toolbox for rapid prototyping of neural models and batch simulation management. It is designed to speed up and simplify the process of generating, sharing, and exploring network models of neurons with one or more compartments. Models can be specified by equations directly (similar to XPP or the Brian simulator) or by lists of predefined or custom model components. The higher-level specification supports arbitrarily complex population models and networks of interconnected populations. DynaSim also includes a large set of features that simplify exploring model dynamics over parameter spaces, running simulations in parallel using both multicore processors and high-performance computer clusters, and analyzing and plotting large numbers of simulated data sets in parallel. It also includes a graphical user interface (DynaSim GUI) that supports full functionality without requiring user programming. The software has been implemented in MATLAB to enable advanced neural modeling using MATLAB, given its popularity and a growing interest in modeling neural systems. The design of DynaSim incorporates a novel schema for model specification to facilitate future interoperability with other specifications (e.g., NeuroML, SBML), simulators (e.g., NEURON, Brian, NEST), and web-based applications (e.g., Geppetto) outside MATLAB. DynaSim is freely available at http://dynasimtoolbox.org. This tool promises to reduce barriers for investigating dynamics in large neural models, facilitate collaborative modeling, and complement other tools being developed in the neuroinformatics community. PMID:29599715

Results from SIM's Thermo-Opto-Mechanical (TOM3) Testbed

NASA Technical Reports Server (NTRS)

Goullioud, Renaud; Lindensmith, C. A.; Hahn, I.

2006-01-01

Future space-based optical interferometers, such as the Space Interferometer Mission Planet Quest (SIM), require thermal stability of the optical wavefront to the level of picometers in order to produce astrometric data at the micro-arc-second level. In SIM, the internal path of the interferometer will be measured with a small metrology beam whereas the starlight fringe position is estimated from a large concentric annular beam. To achieve the micro-arc-second observation goal for SIM, it is necessary to maintain the optical path difference between the central and the outer annulus portions of the wavefront of the front-end telescope optics to a few tens of picometers. The Thermo-Opto-Mecha nical testbed (TOM3) was developed at the Jet Propulsion Laboratory to measure thermally induced optical deformations of a full-size flight-like beam compressor and siderostat, the two largest optics on SIM, in flight-like thermal environments. A Common Path Heterodyne Interferometer (COPHI) developed at JPL was used for the fine optical path difference measurement as the metrology sensor. The system was integrated inside a large vacuum chamber in order to mitigate the atmospheric and thermal disturbances. The siderostat was installed in a temperature-controlled thermal shroud inside the vacuum chamber, creating a flight-like thermal environment. Detailed thermal and structural models of the test articles (siderostat and compressor) were also developed for model prediction and correlation of the thermal deformations. Experimental data shows SIM required thermal stability of the test articles and good agreement with the model predictions.

DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation.

PubMed

Sherfey, Jason S; Soplata, Austin E; Ardid, Salva; Roberts, Erik A; Stanley, David A; Pittman-Polletta, Benjamin R; Kopell, Nancy J

2018-01-01

DynaSim is an open-source MATLAB/GNU Octave toolbox for rapid prototyping of neural models and batch simulation management. It is designed to speed up and simplify the process of generating, sharing, and exploring network models of neurons with one or more compartments. Models can be specified by equations directly (similar to XPP or the Brian simulator) or by lists of predefined or custom model components. The higher-level specification supports arbitrarily complex population models and networks of interconnected populations. DynaSim also includes a large set of features that simplify exploring model dynamics over parameter spaces, running simulations in parallel using both multicore processors and high-performance computer clusters, and analyzing and plotting large numbers of simulated data sets in parallel. It also includes a graphical user interface (DynaSim GUI) that supports full functionality without requiring user programming. The software has been implemented in MATLAB to enable advanced neural modeling using MATLAB, given its popularity and a growing interest in modeling neural systems. The design of DynaSim incorporates a novel schema for model specification to facilitate future interoperability with other specifications (e.g., NeuroML, SBML), simulators (e.g., NEURON, Brian, NEST), and web-based applications (e.g., Geppetto) outside MATLAB. DynaSim is freely available at http://dynasimtoolbox.org. This tool promises to reduce barriers for investigating dynamics in large neural models, facilitate collaborative modeling, and complement other tools being developed in the neuroinformatics community.

[SIM and SINASC: social representation of nurses and professional in administrative sectors who work in hospitals in the city of São Paulo].

PubMed

Schoeps, Daniela; Almeida, Marcia Furquim de; Raspantini, Priscila Ribeiro; Novaes, Hillegonda Maria Dutilh; Silva, Zilda Pereira da; Lefevre, Fernando

2013-05-01

Few studies have analyzed the SINASC (Live Birth Information System) and MIS (Mortality Information System) applying qualitative methodology seeking to understand data production processes and contexts. This article aims to study the social representation of health professionals about Live Birth Certificates (LBC) and perinatal Death Certificates (DC). A total of 24 interviews were conducted with nurses and other professionals of 16 Unified Health System (SUS) and non-SUS hospitals of the city of São Paulo in 2009. Qualitative methodology was adopted along with the Collective Subject Discourse technique. Professionals acknowledged that they are an integral part of the information production process of SINASC and their reports indicate that they incorporate it in their work routine. They also perceive that training activities are a tool to understand the information produced by them and are aware of the utility of LBC information. Although physicians are legally responsible for the DC, other professionals frequently provide some of the information to complete it. The professionals see themselves as participants of the SINASC. Despite providing information to complete the DC, they do not see themselves as participants of the MIS operation.

DOE/NASA SIMS Prototype Solar System, no. 4. Part 1: Market analysis. Part 2: Modular manufacturing cost estimate

NASA Technical Reports Server (NTRS)

1979-01-01

The findings of the IIT Research Institute (IITRI) market study of the SIMS Prototype System 4, a hot water (DHW) system are documented. The feasibility of prepackaging currently available solar heating components into modular subsystems for site assembly is addressed. A documented design and installation procedure and a performance test report were prepared. The potential markets and applications for this particular system in the nonfederal market are profiled by assessing the needs and requirements of potential users and specifiers, by characterizing the nature of the market and the competitive environment, by identifying the barriers to commercial acceptance, and by estimating the size of the potential market.

The Mask Designs for Space Interferometer Mission (SIM)

NASA Technical Reports Server (NTRS)

Wang, Xu

2008-01-01

The Space Interferometer Mission (SIM) consists of three interferometers (science, guide1, and guide2) and two optical paths (metrology and starlight). The system requirements for each interferometer/optical path combination are different and sometimes work against each other. A diffraction model is developed to design and optimize various masks to simultaneously meet the system requirements of three interferometers. In this paper, the details of this diffraction model will be described first. Later, the mask design for each interferometer will be presented to demonstrate the system performance compliance. In the end, a tolerance sensitivity study on the geometrical dimension, shape, and the alignment of these masks will be discussed.

Improving SysSim's Planetary Occurrence Rate Estimates

NASA Astrophysics Data System (ADS)

Ashby, Keir; Ragozzine, Darin; Hsu, Danley; Ford, Eric B.

2017-10-01

Kepler's catalog of thousands of transiting planet candidates enables statistical characterization of the underlying planet occurrence rates as a function of period and radius. Due to geometric factors and general noise in measurements, we know that many planets--especially those with a small-radius and/or long-period--were not observed by Kepler.To account for Kepler's detection criteria, Hsu et al. 2017 expanded on work in Lissuaer et al. 2011 to develop the Planetary System Simulator or "SysSim". SysSim uses a forward model to generate simulated catalogs of exoplanet systems, determine which of those simulated planets would have been seen by Kepler in the presence of uncertainties, and then compares those “observed planets” to those actually seen by Kepler. It then uses Approximate Bayesian Computation to infer the posterior probability distributions of the input parameters used to generate the forward model. In Hsu et al. 2017, we focused on matching the observed frequency of planets by solving for the underlying occurrence rate for each bin in a 2-dimensional grid of radius and period. After summarizing the results of Hsu et al. 2017, we show new results that investigate the effect on occurrence rates from including more accurate completeness products (from the Kepler DR25 analysis) into SysSim.

Structural analysis of poly-SUMO chain recognition by the RNF4-SIMs domain.

PubMed

Kung, Camy C-H; Naik, Mandar T; Wang, Szu-Huan; Shih, Hsiu-Ming; Chang, Che-Chang; Lin, Li-Ying; Chen, Chia-Lin; Ma, Che; Chang, Chi-Fon; Huang, Tai-Huang

2014-08-15

The E3 ubiquitin ligase RNF4 (RING finger protein 4) contains four tandem SIM [SUMO (small ubiquitin-like modifier)-interaction motif] repeats for selective interaction with poly-SUMO-modified proteins, which it targets for degradation. We employed a multi-faceted approach to characterize the structure of the RNF4-SIMs domain and the tetra-SUMO2 chain to elucidate the interaction between them. In solution, the SIM domain was intrinsically disordered and the linkers of the tetra-SUMO2 were highly flexible. Individual SIMs of the RNF4-SIMs domains bind to SUMO2 in the groove between the β2-strand and the α1-helix parallel to the β2-strand. SIM2 and SIM3 bound to SUMO with a high affinity and together constituted the recognition module necessary for SUMO binding. SIM4 alone bound to SUMO with low affinity; however, its contribution to tetra-SUMO2 binding avidity is comparable with that of SIM3 when in the RNF4-SIMs domain. The SAXS data of the tetra-SUMO2-RNF4-SIMs domain complex indicate that it exists as an ordered structure. The HADDOCK model showed that the tandem RNF4-SIMs domain bound antiparallel to the tetra-SUMO2 chain orientation and wrapped around the SUMO protamers in a superhelical turn without imposing steric hindrance on either molecule.

New Constraints on the Abundance of 60Fe in the Early Solar System

NASA Astrophysics Data System (ADS)

Trappitsch, Reto; Boehnke, Patrick; Stephan, Thomas; Telus, Myriam; Savina, Michael R.; Pardo, Olivia; Davis, Andrew M.; Dauphas, Nicolas; Pellin, Michael J.; Huss, Gary R.

2018-04-01

Establishing the abundance of the extinct radionuclide 60Fe (half-life 2.62 Ma) in the early solar system is important for understanding the astrophysical context of solar system formation. While bulk measurements of early solar system phases show a low abundance consistent with galactic background, some in situ measurements by secondary ion mass spectrometry (SIMS) imply a higher abundance, which would require injection from a nearby supernova (SN). Here we present in situ nickel isotopic analyses by resonance ionization mass spectrometry (RIMS) in a chondrule from the primitive meteorite Semarkona (LL3.00). The same chondrule had been previously analyzed by SIMS. Despite improved precision compared to SIMS, the RIMS nickel isotopic data do not reveal any resolved excesses of 60Ni that could be unambiguously ascribed to in situ 60Fe decay. Linear regression of 60Ni/58Ni versus 56Fe/58Ni yields an initial 60Fe/56Fe ratio for this chondrule of (3.8 ± 6.9) × 10‑8, which is consistent with both the low initial value found by bulk measurements and the low end of the range of initial ratios inferred from some in situ work. The same regression also gives a solar initial 60Ni/58Ni ratio, which shows that this sample was not disturbed by nickel mobilization, thus agreeing with a low initial 60Fe/56Fe ratio. These findings agree with a re-evaluation of previous SIMS measurements of the same sample. Supernova injection of 60Fe into the solar system or its parental cloud material is therefore not necessary to account for the measured solar system’s initial amount of 60Fe.

FUX-Sim: Implementation of a fast universal simulation/reconstruction framework for X-ray systems.

PubMed

Abella, Monica; Serrano, Estefania; Garcia-Blas, Javier; García, Ines; de Molina, Claudia; Carretero, Jesus; Desco, Manuel

2017-01-01

The availability of digital X-ray detectors, together with advances in reconstruction algorithms, creates an opportunity for bringing 3D capabilities to conventional radiology systems. The downside is that reconstruction algorithms for non-standard acquisition protocols are generally based on iterative approaches that involve a high computational burden. The development of new flexible X-ray systems could benefit from computer simulations, which may enable performance to be checked before expensive real systems are implemented. The development of simulation/reconstruction algorithms in this context poses three main difficulties. First, the algorithms deal with large data volumes and are computationally expensive, thus leading to the need for hardware and software optimizations. Second, these optimizations are limited by the high flexibility required to explore new scanning geometries, including fully configurable positioning of source and detector elements. And third, the evolution of the various hardware setups increases the effort required for maintaining and adapting the implementations to current and future programming models. Previous works lack support for completely flexible geometries and/or compatibility with multiple programming models and platforms. In this paper, we present FUX-Sim, a novel X-ray simulation/reconstruction framework that was designed to be flexible and fast. Optimized implementation for different families of GPUs (CUDA and OpenCL) and multi-core CPUs was achieved thanks to a modularized approach based on a layered architecture and parallel implementation of the algorithms for both architectures. A detailed performance evaluation demonstrates that for different system configurations and hardware platforms, FUX-Sim maximizes performance with the CUDA programming model (5 times faster than other state-of-the-art implementations). Furthermore, the CPU and OpenCL programming models allow FUX-Sim to be executed over a wide range of hardware platforms.

Paragenesis and Geochronology of the Nopal I Uranium Deposit, Mexico

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

M. Fayek; M. Ren

2007-02-14

Uranium deposits can, by analogy, provide important information on the long-term performance of radioactive waste forms and radioactive waste repositories. Their complex mineralogy and variable elemental and isotopic compositions can provide important information, provided that analyses are obtained on the scale of several micrometers. Here, we present a structural model of the Nopal I deposit as well as petrography at the nanoscale coupled with preliminary U-Th-Pb ages and O isotopic compositions of uranium-rich minerals obtained by Secondary Ion Mass Spectrometry (SIMS). This multi-technique approach promises to provide ''natural system'' data on the corrosion rate of uraninite, the natural analogue ofmore » spent nuclear fuel.« less

Human face detection using motion and color information

NASA Astrophysics Data System (ADS)

Kim, Yang-Gyun; Bang, Man-Won; Park, Soon-Young; Choi, Kyoung-Ho; Hwang, Jeong-Hyun

2008-02-01

In this paper, we present a hardware implementation of a face detector for surveillance applications. To come up with a computationally cheap and fast algorithm with minimal memory requirement, motion and skin color information are fused successfully. More specifically, a newly appeared object is extracted first by comparing average Hue and Saturation values of background image and a current image. Then, the result of skin color filtering of the current image is combined with the result of a newly appeared object. Finally, labeling is performed to locate a true face region. The proposed system is implemented on Altera Cyclone2 using Quartus II 6.1 and ModelSim 6.1. For hardware description language (HDL), Verilog-HDL is used.

An intelligent virtual human system for providing healthcare information and support.

PubMed

Rizzo, Albert A; Lange, Belinda; Buckwalter, John G; Forbell, Eric; Kim, Julia; Sagae, Kenji; Williams, Josh; Rothbaum, Barbara O; Difede, JoAnn; Reger, Greg; Parsons, Thomas; Kenny, Patrick

2011-01-01

Over the last 15 years, a virtual revolution has taken place in the use of Virtual Reality simulation technology for clinical purposes. Shifts in the social and scientific landscape have now set the stage for the next major movement in Clinical Virtual Reality with the "birth" of intelligent virtual humans. Seminal research and development has appeared in the creation of highly interactive, artificially intelligent and natural language capable virtual human agents that can engage real human users in a credible fashion. No longer at the level of a prop to add context or minimal faux interaction in a virtual world, virtual humans can be designed to perceive and act in a 3D virtual world, engage in spoken dialogues with real users and can be capable of exhibiting human-like emotional reactions. This paper will present an overview of the SimCoach project that aims to develop virtual human support agents to serve as online guides for promoting access to psychological healthcare information and for assisting military personnel and family members in breaking down barriers to initiating care. The SimCoach experience is being designed to attract and engage military Service Members, Veterans and their significant others who might not otherwise seek help with a live healthcare provider. It is expected that this experience will motivate users to take the first step--to empower themselves to seek advice and information regarding their healthcare and general personal welfare and encourage them to take the next step towards seeking more formal resources if needed.

Image recombination transform algorithm for superresolution structured illumination microscopy

PubMed Central

Zhou, Xing; Lei, Ming; Dan, Dan; Yao, Baoli; Yang, Yanlong; Qian, Jia; Chen, Guangde; Bianco, Piero R.

2016-01-01

Abstract. Structured illumination microscopy (SIM) is an attractive choice for fast superresolution imaging. The generation of structured illumination patterns made by interference of laser beams is broadly employed to obtain high modulation depth of patterns, while the polarizations of the laser beams must be elaborately controlled to guarantee the high contrast of interference intensity, which brings a more complex configuration for the polarization control. The emerging pattern projection strategy is much more compact, but the modulation depth of patterns is deteriorated by the optical transfer function of the optical system, especially in high spatial frequency near the diffraction limit. Therefore, the traditional superresolution reconstruction algorithm for interference-based SIM will suffer from many artifacts in the case of projection-based SIM that possesses a low modulation depth. Here, we propose an alternative reconstruction algorithm based on image recombination transform, which provides an alternative solution to address this problem even in a weak modulation depth. We demonstrated the effectiveness of this algorithm in the multicolor superresolution imaging of bovine pulmonary arterial endothelial cells in our developed projection-based SIM system, which applies a computer controlled digital micromirror device for fast fringe generation and multicolor light-emitting diodes for illumination. The merit of the system incorporated with the proposed algorithm allows for a low excitation intensity fluorescence imaging even less than 1  W/cm2, which is beneficial for the long-term, in vivo superresolved imaging of live cells and tissues. PMID:27653935

Reactor Simulator Testing

NASA Technical Reports Server (NTRS)

Schoenfeld, Michael P.; Webster, Kenny L.; Pearson, Boise Jon

2013-01-01

As part of the Nuclear Systems Office Fission Surface Power Technology Demonstration Unit (TDU) project, a reactor simulator test loop (RxSim) was design & built to perform integrated testing of the TDU components. In particular, the objectives of RxSim testing was to verify the operation of the core simulator, the instrumentation and control system, and the ground support gas and vacuum test equipment. In addition, it was decided to include a thermal test of a cold trap purification design and a pump performance test at pump voltages up to 150 V since the targeted mass flow rate of 1.75 kg/s was not obtained in the RxSim at the originally constrained voltage of 120 V. This paper summarizes RxSim testing. The gas and vacuum ground support test equipment performed effectively in NaK fill, loop pressurization, and NaK drain operations. The instrumentation and control system effectively controlled loop temperature and flow rates or pump voltage to targeted settings. The cold trap design was able to obtain the targeted cold temperature of 480 K. An outlet temperature of 636 K was obtained which was lower than the predicted 750 K but 156 K higher than the cold temperature indicating the design provided some heat regeneration. The annular linear induction pump (ALIP) tested was able to produce a maximum flow rate of 1.53 kg/s at 800 K when operated at 150 V and 53 Hz. Keywords: fission, space power, nuclear, liquid metal, NaK.

Hydrologic Conditions in Northwest Florida: 2006 Water Year

USGS Publications Warehouse

Verdi, Richard Jay

2007-01-01

Introduction National data for streamflow, ground-water levels, and quality of water for the 2006 water year are accessible to the public on the U.S. Geological Survey's (USGS) Site Information Management System (SIMS) website http://web10capp.er.usgs.gov/adr06_lookup/search.jsp. This fact sheet describes data and hydrologic conditions throughout northwest Florida during the 2006 water year (fig. 1), when record-low monthly streamflow conditions were reported at several streamgage locations. Prior to 1960, these data were published in various USGS Water-Supply Papers and included water-related data collected by the USGS during the water year (October 1 to September 30). In 1961, a series of annual reports, 'Water Resources Data-Florida,' was introduced that published surface-water data. In 1964, a similar report was introduced for the purposes of publishing water-quality data. In 1975, the reports were merged to a single volume and were expanded to publish data for surface water, water quality, and ground-water levels. Formal publication of the annual report series was discontinued at the end of the 2005 water year, upon activation of the SIMS website database.

Customization of home closed-loop insulin delivery in adult patients with type 1 diabetes, assisted with structured remote monitoring: the pilot WP7 Diabeloop study.

PubMed

Benhamou, Pierre Yves; Huneker, Erik; Franc, Sylvia; Doron, Maeva; Charpentier, Guillaume

2018-06-01

Improvement in closed-loop insulin delivery systems could result from customization of settings to individual needs and remote monitoring. This pilot home study evaluated the efficacy and relevance of this approach. A bicentric clinical trial was conducted for 3 weeks, using an MPC-based algorithm (Diabeloop Artificial Pancreas system) featuring five settings designed to modulate the reactivity of regulation. Remote monitoring was ensured by expert nurses with a web platform generating automatic Secured Information Messages (SIMs) and with a structured procedure. Endpoints were glucose metrics and description of impact of monitoring on regulation parameters. Eight patients with type 1 diabetes (six men, age 41.8 ± 11.4 years, HbA1c 7.7 ± 1.0%) were included. Time spent in the 70-180 mg/dl range was 70.2% [67.5; 76.9]. Time in hypoglycemia < 70 mg/dl was 2.9% [2.1; 3.4]. Eleven SIMs led to phone intervention. Original default settings were modified in all patients by the intervention of the nurses. This pilot trial suggests that the Diabeloop closed-loop system could be efficient regarding metabolic outcomes, whereas its telemedical monitoring feature could contribute to enhanced efficacy and safety. This study is registered at ClinicalTrials.gov with trial registration number NCT02987556.

Reprint Of: Enhanced spatially-resolved trace analysis using combined SIMS-single-stage AMS

NASA Astrophysics Data System (ADS)

Grabowski, K. S.; Groopman, E. E.; Fahey, A. J.

2018-01-01

Secondary ion mass spectrometry (SIMS) provides spatially resolved trace analysis of solid materials, but can be complicated by unresolved abundant molecular isobars. By adding a 300-kV single-stage accelerator mass spectrometer (SSAMS) as a detector for a Cameca ims 4f SIMS, one can measure more abundant positive ions from the SIMS while removing molecular isobars, thus improving very low abundance trace element and isotope analysis. This paper describes important features and capabilities of such an integrated system at the Naval Research Laboratory using charge state +1 ions. Transmission loss is compared to molecule destruction as gas flow to the molecule-destruction cell increases. As most measurements tolerate more modest abundance sensitivities than for 14C analysis, a lower gas flow is acceptable, so good transmission of 20-50% for ions of interest can be maintained for a broad range of ion masses. This new instrument has measured isotope ratios for uranium, lead, rare earths, and other elements from particulates and localized regions, with molecule destruction enabling the measurement at low SIMS mass resolving power and thus high transmission, as examples will show. This new and world-unique instrument provides improved capabilities for applications in nuclear and other forensics, geochemistry, cosmochemistry, and the development of optical, electronic, multifunctional, and structural materials.

Enhanced spatially-resolved trace analysis using combined SIMS-single-stage AMS

NASA Astrophysics Data System (ADS)

Grabowski, K. S.; Groopman, E. E.; Fahey, A. J.

2017-11-01

Secondary ion mass spectrometry (SIMS) provides spatially resolved trace analysis of solid materials, but can be complicated by unresolved abundant molecular isobars. By adding a 300-kV single-stage accelerator mass spectrometer (SSAMS) as a detector for a Cameca ims 4f SIMS, one can measure more abundant positive ions from the SIMS while removing molecular isobars, thus improving very low abundance trace element and isotope analysis. This paper describes important features and capabilities of such an integrated system at the Naval Research Laboratory using charge state +1 ions. Transmission loss is compared to molecule destruction as gas flow to the molecule-destruction cell increases. As most measurements tolerate more modest abundance sensitivities than for 14C analysis, a lower gas flow is acceptable, so good transmission of 20-50% for ions of interest can be maintained for a broad range of ion masses. This new instrument has measured isotope ratios for uranium, lead, rare earths, and other elements from particulates and localized regions, with molecule destruction enabling the measurement at low SIMS mass resolving power and thus high transmission, as examples will show. This new and world-unique instrument provides improved capabilities for applications in nuclear and other forensics, geochemistry, cosmochemistry, and the development of optical, electronic, multifunctional, and structural materials.

JASSA: a comprehensive tool for prediction of SUMOylation sites and SIMs.

PubMed

Beauclair, Guillaume; Bridier-Nahmias, Antoine; Zagury, Jean-François; Saïb, Ali; Zamborlini, Alessia

2015-11-01

Post-translational modification by the Small Ubiquitin-like Modifier (SUMO) proteins, a process termed SUMOylation, is involved in many fundamental cellular processes. SUMO proteins are conjugated to a protein substrate, creating an interface for the recruitment of cofactors harboring SUMO-interacting motifs (SIMs). Mapping both SUMO-conjugation sites and SIMs is required to study the functional consequence of SUMOylation. To define the best candidate sites for experimental validation we designed JASSA, a Joint Analyzer of SUMOylation site and SIMs. JASSA is a predictor that uses a scoring system based on a Position Frequency Matrix derived from the alignment of experimental SUMOylation sites or SIMs. Compared with existing web-tools, JASSA displays on par or better performances. Novel features were implemented towards a better evaluation of the prediction, including identification of database hits matching the query sequence and representation of candidate sites within the secondary structural elements and/or the 3D fold of the protein of interest, retrievable from deposited PDB files. JASSA is freely accessible at http://www.jassa.fr/. Website is implemented in PHP and MySQL, with all major browsers supported. guillaume.beauclair@inserm.fr Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Changing learning with new interactive and media-rich instruction environments: virtual labs case study report.

PubMed

Huang, Camillan

2003-01-01

Technology has created a new dimension for visual teaching and learning with web-delivered interactive media. The Virtual Labs Project has embraced this technology with instructional design and evaluation methodologies behind the simPHYSIO suite of simulation-based, online interactive teaching modules in physiology for the Stanford students. In addition, simPHYSIO provides the convenience of anytime web-access and a modular structure that allows for personalization and customization of the learning material. This innovative tool provides a solid delivery and pedagogical backbone that can be applied to developing an interactive simulation-based training tool for the use and management of the Picture Archiving and Communication System (PACS) image information system. The disparity in the knowledge between health and IT professionals can be bridged by providing convenient modular teaching tools to fill the gaps in knowledge. An innovative teaching method in the whole PACS is deemed necessary for its successful implementation and operation since it has become widely distributed with many interfaces, components, and customizations. This paper will discuss the techniques for developing an interactive-based teaching tool, a case study of its implementation, and a perspective for applying this approach to an online PACS training tool. Copyright 2002 Elsevier Science Ltd.

Interrogating Host-virus Interactions and Elemental Transfer Using NanoSIMS

NASA Astrophysics Data System (ADS)

Pasulka, A.; Thamatrakoln, K.; Poulos, B.; Bidle, K. D.; Sullivan, M. B.; Orphan, V. J.

2016-02-01

Marine viruses (bacteriophage and eukaryotic viruses) impact microbial food webs by influencing microbial community structure, carbon and nutrient flow, and serving as agents of gene transfer. While the collective impact of viral activity has become more apparent over the last decade, there is a growing need for single-cell and single-virus level measurements of the associated carbon and nitrogen transfer, which ultimately shape the biogeochemical impact of viruses in the upper ocean. Stable isotopes have been used extensively for understanding trophic relationships and elemental cycling in marine food webs. While single-cell isotope approaches such as nanoscale secondary ion mass spectrometry (nanoSIMS) have been more readily used to study trophic interactions between microorganisms, isotopic enrichment in viruses has not been described. Here we used nanoSIMS to quantify the transfer of stable isotopes (13C and 15N) from host to individual viral particles in two distinct unicellular algal-virus model systems. These model systems represent a eukaryotic phytoplankton (Emiliania huxleyi strain CCMP374) and its 200nm coccolithovirus (EhV207), as well as a cyanobacterial phytoplankton (Synechococcus WH8101) and its 80nm virus (Syn1). Host cells were grown on labeled media for multiple generations, subjected to viral infection, and then viruses were harvested after lysis. In both cases, nanoSIMS measurements were able to detect 13C and 15N in the resulting viral particles significantly above the background noise. The isotopic enrichment in the viral particles mirrored that of the host. Through use of these laboratory model systems, we quantified the sensitivity (ion counts), spatial resolution, and reproducibility, including sources of methodological and biological variability, in stable isotope incorporation into viral particles. Our findings suggest that nanoSIMS can be successfully employed to directly probe virus-host interactions at the resolution of individual viral particles and quantify the amount of carbon and nitrogen transferred into viruses during infection of autotrophic phytoplankton.

75 FR 19658 - Agency Information Collection Activities: Proposed Collection; Comments Requested: National...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-15

... Division Counsel, El Paso Intelligence Center, 11339 SSG Sims Blvd., El Paso, TX 79908. Written comments... of the methodology and assumptions used; Enhance the quality, utility, and clarity of the information... collection: Form number: EPIC Form 143. Component: El Paso Intelligence Center, Drug Enforcement...

Effect of alternate and simultaneous grazing on endoparasite infection in sheep and cattle.

PubMed

Brito, Daiana Lima; Dallago, Bruno Stéfano Lima; Louvandini, Helder; dos Santos, Viviane Rodrigues Verdolin; Torres, Sonia Emília Figueirêdo de Araújo; Gomes, Edgard Franco; do Amarante, Alessandro Francisco Talamini; de Melo, Cristiano Barros; McManus, Concepta Margaret

2013-01-01

This experiment was carried out on 8 ha of Panicum maximum cv. Tanzania pastures, with rotational grazing consisting of 7 days of occupation and 21 days of rest. Four treatments were evaluated: cattle grazing alone (BOV), sheep grazing alone (OVI), cattle and sheep grazing simultaneously (SIM) and cattle grazing followed by sheep (alternate - ALT). Twenty heifers and 30 male Santa Inês lambs were used. Fecal egg count (FEC) and fecal cultures were carried out. Blood was also collected to examine red and white cell series, total plasma protein (TPP), albumin and hemoglobin. FEC and estimated nematode pathogenicity index in sheep were lower in the SIM treatment. The Haemonchus spp. proportion was higher in isolated grazing systems. For sheep, mixed grazing was shown to reduce endoparasite infection, and SIM was better than ALT. For cattle, no difference between grazing systems was seen. Therefore, simultaneous grazing (sheep and cattle) may be a tool for reducing the need for anthelmintic treatments in sheep.

Cross-correlating 2D and 3D galaxy surveys

DOE PAGES

Passaglia, Samuel; Manzotti, Alessandro; Dodelson, Scott

2017-06-08

Galaxy surveys probe both structure formation and the expansion rate, making them promising avenues for understanding the dark universe. Photometric surveys accurately map the 2D distribution of galaxy positions and shapes in a given redshift range, while spectroscopic surveys provide sparser 3D maps of the galaxy distribution. We present a way to analyse overlapping 2D and 3D maps jointly and without loss of information. We represent 3D maps using spherical Fourier-Bessel (sFB) modes, which preserve radial coverage while accounting for the spherical sky geometry, and we decompose 2D maps in a spherical harmonic basis. In these bases, a simple expression exists for the cross-correlation of the two fields. One very powerful application is the ability to simultaneously constrain the redshift distribution of the photometric sample, the sample biases, and cosmological parameters. We use our framework to show that combined analysis of DESI and LSST can improve cosmological constraints by factors ofmore » $${\\sim}1.2$$ to $${\\sim}1.8$$ on the region where they overlap relative to identically sized disjoint regions. We also show that in the overlap of DES and SDSS-III in Stripe 82, cross-correlating improves photo-$z$ parameter constraints by factors of $${\\sim}2$$ to $${\\sim}12$$ over internal photo-$z$ reconstructions.« less

Water Planning in Phoenix: Managing Risk in the Face of Climatic Uncertainty

NASA Astrophysics Data System (ADS)

Gober, P.

2009-12-01

The Decision Center for a Desert City (DCDC) was founded in 2004 to develop scientifically-credible support tools to improve water management decisions in the face of growing climatic uncertainty and rapid urbanization in metropolitan Phoenix. At the center of DCDC's effort is WaterSim, a model that integrates information about water supply from groundwater, the Colorado River, and upstream watersheds and water demand from land use change and population growth. Decision levers enable users to manipulate model outcomes in response to climate change scenarios, drought conditions, population growth rates, technology innovations, lifestyle changes, and policy decisions. WaterSim allows users to examine the risks of water shortage from global climate change, the tradeoffs between groundwater sustainability and lifestyle choices, the effects of various policy decisions, and the consequences of delaying policy for the exposure to risk. WaterSim is an important point of contact for DCDC’s relationships with local decision makers. Knowledge, tools, and visualizations are co-produced—by scientists and policy makers, and the Center’s social scientists mine this co-production process for new insights about model development and application. WaterSim is less a static scientific product and more a dynamic process of engagement between decision makers and scientists.

Cross-correlating 2D and 3D galaxy surveys

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

Passaglia, Samuel; Manzotti, Alessandro; Dodelson, Scott

Galaxy surveys probe both structure formation and the expansion rate, making them promising avenues for understanding the dark universe. Photometric surveys accurately map the 2D distribution of galaxy positions and shapes in a given redshift range, while spectroscopic surveys provide sparser 3D maps of the galaxy distribution. We present a way to analyse overlapping 2D and 3D maps jointly and without loss of information. We represent 3D maps using spherical Fourier-Bessel (sFB) modes, which preserve radial coverage while accounting for the spherical sky geometry, and we decompose 2D maps in a spherical harmonic basis. In these bases, a simple expression exists for the cross-correlation of the two fields. One very powerful application is the ability to simultaneously constrain the redshift distribution of the photometric sample, the sample biases, and cosmological parameters. We use our framework to show that combined analysis of DESI and LSST can improve cosmological constraints by factors ofmore » $${\\sim}1.2$$ to $${\\sim}1.8$$ on the region where they overlap relative to identically sized disjoint regions. We also show that in the overlap of DES and SDSS-III in Stripe 82, cross-correlating improves photo-$z$ parameter constraints by factors of $${\\sim}2$$ to $${\\sim}12$$ over internal photo-$z$ reconstructions.« less

Effect of Simvastatin Prodrug on Experimental Periodontitis.

PubMed

Bradley, Aaron D; Zhang, Yijia; Jia, Zhenshan; Zhao, Gang; Wang, Xiaobei; Pranke, Laura; Schmid, Marian J; Wang, Dong; Reinhardt, Richard A

2016-05-01

Local application of statins has shown potential in preventing and regenerating bone loss associated with experimental periodontitis. This study evaluates the effect of a novel simvastatin (SIM) prodrug (capable of delivering high doses to periodontitis inflammatory lesion and cells) on experimental periodontitis bone loss and inflammation. Forty mature female Sprague Dawley rats were subjected to ligature-induced experimental periodontitis between maxillary first and second molars (M1-M2). Equal groups were treated with three weekly doses of: 1) prodrug carrier alone (mPEG); 2) 0.5 mg SIM dose equivalent in carrier (SIM/SIM-mPEG); 3) 1.0 mg SIM/SIM-mPEG; 4) 1.5 mg SIM/SIM-mPEG; or 5) ligature alone. Contralateral molars served as unmanipulated controls. Four weeks after initiation of periodontitis, animals were euthanized, the M1-M2 interproximal was evaluated with microcomputed tomography and histology, and data were analyzed with one-way analysis of variance. Ligature alone caused a mean bone loss of 1.01 ± 0.06 mm from the cemento-enamel junction, whereas all doses of SIM/SIM-mPEG reduced bone loss, especially 1.5 mg SIM/SIM-mPEG (0.68 ± 0.05 mm, P <0.001), which was not statistically different from contralateral control (0.47 ± 0.06 mm). A dose of 1.5 mg SIM/SIM-mPEG also reduced percentage of neutrophils compared with carrier alone (2.0% ± 1.0% versus 5.7% ± 1.1%; P <0.05), and increased amount of uninflamed connective tissue in the M1-M2 interproximal area (65.2% ± 3.3% versus 46.3% ± 3.3%; P <0.001). The mPEG carrier alone did not have bone-sparing or anti-inflammatory properties. Multiple local 1.5-mg doses of a macromolecular SIM prodrug decreases amount of experimental periodontitis bone loss and inflammation in rats.

Dim star fringe stabilization demonstration using pathlength feed-forward on the SIM testbed 3 (STB3)

NASA Astrophysics Data System (ADS)

Goullioud, Renaud; Alvarez-Salazar, Oscar S.; Nemati, Bijan

2003-02-01

Future space-based optical interferometers such as the Space Interferometer Mission require fringe stabilization to the level of nanometers in order to produce astrometric data at the micro-arc-second level. Even the best attitude control system available to date will not be able to stabilize the attitude of a several thousand pound spacecraft to a few milli-arc-seconds. Active pathlength control is usually implemented to compensate for attitude drift of the spacecraft. This issue has been addressed in previous experiments while tracking bright stars. In the case of dim stars, as the sensor bandwidth falls below one hertz, feedback control will not provide sufficient rejection. However, stabilization of the fringes from a dim-star down to the nanometer level can be done open loop using information from additional interferometers looking at bright guide stars. The STB3 testbed developed at the Jet Propulsion Laboratory features three optical interferometers sharing a common baseline, dynamically representative to the SIM interferometer. An artificial star feeding the interferometers is installed on a separate optics bench. Voice coils are used to simulate the attitude motion of the spacecraft by moving the entire bench. Data measured on STB3 show that fringe motion of a dim star due to spacecraft attitude changes can be attenuated by 80 dB at 0.1Hz without feedback control, using only information from two guide stars. This paper describes the STB3 setup, the pathlength feed-forward architecture, implementation issues and data collected with the system.

SU-F-P-54: Guidelines to Check Image Registration QA of a Clinical Deformation Registration Software: A Single Institution Preliminary Study

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

Gill, G; Souri, S; Rea, A

Purpose: The objective of this study is to verify and analyze the accuracy of a clinical deformable image registration (DIR) software. Methods: To test clinical DIR software qualitatively and quantitatively, we focused on lung radiotherapy and analyzed a single (Lung) patient CT scan. Artificial anatomical changes were applied to account for daily variations during the course of treatment including the planning target volume (PTV) and organs at risk (OAR). The primary CT (pCT) and the structure set (pST) was deformed with commercial tool (ImSimQA-Oncology Systems Limited) and after artificial deformation (dCT and dST) sent to another commercial tool (VelocityAI-Varian Medicalmore » Systems). In Velocity, the deformed CT and structures (dCT and dST) were inversely deformed back to original primary CT (dbpCT and dbpST). We compared the dbpST and pST structure sets using similarity metrics. Furthermore, a binary deformation field vector (BDF) was created and sent to ImSimQA software for comparison with known “ground truth” deformation vector fields (DVF). Results: An image similarity comparison was made by using “ground truth” DVF and “deformed output” BDF with an output of normalized “cross correlation (CC)” and “mutual information (MI)” in ImSimQA software. Results for the lung case were MI=0.66 and CC=0.99. The artificial structure deformation in both pST and dbpST was analyzed using DICE coefficient, mean distance to conformity (MDC) and deformation field error volume histogram (DFEVH) by comparing them before and after inverse deformation. We have noticed inadequate structure match for CTV, ITV and PTV due to close proximity of heart and overall affected by lung expansion. Conclusion: We have seen similarity between pCT and dbpCT but not so well between pST and dbpST, because of inadequate structure deformation in clinical DIR system. This system based quality assurance test will prepare us for adopting the guidelines of upcoming AAPM task group 132 protocol.« less

Automated Discovery of Simulation Between Programs

DTIC Science & Technology

2014-10-18

relation. These relations enable the refinement-step of SimAbs. We have implemented SimAbs using UFO framework and Z3 SMT-solver and applied it to...step of SimAbs. We implemented SimAbs and AE-VAL on the top of the UFO framework [1, 15] and an SMT-solver Z3 [8], respectively. We have evaluated SimAbs...ut 6 Evaluation We have implemented SimAbs in the UFO framework, and evaluated it on the Software Verification Competition (SVCOMP’14) benchmarks and

Data management applications

NASA Technical Reports Server (NTRS)

1983-01-01

Kennedy Space Center's primary institutional computer is a 4 megabyte IBM 4341 with 3.175 billion characters of IBM 3350 disc storage. This system utilizes the Software AG product known as ADABAS with the on line user oriented features of NATURAL and COMPLETE as a Data Base Management System (DBMS). It is operational under the OS/VSI and is currently supporting batch/on line applications such as Personnel, Training, Physical Space Management, Procurement, Office Equipment Maintenance, and Equipment Visibility. A third and by far the largest DBMS application is known as the Shuttle Inventory Management System (SIMS) which is operational on a Honeywell 6660 (dedicated) computer system utilizing Honeywell Integrated Data Storage I (IDSI) as the DBMS. The SIMS application is designed to provide central supply system acquisition, inventory control, receipt, storage, and issue of spares, supplies, and materials.

Secondary Ion Mass Spectrometry SIMS XI

NASA Astrophysics Data System (ADS)

Gillen, G.; Lareau, R.; Bennett, J.; Stevie, F.

2003-05-01

This volume contains 252 contributions presented as plenary, invited and contributed poster and oral presentations at the 11th International Conference on Secondary Ion Mass Spectrometry (SIMS XI) held at the Hilton Hotel, Walt Disney World Village, Orlando, Florida, 7 12 September, 1997. The book covers a diverse range of research, reflecting the rapid growth in advanced semiconductor characterization, ultra shallow depth profiling, TOF-SIMS and the new areas in which SIMS techniques are being used, for example in biological sciences and organic surface characterization. Papers are presented under the following categories: Isotopic SIMS Biological SIMS Semiconductor Characterization Techniques and Applications Ultra Shallow Depth Profiling Depth Profiling Fundamental/Modelling and Diffusion Sputter-Induced Topography Fundamentals of Molecular Desorption Organic Materials Practical TOF-SIMS Polyatomic Primary Ions Materials/Surface Analysis Postionization Instrumentation Geological SIMS Imaging Fundamentals of Sputtering Ion Formation and Cluster Formation Quantitative Analysis Environmental/Particle Characterization Related Techniques These proceedings provide an invaluable source of reference for both newcomers to the field and experienced SIMS users.

Model for Sucker-Rod Pumping Unit Operating Modes Analysis Based on SimMechanics Library

NASA Astrophysics Data System (ADS)

Zyuzev, A. M.; Bubnov, M. V.

2018-01-01

The article provides basic information about the process of a sucker-rod pumping unit (SRPU) model developing by means of SimMechanics library in the MATLAB Simulink environment. The model is designed for the development of a pump productivity optimal management algorithms, sensorless diagnostics of the plunger pump and pumpjack, acquisition of the dynamometer card and determination of a dynamic fluid level in the well, normalization of the faulty unit operation before troubleshooting is performed by staff as well as equilibrium ratio determining by energy indicators and outputting of manual balancing recommendations to achieve optimal power consumption efficiency. Particular attention is given to the application of various blocks from SimMechanics library to take into account the pumpjack construction principal characteristic and to obtain an adequate model. The article explains in depth the developed tools features for collecting and analysis of simulated mechanism data. The conclusions were drawn about practical implementation possibility of the SRPU modelling results and areas for further development of investigation.

RNA 3D Structure Modeling by Combination of Template-Based Method ModeRNA, Template-Free Folding with SimRNA, and Refinement with QRNAS.

PubMed

Piatkowski, Pawel; Kasprzak, Joanna M; Kumar, Deepak; Magnus, Marcin; Chojnowski, Grzegorz; Bujnicki, Janusz M

2016-01-01

RNA encompasses an essential part of all known forms of life. The functions of many RNA molecules are dependent on their ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is laborious and challenging, and therefore, the majority of known RNAs remain structurally uncharacterized. To address this problem, computational structure prediction methods were developed that either utilize information derived from known structures of other RNA molecules (by way of template-based modeling) or attempt to simulate the physical process of RNA structure formation (by way of template-free modeling). All computational methods suffer from various limitations that make theoretical models less reliable than high-resolution experimentally determined structures. This chapter provides a protocol for computational modeling of RNA 3D structure that overcomes major limitations by combining two complementary approaches: template-based modeling that is capable of predicting global architectures based on similarity to other molecules but often fails to predict local unique features, and template-free modeling that can predict the local folding, but is limited to modeling the structure of relatively small molecules. Here, we combine the use of a template-based method ModeRNA with a template-free method SimRNA. ModeRNA requires a sequence alignment of the target RNA sequence to be modeled with a template of the known structure; it generates a model that predicts the structure of a conserved core and provides a starting point for modeling of variable regions. SimRNA can be used to fold small RNAs (<80 nt) without any additional structural information, and to refold parts of models for larger RNAs that have a correctly modeled core. ModeRNA can be either downloaded, compiled and run locally or run through a web interface at http://genesilico.pl/modernaserver/ . SimRNA is currently available to download for local use as a precompiled software package at http://genesilico.pl/software/stand-alone/simrna and as a web server at http://genesilico.pl/SimRNAweb . For model optimization we use QRNAS, available at http://genesilico.pl/qrnas .

Principal component analysis of TOF-SIMS spectra, images and depth profiles: an industrial perspective

NASA Astrophysics Data System (ADS)

Pacholski, Michaeleen L.

2004-06-01

Principal component analysis (PCA) has been successfully applied to time-of-flight secondary ion mass spectrometry (TOF-SIMS) spectra, images and depth profiles. Although SIMS spectral data sets can be small (in comparison to datasets typically discussed in literature from other analytical techniques such as gas or liquid chromatography), each spectrum has thousands of ions resulting in what can be a difficult comparison of samples. Analysis of industrially-derived samples means the identity of most surface species are unknown a priori and samples must be analyzed rapidly to satisfy customer demands. PCA enables rapid assessment of spectral differences (or lack there of) between samples and identification of chemically different areas on sample surfaces for images. Depth profile analysis helps define interfaces and identify low-level components in the system.

Quantitative Surface Analysis of a Binary Drug Mixture—Suppression Effects in the Detection of Sputtered Ions and Post-Ionized Neutrals

NASA Astrophysics Data System (ADS)

Karras, Gabriel; Lockyer, Nicholas P.

2014-05-01

A systematic mass spectrometric study of two of the most common analgesic drugs, paracetamol and ibuprofen, is reported. The drugs were studied by means of secondary ion mass spectrometry (SIMS) and secondary neutral mass spectrometry (SNMS) using laser post-ionization (LPI) both in pure samples and in a two-component mixture. Ion suppression within the two-component system observed in SIMS mode is ameliorated using LPI under room temperature analysis. However, suppression effects are apparent in LPI mode on performing the analysis at cryogenic temperatures, which we attribute to changes in the desorption characteristics of sputtered molecules, which influences the subsequent post-ionization efficiency. This suggests different mechanisms of ion suppression in SIMS and LPI modes.

Sim1 haploinsufficiency impairs melanocortin-mediated anorexia and activation of paraventricular nucleus neurons.

PubMed

Kublaoui, Bassil M; Holder, J Lloyd; Gemelli, Terry; Zinn, Andrew R

2006-10-01

Single-minded 1 (SIM1) is one of only six genes implicated in human monogenic obesity. Haploinsufficiency of this hypothalamic transcription factor is associated with hyperphagic obesity and increased linear growth in both humans and mice. Additionally, Sim1 heterozygous mice show enhanced hyperphagia and obesity in response to a high-fat diet. Thus the phenotype of Sim1 haploinsufficiency is similar to that of agouti yellow (Ay), and melanocortin 4 receptor (Mc4r) knockout mice, both of which are defective in hypothalamic melanocortin signaling. Sim1 and Mc4r are both expressed in the paraventricular nucleus (PVN). Here we report that Sim1 heterozygous mice, which have normal energy expenditure, are hyperphagic despite having elevated hypothalamic proopiomelanocortin (Pomc) expression. In response to the melanocortin agonist melanotan-2 (MTII) they exhibit a blunted suppression of feeding yet increase their energy expenditure normally. They also fail to activate PVN neurons in response to the drug at a dose that induces robust c-Fos expression in a subset of Sim1 PVN neurons in wild-type mice. The resistance to melanocortin signaling in Sim1 heterozygotes is not due to a reduced number of Sim1 neurons in the PVN. Hypothalamic Sim1 gene expression is induced by leptin and MTII treatment. Our results demonstrate that Sim1 heterozygotes are resistant to hypothalamic melanocortin signaling and suggest that Sim1-expressing PVN neurons regulate feeding, but not energy expenditure, in response to melanocortin signaling.

Structures of the TetR-like simocyclinone efflux pump repressor, SimR, and the mechanism of ligand-mediated derepression.

PubMed

Le, Tung B K; Stevenson, Clare E M; Fiedler, Hans-Peter; Maxwell, Anthony; Lawson, David M; Buttner, Mark J

2011-04-22

Simocyclinone D8 (SD8), a potent DNA gyrase inhibitor made by Streptomyces antibioticus, is exported from the producing organism by the SimX efflux pump. The expression of simX is under the control of SimR, a member of the TetR family of transcriptional regulators. SimR represses simX transcription by binding to operators in the intergenic region between simR and simX. Previously, we have shown that the mature antibiotic SD8 or its biosynthetic intermediate, simocyclinone C4, can dissociate SimR from its operators, leading to derepression of simX and export of SD8 from the cell. This provides a mechanism that couples the biosynthesis of the antibiotic to its export. Here, we report the crystal structures of SimR alone and in complex with either SD8 or simocyclinone C4. The ligand-binding pocket is unusual compared to those of other characterized TetR-family transcriptional regulators: the structures show an extensive ligand-binding pocket spanning both monomers in the functional dimeric unit, with the aminocoumarin moiety of SD8 buried in the protein core, while the angucyclic polyketide moiety is partially exposed to bulk solvent. Through comparisons of the structures, we postulate a derepression mechanism for SimR that invokes rigid-body motions of the subunits relative to one another, coupled with a putative locking mechanism to restrict further conformational change. Copyright © 2011 Elsevier Ltd. All rights reserved.

Software for Simulating a Complex Robot

NASA Technical Reports Server (NTRS)

Goza, S. Michael

2003-01-01

RoboSim (Robot Simulation) is a computer program that simulates the poses and motions of the Robonaut a developmental anthropomorphic robot that has a complex system of joints with 43 degrees of freedom and multiple modes of operation and control. RoboSim performs a full kinematic simulation of all degrees of freedom. It also includes interface components that duplicate the functionality of the real Robonaut interface with control software and human operators. Basically, users see no difference between the real Robonaut and the simulation. Consequently, new control algorithms can be tested by computational simulation, without risk to the Robonaut hardware, and without using excessive Robonaut-hardware experimental time, which is always at a premium. Previously developed software incorporated into RoboSim includes Enigma (for graphical displays), OSCAR (for kinematical computations), and NDDS (for communication between the Robonaut and external software). In addition, RoboSim incorporates unique inverse-kinematical algorithms for chains of joints that have fewer than six degrees of freedom (e.g., finger joints). In comparison with the algorithms of OSCAR, these algorithms are more readily adaptable and provide better results when using equivalent sets of data.

Laparoscopic virtual reality and box trainers: is one superior to the other?

PubMed

Munz, Y; Kumar, B D; Moorthy, K; Bann, S; Darzi, A

2004-03-01

Virtual reality (VR) simulators now have the potential to replace traditional methods of laparoscopic training. The aim of this study was to compare the VR simulator with the classical box trainer and determine whether one has advantages over the other. Twenty four novices were tested to determine their baseline laparoscopic skills and then randomized into the following three group: LapSim, box trainer, and no training (control). After 3 weekly training sessions lasting 30-min each, all subjects were reassessed. Assessment included motion analysis and error scores. Nonparametric tests were applied, and p < 0.05 was deemed significant. Both trained groups made significant improvements in all parameters measured ( p < 0.05). Compared to the controls, the box trainer group performed significantly better on most of the parameters, whereas the LapSim group performed significantly better on some parameters. There were no significant differences between the LapSim and box trainer groups. LapSim is effective in teaching skills that are transferable to a real laparoscopic task. However, there appear to be no substantial advantages of one system over the other.

Submicron mass spectrometry imaging of single cells by combined use of mega electron volt time-of-flight secondary ion mass spectrometry and scanning transmission ion microscopy

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

Siketić, Zdravko; Bogdanović Radović, Ivančica; Jakšić, Milko

In order to better understand biochemical processes inside an individual cell, it is important to measure the molecular composition at the submicron level. One of the promising mass spectrometry imaging techniques that may be used to accomplish this is Time-of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS), using MeV energy heavy ions for excitation. MeV ions have the ability to desorb large intact molecules with a yield that is several orders of magnitude higher than conventional SIMS using keV ions. In order to increase the spatial resolution of the MeV TOF-SIMS system, we propose an independent TOF trigger using a STIM (scanningmore » transmission ion microscopy) detector that is placed just behind the thin transmission target. This arrangement is suitable for biological samples in which the STIM detector simultaneously measures the mass distribution in scanned samples. The capability of the MeV TOF-SIMS setup was demonstrated by imaging the chemical composition of CaCo-2 cells.« less

Quantum Monte Carlo calculations of weak transitions in A = 6 – 10 nuclei

DOE PAGES

Pastore, S.; Baroni, A.; Carlson, J.; ...

2018-02-26

{\\it Ab initio} calculations of the Gamow-Teller (GT) matrix elements in themore » $$\\beta$$ decays of $^6$He and $$^{10}$$C and electron captures in $^7$Be are carried out using both variational and Green's function Monte Carlo wave functions obtained from the Argonne $$v_{18}$$ two-nucleon and Illinois-7 three-nucleon interactions, and axial many-body currents derived from either meson-exchange phenomenology or chiral effective field theory. The agreement with experimental data is excellent for the electron captures in $^7$Be, while theory overestimates the $^6$He and $$^{10}$$C data by $$\\sim 2\\%$$ and $$\\sim 10\\%$$, respectively. We show that for these systems correlations in the nuclear wave functions are crucial to explain the data, while many-body currents increase by $$\\sim 2$$--$$3\\%$$ the one-body GT contributions. These findings suggest that the longstanding $$g_A$$-problem, {\\it i.e.}, the systematic overprediction ($$\\sim 20 \\%$$ in $$A\\le 18$$ nuclei) of GT matrix elements in shell-model calculations, may be resolved, at least partially, by correlation effects.« less

TankSIM: A Cryogenic Tank Performance Prediction Program

NASA Technical Reports Server (NTRS)

Bolshinskiy, L. G.; Hedayat, A.; Hastings, L. J.; Moder, J. P.; Schnell, A. R.; Sutherlin, S. G.

2015-01-01

Accurate prediction of the thermodynamic state of the cryogenic propellants in launch vehicle tanks is necessary for mission planning and successful execution. Cryogenic propellant storage and transfer in space environments requires that tank pressure be controlled. The pressure rise rate is determined by the complex interaction of external heat leak, fluid temperature stratification, and interfacial heat and mass transfer. If the required storage duration of a space mission is longer than the period in which the tank pressure reaches its allowable maximum, an appropriate pressure control method must be applied. Therefore, predictions of the pressurization rate and performance of pressure control techniques in cryogenic tanks are required for development of cryogenic fluid long-duration storage technology and planning of future space exploration missions. This paper describes an analytical tool, Tank System Integrated Model (TankSIM), which can be used for modeling pressure control and predicting the behavior of cryogenic propellant for long-term storage for future space missions. It is written in the FORTRAN 90 language and can be compiled with any Visual FORTRAN compiler. A thermodynamic vent system (TVS) is used to achieve tank pressure control. Utilizing TankSIM, the following processes can be modeled: tank self-pressurization, boiloff, ullage venting, and mixing. Details of the TankSIM program and comparisons of its predictions with test data for liquid hydrogen and liquid methane will be presented in the final paper.

Pressure Loss Predictions of the Reactor Simulator Subsystem at NASA GRC

NASA Technical Reports Server (NTRS)

Reid, Terry V.

2015-01-01

Testing of the Fission Power System (FPS) Technology Demonstration Unit (TDU) is being conducted at NASA GRC. The TDU consists of three subsystems: the Reactor Simulator (RxSim), the Stirling Power Conversion Unit (PCU), and the Heat Exchanger Manifold (HXM). An Annular Linear Induction Pump (ALIP) is used to drive the working fluid. A preliminary version of the TDU system (which excludes the PCU for now), is referred to as the RxSim subsystem and was used to conduct flow tests in Vacuum Facility 6 (VF 6). In parallel, a computational model of the RxSim subsystem was created based on the CAD model and was used to predict loop pressure losses over a range of mass flows. This was done to assess the ability of the pump to meet the design intent mass flow demand. Measured data indicates that the pump can produce 2.333 kg/sec of flow, which is enough to supply the RxSim subsystem with a nominal flow of 1.75 kg/sec. Computational predictions indicated that the pump could provide 2.157 kg/sec (using the Spalart-Allmaras turbulence model), and 2.223 kg/sec (using the k-? turbulence model). The computational error of the predictions for the available mass flow is -0.176 kg/sec (with the S-A turbulence model) and -0.110 kg/sec (with the k-epsilon turbulence model) when compared to measured data.

An inversion-based self-calibration for SIMS measurements: Application to H, F, and Cl in apatite

NASA Astrophysics Data System (ADS)

Boyce, J. W.; Eiler, J. M.

2011-12-01

Measurements of volatile abundances in igneous apatites can provide information regarding the abundances and evolution of volatiles in magmas, with applications to terrestrial volcanism and planetary evolution. Secondary ion mass spectrometry (SIMS) measurements can produce accurate and precise measurements of H and other volatiles in many materials including apatite. SIMS standardization generally makes use of empirical linear transfer functions that relate measured ion ratios to independently known concentrations. However, this approach is often limited by the lack of compositionally diverse, well-characterized, homogeneous standards. In general, SIMS calibrations are developed for minor and trace elements, and any two are treated as independent of one another. However, in crystalline materials, additional stoichiometric constraints may apply. In the case of apatite, the sum of concentrations of abundant volatile elements (H, Cl, and F) should closely approach 100% occupancy of their collective structural site. Here we propose and document the efficacy of a method for standardizing SIMS analyses of abundant volatiles in apatites that takes advantage of this stoichiometric constraint. The principle advantage of this method is that it is effectively self-standardizing; i.e., it requires no independently known homogeneous reference standards. We define a system of independent linear equations relating measured ion ratios (H/P, Cl/P, F/P) and unknown calibration slopes. Given sufficient range in the concentrations of the different elements among apatites measured in a single analytical session, solving this system of equations allows for the calibration slope for each element to be determined without standards, using only blank-corrected ion ratios. In the case that a data set of this kind lacks sufficient range in measured compositions of one or more of the relevant ion ratios, one can employ measurements of additional apatites of a variety of compositions to increase the statistical range and make the inversion more accurate and precise. These additional non-standard apatites need only be wide-ranging in composition: They need not be homogenous nor have known H, F, or Cl concentrations. Tests utilizing synthetic data and data generated in the laboratory indicate that this method should yield satisfactory results provided apatites meet the criteria of the model. The inversion method is able to reproduce conventional calibrations to within <2.5%, a level of accuracy comparable to or even better than the uncertainty of the conventional calibration, and one that includes both error in the inversion method as well as any true error in the independently determined values of the standards. Uncertainties in the inversion calibrations range from 0.1-1.7% (2σ), typically an order of magnitude smaller than the uncertainties in conventional calibrations (~4-5% for H2O, 1-19% for F and Cl). However, potential systematic errors stem from the model assumption of 100% occupancy of this site by the measured elements. Use of this method simplifies analysis of H, F, and Cl in apatites by SIMS, and may also be amenable to other stoichiometrically limited substitution groups, including P+As+S+Si+C in apatite, and Zr+Hf+U+Th in non-metamict zircon.

NICeSim: an open-source simulator based on machine learning techniques to support medical research on prenatal and perinatal care decision making.

PubMed

Cerqueira, Fabio Ribeiro; Ferreira, Tiago Geraldo; de Paiva Oliveira, Alcione; Augusto, Douglas Adriano; Krempser, Eduardo; Corrêa Barbosa, Helio José; do Carmo Castro Franceschini, Sylvia; de Freitas, Brunnella Alcantara Chagas; Gomes, Andreia Patricia; Siqueira-Batista, Rodrigo

2014-11-01

This paper describes NICeSim, an open-source simulator that uses machine learning (ML) techniques to aid health professionals to better understand the treatment and prognosis of premature newborns. The application was developed and tested using data collected in a Brazilian hospital. The available data were used to feed an ML pipeline that was designed to create a simulator capable of predicting the outcome (death probability) for newborns admitted to neonatal intensive care units. However, unlike previous scoring systems, our computational tool is not intended to be used at the patients bedside, although it is possible. Our primary goal is to deliver a computational system to aid medical research in understanding the correlation of key variables with the studied outcome so that new standards can be established for future clinical decisions. In the implemented simulation environment, the values of key attributes can be changed using a user-friendly interface, where the impact of each change on the outcome is immediately reported, allowing a quantitative analysis, in addition to a qualitative investigation, and delivering a totally interactive computational tool that facilitates hypothesis construction and testing. Our statistical experiments showed that the resulting model for death prediction could achieve an accuracy of 86.7% and an area under the receiver operating characteristic curve of 0.84 for the positive class. Using this model, three physicians and a neonatal nutritionist performed simulations with key variables correlated with chance of death. The results indicated important tendencies for the effect of each variable and the combination of variables on prognosis. We could also observe values of gestational age and birth weight for which a low Apgar score and the occurrence of respiratory distress syndrome (RDS) could be less or more severe. For instance, we have noticed that for a newborn with 2000 g or more the occurrence of RDS is far less problematic than for neonates weighing less. The significant accuracy demonstrated by our predictive model shows that NICeSim might be used for hypothesis testing to minimize in vivo experiments. We observed that the model delivers predictions that are in very good agreement with the literature, demonstrating that NICeSim might be an important tool for supporting decision making in medical practice. Other very important characteristics of NICeSim are its flexibility and dynamism. NICeSim is flexible because it allows the inclusion and deletion of variables according to the requirements of a particular study. It is also dynamic because it trains a just-in-time model. Therefore, the system is improved as data from new patients become available. Finally, NICeSim can be extended in a cooperative manner because it is an open-source system. Copyright © 2014 Elsevier B.V. All rights reserved.

SIM Configuration Evolution

NASA Technical Reports Server (NTRS)

Aaron, Kim M.

2000-01-01

The Space Interferometry Mission (SIM) is a space-based 10 m baseline Michelson interferometer. Planned for launch in 2005 aboard a Delta III launch vehicle, or equivalent, its primary objective is to measure the positions of stars and other celestial objects with an unprecedented accuracy of 4 micro arc seconds. With such an instrument, tremendous advancement can be expected in our understanding of stellar and galactic dynamics. Using triangulation from opposite sides of the orbit around the sun (i.e. by using parallax) one can measure the distance to any observable object in our galaxy. By directly measuring the orbital wobble of nearby stars, the mass and orbit of planets can be determined over a wide range of parameters. The distribution of velocity within nearby galaxies will be measurable. Observations of these and other objects will improve the calibration of distance estimators by more than an order of magnitude. This will permit a much better determination of the Hubble Constant as well as improving our overall understanding of the evolution of the universe. SIM has undergone several transformations, especially over the past year and a half since the start of Phase A. During this phase of a project, it is desirable to perform system-level trade studies, so the substantial evolution of the design that has occurred is quite appropriate. Part of the trade-off process has addressed two major underlying architectures: SIM Classic; and Son of SIM. The difference between these two architectures is related to the overall arrangement of the optical elements and the associated metrology system. Several different configurations have been developed for each architecture. Each configuration is the result of design choices that are influenced by many competing considerations. Some of the more important aspects will be discussed. The Space Interferometry Mission has some extremely challenging goals: millikelvin thermal stability, nanometer stabilization of optics, picometer measurement of wavefront, and others. In order to meet these goals, a significant amount of technological development is required. Although there has been a program operating for about a decade developing technologies specifically to address the challenges of space-based interferometry, there still remains a tremendous effort to achieve the incredible accuracy required of SIM. The projected viability of some of these areas has influenced design choices during the evolution of the many configurations that have been developed. For instance, the perceived complexity of the IR laser metrology system used to measure and control the positions of key optical elements was the strongest discriminator between the two architectures, and led to a decision to select SOS rather than Classic in early 1998. More recently, an appreciation of the sensitivity to beam-walk within the SOS architecture is forcing a reconsideration of that decision. At the time of submission of this abstract, there is some hope that a full-aperture metrology system may alleviate this issue. In addition to describing the current configuration of SIM, the influence of a few selected areas on the evolution of the configuration will be discussed.

SimSchool: An Opportunity for Using Serious Gaming for Training Teachers in Rural Areas

ERIC Educational Resources Information Center

Tyler-Wood, Tandra; Estes, Mary; Christensen, Rhonda; Knezek, Gerald; Gibson, David

2015-01-01

This article examines the use of simSchool as a training tool for educators working with students with special needs in rural districts. SimSchool is a game that emulates a classroom utilizing a virtual environment. The theory supporting simSchool is explored and current research associated with simSchool is reviewed. The issues surrounding…

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

Chan, James H. H.; Suyu, Sherry H.; Chiueh, Tzihong

Strong gravitationally lensed quasars provide powerful means to study galaxy evolution and cosmology. Current and upcoming imaging surveys will contain thousands of new lensed quasars, augmenting the existing sample by at least two orders of magnitude. To find such lens systems, we built a robot, Chitah, that hunts for lensed quasars by modeling the configuration of the multiple quasar images. Specifically, given an image of an object that might be a lensed quasar, Chitah first disentangles the light from the supposed lens galaxy and the light from the multiple quasar images based on color information. A simple rule is designed to categorize the given object as a potential four-image (quad) or two-image (double) lensed quasar system. The configuration of the identified quasar images is subsequently modeled to classify whether the object is a lensed quasar system. We test the performance of Chitah using simulated lens systems based on the Canada–France–Hawaii Telescope Legacy Survey. For bright quads with large image separations (with Einstein radiusmore » $${r}_{\\mathrm{ein}}\\gt 1\\buildrel{\\prime\\prime}\\over{.} 1$$) simulated using Gaussian point-spread functions, a high true-positive rate (TPR) of $$\\sim 90\\%$$ and a low false-positive rate of $$\\sim 3\\%$$ show that this is a promising approach to search for new lens systems. We obtain high TPR for lens systems with $${r}_{\\mathrm{ein}}\\gtrsim 0\\buildrel{\\prime\\prime}\\over{.} 5$$, so the performance of Chitah is set by the seeing. We further feed a known gravitational lens system, COSMOS 5921+0638, to Chitah, and demonstrate that Chitah is able to classify this real gravitational lens system successfully. Our newly built Chitah is omnivorous and can hunt in any ground-based imaging surveys.« less

Computer simulation of the human respiratory system for educational purposes.

PubMed

Botsis, Taxiarhis; Halkiotis, Stelios-Chris; Kourlaba, Georgia

2004-01-01

The main objective of this study was the development of a computer simulation system for the human respiratory system, in order to educate students of nursing. This approach was based on existing mathematical models and on our own constructed specific functions. For the development of this educational tool the appropriate software packages were used according to the special demands of this process. This system is called ReSim (Respiratory Simulation) and consists of two parts: the first part deals with pulmonary volumes and the second one represents the mechanical behavior of lungs. The target group evaluated ReSim. The outcomes of the evaluation process were positive and helped us realize the system characteristics that needed improvements. Our basic conclusion is that the extended use of such systems supports the educational process and offers new potential for learning.

SimZones: An Organizational Innovation for Simulation Programs and Centers.

PubMed

Roussin, Christopher J; Weinstock, Peter

2017-08-01

The complexity and volume of simulation-based learning programs have increased dramatically over the last decade, presenting several major challenges for those who lead and manage simulation programs and centers. The authors present five major issues affecting the organization of simulation programs: (1) supporting both single- and double-loop learning experiences; (2) managing the training of simulation teaching faculty; (3) optimizing the participant mix, including individuals, professional groups, teams, and other role-players, to ensure learning; (4) balancing in situ, node-based, and center-based simulation delivery; and (5) organizing simulation research and measuring value. They then introduce the SimZones innovation, a system of organization for simulation-based learning, and explain how it can alleviate the problems associated with these five issues.Simulations are divided into four zones (Zones 0-3). Zone 0 simulations include autofeedback exercises typically practiced by solitary learners, often using virtual simulation technology. Zone 1 simulations include hands-on instruction of foundational clinical skills. Zone 2 simulations include acute situational instruction, such as clinical mock codes. Zone 3 simulations involve authentic, native teams of participants and facilitate team and system development.The authors also discuss the translation of debriefing methods from Zone 3 simulations to real patient care settings (Zone 4), and they illustrate how the SimZones approach can enable the development of longitudinal learning systems in both teaching and nonteaching hospitals. The SimZones approach was initially developed in the context of the Boston Children's Hospital Simulator Program, which the authors use to illustrate this innovation in action.

SimPhy: a simulation game to lessen the impact of phytosanitaries on health and the environment--the case of Merja Zerga in Morocco.

PubMed

Ayadi, H; Le Bars, M; Le Grusse, Ph; Mandart, E; Fabre, J; Bouaziz, A; Bord, J P

2014-04-01

Diffuse phytosanitary pollution is a complex phenomenon to manage. Reducing this type of pollution is one of today's key socio-economic and environmental challenges. At the regional level, few approaches enable the actors concerned to implement agricultural management strategies to reduce the use and impact of phytosanitary products. Our research problem focused on the consequences of intensive agriculture and, in particular, how to evaluate the impact of phytosanitary products on human health and the environment. In this article, we present the SimPhy simulation game which places the actors from a given region directly into a situation in which they manage farms whilst under pressure to reduce phytosanitaries (quantity and toxicity). The application focused on the Merja Zerga catchment area in Morocco. The region is dominated by intensive agriculture which is located upstream from a Ramsar-classified wetland area. The SimPhy simulation game is based on a decision support system-type tool. It allows us to anticipate the impact of regulations on farming systems. It also enables us to analyse the consequences of the actors' strategies on farm economies, human health and the quality of ecosystems. Initial results from the SimPhy simulation game enabled the technicians from Agricultural Development Center (CDA) themselves to learn about managing agricultural production systems in a dynamic and interactive fashion. With the simulation game, it was possible to learn about the farmer's ability to adapt to new regulatory constraints, and the involved consequences for toxicity risks for human health and the environment.

Genome-wide analysis of the bHLH gene family in planarians identifies factors required for adult neurogenesis and neuronal regeneration.

PubMed

Cowles, Martis W; Brown, David D R; Nisperos, Sean V; Stanley, Brianna N; Pearson, Bret J; Zayas, Ricardo M

2013-12-01

In contrast to most well-studied model organisms, planarians have a remarkable ability to completely regenerate a functional nervous system from a pluripotent stem cell population. Thus, planarians provide a powerful model to identify genes required for adult neurogenesis in vivo. We analyzed the basic helix-loop-helix (bHLH) family of transcription factors, many of which are crucial for nervous system development and have been implicated in human diseases. However, their potential roles in adult neurogenesis or central nervous system (CNS) function are not well understood. We identified 44 planarian bHLH homologs, determined their patterns of expression in the animal and assessed their functions using RNAi. We found nine bHLHs expressed in stem cells and neurons that are required for CNS regeneration. Our analyses revealed that homologs of coe, hes (hesl-3) and sim label progenitors in intact planarians, and following amputation we observed an enrichment of coe(+) and sim(+) progenitors near the wound site. RNAi knockdown of coe, hesl-3 or sim led to defects in CNS regeneration, including failure of the cephalic ganglia to properly pattern and a loss of expression of distinct neuronal subtype markers. Together, these data indicate that coe, hesl-3 and sim label neural progenitor cells, which serve to generate new neurons in uninjured or regenerating animals. Our study demonstrates that this model will be useful to investigate how stem cells interpret and respond to genetic and environmental cues in the CNS and to examine the role of bHLH transcription factors in adult tissue regeneration.

ICP-MS Workshop

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

Carman, April J.; Eiden, Gregory C.

2014-11-01

This is a short document that explains the materials that will be transmitted to LLNL and DNN HQ regarding the ICP-MS Workshop held at PNNL June 17-19th. The goal of the information is to pass on to LLNL information regarding the planning and preparations for the Workshop at PNNL in preparation of the SIMS workshop at LLNL.

Ablation of Sim1 Neurons Causes Obesity through Hyperphagia and Reduced Energy Expenditure

PubMed Central

Xi, Dong; Gandhi, Nilay; Lai, Meizan; Kublaoui, Bassil M.

2012-01-01

Single-minded 1 (Sim1) is a transcription factor necessary for development of the paraventricular nucleus of the hypothalamus (PVH). This nucleus is a critical regulator of appetite, energy expenditure and body weight. Previously we showed that Sim1+/− mice and conditional postnatal Sim1−/− mice exhibit hyperphagia, obesity, increased linear growth and susceptibility to diet-induced obesity, but no decrease in energy expenditure. Bilateral ablation of the PVH causes obesity due to hyperphagia and reduced energy expenditure. It remains unknown whether Sim1 neurons regulate energy expenditure. In this study, Sim1cre mice were bred to homozygous inducible diphtheria toxin receptor (iDTR) mice to generate mice expressing the simian DTR in Sim1 cells. In these mice, Sim1 neuron ablation was performed by intracerebroventricular (ICV) injection of diphtheria toxin. Compared to controls, mice with Sim1 neuron ablation became obese (with increased fat mass) on a chow diet due to increased food intake and reduced energy expenditure. In post-injection mice, we observed a strong inverse correlation between the degree of obesity and hypothalamic Sim1 expression. The reduction in baseline energy expenditure observed in these mice was accompanied by a reduction in activity. This reduction in activity did not fully account for the reduced energy expenditure as these mice exhibited decreased resting energy expenditure, decreased body temperature, decreased brown adipose tissue temperature, and decreased UCP1 expression suggesting an impairment of thermogenesis. In injected mice, hypothalamic gene expression of Sim1, oxytocin (OXT) and thyrotropin releasing hormone (TRH) was reduced by about 50%. These results demonstrate that Sim1 neurons in adult mice regulate both food intake and energy expenditure. Based on the body of work in the field, feeding regulation by Sim1 neurons likely occurs in both the PVH and medial amygdala, in contrast to energy expenditure regulation by Sim1 neurons, which likely is localized to the PVH. PMID:22558467

Ablation of Sim1 neurons causes obesity through hyperphagia and reduced energy expenditure.

PubMed

Xi, Dong; Gandhi, Nilay; Lai, Meizan; Kublaoui, Bassil M

2012-01-01

Single-minded 1 (Sim1) is a transcription factor necessary for development of the paraventricular nucleus of the hypothalamus (PVH). This nucleus is a critical regulator of appetite, energy expenditure and body weight. Previously we showed that Sim1(+/-) mice and conditional postnatal Sim1(-/-) mice exhibit hyperphagia, obesity, increased linear growth and susceptibility to diet-induced obesity, but no decrease in energy expenditure. Bilateral ablation of the PVH causes obesity due to hyperphagia and reduced energy expenditure. It remains unknown whether Sim1 neurons regulate energy expenditure. In this study, Sim1cre mice were bred to homozygous inducible diphtheria toxin receptor (iDTR) mice to generate mice expressing the simian DTR in Sim1 cells. In these mice, Sim1 neuron ablation was performed by intracerebroventricular (ICV) injection of diphtheria toxin. Compared to controls, mice with Sim1 neuron ablation became obese (with increased fat mass) on a chow diet due to increased food intake and reduced energy expenditure. In post-injection mice, we observed a strong inverse correlation between the degree of obesity and hypothalamic Sim1 expression. The reduction in baseline energy expenditure observed in these mice was accompanied by a reduction in activity. This reduction in activity did not fully account for the reduced energy expenditure as these mice exhibited decreased resting energy expenditure, decreased body temperature, decreased brown adipose tissue temperature, and decreased UCP1 expression suggesting an impairment of thermogenesis. In injected mice, hypothalamic gene expression of Sim1, oxytocin (OXT) and thyrotropin releasing hormone (TRH) was reduced by about 50%. These results demonstrate that Sim1 neurons in adult mice regulate both food intake and energy expenditure. Based on the body of work in the field, feeding regulation by Sim1 neurons likely occurs in both the PVH and medial amygdala, in contrast to energy expenditure regulation by Sim1 neurons, which likely is localized to the PVH.

Microarcsecond Astrometry As A Probe Of Circumstellar Structure

NASA Astrophysics Data System (ADS)

Velusamy, T.; Turyshev, S. G.

1999-12-01

The Space Interferometry Mission (SIM) is a space-based long-baseline optical interferometer for precision astrometry. This mission will open up many areas of astrophysics, via astrometry with unprecedented accuracy. Wide-angle measurements, which include annual parallax, will reach a design accuracy of 4 μ as. Over a narrow field of view the relative accuracy is better, and SIM is expected to achieve an accuracy of 1 μ as. In this mode, SIM will search for planetary companions to nearby stars, by detecting the astrometric `wobble' relative to a nearby (<= 1o) reference star. The expected proper motion accuracy is 2 μ as yr-1, corresponding to a transverse velocity of 10 m s-1 at a distance of 1 kpc. Such an accuracy of the future SIM instrument provides a very useful astrometric tool for probing the circumstellar structure. The motion of the photo center as detected by SIM is not necessarily that of the center of mass. It is expected that unmodelled dynamics of the stellar systems may be a potential source for systematic astrometric errors. In this paper we discuss the possibility of using SIM's precision astrometry not only to detect Keplerian signatures due to the planetary motion around nearby stars, but also to characterize the structure of the planetary and proto-planetary orbits, accretions disks, debris disks, circumstellar material, jets and other types of the mass transfer mechanisms. We evaluate possible astrometric signatures due to different types of dynamical processes (both gravitational, non-gravitational) and characterize the magnitude of the corresponding astrometric signal. We attempt to address the most natural scenario of non-Keplerian motion, caused by an extended structure and complex dynamics of the stellar systems that may produce a detectable wobble in the motion of the optical center of a target star. We examine the use of μ as astrometry, as complementary to high resolution imaging, to detect some of the structures present around stars. This work was performed by the Jet Propulsion Laboratory, California Institute of Technology, under contract with the National Aeronautics and Space Administration.

Evolving virtual creatures and catapults.

PubMed

Chaumont, Nicolas; Egli, Richard; Adami, Christoph

2007-01-01

We present a system that can evolve the morphology and the controller of virtual walking and block-throwing creatures (catapults) using a genetic algorithm. The system is based on Sims' work, implemented as a flexible platform with an off-the-shelf dynamics engine. Experiments aimed at evolving Sims-type walkers resulted in the emergence of various realistic gaits while using fairly simple objective functions. Due to the flexibility of the system, drastically different morphologies and functions evolved with only minor modifications to the system and objective function. For example, various throwing techniques evolved when selecting for catapults that propel a block as far as possible. Among the strategies and morphologies evolved, we find the drop-kick strategy, as well as the systematic invention of the principle behind the wheel, when allowing mutations to the projectile.

Development of a quadrupole-based Secondary-Ion Mass Spectrometry (SIMS) system at Lewis Research Center

NASA Technical Reports Server (NTRS)

Vargas-Aburto, Carlos; Aron, Paul R.; Liff, Dale R.

1990-01-01

The design, construction, and initial use of an ion microprobe to carry out secondary ion mass spectrometry (SIMS) of solid samples is reported. The system is composed of a differentially pumped custom-made UHV (Ultra High Vacuum) chamber, a quadrupole mass spectrometer and a telefocus A-DIDA ion gun with the capability of producing beams of Cesium, as well as inert and reactive gases. The computer control and acquisition of the data were designed and implemented using a personal computer with plug-in boards, and external circuitry built as required to suit the system needs. The software is being developed by using a FORTH-like language. Initial tests aimed at characterizing the system, as well as preliminary surface and depth-profiling studies are presently underway.

A Micro-Grid Simulator Tool (SGridSim) using Effective Node-to-Node Complex Impedance (EN2NCI) Models

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

Udhay Ravishankar; Milos manic

2013-08-01

This paper presents a micro-grid simulator tool useful for implementing and testing multi-agent controllers (SGridSim). As a common engineering practice it is important to have a tool that simplifies the modeling of the salient features of a desired system. In electric micro-grids, these salient features are the voltage and power distributions within the micro-grid. Current simplified electric power grid simulator tools such as PowerWorld, PowerSim, Gridlab, etc, model only the power distribution features of a desired micro-grid. Other power grid simulators such as Simulink, Modelica, etc, use detailed modeling to accommodate the voltage distribution features. This paper presents a SGridSimmore » micro-grid simulator tool that simplifies the modeling of both the voltage and power distribution features in a desired micro-grid. The SGridSim tool accomplishes this simplified modeling by using Effective Node-to-Node Complex Impedance (EN2NCI) models of components that typically make-up a micro-grid. The term EN2NCI models means that the impedance based components of a micro-grid are modeled as single impedances tied between their respective voltage nodes on the micro-grid. Hence the benefit of the presented SGridSim tool are 1) simulation of a micro-grid is performed strictly in the complex-domain; 2) faster simulation of a micro-grid by avoiding the simulation of detailed transients. An example micro-grid model was built using the SGridSim tool and tested to simulate both the voltage and power distribution features with a total absolute relative error of less than 6%.« less

A simulated emergency department for medical students.

PubMed

Johnson, Patricia; Brazil, Victoria; Raymond-Dufresne, Éliane; Nielson, Tracy

2017-08-01

During their training, medical students often undertake a rotation in an emergency department (ED), where they are exposed to a wide variety of patient presentations. Simulation can be an effective teaching strategy to help prepare learners for the realities of the clinical environment. Simulating an ED shift can provide students with the opportunity to perform a range of clinical activities, within their scope of practice, in a supervised and supportive learning environment. Medical students often undertake a rotation in an emergency department CONTEXT: There is limited literature describing the structure, syllabus, feasibility and perceived usefulness of simulating a typical ED for medical student training. We developed a simulated ED (simED) teaching session for medical students at our university. Students were informed of the purpose and learning tasks of the session prior to attendance. At the start of their 2-hour simED shift students were allocated 'patients' by the Triage nurse. At the completion of their shift, students attended a debriefing discussion. Student feedback indicated that they felt that the simED: provided a good opportunity to practise skills and apply theory to practice; was realistic and challenging; highlighted the importance of teamwork; and enabled them to identify skills requiring further practise. Suggestions for improvements included a longer time spent in the simED and the opportunity to see more patients. The simED approach seemed to be well received and perceived by medical students as useful preparation for the ED. An overview of the structure, materials and resources used is provided to assist educators seeking to implement similar ED clinical scenarios in their curriculum. © 2016 John Wiley & Sons Ltd and The Association for the Study of Medical Education.

Analysis of antioxidants in insulation cladding of copper wire: a comparison of different mass spectrometric techniques (ESI-IT, MALDI-RTOF and RTOF-SIMS).

PubMed

Schnöller, Johannes; Pittenauer, Ernst; Hutter, Herbert; Allmaier, Günter

2009-12-01

Commercial copper wire and its polymer insulation cladding was investigated for the presence of three synthetic antioxidants (ADK STAB AO412S, Irganox 1010 and Irganox MD 1024) by three different mass spectrometric techniques including electrospray ionization-ion trap-mass spectrometry (ESI-IT-MS), matrix-assisted laser desorption/ionization reflectron time-of-flight (TOF) mass spectrometry (MALDI-RTOF-MS) and reflectron TOF secondary ion mass spectrometry (RTOF-SIMS). The samples were analyzed either directly without any treatment (RTOF-SIMS) or after a simple liquid/liquid extraction step (ESI-IT-MS, MALDI-RTOF-MS and RTOF-SIMS). Direct analysis of the copper wire itself or of the insulation cladding by RTOF-SIMS allowed the detection of at least two of the three antioxidants but at rather low sensitivity as molecular radical cations and with fairly strong fragmentation (due to the highly energetic ion beam of the primary ion gun). ESI-IT- and MALDI-RTOF-MS-generated abundant protonated and/or cationized molecules (ammoniated or sodiated) from the liquid/liquid extract. Only ESI-IT-MS allowed simultaneous detection of all three analytes in the extract of insulation claddings. The latter two so-called 'soft' desorption/ionization techniques exhibited intense fragmentation only by applying low-energy collision-induced dissociation (CID) tandem MS on a multistage ion trap-instrument and high-energy CID on a tandem TOF-instrument (TOF/RTOF), respectively. Strong differences in the fragmentation behavior of the three analytes could be observed between the different CID spectra obtained from either the IT-instrument (collision energy in the very low eV range) or the TOF/RTOF-instrument (collision energy 20 keV), but both delivered important structural information. Copyright 2009 John Wiley & Sons, Ltd.

Preparation of Flight Operations and IWS Integration of the CELIAS Experiment on the SOHO Spacecraft

NASA Technical Reports Server (NTRS)

Ipavich, Fred

1996-01-01

During this reporting time period, the following activities took place: (1) generation of several versions of the CELIAS (STOF/SEM/CTOF/MTOF/DPU) commissioning timeline for the first 180 days after launch; (2) identification of several problems with the CELIAS portion of the Project Data Base (PDB); (3) attendance of the Science Operations Working Group (SOWG) Meetings (November 1994, February 1995, May 1995) and Flight Operations Review Meeting (July 1995); (4) participation in Flight Operation Simulations SIM 1 (November 14-18, 1994), SIM 2 (May 1-4, 1995) and SIM3 (August 7-11, 1995); and (5) participation in the Ground System Compatibility Test Rehearsal (April 24-28) 1995), GSCT #2 (May 30-June 14, 1995), GSCT #3 (September 12-22 1995), and GSCT #4b (October 30-November 5, 1995).

Continuous monitoring of large civil structures using a digital fiber optic motion sensor system

NASA Astrophysics Data System (ADS)

Hodge, Malcolm H.; Kausel, Theodore C., Jr.

1998-03-01

There is no single attribute which can always predict structural deterioration. Accordingly, we have developed a scheme for monitoring a wide range of incipient deterioration parameters, all based on a single motion sensor concept. In this presentation, we describe how an intrinsically low power- consumption fiber optic harness can be permanently deployed to poll an array of optical sensors. The function and design of these simple, durable, and naturally digital sensors is described, along with the manner in which they have been configured to collect information for changes in the most important structural aspects. The SIMS system is designed to interrogate each sensor up to five-thousand times per second for the life of the structure, and to report sensor data back to a remote computer base for current and long-term analysis, and is directed primarily towards bridges. By suitably modifying the actuation of this very precise motion sensor, SIMS is able to track bridge deck deflection and vibration, expansion joint travel, concrete and rebar corrosion, pothole development, pier scour and tilt. Other sensors will track bolt clamp load, cable tension, and metal fatigue. All of these data are received within microseconds, which means that appropriate computer algorithm manipulations can be carried out to correlate one sensor with other sensors in real time. This internal verification feature automatically enhances confidence in the system's predictive ability and alerts the user to any anomalous behavior.

SU-F-303-12: Implementation of MR-Only Simulation for Brain Cancer: A Virtual Clinical Trial

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

Glide-Hurst, C; Zheng, W; Kim, J

2015-06-15

Purpose: To perform a retrospective virtual clinical trial using an MR-only workflow for a variety of brain cancer cases by incorporating novel imaging sequences, tissue segmentation using phase images, and an innovative synthetic CT (synCT) solution. Methods: Ten patients (16 lesions) were evaluated using a 1.0T MR-SIM including UTE-DIXON imaging (TE = 0.144/3.4/6.9ms). Bone-enhanced images were generated from DIXON-water/fat and inverted UTE. Automated air segmentation was performed using unwrapped UTE phase maps. Segmentation accuracy was assessed by calculating intersection and Dice similarity coefficients (DSC) using CT-SIM as ground truth. SynCTs were generated using voxel-based weighted summation incorporating T2, FLAIR, UTE1,more » and bone-enhanced images. Mean absolute error (MAE) characterized HU differences between synCT and CT-SIM. Dose was recalculated on synCTs; differences were quantified using planar gamma analysis (2%/2 mm dose difference/distance to agreement) at isocenter. Digitally reconstructed radiographs (DRRs) were compared. Results: On average, air maps intersected 80.8 ±5.5% (range: 71.8–88.8%) between MR-SIM and CT-SIM yielding DSCs of 0.78 ± 0.04 (range: 0.70–0.83). Whole-brain MAE between synCT and CT-SIM was 160.7±8.8 HU, with the largest uncertainty arising from bone (MAE = 423.3±33.2 HU). Gamma analysis revealed pass rates of 99.4 ± 0.04% between synCT and CT-SIM for the cohort. Dose volume histogram analysis revealed that synCT tended to yield slightly higher doses. Organs at risk such as the chiasm and optic nerves were most sensitive due to their proximities to air/bone interfaces. DRRs generated via synCT and CT-SIM were within clinical tolerances. Conclusion: Our approach for MR-only simulation for brain cancer treatment planning yielded clinically acceptable results relative to the CT-based benchmark. While slight dose differences were observed, reoptimization of treatment plans and improved image registration can address this limitation. Future work will incorporate automated registration between setup images (cone-beam CT and kilovoltage images) for synCT and CT-SIM. Submitting institution holds research agreements with Philips HealthCare, Best, Netherlands and Varian Medical Systems, Palo Alto, CA. Research partially sponsored via an Internal Mentored Research Grant.« less

The central role of chloride in the metabolic acid-base changes in canine parvoviral enteritis.

PubMed

Burchell, Richard K; Schoeman, Johan P; Leisewitz, Andrew L

2014-04-01

The acid-base disturbances in canine parvoviral (CPV) enteritis are not well described. In addition, the mechanisms causing these perturbations have not been fully elucidated. The purpose of the present study was to assess acid-base changes in puppies suffering from CPV enteritis, using a modified strong ion model (SIM). The hypothesis of the study was that severe acid-base disturbances would be present and that the SIM would provide insights into pathological mechanisms, which have not been fully appreciated by the Henderson-Hasselbalch model. The study analysed retrospective data, obtained from 42 puppies with confirmed CPV enteritis and 10 healthy control dogs. The CPV-enteritis group had been allocated a clinical score, to allow classification of the data according to clinical severity. The effects of changes in free water, chloride, l-lactate, albumin and phosphate were calculated, using a modification of the base excess algorithm. When the data were summated for each patient, and correlated to each individual component, the most important contributor to the metabolic acid-base changes, according to the SIM, was chloride (P<0.001). Severely-affected animals tended to demonstrate hypochloraemic alkalosis, whereas mildly-affected puppies had a hyperchloraemic acidosis (P=0.007). In conclusion, the acid-base disturbances in CPV enteritis are multifactorial and complex, with the SIM providing information in terms of the origin of these changes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Surface components of PM2.5 during clear and hazy days in Shanghai by ToF-SIMS

NASA Astrophysics Data System (ADS)

Huang, Di; Xiu, Guangli; Li, Meng; Hua, Xin; Long, Yitao

2017-01-01

The compositions of atmospheric particles change greatly on hazy days and could threaten human health. In this study, fine mode particles (PM2.5) were collected and divided according to hazy and non-hazy days in Shanghai from December 8th, 2015 to January 12th, 2016. Versatile ToF-SIMS was performed on the samples to reveal chemical information from the surface of PM2.5. Normalized intensities of Na, Mn, K, V, Al, Fe, Ca, Ti, Cl, NOx and ammonia were higher on clear days while peak intensities of detected bromine and sulfur-contained species were much higher on hazy days. Some hazardous species (Pb, Cr, Ni, As, CHS, SO2) and high-mass aromatic hydrocarbon fractions could only be detected by ToF-SIMS from PM2.5 collected on hazy days. Comparison of metallic elements and phthalates implied that haze pollution in Shanghai was mainly the mixing of coal combustion with vehicle emission. In addition, comparison of different haze pollution was also exhibited. Some nitrogen-containing organic compounds were detected only from PM2.5 of December 15th, and ToF-SIMS ion signals of N2H5+, NH4+, CN-, NO2- and NO3- from PM2.5 of December 15th were much more intense, compared with PM2.5 collected on December 25th.

Using a simulation cell for exercise realism.

PubMed

Lerner, Ken

2013-01-01

A simulation cell or SimCell is an effective and flexible tool for control of emergency management exercises. It allows exercise participants to interact, via simulation, with a wide variety of nonplaying organizations and officials. Adapted from military application, the Chemical Stockpile Emergency Preparedness Program (CSEPP) applied, developed, and refined the SimCell concept for emergency management exercises. It has now been incorporated into national exercise guidance through the Homeland Security Exercise and Evaluation Program, and has been used in a wide variety of national, regional, and local exercises. This article reviews development of the SimCell concept in CSEPP, briefly surveys current practice incorporating SimCells in exercise control, and offers practical lessons-learned and tips on using a SimCell to best advantage. Lessons learned include using a SimCell as an exercise-control hub; preparing inject material for exercise controllers as part of the Master Scenario Event List; laying the groundwork for success through exercise player and controller training; developing protocol for SimCell communications; and capturing feedback from SimCell controllers for inclusion in the exercise evaluation reporting process. The SimCell concept is flexible and can be applied to a variety of exercise types and through a variety of methods.

Pressure Loss Predictions of the Reactor Simulator Subsystem at NASA Glenn Research Center

NASA Technical Reports Server (NTRS)

Reid, Terry V.

2016-01-01

Testing of the Fission Power System (FPS) Technology Demonstration Unit (TDU) is being conducted at NASA Glenn Research Center. The TDU consists of three subsystems: the reactor simulator (RxSim), the Stirling Power Conversion Unit (PCU), and the heat exchanger manifold (HXM). An annular linear induction pump (ALIP) is used to drive the working fluid. A preliminary version of the TDU system (which excludes the PCU for now) is referred to as the "RxSim subsystem" and was used to conduct flow tests in Vacuum Facility 6 (VF 6). In parallel, a computational model of the RxSim subsystem was created based on the computer-aided-design (CAD) model and was used to predict loop pressure losses over a range of mass flows. This was done to assess the ability of the pump to meet the design intent mass flow demand. Measured data indicates that the pump can produce 2.333 kg/sec of flow, which is enough to supply the RxSim subsystem with a nominal flow of 1.75 kg/sec. Computational predictions indicated that the pump could provide 2.157 kg/sec (using the Spalart-Allmaras (S?A) turbulence model) and 2.223 kg/sec (using the k- turbulence model). The computational error of the predictions for the available mass flow is ?0.176 kg/sec (with the S-A turbulence model) and -0.110 kg/sec (with the k- turbulence model) when compared to measured data.

Solving Nonlinear Differential Equations in the Engineering Curriculum

ERIC Educational Resources Information Center

Auslander, David M.

1977-01-01

Described is the Dynamic System Simulation Language (SIM) mini-computer system utilized at the University of California, Los Angeles. It is used by engineering students for solving nonlinear differential equations. (SL)

Does training novices to criteria and does rapid acquisition of skills on laparoscopic simulators have predictive validity or are we just playing video games?

PubMed

Hogle, Nancy J; Widmann, Warren D; Ude, Aku O; Hardy, Mark A; Fowler, Dennis L

2008-01-01

To determine whether LapSim training (version 3.0; Surgical Science Ltd, Göteborg, Sweden) to criteria for novice PGY1 surgical residents had predictive validity for improvement in the performance of laparoscopic cholecystectomy. In all, 21 PGY1 residents performed laparoscopic cholecystectomies in pigs after minimal training; their performance was evaluated by skilled laparoscopic surgeons using the validated tool GOALS (global operative assessment of laparoscopic operative skills: depth perception, bimanual dexterity, efficiency, tissue handling, and overall competence). From the group, 10 residents trained to competency on the LapSim Basic Skills Programs (camera navigation, instrument navigation, coordination, grasping, lifting and grasping, cutting, and clip applying). All 21 PGY1 residents again performed laparoscopic cholecystectomies on pigs; their performance was again evaluated by skilled laparoscopic surgeons using GOALS. Additionally, we studied the rate of learning to determine whether the slow or fast learners on the LapSim performed equivalently when performing actual cholecystectomies in pigs. Finally, 6 categorical residents were tracked, and their clinical performance on all of the laparoscopic cholecystectomies in which they were "surgeon, junior" was prospectively evaluated using the GOALS criteria. We found a statistical improvement of depth perception in the operative performance of cholecystectomies in pigs in the group trained on the LapSim. In the other 4 domains, a trend toward improvement was observed. No correlation between being a fast learner and the ultimate skill was demonstrated in the clinical performance of laparoscopic cholecystectomies. We did find that the fast learners on LapSim all were past or current video game players ("gamers"); however, that background did not translate into better clinical performance. Using current criteria, we doubt that the time and effort spent training novice PGY1 Surgical Residents on the basic LapSim training programs is justified, as such training to competence lacks predictive validity in most domains of the GOALS program. We are investigating 2 other approaches: more difficult training exercises using the LapSim system and an entirely different approach using haptic technology (ProMis; Haptica Ltd., Ireland), which uses real instruments, with training on realistic 3-dimensional models with real rather than simulated cutting, sewing, and dissection. Although experienced video gamers achieve competency faster than nongamers on LapSim programs, that skill set does not translate into improved clinical performance.

The Global Streamflow Indices and Metadata archive (G-SIM): A compilation of global streamflow time series indices and meta-data

NASA Astrophysics Data System (ADS)

Do, Hong; Gudmundsson, Lukas; Leonard, Michael; Westra, Seth; Senerivatne, Sonia

2017-04-01

In-situ observations of daily streamflow with global coverage are a crucial asset for understanding large-scale freshwater resources which are an essential component of the Earth system and a prerequisite for societal development. Here we present the Global Streamflow Indices and Metadata archive (G-SIM), a collection indices derived from more than 20,000 daily streamflow time series across the globe. These indices are designed to support global assessments of change in wet and dry extremes, and have been compiled from 12 free-to-access online databases (seven national databases and five international collections). The G-SIM archive also includes significant metadata to help support detailed understanding of streamflow dynamics, with the inclusion of drainage area shapefile and many essential catchment properties such as land cover type, soil and topographic characteristics. The automated procedure in data handling and quality control of the project makes G-SIM a reproducible, extendible archive and can be utilised for many purposes in large-scale hydrology. Some potential applications include the identification of observational trends in hydrological extremes, the assessment of climate change impacts on streamflow regimes, and the validation of global hydrological models.

Model Comparison in Subsurface Science: The DECOVALEX and Sim-SEQ Initiatives (Invited)

NASA Astrophysics Data System (ADS)

Birkholzer, J. T.; Mukhopadhyay, S.; Rutqvist, J.; Tsang, C.

2013-12-01

Building predictive model for flow and transport processes in the subsurface is a challenging task, even more so if these processes are coupled to geomechanical and/or geochemical effects. Modelers must take into consideration a multiplicity of length scales, a wide range of time scales, the coupling between processes, different model components, and the spatial variability in the value of most model input parameters (and often limited knowledge about them). Consequently, modelers have to make choices while developing their conceptual models. Such model choices may cause a wide range in the predictions made by different models and different modeling groups, even if each of the underlying simulators has been perfectly verified against appropriate benchmarks. In other words, the modeling activity itself is prone to uncertainty and bias. This uncertainty, referred to here as model selection uncertainty, forms one of the greatest sources of uncertainty for predictive modeling. In this paper, we discuss two examples of model intercomparison exercises that are currently undertaken to better understand model selection uncertainty, elucidate system behavior, inform needs for data collection and better physics parameterizations, and enhance community understanding of capabilities. The first example is the international DECOVALEX project, which was launched in 1992 by a group of countries dealing with modeling issues related to geologic disposal of radioactive waste. DECOVALEX is an acronym for DEvelopment of COupled THM models and their VALidation against Experiments. To date, the project has progressed successfully through five stages, each of which featuring a small number of test cases for model comparison related to coupled thermo-hydro-mechanical (THM) processes in geologic systems. The test cases are proposed and developed by the organizations participating in DECOVALEX; they typically involve results from major field and laboratory experiments. Over the past decades, the DECOVALEX project has played a major role in improving our understanding of coupled THM processes in fractured rock and buffer/backfill materials, a subject of importance to performance assessment of a radioactive waste geologic repository. The second example is the Sim-SEQ project, a relatively recent model comparison initiative addressing multi-phase processes relevant in geologic carbon sequestration. Like DECOVALEX, Sim-SEQ is not about benchmarking, but rather about evaluating model building efforts in a broad and comprehensive sense. In Sim-SEQ, sixteen international modeling teams are building their own models for a specific carbon sequestration site referred to as the Sim-SEQ Study site (the S-3 site). The S-3 site is patterned after the ongoing SECARB Phase III Early Test site in southwestern Mississippi, where CO2 is injected into a fluvial sandstone unit with high vertical and lateral heterogeneity. The complex geology of the S-3 site, its location in the water leg of a CO2-EOR field with a strong water drive, and the presence of methane in the reservoir brine make this a challenging task, requiring the modelers to use their best judgment in making a large number of choices about how to model various processes and properties of the system.

Reconstructing Holocene climate using a climate model: Model strategy and preliminary results

NASA Astrophysics Data System (ADS)

Haberkorn, K.; Blender, R.; Lunkeit, F.; Fraedrich, K.

2009-04-01

An Earth system model of intermediate complexity (Planet Simulator; PlaSim) is used to reconstruct Holocene climate based on proxy data. The Planet Simulator is a user friendly general circulation model (GCM) suitable for palaeoclimate research. Its easy handling and the modular structure allow for fast and problem dependent simulations. The spectral model is based on the moist primitive equations conserving momentum, mass, energy and moisture. Besides the atmospheric part, a mixed layer-ocean with sea ice and a land surface with biosphere are included. The present-day climate of PlaSim, based on an AMIP II control-run (T21/10L resolution), shows reasonable agreement with ERA-40 reanalysis data. Combining PlaSim with a socio-technological model (GLUES; DFG priority project INTERDYNAMIK) provides improved knowledge on the shift from hunting-gathering to agropastoral subsistence societies. This is achieved by a data assimilation approach, incorporating proxy time series into PlaSim to initialize palaeoclimate simulations during the Holocene. For this, the following strategy is applied: The sensitivities of the terrestrial PlaSim climate are determined with respect to sea surface temperature (SST) anomalies. Here, the focus is the impact of regionally varying SST both in the tropics and the Northern Hemisphere mid-latitudes. The inverse of these sensitivities is used to determine the SST conditions necessary for the nudging of land and coastal proxy climates. Preliminary results indicate the potential, the uncertainty and the limitations of the method.

Single Cell Profiling using Ionic Liquid Matrix-Enhanced Secondary Ion Mass Spectrometry for Neuronal Cell Type Differentiation

PubMed Central

Do, Thanh D.; Comi, Troy J.; Dunham, Sage J. B.; Rubakhin, Stanislav S.; Sweedler, Jonathan V.

2017-01-01

A high-throughput single cell profiling method has been developed for matrix-enhanced secondary ion mass spectrometry (ME-SIMS) to investigate the lipid profiles of neuronal cells. Populations of cells are dispersed onto the substrate, their locations determined using optical microscopy, and the cell locations used to guide the acquisition of SIMS spectra from the cells. Up to 2,000 cells can be assayed in one experiment at a rate of 6 s per cell. Multiple saturated and unsaturated phosphatidylcholines (PCs) and their fragments are detected and verified with tandem mass spectrometry from individual cells when ionic liquids are employed as a matrix. Optically guided single cell profiling with ME-SIMS is suitable for a range of cell sizes, from Aplysia californica neurons larger than 75 μm to 7-μm rat cerebellar neurons. ME-SIMS analysis followed by t-distributed stochastic neighbor embedding of peaks in the lipid molecular mass range (m/z 700–850) distinguishes several cell types from the rat central nervous system, largely based on the relative proportions of the four dominant lipids, PC(32:0), PC(34:1), PC(36:1), and PC(38:5). Furthermore, subpopulations within each cell type are tentatively classified consistent with their endogenous lipid ratios. The results illustrate the efficacy of a new approach to classify single cell populations and subpopulations using SIMS profiling of lipid and metabolite contents. These methods are broadly applicable for high throughput single cell chemical analyses. PMID:28194949

SIMS prototype system 4 - performance test report

NASA Technical Reports Server (NTRS)

1978-01-01

A self-contained, preassembled air type solar system, designed for installation remote from the dwelling, to provide space heating and hot water was evaluated. Data analysis is included which documents the system performance and verifies its suitability for field installation.

Real-time inverse kinematics and inverse dynamics for lower limb applications using OpenSim

PubMed Central

Modenese, L.; Lloyd, D.G.

2017-01-01

Real-time estimation of joint angles and moments can be used for rapid evaluation in clinical, sport, and rehabilitation contexts. However, real-time calculation of kinematics and kinetics is currently based on approximate solutions or generic anatomical models. We present a real-time system based on OpenSim solving inverse kinematics and dynamics without simplifications at 2000 frame per seconds with less than 31.5ms of delay. We describe the software architecture, sensitivity analyses to minimise delays and errors, and compare offline and real-time results. This system has the potential to strongly impact current rehabilitation practices enabling the use of personalised musculoskeletal models in real-time. PMID:27723992

Visualising interacting binaries in 3D

NASA Astrophysics Data System (ADS)

Hynes, R. I.

2002-01-01

I have developed a code which allows images to be produced of a variety of interacting binaries for any system parameters. The resulting images are not only helpful in visualising the geometry of a given system but are also helpful in talks and educational work. I would like to acknowledge financial support from the Leverhulme Trust, and to thank Dan Rolfe for many discussions on how to represent interacting binaries and the users of BinSim who have provided valuable testing and feedback. BinSim would not have been possible without the efforts of Brian Paul and others responsible for the Mesa 3-D graphics library -- Mesa 3-D graphics .

Real-time inverse kinematics and inverse dynamics for lower limb applications using OpenSim.

PubMed

Pizzolato, C; Reggiani, M; Modenese, L; Lloyd, D G

2017-03-01

Real-time estimation of joint angles and moments can be used for rapid evaluation in clinical, sport, and rehabilitation contexts. However, real-time calculation of kinematics and kinetics is currently based on approximate solutions or generic anatomical models. We present a real-time system based on OpenSim solving inverse kinematics and dynamics without simplifications at 2000 frame per seconds with less than 31.5 ms of delay. We describe the software architecture, sensitivity analyses to minimise delays and errors, and compare offline and real-time results. This system has the potential to strongly impact current rehabilitation practices enabling the use of personalised musculoskeletal models in real-time.

Development Towards a Space Qualified Laser Stabilization System in Support of Space-Based Optical Interferometers

NASA Technical Reports Server (NTRS)

Seidel, David J.; Dubovitsky, Serge

2000-01-01

We report on the development, functional performance and space-qualification status of a laser stabilization system supporting a space-based metrology source used to measure changes in optical path lengths in space-based stellar interferometers. The Space Interferometry Mission (SIM) and Deep Space 3 (DS-3) are two missions currently funded by the National Aeronautics and Space Administration (NASA) that are space-based optical interferometers. In order to properly recombine the starlight received at each telescope of the interferometer it is necessary to perform high resolution laser metrology to stabilize the interferometer. A potentially significant error source in performing high resolution metrology length measurements is the potential for fluctuations in the laser gauge itself. If the laser frequency or wavelength is changing over time it will be misinterpreted as a length change in one of the legs of the interferometer. An analysis of the frequency stability requirement for SIM resulted in a fractional frequency stability requirement of square root (S(sub y)(f)) = <2 x 10(exp -12)/square root(Hz) at Fourier frequencies between 10 Hz and 1000 Hz. The DS-3 mission stability requirement is further increased to square root (S(sub y)(f)) = <5 x 10(exp -14)/Square root(Hz) at Fourier frequencies between 0.2 Hz and 10 kHz with a goal of extending the low frequency range to 0.05 Hz. The free running performance of the Lightwave Electronics NPRO lasers, which are the baseline laser for both SIM and DS-3 vary in stability and we have measured them to perform as follows (9 x l0(exp -11)/ f(Hz))(Hz)/square root(Hz)) = <( square root (S(sub y)(f)) = <(1.3 x l0(exp -8)/ f(Hz))/Square root(Hz). In order to improve the frequency stability of the laser we stabilize the laser to a high finesse optical cavity by locking the optical frequency of the laser to one of the transmission modes of the cavity. At JPL we have built a prototype space-qualifiable system meeting the stability requirements of SIM, which has been delivered to one of the SIM testbeds. We have also started on the development of a system to meet the stability needs of DS-3.

Sample processing, protocol, and statistical analysis of the time-of-flight secondary ion mass spectrometry (ToF-SIMS) of protein, cell, and tissue samples.

PubMed

Barreto, Goncalo; Soininen, Antti; Sillat, Tarvo; Konttinen, Yrjö T; Kaivosoja, Emilia

2014-01-01

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is increasingly being used in analysis of biological samples. For example, it has been applied to distinguish healthy and osteoarthritic human cartilage. This chapter discusses ToF-SIMS principle and instrumentation including the three modes of analysis in ToF-SIMS. ToF-SIMS sets certain requirements for the samples to be analyzed; for example, the samples have to be vacuum compatible. Accordingly, sample processing steps for different biological samples, i.e., proteins, cells, frozen and paraffin-embedded tissues and extracellular matrix for the ToF-SIMS are presented. Multivariate analysis of the ToF-SIMS data and the necessary data preprocessing steps (peak selection, data normalization, mean-centering, and scaling and transformation) are discussed in this chapter.

Rapid discrimination of the causal agents of urinary tract infection using ToF-SIMS with chemometric cluster analysis

NASA Astrophysics Data System (ADS)

Fletcher, John S.; Henderson, Alexander; Jarvis, Roger M.; Lockyer, Nicholas P.; Vickerman, John C.; Goodacre, Royston

2006-07-01

Advances in time of flight secondary ion mass spectrometry (ToF-SIMS) have enabled this technique to become a powerful tool for the analysis of biological samples. Such samples are often very complex and as a result full interpretation of the acquired data can be extremely difficult. To simplify the interpretation of these information rich data, the use of chemometric techniques is becoming widespread in the ToF-SIMS community. Here we discuss the application of principal components-discriminant function analysis (PC-DFA) to the separation and classification of a number of bacterial samples that are known to be major causal agents of urinary tract infection. A large data set has been generated using three biological replicates of each isolate and three machine replicates were acquired from each biological replicate. Ordination plots generated using the PC-DFA are presented demonstrating strain level discrimination of the bacteria. The results are discussed in terms of biological differences between certain species and with reference to FT-IR, Raman spectroscopy and pyrolysis mass spectrometric studies of similar samples.

Gamma-Ray Bursts and Cosmology

NASA Technical Reports Server (NTRS)

Norris, Jay P.

2003-01-01

The unrivalled, extreme luminosities of gamma-ray bursts (GRBs) make them the favored beacons for sampling the high redshift Universe. To employ GRBs to study the cosmic terrain -- e.g., star and galaxy formation history -- GRB luminosities must be calibrated, and the luminosity function versus redshift must be measured or inferred. Several nascent relationships between gamma-ray temporal or spectral indicators and luminosity or total energy have been reported. These measures promise to further our understanding of GRBs once the connections between the luminosity indicators and GRB jets and emission mechanisms are better elucidated. The current distribution of 33 redshifts determined from host galaxies and afterglows peaks near z $\\sim$ 1, whereas for the full BATSE sample of long bursts, the lag-luminosity relation predicts a broad peak z $\\sim$ 1--4 with a tail to z $\\sim$ 20, in rough agreement with theoretical models based on star formation considerations. For some GRB subclasses and apparently related phenomena -- short bursts, long-lag bursts, and X-ray flashes -- the present information on their redshift distributions is sparse or entirely lacking, and progress is expected in Swift era when prompt alerts become numerous.

Improving Secondary Ion Mass Spectrometry Image Quality with Image Fusion

NASA Astrophysics Data System (ADS)

Tarolli, Jay G.; Jackson, Lauren M.; Winograd, Nicholas

2014-12-01

The spatial resolution of chemical images acquired with cluster secondary ion mass spectrometry (SIMS) is limited not only by the size of the probe utilized to create the images but also by detection sensitivity. As the probe size is reduced to below 1 μm, for example, a low signal in each pixel limits lateral resolution because of counting statistics considerations. Although it can be useful to implement numerical methods to mitigate this problem, here we investigate the use of image fusion to combine information from scanning electron microscope (SEM) data with chemically resolved SIMS images. The advantage of this approach is that the higher intensity and, hence, spatial resolution of the electron images can help to improve the quality of the SIMS images without sacrificing chemical specificity. Using a pan-sharpening algorithm, the method is illustrated using synthetic data, experimental data acquired from a metallic grid sample, and experimental data acquired from a lawn of algae cells. The results show that up to an order of magnitude increase in spatial resolution is possible to achieve. A cross-correlation metric is utilized for evaluating the reliability of the procedure.

Purchase and Installation of NanoSIMS 50

NASA Technical Reports Server (NTRS)

Walker, Robert M.

2001-01-01

Although this is a final report on NASA grant number NAG5-8729 we wish to state at the outset that it was mistakenly written as a two-year grant instead of a three-year grant as should have been done. The grant was made for the purpose of purchasing and installing a novel ion microprobe initially called the NanoSIMS 50 and now called the NanoSIMS. The total cost to NASA for purchasing the instrument and refurbishing a laboratory to house it was $1.1 M, split into three installments of $400 (FY 1999), $350K (FY2000), and $350K (FY-2001). We received the first installment in full and $335K in FY2000 for the second installment. The final $350K necessary to complete the purchase and installation was expected by us in the spring of 2001. However, we were recently informed that no more money can be transferred on this grant since it was originally written as a two-year grant. Therefore, we are closing out the current grant and simultaneously writing a new proposal to obtain the final $350K needed to complete the purchase.

Approximate Bayesian Computation by Subset Simulation using hierarchical state-space models

NASA Astrophysics Data System (ADS)

Vakilzadeh, Majid K.; Huang, Yong; Beck, James L.; Abrahamsson, Thomas

2017-02-01

A new multi-level Markov Chain Monte Carlo algorithm for Approximate Bayesian Computation, ABC-SubSim, has recently appeared that exploits the Subset Simulation method for efficient rare-event simulation. ABC-SubSim adaptively creates a nested decreasing sequence of data-approximating regions in the output space that correspond to increasingly closer approximations of the observed output vector in this output space. At each level, multiple samples of the model parameter vector are generated by a component-wise Metropolis algorithm so that the predicted output corresponding to each parameter value falls in the current data-approximating region. Theoretically, if continued to the limit, the sequence of data-approximating regions would converge on to the observed output vector and the approximate posterior distributions, which are conditional on the data-approximation region, would become exact, but this is not practically feasible. In this paper we study the performance of the ABC-SubSim algorithm for Bayesian updating of the parameters of dynamical systems using a general hierarchical state-space model. We note that the ABC methodology gives an approximate posterior distribution that actually corresponds to an exact posterior where a uniformly distributed combined measurement and modeling error is added. We also note that ABC algorithms have a problem with learning the uncertain error variances in a stochastic state-space model and so we treat them as nuisance parameters and analytically integrate them out of the posterior distribution. In addition, the statistical efficiency of the original ABC-SubSim algorithm is improved by developing a novel strategy to regulate the proposal variance for the component-wise Metropolis algorithm at each level. We demonstrate that Self-regulated ABC-SubSim is well suited for Bayesian system identification by first applying it successfully to model updating of a two degree-of-freedom linear structure for three cases: globally, locally and un-identifiable model classes, and then to model updating of a two degree-of-freedom nonlinear structure with Duffing nonlinearities in its interstory force-deflection relationship.

Cosensitized Porphyrin System for High-Performance Solar Cells with TOF-SIMS Analysis.

PubMed

Wu, Wenjun; Xiang, Huaide; Fan, Wei; Wang, Jinglin; Wang, Haifeng; Hua, Xin; Wang, Zhaohui; Long, Yitao; Tian, He; Zhu, Wei-Hong

2017-05-17

To date, development of organic sensitizers has been predominately focused on light harvesting, highest occupied molecular orbital and lowest unoccupied molecular orbital energy levels, and the electron transferring process. In contrast, their adsorption mode as well as the dynamic loading behavior onto nanoporous TiO 2 is rarely considered. Herein, we have employed the time-of-flight secondary ion mass spectrometry (TOF-SIMS) to gain insight into the competitive dye adsorption mode and kinetics in the cosensitized porphyrin system. Using novel porphyrin dye FW-1 and D-A-π-A featured dye WS-5, the different bond-breaking mode in TOF-SIMS and dynamic dye-loading amount during the coadsorption process are well-compared with two different anchoring groups, such as benzoic acid and cyanoacrylic acid. With the bombardment mode in TOF-SIMS spectra, we have speculated that the cyano group grafts onto nanoporous TiO 2 as tridentate binding for the common anchoring unit of cyanoacrylic acid and confirmed it through extensive first-principles density functional theory calculation by anchoring either the carboxyl or cyano group, which shows that the cyano group can efficiently participate in the adsorption of the WS-5 molecule onto the TiO 2 nanocrystal. The grafting reinforcement interaction between the cyano group and TiO 2 in WS-5 can well-explain the rapid adsorption characteristics. A strong coordinate bond between the lone pair of electrons on the nitrogen or oxygen atom and the Lewis acid sites of TiO 2 can increase electron injection efficiencies with respect to those from the bond between the benzoic acid group and the Brønsted acid sites of the TiO 2 surface. Upon optimization of the coadsorption process with dye WS-5, the photoelectric conversion efficiency based on porphyrin dye FW-1 is increased from 6.14 to 9.72%. The study on the adsorption dynamics of organic sensitizers with TOF-SIMS analysis might provide a new venue for improvement of cosensitized solar cells.

A Cluster-Randomized Controlled Trial of a Simplified Multifaceted Management Program for Individuals at High Cardiovascular Risk (SimCard Trial) in Rural Tibet, China and Haryana, India

PubMed Central

Tian, Maoyi; Ajay, Vamadevan S.; Dunzhu, Danzeng; Hameed, Safraj S.; Li, Xian; Liu, Zhong; Li, Cong; Chen, Hao; Cho, KaWing; Li, Ruilai; Zhao, Xingshan; Jindal, Devraj; Rawal, Ishita; Ali, Mohammed K.; Peterson, Eric D.; Ji, Jiachao; Amarchand, Ritvik; Krishnan, Anand; Tandon, Nikhil; Xu, Li-Qun; Wu, Yangfeng; Prabhakaran, Dorairaj; Yan, Lijing L.

2015-01-01

Background In rural areas in China and India, cardiovascular disease burden is high but economic and healthcare resources are limited. This study aims to develop and evaluate a simplified cardiovascular management program (SimCard) delivered by community health workers (CHWs) with the aid of a smartphone-based electronic decision support system. Methods and Results The SimCard study was a yearlong cluster-randomized controlled trial conducted in 47 villages (27 in China and 20 in India). 2,086 ‘high cardiovascular risk’ individuals (aged 40 years or older with self-reported history of coronary heart disease, stroke, diabetes, and/or measured systolic blood pressure ≥160 mmHg) were recruited. Participants in the intervention villages were managed by CHWs through an Android-powered “app” on a monthly basis focusing on two medication use and two lifestyle modifications. Compared with the control group, the intervention group had a 25.5% (P<0.001) higher net increase in the primary outcome of the proportion of patient-reported anti-hypertensive medication use pre-and-post intervention. There were also significant differences in certain secondary outcomes: aspirin use (net difference 17.1%, P<0.001) and systolic blood pressure (−2.7 mmHg, P=0.04). However, no significant changes were observed in the lifestyle factors. The intervention was culturally tailored and country-specific results revealed important differences between the regions. Conclusions The results indicate that the simplified cardiovascular management program improved quality of primary care and clinical outcomes in resource-poor settings in China and India. Larger trials in more places are needed to ascertain potential impacts on mortality and morbidity outcomes. Clinical Trial Registration Information clinicaltrials.gov. Identifier: NCT01503814. PMID:26187183

Conceptual design of initial opacity experiments on the national ignition facility

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

Heeter, R.  F.; Bailey, J.  E.; Craxton, R.  S.

Accurate models of X-ray absorption and re-emission in partly stripped ions are necessary to calculate the structure of stars, the performance of hohlraums for inertial confinement fusion and many other systems in high-energy-density plasma physics. Despite theoretical progress, a persistent discrepancy exists with recent experiments at the Sandia Z facility studying iron in conditions characteristic of the solar radiative–convective transition region. The increased iron opacity measured at Z could help resolve a longstanding issue with the standard solar model, but requires a radical departure for opacity theory. To replicate the Z measurements, an opacity experiment has been designed for the National Facility (NIF). The design uses established techniques scaled to NIF. A laser-heated hohlraum will produce X-ray-heated uniform iron plasmas in local thermodynamic equilibrium (LTE) at temperaturesmore » $${\\geqslant}150$$ eV and electron densities$${\\geqslant}7\\times 10^{21}~\\text{cm}^{-3}$$. The iron will be probed using continuum X-rays emitted in a$${\\sim}200$$ ps,$${\\sim}200~\\unicode[STIX]{x03BC}\\text{m}$$diameter source from a 2 mm diameter polystyrene (CH) capsule implosion. In this design,$2/3$$of the NIF beams deliver 500 kJ to the$${\\sim}6$$ mm diameter hohlraum, and the remaining$$1/3$directly drive the CH capsule with 200 kJ. Calculations indicate this capsule backlighter should outshine the iron sample, delivering a point-projection transmission opacity measurement to a time-integrated X-ray spectrometer viewing down the hohlraum axis. Preliminary experiments to develop the backlighter and hohlraum are underway, informing simulated measurements to guide the final design.« less

MOtoNMS: A MATLAB toolbox to process motion data for neuromusculoskeletal modeling and simulation.

PubMed

Mantoan, Alice; Pizzolato, Claudio; Sartori, Massimo; Sawacha, Zimi; Cobelli, Claudio; Reggiani, Monica

2015-01-01

Neuromusculoskeletal modeling and simulation enable investigation of the neuromusculoskeletal system and its role in human movement dynamics. These methods are progressively introduced into daily clinical practice. However, a major factor limiting this translation is the lack of robust tools for the pre-processing of experimental movement data for their use in neuromusculoskeletal modeling software. This paper presents MOtoNMS (matlab MOtion data elaboration TOolbox for NeuroMusculoSkeletal applications), a toolbox freely available to the community, that aims to fill this lack. MOtoNMS processes experimental data from different motion analysis devices and generates input data for neuromusculoskeletal modeling and simulation software, such as OpenSim and CEINMS (Calibrated EMG-Informed NMS Modelling Toolbox). MOtoNMS implements commonly required processing steps and its generic architecture simplifies the integration of new user-defined processing components. MOtoNMS allows users to setup their laboratory configurations and processing procedures through user-friendly graphical interfaces, without requiring advanced computer skills. Finally, configuration choices can be stored enabling the full reproduction of the processing steps. MOtoNMS is released under GNU General Public License and it is available at the SimTK website and from the GitHub repository. Motion data collected at four institutions demonstrate that, despite differences in laboratory instrumentation and procedures, MOtoNMS succeeds in processing data and producing consistent inputs for OpenSim and CEINMS. MOtoNMS fills the gap between motion analysis and neuromusculoskeletal modeling and simulation. Its support to several devices, a complete implementation of the pre-processing procedures, its simple extensibility, the available user interfaces, and its free availability can boost the translation of neuromusculoskeletal methods in daily and clinical practice.

Complementary Imaging of Silver Nanoparticle Interactions with Green Algae: Dark-Field Microscopy, Electron Microscopy, and Nanoscale Secondary Ion Mass Spectrometry.

PubMed

Sekine, Ryo; Moore, Katie L; Matzke, Marianne; Vallotton, Pascal; Jiang, Haibo; Hughes, Gareth M; Kirby, Jason K; Donner, Erica; Grovenor, Chris R M; Svendsen, Claus; Lombi, Enzo

2017-11-28

Increasing consumer use of engineered nanomaterials has led to significantly increased efforts to understand their potential impact on the environment and living organisms. Currently, no individual technique can provide all the necessary information such as their size, distribution, and chemistry in complex biological systems. Consequently, there is a need to develop complementary instrumental imaging approaches that provide enhanced understanding of these "bio-nano" interactions to overcome the limitations of individual techniques. Here we used a multimodal imaging approach incorporating dark-field light microscopy, high-resolution electron microscopy, and nanoscale secondary ion mass spectrometry (NanoSIMS). The aim was to gain insight into the bio-nano interactions of surface-functionalized silver nanoparticles (Ag-NPs) with the green algae Raphidocelis subcapitata, by combining the fidelity, spatial resolution, and elemental identification offered by the three techniques, respectively. Each technique revealed that Ag-NPs interact with the green algae with a dependence on the size (10 nm vs 60 nm) and surface functionality (tannic acid vs branched polyethylenimine, bPEI) of the NPs. Dark-field light microscopy revealed the presence of strong light scatterers on the algal cell surface, and SEM imaging confirmed their nanoparticulate nature and localization at nanoscale resolution. NanoSIMS imaging confirmed their chemical identity as Ag, with the majority of signal concentrated at the cell surface. Furthermore, SEM and NanoSIMS provided evidence of 10 nm bPEI Ag-NP internalization at higher concentrations (40 μg/L), correlating with the highest toxicity observed from these NPs. This multimodal approach thus demonstrated an effective approach to complement dose-response studies in nano-(eco)-toxicological investigations.

Fundamental Studies of Molecular Secondary Ion Mass Spectrometry Ionization Probability Measured With Femtosecond, Infrared Laser Post-Ionization

NASA Astrophysics Data System (ADS)

Popczun, Nicholas James

The work presented in this dissertation is focused on increasing the fundamental understanding of molecular secondary ion mass spectrometry (SIMS) ionization probability by measuring neutral molecule behavior with femtosecond, mid-infrared laser post-ionization (LPI). To accomplish this, a model system was designed with a homogeneous organic film comprised of coronene, a polycyclic hydrocarbon which provides substantial LPI signal. Careful consideration was given to signal lost to photofragmentation and undersampling of the sputtered plume that is contained within the extraction volume of the mass spectrometer. This study provided the first ionization probability for an organic compound measured directly by the relative secondary ions and sputtered neutral molecules using a strong-field ionization (SFI) ionization method. The measured value of ˜10-3 is near the upper limit of previous estimations of ionization probability for organic molecules. The measurement method was refined, and then applied to a homogeneous guanine film, which produces protonated secondary ions. This measurement found the probability of protonation to occur to be on the order of 10-3, although with less uncertainty than that of the coronene. Finally, molecular depth profiles were obtained for SIMS and LPI signals as a function of primary ion fluence to determine the effect of ionization probability on the depth resolution of chemical interfaces. The interfaces chosen were organic/inorganic interfaces to limit chemical mixing. It is shown that approaching the inorganic chemical interface can enhance or suppress the ionization probability for the organic molecule, which can lead to artificially sharpened or broadened depths, respectively. Overall, the research described in this dissertation provides new methods for measuring ionization efficiency in SIMS in both absolute and relative terms, and will inform both innovation in the technique, as well as increase understanding of depth-dependent experiments.

Poly-Small Ubiquitin-like Modifier (PolySUMO)-binding Proteins Identified through a String Search*

PubMed Central

Sun, Huaiyu; Hunter, Tony

2012-01-01

Polysumoylation is a crucial cellular response to stresses against genomic integrity or proteostasis. Like the small ubiquitin-like modifier (SUMO)-targeted ubiquitin ligase RNF4, proteins with clustered SUMO-interacting motifs (SIMs) can be important signal transducers downstream of polysumoylation. To identify novel polySUMO-binding proteins, we conducted a computational string search with a custom Python script. We found clustered SIMs in another RING domain protein Arkadia/RNF111. Detailed biochemical analysis of the Arkadia SIMs revealed that dominant SIMs in a SIM cluster often contain a pentameric VIDLT ((V/I/L/F/Y)(V/I)DLT) core sequence that is also found in the SIMs in PIAS family E3s and is likely the best-fitted structure for SUMO recognition. This idea led to the identification of additional novel SIM clusters in FLASH/CASP8AP2, C5orf25, and SOBP/JXC1. We suggest that the clustered SIMs in these proteins form distinct SUMO binding domains to recognize diverse forms of protein sumoylation. PMID:23086935

Campaign 1.7 Pu Aging. Development of Time of Flight Secondary Ion Mass Spectroscopy

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

Venhaus, Thomas J.

2015-09-09

The first application of Time-of-Flight Secondary Ion Mass Spectroscopy (ToF-SIMS) to an aged plutonium surface has resulted in a rich set of surface chemistry data, as well as some unexpected results. FY15 was highlighted by not only the first mapping of hydrogen-containing features within the metal, but also a prove-in series of experiments using the system’s Sieverts Reaction Cell. These experiments involved successfully heating the sample to ~450 oC for nearly 24 hours while the sample was dosed several times with hydrogen, followed by an in situ ToF-SIMS analysis. During this year, the data allowed for better and more consistentmore » identification of the myriad peaks that result from the SIMS sputter process. In collaboration with the AWE (U.K), the system was also fully aligned for sputter depth profiling for future experiments.« less

xLPR Sim Editor 1.0 User's Guide

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

Mariner, Paul E.

2017-03-01

The United States Nuclear Regulatory Commission in cooperation with the Electric Power Research Institute contracted Sandia National Laboratories to develop the framework of a probabilistic fracture mechanics assessment code called xLPR ( Extremely Low Probability of Rupture) Version 2.0 . The purpose of xLPR is to evaluate degradation mechanisms in piping systems at nuclear power plants and to predict the probability of rupture. This report is a user's guide for xLPR Sim Editor 1.0 , a graphical user interface for creating and editing the xLPR Version 2.0 input file and for creating, editing, and using the xLPR Version 2.0 databasemore » files . The xLPR Sim Editor, provides a user - friendly way for users to change simulation options and input values, s elect input datasets from xLPR data bases, identify inputs needed for a simulation, and create and modify an input file for xLPR.« less

Health, drugs and service use among deprived single men: comparing (subgroups) of single male welfare recipients against employed single men in Amsterdam.

PubMed

Kamann, Tjerk C; de Wit, Matty A S; Cremer, Stephan; Beekman, Aartjan T F

2014-02-20

To aid public health policy in preventing severe social exclusion (like homelessness) and promoting social inclusion (like labour market participation), we aimed to quantify (unmet) health needs of an expectedly vulnerable population on which little was known about: single male welfare recipients (SIM-welfare). One of the main policy questions was: is there need to promote access to healthcare for this specific group? A cross-sectional study incorporating peer-to-peer methodology to approach and survey SIM-welfare. Sociodemographics, prevalence of ill health, harmful drug use and healthcare utilisation for subgroups of SIM-welfare assessed with a different distance to the labour market and exposed to different reintegration policy were described and compared against single employed men (SIM-work). Men between the age of 23 and 64, living in single person households in Amsterdam. A random and representative sample of 472 SIM-welfare was surveyed during 2009-2010. A reference sample of 212 SIM-work was taken from the 2008 Amsterdam Health Survey. Standardised instruments were used to assess self-reported ill somatic and mental health, harmful drug use and service use. SIM-welfare are mostly long-term jobless, low educated, older men; 70% are excluded from re-employment policy due to multiple personal barriers. Health: 50% anxiety and depression; 47% harmful drug use; 41% multiple somatic illnesses. Health differences compared with SIM-work: (1) controlled for background characteristics, SIM-welfare report more mental (OR 4.0; 95% CI 2.1 to 4.7) and somatic illnesses (OR 3.1; 95% CI 2.7 to 6.0); (2) SIM-welfare assessed with the largest distance to the labour market report most combined health problems. Controlled for ill health, SIM-welfare are more likely to have service contacts than SIM-work. SIM-welfare form a selection of men with disadvantaged human capital and health. Findings do not support a need to improve access to healthcare. The stratification of welfare clients distinguishes between health needs.

Health, drugs and service use among deprived single men: comparing (subgroups) of single male welfare recipients against employed single men in Amsterdam

PubMed Central

Kamann, Tjerk C; de Wit, Matty A S; Cremer, Stephan; Beekman, Aartjan T F

2014-01-01

Objectives To aid public health policy in preventing severe social exclusion (like homelessness) and promoting social inclusion (like labour market participation), we aimed to quantify (unmet) health needs of an expectedly vulnerable population on which little was known about: single male welfare recipients (SIM-welfare). One of the main policy questions was: is there need to promote access to healthcare for this specific group? Design A cross-sectional study incorporating peer-to-peer methodology to approach and survey SIM-welfare. Sociodemographics, prevalence of ill health, harmful drug use and healthcare utilisation for subgroups of SIM-welfare assessed with a different distance to the labour market and exposed to different reintegration policy were described and compared against single employed men (SIM-work). Setting Men between the age of 23 and 64, living in single person households in Amsterdam. Participants A random and representative sample of 472 SIM-welfare was surveyed during 2009–2010. A reference sample of 212 SIM-work was taken from the 2008 Amsterdam Health Survey. Outcome measures Standardised instruments were used to assess self-reported ill somatic and mental health, harmful drug use and service use. Results SIM-welfare are mostly long-term jobless, low educated, older men; 70% are excluded from re-employment policy due to multiple personal barriers. Health: 50% anxiety and depression; 47% harmful drug use; 41% multiple somatic illnesses. Health differences compared with SIM-work: (1) controlled for background characteristics, SIM-welfare report more mental (OR 4.0; 95% CI 2.1 to 4.7) and somatic illnesses (OR 3.1; 95% CI 2.7 to 6.0); (2) SIM-welfare assessed with the largest distance to the labour market report most combined health problems. Controlled for ill health, SIM-welfare are more likely to have service contacts than SIM-work. Conclusions SIM-welfare form a selection of men with disadvantaged human capital and health. Findings do not support a need to improve access to healthcare. The stratification of welfare clients distinguishes between health needs. PMID:24556242

Automated Re-Entry System using FNPEG

NASA Technical Reports Server (NTRS)

Johnson, Wyatt R.; Lu, Ping; Stachowiak, Susan J.

2017-01-01

This paper discusses the implementation and simulated performance of the FNPEG (Fully Numerical Predictor-corrector Entry Guidance) algorithm into GNC FSW (Guidance, Navigation, and Control Flight Software) for use in an autonomous re-entry vehicle. A few modifications to FNPEG are discussed that result in computational savings -- a change to the state propagator, and a modification to cross-range lateral logic. Finally, some Monte Carlo results are presented using a representative vehicle in both a high-fidelity 6-DOF (degree-of-freedom) sim as well as in a 3-DOF sim for independent validation.

Higher Signal-to-Noise Measurements of Alpha-element Abundances in the M31 System

NASA Astrophysics Data System (ADS)

Escala, Ivanna; Kirby, Evan N.

2018-06-01

The stellar halo and tidal streams of M31 provide an essential counterpoint to the same structures around the Milky Way (MW). While measurements of [Fe/H] and [$\\alpha$/Fe] have been made in the MW, little is known about the detailed chemical abundances of the M31 system. To make progress with existing telescopes, we expand upon the technique first presented by Kirby et al., applying spectral synthesis to medium-resolution spectroscopy at lower spectral resolution (R $\\sim$ 1800) across an optical range (4100~\\AA \\ $<$ $\\lambda$ $<$ 9100~\\AA) that extends down the blue. We have obtained deep spectra of red giants in the tidal streams, smooth halo, and disk of M31 using the DEIMOS 600ZD grating, resulting in higher signal-to-noise per spectral resolution element (S/N $\\sim$ 30 \\AA$^{-1}$). By applying our technique to red giant stars in MW globular clusters with higher-resolution ($R$ $\\sim$ 6000) spectra in the blue (4100 - 6300 \\AA), we demonstrate that our technique reproduces previous measurements derived from the red side of the optical (6300 - 9100 \\AA). For the first time, we present measurements of [Fe/H] and [$\\alpha$/Fe] of sufficient quality and sample size to construct quantitative models of galactic chemical evolution in the M31 system.

Design data brochure: SIMS prototype system 3

NASA Technical Reports Server (NTRS)

1978-01-01

A closed hydronic solar system is reported for space and hot water heating. Design, performance, and hardware specifications are presented sufficient for architectural engineers and contractors to procure, install, operate, and maintain a similar solar application.

Return to the Moon in Second Life, a 3D Metaverse

NASA Astrophysics Data System (ADS)

Ireton, F.; Day, B.; Mitchell, B.; Stockman, S.

2008-12-01

Second Life (SL) is one of several virtual 3D simulations or metaverses. Presently there over nine million SL users worldwide with a growth rate of about 10 percent per month. SL has seen explosive growth in the five years it has been available and hosts a number of educational and institutional 'islands' or sims. There are over 200 educational institutions and education specific sims in SL. The SL education group hosts an educational mailing list of over 1,800 and at the recent SL conference conducted education strands all three days. Federal agencies with an SL presence include NASA, NOAA, and EPA. At any one time there may be 40,000-50,000 users on line. Users develop a persona and are seen on screen as a human figure or avatar. Avatars are able to move around the sim islands by walking or flying and move from island to island or remote locations by teleporting. While a big part of the Second Life experience deals with avatar interactions and exploring, there is an active community of builders who create the scenery, buildings, and other artifacts of the SL world including clothing and other personal items. SL builders start with basic shapes and through size manipulation on three axis and adding texture to the shapes create a myriad of objects-a 3D world. This paper will deal with the design and creation of an exhibit hall for NASA's Lunar Precursor Robotics Program (LPRP) and the LRO/LCROSS mission slated for launch in 2009. A Return to the Moon exhibit hall has been placed in the NASA sponsored Co-Lab sim located in the Sci Lands area of Second Life. Storyboards with information about the mission interpret the exhibits for visitors. Links to external websites provide for further information on the missions, both spacecraft instrument suites, and EPO efforts. Future plans for the exhibit include live broadcast of the launch and LCROSS impact.

ImagingSIMS

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

2017-11-06

ImagingSIMS is an open source application for loading, processing, manipulating and visualizing secondary ion mass spectrometry (SIMS) data. At PNNL, a separate branch has been further developed to incorporate application specific features for dynamic SIMS data sets. These include loading CAMECA IMS-1280, NanoSIMS and modified IMS-4f raw data, creating isotopic ratio images and stitching together images from adjacent interrogation regions. In addition to other modifications of the parent open source version, this version is equipped with a point-by-point image registration tool to assist with streamlining the image fusion process.

Development of a TOF SIMS setup at the Zagreb heavy ion microbeam facility

NASA Astrophysics Data System (ADS)

Tadić, Tonči; Bogdanović Radović, Iva; Siketić, Zdravko; Cosic, Donny Domagoj; Skukan, Natko; Jakšić, Milko; Matsuo, Jiro

2014-08-01

We describe a new Time-of-flight Secondary Ion Mass Spectrometry (TOF SIMS) setup for MeV SIMS application, which is constructed and installed at the heavy ion microbeam facility at the Ruđer Bošković Institute in Zagreb. The TOF-SIMS setup is developed for high sensitivity molecular imaging using a heavy ion microbeam that focuses ion beams (from C to I) with sub-micron resolution. Dedicated pulse processing electronics for MeV SIMS application have been developed, enabling microbeam-scanning control, incoming ion microbeam pulsing and molecular mapping. The first results showing measured MeV SIMS spectra as well as molecular maps for samples of interest are presented and discussed.

Snakebites as cause of deaths in the Western Brazilian Amazon: Why and who dies? Deaths from snakebites in the Amazon.

PubMed

da Silva Souza, Anderson; de Almeida Gonçalves Sachett, Jacqueline; Alcântara, João Arthur; Freire, Monique; Alecrim, Maria das Graças Costa; Lacerda, Marcus; de Lima Ferreira, Luiz Carlos; Fan, Hui Wen; de Souza Sampaio, Vanderson; Monteiro, Wuelton Marcelo

2018-04-01

Snake envenoming represents a major burden for public health worldwide. In the Amazon, the official number of cases and deaths detected is probably underestimated because of the difficulty riverine and indigenous populations have reaching health centers in order to receive medical assistance. Thus, integrated analysis of health information systems must be used in order to improve adequate health policies. The aim of this work is to describe a series of deaths and identify risk factors for lethality from snakebites in the state of Amazonas, Brazil. All deaths from snakebites reported to the Brazilian Notifiable Diseases Surveillance System (SINAN) and to the Mortality Information System (SIM; ICD10-10th revision, X.29), from 2007 to 2015, were included. Variables were assessed by blocks with distal (ecological variables), intermediate (demographics) and proximal (clinical variables) components to identify predictors of case fatality. A total of 127 deaths from snakebites were recorded, with 58 pairs found through linkage of the SINAN and SIM databases (45.7%), 37 (29.1%) deaths found only in SINAN and 32 (25.2%) found only in the SIM. Deaths occurred mostly in males (95 cases; 74.8%) living in rural areas (78.6%). The most affected age group was the ≥61 years old (36 cases; 28.4%). Snakebites were presumably due to Bothrops snakes in 68.5% of the cases and Lachesis in 29.5% based on clinico-epidemiological diagnosis. A proportion of 26.2% of the cases received treatment over 24 h after the bite ocurred. On admission, cases were mostly classified as severe (65.6%). Overall, 28 patients (22.0%). Deceased without any medical assistance Antivenom was given to 53.5%. In the multivariate analysis, a distance from Manaus >300 km [OR = 3.40 (95%CI = 1.99-5.79); (p < 0.001)]; age ≥61 years [OR = 4.31 (95%CI = 1.22-15.21); (p = 0.023)] and Indigenous status [OR = 5.47 (95%CI = 2.37-12.66); (p < 0.001)] were independently associated with case fatality from snakebites. Severe snakebites [OR = 16.24 (95%CI = 4.37-60.39); (p < 0.001)] and a lack of antivenom administration [OR = 4.21 (95%CI = 1.30-13.19); (p = 0.014)] were also independently associated with case fatality. Respiratory failure/dyspnea, systemic bleeding, sepsis and shock were recorded only among fatal cases. In conclusion, i) death from snakebites was underreported in the mortality surveillance system; ii) older age groups living in remote municipalities and indigenous peoples were the population groups most prone to death; iii) lack or underdosage of antivenom resulted in higher case fatality and iv) systemic bleeding, circulatory shock, sepsis and acute respiratory failure were strongly associated to fatal outcome. Copyright © 2018 Elsevier Ltd. All rights reserved.

SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees

PubMed Central

Mallo, Diego; De Oliveira Martins, Leonardo; Posada, David

2016-01-01

We present a fast and flexible software package—SimPhy—for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer—all three potentially leading to species tree/gene tree discordance—and gene conversion. SimPhy implements a hierarchical phylogenetic model in which the evolution of species, locus, and gene trees is governed by global and local parameters (e.g., genome-wide, species-specific, locus-specific), that can be fixed or be sampled from a priori statistical distributions. SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon, and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validate SimPhy's output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large trees, being an order of magnitude faster than the most similar program (DLCoal-Sim). In addition, we demonstrate how SimPhy can be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods. SimPhy is available at https://github.com/adamallo/SimPhy, where users can find the source code, precompiled executables, a detailed manual and example cases. PMID:26526427

Search for a scalar partner of the top quark in the jets plus missing transverse momentum final state at $$\\sqrt{s}=13 $$ TeV with the ATLAS detector

DOE PAGES

Aaboud, M.; Aad, G.; Abbott, B.; ...

2017-12-15

A search for pair production of a scalar partner of the top quark in events with four or more jets plus missing transverse momentum is presented. Here, an analysis of 36.1 fb -1 ofmore » $$ \\sqrt{s}=13 $$ TeV proton-proton collisions collected using the ATLAS detector at the LHC yields no significant excess over the expected Standard Model background. To interpret the results a simplified supersymmetric model is used where the top squark is assumed to decay via $$\\sim\\atop{t}$$ 1→t(*)$$\\sim\\atop{χ}$$ $$0\\atop{1}$$ and $$\\sim\\atop{t}$$ 1→b$$\\sim\\atop{χ}$$ $$±\\atop{1}$$→bW(*)$$\\sim\\atop{χ}$$ $$0\\atop{1}$$, where χ 1 0 (χ 1 ± ) denotes the lightest neutralino (chargino). Exclusion limits are placed in terms of the top-squark and neutralino masses. Assuming a branching ratio of 100% to t$$\\sim\\atop{χ}$$ $$0\\atop{1}$$, top-squark masses in the range 450–1000 GeV are excluded for $$\\sim\\atop{χ}$$ $$0\\atop{1}$$ masses below 160 GeV. In the case where m$$\\sim\\atop{t}$$ 1-m t+m $$\\sim\\atop{χ}$$ $$0\\atop{1}$$ , top-squark masses in the range 235–590 GeV are excluded.« less

Search for a scalar partner of the top quark in the jets plus missing transverse momentum final state at $$\\sqrt{s}=13 $$ TeV with the ATLAS detector

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

Aaboud, M.; Aad, G.; Abbott, B.

A search for pair production of a scalar partner of the top quark in events with four or more jets plus missing transverse momentum is presented. Here, an analysis of 36.1 fb -1 ofmore » $$ \\sqrt{s}=13 $$ TeV proton-proton collisions collected using the ATLAS detector at the LHC yields no significant excess over the expected Standard Model background. To interpret the results a simplified supersymmetric model is used where the top squark is assumed to decay via $$\\sim\\atop{t}$$ 1→t(*)$$\\sim\\atop{χ}$$ $$0\\atop{1}$$ and $$\\sim\\atop{t}$$ 1→b$$\\sim\\atop{χ}$$ $$±\\atop{1}$$→bW(*)$$\\sim\\atop{χ}$$ $$0\\atop{1}$$, where χ 1 0 (χ 1 ± ) denotes the lightest neutralino (chargino). Exclusion limits are placed in terms of the top-squark and neutralino masses. Assuming a branching ratio of 100% to t$$\\sim\\atop{χ}$$ $$0\\atop{1}$$, top-squark masses in the range 450–1000 GeV are excluded for $$\\sim\\atop{χ}$$ $$0\\atop{1}$$ masses below 160 GeV. In the case where m$$\\sim\\atop{t}$$ 1-m t+m $$\\sim\\atop{χ}$$ $$0\\atop{1}$$ , top-squark masses in the range 235–590 GeV are excluded.« less

Static Time-of-Flight Secondary Ion Mass Spectrometry (SIMS) | Materials

Science.gov Websites

-Flight Secondary Ion Mass Spectrometry (SIMS) Image of high mass resolution and mass accuracy provided by TOF SIMS We used the high mass resolution and mass accuracy of TOF SIMS to study surface cleanliness acidic wash resulted in contamination by Fe and other metals. Without high mass accuracy, the CaO signal

78 FR 8587 - American Showa, Inc.; Blanchester Plant, Including On-Site Leased Workers From Adecco and Sims...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-06

....; Blanchester Plant, Including On-Site Leased Workers From Adecco and Sims Bros., Inc.; Blanchester, OH; Amended... workers from Sims Bros., Inc. were working on-site at the subject firm during the relevant period and that the services supplied by Sims Bros., Inc. were related to the production of gear boxes (and parts...

Teaching the Teacher: Tutoring SimStudent Leads to More Effective Cognitive Tutor Authoring

ERIC Educational Resources Information Center

Matsuda, Noboru; Cohen, William W.; Koedinger, Kenneth R.

2015-01-01

SimStudent is a machine-learning agent initially developed to help novice authors to create cognitive tutors without heavy programming. Integrated into an existing suite of software tools called Cognitive Tutor Authoring Tools (CTAT), SimStudent helps authors to create an expert model for a cognitive tutor by tutoring SimStudent on how to solve…

SimGraph: A Flight Simulation Data Visualization Workstation

NASA Technical Reports Server (NTRS)

Kaplan, Joseph A.; Kenney, Patrick S.

1997-01-01

Today's modern flight simulation research produces vast amounts of time sensitive data, making a qualitative analysis of the data difficult while it remains in a numerical representation. Therefore, a method of merging related data together and presenting it to the user in a more comprehensible format is necessary. Simulation Graphics (SimGraph) is an object-oriented data visualization software package that presents simulation data in animated graphical displays for easy interpretation. Data produced from a flight simulation is presented by SimGraph in several different formats, including: 3-Dimensional Views, Cockpit Control Views, Heads-Up Displays, Strip Charts, and Status Indicators. SimGraph can accommodate the addition of new graphical displays to allow the software to be customized to each user s particular environment. A new display can be developed and added to SimGraph without having to design a new application, allowing the graphics programmer to focus on the development of the graphical display. The SimGraph framework can be reused for a wide variety of visualization tasks. Although it was created for the flight simulation facilities at NASA Langley Research Center, SimGraph can be reconfigured to almost any data visualization environment. This paper describes the capabilities and operations of SimGraph.

CatSim: a new computer assisted tomography simulation environment

NASA Astrophysics Data System (ADS)

De Man, Bruno; Basu, Samit; Chandra, Naveen; Dunham, Bruce; Edic, Peter; Iatrou, Maria; McOlash, Scott; Sainath, Paavana; Shaughnessy, Charlie; Tower, Brendon; Williams, Eugene

2007-03-01

We present a new simulation environment for X-ray computed tomography, called CatSim. CatSim provides a research platform for GE researchers and collaborators to explore new reconstruction algorithms, CT architectures, and X-ray source or detector technologies. The main requirements for this simulator are accurate physics modeling, low computation times, and geometrical flexibility. CatSim allows simulating complex analytic phantoms, such as the FORBILD phantoms, including boxes, ellipsoids, elliptical cylinders, cones, and cut planes. CatSim incorporates polychromaticity, realistic quantum and electronic noise models, finite focal spot size and shape, finite detector cell size, detector cross-talk, detector lag or afterglow, bowtie filtration, finite detector efficiency, non-linear partial volume, scatter (variance-reduced Monte Carlo), and absorbed dose. We present an overview of CatSim along with a number of validation experiments.

Simulated electronic health record (Sim-EHR) curriculum: teaching EHR skills and use of the EHR for disease management and prevention.

PubMed

Milano, Christina E; Hardman, Joseph A; Plesiu, Adeline; Rdesinski, Rebecca E; Biagioli, Frances E

2014-03-01

Electronic health records (EHRs) can improve many aspects of patient care, yet few formal EHR curricula exist to teach optimal use to students and other trainees. The Simulated EHR (Sim-EHR) curriculum was introduced in January 2011 at Oregon Health & Science University (OHSU) to provide learners with a safe hands-on environment in which to apply evidence-based guidelines while learning EHR skills. Using an EHR training platform identical to the OHSU EHR system, learners review and correct a simulated medical chart for a complex virtual patient with chronic diseases and years of fragmented care. They write orders and prescriptions, create an evidence-based plan of care for indicated disease prevention and management, and review their work in a small-group setting. Third-year students complete the Sim-EHR curriculum as part of the required family medicine clerkship; their chart work is assessed using a rubric tied to the curriculum's general and specific objectives. As of January 2014, 406 third-year OHSU medical students, on campus or at remote clerkship sites, and 21 OHSU internal medicine interns had completed simulated charts.In this article, the authors describe the development and implementation of the Sim-EHR curriculum, with a focus on use of the curriculum in the family medicine clerkship. They also share preliminary findings and lessons learned. They suggest that the Sim-EHR curriculum is an effective, interactive method for providing learners with EHR skills education while demonstrating how a well-organized chart helps ensure safe, efficient, and quality patient care.

Laser acupuncture causes thermal changes in small intestine meridian pathway.

PubMed

de Souza, Regina Célia; Pansini, Mario; Arruda, Gisele; Valente, Caroline; Brioschi, Marcos Leal

2016-11-01

The acupuncture meridians represent the flow of corporal energy which contains the acupuncture points. Laser acupuncture is a form of acupuncture stimulation by the use of laser. Thermographic images represent the propagation of heat in micro-environmental systems. The objective of this study was to investigate the use of thermographic images to document the changes on the small intestine meridian (S.I.M.) when submitted to laser acupuncture. Another important issue regards to the analysis of the flow direction if it is upward when stimulated by acupuncture points. For the execution of this work, a laser acupuncture pen was used in points of the meridian in the S.I.M. Two healthy male volunteers were selected (18 and 60 years old, respectively), and doses of 576,92 J/cm 2 with low-power infrared laser equipment with a wavelength of 780 nm in the SI.3 and SI.19 points were applied. An infrared thermal camera was used to measure the temperature of the S.I.M. during the 6 min laser acupuncture pen stimulus. When the laser acupuncture of both volunteers was conducted in the SI.3 point, it presented hyper-radiation of the hemi face in the same side, far from the application site. When this was applied in the SI.19 point, hyper-radiation in the same point and temperature lowering at the end of the meridian were observed. The laser energy caused thermal changes along the path of the S.I.M., distal, and proximal at the same time, proving the existence of the S.I.M.

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

Yao, Juan; Zhou, Yufan; Sui, Xiao

Switchable ionic liquids (SWIL) play an important role in green chemistry. Due to the nature of SWIL chemistry, such as air sensitivity and pressure and temperature dependence, it is difficult to characterize SWIL using vacuum-based surface techniques. The fully CO2 loaded and none-loaded DBU and hexanol mixtures, a SWIL system, were analyzed in situ by time-of-flight secondary ion mass spectrometry (ToF-SIMS) coupled with the System for Analysis at the Liquid Vacuum Interface (SALVI), respectively. The DBU/Hexanol/CO2 SWIL was injected into the microchannel before liquid SIMS analysis. Bi3+ primary ion beam was used. The positive and negative spectra of the SWILmore » chemical components are presented. The characteristic peaks m/z 153 (reduced DBU) in the positive mode and m/z 101 (oxidized hexanol) in negative mode were observed. In addition, ion pair peaks including m/z 253, 319, 305, 451 in the positive mode and m/z 145, 223, 257 in the negative mode are first observed using this approach. These results demonstrate that the SALVI microfluidic reactor enables the vacuum-based surface technique (i.e., ToF-SIMS) for in situ characterization of challenging liquid samples such as ionic liquids.« less

Reducing the Matrix Effect in Organic Cluster SIMS Using Dynamic Reactive Ionization

NASA Astrophysics Data System (ADS)

Tian, Hua; Wucher, Andreas; Winograd, Nicholas

2016-12-01

Dynamic reactive ionization (DRI) utilizes a reactive molecule, HCl, which is doped into an Ar cluster projectile and activated to produce protons at the bombardment site on the cold sample surface with the presence of water. The methodology has been shown to enhance the ionization of protonated molecular ions and to reduce salt suppression in complex biomatrices. In this study, we further examine the possibility of obtaining improved quantitation with DRI during depth profiling of thin films. Using a trehalose film as a model system, we are able to define optimal DRI conditions for depth profiling. Next, the strategy is applied to a multilayer system consisting of the polymer antioxidants Irganox 1098 and 1010. These binary mixtures have demonstrated large matrix effects, making quantitative SIMS measurement not feasible. Systematic comparisons of depth profiling of this multilayer film between directly using GCIB, and under DRI conditions, show that the latter enhances protonated ions for both components by 4- to 15-fold, resulting in uniform depth profiling in positive ion mode and almost no matrix effect in negative ion mode. The methodology offers a new strategy to tackle the matrix effect and should lead to improved quantitative measurement using SIMS.

Direct-method SAD phasing with partial-structure iteration: towards automation.

PubMed

Wang, J W; Chen, J R; Gu, Y X; Zheng, C D; Fan, H F

2004-11-01

The probability formula of direct-method SAD (single-wavelength anomalous diffraction) phasing proposed by Fan & Gu (1985, Acta Cryst. A41, 280-284) contains partial-structure information in the form of a Sim-weighting term. Previously, only the substructure of anomalous scatterers has been included in this term. In the case that the subsequent density modification and model building yields only structure fragments, which do not straightforwardly lead to the complete solution, the partial structure can be fed back into the Sim-weighting term of the probability formula in order to strengthen its phasing power and to benefit the subsequent automatic model building. The procedure has been tested with experimental SAD data from two known proteins with copper and sulfur as the anomalous scatterers.

QCM-D and ToF-SIMS Investigation to Deconvolute the Relationship between Lipid Adsorption and Orientation on Lipase Activity.

PubMed

Joyce, Paul; Kempson, Ivan; Prestidge, Clive A

2015-09-22

Quartz crystal microbalance with dissipation (QCM-D) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) were used to provide insights into the relationship between lipid adsorption kinetics and molecular behavior in porous silica particles of varying hydrophobicities on lipase activity. Lipase (an interfacial enzyme that cleaves ester bonds to break down lipids to fatty acids and monoglycerides) activity was controlled by loading triglycerides at different surface coverages in hydrophilic and hydrophobic porous silica particles. The rate of lipid adsorption increased 2-fold for the hydrophobic surface compared to the hydrophilic surface. However, for submonolayer lipid coverage, the hydrophilic surface enhanced lipase activity 4-fold, whereas the hydrophobic surface inhibited lipase activity 16-fold, compared to lipid droplets in water. A difference in lipid orientation for low surface coverage, evidenced by ToF-SIMS, indicated that lipid adsorbs to hydrophilic silica in a conformation promoting hydrolysis. Multilayer coverage on hydrophobic and hydrophilic surfaces was indistinguishable with ToF-SIMS analysis. Increased lipid adsorption for both substrates facilitated digestion kinetics comparable to a conventional emulsion. Improved understanding of the interfacial adsorption and orientation of lipid and its digestibility in porous silica has implications in improving the uptake of pharmaceuticals and nutrients from lipid-based delivery systems.

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

Hua, Xin; Yu, Xiao-Ying; Wang, Zhaoying

The first results of using a novel single channel microfluidic reactor to enable Shewanella biofilm growth and in situ characterization using time-of-flight secondary ion mass spectrometry (ToF-SIMS) in the hydrated environment are presented. The new microfluidic interface allows direct probing of the liquid surface using ToF-SIMS, a vacuum surface technique. The detection window is an aperture of 2 m in diameter on a thin silicon nitride (SiN) membrane and it allows direct detection of the liquid surface. Surface tension of the liquid flowing inside the microchannel holds the liquid within the aperture. ToF-SIMS depth profiling was used to drill throughmore » the SiN membrane and the biofilm grown on the substrate. In situ 2D imaging of the biofilm in hydrated state was acquired, providing spatial distribution of the chemical compounds in the biofilm system. This data was compared with a medium filled microfluidic reactor devoid of biofilm and dried biofilm samples deposited on clean silicon wafers. Principle Component Analysis (PCA) was used to investigate these observations. Our results show that imaging biofilms in the hydrated environment using ToF-SIMS is possible using the unique microfluidic reactor. Moreover, characteristic biofilm fatty acids fragments were observed in the hydrated biofilm grown in the microfluidic channel, illustrating the advantage of imaging biofilm in its native environment.« less

SimPhospho: a software tool enabling confident phosphosite assignment.

PubMed

Suni, Veronika; Suomi, Tomi; Tsubosaka, Tomoya; Imanishi, Susumu Y; Elo, Laura L; Corthals, Garry L

2018-03-27

Mass spectrometry combined with enrichment strategies for phosphorylated peptides has been successfully employed for two decades to identify sites of phosphorylation. However, unambiguous phosphosite assignment is considered challenging. Given that site-specific phosphorylation events function as different molecular switches, validation of phosphorylation sites is of utmost importance. In our earlier study we developed a method based on simulated phosphopeptide spectral libraries, which enables highly sensitive and accurate phosphosite assignments. To promote more widespread use of this method, we here introduce a software implementation with improved usability and performance. We present SimPhospho, a fast and user-friendly tool for accurate simulation of phosphopeptide tandem mass spectra. Simulated phosphopeptide spectral libraries are used to validate and supplement database search results, with a goal to improve reliable phosphoproteome identification and reporting. The presented program can be easily used together with the Trans-Proteomic Pipeline and integrated in a phosphoproteomics data analysis workflow. SimPhospho is available for Windows, Linux and Mac operating systems at https://sourceforge.net/projects/simphospho/. It is open source and implemented in C ++. A user's manual with detailed description of data analysis using SimPhospho as well as test data can be found as supplementary material of this article. Supplementary data are available at https://www.btk.fi/research/ computational-biomedicine/software/.

Interpreting Musculoskeletal Models and Dynamic Simulations: Causes and Effects of Differences Between Models.

PubMed

Roelker, Sarah A; Caruthers, Elena J; Baker, Rachel K; Pelz, Nicholas C; Chaudhari, Ajit M W; Siston, Robert A

2017-11-01

With more than 29,000 OpenSim users, several musculoskeletal models with varying levels of complexity are available to study human gait. However, how different model parameters affect estimated joint and muscle function between models is not fully understood. The purpose of this study is to determine the effects of four OpenSim models (Gait2392, Lower Limb Model 2010, Full-Body OpenSim Model, and Full Body Model 2016) on gait mechanics and estimates of muscle forces and activations. Using OpenSim 3.1 and the same experimental data for all models, six young adults were scaled in each model, gait kinematics were reproduced, and static optimization estimated muscle function. Simulated measures differed between models by up to 6.5° knee range of motion, 0.012 Nm/Nm peak knee flexion moment, 0.49 peak rectus femoris activation, and 462 N peak rectus femoris force. Differences in coordinate system definitions between models altered joint kinematics, influencing joint moments. Muscle parameter and joint moment discrepancies altered muscle activations and forces. Additional model complexity yielded greater error between experimental and simulated measures; therefore, this study suggests Gait2392 is a sufficient model for studying walking in healthy young adults. Future research is needed to determine which model(s) is best for tasks with more complex motion.

Visual Analysis of Social Networks in a Counter-Insurgency Context

DTIC Science & Technology

2011-06-01

Batagelj and Mrvar 2003] specifically focus on the analysis and visualisation of extremely large networks. Moreover, on top of these data about the...and behavioral components of a complex conflict ecosystem, SpringSim: 23. Batagelj , V. & Mrvar , A., (2003), Pajek - analysis and visualisation of...information regarding network patterns and structures, no spatial information is usually encoded. This is despite the fact that already Wellman [ 1996

Clinical Placement Before or After Simulated Learning Environments?: A Naturalistic Study of Clinical Skills Acquisition Among Early-Stage Paramedicine Students.

PubMed

Mills, Brennen W; Carter, Owen B J; Rudd, Cobie J; Ross, Nathan P; Claxton, Louise A

2015-10-01

There is conflicting evidence surrounding the merit of clinical placements (CPs) for early-stage health-profession students. Some contend that early-stage CPs facilitate contextualization of a subsequently learned theory. Others argue that training in simulated-learning experiences (SLEs) should occur before CP to ensure that students possess at least basic competency. We sought to investigate both claims. First-year paramedicine students (n = 85) undertook 3 days of CP and SLEs as part of course requirements. Students undertook CP either before or after participation in SLEs creating 2 groups (Clin → Sim/Sim → Clin). Clinical skills acquisition was measured via direct scenario-based clinical assessments with expert observers conducted at 4 intervals during the semester. Perceptions of difficulty of CP and SLE were measured via the National Aeronautics and Space Administration Task Load Index. Students' clinical assessment scores in both groups improved significantly from beginning to end of semester (P < 0.001). However, at semester's end, clinical assessment scores for the Sim → Clin group were statistically significantly greater than those of the Clin → Sim group (P = 0.021). Both groups found SLEs more demanding than CP (P < 0.001). However, compared with the Sim → Clin group, the Clin → Sim group rated SLE as substantially more time-demanding than CP (P = 0.003). Differences in temporal demand suggest that the Clin → Sim students had fewer opportunities to practice clinical skills during CP than the Sim → Clin students due to a more limited scope of practice. The Sim → Clin students contextualized SLE within subsequent CP resulting in greater improvement in clinical competency by semester's end in comparison with the Clin → Sim students who were forced to contextualize skills retrospectively.

The eponymous Dr James Marion Sims MD, LLD (1813-1883).

PubMed

West, M J; Irvine, L M

2015-02-01

Dr James Marion Sims was born in 1813 in Lancaster County, South Carolina. It was while pioneering numerous surgical procedures in Alabama that in 1849 he achieved the outstanding landmark in medical history of successfully, and consistently, repairing vesicovaginal fistulae. Sims soon developed a reputation as a fine surgeon, with new operations and techniques, using novel surgical instruments and his innovative approaches frequently published. Moving to New York City in 1853, he further established hospitals devoted entirely to women's health. Sims was controversial, with flamboyant descriptions of self-confident success, yet they were tempered with sober reflection of failure and loss. Today we remain with the Sims speculum and Sims position, eponymous tributes to his accomplishments as the 'Father of Gynaecology'. © The Author(s) 2013 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Evaluation of vSim for Nursing in an Adult Health Nursing Course: A Multisite Pilot Study.

PubMed

Wright, Renée R; Tinnon, Elizabeth A; Newton, Rebecca H

2018-02-01

Virtual simulation technology is the next step in using simulation as an accepted teaching-learning pedagogy in nursing. The purpose of this multisite, quasi-experimental, three-group, posttest-only design was to evaluate the effectiveness and participant satisfaction of vSim for Nursing in an Adult Health Nursing course. Although the quantitative findings (examination scores and postsimulation scores) were not statistically significant, participants overwhelmingly found vSim for Nursing to be a positive experiential learning endeavor. Ninety-one percent of the participants (n = 61) indicated that vSim for Nursing helped them understand adult health concepts and that vSim for Nursing was beneficial to learning. vSim for Nursing warrants further investigation, using other methods to measure effectiveness to ascertain whether knowledge acquisition is indeed improved as indicated by participant data in this study.

WEC-SIM Phase 1 Validation Testing -- Numerical Modeling of Experiments: Preprint

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

Ruehl, Kelley; Michelen, Carlos; Bosma, Bret

2016-08-01

The Wave Energy Converter Simulator (WEC-Sim) is an open-source code jointly developed by Sandia National Laboratories and the National Renewable Energy Laboratory. It is used to model wave energy converters subjected to operational and extreme waves. In order for the WEC-Sim code to be beneficial to the wave energy community, code verification and physical model validation is necessary. This paper describes numerical modeling of the wave tank testing for the 1:33-scale experimental testing of the floating oscillating surge wave energy converter. The comparison between WEC-Sim and the Phase 1 experimental data set serves as code validation. This paper is amore » follow-up to the WEC-Sim paper on experimental testing, and describes the WEC-Sim numerical simulations for the floating oscillating surge wave energy converter.« less

SimC7 Is a Novel NAD(P)H-Dependent Ketoreductase Essential for the Antibiotic Activity of the DNA Gyrase Inhibitor Simocyclinone.

PubMed

Schäfer, Martin; Le, Tung B K; Hearnshaw, Stephen J; Maxwell, Anthony; Challis, Gregory L; Wilkinson, Barrie; Buttner, Mark J

2015-06-19

Simocyclinone D8 (SD8) is a potent DNA gyrase inhibitor produced by Streptomyces antibioticus Tü6040. The simocyclinone (sim) biosynthetic gene cluster has been sequenced and a hypothetical biosynthetic pathway has been proposed. The tetraene linker in SD8 was suggested to be the product of a modular type I polyketide synthase working in trans with two monofunctional enzymes. One of these monofunctional enzymes, SimC7, was proposed to supply a dehydratase activity missing from two modules of the polyketide synthase. In this study, we report the function of SimC7. We isolated the entire ~72-kb sim cluster on a single phage artificial chromosome clone and produced simocyclinone heterologously in a Streptomyces coelicolor strain engineered for improved antibiotic production. Deletion of simC7 resulted in the production of a novel simocyclinone, 7-oxo-SD8, which unexpectedly carried a normal tetraene linker but was altered in the angucyclinone moiety. We demonstrate that SimC7 is an NAD(P)H-dependent ketoreductase that catalyzes the conversion of 7-oxo-SD8 into SD8. 7-oxo-SD8 was essentially inactive as a DNA gyrase inhibitor, and the reduction of the keto group by SimC7 was shown to be crucial for high-affinity binding to the enzyme. Thus, SimC7 is an angucyclinone ketoreductase that is essential for the biological activity of simocyclinone. Copyright © 2015. Published by Elsevier Ltd.

The Evaluation Of Therapeutic Efficacy and Safety Profile of Simvastatin Prodrug Micelles in a Closed Fracture Mouse Model

PubMed Central

Zhang, Yijia; Jia, Zhenshan; Yuan, Hongjiang; Dusad, Anand; Ren, Ke; Wei, Xin; Fehringer, Edward V.; Purdue, P. Edward; Daluiski, Aaron; Goldring, Steven R.; Wang, Dong

2016-01-01

Purpose To evaluate the therapeutic efficiency of a micellar prodrug formulation of simvastatin (SIM/SIM-mPEG) and explore its safety in a closed femoral fracture mouse model. Methods The amphiphilic macromolecular prodrug of simvastatin (SIM-mPEG) was synthesized and formulated together with free simvastatin into micelles. It was also labeled with a near infrared dye for in vivo imaging purpose. A closed femoral fracture mouse model was established using a three-point bending device. The mice with established closed femoral fracture were treated with SIM/SIM-mPEG micelle, using free simvastatin and saline as controls. The therapeutic efficacy of the micelles was evaluated using a high-resolution micro-CT. Serum biochemistry and histology analyses were performed to explore the potential toxicity of the micelle formulation. Results Near Infrared Fluorescence (NIRF) imaging confirmed the passive targeting of SIM/SIM-mPEG micelles to the bone lesion of the mice with closed femoral fracture. The micelle was found to promote fracture healing with an excellent safety profile. In addition, the accelerated healing of the femoral fracture also helped to prevent disuse-associated same-side tibia bone loss accompanying the femur fracture. Conclusion SIM/SIM-mPEG micelle was found to be an effective and safe treatment for closed femoral fracture repair in mice. The evidence obtained in this study suggests that it may have the potential to be translated into a novel therapy for clinical management of skeletal fractures and non-union. PMID:27164897

Development of a patient-specific dosimetry estimation system in nuclear medicine examination

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

Lin, H. H.; Dong, S. L.; Yang, H. J.

2011-07-01

The purpose of this study is to develop a patient-specific dosimetry estimation system in nuclear medicine examination using a SimSET-based Monte Carlo code. We added a dose deposition routine to store the deposited energy of the photons during their flights in SimSET and developed a user-friendly interface for reading PET and CT images. Dose calculated on ORNL phantom was used to validate the accuracy of this system. The S values for {sup 99m}Tc, {sup 18}F and {sup 131}I obtained by the system were compared to those from the MCNP4C code and OLINDA. The ratios of S values computed by thismore » system to those obtained with OLINDA for various organs were ranged from 0.93 to 1.18, which are comparable to that obtained from MCNP4C code (0.94 to 1.20). The average ratios of S value were 0.99{+-}0.04, 1.03{+-}0.05, and 1.00{+-}0.07 for isotopes {sup 131}I, {sup 18}F, and {sup 99m}Tc, respectively. The simulation time of SimSET was two times faster than MCNP4C's for various isotopes. A 3D dose calculation was also performed on a patient data set with PET/CT examination using this system. Results from the patient data showed that the estimated S values using this system differed slightly from those of OLINDA for ORNL phantom. In conclusion, this system can generate patient-specific dose distribution and display the isodose curves on top of the anatomic structure through a friendly graphic user interface. It may also provide a useful tool to establish an appropriate dose-reduction strategy to patients in nuclear medicine environments. (authors)« less

Search for direct top squark pair production in events with a $Z$ boson, $b$-jets and missing transverse momentum in $$\\sqrt{s}$$= 8 TeV $pp$ collisions with the ATLAS detector

DOE PAGES

Aad, G.; Abbott, B.; Abdallah, J.; ...

2014-06-01

Here, a search is presented for direct top squark pair production using events with at least two leptons including a same-flavour opposite-sign pair with invariant mass consistent with the Z boson mass, jets tagged as originating from b-quarks and missing transverse momentum. The analysis is performed with proton–proton collision data at √s = 8 TeV collected with the ATLAS detector at the LHC in 2012 corresponding to an integrated luminosity of 20.3 fb -1. No excess beyond the Standard Model expectation is observed. Interpretations of the results are provided in models based on the direct pair production of the heavier top squark state (more » $$\\sim\\atop{t}_2$$) followed by the decay to the lighter top squark state ($$\\sim\\atop{t}_1$$) via $$\\sim\\atop{t}_2$$ → Z$$\\sim\\atop{t}_1$$, and for $$\\sim\\atop{t}_1$$ pair production in natural gauge-mediated supersymmetry breaking scenarios where the neutralino ($$\\sim\\atop{χ}$$$0\\atop{1}$$) is the next-to-lightest supersymmetric particle and decays producing a Z boson and a gravitino ($$\\sim\\atop{G}$$) via the $$\\sim\\atop{χ}$$$0\\atop{1}$$ → Z G process.« less

Effects of Preoperative Simulation on Minimally Invasive Hybrid Lumbar Interbody Fusion.

PubMed

Rieger, Bernhard; Jiang, Hongzhen; Reinshagen, Clemens; Molcanyi, Marek; Zivcak, Jozef; Grönemeyer, Dietrich; Bosche, Bert; Schackert, Gabriele; Ruess, Daniel

2017-10-01

The main focus of this study was to evaluate how preoperative simulation affects the surgical work flow, radiation exposure, and outcome of minimally invasive hybrid lumbar interbody fusion (MIS-HLIF). A total of 132 patients who underwent single-level MIS-HLIF were enrolled in a cohort study design. Dose area product was analyzed in addition to surgical data. Once preoperative simulation was established, 66 cases (SIM cohort) were compared with 66 patients who had previously undergone MIS-HLIF without preoperative simulation (NO-SIM cohort). Dose area product was reduced considerably in the SIM cohort (320 cGy·cm 2 NO-SIM cohort: 470 cGy·cm 2 ; P < 0.01). Surgical time was shorter for the SIM cohort (155 minutes; NO-SIM cohort, 182 minutes; P < 0.05). SIM cohort had a better outcome in Numeric Rating Scale back at 6 months follow-up compared with the NO-SIM cohort (P < 0.05). Preoperative simulation reduced radiation exposure and resulted in less back pain at the 6 months follow-up time point. Preoperative simulation provided guidance in determining the correct cage height. Outcome controls enabled the surgeon to improve the procedure and the software algorithm. Copyright © 2017 Elsevier Inc. All rights reserved.

Enumeration of total aerobic microorganisms in foods by SimPlate Total Plate Count-Color Indicator methods and conventional culture methods: collaborative study.

PubMed

Feldsine, Philip T; Leung, Stephanie C; Lienau, Andrew H; Mui, Linda A; Townsend, David E

2003-01-01

The relative efficacy of the SimPlate Total Plate Count-Color Indicator (TPC-CI) method (SimPlate 35 degrees C) was compared with the AOAC Official Method 966.23 (AOAC 35 degrees C) for enumeration of total aerobic microorganisms in foods. The SimPlate TPC-CI method, incubated at 30 degrees C (SimPlate 30 degrees C), was also compared with the International Organization for Standardization (ISO) 4833 method (ISO 30 degrees C). Six food types were analyzed: ground black pepper, flour, nut meats, frozen hamburger patties, frozen fruits, and fresh vegetables. All foods tested were naturally contaminated. Nineteen laboratories throughout North America and Europe participated in the study. Three method comparisons were conducted. In general, there was <0.3 mean log count difference in recovery among the SimPlate methods and their corresponding reference methods. Mean log counts between the 2 reference methods were also very similar. Repeatability (Sr) and reproducibility (SR) standard deviations were similar among the 3 method comparisons. The SimPlate method (35 degrees C) and the AOAC method were comparable for enumerating total aerobic microorganisms in foods. Similarly, the SimPlate method (30 degrees C) was comparable to the ISO method when samples were prepared and incubated according to the ISO method.

Microscope mode secondary ion mass spectrometry imaging with a Timepix detector.

PubMed

Kiss, Andras; Jungmann, Julia H; Smith, Donald F; Heeren, Ron M A

2013-01-01

In-vacuum active pixel detectors enable high sensitivity, highly parallel time- and space-resolved detection of ions from complex surfaces. For the first time, a Timepix detector assembly was combined with a secondary ion mass spectrometer for microscope mode secondary ion mass spectrometry (SIMS) imaging. Time resolved images from various benchmark samples demonstrate the imaging capabilities of the detector system. The main advantages of the active pixel detector are the higher signal-to-noise ratio and parallel acquisition of arrival time and position. Microscope mode SIMS imaging of biomolecules is demonstrated from tissue sections with the Timepix detector.

Prediction and Validation of Disease Genes Using HeteSim Scores.

PubMed

Zeng, Xiangxiang; Liao, Yuanlu; Liu, Yuansheng; Zou, Quan

2017-01-01

Deciphering the gene disease association is an important goal in biomedical research. In this paper, we use a novel relevance measure, called HeteSim, to prioritize candidate disease genes. Two methods based on heterogeneous networks constructed using protein-protein interaction, gene-phenotype associations, and phenotype-phenotype similarity, are presented. In HeteSim_MultiPath (HSMP), HeteSim scores of different paths are combined with a constant that dampens the contributions of longer paths. In HeteSim_SVM (HSSVM), HeteSim scores are combined with a machine learning method. The 3-fold experiments show that our non-machine learning method HSMP performs better than the existing non-machine learning methods, our machine learning method HSSVM obtains similar accuracy with the best existing machine learning method CATAPULT. From the analysis of the top 10 predicted genes for different diseases, we found that HSSVM avoid the disadvantage of the existing machine learning based methods, which always predict similar genes for different diseases. The data sets and Matlab code for the two methods are freely available for download at http://lab.malab.cn/data/HeteSim/index.jsp.

Detecting feigned postconcussional and posttraumatic stress symptoms with the structured inventory of malingered symptomatology (SIMS).

PubMed

Parks, Adam C; Gfeller, Jeffrey; Emmert, Natalie; Lammert, Hannah

2017-01-01

The Structured Inventory of Malingered Symptomatology (SIMS) is a standalone symptom validity test (SVT) designed as a screening measure to detect a variety of exaggerated psychological symptoms. A number of studies have explored the accuracy of the SIMS in litigious and clinical populations, yet few have examined the validity of the SIMS in detecting feigned symptoms of postconcussional disorder (PCD) and posttraumatic stress disorder (PTSD). The present study examined the sensitivity of the SIMS in detecting undergraduate simulators (N = 78) feigning symptoms of PCD, PTSD, and the comorbid presentation of both PCD and PTSD symptomatologies. Overall, the SIMS Total score produced the highest sensitivities for the PCD symptoms and PCD+PTSD symptoms groups (.89 and .85, respectively), and to a lesser extent, the PTSD symptoms group (.69). The Affective Disorders (AF) subscale was most sensitive to the PTSD symptoms group compared to the PCD and PCD+PTSD symptoms groups. Additional sensitivity values are presented and examined at multiple scale cutoff scores. These findings support the use of the SIMS as a SVT screening measure for PCD and PTSD symptom exaggeration in neuropsychological assessment.

Modeling wildlife populations with HexSim

EPA Science Inventory

HexSim is a framework for constructing spatially-explicit, individual-based computer models designed for simulating terrestrial wildlife population dynamics and interactions. HexSim is useful for a broad set of modeling applications including population viability analysis for on...

Alpha particle spectroscopy using FNTD and SIM super-resolution microscopy.

PubMed

Kouwenberg, J J M; Kremers, G J; Slotman, J A; Wolterbeek, H T; Houtsmuller, A B; Denkova, A G; Bos, A J J

2018-06-01

Structured illumination microscopy (SIM) for the imaging of alpha particle tracks in fluorescent nuclear track detectors (FNTD) was evaluated and compared to confocal laser scanning microscopy (CLSM). FNTDs were irradiated with an external alpha source and imaged using both methodologies. SIM imaging resulted in improved resolution, without increase in scan time. Alpha particle energy estimation based on the track length, direction and intensity produced results in good agreement with the expected alpha particle energy distribution. A pronounced difference was seen in the spatial scattering of alpha particles in the detectors, where SIM showed an almost 50% reduction compared to CLSM. The improved resolution of SIM allows for more detailed studies of the tracks induced by ionising particles. The combination of SIM and FNTDs for alpha radiation paves the way for affordable and fast alpha spectroscopy and dosimetry. © 2018 The Authors. Journal of Microscopy published by JohnWiley & Sons Ltd on behalf of Royal Microscopical Society.

Model Package Report: Hanford Soil Inventory Model SIM v.2 Build 1

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

Nichols, Will E.; Zaher, U.; Mehta, S.

The Hanford Soil Inventory Model (SIM) is a tool for the estimation of inventory of contaminants that were released to soil from liquid discharges during the U.S. Department of Energy’s Hanford Site operations. This model package report documents the construction and development of a second version of SIM (SIM-v2) to support the needs of Hanford Site Composite Analysis. The SIM-v2 is implemented using GoldSim Pro®1 software with a new model architecture that preserves the uncertainty in inventory estimates while reducing the computational burden (compared to the previous version) and allowing more traceability and transparency in calculation methodology. The calculation architecturemore » is designed in such a manner that future updates to the waste stream composition along with addition or deletion of waste sites can be performed with relative ease. In addition, the new computational platform allows for continued hardware upgrade.« less

uleSIMS characterization of silver reference surfaces

NASA Astrophysics Data System (ADS)

Palitsin, V. V.; Dowsett, M. G.; Mata, B. Guzmán de la; Oloff, I. W.; Gibbons, R.

2006-07-01

Ultra low energy SIMS (uleSIMS) is a high sensitivity analytical technique that is normally used for ultra shallow profiling at a depth resolution of up to1 nm. This work describes the use of uleSIMS as both a spectroscopic and depth-profiling tool for the characterization of the early stages of corrosion formed on reference surfaces of silver. These samples are being developed to help with the characterization of tarnished surfaces in a cultural heritage context, and uleSIMS enables the tarnishing to be studied from its very earliest stages due to its high sensitivity (ppm-ppb) and surface specificity. We show that, uleSIMS can be used effectively to study the surface chemistry and aid the development of reference surfaces themselves. In particular, handling contaminants, surface dust, and residues from polishing are relatively easy to identify allowing them to be separated from the parts of the mass spectrum specific to the early stages of corrosion.

Nephron proximal tubule patterning and corpuscles of Stannius formation are regulated by the sim1a transcription factor and retinoic acid in zebrafish.

PubMed

Cheng, Christina N; Wingert, Rebecca A

2015-03-01

The mechanisms that establish nephron segments are poorly understood. The zebrafish embryonic kidney, or pronephros, is a simplified yet conserved genetic model to study this renal development process because its nephrons contain segments akin to other vertebrates, including the proximal convoluted and straight tubules (PCT, PST). The zebrafish pronephros is also associated with the corpuscles of Stannius (CS), endocrine glands that regulate calcium and phosphate homeostasis, but whose ontogeny from renal progenitors is largely mysterious. Initial patterning of zebrafish renal progenitors in the intermediate mesoderm (IM) involves the formation of rostral and caudal domains, the former being reliant on retinoic acid (RA) signaling, and the latter being repressed by elevated RA levels. Here, using expression profiling to gain new insights into nephrogenesis, we discovered that the gene single minded family bHLH transcription factor 1a (sim1a) is dynamically expressed in the renal progenitors-first marking the caudal domain, then becoming restricted to the proximal segments, and finally exhibiting specific CS expression. In loss of function studies, sim1a knockdown expanded the PCT and abrogated both the PST and CS populations. Conversely, overexpression of sim1a modestly expanded the PST and CS, while it reduced the PCT. These results show that sim1a activity is necessary and partially sufficient to induce PST and CS fates, and suggest that sim1a may inhibit PCT fate and/or negotiate the PCT/PST boundary. Interestingly, the sim1a expression domain in renal progenitors is responsive to altered levels of RA, suggesting that RA regulates sim1a, directly or indirectly, during nephrogenesis. sim1a deficient embryos treated with exogenous RA formed nephrons that were predominantly composed of PCT segments, but lacked the enlarged PST observed in RA treated wild-types, indicating that RA is not sufficient to rescue the PST in the absence of sim1a expression. Alternately, when sim1a knockdowns were exposed to the RA inhibitor diethylaminobenzaldehyde (DEAB), the CS was abrogated rather than expanded as seen in DEAB treated wild-types, revealing that CS formation in the absence of sim1a cannot be rescued by RA biosynthesis abrogation. Taken together, these data reveal previously unappreciated roles for sim1a in zebrafish pronephric proximal tubule and CS patterning, and are consistent with the model that sim1a acts downstream of RA to mitigate the formation of these lineages. These findings provide new insights into the genetic pathways that direct nephron development, and may have implications for understanding renal birth defects and kidney reprogramming. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Evaluation of blood adsorption onto dialysis membranes by time-of-flight secondary ion mass spectrometry and near-field infrared microscopy.

PubMed

Aoyagi, Satoka; Abe, Kiyoshi; Yamagishi, Takayuki; Iwai, Hideo; Yamaguchi, Satoru; Sunohara, Takashi

2017-11-01

Blood adsorption onto the inside surface of hollow fiber dialysis membranes was investigated by means of time-of-flight secondary ion mass spectrometry (TOF-SIMS) and near-field infrared microscopy (NFIR) in order to evaluate the biocompatibility and permeability of dialysis membranes. TOF-SIMS is useful for the imaging of particular molecules with a high spatial resolution of approximately 100 nm. In contrast, infrared spectra provide quantitative information and NFIR enables analysis with a high spatial resolution of less than 1 μm, which is close to the resolution of TOF-SIMS. A comparison was made of one of the most widely used dialysis membranes made of polysulfone (PSf), that has an asymmetric and inhomogeneous pore structure, and a newly developed asymmetric cellulose triacetate (ATA) membrane that also has an asymmetric pore structure, even though the conventional cellulose triacetate membrane has a symmetric and homogeneous pore structure. As a result, it was demonstrated that blood adsorption on the inside surface of the ATA membrane is more reduced than that on the PSf membrane. Graphical abstract Analysis of blood adsorption on inside surface of hollow fiber membrane.

Improving Secondary Ion Mass Spectrometry Image Quality with Image Fusion

PubMed Central

Tarolli, Jay G.; Jackson, Lauren M.; Winograd, Nicholas

2014-01-01

The spatial resolution of chemical images acquired with cluster secondary ion mass spectrometry (SIMS) is limited not only by the size of the probe utilized to create the images, but also by detection sensitivity. As the probe size is reduced to below 1 µm, for example, a low signal in each pixel limits lateral resolution due to counting statistics considerations. Although it can be useful to implement numerical methods to mitigate this problem, here we investigate the use of image fusion to combine information from scanning electron microscope (SEM) data with chemically resolved SIMS images. The advantage of this approach is that the higher intensity and, hence, spatial resolution of the electron images can help to improve the quality of the SIMS images without sacrificing chemical specificity. Using a pan-sharpening algorithm, the method is illustrated using synthetic data, experimental data acquired from a metallic grid sample, and experimental data acquired from a lawn of algae cells. The results show that up to an order of magnitude increase in spatial resolution is possible to achieve. A cross-correlation metric is utilized for evaluating the reliability of the procedure. PMID:24912432

Metal-assisted SIMS and cluster ion bombardment for ion yield enhancement

NASA Astrophysics Data System (ADS)

Heile, A.; Lipinsky, D.; Wehbe, N.; Delcorte, A.; Bertrand, P.; Felten, A.; Houssiau, L.; Pireaux, J.-J.; De Mondt, R.; Van Vaeck, L.; Arlinghaus, H. F.

2008-12-01

In addition to structural information, a detailed knowledge of the local chemical environment proves to be of ever greater importance, for example for the development of new types of materials as well as for specific modifications of surfaces and interfaces in multiple fields of materials science or various biomedical and chemical applications. But the ongoing miniaturization and therefore reduction of the amount of material available for analysis constitute a challenge to the detection limits of analytical methods. In the case of time-of-flight secondary ion mass spectrometry (TOF-SIMS), several methods of secondary ion yield enhancement have been proposed. This paper focuses on the investigation of the effects of two of these methods, metal-assisted SIMS and polyatomic primary ion bombardment. For this purpose, thicker layers of polystyrene (PS), both pristine and metallized with different amounts of gold, were analyzed using monoatomic (Ar +, Ga +, Xe +, Bi +) and polyatomic (SF 5+, Bi 3+, C 60+) primary ions. It was found that polyatomic ions generally induce a significant increase of the secondary ion yield. On the other hand, with gold deposition, a yield enhancement can only be detected for monoatomic ion bombardment.

Shear induced migration of particles in a yield stress fluid: experiment

NASA Astrophysics Data System (ADS)

Hormozi, Sarah; Gholami, Mohammad; Rashedi, Ahmadreza; Lenoir, Nicolas; Ovarlez, Guillaume

2017-11-01

We have performed rheometry coupled with X-ray radiography in a narrow gap Couette cell filled with a suspension of spherical particles in a yield stress fluid. In this setup, the shear rate is discontinuous changing from a constant value in the gap to zero in the reservoir located at the top. This shear rate inhomogeneity results in the migration of particles from the gap to the reservoir, so-called Shear Induced Migration (SIM). The rheometry results give us insight into understanding the bulk rheology in the presence of shear rate and solid volume fraction inhomogeneities. In addition to that, our recent X-ray radiography technique (Gholami et al., JOR. 2017) provides detailed information about the evolution of the solid volume fraction in the domain. These measurements allow us to refine the recent continuum model frameworks (Hormozi & Frigaard, JFM 2017) for SIM of particles in a yield stress suspending fluid. We show that complex rheology of the yield stress suspending fluid and formation of the islands of unyielded regions in the reservoir strongly affects the SIM of particles. This feature is absent when we deal with a Newtonian suspending fluid. NSF (Grant No. CBET-1554044- CAREER), ACS PRF (Grant No. 55661-DNI9).

SimLabel: a graphical user interface to simulate continuous wave EPR spectra from site-directed spin labeling experiments.

PubMed

Etienne, E; Le Breton, N; Martinho, M; Mileo, E; Belle, V

2017-08-01

Site-directed spin labeling (SDSL) combined with continuous wave electron paramagnetic resonance (cw EPR) spectroscopy is a powerful technique to reveal, at the residue level, structural transitions in proteins. SDSL-EPR is based on the selective grafting of a paramagnetic label on the protein under study, followed by cw EPR analysis. To extract valuable quantitative information from SDSL-EPR spectra and thus give reliable interpretation on biological system dynamics, numerical simulations of the spectra are required. Such spectral simulations can be carried out by coding in MATLAB using functions from the EasySpin toolbox. For non-expert users of MATLAB, this could be a complex task or even impede the use of such simulation tool. We developed a graphical user interface called SimLabel dedicated to run cw EPR spectra simulations particularly coming from SDSL-EPR experiments. Simlabel provides an intuitive way to visualize, simulate, and fit such cw EPR spectra. An example of SDSL-EPR spectra simulation concerning the study of an intrinsically disordered region undergoing a local induced folding is described and discussed. We believe that this new tool will help the users to rapidly obtain reliable simulated spectra and hence facilitate the interpretation of their results. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Towards a Hybrid Agent-based Model for Mosquito Borne Disease.

PubMed

Mniszewski, S M; Manore, C A; Bryan, C; Del Valle, S Y; Roberts, D

2014-07-01

Agent-based models (ABM) are used to simulate the spread of infectious disease through a population. Detailed human movement, demography, realistic business location networks, and in-host disease progression are available in existing ABMs, such as the Epidemic Simulation System (EpiSimS). These capabilities make possible the exploration of pharmaceutical and non-pharmaceutical mitigation strategies used to inform the public health community. There is a similar need for the spread of mosquito borne pathogens due to the re-emergence of diseases such as chikungunya and dengue fever. A network-patch model for mosquito dynamics has been coupled with EpiSimS. Mosquitoes are represented as a "patch" or "cloud" associated with a location. Each patch has an ordinary differential equation (ODE) mosquito dynamics model and mosquito related parameters relevant to the location characteristics. Activities at each location can have different levels of potential exposure to mosquitoes based on whether they are inside, outside, or somewhere in-between. As a proof of concept, the hybrid network-patch model is used to simulate the spread of chikungunya through Washington, DC. Results are shown for a base case, followed by varying the probability of transmission, mosquito count, and activity exposure. We use visualization to understand the pattern of disease spread.

Surface studies of heterogeneous catalysts by time-of-flight secondary ion mass spectrometry.

PubMed

Grams, Jacek

2010-01-01

The aim of this paper was to present potentialities of time-of-flight secondary ion mass spectrometry (ToF- SIMS) in the studies of heterogeneous catalysts. The results of ToF-SIMS investigations of Co/Al2O3, Mo/Al2O3, Co-Mo/Al2O3, Au/Al2O3, Pt/TiO2 and Pd/TiO2 systems were described. It was demonstrated that, in this case, an application of ToF-SIMS makes possible the determination of surface composition of investigated catalysts (including an identification of surface contaminants), characterization of interactions between an active phase and support, estimation of active phase dispersion on the analyzed surface, comparison of the degree of metal oxidation after treatment of the catalyst in different conditions, investigation of catalyst deactivation processes (formation of new chemical compounds, adsorption of various impurities and poisons on the catalyst surface) and determination of organic precursors of catalysts.

Effect of Ceramic Ball and Hybrid Stainless Steel Bearing/Wheel Combinations on the Lifetime of a Precision Translation Stage for the SIM Flight Project

NASA Technical Reports Server (NTRS)

Lo, C. John; Klein, Kerry; Jones, William R., Jr.; Jansen, Mark J.; Wemhoner, Jens

2009-01-01

A study of hybrid material couples using the Spiral Orbit Tribometer (SOT) was initiated to investigate both lubricated (Pennzane X2000 and Brayco 815Z) and unlubricated Si3N4, 440C SS, Rex 20, Cronidur X30 and X40 plates with Cerbec SN-101-C (Si3N4) and 440C balls. The hybrid wheel/bearing assembly will be used on the Linear Optical Delay Line (LODL) stage as an element of the NASA Space Interferometry Mission (SIM). SIM is an orbiting interferometer linking a pair of telescopes within the spacecraft and, by using an interferometry technique and several precision optical stages, is able to measure the motions of known stars much better than current ground or space based systems. This measurement will provide the data to "infer" the existence of any plants, undetectable by other methods, orbiting these known stars.

SIMS prototype system 1: Design data brochure. [solar heating system

NASA Technical Reports Server (NTRS)

1978-01-01

A prototype solar heating and hot water system using air as the collector fluid and a pebble bed for heat storage was designed for installation into a single family dwelling. The system, subsystem, and installation requirements are described. System operation and performance are discussed, and procedures for sizing the system to a specific site are presented.

Solar energy system performance evaluation: Seasonal report for IBM System 2, Togus, Maine

NASA Technical Reports Server (NTRS)

1980-01-01

The solar energy system, SIMS Prototype System 2, was designed to supply domestic hot water to single family residences. The system consists of flat plate collectors, silicone working fluid, storage tanks, pumps, heat exchanger, controls, and associated plumbing. The long term field performance of the installed system was analyzed and the results are described.

Sim1 is required for the migration and axonal projections of V3 interneurons in the developing mouse spinal cord.

PubMed

Blacklaws, Jake; Deska-Gauthier, Dylan; Jones, Christopher T; Petracca, Yanina L; Liu, Mingwei; Zhang, Han; Fawcett, James P; Glover, Joel C; Lanuza, Guillermo M; Zhang, Ying

2015-09-01

V3 spinal interneurons (INs) are a group of excitatory INs that play a crucial role in producing balanced and stable gaits in vertebrate animals. In the developing mouse spinal cord, V3 INs arise from the most ventral progenitor domain and form anatomically distinctive subpopulations in adult spinal cords. They are marked by the expression of transcription factor Sim1 postmitotically, but the function of Sim1 in V3 development remains unknown. Here, we used Sim1(Cre) ;tdTomato mice to trace the fate of V3 INs in a Sim1 mutant versus control genetic background during development. In Sim1 mutants, V3 INs are produced normally and maintain a similar position and organization as in wild types before E12.5. Further temporal analysis revealed that the V3 INs in the mutants failed to migrate properly to form V3 subgroups along the dorsoventral axis of the spinal cord. At birth, in the Sim1 mutant the number of V3 INs in the ventral subgroup was normal, but they were significantly reduced in the dorsal subgroup with a concomitant increase in the intermediate subgroup. Retrograde labeling at lumbar level revealed that loss of Sim1 led to a reduction in extension of contralateral axon projections both at E14.5 and P0 without affecting ipsilateral axon projections. These results demonstrate that Sim1 is essential for proper migration and the guidance of commissural axons of the spinal V3 INs. © 2015 Wiley Periodicals, Inc.

Installation package - SIMS prototype system 1A

NASA Technical Reports Server (NTRS)

1976-01-01

This report consists of details for the installation, operation and maintenance of a prototype heating and hot water system, designed for residential or light commercial applications. This system consists of the following subsystems: air type collectors, pebble bed thermal storage, air handling unit, air to water heat exchanger, hot water preheat tank, auxiliary energy, ducting system.

Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes.

PubMed

Sedwards, Sean; Mazza, Tommaso

2007-10-15

Compartments and membranes are the basis of cell topology and more than 30% of the human genome codes for membrane proteins. While it is possible to represent compartments and membrane proteins in a nominal way with many mathematical formalisms used in systems biology, few, if any, explicitly model the topology of the membranes themselves. Discrete stochastic simulation potentially offers the most accurate representation of cell dynamics. Since the details of every molecular interaction in a pathway are often not known, the relationship between chemical species in not necessarily best described at the lowest level, i.e. by mass action. Simulation is a form of computer-aided analysis, relying on human interpretation to derive meaning. To improve efficiency and gain meaning in an automatic way, it is necessary to have a formalism based on a model which has decidable properties. We present Cyto-Sim, a stochastic simulator of membrane-enclosed hierarchies of biochemical processes, where the membranes comprise an inner, outer and integral layer. The underlying model is based on formal language theory and has been shown to have decidable properties (Cavaliere and Sedwards, 2006), allowing formal analysis in addition to simulation. The simulator provides variable levels of abstraction via arbitrary chemical kinetics which link to ordinary differential equations. In addition to its compact native syntax, Cyto-Sim currently supports models described as Petri nets, can import all versions of SBML and can export SBML and MATLAB m-files. Cyto-Sim is available free, either as an applet or a stand-alone Java program via the web page (http://www.cosbi.eu/Rpty_Soft_CytoSim.php). Other versions can be made available upon request.

Creating a Software Framework for Simulating Satellite Geolocation

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

Koch, Daniel B

2011-01-01

It is hard to imagine life these days without having some sort of electronic indication of one's current location. Whether the purpose is for business, personal, or emergency use, utilizing smart cell phones, in-vehicle navigation systems, or location beacons, dependence on the Global Positioning System (GPS) is pervasive. Yet the availability of the GPS should not be taken for granted. Both environmental (e.g., terrain, weather) and intentional interference (i.e., jamming) can reduce or deny satellite access. In order to investigate these and other issues, as well as to explore possible alternative satellite constellations, an application called the Satellite Simulation Toolkitmore » (SatSim) was created. This paper presents a high-level overview of SatSim and an example of how it may be used to study geolocation.« less

Applications of time-of-flight secondary ion mass spectrometry (TOF-SIMS) and X-ray photoelectron spectroscopy (XPS) to study interactions of genetically engineered proteins with noble metal films

NASA Astrophysics Data System (ADS)

Suzuki, Noriaki

Genetically engineered proteins for inorganics (GEPIs) belong to a new class of polypeptides that are designed to have specific affinities to inorganic materials. A "gold binding protein (GBP)" was chosen as a model protein for GEPIs to study the molecular origins of binding specificity to gold using Time-of-flight secondary ion mass spectrometry (TOF-SIMS) and X-ray photoelectron spectroscopy (XPS). TOF-SIMS, a surface-sensitive analytical instrument with extremely high mass resolutions, provides information on specific amino acid-surface interactions. We used "principal component analysis (PCA)" to analyze the data. We also introduced a new multivariate technique, "hierarchical cluster analysis (HCA)" to organize the data into meaningful structures by measuring a degree of "similarity" and "dissimilarity" of the data. This report discusses a combined use of PCA and HCA to elucidate the binding specificity of GBP to Au. Based on the knowledge gained from TOF-SIMS measurements, we further investigated the nature of the interaction between selected amino acids and noble metal surfaces by using X-ray photoelectron spectroscopy (XPS). We developed a unique capability to introduce water vapor during the adsorption of a single amino acid and applied this method to study the intrinsic nature of sidechain/Au interactions. To further apply this unique research protocol, we characterized another type of GEPI, "quartz binding protein (QBP)," to identify the possible binding sites. This thesis research aims to provide experimental protocols for analyzing short peptide-substrate interface from complex spectroscopic data by using multivariate analysis techniques.

SimITK: visual programming of the ITK image-processing library within Simulink.

PubMed

Dickinson, Andrew W L; Abolmaesumi, Purang; Gobbi, David G; Mousavi, Parvin

2014-04-01

The Insight Segmentation and Registration Toolkit (ITK) is a software library used for image analysis, visualization, and image-guided surgery applications. ITK is a collection of C++ classes that poses the challenge of a steep learning curve should the user not have appropriate C++ programming experience. To remove the programming complexities and facilitate rapid prototyping, an implementation of ITK within a higher-level visual programming environment is presented: SimITK. ITK functionalities are automatically wrapped into "blocks" within Simulink, the visual programming environment of MATLAB, where these blocks can be connected to form workflows: visual schematics that closely represent the structure of a C++ program. The heavily templated C++ nature of ITK does not facilitate direct interaction between Simulink and ITK; an intermediary is required to convert respective data types and allow intercommunication. As such, a SimITK "Virtual Block" has been developed that serves as a wrapper around an ITK class which is capable of resolving the ITK data types to native Simulink data types. Part of the challenge surrounding this implementation involves automatically capturing and storing the pertinent class information that need to be refined from an initial state prior to being reflected within the final block representation. The primary result from the SimITK wrapping procedure is multiple Simulink block libraries. From these libraries, blocks are selected and interconnected to demonstrate two examples: a 3D segmentation workflow and a 3D multimodal registration workflow. Compared to their pure-code equivalents, the workflows highlight ITK usability through an alternative visual interpretation of the code that abstracts away potentially confusing technicalities.

Rim Sim: A Role-Play Simulation

USGS Publications Warehouse

Barrett, Robert C.; Frew, Suzanne L.; Howell, David G.; Karl, Herman A.; Rudin, Emily B.

2003-01-01

Rim Sim is a 6-hour, eight-party negotiation that focuses on creating a framework for the long-term disaster-recovery efforts. It involves a range of players from five countries affected by two natural disasters: a typhoon about a year ago and an earthquake about 6 months ago. The players are members of an International Disaster Working Group (IDWG) that has been created by an international commission. The IDWG has been charged with drawing up a framework for managing two issues: the reconstruction of regionally significant infrastructure and the design of a mechanism for allocating funding to each country for reconstruction of local infrastructure and ongoing humanitarian needs. The first issue will involve making choices among five options (two harbor options, two airport options, and one rail-line option), each of which will have three levels at which to rebuild. The second issue will involve five starting-point options. Participants are encouraged to invent other options for both issues. The goal of Rim Sim is to raise questions about traditional approaches to disaster-preparedness planning and reconstruction efforts in an international setting, in this case the Pacific Rim. Players must confront the reverberating effects of disasters and the problems of using science and technical information in decisionmaking, and are introduced to a consensus-building approach emphasizing face-to-face dialog and multinational cooperation in dealing with humanitarian concerns, as well as long-term efforts to reconstruct local and regional infrastructure. The Rim Sim simulation raises four key points: ripple effects of disasters, role of science, multiparty negotiation, and building personal relationships.

Artist concept of SIM PlanetQuest Artist Concept

NASA Image and Video Library

2002-12-21

Artist's concept of the current mission configuration. SIM PlanetQuest (formerly called Space Interferometry Mission), currently under development, will determine the positions and distances of stars several hundred times more accurately than any previous program. This accuracy will allow SIM to determine the distances to stars throughout the galaxy and to probe nearby stars for Earth-sized planets. SIM will open a window to a new world of discoveries. http://photojournal.jpl.nasa.gov/catalog/PIA04248

Transfer of skills on LapSim virtual reality laparoscopic simulator into the operating room in urology.

PubMed

Alwaal, Amjad; Al-Qaoud, Talal M; Haddad, Richard L; Alzahrani, Tarek M; Delisle, Josee; Anidjar, Maurice

2015-01-01

Assessing the predictive validity of the LapSim simulator within a urology residency program. Twelve urology residents at McGill University were enrolled in the study between June 2008 and December 2011. The residents had weekly training on the LapSim that consisted of 3 tasks (cutting, clip-applying, and lifting and grasping). They underwent monthly assessment of their LapSim performance using total time, tissue damage and path length among other parameters as surrogates for their economy of movement and respect for tissue. The last residents' LapSim performance was compared with their first performance of radical nephrectomy on anesthetized porcine models in their 4(th) year of training. Two independent urologic surgeons rated the resident performance on the porcine models, and kappa test with standardized weight function was used to assess for inter-observer bias. Nonparametric spearman correlation test was used to compare each rater's cumulative score with the cumulative score obtained on the porcine models in order to test the predictive validity of the LapSim simulator. The kappa results demonstrated acceptable agreement between the two observers among all domains of the rating scale of performance except for confidence of movement and efficiency. In addition, poor predictive validity of the LapSim simulator was demonstrated. Predictive validity was not demonstrated for the LapSim simulator in the context of a urology residency training program.

SIMS: A Hybrid Method for Rapid Conformational Analysis

PubMed Central

Gipson, Bryant; Moll, Mark; Kavraki, Lydia E.

2013-01-01

Proteins are at the root of many biological functions, often performing complex tasks as the result of large changes in their structure. Describing the exact details of these conformational changes, however, remains a central challenge for computational biology due the enormous computational requirements of the problem. This has engendered the development of a rich variety of useful methods designed to answer specific questions at different levels of spatial, temporal, and energetic resolution. These methods fall largely into two classes: physically accurate, but computationally demanding methods and fast, approximate methods. We introduce here a new hybrid modeling tool, the Structured Intuitive Move Selector (sims), designed to bridge the divide between these two classes, while allowing the benefits of both to be seamlessly integrated into a single framework. This is achieved by applying a modern motion planning algorithm, borrowed from the field of robotics, in tandem with a well-established protein modeling library. sims can combine precise energy calculations with approximate or specialized conformational sampling routines to produce rapid, yet accurate, analysis of the large-scale conformational variability of protein systems. Several key advancements are shown, including the abstract use of generically defined moves (conformational sampling methods) and an expansive probabilistic conformational exploration. We present three example problems that sims is applied to and demonstrate a rapid solution for each. These include the automatic determination of “active” residues for the hinge-based system Cyanovirin-N, exploring conformational changes involving long-range coordinated motion between non-sequential residues in Ribose-Binding Protein, and the rapid discovery of a transient conformational state of Maltose-Binding Protein, previously only determined by Molecular Dynamics. For all cases we provide energetic validations using well-established energy fields, demonstrating this framework as a fast and accurate tool for the analysis of a wide range of protein flexibility problems. PMID:23935893

Role of ghrelin in small intestinal motility following pediatric intracerebral hemorrhage in mice.

PubMed

Zan, Jieyu; Song, Lei; Wang, Jiejie; Zou, Rong; Hong, Fei; Zhao, Jinhua; Cheng, Yijun; Xu, Ming

2017-11-01

Small intestinal motility (SIM) disorder is a common complication following pediatric intracerebral hemorrhage (ICH), leading to a poor prognosis in patients. Previous studies have shown that ghrelin is involved in SIM in various diseases; however, the role of ghrelin in pediatric ICH‑induced SIM disorder remains to be elucidated. The present study was designed to investigate the association between ghrelin and SIM post‑ICH, and to examine the effect of exogenous ghrelin administration on SIM in vivo. An ICH model was induced in mice by autologous blood infusion. Neurobehavioral deficits were evaluated using a Rotarod test, forelimb placing test, and corner turn test. Intestinal mucosal damage was examined using hematoxylin and eosin staining. SIM was measured using charcoal meal staining. An enzyme‑linked immunosorbent assay was used to evaluate serum levels of ghrelin and nitric oxide (NO). Reverse transcription‑quantitative polymerase chain reaction and western blot analyses were performed to determine the levels of inducible nitric oxide synthase (iNOS), neuronal nitric oxide synthase (nNOS) and endothelial nitric oxide synthase (eNOS) at the mRNA and protein levels. Nω‑nitro‑L‑arginine methyl ester hydrochloride (L‑NAME), L‑arginine, atropine, phentolamine and propranolol were used to manipulate the putative pathways induced by ghrelin. Neurological dysfunction was observed post‑ICH. ICH caused damage to the intestinal mucosa and delayed SIM. Serum levels of ghrelin increased between 3 h and 3 days, peaking at 12 h, and showed a significant negative correlation with SIM post‑ICH. Ghrelin administration dose‑dependently attenua-ted ICH‑induced SIM disorder. Ghrelin also decreased NO levels by downregulating the mRNA and protein expression levels of iNOS, but not those of nNOS or eNOS, post‑ICH. Consistently, the effect was enhanced by L‑NAME and weakened by L‑arginine, respectively. The protective effect of ghrelin was eradicated by atropine, but not phentolamine or propranolol. These findings suggested that ghrelin ameliorated SIM disorder by downregulating iNOS/NO via the cholinergic pathway. Therefore, ghrelin may serve as a potential biomarker and useful target in ICH‑induced SIM disorder.

Improved Response to Disasters and Outbreaks by Tracking Population Movements with Mobile Phone Network Data: A Post-Earthquake Geospatial Study in Haiti

PubMed Central

Bengtsson, Linus; Lu, Xin; Thorson, Anna; Garfield, Richard; von Schreeb, Johan

2011-01-01

Background Population movements following disasters can cause important increases in morbidity and mortality. Without knowledge of the locations of affected people, relief assistance is compromised. No rapid and accurate method exists to track population movements after disasters. We used position data of subscriber identity module (SIM) cards from the largest mobile phone company in Haiti (Digicel) to estimate the magnitude and trends of population movements following the Haiti 2010 earthquake and cholera outbreak. Methods and Findings Geographic positions of SIM cards were determined by the location of the mobile phone tower through which each SIM card connects when calling. We followed daily positions of SIM cards 42 days before the earthquake and 158 days after. To exclude inactivated SIM cards, we included only the 1.9 million SIM cards that made at least one call both pre-earthquake and during the last month of study. In Port-au-Prince there were 3.2 persons per included SIM card. We used this ratio to extrapolate from the number of moving SIM cards to the number of moving persons. Cholera outbreak analyses covered 8 days and tracked 138,560 SIM cards. An estimated 630,000 persons (197,484 Digicel SIM cards), present in Port-au-Prince on the day of the earthquake, had left 19 days post-earthquake. Estimated net outflow of people (outflow minus inflow) corresponded to 20% of the Port-au-Prince pre-earthquake population. Geographic distribution of population movements from Port-au-Prince corresponded well with results from a large retrospective, population-based UN survey. To demonstrate feasibility of rapid estimates and to identify areas at potentially increased risk of outbreaks, we produced reports on SIM card movements from a cholera outbreak area at its immediate onset and within 12 hours of receiving data. Conclusions Results suggest that estimates of population movements during disasters and outbreaks can be delivered rapidly and with potentially high validity in areas with high mobile phone use. Please see later in the article for the Editors' Summary PMID:21918643

SimRiver: Environmental Modeling Software for the Science Classroom

ERIC Educational Resources Information Center

Hoffer, Jeannette; Mayama, Shigeki; Lingle, Kristin; Conroy, Kathryn; Julius, Matthew

2011-01-01

While students may acknowledge the impact that land use and development have on our environment, they do not necessarily understand the relationship between human activities and ecosystem responses. Therefore, the nature of the relationships leaves the science teacher to most often present information in a purely narrative form without any…

78 FR 58348 - Agency Information Collection Activities; Proposed Collection; Comments Requested: National...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-23

.... Fleming, Field Division Counsel, El Paso Intelligence Center, 11339 SSG Sims Blvd., El Paso, TX 79908... validity of the methodology and assumptions used; Enhance the quality, utility, and clarity of the... sponsoring the collection: Form number: EPIC Form 143. Component: El Paso Intelligence Center, Drug...

Automated road segment creation process : a report on research sponsored by SaferSim.

DOT National Transportation Integrated Search

2016-08-01

This report provides a summary of a set of tools that can be used to automate the process : of generating roadway surfaces from alignment and texture information. The tools developed : were created in Python 3.x and rely on the availability of two da...

Graph-based analysis of connectivity in spatially-explicit population models: HexSim and the Connectivity Analysis Toolkit

EPA Science Inventory

Background / Question / Methods Planning for the recovery of threatened species is increasingly informed by spatially-explicit population models. However, using simulation model results to guide land management decisions can be difficult due to the volume and complexity of model...

Solid-State Molecular Nanomagnet Inclusion into a Magnetic Metal-Organic Framework: Interplay of the Magnetic Properties.

PubMed

Mon, Marta; Pascual-Álvarez, Alejandro; Grancha, Thais; Cano, Joan; Ferrando-Soria, Jesús; Lloret, Francesc; Gascon, Jorge; Pasán, Jorge; Armentano, Donatella; Pardo, Emilio

2016-01-11

Single-ion magnets (SIMs) are the smallest possible magnetic devices and are a controllable, bottom-up approach to nanoscale magnetism with potential applications in quantum computing and high-density information storage. In this work, we take advantage of the promising, but yet insufficiently explored, solid-state chemistry of metal-organic frameworks (MOFs) to report the single-crystal to single-crystal inclusion of such molecular nanomagnets within the pores of a magnetic MOF. The resulting host-guest supramolecular aggregate is used as a playground in the first in-depth study on the interplay between the internal magnetic field created by the long-range magnetic ordering of the structured MOF and the slow magnetic relaxation of the SIM. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

HexSim: a modeling environment for ecology and conservation.

EPA Science Inventory

HexSim is a powerful and flexible new spatially-explicit, individual based modeling environment intended for use in ecology, conservation, genetics, epidemiology, toxicology, and other disciplines. We describe HexSim, illustrate past applications that contributed to our >10 year ...

Bio-SimVerb and Bio-SimLex: wide-coverage evaluation sets of word similarity in biomedicine.

PubMed

Chiu, Billy; Pyysalo, Sampo; Vulić, Ivan; Korhonen, Anna

2018-02-05

Word representations support a variety of Natural Language Processing (NLP) tasks. The quality of these representations is typically assessed by comparing the distances in the induced vector spaces against human similarity judgements. Whereas comprehensive evaluation resources have recently been developed for the general domain, similar resources for biomedicine currently suffer from the lack of coverage, both in terms of word types included and with respect to the semantic distinctions. Notably, verbs have been excluded, although they are essential for the interpretation of biomedical language. Further, current resources do not discern between semantic similarity and semantic relatedness, although this has been proven as an important predictor of the usefulness of word representations and their performance in downstream applications. We present two novel comprehensive resources targeting the evaluation of word representations in biomedicine. These resources, Bio-SimVerb and Bio-SimLex, address the previously mentioned problems, and can be used for evaluations of verb and noun representations respectively. In our experiments, we have computed the Pearson's correlation between performances on intrinsic and extrinsic tasks using twelve popular state-of-the-art representation models (e.g. word2vec models). The intrinsic-extrinsic correlations using our datasets are notably higher than with previous intrinsic evaluation benchmarks such as UMNSRS and MayoSRS. In addition, when evaluating representation models for their abilities to capture verb and noun semantics individually, we show a considerable variation between performances across all models. Bio-SimVerb and Bio-SimLex enable intrinsic evaluation of word representations. This evaluation can serve as a predictor of performance on various downstream tasks in the biomedical domain. The results on Bio-SimVerb and Bio-SimLex using standard word representation models highlight the importance of developing dedicated evaluation resources for NLP in biomedicine for particular word classes (e.g. verbs). These are needed to identify the most accurate methods for learning class-specific representations. Bio-SimVerb and Bio-SimLex are publicly available.

The medical ethics of Dr J Marion Sims: a fresh look at the historical record

PubMed Central

Wall, L L

2006-01-01

Vesicovaginal fistula was a catastrophic complication of childbirth among 19th century American women. The first consistently successful operation for this condition was developed by Dr J Marion Sims, an Alabama surgeon who carried out a series of experimental operations on black slave women between 1845 and 1849. Numerous modern authors have attacked Sims's medical ethics, arguing that he manipulated the institution of slavery to perform ethically unacceptable human experiments on powerless, unconsenting women. This article reviews these allegations using primary historical source material and concludes that the charges that have been made against Sims are largely without merit. Sims's modern critics have discounted the enormous suffering experienced by fistula victims, have ignored the controversies that surrounded the introduction of anaesthesia into surgical practice in the middle of the 19th century, and have consistently misrepresented the historical record in their attacks on Sims. Although enslaved African American women certainly represented a “vulnerable population” in the 19th century American South, the evidence suggests that Sims's original patients were willing participants in his surgical attempts to cure their affliction—a condition for which no other viable therapy existed at that time. PMID:16731734

WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions

PubMed Central

Karr, Jonathan R.; Phillips, Nolan C.; Covert, Markus W.

2014-01-01

Mechanistic ‘whole-cell’ models are needed to develop a complete understanding of cell physiology. However, extracting biological insights from whole-cell models requires running and analyzing large numbers of simulations. We developed WholeCellSimDB, a database for organizing whole-cell simulations. WholeCellSimDB was designed to enable researchers to search simulation metadata to identify simulations for further analysis, and quickly slice and aggregate simulation results data. In addition, WholeCellSimDB enables users to share simulations with the broader research community. The database uses a hybrid relational/hierarchical data format architecture to efficiently store and retrieve both simulation setup metadata and results data. WholeCellSimDB provides a graphical Web-based interface to search, browse, plot and export simulations; a JavaScript Object Notation (JSON) Web service to retrieve data for Web-based visualizations; a command-line interface to deposit simulations; and a Python API to retrieve data for advanced analysis. Overall, we believe WholeCellSimDB will help researchers use whole-cell models to advance basic biological science and bioengineering. Database URL: http://www.wholecellsimdb.org Source code repository URL: http://github.com/CovertLab/WholeCellSimDB PMID:25231498

A NASP (N1/N2)-Related Protein, Sim3, Binds CENP-A and Is Required for Its Deposition at Fission Yeast Centromeres

PubMed Central

Dunleavy, Elaine M.; Pidoux, Alison L.; Monet, Marie; Bonilla, Carolina; Richardson, William; Hamilton, Georgina L.; Ekwall, Karl; McLaughlin, Paul J.; Allshire, Robin C.

2007-01-01

Summary A defining feature of centromeres is the presence of the histone H3 variant CENP-ACnp1. It is not known how CENP-ACnp1 is specifically delivered to, and assembled into, centromeric chromatin. Through a screen for factors involved in kinetochore integrity in fission yeast, we identified Sim3. Sim3 is homologous to known histone binding proteins NASPHuman and N1/N2Xenopus and aligns with Hif1S. cerevisiae, defining the SHNi-TPR family. Sim3 is distributed throughout the nucleoplasm, yet it associates with CENP-ACnp1 and also binds H3. Cells defective in Sim3 function have reduced levels of CENP-ACnp1 at centromeres (and increased H3) and display chromosome segregation defects. Sim3 is required to allow newly synthesized CENP-ACnp1 to accumulate at centromeres in S and G2 phase-arrested cells in a replication-independent mechanism. We propose that one function of Sim3 is to act as an escort that hands off CENP-ACnp1 to chromatin assembly factors, allowing its incorporation into centromeric chromatin. PMID:18158900

The Structured Inventory of Malingered Symptomatology (SIMS): a systematic review and meta-analysis.

PubMed

van Impelen, Alfons; Merckelbach, Harald; Jelicic, Marko; Merten, Thomas

2014-01-01

We meta-analytically reviewed studies that used the Structured Inventory of Malingered Symptomatology (SIMS) to detect feigned psychopathology. We present weighted mean diagnostic accuracy and predictive power indices in various populations, based on 31 studies, including 61 subsamples and 4009 SIMS protocols. In addition, we provide normative data of patients, claimants, defendants, nonclinical adults, and various experimental feigners, based on 41 studies, including 125 subsamples and 4810 SIMS protocols. We conclude that the SIMS (1) is able to differentiate well between instructed feigners and honest responders; (2) generates heightened scores in groups that are known to have a raised prevalence of feigning (e.g., offenders who claim crime-related amnesia); (3) may overestimate feigning in patients who suffer from schizophrenia, intellectual disability, or psychogenic non-epileptic seizures; and (4) is fairly robust against coaching. The diagnostic power of the traditional cut scores of the SIMS (i.e., > 14 and > 16) is not so much limited by their sensitivity—which is satisfactory—but rather by their substandard specificity. This, however, can be worked around by combining the SIMS with other symptom validity measures and by raising the cut score, although the latter solution sacrifices sensitivity for specificity.

GLABROUS INFLORESCENCE STEMS regulates trichome branching by genetically interacting with SIM in Arabidopsis.

PubMed

Sun, Li-Li; Zhou, Zhong-Jing; An, Li-Jun; An, Yan; Zhao, Yong-Qin; Meng, Xiao-Fang; Steele-King, Clare; Gan, Yin-Bo

2013-07-01

Arabidopsis trichomes are large branched single cells that protrude from the epidermis. The first morphological indication of trichome development is an increase in nuclear content resulting from an initial cycle of endoreduplication. Our previous study has shown that the C2H2 zinc finger protein GLABROUS INFLORESCENCE STEMS (GIS) is required for trichome initiation in the inflorescence organ and for trichome branching in response to gibberellic acid signaling, although GIS gene does not play a direct role in regulating trichome cell division. Here, we describe a novel role of GIS, controlling trichome cell division indirectly by interacting genetically with a key endoreduplication regulator SIAMESE (SIM). Our molecular and genetic studies have shown that GIS might indireclty control cell division and trichome branching by acting downstream of SIM. A loss of function mutation of SIM signficantly reduced the expression of GIS. Futhermore, the overexpression of GIS rescued the trichome cluster cell phenotypes of sim mutant. The gain or loss of function of GIS had no significant effect on the expression of SIM. These results suggest that GIS may play an indirect role in regulating trichome cell division by genetically interacting with SIM.

The medical ethics of Dr J Marion Sims: a fresh look at the historical record.

PubMed

Wall, L L

2006-06-01

Vesicovaginal fistula was a catastrophic complication of childbirth among 19th century American women. The first consistently successful operation for this condition was developed by Dr J Marion Sims, an Alabama surgeon who carried out a series of experimental operations on black slave women between 1845 and 1849. Numerous modern authors have attacked Sims's medical ethics, arguing that he manipulated the institution of slavery to perform ethically unacceptable human experiments on powerless, unconsenting women. This article reviews these allegations using primary historical source material and concludes that the charges that have been made against Sims are largely without merit. Sims's modern critics have discounted the enormous suffering experienced by fistula victims, have ignored the controversies that surrounded the introduction of anaesthesia into surgical practice in the middle of the 19th century, and have consistently misrepresented the historical record in their attacks on Sims. Although enslaved African American women certainly represented a "vulnerable population" in the 19th century American South, the evidence suggests that Sims's original patients were willing participants in his surgical attempts to cure their affliction-a condition for which no other viable therapy existed at that time.

A Computational Dual-Process Model of Social Interaction

DTIC Science & Technology

2014-01-30

that portray the model’s behaviors when OMAR was adapted to operate first with Neverwinter Night and then with OpenSim . 3.1 Overview of Human...the Neverwinter Night (NwN; http://nwn.wikia.com) environment and more recently adapted to run with OpenSim (http://opensimulator.org). Figure 1...provides a screenshot of a scene from the NwN world while Figure 2 provides a screenshot from the OpenSim world. The NwN and OpenSim avatars and scenes

Magnifying endoscopy for the diagnosis of specialized intestinal metaplasia in short-segment Barrett's esophagus.

PubMed

Ham, Nam Seok; Jang, Jae Young; Ryu, Sung Woo; Kim, Ji Hye; Park, Eui Ju; Lee, Woong Cheul; Shim, Kwang Yeun; Jeong, Soung Won; Kim, Hyun Gun; Lee, Tae Hee; Jeon, Sung Ran; Cho, Jun Hyung; Cho, Joo Young; Jin, So Young; Lee, Ji Sung

2013-11-07

To determine whether magnified observation of short-segment Barrett's esophagus (BE) is useful for the detection of specialized intestinal metaplasia (SIM). Thirty patients with suspected short-segment BE underwent magnifying endoscopy up to × 80. The magnified images were analyzed with respect to their pit-patterns, which were simultaneously classified into five epithelial types [I (small round), II (straight), III (long oval), IV (tubular), V (villous)] by Endo's classification. Then, a 0.5% solution of methylene blue (MB) was sprayed over columnar mucosa. The patterns of the magnified image and MB staining were analyzed. Biopsies were obtained from the regions previously observed by magnifying endoscopy and MB chromoendoscopy. Three of five patients with a type V (villous) epithelial pattern had SIM, whereas 21 patients with a non-type V epithelial patterns did not have SIM. The sensitivity, specificity, accuracy, positive predictive value, and negative predictive value of pit-patterns in detecting SIM were 100%, 91.3%, 92.3%, 60% and 100%, respectively (P = 0.004). Three of the 12 patients with positive MB staining had SIM, whereas 14 patients with negative MB staining did not have SIM. The sensitivity, specificity, accuracy, positive predictive value, and negative predictive value of MB staining in detecting SIM were 100%, 60.9%, 65.4%, 25% and 100%, respectively (P = 0.085). The specificity and accuracy of pit-pattern evaluation were significantly superior compared with MB staining for detecting SIM by comparison with the exact McNemar's test (P = 0.0391). The magnified observation of a short-segment BE according to the mucosal pattern and its classification can be predictive of SIM.

Numerical investigation of depth profiling capabilities of helium and neon ions in ion microscopy

PubMed Central

Rzeznik, Lukasz; Wirtz, Tom

2016-01-01

The analysis of polymers by secondary ion mass spectrometry (SIMS) has been a topic of interest for many years. In recent years, the primary ion species evolved from heavy monatomic ions to cluster and massive cluster primary ions in order to preserve a maximum of organic information. The progress in less-damaging sputtering goes along with a loss in lateral resolution for 2D and 3D imaging. By contrast the development of a mass spectrometer as an add-on tool for the helium ion microscope (HIM), which uses finely focussed He+ or Ne+ beams, allows for the analysis of secondary ions and small secondary cluster ions with unprecedented lateral resolution. Irradiation induced damage and depth profiling capabilities obtained with these light rare gas species have been far less investigated than ion species used classically in SIMS. In this paper we simulated the sputtering of multi-layered polymer samples using the BCA (binary collision approximation) code SD_TRIM_SP to study preferential sputtering and atomic mixing in such samples up to a fluence of 1018 ions/cm2. Results show that helium primary ions are completely inappropriate for depth profiling applications with this kind of sample materials while results for neon are similar to argon. The latter is commonly used as primary ion species in SIMS. For the two heavier species, layers separated by 10 nm can be distinguished for impact energies of a few keV. These results are encouraging for 3D imaging applications where lateral and depth information are of importance. PMID:28144525

WHAT IS A MOMENT ARM? CALCULATING MUSCLE EFFECTIVENESS IN BIOMECHANICAL MODELS USING GENERALIZED COORDINATES

PubMed Central

Seth, Ajay; Delp, Scott L.

2015-01-01

Biomechanics researchers often use multibody models to represent biological systems. However, the mapping from biology to mechanics and back can be problematic. OpenSim is a popular open source tool used for this purpose, mapping between biological specifications and an underlying generalized coordinate multibody system called Simbody. One quantity of interest to biomechanical researchers and clinicians is “muscle moment arm,” a measure of the effectiveness of a muscle at contributing to a particular motion over a range of configurations. OpenSim can automatically calculate these quantities for any muscle once a model has been built. For simple cases, this calculation is the same as the conventional moment arm calculation in mechanical engineering. But a muscle may span several joints (e.g., wrist, neck, back) and may follow a convoluted path over various curved surfaces. A biological joint may require several bodies or even a mechanism to accurately represent in the multibody model (e.g., knee, shoulder). In these situations we need a careful definition of muscle moment arm that is analogous to the mechanical engineering concept, yet generalized to be of use to biomedical researchers. Here we present some biomechanical modeling challenges and how they are resolved in OpenSim and Simbody to yield biologically meaningful muscle moment arms. PMID:25905111

WHAT IS A MOMENT ARM? CALCULATING MUSCLE EFFECTIVENESS IN BIOMECHANICAL MODELS USING GENERALIZED COORDINATES.

PubMed

Sherman, Michael A; Seth, Ajay; Delp, Scott L

2013-08-01

Biomechanics researchers often use multibody models to represent biological systems. However, the mapping from biology to mechanics and back can be problematic. OpenSim is a popular open source tool used for this purpose, mapping between biological specifications and an underlying generalized coordinate multibody system called Simbody. One quantity of interest to biomechanical researchers and clinicians is "muscle moment arm," a measure of the effectiveness of a muscle at contributing to a particular motion over a range of configurations. OpenSim can automatically calculate these quantities for any muscle once a model has been built. For simple cases, this calculation is the same as the conventional moment arm calculation in mechanical engineering. But a muscle may span several joints (e.g., wrist, neck, back) and may follow a convoluted path over various curved surfaces. A biological joint may require several bodies or even a mechanism to accurately represent in the multibody model (e.g., knee, shoulder). In these situations we need a careful definition of muscle moment arm that is analogous to the mechanical engineering concept, yet generalized to be of use to biomedical researchers. Here we present some biomechanical modeling challenges and how they are resolved in OpenSim and Simbody to yield biologically meaningful muscle moment arms.

Imaging of arsenic traces in human hair by nano-SIMS 50

NASA Astrophysics Data System (ADS)

Audinot, J.-N.; Schneider, S.; Yegles, M.; Hallegot, P.; Wennig, R.; Migeon, H.-N.

2004-06-01

The nano-SIMS 50 allows ion imaging to be performed on microtomed hair cross-sections in order to determine the concentration and to localize the distribution of arsenic traces in hairs. Our study shows a linear relationship between the SIMS signal (As normalized with respect to CN) and the concentration determined by other analytical techniques. The advantages of SIMS imaging can be clearly proved by the capability to record quantitative distributions of As in the cross section. As a matter of fact, the nano-SIMS 50 images may allow differentiation between As located in the medulla, the cortex and the cuticle of the hair and thus distinguish between intoxication by indigestion and surface pollution of the sample.

Commissioning an in-room mobile CT for adaptive proton therapy with a compact proton system.

PubMed

Oliver, Jasmine A; Zeidan, Omar; Meeks, Sanford L; Shah, Amish P; Pukala, Jason; Kelly, Patrick; Ramakrishna, Naren R; Willoughby, Twyla R

2018-05-01

To describe the commissioning of AIRO mobile CT system (AIRO) for adaptive proton therapy on a compact double scattering proton therapy system. A Gammex phantom was scanned with varying plug patterns, table heights, and mAs on a CT simulator (CT Sim) and on the AIRO. AIRO-specific CT-stopping power ratio (SPR) curves were created with a commonly used stoichiometric method using the Gammex phantom. A RANDO anthropomorphic thorax, pelvis, and head phantom, and a CIRS thorax and head phantom were scanned on the CT Sim and AIRO. Clinically realistic treatment plans and nonclinical plans were generated on the CT Sim images and subsequently copied onto the AIRO CT scans for dose recalculation and comparison for various AIRO SPR curves. Gamma analysis was used to evaluate dosimetric deviation between both plans. AIRO CT values skewed toward solid water when plugs were scanned surrounded by other plugs in phantom. Low-density materials demonstrated largest differences. Dose calculated on AIRO CT scans with stoichiometric-based SPR curves produced over-ranged proton beams when large volumes of low-density material were in the path of the beam. To create equivalent dose distributions on both data sets, the AIRO SPR curve's low-density data points were iteratively adjusted to yield better proton beam range agreement based on isodose lines. Comparison of the stoichiometric-based AIRO SPR curve and the "dose-adjusted" SPR curve showed slight improvement on gamma analysis between the treatment plan and the AIRO plan for single-field plans at the 1%, 1 mm level, but did not affect clinical plans indicating that HU number differences between the CT Sim and AIRO did not affect dose calculations for robust clinical beam arrangements. Based on this study, we believe the AIRO can be used offline for adaptive proton therapy on a compact double scattering proton therapy system. © 2018 Orlando Health UF Health Cancer Center. Journal of Applied Clinical Medical Physics published by Wiley Periodicals, Inc. on behalf of American Association of Physicists in Medicine.

Synchromodal optical in vivo imaging employing microlens array optics: a complete framework

NASA Astrophysics Data System (ADS)

Peter, Joerg

2013-03-01

A complete mathematical framework for preclinical optical imaging (OI) support comprising bioluminescence imaging (BLI), fluorescence surface imaging (FSI) and fluorescence optical tomography (FOT) is presented in which optical data is acquired by means of a microlens array (MLA) based light detector (MLA-D). The MLA-D has been developed to enable unique OI, especially in synchromodal operation with secondary imaging modalities (SIM) such as positron emission tomography (PET) or magnetic resonance imaging (MRI). An MLA-D consists of a (large-area) photon sensor array, a matched MLA for field-of-view definition, and a septum mask of specific geometry made of anodized aluminum that is positioned between the sensor and the MLA to suppresses light cross-talk and to shield the sensor's radiofrequency interference signal (essential when used inside an MRI system). The software framework, while freely parameterizable for any MLA-D, is tailored towards an OI prototype system for preclinical SIM application comprising a multitude of cylindrically assembled, gantry-mounted, simultaneously operating MLA-D's. Besides the MLA-D specificity, the framework incorporates excitation and illumination light-source declarations of large-field and point geometry to facilitate multispectral FSI and FOT as well as three-dimensional object recognition. When used in synchromodal operation, reconstructed tomographic SIM volume data can be used for co-modal image fusion and also as a prior for estimating the imaged object's 3D surface by means of gradient vector flow. Superimposed planar (without object prior) or surface-aligned inverse mapping can be performed to estimate and to fuse the emission light map with the boundary of the imaged object. Triangulation and subsequent optical reconstruction (FOT) or constrained flow estimation (BLI), both including the possibility of SIM priors, can be performed to estimate the internal three-dimensional emission light distribution. The framework is susceptible to a number of variables controlling convergence and computational speed. Utilization and performance is illustrated on experimentally acquired data employing the OI prototype system in stand-alone operation, and when integrated into an unmodified preclinical PET system performing synchromodal BLI-PET in vivo imaging.

Graphene Oxide as a Novel Evenly Continuous Phase Matrix for TOF-SIMS.

PubMed

Cai, Lesi; Sheng, Linfeng; Xia, Mengchan; Li, Zhanping; Zhang, Sichun; Zhang, Xinrong; Chen, Hongyuan

2017-03-01

Using matrix to enhance the molecular ion signals for biomolecule identification without loss of spatial resolution caused by matrix crystallization is a great challenge for the application of TOF-SIMS in real-world biological research. In this report, graphene oxide (GO) was used as a matrix for TOF-SIMS to improve the secondary ion yields of intact molecular ions ([M + H] + ). Identifying and distinguishing the molecular ions of lipids (m/z >700) therefore became straightforward. The spatial resolution of TOF-SIMS imaging could also be improved as GO can form a homogeneous layer of matrix instead of crystalline domain, which prevents high spatial resolution in TOF-SIMS imaging. Lipid mapping in presence of GO revealed the delicate morphology and distribution of single vesicles with a diameter of 800 nm. On GO matrix, the vesicles with similar shape but different chemical composition could be distinguished using molecular ions. This novel matrix holds potentials in such applications as the analysis and imaging of complex biological samples by TOF-SIMS. Graphical Abstract ᅟ.

Graphene Oxide as a Novel Evenly Continuous Phase Matrix for TOF-SIMS

NASA Astrophysics Data System (ADS)

Cai, Lesi; Sheng, Linfeng; Xia, Mengchan; Li, Zhanping; Zhang, Sichun; Zhang, Xinrong; Chen, Hongyuan

2017-03-01

Using matrix to enhance the molecular ion signals for biomolecule identification without loss of spatial resolution caused by matrix crystallization is a great challenge for the application of TOF-SIMS in real-world biological research. In this report, graphene oxide (GO) was used as a matrix for TOF-SIMS to improve the secondary ion yields of intact molecular ions ([M + H]+). Identifying and distinguishing the molecular ions of lipids ( m/z >700) therefore became straightforward. The spatial resolution of TOF-SIMS imaging could also be improved as GO can form a homogeneous layer of matrix instead of crystalline domain, which prevents high spatial resolution in TOF-SIMS imaging. Lipid mapping in presence of GO revealed the delicate morphology and distribution of single vesicles with a diameter of 800 nm. On GO matrix, the vesicles with similar shape but different chemical composition could be distinguished using molecular ions. This novel matrix holds potentials in such applications as the analysis and imaging of complex biological samples by TOF-SIMS.

1393 Ring Bus at JPL: Description and Status

NASA Technical Reports Server (NTRS)

Wysocky, Terry R.

2007-01-01

Completed Ring Bus IC V&V Phase - Ring Bus Test Plan Completed for SIM Project - Applicable to Other Projects Implemented a Avionics Bus Based upon the IEEE 1393 Standard - Excellent Starting Point for a General Purpose High-Speed Spacecraft Bus - Designed to Meet SIM Requirements for - Real-time deterministic, distributed systems. - Control system requirements - Fault detection and recovery Other JPL Projects Considering Implementation F'light Software Ring Bus Driver Module Began in 2006, Continues Participating in Standard Revision. Search for Earth-like planets orbiting nearby stars and measure the masses and orbits of the planets it finds. Survey 2000 nearby stars for planetary systems to learn whether our Solar System is unusual, or typical. Make a new catalog of star position 100 times more accurate than current measurements. Learn how our galaxy formed and will evolve by studying the dynamics of its stars. Critically test models of exactly how stars shine, including exotic objects like black holes, neutron stars and white dwarfs.

Educating resident physicians using virtual case-based simulation improves diabetes management: a randomized controlled trial.

PubMed

Sperl-Hillen, JoAnn; O'Connor, Patrick J; Ekstrom, Heidi L; Rush, William A; Asche, Stephen E; Fernandes, Omar D; Appana, Deepika; Amundson, Gerald H; Johnson, Paul E; Curran, Debra M

2014-12-01

To test a virtual case-based Simulated Diabetes Education intervention (SimDE) developed to teach primary care residents how to manage diabetes. Nineteen primary care residency programs, with 341 volunteer residents in all postgraduate years (PGY), were randomly assigned to a SimDE intervention group or control group (CG). The Web-based interactive educational intervention used computerized virtual patients who responded to provider actions through programmed simulation models. Eighteen distinct learning cases (L-cases) were assigned to SimDE residents over six months from 2010 to 2011. Impact was assessed using performance on four virtual assessment cases (A-cases), an objective knowledge test, and pre-post changes in self-assessed diabetes knowledge and confidence. Group comparisons were analyzed using generalized linear mixed models, controlling for clustering of residents within residency programs and differences in baseline knowledge. The percentages of residents appropriately achieving A-case composite clinical goals for glucose, blood pressure, and lipids were as follows: A-case 1: SimDE = 21.2%, CG = 1.8%, P = .002; A-case 2: SimDE = 15.7%, CG = 4.7%, P = .02; A-case 3: SimDE = 48.0%, CG = 10.4%, P < .001; and A-case 4: SimDE = 42.1%, CG = 18.7%, P = .004. The mean knowledge score and pre-post changes in self-assessed knowledge and confidence were significantly better for SimDE group than CG participants. A virtual case-based simulated diabetes education intervention improved diabetes management skills, knowledge, and confidence for primary care residents.

Observation of endoplasmic reticulum tubules via TOF-SIMS tandem mass spectrometry imaging of transfected cells.

PubMed

Chini, Corryn E; Fisher, Gregory L; Johnson, Ben; Tamkun, Michael M; Kraft, Mary L

2018-02-26

Advances in three-dimensional secondary ion mass spectrometry (SIMS) imaging have enabled visualizing the subcellular distributions of various lipid species within individual cells. However, the difficulty of locating organelles using SIMS limits efforts to study their lipid compositions. Here, the authors have assessed whether endoplasmic reticulum (ER)-Tracker Blue White DPX ® , which is a commercially available stain for visualizing the endoplasmic reticulum using fluorescence microscopy, produces distinctive ions that can be used to locate the endoplasmic reticulum using SIMS. Time-of-flight-SIMS tandem mass spectrometry (MS 2 ) imaging was used to identify positively and negatively charged ions produced by the ER-Tracker stain. Then, these ions were used to localize the stain and thus the endoplasmic reticulum, within individual human embryonic kidney cells that contained higher numbers of endoplasmic reticulum-plasma membrane junctions on their surfaces. By performing MS 2 imaging of selected ions in parallel with the precursor ion (MS 1 ) imaging, the authors detected a chemical interference native to the cell at the same nominal mass as the pentafluorophenyl fragment from the ER-Tracker stain. Nonetheless, the fluorine secondary ions produced by the ER-Tracker stain provided a distinctive signal that enabled locating the endoplasmic reticulum using SIMS. This simple strategy for visualizing the endoplasmic reticulum in individual cells using SIMS could be combined with existing SIMS methodologies for imaging intracellular lipid distribution and to study the lipid composition within the endoplasmic reticulum.

Finding Space in Second Life, NASA Education and Public Outreach in a 3D Metaverse

NASA Astrophysics Data System (ADS)

Ireton, F. M.

2007-12-01

Second Life (SL) is a virtual 3D simulation or metaverse with almost eight million users worldwide. SL has seen explosive growth in the four years it has been available and hosts a number of educational and institutional "islands" or sims. Federal agencies with an SL presence include NASA and NOAA. There are several educational institutions and education specific sims in SL. At any one time there may be as many as 40,000 users on line. Users develop a persona and are seen on screen as a human figure or avatar. Avatars are able to move around the sim islands by walking or flying and move from island to island or remote locations by teleporting. While a big part of the Second Life experience deals with avatar interactions and exploring, there is an active community of builders who create the scenery, buildings, and other artifacts of the SL world including clothing and other personal items. SL builders start with basic shapes and through size manipulation on three axis and adding texture to the shapes create a myriad of objects - a 3D world. This paper will deal with the design and creation of exhibits halls for NASA's LRO/LCROSS mission slated for launch October 2008 and a NASA sponsored aeronautical engineering student challenge contest. The exhibit halls will be placed on the NASA sponsored Co-Lab sim and will feature models of the spacecraft and the instruments carried on board and student exhibits. There also will be storyboards with information about the mission and contest. Where appropriate there will be links to external websites for further information. The exhibits will be interactive to support the outreach efforts associated with the mission and the contest. Upon completion of the visit to the LRO/LCROSS hall participants will have the opportunity to visit a near by sandbox - SL parlance for a building area - to design and build a spacecraft from a suite of instruments provided for them depending on their area of interest. Real limitations such as mass, power, and cost will be included in the guidelines for building their spacecraft.

The HexSim Model

EPA Science Inventory

HexSim version 2.0 is soon to be released by EPA's Western Ecology Division (WED). More than three years of work have gone into the development of this tool, which grew out of an EPA model called PATCH. HexSim makes it possible for non-programmers to develop sophisticated simula...

HexSim - A general purpose framework for spatially-explicit, individual-based modeling

EPA Science Inventory

HexSim is a framework for constructing spatially-explicit, individual-based computer models designed for simulating terrestrial wildlife population dynamics and interactions. HexSim is useful for a broad set of modeling applications. This talk will focus on a subset of those ap...

Wisconsin System for Instructional Management: Terminal Operator Manual. Practical Paper No. 19.

ERIC Educational Resources Information Center

Bozeman, William C.; And Others

The Wisconsin System for Instructional Management (WIS-SIM) is a computer managed instruction (CMI) system designed to improve instructional decision making in order to maximize the educational progress of each child while making efficient use of the available human, material, and financial resources within an organizational structure such as the…

Estimating and validating harvesting system production through computer simulation

Treesearch

John E. Baumgras; Curt C. Hassler; Chris B. LeDoux

1993-01-01

A Ground Based Harvesting System Simulation model (GB-SIM) has been developed to estimate stump-to-truck production rates and multiproduct yields for conventional ground-based timber harvesting systems in Appalachian hardwood stands. Simulation results reflect inputs that define harvest site and timber stand attributes, wood utilization options, and key attributes of...

An Interactive Teaching System for Bond Graph Modeling and Simulation in Bioengineering

ERIC Educational Resources Information Center

Roman, Monica; Popescu, Dorin; Selisteanu, Dan

2013-01-01

The objective of the present work was to implement a teaching system useful in modeling and simulation of biotechnological processes. The interactive system is based on applications developed using 20-sim modeling and simulation software environment. A procedure for the simulation of bioprocesses modeled by bond graphs is proposed and simulators…

Installation package for SIMS prototype system 2, solar hot water

NASA Technical Reports Server (NTRS)

1978-01-01

The prototype system 2 solar hot water was designed for use in a single family dwelling and consists of the following subsystems: collector, storage, energy transport, and control. Guidelines are presented for utilization in the development of detailed installation plans and specifications. Instruction on operation, maintenance, and repair of the system is discussed.

Comparing pre- and post-chemical abrasion ages for Miocene Peach Springs Tuff zircon from ID-TIMS and SIMS analyses

NASA Astrophysics Data System (ADS)

Lidzbarski, M. I.; Mundil, R.; Miller, J. S.; Vazquez, J. A.

2012-12-01

The Miocene Peach Spring Tuff (PST) is a voluminous (>600 km3), zoned ignimbrite (trachyte to high-SiO2 rhyolite) that is exposed widely in eastern California, western Arizona, and southernmost Nevada, which was erupted from the Silver Creek caldera in the southwestern Black Mountains, AZ. PST serves as a regionally widespread marker unit and its eruption age has been determined to 18.8 to 18.9 Ma by 40Ar/39Ar methods, when corrected for systematic bias and normalized to the U-Pb system (Renne et al., 2010,). We performed ion-microprobe (SIMS) U-Pb dating of zircon from individual pumice clasts from PST to evaluate the growth history of zircon in the PST magma system. Sectioned, polished zircon from conventional epoxy mounts allows dating of internal growth domains (e.g. cores, interiors, and near-rim), whereas mounting unpolished zircon in indium and analyzing unpolished crystal faces provides a means to selectively sample the final increments of crystal growth (Reid and Coath, 2000). Combining U-Pb ages of unpolished zircon rims with near-rim interior analyses on sectioned grains yields a mean age of ca. 18.3 Ma, whereas ages of cores of sectioned crystals yield a mean of ca. 18.9 Ma. Several zircons have rim and/or core ages that are several hundred thousand years older or younger than these means (up to 1 m.y. total spread), although the uncertainties for individual SIMS ages are 2 to 5% (2 sigma uncertainty). Therefore, the distribution of ages is challenging to resolve. A modest number of the older grains are plausibly recycled antecrysts, but we suspect that the youngest zircons may have experienced Pb-loss. Failure to account for the possibility of inheritance and Pb-loss may lead to erroneous interpretations about crystallization in the PST system. In order to evaluate and mitigate the effects of Pb-loss, we employed the chemical abrasion (CA) technique of Mattinson (2005), which effectively eliminates domains in zircon that have suffered Pb-loss, and removes micro-inclusions that typically contain common Pb. Thermal annealing followed by CA techniques were used for ID-TIMS dating of a sub-set of zircon crystals previously analyzed by SIMS. Prior to TIMS analyses, zircon crystals were imaged by scanning electron microscopy (SEM) to evaluate the effects of CA on crystal domains sampled by SIMS. SEM images reveal that whole portions of crystals were removed by the CA technique, and a heterogeneous pattern of etching that was not confined to specific compositional zones visible in cathodoluminescence. Most of the SIMS sputter pits that yield spurious ages, are associated with etching and/or preferential annealing by the combined annealing and CA technique, suggesting that the young ages relative to the 40Ar/39Ar age may be due to Pb loss. ID-TIMS yields a coherent U-Pb age population of 18.8 Ma, with several older and younger crystals that might reflect xenocrysts, Pb-loss, and/or younger crystallization. In order to maintain spatial resolution and further evaluate the effects of Pb-loss in PST zircon, the annealing and CA-technique will be applied to zircon prior to SIMS dating. References: Reid and Coath, 2000, Geology 28: 443 Renne et al., 2010, GCA 78: 5349

Revisiting "Beyond Instructional Design"

ERIC Educational Resources Information Center

Sims, Rod

2015-01-01

Since the article "Beyond Instructional Design: Making Learning Design a Reality" (Sims, 2006) was published, much has changed in the opportunities we have for learning, and Professor Rod Sims's thinking has evolved. In this article, Professor Rod Sims reflects upon his original article, and he offers an evolved model of learning design,…

A novel ToF-SIMS operation mode for sub 100 nm lateral resolution: Application and performance.

PubMed

Kubicek, Markus; Holzlechner, Gerald; Opitz, Alexander K; Larisegger, Silvia; Hutter, Herbert; Fleig, Jürgen

2014-01-15

A novel operation mode for time of flight-secondary ion mass spectrometry (ToF-SIMS) is described for a TOF.SIMS 5 instrument with a Bi-ion gun. It features sub 100 nm lateral resolution, adjustable primary ion currents and the possibility to measure with high lateral resolution as well as high mass resolution. The adjustment and performance of the novel operation mode are described and compared to established ToF-SIMS operation modes. Several examples of application featuring novel scientific results show the capabilities of the operation mode in terms of lateral resolution, accuracy of isotope analysis of oxygen, and combination of high lateral and mass resolution. The relationship between high lateral resolution and operation of SIMS in static mode is discussed.

Recent developments in the evolution of morphologies and controllers for physically simulated creatures.

PubMed

Taylor, T; Massey, C

2001-01-01

Karl Sims' work on evolving body shapes and controllers for three-dimensional, physically simulated creatures generated wide interest on its publication in 1994. The purpose of this article is threefold: (a) to highlight a spate of recent work by a number of researchers in replicating, and in some cases extending, Sims' results using standard PCs (Sims' original work was done on a Connection Machine CM-5 parallel computer). In particular, a re-implementation of Sims' work by the authors will be described and discussed; (b) to illustrate how off-the-shelf physics engines can be used in this sort of work, and also to highlight some deficiencies of these engines and pitfalls when using them; and (c) to indicate how these recent studies stand in respect to Sims' original work.

Wind-farm simulation over moderately complex terrain

NASA Astrophysics Data System (ADS)

Segalini, Antonio; Castellani, Francesco

2017-05-01

A comparison between three independent software to estimate the power production and the flow field in a wind farm is conducted, validating them against SCADA (Supervisory, Control And Data Acquisition) data. The three software were ORFEUS, WindSim and WAsP: ORFEUS and WAsP are linearised solvers, while WindSim is fully nonlinear. A wake model (namely a prescribed velocity deficit associated to the turbines) is used by WAsP, while ORFEUS and WindSim use the actuator-disc method to account for the turbines presence. The comparison indicates that ORFEUS and WAsP perform slightly better than WindSim in the assessment of the polar efficiency. The wakes simulated with ORFEUS appear more persistent than the ones of WindSim, which uses a two-equation closure model for the turbulence effects.

Scalable and Axiomatic Ranking of Network Role Similarity

PubMed Central

Jin, Ruoming; Lee, Victor E.; Li, Longjie

2014-01-01

A key task in analyzing social networks and other complex networks is role analysis: describing and categorizing nodes according to how they interact with other nodes. Two nodes have the same role if they interact with equivalent sets of neighbors. The most fundamental role equivalence is automorphic equivalence. Unfortunately, the fastest algorithms known for graph automorphism are nonpolynomial. Moreover, since exact equivalence is rare, a more meaningful task is measuring the role similarity between any two nodes. This task is closely related to the structural or link-based similarity problem that SimRank addresses. However, SimRank and other existing similarity measures are not sufficient because they do not guarantee to recognize automorphically or structurally equivalent nodes. This paper makes two contributions. First, we present and justify several axiomatic properties necessary for a role similarity measure or metric. Second, we present RoleSim, a new similarity metric which satisfies these axioms and which can be computed with a simple iterative algorithm. We rigorously prove that RoleSim satisfies all these axiomatic properties. We also introduce Iceberg RoleSim, a scalable algorithm which discovers all pairs with RoleSim scores above a user-defined threshold θ. We demonstrate the interpretative power of RoleSim on both both synthetic and real datasets. PMID:25383066

WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions.

PubMed

Karr, Jonathan R; Phillips, Nolan C; Covert, Markus W

2014-01-01

Mechanistic 'whole-cell' models are needed to develop a complete understanding of cell physiology. However, extracting biological insights from whole-cell models requires running and analyzing large numbers of simulations. We developed WholeCellSimDB, a database for organizing whole-cell simulations. WholeCellSimDB was designed to enable researchers to search simulation metadata to identify simulations for further analysis, and quickly slice and aggregate simulation results data. In addition, WholeCellSimDB enables users to share simulations with the broader research community. The database uses a hybrid relational/hierarchical data format architecture to efficiently store and retrieve both simulation setup metadata and results data. WholeCellSimDB provides a graphical Web-based interface to search, browse, plot and export simulations; a JavaScript Object Notation (JSON) Web service to retrieve data for Web-based visualizations; a command-line interface to deposit simulations; and a Python API to retrieve data for advanced analysis. Overall, we believe WholeCellSimDB will help researchers use whole-cell models to advance basic biological science and bioengineering. http://www.wholecellsimdb.org SOURCE CODE REPOSITORY: URL: http://github.com/CovertLab/WholeCellSimDB. © The Author(s) 2014. Published by Oxford University Press.

GneimoSim: A Modular Internal Coordinates Molecular Dynamics Simulation Package

PubMed Central

Larsen, Adrien B.; Wagner, Jeffrey R.; Kandel, Saugat; Salomon-Ferrer, Romelia; Vaidehi, Nagarajan; Jain, Abhinandan

2014-01-01

The Generalized Newton Euler Inverse Mass Operator (GNEIMO) method is an advanced method for internal coordinates molecular dynamics (ICMD). GNEIMO includes several theoretical and algorithmic advancements that address longstanding challenges with ICMD simulations. In this paper we describe the GneimoSim ICMD software package that implements the GNEIMO method. We believe that GneimoSim is the first software package to include advanced features such as the equipartition principle derived for internal coordinates, and a method for including the Fixman potential to eliminate systematic statistical biases introduced by the use of hard constraints. Moreover, by design, GneimoSim is extensible and can be easily interfaced with third party force field packages for ICMD simulations. Currently, GneimoSim includes interfaces to LAMMPS, OpenMM, Rosetta force field calculation packages. The availability of a comprehensive Python interface to the underlying C++ classes and their methods provides a powerful and versatile mechanism for users to develop simulation scripts to configure the simulation and control the simulation flow. GneimoSim has been used extensively for studying the dynamics of protein structures, refinement of protein homology models, and for simulating large scale protein conformational changes with enhanced sampling methods. GneimoSim is not limited to proteins and can also be used for the simulation of polymeric materials. PMID:25263538

Phytoremediation of the organic Xenobiotic simazine by p450-1a2 transgenic Arabidopsis thaliana plants.

PubMed

Azab, Ehab; Hegazy, Ahmad K; El-Sharnouby, Mohamed E; Abd Elsalam, Hassan E

2016-01-01

The potential use of human P450-transgenic plants for phytoremediation of pesticide contaminated soils was tested in laboratory and greenhouse experiments. The transgenic P450 CYP1A2 gene Arabidopsis thaliana plants metabolize number of herbicides, insecticides and industrial chemicals. The P450 isozymes CYP1A2 expressed in A. thaliana were examined regarding the herbicide simazine (SIM). Transgenic A. thaliana plants expressing CYP1A2 gene showed significant resistance to SIM supplemented either in plant growth medium or sprayed on foliar parts. The results showed that SIM produces harmful effect on both rosette diameter and primary root length of the wild type (WT) plants. In transgenic A. thaliana lines, the rosette diameter and primary root length were not affected by SIM concentrations used in this experiment. The results indicate that CYP1A2 can be used as a selectable marker for plant transformation, allowing efficient selection of transgenic lines in growth medium and/or in soil-grown plants. The transgenic A. thaliana plants exhibited a healthy growth using doses of up to 250 μmol SIM treatments, while the non-transgenic A. thaliana plants were severely damaged with doses above 50 μmol SIM treatments. The transgenic A. thaliana plants can be used as phytoremediator of environmental SIM contaminants.

GneimoSim: a modular internal coordinates molecular dynamics simulation package.

PubMed

Larsen, Adrien B; Wagner, Jeffrey R; Kandel, Saugat; Salomon-Ferrer, Romelia; Vaidehi, Nagarajan; Jain, Abhinandan

2014-12-05

The generalized Newton-Euler inverse mass operator (GNEIMO) method is an advanced method for internal coordinates molecular dynamics (ICMD). GNEIMO includes several theoretical and algorithmic advancements that address longstanding challenges with ICMD simulations. In this article, we describe the GneimoSim ICMD software package that implements the GNEIMO method. We believe that GneimoSim is the first software package to include advanced features such as the equipartition principle derived for internal coordinates, and a method for including the Fixman potential to eliminate systematic statistical biases introduced by the use of hard constraints. Moreover, by design, GneimoSim is extensible and can be easily interfaced with third party force field packages for ICMD simulations. Currently, GneimoSim includes interfaces to LAMMPS, OpenMM, and Rosetta force field calculation packages. The availability of a comprehensive Python interface to the underlying C++ classes and their methods provides a powerful and versatile mechanism for users to develop simulation scripts to configure the simulation and control the simulation flow. GneimoSim has been used extensively for studying the dynamics of protein structures, refinement of protein homology models, and for simulating large scale protein conformational changes with enhanced sampling methods. GneimoSim is not limited to proteins and can also be used for the simulation of polymeric materials. © 2014 Wiley Periodicals, Inc.

Enhancing the isotropy of lateral resolution in coherent structured illumination microscopy

PubMed Central

Park, Joo Hyun; Lee, Jae Yong; Lee, Eun Seong

2014-01-01

We present a method to improve the isotropy of spatial resolution in a structured illumination microscopy (SIM) implemented for imaging non-fluorescent samples. To alleviate the problem of anisotropic resolution involved with the previous scheme of coherent SIM that employs the two orthogonal standing-wave illumination, referred to as the orthogonal SIM, we introduce a hexagonal-lattice illumination that incorporates three standing-wave fields simultaneously superimposed at the orientations equally divided in the lateral plane. A theoretical formulation is worked out rigorously for the coherent image formation with such a simultaneous multiple-beam illumination and an explicit Fourier-domain framework is derived for reconstructing an image with enhanced resolution. Using a computer-synthesized resolution target as a 2D coherent sample, we perform numerical simulations to examine the imaging characteristics of our three-angle SIM compared with the orthogonal SIM. The investigation on the 2D resolving power with the various test patterns of different periods and orientations reveal that the orientation-dependent undulation of lateral resolution can be reduced from 27% to 8% by using the three-angle SIM while the best resolution (0.54 times the resolution limit of conventional coherent imaging) in the directions of structured illumination is slightly deteriorated by 4.6% from that of the orthogonal SIM. PMID:24940548

Efficient simulation of voxelized phantom in GATE with embedded SimSET multiple photon history generator.

PubMed

Lin, Hsin-Hon; Chuang, Keh-Shih; Lin, Yi-Hsing; Ni, Yu-Ching; Wu, Jay; Jan, Meei-Ling

2014-10-21

GEANT4 Application for Tomographic Emission (GATE) is a powerful Monte Carlo simulator that combines the advantages of the general-purpose GEANT4 simulation code and the specific software tool implementations dedicated to emission tomography. However, the detailed physical modelling of GEANT4 is highly computationally demanding, especially when tracking particles through voxelized phantoms. To circumvent the relatively slow simulation of voxelized phantoms in GATE, another efficient Monte Carlo code can be used to simulate photon interactions and transport inside a voxelized phantom. The simulation system for emission tomography (SimSET), a dedicated Monte Carlo code for PET/SPECT systems, is well-known for its efficiency in simulation of voxel-based objects. An efficient Monte Carlo workflow integrating GATE and SimSET for simulating pinhole SPECT has been proposed to improve voxelized phantom simulation. Although the workflow achieves a desirable increase in speed, it sacrifices the ability to simulate decaying radioactive sources such as non-pure positron emitters or multiple emission isotopes with complex decay schemes and lacks the modelling of time-dependent processes due to the inherent limitations of the SimSET photon history generator (PHG). Moreover, a large volume of disk storage is needed to store the huge temporal photon history file produced by SimSET that must be transported to GATE. In this work, we developed a multiple photon emission history generator (MPHG) based on SimSET/PHG to support a majority of the medically important positron emitters. We incorporated the new generator codes inside GATE to improve the simulation efficiency of voxelized phantoms in GATE, while eliminating the need for the temporal photon history file. The validation of this new code based on a MicroPET R4 system was conducted for (124)I and (18)F with mouse-like and rat-like phantoms. Comparison of GATE/MPHG with GATE/GEANT4 indicated there is a slight difference in energy spectra for energy below 50 keV due to the lack of x-ray simulation from (124)I decay in the new code. The spatial resolution, scatter fraction and count rate performance are in good agreement between the two codes. For the case studies of (18)F-NaF ((124)I-IAZG) using MOBY phantom with 1  ×  1 × 1 mm(3) voxel sizes, the results show that GATE/MPHG can achieve acceleration factors of approximately 3.1 × (4.5 ×), 6.5 × (10.7 ×) and 9.5 × (31.0 ×) compared with GATE using the regular navigation method, the compressed voxel method and the parameterized tracking technique, respectively. In conclusion, the implementation of MPHG in GATE allows for improved efficiency of voxelized phantom simulations and is suitable for studying clinical and preclinical imaging.

TOF-SIMS investigation of Streptomyces coelicolor, a mycelial bacterium

NASA Astrophysics Data System (ADS)

Vaidyanathan, Seetharaman; Fletcher, John S.; Lockyer, Nicholas P.; Vickerman, John C.

2008-12-01

Streptomyces coelicolor is a mycelial microorganism that produces several secondary metabolites, including antibiotics. The physiology of the organism has largely been investigated in liquid cultures due to ease of monitoring different physiological parameters and more homogeneous culture conditions. However, solid cultures reflect the natural physiology of the microorganism better, given that in its natural state it grows in the soil. Imaging mass spectrometry with TOF-SIMS and C 60+ primary ion beams offers a potential route to studying chemical changes at the molecular level, both intracellular and extracellular that can help in understanding the natural physiology of the microorganism. Here, we report the application of the technique for studying the lateral distribution of the chemical species detected in a population, grown in both liquid and solid cultures. The capability of the technique for studying biological systems with minimal system intervention is demonstrated.

Small molecule analysis and imaging of fatty acids in the zebra finch song system using time-of-flight-secondary ion mass spectrometry.

PubMed

Amaya, Kensey R; Sweedler, Jonathan V; Clayton, David F

2011-08-01

Fatty acids are central to brain metabolism and signaling, but their distributions within complex brain circuits have been difficult to study. Here we applied an emerging technique, time-of-flight secondary ion mass spectrometry (ToF-SIMS), to image specific fatty acids in a favorable model system for chemical analyses of brain circuits, the zebra finch (Taeniopygia guttata). The zebra finch, a songbird, produces complex learned vocalizations under the control of an interconnected set of discrete, dedicated brain nuclei 'song nuclei'. Using ToF-SIMS, the major song nuclei were visualized by virtue of differences in their content of essential and non-essential fatty acids. Essential fatty acids (arachidonic acid and docosahexaenoic acid) showed distinctive distributions across the song nuclei, and the 18-carbon fatty acids stearate and oleate discriminated the different core and shell subregions of the lateral magnocellular nucleus of the anterior nidopallium. Principal component analysis of the spectral data set provided further evidence of chemical distinctions between the song nuclei. By analyzing the robust nucleus of the arcopallium at three different ages during juvenile song learning, we obtain the first direct evidence of changes in lipid content that correlate with progression of song learning. The results demonstrate the value of ToF-SIMS to study lipids in a favorable model system for probing the function of lipids in brain organization, development and function. © 2011 The Authors. Journal of Neurochemistry © 2011 International Society for Neurochemistry.

Analysis of the Boeing 747-100 using CEASIOM

NASA Astrophysics Data System (ADS)

Richardson, Thomas S.; Beaverstock, Chris; Isikveren, Askin; Meheri, Alireza; Badcock, Ken; Da Ronch, Andrea

2011-11-01

One of the requirements for the SimSAC project was to use existing aircraft to act as benchmarks for comparison with CEASIOM generated models. Within this paper, results are given for one of these examples, the Boeing 747-100. This aircraft was selected because a complete dataset exists in the open domain, which can be used to validate SimSAC generated data. The purpose of this paper is to both give confidence in, and to demonstrate the capabilities of, the CEASIOM environment when used for preliminary aircraft and control system design. CEASIOM is the result of the integration of a set of sophisticated tools by the European Union funded, Framework 6 SimSAC program. The first part of this paper presents a comparison of the aerodynamic results for each of the solvers available within CEASIOM together with data from the 747-100 model published by NASA. The resulting nonlinear model is then trimmed and analysed using the Flight Control System Designer Toolkit (FCSDT) module. In the final section of the paper a state-feedback controller is designed within CEASIOM in order to modify the longitudinal dynamics of the aircraft. The open and closed loop models are subsequently evaluated with selected failed aerodynamic surfaces and for the case of a single failed engine. Through these results, the CEASIOM software suite is shown to be able to generate excellent quality adaptive-fidelity aerodynamic data. This data is contained within a full nonlinear aircraft model to which linear analysis and control system design can be easily applied.

BeeSim: Leveraging Wearable Computers in Participatory Simulations with Young Children

ERIC Educational Resources Information Center

Peppler, Kylie; Danish, Joshua; Zaitlen, Benjamin; Glosson, Diane; Jacobs, Alexander; Phelps, David

2010-01-01

New technologies have enabled students to become active participants in computational simulations of dynamic and complex systems (called Participatory Simulations), providing a "first-person"perspective on complex systems. However, most existing Participatory Simulations have targeted older children, teens, and adults assuming that such concepts…

The Social Information Processing Model of Task Design: A Review of the Literature.

DTIC Science & Technology

1983-02-01

The Job Characteristics Inventory (JCI) (Sims, Szilagyi , & Keller, 1976) was used as a measure of task characteristics in four studies. Table 2...KD:716:enj 78u452-883 LIST 15 (Continued) 24 June 1981 Dr. H. Wallace Sinaiko Program Director, Manpower Research and Advisory Services Smithsonian

Social Information Processing and Group-Induced Response Shifts

DTIC Science & Technology

1984-01-01

34). The rationale for not using a standard task attributes measure such as the JDS (Hackman . & Oldham, 1975) or JCI (Sims, Szilagyi , & Keller, 1976...68588 P4-5/B5 LIST 15 (Continued) 452:KD:716:enj 78u452-883 24 June 1981 Dr. H. Wallace Sinaiko Program Director, Manpower Research and

75 FR 74073 - Endangered and Threatened Wildlife and Plants; Draft Revised Recovery Plan for the Northern...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-30

... population program HexSim. Though still at preliminary draft stage, population response simulations from this portion of the modeling process are available for public review by request from our office. These simulations do not estimate what will occur in the future, but provide comparative information on potential...

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

Hadgu, Teklu; Appel, Gordon John

Sandia National Laboratories (SNL) continued evaluation of total system performance assessment (TSPA) computing systems for the previously considered Yucca Mountain Project (YMP). This was done to maintain the operational readiness of the computing infrastructure (computer hardware and software) and knowledge capability for total system performance assessment (TSPA) type analysis, as directed by the National Nuclear Security Administration (NNSA), DOE 2010. This work is a continuation of the ongoing readiness evaluation reported in Lee and Hadgu (2014) and Hadgu et al. (2015). The TSPA computing hardware (CL2014) and storage system described in Hadgu et al. (2015) were used for the currentmore » analysis. One floating license of GoldSim with Versions 9.60.300, 10.5 and 11.1.6 was installed on the cluster head node, and its distributed processing capability was mapped on the cluster processors. Other supporting software were tested and installed to support the TSPA-type analysis on the server cluster. The current tasks included verification of the TSPA-LA uncertainty and sensitivity analyses, and preliminary upgrade of the TSPA-LA from Version 9.60.300 to the latest version 11.1. All the TSPA-LA uncertainty and sensitivity analyses modeling cases were successfully tested and verified for the model reproducibility on the upgraded 2014 server cluster (CL2014). The uncertainty and sensitivity analyses used TSPA-LA modeling cases output generated in FY15 based on GoldSim Version 9.60.300 documented in Hadgu et al. (2015). The model upgrade task successfully converted the Nominal Modeling case to GoldSim Version 11.1. Upgrade of the remaining of the modeling cases and distributed processing tasks will continue. The 2014 server cluster and supporting software systems are fully operational to support TSPA-LA type analysis.« less

System-level modeling for economic evaluation of geological CO2storage in gas reservoirs

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

Zhang, Yingqi; Oldenburg, Curtis M.; Finsterle, Stefan

2006-03-02

One way to reduce the effects of anthropogenic greenhousegases on climate is to inject carbon dioxide (CO2) from industrialsources into deep geological formations such as brine aquifers ordepleted oil or gas reservoirs. Research is being conducted to improveunderstanding of factors affecting particular aspects of geological CO2storage (such as storage performance, storage capacity, and health,safety and environmental (HSE) issues) as well as to lower the cost ofCO2 capture and related processes. However, there has been less emphasisto date on system-level analyses of geological CO2 storage that considergeological, economic, and environmental issues by linking detailedprocess models to representations of engineering components andassociatedmore » economic models. The objective of this study is to develop asystem-level model for geological CO2 storage, including CO2 capture andseparation, compression, pipeline transportation to the storage site, andCO2 injection. Within our system model we are incorporating detailedreservoir simulations of CO2 injection into a gas reservoir and relatedenhanced production of methane. Potential leakage and associatedenvironmental impacts are also considered. The platform for thesystem-level model is GoldSim [GoldSim User's Guide. GoldSim TechnologyGroup; 2006, http://www.goldsim.com]. The application of the system modelfocuses on evaluating the feasibility of carbon sequestration withenhanced gas recovery (CSEGR) in the Rio Vista region of California. Thereservoir simulations are performed using a special module of the TOUGH2simulator, EOS7C, for multicomponent gas mixtures of methane and CO2.Using a system-level modeling approach, the economic benefits of enhancedgas recovery can be directly weighed against the costs and benefits ofCO2 injection.« less

Randomized, double-blind, placebo-controlled clinical trial of loperamide plus simethicone versus loperamide alone and simethicone alone in the treatment of acute diarrhea with gas-related abdominal discomfort.

PubMed

Hanauer, Stephen B; DuPont, Herbert L; Cooper, Kimberly M; Laudadio, Charles

2007-05-01

To compare efficacy and tolerability of a loperamide/simethicone (LOP/SIM) combination product with that of loperamide (LOP) alone, simethicone (SIM) alone, and placebo (PBO) for acute nonspecific diarrhea with gas-related abdominal discomfort. In this multicenter, double-blind, 48-h study, patients were randomly assigned to receive two tablets, each containing either LOP/SIM 2 mg/125 mg (n = 121), LOP 2 mg (n = 120), SIM 125 mg (n = 123), or PBO (n = 121), followed by one tablet after each unformed stool, up to four tablets in any 24-h period. The primary outcome measures were time to last unformed stool and time to complete relief of gas-related abdominal discomfort. For time to last unformed stool, an unformed stool after a 24-h period of formed stools or no stools was considered a continuance of the original episode (stricter definition) or a new episode (alternate definition). A total of 483 patients were included in the intent-to-treat analysis. The median time to last unformed stool for LOP/SIM (7.6 h) was significantly shorter than that of LOP (11.5 h), SIM (26.0 h), and PBO (29.4 h) (p < or = 0.0232 in comparison with survival curves) using the alternate definition; it was numerically but not significantly shorter than that of LOP (p = 0.0709) and significantly shorter than that of SIM and PBO (p = 0.0001) using the stricter definition. LOP/SIM-treated patients had a shorter time to complete relief of gas-related abdominal discomfort than patients who received either ingredient alone or placebo (all p = 0.0001). Few patients reported adverse events in the four treatment groups, none of which were serious in nature. Potential study limitations include the ability to generalize study results to the population at large, variability in total dose consumed, and subjectivity of patient diary data. LOP/SIM was well-tolerated and more efficacious than LOP alone, SIM alone, or placebo for acute nonspecific diarrhea and gas-related abdominal discomfort.

Enhancing the ATIC Charge Resolution

NASA Technical Reports Server (NTRS)

Guzik, T. G.; Adams, J. H., Jr.; Ahn, H. S.; Bashindzhagyan, G. L.; Batkov, K. E.; Chang, J.; Christl, M.; Fazely, A. R.; Ganel, O.; Gunashingha, R. M.

2006-01-01

The Advanced Thin Ionization Calorimeter (ATIC) experiment measures the energy spectra of elements, from H to Fe, in the energy region from about 100 GeV to tens of TeV. The ATIC instrument was flown twice in long-duration balloon flights around the South Pole; the ATIC-1 test flight during Dec. 2000 - Jan. 2001 and the ATIC-2 science flight during Dec. 2002 - Jan. 2003. Analyses of both datasets have, to date, relied upon the highly segmented Silicon Matrix (SiM) detector to separate the incident cosmic ray from the calorimeter backscatter and to identify the charge. This method has worked well, enabling ATIC to separate protons from helium and to resolve all the major species up through iron. This charge resolution can be significantly improved by restricting the analysis to particle trajectories that pass through two SiM pixels at the cost of using only a fraction of the potential instrument geometry. However, immediately below the SiM is the two layer SI hodoscope (x, y) consisting of Bicron BC-408 plastic scintillator 2 cm wide, 1 cm thick, 88.2 cm long strips viewed by Hamamatsu R5611 photomultiplier tubes on each end of each strip. The primary purpose of the ATIC hodoscopes is to provide a fast trigger, and each hodoscope includes two crossed layers of strips (42 per layer in the case of Sl) providing supplemental particle trajectory information. The hodoscope readout electronics were designed to provide reasonable charge resolution over the dynamic range from protons through iron. This presentation discusses the S 1 hodoscope energy deposit calibrations, examines the charge resolution possible with this detector and investigates combining the S1 and SiM charge measurements to improve the overall ATIC charge resolution while minimizing degradation of the instrument geometry.

Comparison between thaw-mounting and use of conductive tape for sample preparation in ToF-SIMS imaging of lipids in Drosophila microRNA-14 model.

PubMed

Le, Minh Uyen Thi; Son, Jin Gyeong; Shon, Hyun Kyoung; Park, Jeong Hyang; Lee, Sung Bae; Lee, Tae Geol

2018-03-30

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging elucidates molecular distributions in tissue sections, providing useful information about the metabolic pathways linked to diseases. However, delocalization of the analytes and inadequate tissue adherence during sample preparation are among some of the unfortunate phenomena associated with this technique due to their role in the reduction of the quality, reliability, and spatial resolution of the ToF-SIMS images. For these reasons, ToF-SIMS imaging requires a more rigorous sample preparation method in order to preserve the natural state of the tissues. The traditional thaw-mounting method is particularly vulnerable to altered distributions of the analytes due to thermal effects, as well as to tissue shrinkage. In the present study, the authors made comparisons of different tissue mounting methods, including the thaw-mounting method. The authors used conductive tape as the tissue-mounting material on the substrate because it does not require heat from the finger for the tissue section to adhere to the substrate and can reduce charge accumulation during data acquisition. With the conductive-tape sampling method, they were able to acquire reproducible tissue sections and high-quality images without redistribution of the molecules. Also, the authors were successful in preserving the natural states and chemical distributions of the different components of fat metabolites such as diacylglycerol and fatty acids by using the tape-supported sampling in microRNA-14 (miR-14) deleted Drosophila models. The method highlighted here shows an improvement in the accuracy of mass spectrometric imaging of tissue samples.

Comparison of Two Intervention Strategies on Prevention of Bedsores among the Bedridden Patients: A Quasi Experimental Community-based Trial.

PubMed

Kaur, Sukhpal; Singh, Amarjeet; Tewari, Manoj K; Kaur, Tejinder

2018-01-01

More than 80% of bedridden patients develop bedsores in home care settings. Training of informal caregivers can significantly affect the quality of care to these patients. The objective of this study is to compare the effectiveness of two caregiver training strategies on prevention of bedsores among bedridden patients. The study was carried out in Chandigarh. The study center was at PGIMER, Chandigarh. Seventy-eight bedridden patients being taken care in their homes were identified. These were randomly allocated into two groups. Group A received Prevention Package I, i.e., self-instruction Manual (SIM), training, and counseling. Group B received Prevention Package 2, i.e., only SIM. All these patients were followed up periodically for 1 year. During each follow-up, patients were observed for bedsore development. Braden scale was used to assess the risk factors of bedsores. Katz scale was used to evaluate the level of functional dependence of patients. Descriptive statistics was used to analyze the data. The percentage reduction of number of patients at risk of bedsore development as per various domains of Braden Scale was more in Group A as compared to Group B on each successive visit. There was 100% improvement in mobility level in the patients who were totally dependent in both the groups. However, in moderately dependant patients, the improvement in mobility level was more (87%) in Group A as compared to Group B (75%). All the caregivers complied fully with instructions postintervention. Training of caregivers for the prevention of bedsores among the bedridden patients was effective in improving the practices of the caregivers and also in reducing the risk factors of bedsores. One-to-one training with SIM distribution yielded better results than the use of only SIM.

Comparison of Two Intervention Strategies on Prevention of Bedsores among the Bedridden Patients: A Quasi Experimental Community-based Trial

PubMed Central

Kaur, Sukhpal; Singh, Amarjeet; Tewari, Manoj K; Kaur, Tejinder

2018-01-01

Background: More than 80% of bedridden patients develop bedsores in home care settings. Training of informal caregivers can significantly affect the quality of care to these patients. Objective: The objective of this study is to compare the effectiveness of two caregiver training strategies on prevention of bedsores among bedridden patients. Methods: The study was carried out in Chandigarh. The study center was at PGIMER, Chandigarh. Seventy-eight bedridden patients being taken care in their homes were identified. These were randomly allocated into two groups. Group A received Prevention Package I, i.e., self-instruction Manual (SIM), training, and counseling. Group B received Prevention Package 2, i.e., only SIM. All these patients were followed up periodically for 1 year. During each follow-up, patients were observed for bedsore development. Braden scale was used to assess the risk factors of bedsores. Katz scale was used to evaluate the level of functional dependence of patients. Descriptive statistics was used to analyze the data. Results: The percentage reduction of number of patients at risk of bedsore development as per various domains of Braden Scale was more in Group A as compared to Group B on each successive visit. There was 100% improvement in mobility level in the patients who were totally dependent in both the groups. However, in moderately dependant patients, the improvement in mobility level was more (87%) in Group A as compared to Group B (75%). All the caregivers complied fully with instructions postintervention. Conclusion: Training of caregivers for the prevention of bedsores among the bedridden patients was effective in improving the practices of the caregivers and also in reducing the risk factors of bedsores. One-to-one training with SIM distribution yielded better results than the use of only SIM. PMID:29440803

A tutorial platform suitable for surgical simulator training (SimMentor).

PubMed

Røtnes, Jan Sigurd; Kaasa, Johannes; Westgaard, Geir; Eriksen, Eivind Myrold; Hvidsten, Per Oyvind; Strøm, Kyrre; Sørhus, Vidar; Halbwachs, Yvon; Haug, Einar; Grimnes, Morten; Fontenelle, Hugues; Ekeberg, Tom; Thomassen, Jan B; Elle, Ole Jakob; Fosse, Erik

2002-01-01

The introduction of simulators in surgical training entails the need to develop pedagogic platforms adapted to the potentials and limitations provided by the information technology. As a solution to the technical challenges in treating all possible interaction events and to obtain a suitable pedagogic approach, we have developed a pedagogic platform for surgical training, SimMentor. In SimMentor the procedure to be practiced is divided into a number of natural phases. The trainee will practice on one phase at a time, however he can select the sequence of phases arbitrarily. A phase is taught by letting the trainee alternate freely between 2 modes: 1: A 3-dimensional animated guidance designed for learning the objectives and challenges in a procedure. 2: An interactive training session through the instrument manipulator device designed for training motoric responses based on visual and tactile responses produced by the simulator. The two modes are interfaced with the same virtual reality platform, thus SimMentor allows a seamless transition between the modes. We have developed a prototype simulator for robotic assisted endoscopic CABG (Coronary Artery Bypass Grafting) procedure by first focusing on the anastomosis part of the operation. Tissue, suture and instrument models have been developed and integrated with a simulated model of a beating heart comprises the elements in the simulator engine that is used in construction a training platform for learning different methods for performing a coronary anastomosis procedure. The platform is designed for integrating the following features: 1) practical approach to handle interactivity events with flexible-objects 3D simulators, 2) methods for quantitative evaluations of performance, 3) didactic presentations, 4) effective ways of producing diversity of clinical and pathological training scenarios.

Evaluation of a signal intensity mask in the interpretation of functional MR imaging activation maps.

PubMed

Strigel, Roberta M; Moritz, Chad H; Haughton, Victor M; Badie, Behnam; Field, Aaron; Wood, David; Hartman, Michael; Rowley, Howard A

2005-03-01

The purpose of this study was to determine the incidence of susceptibility artifacts on functional MR imaging (fMRI) studies and their effect on fMRI readings. We hypothesized that the availability of the signal intensity maps (SIMs) changes the interpretation of fMRI studies in which susceptibility artifacts affected eloquent brain regions. We reviewed 152 consecutive clinical fMRI studies performed with a SIM. The SIM consisted of the initial echo-planar images (EPI) in each section thresholded to eliminate signal intensity from outside the brain and then overlaid on anatomic images. The cause of the artifact was then determined by examining the images. Cases with a susceptibility artifact in eloquent brain were included in a blinded study read by four readers, first without and then with the SIM. For each reader, the number of times the interpretation changed on viewing the SIM was counted. Of 152 patients, 44% had signal intensity loss involving cerebral cortex and 18% involving an eloquent brain region. Causes of the artifacts were: surgical site artifact, blood products, dental devices, calcium, basal ganglia calcifications, ICP monitors, embolization materials, and air. When provided with the SIM, readers changed interpretations in 8-38% of patient cases, depending on reader experience and size and location of susceptibility artifact. Patients referred for clinical fMRI have a high incidence of susceptibility artifacts, whose presence and size can be determined by inspection of the SIM but not anatomic images. The availability of the SIM may affect interpretation of the fMRI.