Attention to individual identities modulates face processing.

PubMed

Ruz, María; Aranda, Clara; Sarmiento, Beatriz R; Sanabria, Daniel

2015-05-01

The ability of attention to apply in a flexible manner to several types of information at various stages of processing has been studied extensively. However, the susceptibility of these effects to the nature of the idiosyncratic items being attended is less understood. In the current study, we used symbolic cues to orient the attention of participants to the subsequent appearance of the face of a famous person (the former king of Spain) or an unfamiliar face. These were matched in perceptual characteristics. Behavioral effects showed that face-specific attention optimized response speed in an orthogonal task when the target matched the cue (valid trials) compared to when it did not (invalid trials). According to topographical analyses of the electrophysiological data, the famous and unfamiliar faces engaged dissociable brain circuits in two different temporal windows, from 144 to 300 ms after target processing, and at a later 456-492 ms epoch. In addition, orienting attention to specific faces modulated the perceptual stages reflected in the P1 and N170 potentials but with a different laterality pattern that depended on the familiarity of the faces. Whereas only attention to the famous face enhanced the P1 potential at left posterior electrodes, with no corresponding effect for the unfamiliar face at this stage, the N170 was modulated at left posterior sites for the famous item and at right homologous electrodes for the unfamiliar face. Intermediate processing stages, previously linked to facial identity processing indexed by the P2 and N2 potentials, reflected item familiarity but were not affected by the cueing manipulation. At the P3 level, attention influenced again item processing but did so in an equivalent manner for the famous and unfamiliar face. Our results, showing that identity-specific attention modulates perceptual stages of facial processing at different locations depending on idiosyncratic stimulus familiarity, may inform comparison of studies

Line drawing Scientific Instrument Module and lunar orbital science package

NASA Technical Reports Server (NTRS)

1970-01-01

A line drawing of the Scientific Instrument Module (SIM) with its lunar orbital science package. The SIM will be mounted in a previously vacant sector of the Apollo Service Module. It will carry specialized cameras and instrumentation for gathering lunar orbit scientific data.

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

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.

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.

SimCell Status Board

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

Tanzman, Edward; Dactelides, John M; Sharp, Robert

The Virtual SimCell is a method embodied in several software applications based on the Virtual Community Platform (VCP) (ANL-SF-11-049) and its Real-Time Dashboard (RTD) app. The purpose of this method is to more efficiently facilitate emergency preparedness exercises by allowing emergency preparedness exercise Simulation Cells -- SimCells -- to be established and managed through a computer network. SimCells take the place of organizations that would respond to actual emergencies, but are not participants in exercises of emergency preparedness plans. In effect, SimCells serve as actors portraying how those organizations would respond during real emergency events. The SimCell Status Board (SSB)more » is an RTD mini-app for controllers to communicate exercise events to players and each other by entering information into an integrated system of pre-defined data fields, displaying those data effectively, and preserving them for easy access during exercise evaluations.« less

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.

SIM Lite Astrometric Observatory progress report

NASA Astrophysics Data System (ADS)

Marr, James C., IV; Shao, Michael; Goullioud, Renaud

2010-07-01

The SIM Lite Astrometric Observatory (aka SIM Lite), a micro-arcsecond astrometry space mission, has been developed in response to NASA's indefinite deferral of the SIM PlanetQuest mission. The SIM Lite mission, while significantly more affordable than the SIM PlanetQuest mission concept, still addresses the full breadth of SIM science envisioned by two previous National Research Council (NRC) Astrophysics Decadal Surveys at the most stringent "Goal" level of astrometric measurement performance envisioned in those surveys. Over the past two years, the project has completed the conceptual design of the SIM Lite mission using only the completed SIM technology; published a 250 page book describing the science and mission design (available at the SIM website: http://sim.jpl.nasa.gov); been subject to an independent cost and technical readiness assessment by the Aerospace Corporation; and submitted a number of information responses to the NRC Astro2010 Decadal Survey. The project also conducted an exoplanet-finding capability double blind study that clearly demonstrated the ability of the mission to survey 60 to 100 nearby sun-like dwarf stars for terrestrial, habitable zone planets in complex planetary systems. Additionally, the project has continued Engineering Risk Reduction activities by building brassboard (form, fit & function to flight) version of key instrument elements and subjecting them to flight qualification environmental and performance testing. This paper summarizes the progress over the last two years and the current state of the SIM Lite project.

View of Scientific Instrument Module to be flown on Apollo 15

NASA Technical Reports Server (NTRS)

1971-01-01

Close-up view of the Scientific Instrument Module (SIM) to be flown for the first time on the Apollo 15 mission. Mounted in a previously vacant sector of the Apollo Service Module, the SIM carries specialized cameras and instrumentation for gathering lunar orbit scientific data.

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.

The Heuristic Sandbox: Developing Teacher Know-How through Play in simSchool

ERIC Educational Resources Information Center

Hopper, Susan B.

2018-01-01

simSchool is a game-based, virtual, and interactive tool that allows pre-service teachers to acquire new skills while constructing knowledge through experimentation with learning situations. Pre-service teachers develop know-how--or heuristic knowledge--through repeated practice in the "Personality Plus Higher-Order Thinking" module to…

Adaptor Identity Modulates Adaptation Effects in Familiar Face Identification and Their Neural Correlates

PubMed Central

Walther, Christian; Schweinberger, Stefan R.; Kovács, Gyula

2013-01-01

Adaptation-related aftereffects (AEs) show how face perception can be altered by recent perceptual experiences. Along with contrastive behavioural biases, modulations of the early event-related potentials (ERPs) were typically reported on categorical levels. Nevertheless, the role of the adaptor stimulus per se for face identity-specific AEs is not completely understood and was therefore investigated in the present study. Participants were adapted to faces (S1s) varying systematically on a morphing continuum between pairs of famous identities (identities A and B), or to Fourier phase-randomized faces, and had to match the subsequently presented ambiguous faces (S2s; 50/50% identity A/B) to one of the respective original faces. We found that S1s identical with or near to the original identities led to strong contrastive biases with more identity B responses following A adaptation and vice versa. In addition, the closer S1s were to the 50/50% S2 on the morphing continuum, the smaller the magnitude of the AE was. The relation between S1s and AE was, however, not linear. Additionally, stronger AEs were accompanied by faster reaction times. Analyses of the simultaneously recorded ERPs revealed categorical adaptation effects starting at 100 ms post-stimulus onset, that were most pronounced at around 125–240 ms for occipito-temporal sites over both hemispheres. S1-specific amplitude modulations were found at around 300–400 ms. Response-specific analyses of ERPs showed reduced voltages starting at around 125 ms when the S1 biased perception in a contrastive way as compared to when it did not. Our results suggest that face identity AEs do not only depend on physical differences between S1 and S2, but also on perceptual factors, such as the ambiguity of S1. Furthermore, short-term plasticity of face identity processing might work in parallel to object-category processing, and is reflected in the first 400 ms of the ERP. PMID:23990908

Image restoration approach to address reduced modulation contrast in structured illumination microscopy

PubMed Central

Patwary, Nurmohammed; Doblas, Ana; Preza, Chrysanthe

2018-01-01

The performance of structured illumination microscopy (SIM) is hampered in many biological applications due to the inability to modulate the light when imaging deep into the sample. This is in part because sample-induced aberration reduces the modulation contrast of the structured pattern. In this paper, we present an image restoration approach suitable for processing raw incoherent-grid-projection SIM data with a low fringe contrast. Restoration results from simulated and experimental ApoTome SIM data show results with improved signal-to-noise ratio (SNR) and optical sectioning compared to the results obtained from existing methods, such as 2D demodulation and 3D SIM deconvolution. Our proposed method provides satisfactory results (quantified by the achieved SNR and normalized mean square error) even when the modulation contrast of the illumination pattern is as low as 7%. PMID:29675307

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

View of model of Scientific Instrument Module to be flown on Apollo 15

NASA Technical Reports Server (NTRS)

1970-01-01

Close-up view of a scale model of the Scientific Instrument Module (SIM) to be flown for the first time on the Apollo 15 mission. Mounted in a previously vacant sector of the Apollo service module, the SIM carries specialized cameras and instrumentation for gathering lunar orbit scientific data.

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...

fastSIM: a practical implementation of fast structured illumination microscopy

NASA Astrophysics Data System (ADS)

Lu-Walther, Hui-Wen; Kielhorn, Martin; Förster, Ronny; Jost, Aurélie; Wicker, Kai; Heintzmann, Rainer

2015-03-01

A significant improvement in acquisition speed of structured illumination microscopy (SIM) opens a new field of applications to this already well-established super-resolution method towards 3D scanning real-time imaging of living cells. We demonstrate a method of increased acquisition speed on a two-beam SIM fluorescence microscope with a lateral resolution of ~100 nm at a maximum raw data acquisition rate of 162 frames per second (fps) with a region of interest of 16.5  ×  16.5 µm2, free of mechanically moving components. We use a programmable spatial light modulator (ferroelectric LCOS) which promises precise and rapid control of the excitation pattern in the sample plane. A passive Fourier filter and a segmented azimuthally patterned polarizer are used to perform structured illumination with maximum contrast. Furthermore, the free running mode in a modern sCMOS camera helps to achieve faster data acquisition.

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.

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.

Tracking microbial interactions with NanoSIMS

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

Musat, Niculina; Musat, Florin; Weber, Peter Kilian

The combination of stable isotope probing (SIP), NanoSIMS imaging and microbe identification via fluorescence in situ hybridization (FISH) is often used to link identity to function at the cellular level in microbial communities. Many opportunities remain for nanoSIP to identify metabolic interactions and nutrient fluxes within syntrophic associations and obligate symbioses where exchanges can be extremely rapid. However, additional data, such as genomic potential, gene expression or other imaging modalities are often critical to deciphering the mechanisms underlying specific interactions, and researchers must keep sample preparation artefacts in mind. Here we focus on recent applications of nanoSIP, particularly where usedmore » to track exchanges of isotopically labelled molecules between organisms. Here, we highlight metabolic interactions within syntrophic consortia, carbon/nitrogen fluxes between phototrophs and their heterotrophic partners, and symbiont–host nutrient sharing.« less

Tracking microbial interactions with NanoSIMS

DOE PAGES

Musat, Niculina; Musat, Florin; Weber, Peter Kilian; ...

2016-07-12

The combination of stable isotope probing (SIP), NanoSIMS imaging and microbe identification via fluorescence in situ hybridization (FISH) is often used to link identity to function at the cellular level in microbial communities. Many opportunities remain for nanoSIP to identify metabolic interactions and nutrient fluxes within syntrophic associations and obligate symbioses where exchanges can be extremely rapid. However, additional data, such as genomic potential, gene expression or other imaging modalities are often critical to deciphering the mechanisms underlying specific interactions, and researchers must keep sample preparation artefacts in mind. Here we focus on recent applications of nanoSIP, particularly where usedmore » to track exchanges of isotopically labelled molecules between organisms. Here, we highlight metabolic interactions within syntrophic consortia, carbon/nitrogen fluxes between phototrophs and their heterotrophic partners, and symbiont–host nutrient sharing.« less

fastSIM: a practical implementation of fast structured illumination microscopy.

PubMed

Lu-Walther, Hui-Wen; Kielhorn, Martin; Förster, Ronny; Jost, Aurélie; Wicker, Kai; Heintzmann, Rainer

2015-01-16

A significant improvement in acquisition speed of structured illumination microscopy (SIM) opens a new field of applications to this already well-established super-resolution method towards 3D scanning real-time imaging of living cells. We demonstrate a method of increased acquisition speed on a two-beam SIM fluorescence microscope with a lateral resolution of ~100 nm at a maximum raw data acquisition rate of 162 frames per second (fps) with a region of interest of 16.5  ×  16.5 µm 2 , free of mechanically moving components. We use a programmable spatial light modulator (ferroelectric LCOS) which promises precise and rapid control of the excitation pattern in the sample plane. A passive Fourier filter and a segmented azimuthally patterned polarizer are used to perform structured illumination with maximum contrast. Furthermore, the free running mode in a modern sCMOS camera helps to achieve faster data acquisition.

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

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

CrossSim

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

Plimpton, Steven J.; Agarwal, Sapan; Schiek, Richard

2016-09-02

CrossSim is a simulator for modeling neural-inspired machine learning algorithms on analog hardware, such as resistive memory crossbars. It includes noise models for reading and updating the resistances, which can be based on idealized equations or experimental data. It can also introduce noise and finite precision effects when converting values from digital to analog and vice versa. All of these effects can be turned on or off as an algorithm processes a data set and attempts to learn its salient attributes so that it can be categorized in the machine learning training/classification context. CrossSim thus allows the robustness, accuracy, andmore » energy usage of a machine learning algorithm to be tested on simulated hardware.« less

QuakeSim Project Networking

NASA Astrophysics Data System (ADS)

Kong, D.; Donnellan, A.; Pierce, M. E.

2012-12-01

QuakeSim is an online computational framework focused on using remotely sensed geodetic imaging data to model and understand earthquakes. With the rise in online social networking over the last decade, many tools and concepts have been developed that are useful to research groups. In particular, QuakeSim is interested in the ability for researchers to post, share, and annotate files generated by modeling tools in order to facilitate collaboration. To accomplish this, features were added to the preexisting QuakeSim site that include single sign-on, automated saving of output from modeling tools, and a personal user space to manage sharing permissions on these saved files. These features implement OpenID and Lightweight Data Access Protocol (LDAP) technologies to manage files across several different servers, including a web server running Drupal and other servers hosting the computational tools themselves.

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.

SimEngine v. 1.0

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

Le, Hai D.

2017-03-02

SimEngine provides the core functionalities and components that are key to the development of discrete event simulation tools. These include events, activities, event queues, random number generators, and basic result tracking classes. SimEngine was designed for high performance, integrates seamlessly into any Microsoft .Net development environment, and provides a flexible API for simulation developers.

TOF-SIMS imaging technique with information entropy

NASA Astrophysics Data System (ADS)

Aoyagi, Satoka; Kawashima, Y.; Kudo, Masahiro

2005-05-01

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is capable of chemical imaging of proteins on insulated samples in principal. However, selection of specific peaks related to a particular protein, which are necessary for chemical imaging, out of numerous candidates had been difficult without an appropriate spectrum analysis technique. Therefore multivariate analysis techniques, such as principal component analysis (PCA), and analysis with mutual information defined by information theory, have been applied to interpret SIMS spectra of protein samples. In this study mutual information was applied to select specific peaks related to proteins in order to obtain chemical images. Proteins on insulated materials were measured with TOF-SIMS and then SIMS spectra were analyzed by means of the analysis method based on the comparison using mutual information. Chemical mapping of each protein was obtained using specific peaks related to each protein selected based on values of mutual information. The results of TOF-SIMS images of proteins on the materials provide some useful information on properties of protein adsorption, optimality of immobilization processes and reaction between proteins. Thus chemical images of proteins by TOF-SIMS contribute to understand interactions between material surfaces and proteins and to develop sophisticated biomaterials.

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...

Objective assessment of gynecologic laparoscopic skills using the LapSimGyn virtual reality simulator.

PubMed

Larsen, C R; Grantcharov, T; Aggarwal, R; Tully, A; Sørensen, J L; Dalsgaard, T; Ottesen, B

2006-09-01

Safe realistic training and unbiased quantitative assessment of technical skills are required for laparoscopy. Virtual reality (VR) simulators may be useful tools for training and assessing basic and advanced surgical skills and procedures. This study aimed to investigate the construct validity of the LapSimGyn VR simulator, and to determine the learning curves of gynecologists with different levels of experience. For this study, 32 gynecologic trainees and consultants (juniors or seniors) were allocated into three groups: novices (0 advanced laparoscopic procedures), intermediate level (>20 and <60 procedures), and experts (>100 procedures). All performed 10 sets of simulations consisting of three basic skill tasks and an ectopic pregnancy program. The simulations were carried out on 3 days within a maximum period of 2 weeks. Assessment of skills was based on time, economy of movement, and error parameters measured by the simulator. The data showed that expert gynecologists performed significantly and consistently better than intermediate and novice gynecologists. The learning curves differed significantly between the groups, showing that experts start at a higher level and more rapidly reach the plateau of their learning curve than do intermediate and novice groups of surgeons. The LapSimGyn VR simulator package demonstrates construct validity on both the basic skills module and the procedural gynecologic module for ectopic pregnancy. Learning curves can be obtained, but to reach the maximum performance for the more complex tasks, 10 repetitions do not seem sufficient at the given task level and settings. LapSimGyn also seems to be flexible and widely accepted by the users.

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.

Virtual Learning Environments in Social Psychology: Using "The SIMs[superscript 3]" to Teach Self-Related Processes

ERIC Educational Resources Information Center

Stansbury, Jessica A.

2017-01-01

An interactive learning module was developed and implemented in a social psychology course to teach concepts of the "self" via self-exploration and game play using "The SIMS[superscript 3]." Students volunteered to play the computer video game throughout a 5-week summer session as a supplement to reading the chapter in the…

GSM Network Employment on a Man-Portable UAS

DTIC Science & Technology

2012-09-01

23  Figure 12.  3D Robotics’ ArduCopter kit (From DIY Drones, 2012) ................................24  Figure 13...San Diego, CA (Figure 12) and a base kit retails for under $600.00. 24 Figure 12. 3D Robotics’ ArduCopter kit (From DIY Drones, 2012) Due to...generic until it is associated with a subscriber identity module (SIM), commonly referred to as a SIM card (Figure 17). The SIM contains the identifiers

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.

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.

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.

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.

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

View of Scientific Instrument Module to be flown on Apollo 15

NASA Image and Video Library

1971-06-27

S71-2250X (June 1971) --- A close-up view of the Scientific Instrument Module (SIM) to be flown for the first time on the Apollo 15 lunar landing mission. Mounted in a previously vacant sector of the Apollo Service Module (SM), the SIM carries specialized cameras and instrumentation for gathering lunar orbit scientific data. SIM equipment includes a laser altimeter for accurate measurement of height above the lunar surface; a large-format panoramic camera for mapping, correlated with a metric camera and the laser altimeter for surface mapping; a gamma ray spectrometer on a 25-feet extendible boom; a mass spectrometer on a 21-feet extendible boom; X-ray and alpha particle spectrometers; and a subsatellite which will be injected into lunar orbit carrying a particle and magnetometer, and the S-Band transponder.

Identity-Specific Reward Representations in Orbitofrontal Cortex Are Modulated by Selective Devaluation.

PubMed

Howard, James D; Kahnt, Thorsten

2017-03-08

Goal-directed behavior is sensitive to the current value of expected outcomes. This requires independent representations of specific rewards, which have been linked to orbitofrontal cortex (OFC) function. However, the mechanisms by which the human brain updates specific goals on the fly, and translates those updates into choices, have remained unknown. Here we implemented selective devaluation of appetizing food odors in combination with pattern-based neuroimaging and a decision-making task. We found that in a hungry state, participants chose to smell high-intensity versions of two value-matched food odor rewards. After eating a meal corresponding to one of the two odors, participants switched choices toward the low intensity of the sated odor but continued to choose the high intensity of the nonsated odor. This sensory-specific behavioral effect was mirrored by pattern-based changes in fMRI signal in lateral posterior OFC, where specific reward identity representations were altered after the meal for the sated food odor but retained for the nonsated counterpart. In addition, changes in functional connectivity between the OFC and general value coding in ventromedial prefrontal cortex (vmPFC) predicted individual differences in satiety-related choice behavior. These findings demonstrate how flexible representations of specific rewards in the OFC are updated by devaluation, and how functional connections to vmPFC reflect the current value of outcomes and guide goal-directed behavior. SIGNIFICANCE STATEMENT The orbitofrontal cortex (OFC) is critical for goal-directed behavior. A recent proposal is that OFC fulfills this function by representing a variety of state and task variables ("cognitive maps"), including a conjunction of expected reward identity and value. Here we tested how identity-specific representations of food odor reward are updated by satiety. We found that fMRI pattern-based signatures of reward identity in lateral posterior OFC were modulated after

Identity-Specific Reward Representations in Orbitofrontal Cortex Are Modulated by Selective Devaluation

PubMed Central

Howard, James D.

2017-01-01

Goal-directed behavior is sensitive to the current value of expected outcomes. This requires independent representations of specific rewards, which have been linked to orbitofrontal cortex (OFC) function. However, the mechanisms by which the human brain updates specific goals on the fly, and translates those updates into choices, have remained unknown. Here we implemented selective devaluation of appetizing food odors in combination with pattern-based neuroimaging and a decision-making task. We found that in a hungry state, participants chose to smell high-intensity versions of two value-matched food odor rewards. After eating a meal corresponding to one of the two odors, participants switched choices toward the low intensity of the sated odor but continued to choose the high intensity of the nonsated odor. This sensory-specific behavioral effect was mirrored by pattern-based changes in fMRI signal in lateral posterior OFC, where specific reward identity representations were altered after the meal for the sated food odor but retained for the nonsated counterpart. In addition, changes in functional connectivity between the OFC and general value coding in ventromedial prefrontal cortex (vmPFC) predicted individual differences in satiety-related choice behavior. These findings demonstrate how flexible representations of specific rewards in the OFC are updated by devaluation, and how functional connections to vmPFC reflect the current value of outcomes and guide goal-directed behavior. SIGNIFICANCE STATEMENT The orbitofrontal cortex (OFC) is critical for goal-directed behavior. A recent proposal is that OFC fulfills this function by representing a variety of state and task variables (“cognitive maps”), including a conjunction of expected reward identity and value. Here we tested how identity-specific representations of food odor reward are updated by satiety. We found that fMRI pattern-based signatures of reward identity in lateral posterior OFC were modulated

Cultural modulation of self-referential brain activity for personality traits and social identities.

PubMed

Sul, Sunhae; Choi, Incheol; Kang, Pyungwon

2012-01-01

Cross-cultural studies have shown that personality traits are less central and social identities are more important to the selfhood of collectivistic people. However, most cultural neuroscience studies using the self-reference effect (SRE) paradigm have only used personality traits to explore cultural differences in the neural circuits of self-referential processes. In the present study, we used both personality traits and social identities as stimuli in the SRE paradigm and investigated whether and how one's cultural orientation (i.e., individualism vs. collectivism) affects the SRE in the brain. The results showed that the medial prefrontal cortex, anterior cingulate, bilateral temporoparietal regions, and precuneus were involved in self-representation for both personality traits and social identities. Importantly, cultural orientation predicted differential activation patterns in these regions. Collectivists showed stronger activation in the left temporoparietal regions than individualists, who mainly recruited the medial prefrontal regions. Our findings suggest that the personal and social self share common neural substrates, the activation of which can be modulated by one's cultural orientation.

simSchool: The Game of Teaching

ERIC Educational Resources Information Center

Zibit, Melanie; Gibson, David

2005-01-01

"simSchool" is a classroom simulation program funded by the Preparing Tomorrow's Teachers to Teach with Technology (PT3) program of the U.S. Department of Education. Just as a flight-simulator immerses a player in the complexities of flying a plane, "simSchool" immerses novice teachers in some of the complexities of teaching 7th-12th grade…

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.

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.

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.

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.

"She's Always Been the Smart One. I've Always Been the Dumb One": Identities in the Mathematics Classroom

ERIC Educational Resources Information Center

Bishop, Jessica Pierson

2012-01-01

The moment-to-moment dynamics of student discourse plays a large role in students' enacted mathematics identities. Discourse analysis was used to describe meaningful discursive patterns in the interactions of 2 students in a 7th-grade, technology-based, curricular unit (SimCalc MathWorlds[R]) and to show how mathematics identities are enacted at…

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.

Identification of diazotrophic microorganisms in marine sediment via fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS).

PubMed

Dekas, Anne E; Orphan, Victoria J

2011-01-01

Growing appreciation for the biogeochemical significance of uncultured microorganisms is changing the focus of environmental microbiology. Techniques designed to investigate microbial metabolism in situ are increasingly popular, from mRNA-targeted fluorescence in situ hybridization (FISH) to the "-omics" revolution, including metagenomics, transcriptomics, and proteomics. Recently, the coupling of FISH with nanometer-scale secondary ion mass spectrometry (NanoSIMS) has taken this movement in a new direction, allowing single-cell metabolic analysis of uncultured microbial phylogenic groups. The main advantage of FISH-NanoSIMS over previous noncultivation-based techniques to probe metabolism is its ability to directly link 16S rRNA phylogenetic identity to metabolic function. In the following chapter, we describe the procedures necessary to identify nitrogen-fixing microbes within marine sediment via FISH-NanoSIMS, using our work on nitrogen fixation by uncultured deep-sea methane-consuming archaea as a case study. Copyright © 2011 Elsevier Inc. All rights reserved.

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

SIMS: addressing the problem of heterogeneity in databases

NASA Astrophysics Data System (ADS)

Arens, Yigal

1997-02-01

The heterogeneity of remotely accessible databases -- with respect to contents, query language, semantics, organization, etc. -- presents serious obstacles to convenient querying. The SIMS (single interface to multiple sources) system addresses this global integration problem. It does so by defining a single language for describing the domain about which information is stored in the databases and using this language as the query language. Each database to which SIMS is to provide access is modeled using this language. The model describes a database's contents, organization, and other relevant features. SIMS uses these models, together with a planning system drawing on techniques from artificial intelligence, to decompose a given user's high-level query into a series of queries against the databases and other data manipulation steps. The retrieval plan is constructed so as to minimize data movement over the network and maximize parallelism to increase execution speed. SIMS can recover from network failures during plan execution by obtaining data from alternate sources, when possible. SIMS has been demonstrated in the domains of medical informatics and logistics, using real databases.

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

The Levi-Civita Tensor and Identities in Vector Analysis. Vector Field Identities. Modules and Monographs in Undergraduate Mathematics and Its Applications Project. UMAP Unit 427.

ERIC Educational Resources Information Center

Yiu, Chang-li; Wilde, Carroll O.

Vector analysis is viewed to play a key role in many branches of engineering and the physical sciences. This unit is geared towards deriving identities and establishing "machinery" to make derivations a routine task. It is noted that the module is not an applications unit, but has as its primary objective the goal of providing science,…

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

Modulational Instability in a Pair of Non-identical Coupled Nonlinear Electrical Transmission Lines

NASA Astrophysics Data System (ADS)

Eric, Tala-Tebue; Aurelien, Kenfack-Jiotsa; Marius Hervé, Tatchou-Ntemfack; Timoléon Crépin, Kofané

2013-07-01

In this work, we investigate the dynamics of modulated waves non-identical coupled nonlinear transmission lines. Traditional methods for avoiding mode mixing in identical coupled nonlinear electrical lines consist of adding the same number of linear inductors in each branch. Adding linear inductors in a single line leads to asymmetric coupled nonlinear electrical transmission lines which propagate the signal and the mode mixing. On one hand, the difference between the two lines induced the fission for only one mode of propagation. This fission is influenced by the amplitude of the signal and the amount of the input energy as well; it also narrows the width of the input pulse soliton, leading to a possible increasing of the bit rate. On the other hand, the dissymmetry of the two lines converts the network into a good amplifier for the ω_ mode which corresponds to the regime admitting low frequencies.

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.

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

Sim-based detection tools to minimize motorcycle theft

NASA Astrophysics Data System (ADS)

Triansyah, F. A.; Mudhafar, Z.; Lestari, C.; Amilia, S.; Ruswana, N. D.; Junaeti, E.

2018-05-01

The number of motorcycles in Indonesia spurs the increased criminal acts of motorcycle theft. In addition, the number of motorcycles increases the number of traffic accidents caused by improper motorists. The purpose of this research is to make METEOR (SIM Detector) which is a tool to detect the feasibility of SIM (driver license) which is used to operate and protect motorcycle against theft. METEOR is made through the assembly, encoding, testing, and sequencing stages of the motorcycle. Based on the research that has been done, METEOR generated that can detect the SIM by using additional RFID chip and can be set on the motorcycle. Without the proper SIM, motorized chests coupled with METEOR cannot be turned on. So it can be concluded that motorcycles with additional METEOR is able to be a safety device against theft and as a tool to test the feasibility of motorcycle riders.

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.

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

Social Identity Mapping: A procedure for visual representation and assessment of subjective multiple group memberships.

PubMed

Cruwys, Tegan; Steffens, Niklas K; Haslam, S Alexander; Haslam, Catherine; Jetten, Jolanda; Dingle, Genevieve A

2016-12-01

In this research, we introduce Social Identity Mapping (SIM) as a method for visually representing and assessing a person's subjective network of group memberships. To provide evidence of its utility, we report validating data from three studies (two longitudinal), involving student, community, and clinical samples, together comprising over 400 participants. Results indicate that SIM is easy to use, internally consistent, with good convergent and discriminant validity. Each study also illustrates the ways that SIM can be used to address a range of novel research questions. Study 1 shows that multiple positive group memberships are a particularly powerful predictor of well-being. Study 2 shows that social support is primarily given and received within social groups and that only in-group support is beneficial for well-being. Study 3 shows that improved mental health following a social group intervention is attributable to an increase in group compatibility. In this way, the studies demonstrate the capacity for SIM to make a contribution both to the development of social-psychological theory and to its practical application. © 2016 The British Psychological Society.

AXAF SIM focus mechanism study

NASA Technical Reports Server (NTRS)

Tananbaum, H. D.; Whitbeck, E.

1994-01-01

The design requirements and initial design concept for the AXAF-I Science Instrument Module (SIM) were reviewed at Ball on September 29, 1993. The concept design SIM focus mechanism utilizes a planetary gearset, with redundant motors, to drive a large ring (called 'main housing bearing') via a spur gearset. This large drive ring actuates three tangent bar links (called 'push rods'), which in turn actuate three levers (called 'pin levers'). Each of the three pin levers rotates an 'eccentric pin,' which in turn moves the base of a bipod flexure in both the radial (normal to optical axis) and axial (focus along optical axis) directions. Three bipod flexures are employed, equally spaced at 120 degrees apart, the base of each being translated in the two directions as described above. A focus adjustment is made by rotating the drive ring, which drives the push rods and therefore the pin levers, which in turn rotate the eccentric pins, finally imparting the two motions to the base of each of the bipod flexures. The axial translation (focus adjustment) of the focused structure is the sum of the direct axial motion plus axial motion which comes from uniformly squeezing the three bipod bases radially inward. SAO documented the following concerns regarding the focus mechanism in memo WAP-FY94-001, dated October 7, 1993: (1) The focus adjustment depends, in large part, on the structural properties (stiffnesses and end fixities) of the bipod flexures, push rods, pin levers and eccentric pins. If these properties are not matched very well, then lateral translations as well as unwanted rotations of the focussed structure will accompany focus motion. In addition, the stackup of linkage tolerances and any nonuniform wear in the linkages will result in the same unwanted motions. Thermal gradients will also affect these motions. At the review Ball did not present supporting analyses to support their choice of this design concept. (2) The proposed 'primary' method of measuring focus

Transforming Mobile Platform with KI-SIM Card into an Open Mobile Identity Tool

NASA Astrophysics Data System (ADS)

Hyppönen, Konstantin; Hassinen, Marko; Trichina, Elena

Recent introduction of Near Field Communication (NFC) in mobile phones has stimulated the development of new proximity payment and identification services. We present an architecture that facilitates the use of the mobile phone as a personalised electronic identity tool. The tool can work as a replacement for numerous ID cards and licenses. Design for privacy principles have been applied, such as minimisation of data collection and informed consent of the user. We describe an implementation of a lightweight version of the of the mobile identity tool using currently available handset technology and off-the-shelf development tools.

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.

Discovery of Planetary Systems With SIM

NASA Technical Reports Server (NTRS)

Marcy, Geoffrey W.; Butler, Paul R.; Frink, Sabine; Fischer, Debra; Oppenheimer, Ben; Monet, David G.; Quirrenbach, Andreas; Scargle, Jeffrey D.

2004-01-01

We are witnessing the birth of a new observational science: the discovery and characterization of extrasolar planetary systems. In the past five years, over 70 extrasolar planets have been discovered by precision Doppler surveys, most by members of this SIM team. We are using the data base of information gleaned from our Doppler survey to choose the best targets for a new SIN planet search. In the same way that our Doppler database now serves SIM, our team will return a reconnaissance database to focus Terrestrial Planet Finder (TPF) into a more productive, efficient mission.

The portrayal of J. Marion Sims' controversial surgical legacy.

PubMed

Spettel, Sara; White, Mark Donald

2011-06-01

In the mid 1800s Dr. J. Marion Sims reported the successful repair of vesicovaginal fistulas with a technique he developed by performing multiple operations on female slaves. A venerated physician in his time, the legacy of Dr. Sims is controversial and represents a significant chapter in the mistreatment of African-Americans by the medical establishment. This review compares the modern debate surrounding his legacy with the presentation of his operation in widely consulted urological texts and journals. A literature review was performed of medical, sociological and periodical sources (1851 to the present) regarding J. Marion Sims and vesicovaginal fistula repair. During the last several decades, while the controversy around Dr. Sims' surgical development has produced a steady stream of articles in the historical and popular literature, relatively little mention is found in standard urology textbooks or journals. With increased public attention, some have debated the removal or modification of public tributes to Dr. Sims. This move has been countered by arguments against the validity of judging a 19th century physician by modern standards. While historians, ethicists and the popular press have debated Dr. Sims' legacy, medical sources have continued to portray him unquestionably as a great figure in medical history. This division keeps the medical profession uninformed and detached from the public debate on his legacy and, thus, the larger issues of ethical treatment of surgical patients. Copyright © 2011 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

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.

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.

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 ...

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

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

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 Sim

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

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

WEC-SIM Validation Testing Plan FY14 Q4.

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

Ruehl, Kelley Michelle

2016-02-01

The WEC-Sim project is currently on track, having met both the SNL and NREL FY14 Milestones, as shown in Table 1 and Table 2. This is also reflected in the Gantt chart uploaded to the WEC-Sim SharePoint site in the FY14 Q4 Deliverables folder. The work completed in FY14 includes code verification through code-to-code comparison (FY14 Q1 and Q2), preliminary code validation through comparison to experimental data (FY14 Q2 and Q3), presentation and publication of the WEC-Sim project at OMAE 2014 [1], [2], [3] and GMREC/METS 2014 [4] (FY14 Q3), WEC-Sim code development and public open-source release (FY14 Q3), andmore » development of a preliminary WEC-Sim validation test plan (FY14 Q4). This report presents the preliminary Validation Testing Plan developed in FY14 Q4. The validation test effort started in FY14 Q4 and will go on through FY15. Thus far the team has developed a device selection method, selected a device, and placed a contract with the testing facility, established several collaborations including industry contacts, and have working ideas on the testing details such as scaling, device design, and test conditions.« less

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.

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.

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

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.

SIM key comparison for luminous flux. SIM.PR-K4

NASA Astrophysics Data System (ADS)

Matamoros, Carlos H.; Ohno, Yoshi; Zwinkels, Joanne; Cogno, Jorge A.; Couceiro, Iakyra B.

2016-01-01

In compliance with the established BIPM and CCPR policies and guidelines on comparisons, the SIM Photometry and Radiometry Working Group decided to conduct a key comparison on total luminous flux in order to provide an opportunity for its member National Metrology Institutes (NMIs) that did not participate in the CCPR-K4 comparison, to get a link to the reference value obtained for this quantity (the lumen) and to derive the corresponding degrees of equivalence. This SIM.PR-K4 was piloted by Centro Nacional de Metrología (CENAM), the NMI of Mexico and included the participation of five laboratories: CENAM (Mexico), INTI (Argentina), INMETRO (Brazil), NIST (USA, linking lab), and NRC (Canada, linking lab). The comparison, conducted in star type scheme, was run using three to four lamps per participant, and results are given in this report, including the unilateral degrees of equivalence. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCPR, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

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).

Top–Down Modulation on the Perception and Categorization of Identical Pitch Contours in Speech and Music

PubMed Central

Weidema, Joey L.; Roncaglia-Denissen, M. P.; Honing, Henkjan

2016-01-01

Whether pitch in language and music is governed by domain-specific or domain-general cognitive mechanisms is contentiously debated. The aim of the present study was to investigate whether mechanisms governing pitch contour perception operate differently when pitch information is interpreted as either speech or music. By modulating listening mode, this study aspired to demonstrate that pitch contour perception relies on domain-specific cognitive mechanisms, which are regulated by top–down influences from language and music. Three groups of participants (Mandarin speakers, Dutch speaking non-musicians, and Dutch musicians) were exposed to identical pitch contours, and tested on their ability to identify these contours in a language and musical context. Stimuli consisted of disyllabic words spoken in Mandarin, and melodic tonal analogs, embedded in a linguistic and melodic carrier phrase, respectively. Participants classified identical pitch contours as significantly different depending on listening mode. Top–down influences from language appeared to alter the perception of pitch contour in speakers of Mandarin. This was not the case for non-musician speakers of Dutch. Moreover, this effect was lacking in Dutch speaking musicians. The classification patterns of pitch contours in language and music seem to suggest that domain-specific categorization is modulated by top–down influences from language and music. PMID:27313552

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...

Evaluating the potential of the MegaSIMS for nuclear forensics

NASA Astrophysics Data System (ADS)

Boehnke, P.; McKeegan, K. D.; Coath, C. D.; Hutcheon, I. D.; Steele, R. C.; Harrison, M.

2013-12-01

Nuclear forensics investigates the illicit movement of nuclear materials. Measurements of uranium isotopic compositions are an important key as they permit provenance tracing and determination of intended use. Traditional secondary ion mass spectrometers (SIMS) are incapable of resolving 235UH from 236U due to the high mass resolving power (MRP ~38,000) needed, significantly limiting their ability to accurately measure 236U/235U, particularly for highly enriched uranium. This limitation can significantly inhibit the ability to establish details about enrichment processes. The MegaSIMS is a unique combination of SIMS and accelerator mass spectrometry (AMS) and allows for molecular interference free measurements, while retaining the spatial resolution and ease of sample preparation common in SIMS analyses. The instrument was primarily designed to measure the oxygen isotope composition of the solar wind [1] and its capability for measuring high mass elements has not been evaluated previously. We evaluated the potential of the MegaSIMS by measuring 236U/235U without hydride interference. While preliminary results show abundance sensitivity of ~E-9 and an MRP of ~1,200 at the high mass side of 238 amu, precision is limited by the detector geometry and slow magnet switching. Future work will include developing electrostatic peak switching as well as refining the measurement precision and abundance sensitivity of the MegaSIMS for nuclear forensics. [1] McKeegan, Kallio, Heber, Jarzebinski, Mao, Coath, Kunihiro, Wiens, Nordholt, Moses Jr., Reisenfeld, Jurewicz, and Burnett, 2011. Science. 332, 1528-1532.

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.

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.

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…

Monolithically integrated InGaAsP/InP laser/modulator using identical layer approach for opto-electronic oscillator

NASA Astrophysics Data System (ADS)

Wu, Chi; Keo, Sam A.; Yao, X. S.; Turner, Tasha E.; Davis, Lawrence J.; Young, Martin G.; Maleki, Lute; Forouhar, Siamak

1998-08-01

The microwave optoelectronic oscillator (OEO) has been demonstrated on a breadboard. The future trend is to integrate the whole OEO on a chip, which requires the development of high power and high efficiency integrated photonic components. In this paper, we will present the design and fabrication of an integrated semiconductor laser/modulator using the identical active layer approach on InGaAsP/InP material. The best devices have threshold currents of 50-mA at room temperature for CW operation. The device length is approximately 3-mm, resulting in a mode spacing of 14 GHz. For only 5-dBm microwave power applied to the modulator section, modulation response with 30 dB resonate enhancement has been observed. This work shows the promise for an on-chip integrated OEO.

SIMS analysis of extended impact features on LDEF experiment

NASA Technical Reports Server (NTRS)

Amari, S.; Foote, J.; Jessberger, E. K.; Simon, C.; Stadermann, F. J.; Swan, P.; Walker, R.; Zinner, E.

1991-01-01

Discussed here are the first Secondary Ion Mass Spectroscopy (SIMS) analysis of projectile material deposited in extended impact features on Ge wafers from the trailing edge. Although most capture cells lost their plastic film covers, they contain extended impact features that apparently were produced by high velocity impacts when the plastic foils were still intact. Detailed optical scanning of all bare capture cells from the trailing edge revealed more than 100 impacts. Fifty-eight were selected by scanning electron microscope (SEM) inspection as prime candidates for SIMS analysis. Preliminary SIMS measurements were made on 15 impacts. More than half showed substantial enhancements of Mg, Al, Si, Ca, and Fe in the impact region, indicating micrometeorites as the projectiles.

RxnSim: a tool to compare biochemical reactions.

PubMed

Giri, Varun; Sivakumar, Tadi Venkata; Cho, Kwang Myung; Kim, Tae Yong; Bhaduri, Anirban

2015-11-15

: Quantitative assessment of chemical reaction similarity aids database searches, classification of reactions and identification of candidate enzymes. Most methods evaluate reaction similarity based on chemical transformation patterns. We describe a tool, RxnSim, which computes reaction similarity based on the molecular signatures of participating molecules. The tool is able to compare reactions based on similarities of substrates and products in addition to their transformation. It allows masking of user-defined chemical moieties for weighted similarity computations. RxnSim is implemented in R and is freely available from the Comprehensive R Archive Network, CRAN (http://cran.r-project.org/web/packages/RxnSim/). anirban.b@samsung.com or ty76.kim@samsung.com 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.

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

FoilSim: Basic Aerodynamics Software Created

NASA Technical Reports Server (NTRS)

Peterson, Ruth A.

1999-01-01

FoilSim is interactive software that simulates the airflow around various shapes of airfoils. The graphical user interface, which looks more like a video game than a learning tool, captures and holds the students interest. The software is a product of NASA Lewis Research Center s Learning Technologies Project, an educational outreach initiative within the High Performance Computing and Communications Program (HPCCP).This airfoil view panel is a simulated view of a wing being tested in a wind tunnel. As students create new wing shapes by moving slider controls that change parameters, the software calculates their lift. FoilSim also displays plots of pressure or airspeed above and below the airfoil surface.

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.

Port-O-Sim Object Simulation Application

NASA Technical Reports Server (NTRS)

Lanzi, Raymond J.

2009-01-01

Port-O-Sim is a software application that supports engineering modeling and simulation of launch-range systems and subsystems, as well as the vehicles that operate on them. It is flexible, distributed, object-oriented, and realtime. A scripting language is used to configure an array of simulation objects and link them together. The script is contained in a text file, but executed and controlled using a graphical user interface. A set of modules is defined, each with input variables, output variables, and settings. These engineering models can be either linked to each other or run as standalone. The settings can be modified during execution. Since 2001, this application has been used for pre-mission failure mode training for many Range Safety Scenarios. It contains range asset link analysis, develops look-angle data, supports sky-screen site selection, drives GPS (Global Positioning System) and IMU (Inertial Measurement Unit) simulators, and can support conceptual design efforts for multiple flight programs with its capacity for rapid six-degrees-of-freedom model development. Due to the assembly of various object types into one application, the application is applicable across a wide variety of launch range problem domains.

SimBA: simulation algorithm to fit extant-population distributions.

PubMed

Parida, Laxmi; Haiminen, Niina

2015-03-14

Simulation of populations with specified characteristics such as allele frequencies, linkage disequilibrium etc., is an integral component of many studies, including in-silico breeding optimization. Since the accuracy and sensitivity of population simulation is critical to the quality of the output of the applications that use them, accurate algorithms are required to provide a strong foundation to the methods in these studies. In this paper we present SimBA (Simulation using Best-fit Algorithm) a non-generative approach, based on a combination of stochastic techniques and discrete methods. We optimize a hill climbing algorithm and extend the framework to include multiple subpopulation structures. Additionally, we show that SimBA is very sensitive to the input specifications, i.e., very similar but distinct input characteristics result in distinct outputs with high fidelity to the specified distributions. This property of the simulation is not explicitly modeled or studied by previous methods. We show that SimBA outperforms the existing population simulation methods, both in terms of accuracy as well as time-efficiency. Not only does it construct populations that meet the input specifications more stringently than other published methods, SimBA is also easy to use. It does not require explicit parameter adaptations or calibrations. Also, it can work with input specified as distributions, without an exemplar matrix or population as required by some methods. SimBA is available at http://researcher.ibm.com/project/5669 .

Expectations about person identity modulate the face-sensitive N170.

PubMed

Johnston, Patrick; Overell, Anne; Kaufman, Jordy; Robinson, Jonathan; Young, Andrew W

2016-12-01

Identifying familiar faces is a fundamentally important aspect of social perception that requires the ability to assign very different (ambient) images of a face to a common identity. The current consensus is that the brain processes face identity at approximately 250-300 msec following stimulus onset, as indexed by the N250 event related potential. However, using two experiments we show compelling evidence that where experimental paradigms induce expectations about person identity, changes in famous face identity are in fact detected at an earlier latency corresponding to the face-sensitive N170. In Experiment 1, using a rapid periodic stimulation paradigm presenting highly variable ambient images, we demonstrate robust effects of low frequency, periodic face-identity changes in N170 amplitude. In Experiment 2, we added infrequent aperiodic identity changes to show that the N170 was larger to both infrequent periodic and infrequent aperiodic identity changes than to high frequency identities. Our use of ambient stimulus images makes it unlikely that these effects are due to adaptation of low-level stimulus features. In line with current ideas about predictive coding, we therefore suggest that when expectations about the identity of a face exist, the visual system is capable of detecting identity mismatches at a latency consistent with the N170. Copyright © 2016 Elsevier Ltd. All rights reserved.

The LapSim virtual reality simulator: promising but not yet proven.

PubMed

Fairhurst, Katherine; Strickland, Andrew; Maddern, Guy

2011-02-01

The acquisition of technical skills using surgical simulators is an area of active research and rapidly evolving technology. The LapSim is a virtual reality simulator that currently allows practice of basic laparoscopic skills and some procedures. To date, no reviews have been published with reference to a single virtual reality simulator. A PubMed search was performed using the keyword "LapSim," with further papers identified from the citations of original search articles. Use of the LapSim to develop surgical skills has yielded overall results, although inconsistencies exist. Data regarding the transferability of learned skills to the operative environment are encouraging as is the validation work, particularly the use of a combination of measured parameters to produce an overall comparative performance score. Although the LapSim currently does not have any proven significant advantages over video trainers in terms of basic skills instruction and although the results of validation studies are variable, the potential for such technology to have a huge impact on surgical training is apparent. Work to determine standardized learning curves and proficiency criteria for different levels of trainees is incomplete. Moreover, defining which performance parameters measured by the LapSim accurately determine laparoscopic skill is complex. Further technological advances will undoubtedly improve the efficacy of the LapSim, and the results of large multicenter trials are anticipated.

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.

Sodium accumulation at potential-induced degradation shunted areas in polycrystalline silicon modules

DOE PAGES

Harvey, Steven P.; Aguiar, Jeffery A.; Hacke, Peter; ...

2016-09-19

Here, we investigated potential-induced degradation (PID) in silicon mini-modules that were subjected to accelerated stressing to induce PID conditions. Shunted areas on the cells were identified with photoluminescence and dark lock-in thermography (DLIT) imaging. The identical shunted areas were then analyzed via time-of-flight secondary-ion mass spectrometry (TOFSIMS) imaging, 3-D tomography, and high-resolution transmission electron microscopy. The TOF-SIMS imaging indicates a high concentration of sodium in the shunted areas, and 3-D tomography reveals that the sodium extends more than 2 um from the surface below shunted regions. Transmission electron microscopy investigation reveals that a stacking fault is present at an areamore » identified as shunted by DLIT imaging. After the removal of surface sodium, tomography reveals persistent sodium present around the junction depth of 300 nm and a drastic difference in sodium content at the junction when comparing shunted and nonshunted regions.« less

Heterogeneity of neuroblastoma cell identity defined by transcriptional circuitries.

PubMed

Boeva, Valentina; Louis-Brennetot, Caroline; Peltier, Agathe; Durand, Simon; Pierre-Eugène, Cécile; Raynal, Virginie; Etchevers, Heather C; Thomas, Sophie; Lermine, Alban; Daudigeos-Dubus, Estelle; Geoerger, Birgit; Orth, Martin F; Grünewald, Thomas G P; Diaz, Elise; Ducos, Bertrand; Surdez, Didier; Carcaboso, Angel M; Medvedeva, Irina; Deller, Thomas; Combaret, Valérie; Lapouble, Eve; Pierron, Gaelle; Grossetête-Lalami, Sandrine; Baulande, Sylvain; Schleiermacher, Gudrun; Barillot, Emmanuel; Rohrer, Hermann; Delattre, Olivier; Janoueix-Lerosey, Isabelle

2017-09-01

Neuroblastoma is a tumor of the peripheral sympathetic nervous system, derived from multipotent neural crest cells (NCCs). To define core regulatory circuitries (CRCs) controlling the gene expression program of neuroblastoma, we established and analyzed the neuroblastoma super-enhancer landscape. We discovered three types of identity in neuroblastoma cell lines: a sympathetic noradrenergic identity, defined by a CRC module including the PHOX2B, HAND2 and GATA3 transcription factors (TFs); an NCC-like identity, driven by a CRC module containing AP-1 TFs; and a mixed type, further deconvoluted at the single-cell level. Treatment of the mixed type with chemotherapeutic agents resulted in enrichment of NCC-like cells. The noradrenergic module was validated by ChIP-seq. Functional studies demonstrated dependency of neuroblastoma with noradrenergic identity on PHOX2B, evocative of lineage addiction. Most neuroblastoma primary tumors express TFs from the noradrenergic and NCC-like modules. Our data demonstrate a previously unknown aspect of tumor heterogeneity relevant for neuroblastoma treatment strategies.

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.

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

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.

Collecting Social Network Data from Mobile Phone SIM Cards

ERIC Educational Resources Information Center

Peseckas, Ryan

2016-01-01

I used a subscriber identity module card reader to copy the lists of saved contacts from 170 mobile phones in Fiji. This approach has both advantages and disadvantages compared to other techniques for collecting telephone network data. Copying phone contacts avoids recall biases associated with survey-based name generators. It also obviates the…

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.

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.

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

The Pedagogical Benefits of "SimCity" in Urban Geography Education

ERIC Educational Resources Information Center

Kim, Minsung; Shin, Jungyeop

2016-01-01

This article investigated the pedagogical potential of the "SimCity" simulation game in an urban geography course. University students used "SimCity" to build their own cities and applied a wide range of theories to support their urban structures. Moreover, the students critically evaluated the logic and functioning of the…

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.

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…

Cognitive Anatomy of Tutor Learning: Lessons Learned with SimStudent

ERIC Educational Resources Information Center

Matsuda, Noboru; Yarzebinski, Evelyn; Keiser, Victoria; Raizada, Rohan; Cohen, William W.; Stylianides, Gabriel J.; Koedinger, Kenneth R.

2013-01-01

This article describes an advanced learning technology used to investigate hypotheses about learning by teaching. The proposed technology is an instance of a teachable agent, called SimStudent, that learns skills (e.g., for solving linear equations) from examples and from feedback on performance. SimStudent has been integrated into an online,…

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.

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…

Metabolic activity of uncultivated magnetotactic bacteria revealed by NanoSIMS

NASA Astrophysics Data System (ADS)

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

2017-12-01

Microorganisms that exhibit magnetotaxis behavior, collectively known as the magnetotactic bacteria (MTB), are those whose motility is influenced by the Earth's magnetic field. MTB are a physiologically diverse group of bacteria with a unique feature of intracellular biomineralization of magnetosomes (Fe3O4 and/or Fe3S4) (Bazylinski et al., 2013). However, the ecophysiology of uncultivated MTB, especially those within the Nitrospirae phylum forming hundreds of bullet-shaped magnetite magnetosomes per cell, is still not well characterized (Lin et al., 2014). Nanoscale secondary ion mass spectrometry (NanoSIMS) is a powerful tool for revealing element distribution in nanometer-scale resolution, which opens exciting possibilities for the study of interactions between microorganisms and environments (Gao et al., 2016; Musat et al., 2016). Here we applied NanoSIMS to investigate the dynamics of carbon and nitrogen assimilations in two magnetotactic Nitrospirae populations at single cell level. Our NanoSIMS results confirmed the metabolic potential of Nitrospirae MTB proposed by genomic and metagenomic analysis and provided additional insights into the ecophysiology of uncultivated MTB. This study suggests that NanoSIMS-based analyses are powerful approaches for investigating and characterizing the ecological function of environmental microorganisms. References: Bazylinski D A., Lefèvre, C T., Schüler D., 2013. Magnetotactic Bacteria. 453-494.Lin W, Bazylinski DA, Xiao T, Wu L- F, Pan Y., 2014. Life with compass: diversity and biogeography of magnetotactic bacteria. Environ Microbiol, 16: 1462-2920.Gao D., Huang X., Tao Y., 2016. A critical review of NanoSIMS in analysis of microbial metabolic activities at single-cell level. Crit Rev Biotechnol, 36: 884-890.Musat N., Musat F., Weber PK., Pett-Ridge J., 2016. Tracking microbial interactions with NanoSIMS. Curr Opin Biotechnol, 41: 114-121.

Modulating conversion of isoflavone glycosides to aglycones using crude beta-glycosidase extracts from almonds and processed soy.

PubMed

Ahn-Jarvis, J H; Teegarden, M D; Schwartz, S J; Lee, K; Vodovotz, Y

2017-12-15

Food processing alters the physicochemical state of soy which can enhance chemical and enzymatic conversion of isoflavones to their aglycone forms. This study investigated the role of β-glycosidase from processed soy-ingredient mixture (SIM) or almonds, and examined the impact of isoflavone composition in mediating conversion to aglycones. β-Glycosidase activity was quantified using p-nitrophenol-β-d-glucopyranoside and SIM isoflavone extracts. Almond β-glycosidase activity was significantly (p<0.001) reduced after roasting (99% reduction) or steaming (97% reduction) compared to raw almonds. SIM β-glycosidase activity, however, increased, with steaming by 66% (p<0.001) and with roasting by 52% (p=0.022), compared to raw SIM. After incubation with β-glycosidase, percentage of aglycone (total aglycone/total isoflavones) in SIM isoflavone extracts increased significantly in raw (35%), fermented (48%), roasted (88%) and steamed (91%) SIM, compared to their initial (∼5%) compositions. Manipulation of β-glycosidase activity and isoflavone composition can be used to modulate aglycone content in soy food products. Copyright © 2017 Elsevier Ltd. All rights reserved.

ChromBiSim: Interactive chromatin biclustering using a simple approach.

PubMed

Noureen, Nighat; Zohaib, Hafiz Muhammad; Qadir, Muhammad Abdul; Fazal, Sahar

2017-10-01

Combinatorial patterns of histone modifications sketch the epigenomic locale. Specific positions of these modifications in the genome are marked by the presence of such signals. Various methods highlight such patterns on global scale hence missing the local patterns which are the actual hidden combinatorics. We present ChromBiSim, an interactive tool for mining subsets of modifications from epigenomic profiles. ChromBiSim efficiently extracts biclusters with their genomic locations. It is the very first user interface based and multiple cell type handling tool for decoding the interplay of subsets of histone modifications combinations along their genomic locations. It displays the results in the forms of charts and heat maps in accordance with saving them in files which could be used for post analysis. ChromBiSim tested on multiple cell types produced in total 803 combinatorial patterns. It could be used to highlight variations among diseased versus normal cell types of any species. ChromBiSim is available at (http://sourceforge.net/projects/chrombisim) in C-sharp and python languages. Copyright © 2017 Elsevier Inc. All rights reserved.

Sims for Science: Powerful Tools to Support Inquiry-Based Teaching

ERIC Educational Resources Information Center

Perkins, Katherine K.; Loeblein, Patricia J.; Dessau, Kathryn L.

2010-01-01

Since 2002, the PhET Interactive Simulations project at the University of Colorado has been working to provide learning tools for students and teachers. The project has developed over 85 interactive simulations--or sims--for teaching and learning science. Although these sims can be used in a variety of ways, they are specifically designed to make…

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.

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.

Weakly Coretractable Modules

NASA Astrophysics Data System (ADS)

Hadi, Inaam M. A.; Al-aeashi, Shukur N.

2018-05-01

If R is a ring with identity and M is a unitary right R-module. Here we introduce the class of weakly coretractable module. Some basic properties are investigated and some relationships between these modules and other related one are introduced.

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

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.

EngineSim: Turbojet Engine Simulator Adapted for High School Classroom Use

NASA Technical Reports Server (NTRS)

Petersen, Ruth A.

2001-01-01

EngineSim is an interactive educational computer program that allows users to explore the effect of engine operation on total aircraft performance. The software is supported by a basic propulsion web site called the Beginner's Guide to Propulsion, which includes educator-created, web-based activities for the classroom use of EngineSim. In addition, educators can schedule videoconferencing workshops in which EngineSim's creator demonstrates the software and discusses its use in the educational setting. This software is a product of NASA Glenn Research Center's Learning Technologies Project, an educational outreach initiative within the High Performance Computing and Communications Program.

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 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.

Thermal Expansion of the Cryoprotectant Cocktail DP6 Combined with Synthetic Ice Modulators in Presence and Absence of Biological Tissues

PubMed Central

Eisenberg, David P.; Taylor, Michael J.; Rabin, Yoed

2012-01-01

This study explores physical effects associated with the application of cryopreservation via vitrification using a class of compounds which are defined here as synthetic ice modulators (SIMs). The general classification of SIMs includes molecules that modulate ice nucleation and growth, or possess properties of stabilizing the amorphous state, by virtue of their chemical structure and at concentrations that are not explained on a purely colligative basis. A subcategory of SIMs, referred to in the literature as synthetic ice blockers (SIBs), are compounds that interact directly with ice nuclei or crystals to modify their structure and/or rate of growth. The current study is part of an ongoing effort to characterize thermo-mechanical effects during vitrification, with emphasis on measuring the physical property of thermal expansion—the driving mechanism to thermo-mechanical stress. Materials under investigation are the cryoprotective agent (CPA) cocktail DP6 in combination with one of the following SIMs: 12% polyethylene glycol 400, 6% 1,3 cyclohexanediol, and 6% 2,3 butanediol. Results are presented for the CPA-SIM cocktail in the absence and presence of bovine muscle and goat artery specimens. This study focuses on the upper part of the cryogenic temperature range, where the CPA behaves as a fluid for all practical applications. Results of this study indicate that the addition of SIMs to DP6 allows lower cooling rates to ensure vitrification and extends the range of measurements. It is demonstrated that the combination of SIM with DP6 increases the thermal expansion of the cocktail, with implications for the likelihood of fracture formation—the most dramatic outcome of thermo-mechanical stress. PMID:22579521

NanoSIMS analysis of Bacillus spores for forensics

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

Weber, P K; Davisson, M L; Velsko, S P

2010-02-23

The threat associated with the potential use of radiological, nuclear, chemical and biological materials in terrorist acts has resulted in new fields of forensic science requiring the application of state-of-the-science analytical techniques. Since the anthrax letter attacks in the United States in the fall of 2001, there has been increased interest in physical and chemical characterization of bacterial spores. While molecular methods are powerful tools for identifying genetic differences, other methods may be able to differentiate genetically identical samples based on physical and chemical properties, as well as provide complimentary information, such as methods of production and approximate date ofmore » production. Microanalysis has the potential to contribute significantly to microbial forensics. Bacillus spores are highly structured, consisting of a core, cortex, coat, and in some species, an exosporium. This structure provides a template for constraining elemental abundance differences at the nanometer scale. The primary controls on the distribution of major elements in spores are likely structural and physiological. For example, P and Ca are known to be abundant in the spore core because that is where P-rich nucleic acids and Cadipicolinic acid are located, respectively. Trace elements are known to bind to the spore coat but the controls on these elements are less well understood. Elemental distributions and abundances may be directly related to spore production, purification and stabilization methodologies, which are of particular interest for forensic investigation. To this end, we are developing a high-resolution secondary ion mass spectrometry method using a Cameca NanoSIMS 50 to study the distribution and abundance of trace elements in bacterial spores. In this presentation we will review and compare methods for preparing and analyzing samples, as well as review results on the distribution and abundance of elements in bacterial spores. We use NanoSIMS

Preparing strategic information management plans for hospitals: a practical guideline SIM plans for hospitals: a guideline.

PubMed

Brigl, B; Ammenwerth, E; Dujat, C; Gräber, S; Grosse, A; Häber, A; Jostes, C; Winter, A

2005-01-01

Systematic information management in hospitals demands for a strategic information management plan (SIM plan). As preparing a SIM plan is a considerable challenge we provide a practical guideline that is directly applicable when a SIM plan is going to be prepared. The guideline recommends a detailed structure of a SIM plan and gives advice about its content and the preparation process. It may be used as template, which can be adapted to the individual demands of any hospital. The guideline was used in several hospitals preparing a SIM plan. Experiences showed that the SIM plans could be prepared very efficiently and timely using the guideline, that the proposed SIM plan structure suited well, that the guideline offers enough flexibility to meet the requirements of the individual hospitals and that the specific recommendations of the guideline were very helpful. Nevertheless, we must strive for a more comprehensive theory of strategic information management planning which -- in the sense of enterprise architecture planning -- represents the intrinsic correlations of the different parts of a SIM plan to a greater extent.

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.

Time-of-flight SIMS/MSRI reflectron mass analyzer and method

DOEpatents

Smentkowski, Vincent S.; Gruen, Dieter M.; Krauss, Alan R.; Schultz, J. Albert; Holecek, John C.

1999-12-28

A method and apparatus for analyzing the surface characteristics of a sample by Secondary Ion Mass Spectroscopy (SIMS) and Mass Spectroscopy of Recoiled Ions (MSRI) is provided. The method includes detecting back scattered primary ions, low energy ejected species, and high energy ejected species by ion beam surface analysis techniques comprising positioning a ToF SIMS/MSRI mass analyzer at a predetermined angle .theta., where .theta. is the angle between the horizontal axis of the mass analyzer and the undeflected primary ion beam line, and applying a specific voltage to the back ring of the analyzer. Preferably, .theta. is less than or equal to about 120.degree. and, more preferably, equal to 74.degree.. For positive ion analysis, the extractor, lens, and front ring of the reflectron are set at negative high voltages (-HV). The back ring of the reflectron is set at greater than about +700V for MSRI measurements and between the range of about +15 V and about +50V for SIMS measurements. The method further comprises inverting the polarity of the potentials applied to the extractor, lens, front ring, and back ring to obtain negative ion SIMS and/or MSRI data.

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

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.

Verification of RRA and CMC in OpenSim

NASA Astrophysics Data System (ADS)

Ieshiro, Yuma; Itoh, Toshiaki

2013-10-01

OpenSim is the free software that can handle various analysis and simulation of skeletal muscle dynamics with PC. This study treated RRA and CMC tools in OpenSim. It is remarkable that we can simulate human motion with respect to nerve signal of muscles using these tools. However, these tools seem to still in developmental stages. In order to verify applicability of these tools, we analyze bending and stretching motion data which are obtained from motion capture device using these tools. In this study, we checked the consistency between real muscle behavior and numerical results from these tools.

Did J. Marion Sims deliberately addict his first fistula patients to opium?

PubMed

Wall, L Lewis

2007-07-01

American surgeon J. Marion Sims (1813-83) is regarded by many modern authors as a controversial figure because he carried out a series of experimental surgeries on enslaved African American women between 1846 and 1849 in an attempt to cure them of vesicovaginal fistulas, which they had all developed as a result of prolonged obstructed labor. He operated on one woman, Anarcha Westcott, thirty times before he successfully closed her fistula. Sims performed these fistula repair operations without benefit of anesthesia but gave these women substantial doses of opium afterwards. Several modern writers have alleged that Sims did this in order to addict them to the drug and thereby to enhance his control over them. This article examines the controversy surrounding Sims' use of postoperative opium in these enslaved surgical patients. The evidence suggests that although these women were probably tolerant to the doses of opium that he used, there is no evidence that he deliberately tried to addict them to this drug. Sims' use of postoperative opium appears to have been well supported by the therapeutic practices of his day, and the regimen that he used was enthusiastically supported by many contemporary surgeons.

SimAlba: A Spatial Microsimulation Approach to the Analysis of Health Inequalities

PubMed Central

Campbell, Malcolm; Ballas, Dimitris

2016-01-01

This paper presents applied geographical research based on a spatial microsimulation model, SimAlba, aimed at estimating geographically sensitive health variables in Scotland. SimAlba has been developed in order to answer a variety of “what-if” policy questions pertaining to health policy in Scotland. Using the SimAlba model, it is possible to simulate the distributions of previously unknown variables at the small area level such as smoking, alcohol consumption, mental well-being, and obesity. The SimAlba microdataset has been created by combining Scottish Health Survey and Census data using a deterministic reweighting spatial microsimulation algorithm developed for this purpose. The paper presents SimAlba outputs for Scotland’s largest city, Glasgow, and examines the spatial distribution of the simulated variables for small geographical areas in Glasgow as well as the effects on individuals of different policy scenario outcomes. In simulating previously unknown spatial data, a wealth of new perspectives can be examined and explored. This paper explores a small set of those potential avenues of research and shows the power of spatial microsimulation modeling in an urban context. PMID:27818989

A study of dynamic SIMS analysis of low-k dielectric materials

NASA Astrophysics Data System (ADS)

Mowat, Ian A.; Lin, Xue-Feng; Fister, Thomas; Kendall, Marius; Chao, Gordon; Yang, Ming Hong

2006-07-01

Dynamic SIMS is an established tool for the characterization of dielectric layers in semiconductors, both for contaminant levels and for composition. As the silicon-based semiconductor industry moves towards the use of copper rather than aluminum, there is also a need to use lower k-dielectric materials to reduce RC delays and to reduce cross-talk between closely spaced metal lines. New dielectric materials pose serious challenges for implementation into semiconductor processes and also for the analytical scientist doing measurements on them. The move from inorganic materials such as SiO 2 to organic or carbon-rich low-k materials is a large change for the SIMS analyst. Low-k dielectric films from different sources can be very different materials with different analytical issues. A SIMS challenge for these materials is dealing with their insulating nature and their also fragility, particularly for porous films. These materials can be extremely sensitive to electron beam damage during charge neutralization, leading to difficulties in determining depth scales and introducing unknown errors to secondary ion counts and their subsequent conversion to concentrations. This paper presents details regarding an investigation of the effects of electron beam exposure on a low-k material. These effects and their potential impact on SIMS data will be investigated using FT-IR, TOF-SIMS, AFM and stylus profilometry.

Evaluation of simSchool: An Instructional Simulation for Pre-Service Teachers

ERIC Educational Resources Information Center

Deale, Deb; Pastore, Ray

2014-01-01

This study uses theory-based design principles to evaluate the effectiveness of an instructional simulation, simSchool. It begins by examining the simulation and evaluation literature, followed by an evaluation of the simSchool software. It is a Web-based simulation designed to emulate various students (reactions) in order to provide practice for…

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…

SimVascular: An Open Source Pipeline for Cardiovascular Simulation.

PubMed

Updegrove, Adam; Wilson, Nathan M; Merkow, Jameson; Lan, Hongzhi; Marsden, Alison L; Shadden, Shawn C

2017-03-01

Patient-specific cardiovascular simulation has become a paradigm in cardiovascular research and is emerging as a powerful tool in basic, translational and clinical research. In this paper we discuss the recent development of a fully open-source SimVascular software package, which provides a complete pipeline from medical image data segmentation to patient-specific blood flow simulation and analysis. This package serves as a research tool for cardiovascular modeling and simulation, and has contributed to numerous advances in personalized medicine, surgical planning and medical device design. The SimVascular software has recently been refactored and expanded to enhance functionality, usability, efficiency and accuracy of image-based patient-specific modeling tools. Moreover, SimVascular previously required several licensed components that hindered new user adoption and code management and our recent developments have replaced these commercial components to create a fully open source pipeline. These developments foster advances in cardiovascular modeling research, increased collaboration, standardization of methods, and a growing developer community.

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.;

Students' Expression of Affect in an Inner-City SimCalc Classroom

ERIC Educational Resources Information Center

Schorr, Roberta Y.; Goldin, Gerald A.

2008-01-01

This research focuses on some of the affordances provided by SimCalc software, suggesting that its use can have important consequences for students' mathematical affect and motivation. We describe an episode in an inner-city SimCalc environment illustrating our approach to the study of affect in the mathematics classroom. We infer students'…

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...

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.

Quantitative SIMS Imaging of Agar-Based Microbial Communities.

PubMed

Dunham, Sage J B; Ellis, Joseph F; Baig, Nameera F; Morales-Soto, Nydia; Cao, Tianyuan; Shrout, Joshua D; Bohn, Paul W; Sweedler, Jonathan V

2018-05-01

After several decades of widespread use for mapping elemental ions and small molecular fragments in surface science, secondary ion mass spectrometry (SIMS) has emerged as a powerful analytical tool for molecular imaging in biology. Biomolecular SIMS imaging has primarily been used as a qualitative technique; although the distribution of a single analyte can be accurately determined, it is difficult to map the absolute quantity of a compound or even to compare the relative abundance of one molecular species to that of another. We describe a method for quantitative SIMS imaging of small molecules in agar-based microbial communities. The microbes are cultivated on a thin film of agar, dried under nitrogen, and imaged directly with SIMS. By use of optical microscopy, we show that the area of the agar is reduced by 26 ± 2% (standard deviation) during dehydration, but the overall biofilm morphology and analyte distribution are largely retained. We detail a quantitative imaging methodology, in which the ion intensity of each analyte is (1) normalized to an external quadratic regression curve, (2) corrected for isomeric interference, and (3) filtered for sample-specific noise and lower and upper limits of quantitation. The end result is a two-dimensional surface density image for each analyte. The sample preparation and quantitation methods are validated by quantitatively imaging four alkyl-quinolone and alkyl-quinoline N-oxide signaling molecules (including Pseudomonas quinolone signal) in Pseudomonas aeruginosa colony biofilms. We show that the relative surface densities of the target biomolecules are substantially different from values inferred through direct intensity comparison and that the developed methodologies can be used to quantitatively compare as many ions as there are available standards.

Economic analysis of standard interface modules for use with the multi-mission spacecraft, volume 1

NASA Technical Reports Server (NTRS)

1976-01-01

A preliminary technical and economic feasibility study was made of the use of Standardized Interstate Modules (SIM) to perform electual interfacing functions that were historically incorporated into sensors. Sensor interface functions that are capable of standardization from the set of missions planned for the NASA Multi-Mission Spacecraft (MMS) in the 1981 to 1985 time period were identified. The cost savings that could be achieved through the replacement of nonstandard sensor interface flight hardware that might be used in these missions with SIM were examined.

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.

Analysis and imaging of biocidal agrochemicals using ToF-SIMS.

PubMed

Converso, Valerio; Fearn, Sarah; Ware, Ecaterina; McPhail, David S; Flemming, Anthony J; Bundy, Jacob G

2017-09-06

ToF-SIMS has been increasingly widely used in recent years to look at biological matrices, in particular for biomedical research, although there is still a lot of development needed to maximise the value of this technique in the life sciences. The main issue for biological matrices is the complexity of the mass spectra and therefore the difficulty to specifically and precisely detect analytes in the biological sample. Here we evaluated the use of ToF-SIMS in the agrochemical field, which remains a largely unexplored area for this technique. We profiled a large number of biocidal active ingredients (herbicides, fungicides, and insecticides); we then selected fludioxonil, a halogenated fungicide, as a model compound for more detailed study, including the effect of co-occurring biomolecules on detection limits. There was a wide range of sensitivity of the ToF-SIMS for the different active ingredient compounds, but fludioxonil was readily detected in real-world samples (wheat seeds coated with a commercial formulation). Fludioxonil did not penetrate the seed to any great depth, but was largely restricted to a layer coating the seed surface. ToF-SIMS has clear potential as a tool for not only detecting biocides in biological samples, but also mapping their distribution.

SimHap GUI: An intuitive graphical user interface for genetic association analysis

PubMed Central

Carter, Kim W; McCaskie, Pamela A; Palmer, Lyle J

2008-01-01

Background Researchers wishing to conduct genetic association analysis involving single nucleotide polymorphisms (SNPs) or haplotypes are often confronted with the lack of user-friendly graphical analysis tools, requiring sophisticated statistical and informatics expertise to perform relatively straightforward tasks. Tools, such as the SimHap package for the R statistics language, provide the necessary statistical operations to conduct sophisticated genetic analysis, but lacks a graphical user interface that allows anyone but a professional statistician to effectively utilise the tool. Results We have developed SimHap GUI, a cross-platform integrated graphical analysis tool for conducting epidemiological, single SNP and haplotype-based association analysis. SimHap GUI features a novel workflow interface that guides the user through each logical step of the analysis process, making it accessible to both novice and advanced users. This tool provides a seamless interface to the SimHap R package, while providing enhanced functionality such as sophisticated data checking, automated data conversion, and real-time estimations of haplotype simulation progress. Conclusion SimHap GUI provides a novel, easy-to-use, cross-platform solution for conducting a range of genetic and non-genetic association analyses. This provides a free alternative to commercial statistics packages that is specifically designed for genetic association analysis. PMID:19109877

SimHap GUI: an intuitive graphical user interface for genetic association analysis.

PubMed

Carter, Kim W; McCaskie, Pamela A; Palmer, Lyle J

2008-12-25

Researchers wishing to conduct genetic association analysis involving single nucleotide polymorphisms (SNPs) or haplotypes are often confronted with the lack of user-friendly graphical analysis tools, requiring sophisticated statistical and informatics expertise to perform relatively straightforward tasks. Tools, such as the SimHap package for the R statistics language, provide the necessary statistical operations to conduct sophisticated genetic analysis, but lacks a graphical user interface that allows anyone but a professional statistician to effectively utilise the tool. We have developed SimHap GUI, a cross-platform integrated graphical analysis tool for conducting epidemiological, single SNP and haplotype-based association analysis. SimHap GUI features a novel workflow interface that guides the user through each logical step of the analysis process, making it accessible to both novice and advanced users. This tool provides a seamless interface to the SimHap R package, while providing enhanced functionality such as sophisticated data checking, automated data conversion, and real-time estimations of haplotype simulation progress. SimHap GUI provides a novel, easy-to-use, cross-platform solution for conducting a range of genetic and non-genetic association analyses. This provides a free alternative to commercial statistics packages that is specifically designed for genetic association analysis.

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

Combined SIMS, NanoSIMS, FTIR, and SEM Studies of OH in Nominally Anhydrous Minerals (NAMs)

NASA Astrophysics Data System (ADS)

Mosenfelder, J. L.; Le Voyer, M.; Rossman, G. R.; Guan, Y.; Bell, D. R.; Asimow, P. D.; Eiler, J.

2010-12-01

The accurate analysis of trace concentrations of hydrogen in NAMs is a long-standing problem, with wide-ranging implications in geology and planetology. SIMS and FTIR are two powerful and complementary analytical tools capable of measuring concentrations down to levels of less than 1 ppm H2O. Both methods, however, are subject to matrix effects and rely on other techniques such as manometry or nuclear reaction analysis (NRA) for quantitative calibration. We compared FTIR and SIMS data for a wide variety of NAMs: olivine, orthopyroxene, clinopyroxene, pyrope and grossular garnet, rutile, zircon, kyanite, andalusite, and sillimanite. Some samples were also characterized using high-resolution FE-SEM to assess the potential contribution of submicrocopic inclusions to the analyses. For SIMS, we use high mass resolution (≥5000 MRP) to measure 16O1H, using 30Si and/or 18O as reference isotopes. We use both primary standards, measured independently using manometry or NRA (e.g., [1]), and secondary standards, measured using polarized FTIR referenced back to calibrations developed on primary standards. Our major focus was on on olivine, for which we collected repeated calibration data with both SIMS and NanoSIMS, bracketing measurements of H diffusion profiles in both natural and experimentally annealed crystals at levels of 5-100 ppm H2O. With both instruments we establish low blanks (≤5 ppm) and high precision (typically less than 5% 2-σ errors in 16O1H/30Si), critical requirements for the low concentration levels being measured. Assessment of over 300 analyses on 11 olivines allows us to evaluate the suitability of different standards, several of which are in use in other laboratories [2,3,4]. Seven olivines, with 0-125 ppm H2O, give highly reproducible results and allow us to establish well-constrained calibration slopes with high correlation coefficients (r2 = 0.98-99), in contrast to previous studies [2,3,4]. However, four kimberlitic megacrysts with 140-243 ppm H

Essentially semismall Quasi-Dedekind module relative to a module

NASA Astrophysics Data System (ADS)

Hussain, Mukdad Q.

2018-05-01

Let R be associative ring with identity and M be a unitary R-module. In this paper study the direct summand of essentially semismall quasi-Dedekind module and prove that the direct sum of essentially semismall quasi-Dedekind modules need not be essentially semismall quasi-Dedekind and give the definition of essentially semismall quasi-Dedekind relative to a module with some examples, also give some of their basic properties and some examples that illustrate these properties.

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

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.

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.

Homocysteine is the confounding factor of metabolic syndrome-confirmed by siMS score.

PubMed

Srećković, Branko; Soldatovic, Ivan; Colak, Emina; Mrdovic, Igor; Sumarac-Dumanovic, Mirjana; Janeski, Hristina; Janeski, Nenad; Gacic, Jasna; Dimitrijevic-Sreckovic, Vesna

2018-04-06

Abdominal adiposity has a central role in developing insulin resistance (IR) by releasing pro-inflammatory cytokines. Patients with metabolic syndrome (MS) have higher values of homocysteine. Hyperhomocysteinemia correlates with IR, increasing the oxidative stress. Oxidative stress causes endothelial dysfunction, hypertension and atherosclerosis. The objective of the study was to examine the correlation of homocysteine with siMS score and siMS risk score and with other MS co-founding factors. The study included 69 obese individuals (age over 30, body mass index [BMI] >25 kg/m2), classified into two groups: I-with MS (33 patients); II-without MS (36 patients). Measurements included: anthropometric parameters, lipids, glucose regulation parameters and inflammation parameters. IR was determined by homeostatic model assessment for insulin resistance (HOMA-IR). ATP III classification was applied for diagnosing MS. SiMS score was used as continuous measure of metabolic syndrome. A significant difference between groups was found for C-reactive protein (CRP) (p<0.01) apolipoprotein (Apo) B, HOMA-IR and acidum uricum (p<0.05). siMS risk score showed a positive correlation with homocysteine (p=0.023), while siMS score correlated positively with fibrinogen (p=0.013), CRP and acidum uricum (p=0.000) and homocysteine (p=0.08). Homocysteine correlated positively with ApoB (p=0.036), HbA1c (p=0.047), HOMA-IR (p=0.008) and negatively with ApoE (p=0.042). Correlation of siMS score with homocysteine, fibrinogen, CRP and acidum uricum indicates that they are co-founding factors of MS. siMS risk score correlation with homocysteine indicates that hyperhomocysteinemia increases with age. Hyperhomocysteinemia is linked with genetic factors and family nutritional scheme, increasing the risk for atherosclerosis.

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.

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.

Semi-structured Interview Measure of Stigma (SIMS) in psychosis: Assessment of psychometric properties.

PubMed

Wood, Lisa; Burke, Eilish; Byrne, Rory; Enache, Gabriela; Morrison, Anthony P

2016-10-01

Stigma is a significant difficulty for people who experience psychosis. To date, there have been no outcome measures developed to examine stigma exclusively in people with psychosis. The aim of this study was develop and validate a semi-structured interview measure of stigma (SIMS) in psychosis. The SIMS is an eleven item measure of stigma developed in consultation with service users who have experienced psychosis. 79 participants with experience of psychosis were recruited for the purposes of this study. They were administered the SIMS alongside a battery of other relevant outcome measures to examine reliability and validity. A one-factor solution was identified for the SIMS which encompassed all ten rateable items. The measure met all reliability and validity criteria and illustrated good internal consistency, inter-rater reliability, test retest reliability, criterion validity, construct validity, sensitivity to change and had no floor or ceiling effects. The SIMS is a reliable and valid measure of stigma in psychosis. It may be more engaging and acceptable than other stigma measures due to its semi-structured interview format. Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.

ViscoSim Earthquake Simulator

USGS Publications Warehouse

Pollitz, Fred

2012-01-01

Synthetic seismicity simulations have been explored by the Southern California Earthquake Center (SCEC) Earthquake Simulators Group in order to guide long‐term forecasting efforts related to the Unified California Earthquake Rupture Forecast (Tullis et al., 2012a). In this study I describe the viscoelastic earthquake simulator (ViscoSim) of Pollitz, 2009. Recapitulating to a large extent material previously presented by Pollitz (2009, 2011) I describe its implementation of synthetic ruptures and how it differs from other simulators being used by the group.

Beating the numbers through strategic intervention materials (SIMs): Innovative science teaching for large classes

NASA Astrophysics Data System (ADS)

Alboruto, Venus M.

2017-05-01

The study aimed to find out the effectiveness of using Strategic Intervention Materials (SIMs) as an innovative teaching practice in managing large Grade Eight Science classes to raise the performance of the students in terms of science process skills development and mastery of science concepts. Utilizing experimental research design with two groups of participants, which were purposefully chosen, it was obtained that there existed a significant difference in the performance of the experimental and control groups based on actual class observation and written tests on science process skills with a p-value of 0.0360 in favor of the experimental class. Further, results of written pre-test and post-test on science concepts showed that the experimental group with the mean of 24.325 (SD =3.82) performed better than the control group with the mean of 20.58 (SD =4.94), with a registered p-value of 0.00039. Therefore, the use of SIMs significantly contributed to the mastery of science concepts and the development of science process skills. Based on the findings, the following recommendations are offered: 1. that grade eight science teachers should use or adopt the SIMs used in this study to improve their students' performance; 2. training-workshop on developing SIMs must be conducted to help teachers develop SIMs to be used in their classes; 3. school administrators must allocate funds for the development and reproduction of SIMs to be used by the students in their school; and 4. every division should have a repository of SIMs for easy access of the teachers in the entire division.

SIM Interferometer Testbed (SCDU) Status and Recent Results

NASA Technical Reports Server (NTRS)

Nemati, Bijan; An, Xin; Goullioud, Renaud; Shao, Michael; Shen, Tsae-Pyng; Wehmeier, Udo J.; Weilert, Mark A.; Wang, Xu; Werne, Thomas A.; Wu, Janet P.;

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.

Chemical abrasion-SIMS (CA-SIMS) U-Pb dating of zircon from the late Eocene Caetano caldera, Nevada

USGS Publications Warehouse

Watts, Kathryn E.; Coble, Matthew A.; Vazquez, Jorge A.; Henry, Christopher D.; Colgan, Joseph P.; John, David A.

2016-01-01

Zircon geochronology is a critical tool for establishing geologic ages and time scales of processes in the Earth's crust. However, for zircons compromised by open system behavior, achieving robust dates can be difficult. Chemical abrasion (CA) is a routine step prior to thermal ionization mass spectrometry (TIMS) dating of zircon to remove radiation-damaged parts of grains that may have experienced open system behavior and loss of radiogenic Pb. While this technique has been shown to improve the accuracy and precision of TIMS dating, its application to high-spatial resolution dating methods, such as secondary ion mass spectrometry (SIMS), is relatively uncommon. In our efforts to U-Pb date zircons from the late Eocene Caetano caldera by SIMS (SHRIMP-RG: sensitive high resolution ion microprobe, reverse geometry), some grains yielded anomalously young U-Pb ages that implicated Pb-loss and motivated us to investigate with a comparative CA and non-CA dating study. We present CA and non-CA 206Pb/238U ages and trace elements determined by SHRIMP-RG for zircons from three Caetano samples (Caetano Tuff, Redrock Canyon porphyry, and a silicic ring-fracture intrusion) and for R33 and TEMORA-2 reference zircons. We find that non-CA Caetano zircons have weighted mean or bimodal U-Pb ages that are 2–4% younger than CA zircons for the same samples. CA Caetano zircons have mean U-Pb ages that are 0.4–0.6 Myr older than the 40Ar/39Ar sanidine eruption age (34.00 ± 0.03 Ma; error-weighted mean, 2σ), whereas non-CA zircons have ages that are 0.7–1.3 Myr younger. U-Pb ages do not correlate with U (~ 100–800 ppm), Th (~ 50–300 ppm) or any other measured zircon trace elements (Y, Hf, REE), and CA and non-CA Caetano zircons define identical trace element ranges. No statistically significant difference in U-Pb age is observed for CA versus non-CA R33 or TEMORA-2 zircons. Optical profiler measurements of ion microprobe pits demonstrate consistent depths of ~ 1.6�

VASP, zyxin and TES are tension-dependent members of Focal Adherens Junctions independent of the α-catenin-vinculin module.

PubMed

Oldenburg, Joppe; van der Krogt, Gerard; Twiss, Floor; Bongaarts, Annika; Habani, Yasmin; Slotman, Johan A; Houtsmuller, Adriaan; Huveneers, Stephan; de Rooij, Johan

2015-11-27

Mechanical forces are integrated at cadherin-based adhesion complexes to regulate morphology and strength of cell-cell junctions and organization of associated F-actin. A central mechanosensor at the cadherin complex is α-catenin, whose stretching recruits vinculin to regulate adhesion strength. The identity of the F-actin regulating signals that are also activated by mechanical forces at cadherin-based junctions has remained elusive. Here we identify the actin-regulators VASP, zyxin and TES as members of punctate, tensile cadherin-based junctions called Focal Adherens Junctions (FAJ) and show that they display mechanosensitive recruitment similar to that of vinculin. However, this recruitment is not altered by destroying or over-activating the α-catenin/vinculin module. Structured Illumination Microscopy (SIM) indicates that these tension sensitive proteins concentrate at locations within FAJs that are distinct from the core cadherin complex proteins. Furthermore, localization studies using mutated versions of VASP and zyxin indicate that these two proteins require binding to each other in order to localize to the FAJs. We conclude that there are multiple force sensitive modules present at the FAJ that are activated at distinct locations along the cadherin-F-actin axis and regulate specific aspects of junction dynamics.

Construction of multi-functional open modulized Matlab simulation toolbox for imaging ladar system

NASA Astrophysics Data System (ADS)

Wu, Long; Zhao, Yuan; Tang, Meng; He, Jiang; Zhang, Yong

2011-06-01

Ladar system simulation is to simulate the ladar models using computer simulation technology in order to predict the performance of the ladar system. This paper presents the developments of laser imaging radar simulation for domestic and overseas studies and the studies of computer simulation on ladar system with different application requests. The LadarSim and FOI-LadarSIM simulation facilities of Utah State University and Swedish Defence Research Agency are introduced in details. This paper presents the low level of simulation scale, un-unified design and applications of domestic researches in imaging ladar system simulation, which are mostly to achieve simple function simulation based on ranging equations for ladar systems. Design of laser imaging radar simulation with open and modularized structure is proposed to design unified modules for ladar system, laser emitter, atmosphere models, target models, signal receiver, parameters setting and system controller. Unified Matlab toolbox and standard control modules have been built with regulated input and output of the functions, and the communication protocols between hardware modules. A simulation based on ICCD gain-modulated imaging ladar system for a space shuttle is made based on the toolbox. The simulation result shows that the models and parameter settings of the Matlab toolbox are able to simulate the actual detection process precisely. The unified control module and pre-defined parameter settings simplify the simulation of imaging ladar detection. Its open structures enable the toolbox to be modified for specialized requests. The modulization gives simulations flexibility.

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

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.

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.

CystiSim - An Agent-Based Model for Taenia solium Transmission and Control.

PubMed

Braae, Uffe Christian; Devleesschauwer, Brecht; Gabriël, Sarah; Dorny, Pierre; Speybroeck, Niko; Magnussen, Pascal; Torgerson, Paul; Johansen, Maria Vang

2016-12-01

Taenia solium taeniosis/cysticercosis was declared eradicable by the International Task Force for Disease Eradication in 1993, but remains a neglected zoonosis. To assist in the attempt to regionally eliminate this parasite, we developed cystiSim, an agent-based model for T. solium transmission and control. The model was developed in R and available as an R package (http://cran.r-project.org/package=cystiSim). cystiSim was adapted to an observed setting using field data from Tanzania, but adaptable to other settings if necessary. The model description adheres to the Overview, Design concepts, and Details (ODD) protocol and consists of two entities-pigs and humans. Pigs acquire cysticercosis through the environment or by direct contact with a tapeworm carrier's faeces. Humans acquire taeniosis from slaughtered pigs proportional to their infection intensity. The model allows for evaluation of three interventions measures or combinations hereof: treatment of humans, treatment of pigs, and pig vaccination, and allows for customary coverage and efficacy settings. cystiSim is the first agent-based transmission model for T. solium and suggests that control using a strategy consisting of an intervention only targeting the porcine host is possible, but that coverage and efficacy must be high if elimination is the ultimate goal. Good coverage of the intervention is important, but can be compensated for by including an additional intervention targeting the human host. cystiSim shows that the scenarios combining interventions in both hosts, mass drug administration to humans, and vaccination and treatment of pigs, have a high probability of success if coverage of 75% can be maintained over at least a four year period. In comparison with an existing mathematical model for T. solium transmission, cystiSim also includes parasite maturation, host immunity, and environmental contamination. Adding these biological parameters to the model resulted in new insights in the potential

ToF-SIMS observation for evaluating the interaction between amyloid β and lipid membranes.

PubMed

Aoyagi, Satoka; Shimanouchi, Toshinori; Kawashima, Tomoko; Iwai, Hideo

2015-04-01

The adsorption behaviour of amyloid beta (Aβ), thought to be a key peptide for understanding Alzheimer's disease, was investigated by means of time-of-flight secondary ion mass spectrometry (ToF-SIMS). Aβ aggregates depending on the lipid membrane condition though it has not been fully understood yet. In this study, Aβ samples on different lipid membranes, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), were observed with ToF-SIMS and the complex ToF-SIMS data of the Aβ samples was interpreted using data analysis techniques such as principal component analysis (PCA), gentle-SIMS (G-SIMS) and g-ogram. DOPC and DMPC are liquid crystal at room temperature, while DPPC is gel at room temperature. As primary ion beams, Bi3(+) and Ar cluster ion beams were used and the effect of an Ar cluster ion for evaluating biomolecules was also studied. The secondary ion images of the peptide fragment ions indicated by G-SIMS and g-ogram were consistent with the PCA results. It is suggested that Aβ is adsorbed homogeneously on the liquid-crystalline-phase lipid membranes, while it aggregates along the lipid on the gel-phase lipid membrane. Moreover, in the results using the Ar cluster, the influence of contamination was reduced.

Retention of data in heat-damaged SIM cards and potential recovery methods.

PubMed

Jones, B J; Kenyon, A J

2008-05-02

Examination of various SIM cards and smart card devices indicates that data may be retained in SIM card memory structures even after heating to temperatures up to 450 degrees C, which the National Institute of Standards and Technology (NIST) has determined to be approximately the maximum average sustained temperature at desk height in a house fire. However, in many cases, and certainly for temperatures greater than 450 degrees C, the SIM card chip has suffered structural or mechanical damage that renders simple probing or rewiring ineffective. Nevertheless, this has not necessarily affected the data, which is stored as charge in floating gates, and alternative methods for directly accessing the stored charge may be applicable.

Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis

DOE PAGES

Woebken, Dagmar; Burow, Luke C.; Prufert-Bebout, Leslie; ...

2012-01-12

N 2 fixation is a key process in photosynthetic microbial mats to support the nitrogen demands associated with primary production. Despite its importance, groups that actively fix N 2 and contribute to the input of organic N in these ecosystems still remain largely unclear. To investigate the active diazotrophic community in microbial mats from the Elkhorn Slough estuary, Monterey Bay, CA, USA, we conducted an extensive combined approach, including biogeochemical, molecular and high-resolution secondary ion mass spectrometry (NanoSIMS) analyses. Detailed analysis of dinitrogenase reductase (nifH) transcript clone libraries from mat samples that fixed N 2 at night indicated that cyanobacterialmore » nifH transcripts were abundant and formed a novel monophyletic lineage. Independent NanoSIMS analysis of 15N2-incubated samples revealed significant incorporation of 15N into small, non-heterocystous cyanobacterial filaments. Mat-derived enrichment cultures yielded a unicyanobacterial culture with similar filaments (named Elkhorn Slough Filamentous Cyanobacterium-1 (ESFC-1)) that contained nifH gene sequences grouping with the novel cyanobacterial lineage identified in the transcript clone libraries, displaying up to 100% amino-acid sequence identity. The 16S rRNA gene sequence recovered from this enrichment allowed for the identification of related sequences from Elkhorn Slough mats and revealed great sequence diversity in this cluster. Furthermore, by combining 15N 2 tracer experiments, fluorescence in situ hybridization and NanoSIMS, in situ N 2 fixation activity by the novel ESFC-1 group was demonstrated, suggesting that this group may be the most active cyanobacterial diazotroph in the Elkhorn Slough mat. Pyrotag sequences affiliated with ESFC-1 were recovered from mat samples throughout 2009, demonstrating the prevalence of this group. Here, this work illustrates that combining standard and single-cell analyses can link phylogeny and function to identify

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.

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.

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.

skeleSim: an extensible, general framework for population genetic simulation in R

PubMed Central

Parobek, Christian M.; Archer, Frederick I.; DePrenger-Levin, Michelle E.; Hoban, Sean M.; Liggins, Libby; Strand, Allan E.

2016-01-01

Simulations are a key tool in molecular ecology for inference and forecasting, as well as for evaluating new methods. Due to growing computational power and a diversity of software with different capabilities, simulations are becoming increasingly powerful and useful. However, the widespread use of simulations by geneticists and ecologists is hindered by difficulties in understanding these softwares’ complex capabilities, composing code and input files, a daunting bioinformatics barrier, and a steep conceptual learning curve. skeleSim (an R package) guides users in choosing appropriate simulations, setting parameters, calculating genetic summary statistics, and organizing data output, in a reproducible pipeline within the R environment. skeleSim is designed to be an extensible framework that can ‘wrap’ around any simulation software (inside or outside the R environment) and be extended to calculate and graph any genetic summary statistics. Currently, skeleSim implements coalescent and forward-time models available in the fastsimcoal2 and rmetasim simulation engines to produce null distributions for multiple population genetic statistics and marker types, under a variety of demographic conditions. skeleSim is intended to make simulations easier while still allowing full model complexity to ensure that simulations play a fundamental role in molecular ecology investigations. skeleSim can also serve as a teaching tool: demonstrating the outcomes of stochastic population genetic processes; teaching general concepts of simulations; and providing an introduction to the R environment with a user-friendly graphical user interface (using shiny). PMID:27736016

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

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.

Design data brochure: SIMS prototype system 2

NASA Technical Reports Server (NTRS)

1977-01-01

Information is provided on the design and performance of the IBM SIMS Prototype System 2, solar domestic hot water system, for single family residences. The document provides sufficient data to permit procurement, installation, operation, and maintenance by qualified architectural engineers or contractors.

Comparative assessment of bone pose estimation using Point Cluster Technique and OpenSim.

PubMed

Lathrop, Rebecca L; Chaudhari, Ajit M W; Siston, Robert A

2011-11-01

Estimating the position of the bones from optical motion capture data is a challenge associated with human movement analysis. Bone pose estimation techniques such as the Point Cluster Technique (PCT) and simulations of movement through software packages such as OpenSim are used to minimize soft tissue artifact and estimate skeletal position; however, using different methods for analysis may produce differing kinematic results which could lead to differences in clinical interpretation such as a misclassification of normal or pathological gait. This study evaluated the differences present in knee joint kinematics as a result of calculating joint angles using various techniques. We calculated knee joint kinematics from experimental gait data using the standard PCT, the least squares approach in OpenSim applied to experimental marker data, and the least squares approach in OpenSim applied to the results of the PCT algorithm. Maximum and resultant RMS differences in knee angles were calculated between all techniques. We observed differences in flexion/extension, varus/valgus, and internal/external rotation angles between all approaches. The largest differences were between the PCT results and all results calculated using OpenSim. The RMS differences averaged nearly 5° for flexion/extension angles with maximum differences exceeding 15°. Average RMS differences were relatively small (< 1.08°) between results calculated within OpenSim, suggesting that the choice of marker weighting is not critical to the results of the least squares inverse kinematics calculations. The largest difference between techniques appeared to be a constant offset between the PCT and all OpenSim results, which may be due to differences in the definition of anatomical reference frames, scaling of musculoskeletal models, and/or placement of virtual markers within OpenSim. Different methods for data analysis can produce largely different kinematic results, which could lead to the misclassification

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.

TOFSIMS-P: a web-based platform for analysis of large-scale TOF-SIMS data.

PubMed

Yun, So Jeong; Park, Ji-Won; Choi, Il Ju; Kang, Byeongsoo; Kim, Hark Kyun; Moon, Dae Won; Lee, Tae Geol; Hwang, Daehee

2011-12-15

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) has been a useful tool to profile secondary ions from the near surface region of specimens with its high molecular specificity and submicrometer spatial resolution. However, the TOF-SIMS analysis of even a moderately large size of samples has been hampered due to the lack of tools for automatically analyzing the huge amount of TOF-SIMS data. Here, we present a computational platform to automatically identify and align peaks, find discriminatory ions, build a classifier, and construct networks describing differential metabolic pathways. To demonstrate the utility of the platform, we analyzed 43 data sets generated from seven gastric cancer and eight normal tissues using TOF-SIMS. A total of 87 138 ions were detected from the 43 data sets by TOF-SIMS. We selected and then aligned 1286 ions. Among them, we found the 66 ions discriminating gastric cancer tissues from normal ones. Using these 66 ions, we then built a partial least square-discriminant analysis (PLS-DA) model resulting in a misclassification error rate of 0.024. Finally, network analysis of the 66 ions showed disregulation of amino acid metabolism in the gastric cancer tissues. The results show that the proposed framework was effective in analyzing TOF-SIMS data from a moderately large size of samples, resulting in discrimination of gastric cancer tissues from normal tissues and identification of biomarker candidates associated with the amino acid metabolism.

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.

Deployment and early results from the CanSIM (Canadian Solar Spectral Irradiance Meter) network

NASA Astrophysics Data System (ADS)

Tatsiankou, Viktar; Hinzer, Karin; Schriemer, Henry; McVey-White, Patrick; Beal, Richard

2017-09-01

Three of seven stations have been deployed as part of the Canadian Solar Spectral Irradiance (CanSIM) network situated in Ottawa, Varennes and Egbert to measure long term spectral variation of the direct normal (DNI) and global horizontal irradiances (GHI) across the country. Every station is equipped with a solar tracker, SolarSIM-D2+, SolarSIM-G+, and SR20 pyranometer, reporting the spectral DNI, GHI, diffuse horizontal irradiance (DHI) and aerosol optical depth in the 280-4000 nm range, broadband DNI, GHI, and DHI, atmospheric total column ozone and water vapour amounts. The spectral GHI as measured by the SolarSIM-G+ was within 5% as compared to EKO MS-700 spectroradiometer in 350-1050 nm range on 17 March 2017. The difference in the GHI as reported by SolarSIM-G+ and SR20 pyranometer from all stations was within 2% on 14 April 2017. Furthermore, on this day, the daily GHI sum for the Ottawa, Varennes, and Egbert stations was 7.01, 6.95, and 7.11 kWh/m2, respectively, while the daily DNI sum was 10.65, 10.86, 10.04 kWh/m2, respectively.

Simulation of multi-photon emission isotopes using time-resolved SimSET multiple photon history generator

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

Chiang, Chih-Chieh; Lin, Hsin-Hon; Lin, Chang-Shiun

Abstract-Multiple-photon emitters, such as In-111 or Se-75, have enormous potential in the field of nuclear medicine imaging. For example, Se-75 can be used to investigate the bile acid malabsorption and measure the bile acid pool loss. The simulation system for emission tomography (SimSET) is a well-known Monte Carlo simulation (MCS) code in nuclear medicine for its high computational efficiency. However, current SimSET cannot simulate these isotopes due to the lack of modeling of complex decay scheme and the time-dependent decay process. To extend the versatility of SimSET for simulation of those multi-photon emission isotopes, a time-resolved multiple photon history generatormore » based on SimSET codes is developed in present study. For developing the time-resolved SimSET (trSimSET) with radionuclide decay process, the new MCS model introduce new features, including decay time information and photon time-of-flight information, into this new code. The half-life of energy states were tabulated from the Evaluated Nuclear Structure Data File (ENSDF) database. The MCS results indicate that the overall percent difference is less than 8.5% for all simulation trials as compared to GATE. To sum up, we demonstrated that time-resolved SimSET multiple photon history generator can have comparable accuracy with GATE and keeping better computational efficiency. The new MCS code is very useful to study the multi-photon imaging of novel isotopes that needs the simulation of lifetime and the time-of-fight measurements. (authors)« less

SIM Planetquest Science and Technology: A Status Report

NASA Technical Reports Server (NTRS)

Edberg, Stephen J.; Laskin, Robert A.; Marr, James C., IV; Unwin, Stephen C.; Shao, Michael

2007-01-01

Optical interferometry will open new vistas for astronomy over the next decade. The Space Interferometry Mission (SIM-PlanetQuest), operating unfettered by the Earth's atmosphere, will offer unprecedented astrometric precision that promises the discovery of Earth-analog extra-solar planets as well as a wealth of important astrophysics. Results from SIM will permit the determination of stellar masses to accuracies of 2% or better for objects ranging from brown dwarfs through main sequence stars to evolved white dwarfs, neutron stars, and black holes. Studies of star clusters will yield age determinations and internal dynamics. Microlensing measurements will present the mass spectrum of the Milky Way internal to the Sun while proper motion surveys will show the Sun's orbital radius and speed. Studies of the Galaxy's halo component and companion dwarf galaxies permit the determination of the Milky Way's mass distribution, including its Dark Matter component and the mass distribution and Dark Matter component of the Local Group. Cosmology benefits from precision (1-2%) determination of distances to Cepheid and RR Lyrae standard candles. The emission mechanism of supermassive black holes will be investigated. Finally, radio and optical celestial reference frames will be tied together by an improvement of two orders of magnitude. Optical interferometers present severe technological challenges. The Jet Propulsion Laboratory, with the support of Lockheed Martin Advanced Technology Center (LM ATC) and Northrop Grumman Space Technology (NGST), has addressed these challenges with a technology development program that is now complete. The requirements for SIM have been satisfied, based on outside peer review, using a series of laboratory tests and appropriate computer simulations: laser metrology systems perform with 10 picometer precision; mechanical vibrations have been controlled to nanometers, demonstrating orders of magnitude disturbance rejection; and knowledge of

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.

Analysis of TOF-SIMS spectra from fullerene compounds

NASA Astrophysics Data System (ADS)

Kato, N.; Yamashita, Y.; Iida, S.; Sanada, N.; Kudo, M.

2008-12-01

We analyzed TOF-SIMS spectra obtained from three different size of fullerenes (C 60, C 70 and C 84) by using Ga +, Au + and Au 3+ primary ion beams and investigated the fragmentation patterns, the enhancement of secondary ion yields and the restraint of fragmentation by using cluster primary ion beams compared with monoatomic primary ion beams. In the TOS-SIMS spectra from C 70 and C 84, it was found that a fragment ion, identified as C 60+ ( m/ z = 720), showed a relatively high intensity compared with that of other fragment ions related to C 2 depletion. It was also found that the Au 3+ bombardment caused intensity enhancement of intact molecules (C 60+, C 70+ and C 84+) and restrained the fragmentation due to C 2 depletion.

AmapSim: a structural whole-plant simulator based on botanical knowledge and designed to host external functional models.

PubMed

Barczi, Jean-François; Rey, Hervé; Caraglio, Yves; de Reffye, Philippe; Barthélémy, Daniel; Dong, Qiao Xue; Fourcaud, Thierry

2008-05-01

AmapSim is a tool that implements a structural plant growth model based on a botanical theory and simulates plant morphogenesis to produce accurate, complex and detailed plant architectures. This software is the result of more than a decade of research and development devoted to plant architecture. New advances in the software development have yielded plug-in external functions that open up the simulator to functional processes. The simulation of plant topology is based on the growth of a set of virtual buds whose activity is modelled using stochastic processes. The geometry of the resulting axes is modelled by simple descriptive functions. The potential growth of each bud is represented by means of a numerical value called physiological age, which controls the value for each parameter in the model. The set of possible values for physiological ages is called the reference axis. In order to mimic morphological and architectural metamorphosis, the value allocated for the physiological age of buds evolves along this reference axis according to an oriented finite state automaton whose occupation and transition law follows a semi-Markovian function. Simulations were performed on tomato plants to demonstrate how the AmapSim simulator can interface external modules, e.g. a GREENLAB growth model and a radiosity model. The algorithmic ability provided by AmapSim, e.g. the reference axis, enables unified control to be exercised over plant development parameter values, depending on the biological process target: how to affect the local pertinent process, i.e. the pertinent parameter(s), while keeping the rest unchanged. This opening up to external functions also offers a broadened field of applications and thus allows feedback between plant growth and the physical environment.

Teaching and Learning with SimCity 2000.

ERIC Educational Resources Information Center

Adams, Paul C.

1998-01-01

Introduces "SimCity 2000," a computer simulation, as a tool for teaching urban geography. Argues that, combined with other activities, it can enhance computer literacy, geographical knowledge, and critical skills. Notes gender differences in students' previous exposure to the software; argues that instructors must consider this when…

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...

Thermal Expansion of Vitrified Blood Vessels Permeated with DP6 and Synthetic Ice Modulators

PubMed Central

Eisenberg, David P.; Taylor, Michael J.; Jimenez-Rios, Jorge L.; Rabin, Yoed

2014-01-01

This study provides thermal expansion data for blood vessels permeated with the cryoprotective cocktail DP6, when combined with selected synthetic ice modulators (SIMs): 12% polyethylene glycol 400, 6% 1,3-cyclohexanediol, and 6% 2,3-butanediol. The general classification of SIMs includes molecules that modulate ice nucleation and growth, or possess properties of stabilizing the amorphous state, by virtue of their chemical structure and at concentrations that are not explained on a purely colligative basis. The current study is part of an ongoing effort to characterize thermo-mechanical effects on structural integrity of cryopreserved materials, where thermal expansion is the driving mechanism to thermo-mechanical stress. This study focuses on the lower part of the cryogenic temperature range, where the cryoprotective agent (CPA) behaves as a solid for all practical applications. By combining results obtained in the current study with literature data on the thermal expansion in the upper part of the cryogenic temperature range, unified thermal expansion curves are presented. PMID:24769313

MALDI-MS and NanoSIMS imaging techniques to study cnidarian-dinoflagellate symbioses.

PubMed

Kopp, C; Wisztorski, M; Revel, J; Mehiri, M; Dani, V; Capron, L; Carette, D; Fournier, I; Massi, L; Mouajjah, D; Pagnotta, S; Priouzeau, F; Salzet, M; Meibom, A; Sabourault, C

2015-04-01

Cnidarian-dinoflagellate photosynthetic symbioses are fundamental to biologically diverse and productive coral reef ecosystems. The hallmark of this symbiotic relationship is the ability of dinoflagellate symbionts to supply their cnidarian host with a wide range of nutrients. Many aspects of this association nevertheless remain poorly characterized, including the exact identity of the transferred metabolic compounds, the mechanisms that control their exchange across the host-symbiont interface, and the precise subcellular fate of the translocated materials in cnidarian tissues. This lack of knowledge is mainly attributed to difficulties in investigating such metabolic interactions both in situ, i.e. on intact symbiotic associations, and at high spatial resolution. To address these issues, we illustrate the application of two in situ and high spatial resolution molecular and ion imaging techniques-matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) and the nano-scale secondary-ion mass spectrometry (NanoSIMS) ion microprobe. These imaging techniques provide important new opportunities for the detailed investigation of many aspects of cnidarian-dinoflagellate associations, including the dynamics of cellular interactions. Copyright © 2014 Elsevier GmbH. All rights reserved.

SimArray: a user-friendly and user-configurable microarray design tool

PubMed Central

Auburn, Richard P; Russell, Roslin R; Fischer, Bettina; Meadows, Lisa A; Sevillano Matilla, Santiago; Russell, Steven

2006-01-01

Background Microarrays were first developed to assess gene expression but are now also used to map protein-binding sites and to assess allelic variation between individuals. Regardless of the intended application, efficient production and appropriate array design are key determinants of experimental success. Inefficient production can make larger-scale studies prohibitively expensive, whereas poor array design makes normalisation and data analysis problematic. Results We have developed a user-friendly tool, SimArray, which generates a randomised spot layout, computes a maximum meta-grid area, and estimates the print time, in response to user-specified design decisions. Selected parameters include: the number of probes to be printed; the microtitre plate format; the printing pin configuration, and the achievable spot density. SimArray is compatible with all current robotic spotters that employ 96-, 384- or 1536-well microtitre plates, and can be configured to reflect most production environments. Print time and maximum meta-grid area estimates facilitate evaluation of each array design for its suitability. Randomisation of the spot layout facilitates correction of systematic biases by normalisation. Conclusion SimArray is intended to help both established researchers and those new to the microarray field to develop microarray designs with randomised spot layouts that are compatible with their specific production environment. SimArray is an open-source program and is available from . PMID:16509966

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.

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.

CystiSim – An Agent-Based Model for Taenia solium Transmission and Control

PubMed Central

Gabriël, Sarah; Dorny, Pierre; Speybroeck, Niko; Magnussen, Pascal; Torgerson, Paul; Johansen, Maria Vang

2016-01-01

Taenia solium taeniosis/cysticercosis was declared eradicable by the International Task Force for Disease Eradication in 1993, but remains a neglected zoonosis. To assist in the attempt to regionally eliminate this parasite, we developed cystiSim, an agent-based model for T. solium transmission and control. The model was developed in R and available as an R package (http://cran.r-project.org/package=cystiSim). cystiSim was adapted to an observed setting using field data from Tanzania, but adaptable to other settings if necessary. The model description adheres to the Overview, Design concepts, and Details (ODD) protocol and consists of two entities—pigs and humans. Pigs acquire cysticercosis through the environment or by direct contact with a tapeworm carrier's faeces. Humans acquire taeniosis from slaughtered pigs proportional to their infection intensity. The model allows for evaluation of three interventions measures or combinations hereof: treatment of humans, treatment of pigs, and pig vaccination, and allows for customary coverage and efficacy settings. cystiSim is the first agent-based transmission model for T. solium and suggests that control using a strategy consisting of an intervention only targeting the porcine host is possible, but that coverage and efficacy must be high if elimination is the ultimate goal. Good coverage of the intervention is important, but can be compensated for by including an additional intervention targeting the human host. cystiSim shows that the scenarios combining interventions in both hosts, mass drug administration to humans, and vaccination and treatment of pigs, have a high probability of success if coverage of 75% can be maintained over at least a four year period. In comparison with an existing mathematical model for T. solium transmission, cystiSim also includes parasite maturation, host immunity, and environmental contamination. Adding these biological parameters to the model resulted in new insights in the potential

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.

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

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/.

Use of linkage to improve the completeness of the SIM and SINASC in the Brazilian capitals

PubMed Central

Maia, Lívia Teixeira de Souza; de Souza, Wayner Vieira; Mendes, Antonio da Cruz Gouveia; da Silva, Aline Galdino Soares

2017-01-01

ABSTRACT OBJECTIVE To analyze the contribution of linkage between databases of live births and infant mortality to improve the completeness of the variables common to the Mortality Information System (SIM) and the Live Birth Information System (SINASC) in Brazilian capitals in 2012. METHODS We studied 9,001 deaths of children under one year registered in the SIM in 2012 and 1,424,691 live births present in the SINASC in 2011 and 2012. The databases were related with linkage in two steps – deterministic and probabilistic. We calculated the percentage of incompleteness of the variables common to the SIM and SINASC before and after using the technique. RESULTS We could relate 90.8% of the deaths to their respective declarations of live birth, most of them paired deterministically. We found a higher percentage of pairs in Porto Alegre, Curitiba, and Campo Grande. In the capitals of the North region, the average of pairs was 84.2%; in the South region, this result reached 97.9%. The 11 variables common to the SIM and SINASC had 11,278 incomplete fields cumulatively, and we could recover 91.4% of the data after linkage. Before linkage, five variables presented excellent completeness in the SINASC in all Brazilian capitals, but only one variable had the same status in the SIM. After applying this technique, all 11 variables of the SINASC became excellent, while this occurred in seven variables of the SIM. The city of birth was significantly associated with the death component in the quality of the information. CONCLUSIONS Despite advances in the coverage and quality of the SIM and SINASC, problems in the completeness of the variables can still be identified, especially in the SIM. In this perspective, linkage can be used to qualify important information for the analysis of infant mortality. PMID:29211201

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.

Ansys Fluent versus Sim Vascular for 4-D patient-specific computational hemodynamics in renal arteries

NASA Astrophysics Data System (ADS)

Mumbaraddi, Avinash; Yu, Huidan (Whitney); Sawchuk, Alan; Dalsing, Michael

2015-11-01

The objective of this clinical-need driven research is to investigate the effect of renal artery stenosis (RAS) on the blood flow and wall shear stress in renal arteries through 4-D patient-specific computational hemodynamics (PSCH) and search for possible critical RASs that significantly alter the pressure gradient across the stenosis by manually varying the size of RAS from 50% to 95%. The identification of the critical RAS is important to understand the contribution of RAS to the overall renal resistance thus appropriate clinical therapy can be determined in order to reduce the hypertension. Clinical CT angiographic data together with Doppler Ultra sound images of an anonymous patient are used serving as the required inputs of the PSCH. To validate the PSCH, we use both Ansys Fluent and Sim Vascular and compare velocity, pressure, and wall-shear stress under identical conditions. Renal Imaging Technology Development Program (RITDP) Grant.

An AFM-SIMS Nano Tomography Acquisition System

NASA Astrophysics Data System (ADS)

Swinford, Richard William

An instrument, adding the capability to measure 3D volumetric chemical composition, has been constructed by me as a member of the Sanchez Nano Laboratory. The laboratory's in situ atomic force microscope (AFM) and secondary ion mass spectrometry systems (SIMS) are functional and integrated as one instrument. The SIMS utilizes a Ga focused ion beam (FIB) combined with a quadrupole mass analyzer. The AFM is comprised of a 6-axis stage, three coarse axes and three fine. The coarse stage is used for placing the AFM tip anywhere inside a (13x13x5 mm3) (xyz) volume. Thus the tip can be moved in and out of the FIB processing region with ease. The planned range for the Z-axis piezo was 60 microm, but was reduced after it was damaged from arc events. The repaired Z-axis piezo is now operated at a smaller nominal range of 18 microm (16.7 microm after pre-loading), still quite respectable for an AFM. The noise floor of the AFM is approximately 0.4 nm Rq. The voxel size for the combined instrument is targeted at 50 nm or larger. Thus 0.4 nm of xyz uncertainty is acceptable. The instrument has been used for analyzing samples using FIB beam currents of 250 pA and 5.75 nA. Coarse tip approaches can take a long time so an abbreviated technique is employed. Because of the relatively long thro of the Z piezo, the tip can be disengaged by deactivating the servo PID. Once disengaged, it can be moved laterally out of the way of the FIB-SIMS using the coarse stage. This instrument has been used to acquire volumetric data on AlTiC using AFM tip diameters of 18.9 nm and 30.6 nm. Acquisition times are very long, requiring multiple days to acquire a 50-image stack. New features to be added include auto stigmation, auto beam shift, more software automation, etc. Longer term upgrades to include a new lower voltage Z-piezo with strain-gauge feedback and a new design to extend the life for the coarse XY nano-positioners. This AFM-SIMS instrument, as constructed, has proven to be a great proof

Simazine (SIM) Effects on Serum Testosterone and Testicular Function in the Juvenile Wistar Rat

EPA Science Inventory

Chlorotriazine herbicides, such as SIM, are used extensively in the U.S. each year and both the parent compound and the metabolites are detected in ground water in areas of major usage. Previously we found that SIM exposure from postnatal day 23 to 53 increased serum testosterone...

Search for Terrestrial Planets with SIM Planet Quest

NASA Technical Reports Server (NTRS)

Shao, Michael; Tanner, Angelle M.; Catanzarite, Joseph H.

2006-01-01

SIM is an astrometric mission that will be capable of 1 microarcsec relative astrometric accuracy in a single measurement of approx.1000 sec. The search for terrestrial planets in the habitable zone around nearby stars is one of the main science goals of the project. In 2001, NASA through the peer review process selected 10 key projects, two of which had as its goal, the search for terrestrial planets around nearby stars. The two teams, one led by G. Marcy (UC Berkeley) and one lead by M. Shao (JPL), have an extensive preparatory science program underway. This paper describes the status of this activity as well as the technology status of SIM's narrow angle astrometry capability, to reach 1 uas in a single epoch measure and its ability to average multiple epoch measurements to well below 1 uas.

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.

Using SimCPU in Cooperative Learning Laboratories.

ERIC Educational Resources Information Center

Lin, Janet Mei-Chuen; Wu, Cheng-Chih; Liu, Hsi-Jen

1999-01-01

Reports research findings of an experimental design in which cooperative-learning strategies were applied to closed-lab instruction of computing concepts. SimCPU, a software package specially designed for closed-lab usage was used by 171 high school students of four classes. Results showed that collaboration enhanced learning and that blending…

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

ToF-SIMS imaging of capsaicinoids in Scotch Bonnet peppers (Capsicum chinense).

PubMed

Tyler, Bonnie J; Peterson, Richard E; Lee, Therese G; Draude, Felix; Pelster, Andreas; Arlinghaus, Heinrich F

2016-06-13

Peppers (Capsicum spp.) are well known for their ability to cause an intense burning sensation when eaten. This organoleptic response is triggered by capsaicin and its analogs, collectively called capsaicinoids. In addition to the global popularity of peppers as a spice, there is a growing interest in the use of capsaicinoids to treat a variety of human ailments, including arthritis, chronic pain, digestive problems, and cancer. The cellular localization of capsaicinoid biosynthesis and accumulation has previously been studied by fluorescence microscopy and electron microscopy, both of which require immunostaining. In this work, ToF-SIMS has been used to image the distribution of capsaicinoids in the interlocular septum and placenta of Capsicum chinense (Scotch Bonnet peppers). A unique cryo-ToF-SIMS instrument has been used to prepare and analyze the samples with minimal sample preparation. Samples were frozen in liquid propane, cryosectioned in vacuum, and analyzed without exposure to ambient pressure. ToF-SIMS imaging was performed at -110 °C using a Bi3 (+) primary ion beam. Molecular ions for capsaicin and four other capsaicinoids were identified in both the positive and negative ToF-SIMS spectra. The capsaicinoids were observed concentrated in pockets between the outer walls of the palisade cells and the cuticle of the septum, as well as in the intercellular spaces in both the placenta and interlocular septum. This is the first report of label-free direct imaging of capsaicinoids at the cellular level in Capsicum spp. These images were obtained without the need for labeling or elaborate sample preparation. The study demonstrates the usefulness of ToF-SIMS imaging for studying the distribution of important metabolites in plant tissues.

Investigating the capability of ToF-SIMS to determine the oxidation state of Ce

NASA Astrophysics Data System (ADS)

Seed Ahmed, H. A. A.; Swart, H. C.; Kroon, R. E.

2018-04-01

The capability of time of flight secondary ion mass spectrometry (ToF-SIMS) to determine the oxidation state of Ce ions doped in a phosphor was investigated. Two samples of SiO2:Ce (4 mol%) with known Ce3+/Ce4+ relative concentrations were subjected to ToF-SIMS measurements. The spectra were very similar and no significant differences in the relative peak intensities were observed that would readily allow one to distinguish Ce3+ from Ce4+. Although ToF-SIMS was therefore not useful to distinguish the charge state of Ce ions doped in this phosphor material, the idea in principle was also tested on two other samples, namely CeF3 and CeF4 These contain Ce as part of the host (i.e. much higher concentration) and are fluorides, which is significant because ToF-SIMS has previously been reported to be able to distinguish Eu2+ from Eu3+ in Eu doped Sr5(PO4)3F phosphor. The spectrum of CeF4 contained a small peak related to Ce4+ which was not observed in the CeF3 spectrum, yet the peak related to the Ce3+ ions was found to be much more intense in the spectrum of CeF4 than CeF3, showing that the ToF-SIMS signals cannot be directly interpreted as retaining the charge state of the ions in the original material. Nevertheless, the significant differences in the Ce-related peaks in the ToF-SIMS spectra from CeF3 and CeF4 show that the charge state of Ce may be distinguished. This study shows that while in principle ToF-SIMS may be used to distinguish the charge state of Ce ions, this depends on the sample and it would not be easy to interpret the spectra without a standard or reference.

Assessing the effect of self instructional module on knowledge of menopause & hormone replacement therapy for menopausal women in Moradabad (UP).

PubMed

Khalid, Mehvish; Chhuggani, Manju

2014-01-01

Objectives of the study were to identify the problems faced by menopausal women and to find out the remedial measures adopted by them, to assess the knowledge of menopausal women regarding menopause & hormone replacement therapy (HRT) before and after administration of self-instructional module (SIM) and to find out the acceptability and utility of the SIM. An evaluative research approach, with pre-experimental one group pre-test post-test design was adopted. Purposive sampling technique was used to obtain an adequate size of the sample. The sample comprised of 100 menopausal women living in selected community of Moradabad (UP). A knowledge questionnaire and opinionnaire were administered, and SIM on menopause and HRT administered. It was found that there was deficit in knowledge of menopausal women regarding menopause and HRT. Mean post-test knowledge scores were significantly higher than mean pre-test knowledge scores. SIM was found highly acceptable and useful by menopausal women.

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.

CulSim: A simulator of emergence and resilience of cultural diversity

NASA Astrophysics Data System (ADS)

Ulloa, Roberto

CulSim is an agent-based computer simulation software that allows further exploration of influential and recent models of emergence of cultural groups grounded in sociological theories. CulSim provides a collection of tools to analyze resilience of cultural diversity when events affect agents, institutions or global parameters of the simulations; upon combination, events can be used to approximate historical circumstances. The software provides a graphical and text-based user interface, and so makes this agent-based modeling methodology accessible to a variety of users from different research fields.

The core competencies of James Marion Sims, MD.

PubMed

Straughn, J Michael; Gandy, Roy E; Rodning, Charles B

2012-07-01

The concept of core competencies in graduate medical education was introduced by the Accreditation Council for Graduate Medical Education of the American Medical Association to semiquantitatively assess the professional performance of students, residents, practitioners, and faculty. Many aspects of the career of J. Marion Sims, MD, are exemplary of those core competencies: MEDICAL KNOWLEDGE: Author of the first American textbook related to gynecology. MEDICAL CARE: Innovator of the Sims' Vaginal Speculum, Sims' Position, Sims' Test, and vesico-/rectovaginal fistulorrhaphy; advocated abdominal exploration for penetrating wounds; performed the first cholecystostomy. PROFESSIONALISM: Served as President of the New York Academy of Medicine, the American Medical Association, and the American Gynecologic Society. INTERPERSONAL RELATIONSHIPS/COMMUNICATION: Cared for the indigent, hearthless, indentured, disenfranchised; served as consulting surgeon to the Empress Eugénie (France), the Duchess of Hamilton (Scotland), the Empress of Austria, and other royalty of the aristocratic Houses of Europe; accorded the National Order of the Legion of Honor. PRACTICE-BASED LEARNING: Introduction of silver wire sutures; adoption of the principles of asepsis/antisepsis; adoption of the principles of general anesthesia. SYSTEMS-BASED PRACTICE: Established the Woman's Hospital, New York City, New York, the predecessor of the Memorial Sloan-Kettering Center for the Treatment of Cancer and Allied Diseases; organized the Anglo-American Ambulance Corps under the patronage of Napoleon III. What led him to a life of clinical and humanitarian service? First, he was determined to succeed. His formal medical/surgical education was perhaps the best available to North Americans during that era. Second, he was courageous in experimentation and innovation, applying new developments in operative technique, asepsis/antisepsis, and general anesthesia. Third, his curiosity was not burdened by rigid

SimRNAweb: a web server for RNA 3D structure modeling with optional restraints.

PubMed

Magnus, Marcin; Boniecki, Michał J; Dawson, Wayne; Bujnicki, Janusz M

2016-07-08

RNA function in many biological processes depends on the formation of three-dimensional (3D) structures. However, RNA structure is difficult to determine experimentally, which has prompted the development of predictive computational methods. Here, we introduce a user-friendly online interface for modeling RNA 3D structures using SimRNA, a method that uses a coarse-grained representation of RNA molecules, utilizes the Monte Carlo method to sample the conformational space, and relies on a statistical potential to describe the interactions in the folding process. SimRNAweb makes SimRNA accessible to users who do not normally use high performance computational facilities or are unfamiliar with using the command line tools. The simplest input consists of an RNA sequence to fold RNA de novo. Alternatively, a user can provide a 3D structure in the PDB format, for instance a preliminary model built with some other technique, to jump-start the modeling close to the expected final outcome. The user can optionally provide secondary structure and distance restraints, and can freeze a part of the starting 3D structure. SimRNAweb can be used to model single RNA sequences and RNA-RNA complexes (up to 52 chains). The webserver is available at http://genesilico.pl/SimRNAweb. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

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.

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.

VASP, zyxin and TES are tension-dependent members of Focal Adherens Junctions independent of the α-catenin-vinculin module

PubMed Central

Oldenburg, Joppe; van der Krogt, Gerard; Twiss, Floor; Bongaarts, Annika; Habani, Yasmin; Slotman, Johan A.; Houtsmuller, Adriaan; Huveneers, Stephan; de Rooij, Johan

2015-01-01

Mechanical forces are integrated at cadherin-based adhesion complexes to regulate morphology and strength of cell-cell junctions and organization of associated F-actin. A central mechanosensor at the cadherin complex is α-catenin, whose stretching recruits vinculin to regulate adhesion strength. The identity of the F-actin regulating signals that are also activated by mechanical forces at cadherin-based junctions has remained elusive. Here we identify the actin-regulators VASP, zyxin and TES as members of punctate, tensile cadherin-based junctions called Focal Adherens Junctions (FAJ) and show that they display mechanosensitive recruitment similar to that of vinculin. However, this recruitment is not altered by destroying or over-activating the α-catenin/vinculin module. Structured Illumination Microscopy (SIM) indicates that these tension sensitive proteins concentrate at locations within FAJs that are distinct from the core cadherin complex proteins. Furthermore, localization studies using mutated versions of VASP and zyxin indicate that these two proteins require binding to each other in order to localize to the FAJs. We conclude that there are multiple force sensitive modules present at the FAJ that are activated at distinct locations along the cadherin-F-actin axis and regulate specific aspects of junction dynamics. PMID:26611125

AmapSim: A Structural Whole-plant Simulator Based on Botanical Knowledge and Designed to Host External Functional Models

PubMed Central

Barczi, Jean-François; Rey, Hervé; Caraglio, Yves; de Reffye, Philippe; Barthélémy, Daniel; Dong, Qiao Xue; Fourcaud, Thierry

2008-01-01

Background and Aims AmapSim is a tool that implements a structural plant growth model based on a botanical theory and simulates plant morphogenesis to produce accurate, complex and detailed plant architectures. This software is the result of more than a decade of research and development devoted to plant architecture. New advances in the software development have yielded plug-in external functions that open up the simulator to functional processes. Methods The simulation of plant topology is based on the growth of a set of virtual buds whose activity is modelled using stochastic processes. The geometry of the resulting axes is modelled by simple descriptive functions. The potential growth of each bud is represented by means of a numerical value called physiological age, which controls the value for each parameter in the model. The set of possible values for physiological ages is called the reference axis. In order to mimic morphological and architectural metamorphosis, the value allocated for the physiological age of buds evolves along this reference axis according to an oriented finite state automaton whose occupation and transition law follows a semi-Markovian function. Key Results Simulations were performed on tomato plants to demostrate how the AmapSim simulator can interface external modules, e.g. a GREENLAB growth model and a radiosity model. Conclusions The algorithmic ability provided by AmapSim, e.g. the reference axis, enables unified control to be exercised over plant development parameter values, depending on the biological process target: how to affect the local pertinent process, i.e. the pertinent parameter(s), while keeping the rest unchanged. This opening up to external functions also offers a broadened field of applications and thus allows feedback between plant growth and the physical environment. PMID:17766310

Methodological development of topographic correction in 2D/3D ToF-SIMS images using AFM images

NASA Astrophysics Data System (ADS)

Jung, Seokwon; Lee, Nodo; Choi, Myungshin; Lee, Jungmin; Cho, Eunkyunng; Joo, Minho

2018-02-01

Time-of-flight secondary-ion mass spectrometry (ToF-SIMS) is an emerging technique that provides chemical information directly from the surface of electronic materials, e.g. OLED and solar cell. It is very versatile and highly sensitive mass spectrometric technique that provides surface molecular information with their lateral distribution as a two-dimensional (2D) molecular image. Extending the usefulness of ToF-SIMS, a 3D molecular image can be generated by acquiring multiple 2D images in a stack. These imaging techniques by ToF-SIMS provide an insight into understanding the complex structures of unknown composition in electronic material. However, one drawback in ToF-SIMS is not able to represent topographical information in 2D and 3D mapping images. To overcome this technical limitation, topographic information by ex-situ technique such as atomic force microscopy (AFM) has been combined with chemical information from SIMS that provides both chemical and physical information in one image. The key to combine two different images obtained from ToF-SIMS and AFM techniques is to develop the image processing algorithm, which performs resize and alignment by comparing the specific pixel information of each image. In this work, we present methodological development of the semiautomatic alignment and the 3D structure interpolation system for the combination of 2D/3D images obtained by ToF-SIMS and AFM measurements, which allows providing useful analytical information in a single representation.

OpenSim: A Flexible Distributed Neural Network Simulator with Automatic Interactive Graphics.

PubMed

Jarosch, Andreas; Leber, Jean Francois

1997-06-01

An object-oriented simulator called OpenSim is presented that achieves a high degree of flexibility by relying on a small set of building blocks. The state variables and algorithms put in this framework can easily be accessed through a command shell. This allows one to distribute a large-scale simulation over several workstations and to generate the interactive graphics automatically. OpenSim opens new possibilities for cooperation among Neural Network researchers. Copyright 1997 Elsevier Science Ltd.

Incomplete penetrance and phenotypic variability of 6q16 deletions including SIM1.

PubMed

El Khattabi, Laïla; Guimiot, Fabien; Pipiras, Eva; Andrieux, Joris; Baumann, Clarisse; Bouquillon, Sonia; Delezoide, Anne-Lise; Delobel, Bruno; Demurger, Florence; Dessuant, Hélène; Drunat, Séverine; Dubourg, Christelle; Dupont, Céline; Faivre, Laurence; Holder-Espinasse, Muriel; Jaillard, Sylvie; Journel, Hubert; Lyonnet, Stanislas; Malan, Valérie; Masurel, Alice; Marle, Nathalie; Missirian, Chantal; Moerman, Alexandre; Moncla, Anne; Odent, Sylvie; Palumbo, Orazio; Palumbo, Pietro; Ravel, Aimé; Romana, Serge; Tabet, Anne-Claude; Valduga, Mylène; Vermelle, Marie; Carella, Massimo; Dupont, Jean-Michel; Verloes, Alain; Benzacken, Brigitte; Delahaye, Andrée

2015-08-01

6q16 deletions have been described in patients with a Prader-Willi-like (PWS-like) phenotype. Recent studies have shown that certain rare single-minded 1 (SIM1) loss-of-function variants were associated with a high intra-familial risk for obesity with or without features of PWS-like syndrome. Although SIM1 seems to have a key role in the phenotype of patients carrying 6q16 deletions, some data support a contribution of other genes, such as GRIK2, to explain associated behavioural problems. We describe 15 new patients in whom de novo 6q16 deletions were characterised by comparative genomic hybridisation or single-nucleotide polymorphism (SNP) array analysis, including the first patient with fetopathological data. This fetus showed dysmorphic facial features, cerebellar and cerebral migration defects with neuronal heterotopias, and fusion of brain nuclei. The size of the deletion in the 14 living patients ranged from 1.73 to 7.84 Mb, and the fetus had the largest deletion (14 Mb). Genotype-phenotype correlations confirmed the major role for SIM1 haploinsufficiency in obesity and the PWS-like phenotype. Nevertheless, only 8 of 13 patients with SIM1 deletion exhibited obesity, in agreement with incomplete penetrance of SIM1 haploinsufficiency. This study in the largest series reported to date confirms that the PWS-like phenotype is strongly linked to 6q16.2q16.3 deletions and varies considerably in its clinical expression. The possible involvement of other genes in the 6q16.2q16.3-deletion phenotype is discussed.

Development and application of a Chinese webpage suicide information mining system (sims).

PubMed

Chen, Penglai; Chai, Jing; Zhang, Lu; Wang, Debin

2014-11-01

This study aims at designing and piloting a convenient Chinese webpage suicide information mining system (SIMS) to help search and filter required data from the internet and discover potential features and trends of suicide. SIMS utilizes Microsoft Visual Studio2008, SQL2008 and C# as development tools. It collects webpage data via popular search engines; cleans the data using trained models plus minimum manual help; translates the cleaned texts into quantitative data through models and supervised fuzzy recognition; analyzes and visualizes related variables by self-programmed algorithms. The SIMS developed comprises such functions as suicide news and blogs collection, data filtering, cleaning, extraction and translation, data analysis and presentation. SIMS-mediated mining of one-year webpage revealed that: peak months and hours of web-reported suicide events were June-July and 10-11 am respectively, and the lowest months and hours, September-October and 1-7 am; suicide reports came mostly from Soho, Tecent, Sina etc.; male suicide victims over counted female victims in most sub-regions but southwest China; homes, public places and rented houses were the top three places to commit suicide; poisoning, cutting vein and jumping from building were the most commonly used methods to commit suicide; love disputes, family disputes and mental diseases were the leading causes. SIMS provides a preliminary and supplementary means for monitoring and understanding suicide. It proposes useful aspects as well as tools for analyzing the features and trends of suicide using data derived from Chinese webpages. Yet given the intrinsic "dual nature" of internet-based suicide information and the tremendous difficulties experienced by ourselves and other researchers, there is still a long way to go for us to expand, refine and evaluate the system.

J. Marion Sims and the Vesicovaginal Fistula: Historical Understanding, Medical Ethics, and Modern Political Sensibilities.

PubMed

Wall, L Lewis

To review the historical background surrounding the early work of Dr. J. Marion Sims, who developed the first consistently successful surgical technique for the repair of obstetric vesicovaginal fistulas by operating on a group of young, enslaved, African American women who had this condition between 1846 and 1849. Review of primary source documents on Sims and his operations, early 19th century clinical literature on the treatment of vesicovaginal fistula, the introduction of ether and chloroform anesthesia into surgical practice, and the literature on the early 19th century medical ethics pertaining to surgical innovation. The goals are to understand Sims's operations within the clinical context of the 1840s and to avoid the problems of "presentism," in which beliefs, attitudes, and practices of the 21st century are anachronistically projected backward into the early 19th century. The object is to judge Sims within the context of his time, not to hold him accountable to standards of practice which were not developed until a century after his death. A narrative of what Sims did is presented within the context of the therapeutic options available to those with fistula in the early 19th century. Review of the available material demonstrates that Sims' first fistula operations were legal, that they were carried out with express therapeutic intent for the purpose of repairing these women's injuries, that they conformed to the ethical requirements of his time, and that they were performed with the patients' knowledge, cooperation, assent, and assistance.

SIM PlanetQuest science and technology: a status report

NASA Astrophysics Data System (ADS)

Edberg, Stephen J.; Laskin, Robert A.; Marr, James C., IV; Unwin, Stephen C.; Shao, Michael

2007-09-01

Optical interferometry will open new vistas for astronomy over the next decade. The Space Interferometry Mission (SIM-PlanetQuest), operating unfettered by the Earth's atmosphere, will offer unprecedented astrometric precision that promises the discovery of Earth-analog extra-solar planets as well as a wealth of important astrophysics. Results from SIM will permit the determination of stellar masses to accuracies of 2% or better for objects ranging from brown dwarfs through main sequence stars to evolved white dwarfs, neutron stars, and black holes. Studies of star clusters will yield age determinations and internal dynamics. Microlensing measurements will present the mass spectrum of the Milky Way internal to the Sun while proper motion surveys will show the Sun's orbital radius and speed. Studies of the Galaxy's halo component and companion dwarf galaxies permit the determination of the Milky Way's mass distribution, including its Dark Matter component and the mass distribution and Dark Matter component of the Local Group. Cosmology benefits from precision (1-2%) determination of distances to Cepheid and RR Lyrae standard candles. The emission mechanism of supermassive black holes will be investigated. Finally, radio and optical celestial reference frames will be tied together by an improvement of two orders of magnitude. Optical interferometers present severe technological challenges. The Jet Propulsion Laboratory, with the support of Lockheed Martin Advanced Technology Center (LM ATC) and Northrop Grumman Space Technology (NGST), has addressed these challenges with a technology development program that is now complete. The requirements for SIM have been satisfied, based on outside peer review, using a series of laboratory tests and appropriate computer simulations: laser metrology systems perform with 10 picometer precision; mechanical vibrations have been controlled to nanometers, demonstrating orders of magnitude disturbance rejection; and knowledge of

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

BioNetSim: a Petri net-based modeling tool for simulations of biochemical processes.

PubMed

Gao, Junhui; Li, Li; Wu, Xiaolin; Wei, Dong-Qing

2012-03-01

BioNetSim, a Petri net-based software for modeling and simulating biochemistry processes, is developed, whose design and implement are presented in this paper, including logic construction, real-time access to KEGG (Kyoto Encyclopedia of Genes and Genomes), and BioModel database. Furthermore, glycolysis is simulated as an example of its application. BioNetSim is a helpful tool for researchers to download data, model biological network, and simulate complicated biochemistry processes. Gene regulatory networks, metabolic pathways, signaling pathways, and kinetics of cell interaction are all available in BioNetSim, which makes modeling more efficient and effective. Similar to other Petri net-based softwares, BioNetSim does well in graphic application and mathematic construction. Moreover, it shows several powerful predominances. (1) It creates models in database. (2) It realizes the real-time access to KEGG and BioModel and transfers data to Petri net. (3) It provides qualitative analysis, such as computation of constants. (4) It generates graphs for tracing the concentration of every molecule during the simulation processes.

The Sim-SEQ Project: Comparison of Selected Flow Models for the S-3 Site

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

Mukhopadhyay, Sumit; Doughty, Christine A.; Bacon, Diana H.

Sim-SEQ is an international initiative on model comparison for geologic carbon sequestration, with an objective to understand and, if possible, quantify model uncertainties. Model comparison efforts in Sim-SEQ are at present focusing on one specific field test site, hereafter referred to as the Sim-SEQ Study site (or S-3 site). Within Sim-SEQ, different modeling teams are developing conceptual models of CO2 injection at the S-3 site. In this paper, we select five flow models of the S-3 site and provide a qualitative comparison of their attributes and predictions. These models are based on five different simulators or modeling approaches: TOUGH2/EOS7C, STOMP-CO2e,more » MoReS, TOUGH2-MP/ECO2N, and VESA. In addition to model-to-model comparison, we perform a limited model-to-data comparison, and illustrate how model choices impact model predictions. We conclude the paper by making recommendations for model refinement that are likely to result in less uncertainty in model predictions.« less

Distributed acoustic cues for caller identity in macaque vocalization.

PubMed

Fukushima, Makoto; Doyle, Alex M; Mullarkey, Matthew P; Mishkin, Mortimer; Averbeck, Bruno B

2015-12-01

Individual primates can be identified by the sound of their voice. Macaques have demonstrated an ability to discern conspecific identity from a harmonically structured 'coo' call. Voice recognition presumably requires the integrated perception of multiple acoustic features. However, it is unclear how this is achieved, given considerable variability across utterances. Specifically, the extent to which information about caller identity is distributed across multiple features remains elusive. We examined these issues by recording and analysing a large sample of calls from eight macaques. Single acoustic features, including fundamental frequency, duration and Weiner entropy, were informative but unreliable for the statistical classification of caller identity. A combination of multiple features, however, allowed for highly accurate caller identification. A regularized classifier that learned to identify callers from the modulation power spectrum of calls found that specific regions of spectral-temporal modulation were informative for caller identification. These ranges are related to acoustic features such as the call's fundamental frequency and FM sweep direction. We further found that the low-frequency spectrotemporal modulation component contained an indexical cue of the caller body size. Thus, cues for caller identity are distributed across identifiable spectrotemporal components corresponding to laryngeal and supralaryngeal components of vocalizations, and the integration of those cues can enable highly reliable caller identification. Our results demonstrate a clear acoustic basis by which individual macaque vocalizations can be recognized.

Distributed acoustic cues for caller identity in macaque vocalization

PubMed Central

Doyle, Alex M.; Mullarkey, Matthew P.; Mishkin, Mortimer; Averbeck, Bruno B.

2015-01-01

Individual primates can be identified by the sound of their voice. Macaques have demonstrated an ability to discern conspecific identity from a harmonically structured ‘coo’ call. Voice recognition presumably requires the integrated perception of multiple acoustic features. However, it is unclear how this is achieved, given considerable variability across utterances. Specifically, the extent to which information about caller identity is distributed across multiple features remains elusive. We examined these issues by recording and analysing a large sample of calls from eight macaques. Single acoustic features, including fundamental frequency, duration and Weiner entropy, were informative but unreliable for the statistical classification of caller identity. A combination of multiple features, however, allowed for highly accurate caller identification. A regularized classifier that learned to identify callers from the modulation power spectrum of calls found that specific regions of spectral–temporal modulation were informative for caller identification. These ranges are related to acoustic features such as the call’s fundamental frequency and FM sweep direction. We further found that the low-frequency spectrotemporal modulation component contained an indexical cue of the caller body size. Thus, cues for caller identity are distributed across identifiable spectrotemporal components corresponding to laryngeal and supralaryngeal components of vocalizations, and the integration of those cues can enable highly reliable caller identification. Our results demonstrate a clear acoustic basis by which individual macaque vocalizations can be recognized. PMID:27019727

GSM module for wireless radiation monitoring system via SMS

NASA Astrophysics Data System (ADS)

Rahman, Nur Aira Abd; Hisyam Ibrahim, Noor; Lombigit, Lojius; Azman, Azraf; Jaafar, Zainudin; Arymaswati Abdullah, Nor; Hadzir Patai Mohamad, Glam

2018-01-01

A customised Global System for Mobile communication (GSM) module is designed for wireless radiation monitoring through Short Messaging Service (SMS). This module is able to receive serial data from radiation monitoring devices such as survey meter or area monitor and transmit the data as text SMS to a host server. It provides two-way communication for data transmission, status query, and configuration setup. The module hardware consists of GSM module, voltage level shifter, SIM circuit and Atmega328P microcontroller. Microcontroller provides control for sending, receiving and AT command processing to GSM module. The firmware is responsible to handle task related to communication between device and host server. It process all incoming SMS, extract, and store new configuration from Host, transmits alert/notification SMS when the radiation data reach/exceed threshold value, and transmits SMS data at every fixed interval according to configuration. Integration of this module with radiation survey/monitoring device will create mobile and wireless radiation monitoring system with prompt emergency alert at high-level radiation.

Simvastatin prevents isoproterenol-induced cardiac hypertrophy through modulation of the JAK/STAT pathway

PubMed Central

Al-rasheed, Nouf M; Al-Oteibi, Maha M; Al-Manee, Reem Z; Al-shareef, Sarah A; Al-Rasheed, Nawal M; Hasan, Iman H; Mohamad, Raeesa A; Mahmoud, Ayman M

2015-01-01

Simvastatin (SIM) is a lipid-soluble inhibitor of hydroxy-3-methylglutaryl coenzyme A reductase with multiple reported therapeutic benefits. The present study was designed to investigate the effect of pretreatment with SIM on isoproterenol (ISO)-induced cardiac hypertrophy in rats. Twenty-four male albino Wistar rats weighing 180–200 g were divided into four groups. Groups I and III received normal saline while groups II and IV received SIM (10 mg/kg body weight) for 30 days per gavage. In the last 7 days, rats of groups III and IV were administered ISO (5 mg/kg) intraperitoneally to induce cardiac hypertrophy. Administration of ISO induced an increase in heart-to-body weight (HW/BW) ratio, an increase in serum interleukin-6, and elevated systolic and diastolic blood pressure. Serum levels of lipids, cardiovascular risk indices, and cardiac troponin I and creatine phosphokinase-MB showed significant increase in ISO-induced hypertrophic rats. Histopathological examination of heart tissue revealed focal areas of subendocardium degeneration, mononuclear cellular infiltrations, fibrous tissue deposition, and increased thickness of the myocardium of left ventricle. In addition, ISO-administered rats exhibited significant upregulation of cardiac Janus kinase, phosphorylated signal transducer and activator of transcription, and nuclear factor-kappa B. Pretreatment with SIM significantly prevented ISO-induced cardiac hypertrophy, alleviated the altered biochemical parameters, and improved the heart architecture. In conclusion, our study provides evidence that SIM prevented the development of cardiac hypertrophy via modulation of the Janus kinase/signal transducer and activator of transcription-signaling pathway in the heart of ISO-administered animals. PMID:26150695

Simvastatin prevents isoproterenol-induced cardiac hypertrophy through modulation of the JAK/STAT pathway.

PubMed

Al-Rasheed, Nouf M; Al-Oteibi, Maha M; Al-Manee, Reem Z; Al-Shareef, Sarah A; Al-Rasheed, Nawal M; Hasan, Iman H; Mohamad, Raeesa A; Mahmoud, Ayman M

2015-01-01

Simvastatin (SIM) is a lipid-soluble inhibitor of hydroxy-3-methylglutaryl coenzyme A reductase with multiple reported therapeutic benefits. The present study was designed to investigate the effect of pretreatment with SIM on isoproterenol (ISO)-induced cardiac hypertrophy in rats. Twenty-four male albino Wistar rats weighing 180-200 g were divided into four groups. Groups I and III received normal saline while groups II and IV received SIM (10 mg/kg body weight) for 30 days per gavage. In the last 7 days, rats of groups III and IV were administered ISO (5 mg/kg) intraperitoneally to induce cardiac hypertrophy. Administration of ISO induced an increase in heart-to-body weight (HW/BW) ratio, an increase in serum interleukin-6, and elevated systolic and diastolic blood pressure. Serum levels of lipids, cardiovascular risk indices, and cardiac troponin I and creatine phosphokinase-MB showed significant increase in ISO-induced hypertrophic rats. Histopathological examination of heart tissue revealed focal areas of subendocardium degeneration, mononuclear cellular infiltrations, fibrous tissue deposition, and increased thickness of the myocardium of left ventricle. In addition, ISO-administered rats exhibited significant upregulation of cardiac Janus kinase, phosphorylated signal transducer and activator of transcription, and nuclear factor-kappa B. Pretreatment with SIM significantly prevented ISO-induced cardiac hypertrophy, alleviated the altered biochemical parameters, and improved the heart architecture. In conclusion, our study provides evidence that SIM prevented the development of cardiac hypertrophy via modulation of the Janus kinase/signal transducer and activator of transcription-signaling pathway in the heart of ISO-administered animals.

Junior Leader Innovation: William Sims & Continuous Aim Fire

DTIC Science & Technology

2012-06-06

construction ever perpetrated by the white race.” – LT William S. Sims Admiral Sir Percy Scott , Royal Navy...Admiral Mason, Chief, Bureau of Ordnance Ridley McLean “He continued to be a thorn in the fat flesh of the naval hierarchy during his entire

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.

HepSim: A repository with predictions for high-energy physics experiments

DOE PAGES

Chekanov, S. V.

2015-02-03

A file repository for calculations of cross sections and kinematic distributions using Monte Carlo generators for high-energy collisions is discussed. The repository is used to facilitate effective preservation and archiving of data from theoretical calculations and for comparisons with experimental data. The HepSim data library is publicly accessible and includes a number of Monte Carlo event samples with Standard Model predictions for current and future experiments. The HepSim project includes a software package to automate the process of downloading and viewing online Monte Carlo event samples. Data streaming over a network for end-user analysis is discussed.

Surface Characterization of Polymer Blends by XPS and ToF-SIMS

PubMed Central

Chan, Chi Ming; Weng, Lu-Tao

2016-01-01

The surface properties of polymer blends are important for many industrial applications. The physical and chemical properties at the surface of polymer blends can be drastically different from those in the bulk due to the surface segregation of the low surface energy component. X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary mass spectrometry (ToF-SIMS) have been widely used to characterize surface and bulk properties. This review provides a brief introduction to the principles of XPS and ToF-SIMS and their application to the study of the surface physical and chemical properties of polymer blends. PMID:28773777

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

FunSimMat: a comprehensive functional similarity database

PubMed Central

Schlicker, Andreas; Albrecht, Mario

2008-01-01

Functional similarity based on Gene Ontology (GO) annotation is used in diverse applications like gene clustering, gene expression data analysis, protein interaction prediction and evaluation. However, there exists no comprehensive resource of functional similarity values although such a database would facilitate the use of functional similarity measures in different applications. Here, we describe FunSimMat (Functional Similarity Matrix, http://funsimmat.bioinf.mpi-inf.mpg.de/), a large new database that provides several different semantic similarity measures for GO terms. It offers various precomputed functional similarity values for proteins contained in UniProtKB and for protein families in Pfam and SMART. The web interface allows users to efficiently perform both semantic similarity searches with GO terms and functional similarity searches with proteins or protein families. All results can be downloaded in tab-delimited files for use with other tools. An additional XML–RPC interface gives automatic online access to FunSimMat for programs and remote services. PMID:17932054

Thermal expansion of vitrified blood vessels permeated with DP6 and synthetic ice modulators.

PubMed

Eisenberg, David P; Taylor, Michael J; Jimenez-Rios, Jorge L; Rabin, Yoed

2014-06-01

This study provides thermal expansion data for blood vessels permeated with the cryoprotective cocktail DP6, when combined with selected synthetic ice modulators (SIMs): 12% polyethylene glycol 400, 6% 1,3-cyclohexanediol, and 6% 2,3-butanediol. The general classification of SIMs includes molecules that modulate ice nucleation and growth, or possess properties of stabilizing the amorphous state, by virtue of their chemical structure and at concentrations that are not explained on a purely colligative basis. The current study is part of an ongoing effort to characterize thermo-mechanical effects on structural integrity of cryopreserved materials, where thermal expansion is the driving mechanism to thermo-mechanical stress. This study focuses on the lower part of the cryogenic temperature range, where the cryoprotective agent (CPA) behaves as a solid for all practical applications. By combining results obtained in the current study with literature data on the thermal expansion in the upper part of the cryogenic temperature range, unified thermal expansion curves are presented. Copyright © 2014 Elsevier Inc. All rights reserved.

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.

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.

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.

The medical ethics of the 'father of gynaecology', Dr J Marion Sims.

PubMed Central

Ojanuga, D

1993-01-01

Vesico-vaginal fistula (VVF) was a common ailment among American women in the 19th century. Prior to that time, no successful surgery had been developed for the cure of this condition until Dr J Marion Sims perfected a successful surgical technique in 1849. Dr Sims used female slaves as research subjects over a four-year period of experimentation (1845-1849). This paper discusses the controversy surrounding his use of powerless women and whether his actions were acceptable during that historical period. PMID:8459435

CET exSim: mineral exploration experience via simulation

NASA Astrophysics Data System (ADS)

Wong, Jason C.; Holden, Eun-Jung; Kovesi, Peter; McCuaig, T. Campbell; Hronsky, Jon

2013-08-01

Undercover mineral exploration is a challenging task as it requires understanding of subsurface geology by relying heavily on remotely sensed (i.e. geophysical) data. Cost-effective exploration is essential in order to increase the chance of success using finite budgets. This requires effective decision-making in both the process of selecting the optimum data collection methods and in the process of achieving accuracy during subsequent interpretation. Traditionally, developing the skills, behaviour and practices of exploration decision-making requires many years of experience through working on exploration projects under various geological settings, commodities and levels of available resources. This implies long periods of sub-optimal exploration decision-making, before the necessary experience has been successfully obtained. To address this critical industry issue, our ongoing research focuses on the development of the unique and novel e-learning environment, exSim, which simulates exploration scenarios where users can test their strategies and learn the consequences of their choices. This simulator provides an engaging platform for self-learning and experimentation in exploration decision strategies, providing a means to build experience more effectively. The exSim environment also provides a unique platform on which numerous scenarios and situations (e.g. deposit styles) can be simulated, potentially allowing the user to become virtually familiarised with a broader scope of exploration practices. Harnessing the power of computer simulation, visualisation and an intuitive graphical user interface, the simulator provides a way to assess the user's exploration decisions and subsequent interpretations. In this paper, we present the prototype functionalities in exSim including: simulation of geophysical surveys, follow-up drill testing and interpretation assistive tools.

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

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.

Reference Materials for Trace Element Microanalysis of Carbonates by SIMS and other Mass Spectrometric Techniques

NASA Astrophysics Data System (ADS)

Layne, G. D.

2009-12-01

Today, many areas of geochemical research utilize microanalytical determinations of trace elements in carbonate minerals. In particular, there has been an explosion in the application of Secondary Ion Mass Spectrometry (SIMS) to studies of marine biomineralization. SIMS provides highly precise determinations of Mg and Sr at the concentration levels normally encountered in corals, mollusks or fish otoliths. It is also a highly effective means for determining a wide range of other trace elements at ppm levels (e.g., Na, Fe, Mn, Ba, REE, Pb, Th, and U) in a variety of naturally occurring calcite and aragonite matrices - and so is potentially valuable in studies of diagenesis, hydrothermal fluids and carbonatitic magmas. For SIMS, modest time per spot (often <5 min), lateral spatial resolution (<10 μm), sample volume consumption (<10 ng) and overall reproducibility compare extremely favorably with other microanalytical techniques for these applications. However, accuracy and reproducibility are currently wholly limited by the homogeneity of available solid reference material - which is far inferior to the tenths of a percent levels of precision achieved by SIMS. Due to variation in the sputtered ion yields of most elements with the major element composition of the sample matrix, accuracy of SIMS depends intimately on matrix-matched solid reference materials. Despite its rapidly increasing use for trace element analyses of carbonates, there remains a dearth of certified reference materials suitable for calibrating SIMS. The pressed powders used by some analysts to calibrate LA-ICP-MS do not perform well for SIMS - they are not perfectly dense or homogeneous to the desired level at the micron scale of sampling. Further, they often prove incompatible with the sample high vacuum compatibility requirement for stable SIMS analysis (10-8 to 10-9 torr). Some naturally occurring calcite has apparent utility as a reference material. For example, equigranular calcite from some

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.

Molecular imaging of cannabis leaf tissue with MeV-SIMS method

NASA Astrophysics Data System (ADS)

Jenčič, Boštjan; Jeromel, Luka; Ogrinc Potočnik, Nina; Vogel-Mikuš, Katarina; Kovačec, Eva; Regvar, Marjana; Siketić, Zdravko; Vavpetič, Primož; Rupnik, Zdravko; Bučar, Klemen; Kelemen, Mitja; Kovač, Janez; Pelicon, Primož

2016-03-01

To broaden our analytical capabilities with molecular imaging in addition to the existing elemental imaging with micro-PIXE, a linear Time-Of-Flight mass spectrometer for MeV Secondary Ion Mass Spectrometry (MeV-SIMS) was constructed and added to the existing nuclear microprobe at the Jožef Stefan Institute. We measured absolute molecular yields and damage cross-section of reference materials, without significant alteration of the fragile biological samples during the duration of measurements in the mapping mode. We explored the analytical capability of the MeV-SIMS technique for chemical mapping of the plant tissue of medicinal cannabis leaves. A series of hand-cut plant tissue slices were prepared by standard shock-freezing and freeze-drying protocol and deposited on the Si wafer. We show the measured MeV-SIMS spectra showing a series of peaks in the mass area of cannabinoids, as well as their corresponding maps. The indicated molecular distributions at masses of 345.5 u and 359.4 u may be attributed to the protonated THCA and THCA-C4 acids, and show enhancement in the areas with opened trichome morphology.

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.

The role of public policies in reducing smoking: the Minnesota SimSmoke tobacco policy model.

PubMed

Levy, David T; Boyle, Raymond G; Abrams, David B

2012-11-01

Following the landmark lawsuit and settlement with the tobacco industry, Minnesota pursued the implementation of stricter tobacco control policies, including tax increases, mass media campaigns, smokefree air laws, and cessation treatment policies. Modeling is used to examine policy effects on smoking prevalence and smoking-attributable deaths. To estimate the effect of tobacco control policies in Minnesota on smoking prevalence and smoking-attributable deaths using the SimSmoke simulation model. Minnesota data starting in 1993 are applied to SimSmoke, a simulation model used to examine the effect of tobacco control policies over time on smoking initiation and cessation. Upon validating the model against smoking prevalence, SimSmoke is used to distinguish the effect of policies implemented since 1993 on smoking prevalence. Using standard attribution methods, SimSmoke also estimates deaths averted as a result of the policies. SimSmoke predicts smoking prevalence accurately between 1993 and 2011. Since 1993, a relative reduction in smoking rates of 29% by 2011 and of 41% by 2041 can be attributed to tobacco control policies, mainly tax increases, smokefree air laws, media campaigns, and cessation treatment programs. Moreover, 48,000 smoking-attributable deaths will be averted by 2041. Minnesota SimSmoke demonstrates that tobacco control policies, especially taxes, have substantially reduced smoking prevalence and smoking-attributable deaths. Taxes, smokefree air laws, mass media, cessation treatment policies, and youth-access enforcement contributed to the decline in prevalence and deaths averted, with the strongest component being taxes. With stronger policies, for example, increasing cigarette taxes to $4.00 per pack, Minnesota's smoking rate could be reduced by another 13%, and 7200 deaths could be averted by 2041. Copyright © 2012 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

Chemical Imaging of the Cell Membrane by NanoSIMS

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

Weber, P K; Kraft, M L; Frisz, J F

2010-02-23

The existence of lipid microdomains and their role in cell membrane organization are currently topics of great interest and controversy. The cell membrane is composed of a lipid bilayer with embedded proteins that can flow along the two-dimensional surface defined by the membrane. Microdomains, known as lipid rafts, are believed to play a central role in organizing this fluid system, enabling the cell membrane to carry out essential cellular processes, including protein recruitment and signal transduction. Lipid rafts are also implicated in cell invasion by pathogens, as in the case of the HIV. Therefore, understanding the role of lipid raftsmore » in cell membrane organization not only has broad scientific implications, but also has practical implications for medical therapies. One of the major limitations on lipid organization research has been the inability to directly analyze lipid composition without introducing artifacts and at the relevant length-scales of tens to hundreds of nanometers. Fluorescence microscopy is widely used due to its sensitivity and specificity to the labeled species, but only the labeled components can be observed, fluorophores can alter the behavior of the lipids they label, and the length scales relevant to imaging cell membrane domains are between that probed by fluorescence resonance energy transfer (FRET) imaging (<10 nm) and the diffraction limit of light. Topographical features can be imaged on this length scale by atomic force microscopy (AFM), but the chemical composition of the observed structures cannot be determined. Immuno-labeling can be used to study the distribution of membrane proteins at high resolution, but not lipid composition. We are using imaging mass spectrometry by secondary ion mass spectrometry (SIMS) in concert with other high resolution imaging methods to overcome these limitations. The experimental approach of this project is to combine molecule-specific stable isotope labeling with high-resolution SIMS

TOF-SIMS imaging of chlorhexidine-digluconate transport in frozen hydrated biofilms of the fungus Candida albicans

NASA Astrophysics Data System (ADS)

Tyler, Bonnie J.; Rangaranjan, Srinath; Möller, Jörg; Beumer, Andre'; Arlinghaus, Heinrich F.

2006-07-01

The diffusion of the anti-microbial chlorhexidine digluconate (CHG) has been studied in C. albicans biofilms by time-of-flight secondary-ion mass spectrometry (TOF-SIMS). C. albicans has been shown to become resistant to common anti-microbial agents, including CHG, when growing as a biofilm. Mass transport resistance within biofilms has commonly been suggested as a resistance mechanism, but measurement of transport for most anti-microbial agents in biofilms has proven extremely difficult because of the heterogeneity of the biofilms and the difficulty in detecting these agents within an intact biofilm. In this study, TOF-SIMS has been used to study the transport of CHG and glucose in a frozen hydrated biofilm. The TOF-SIMS images reveal a progression of CHG from the top of the biofilm to its base with time. Images suggest that there are channels within the biofilm and show preferential binding of CHG to cellular components of the biofilm. Additionally, both living and dead cells can be identified in the TOF-SIMS images by the sequestration of K + and the presence of cell markers. This study demonstrates that TOF-SIMS has the unique potential to simultaneously observe the presence of an antimicrobial agent, concentration of nutrients, and the viability of the cell population.

Simulated Study of Organizational Theory: The Use of EXPER-SIM in the Undergraduate Business Curriculum.

ERIC Educational Resources Information Center

Lorton, Paul, Jr.

EXPER-SIM (Experiment Simulation) is an instructional approach (with supporting computer programs) which allows an instructor to build a theory based model of how data would occur if an experiment were actually conducted in a world where the theory held true. The LESS version of EXPER-SIM was adapted to run on the Hewlett-Packard 2000E timesharing…

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

Soccer Injury Movement Screen (SIMS) Composite Score Is Not Associated With Injury Among Semi-Professional Soccer Players.

PubMed

McCunn, Robert; Fünten, Karen Aus der; Whalan, Matthew; Sampson, John A; Meyer, Tim

2018-05-08

Study Design Prospective cohort. Background The association between movement quality and injury is equivocal. No soccer-specific movement assessment has been prospectively investigated in relation to injury risk. Objectives To investigate the association between a soccer-specific movement quality assessment and injury risk among semi-professional soccer players. Methods Semi-professional soccer players (n=306) from 12 clubs completed the Soccer Injury Movement Screen (SIMS) during the pre-season period. Individual training/match exposure and non-contact time loss injuries were recorded prospectively for the entirety of the 2016 season. Relative risks (RR) were calculated, and presented with 90% confidence intervals (CI), for the SIMS composite and individual sub-test scores from generalized linear models with Poisson distribution offset for exposure. Results When considering non-contact time loss lower extremity injuries (primary level of analysis), there was a most likely trivial association with the SIMS composite score. Similarly, SIMS composite score demonstrated most likely to likely trivial associations to all injury categories included in the secondary level of analysis (non-contact time loss hip/groin, thigh, knee and ankle injuries). When considering hamstring strains and ankle sprains specifically (tertiary level of analysis) the SIMS composite score, again, demonstrated very likely trivial associations. A total of 262 non-contact time loss injuries were recorded. The overall (training and match exposure combined) incidence of non-contact time loss injury was 12/1000 hours. Conclusion The SIMS composite score demonstrated no association to any of the investigated categories of soccer-related injury. The SIMS composite score should not be used to group players into 'high' or 'low' risk groups. Level of Evidence Prognosis, level 4. J Orthop Sports Phys Ther, Epub 8 May 2018. doi:10.2519/jospt.2018.8037.

NanoSIMS Imaging Alternation Layers of a Leached SON68 Glass Via A FIB-made Wedged Crater

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

Wang, Yi-Chung; Schreiber, Daniel K.; Neeway, James J.

2014-11-01

Currently, nuclear wastes are commonly immobilized into glasses because of their long-term durability. Exposure to water for long periods of time, however, will eventually corrode the waste form and is the leading potential avenue for radionuclide release into the environment. Because such slow processes cannot be experimentally tested, the prediction of release requires a thorough understanding the mechanisms governing glass corrosion. In addition, due to the exceptional durability of glass, much of the testing must be performed on high-surface-area powders. A technique that can provide accurate compositional profiles with very precise depth resolution for non-flat samples would be a majormore » benefit to the field. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) depth profiling is an excellent tool that has long been used to examine corrosion layers of glass. The roughness of the buried corrosion layers, however, causes the corresponding SIMS depth profiles to exhibit erroneously wide interfaces. In this study, NanoSIMS was used to image the cross-section of the corrosion layers of a leached SON68 glass sample. A wedged crater was prepared by a focused ion beam (FIB) instrument to obtain a 5× improvement in depth resolution for NanoSIMS measurements. This increase in resolution allowed us to confirm that the breakdown of the silica glass network is further from the pristine glass than a second dissolution front for boron, another glass former. The existence of these two distinct interfaces, separated by only ~20 nm distance in depth, was not apparent by traditional ToF-SIMS depth profiling but has been confirmed also by atom probe tomography. This novel sample geometry will be a major benefit to efficient NanoSIMS sampling of irregular interfaces at the nanometer scale that would otherwise be obscured within ToF-SIMS depth profiles.« less

ImaSim, a software tool for basic education of medical x-ray imaging in radiotherapy and radiology

NASA Astrophysics Data System (ADS)

Landry, Guillaume; deBlois, François; Verhaegen, Frank

2013-11-01

Introduction: X-ray imaging is an important part of medicine and plays a crucial role in radiotherapy. Education in this field is mostly limited to textbook teaching due to equipment restrictions. A novel simulation tool, ImaSim, for teaching the fundamentals of the x-ray imaging process based on ray-tracing is presented in this work. ImaSim is used interactively via a graphical user interface (GUI). Materials and methods: The software package covers the main x-ray based medical modalities: planar kilo voltage (kV), planar (portal) mega voltage (MV), fan beam computed tomography (CT) and cone beam CT (CBCT) imaging. The user can modify the photon source, object to be imaged and imaging setup with three-dimensional editors. Objects are currently obtained by combining blocks with variable shapes. The imaging of three-dimensional voxelized geometries is currently not implemented, but can be added in a later release. The program follows a ray-tracing approach, ignoring photon scatter in its current implementation. Simulations of a phantom CT scan were generated in ImaSim and were compared to measured data in terms of CT number accuracy. Spatial variations in the photon fluence and mean energy from an x-ray tube caused by the heel effect were estimated from ImaSim and Monte Carlo simulations and compared. Results: In this paper we describe ImaSim and provide two examples of its capabilities. CT numbers were found to agree within 36 Hounsfield Units (HU) for bone, which corresponds to a 2% attenuation coefficient difference. ImaSim reproduced the heel effect reasonably well when compared to Monte Carlo simulations. Discussion: An x-ray imaging simulation tool is made available for teaching and research purposes. ImaSim provides a means to facilitate the teaching of medical x-ray imaging.

Teaching basic trauma: validating FluoroSim, a digital fluoroscopic simulator for guide-wire insertion in hip surgery.

PubMed

Sugand, Kapil; Wescott, Robert A; Carrington, Richard; Hart, Alister; Van Duren, Bernard H

2018-05-10

Background and purpose - Simulation is an adjunct to surgical education. However, nothing can accurately simulate fluoroscopic procedures in orthopedic trauma. Current options for training with fluoroscopy are either intraoperative, which risks radiation, or use of expensive and unrealistic virtual reality simulators. We introduce FluoroSim, an inexpensive digital fluoroscopy simulator without the need for radiation. Patients and methods - This was a multicenter study with 26 surgeons in which everyone completed 1 attempt at inserting a guide-wire into a femoral dry bone using surgical equipment and FluoroSim. 5 objective performance metrics were recorded in real-time to assess construct validity. The surgeons were categorized based on the number of dynamic hip screws (DHS) performed: novices (< 10), intermediates (10-39) and experts (≥ 40). A 7-point Likert scale questionnaire assessed the face and content validity of FluoroSim. Results - Construct validity was present for 2 clinically validated metrics in DHS surgery. Experts and intermediates statistically significantly outperformed novices for tip-apex distance and for cut-out rate. Novices took the least number of radiographs. Face and content validity were also observed. Interpretation - FluoroSim discriminated between novice and intermediate or expert surgeons based on tip-apex distance and cut-out rate while demonstrating face and content validity. FluoroSim provides a useful adjunct to orthopedic training. Our findings concur with results from studies using other simulation modalities. FluoroSim can be implemented for education easily and cheaply away from theater in a safe and controlled environment.

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

BioFET-SIM web interface: implementation and two applications.

PubMed

Hediger, Martin R; Jensen, Jan H; De Vico, Luca

2012-01-01

We present a web interface which allows us to conveniently set up calculations based on the BioFET-SIM model. With the interface, the signal of a BioFET sensor can be calculated depending on its parameters, as well as the signal dependence on pH. As an illustration, two case studies are presented. In the first case, a generic peptide with opposite charges on both ends is inverted in orientation on a semiconducting nanowire surface leading to a corresponding change in sign of the computed sensitivity of the device. In the second case, the binding of an antibody/antigen complex on the nanowire surface is studied in terms of orientation and analyte/nanowire surface distance. We demonstrate how the BioFET-SIM web interface can aid in the understanding of experimental data and postulate alternative ways of antibody/antigen orientation on the nanowire surface.

SimBRS: A University/Industry Consortium Focused on Simulation Based Solutions for Ground Vehicles

DTIC Science & Technology

2009-07-29

plan is to use the SimBRS contract mechanism to streamline a process that applies research funds into a managed program, that is cognizant to the... designs . Therefore, the challenge for the SimBRS team is to establish an approach based on the capacity of measured data and simulations to support ...by systematically relating appropriate results from measurements and applied research in engineering and science. In turn, basic research and

Elemental imaging at the nanoscale: NanoSIMS and complementary techniques for element localisation in plants.

PubMed

Moore, Katie L; Lombi, Enzo; Zhao, Fang-Jie; Grovenor, Chris R M

2012-04-01

The ability to locate and quantify elemental distributions in plants is crucial to understanding plant metabolisms, the mechanisms of uptake and transport of minerals and how plants cope with toxic elements or elemental deficiencies. High-resolution secondary ion mass spectrometry (SIMS) is emerging as an important technique for the analysis of biological material at the subcellular scale. This article reviews recent work using the CAMECA NanoSIMS to determine elemental distributions in plants. The NanoSIMS is able to map elemental distributions at high resolution, down to 50 nm, and can detect very low concentrations (milligrams per kilogram) for some elements. It is also capable of mapping almost all elements in the periodic table (from hydrogen to uranium) and can distinguish between stable isotopes, which allows the design of tracer experiments. In this review, particular focus is placed upon studying the same or similar specimens with both the NanoSIMS and a wide range of complementary techniques, showing how the advantages of each technique can be combined to provide a fuller data set to address complex scientific questions. Techniques covered include optical microscopy, synchrotron techniques, including X-ray fluorescence and X-ray absorption spectroscopy, transmission electron microscopy, electron probe microanalysis, particle-induced X-ray emission and inductively coupled plasma mass spectrometry. Some of the challenges associated with sample preparation of plant material for SIMS analysis, the artefacts and limitations of the technique and future trends are also discussed.

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

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

Detection and quantification of benzodiazepines in hair by ToF-SIMS: preliminary results

NASA Astrophysics Data System (ADS)

Audinot, J.-N.; Yegles, M.; Labarthe, A.; Ruch, D.; Wennig, R.; Migeon, H.-N.

2003-01-01

Successful results have been obtained in detection and quantification of buprenorphine in urine and hemolysed blood by time of flight-secondary ion mass spectrometry (ToF-SIMS). The present work is focused on four molecules of the benzodiazepine's family: nordiazepam, aminoflunitrozepam, diazepam and oxazepam. These drugs remain difficult to analyse in routine clinical and forensic toxicology because of their thermal instability and low therapeutic range (0.5-5 ng/ml). Internal standards are prepared by means of deuterated molecules. The benzadiazepine and their deuterated form (nordiazepam-D5, amino-flunitrazepam-D3, diazepam-D5 and oxazepam-D5) were added, in known concentration, in urine. These molecules were then extracted with several methods (pH, solvent, etc.) and, after adsorption on a noble metal, analysed by ToF-SIMS. The paper will focus for the different molecules on the comparison of the different preparation procedures, the optimisation of the SIMS conditions, the limits of detection and the limits of quantification.

Extreme isotopologue disequilibrium in molecular SIMS species during SHRIMP geochronology

NASA Astrophysics Data System (ADS)

Magee, Charles W., Jr.; Danišík, Martin; Mernagh, Terry

2017-12-01

The current limitation in the accuracy and precision of inter-element analysis in secondary ion mass spectrometry (SIMS) is the ability to find measurable quantities that allow relative differences in ionization and transmission efficiency of secondary ions to be normalized. In uranium-thorium-lead geochronology, the ability to make these corrections, or "calibrate" the data, results in an accuracy limit of approximately 1 %. This study looks at the ionization of uranium and thorium oxide species, which are traditionally used in U-Pb calibration, to explore the conditions under which isotopologues, or molecular species whose composition differs only in the isotopic composition of one or more atoms in the molecule, remain in or deviate from equilibrium. Isotopologue deficits of up to 0.2 (200 ‰) below ideal mixing are observed in UO2+ species during SIMS gechronological analyses using the SHRIMP IIe SIMS instrument. These are identified by bombarding natural U-bearing minerals with an 18O2- primary beam. The large anomalies are associated with repeat analyses down a single SIMS sputtering crater (Compston et al., 1984), analysis of high-uranium, radiation-damaged zircon, and analysis of baddeleyite. Analysis of zircon under routine conditions yield UO2+ isotopologue anomalies generally within a few percent of equilibrium. The conditions under which the isotopologue anomalies are observed are also conditions in which the UOx-based corrections, or calibration, for relative U vs. Pb ionization efficiencies fail. The existence of these isotopologue anomalies suggest that failure of the various UOx species to equilibrate with each other is the reason that none of them will successfully correct the U  / Pb ratio. No simple isotopologue-based correction is apparent. However, isotopologue disequilibrium appears to be a more sensitive tool for detecting high-U calibration breakdowns than Raman spectroscopy, which showed sharper peaks for ˜ 37 Ma high

GPCR-ModSim: A comprehensive web based solution for modeling G-protein coupled receptors

PubMed Central

Esguerra, Mauricio; Siretskiy, Alexey; Bello, Xabier; Sallander, Jessica; Gutiérrez-de-Terán, Hugo

2016-01-01

GPCR-ModSim (http://open.gpcr-modsim.org) is a centralized and easy to use service dedicated to the structural modeling of G-protein Coupled Receptors (GPCRs). 3D molecular models can be generated from amino acid sequence by homology-modeling techniques, considering different receptor conformations. GPCR-ModSim includes a membrane insertion and molecular dynamics (MD) equilibration protocol, which can be used to refine the generated model or any GPCR structure uploaded to the server, including if desired non-protein elements such as orthosteric or allosteric ligands, structural waters or ions. We herein revise the main characteristics of GPCR-ModSim and present new functionalities. The templates used for homology modeling have been updated considering the latest structural data, with separate profile structural alignments built for inactive, partially-active and active groups of templates. We have also added the possibility to perform multiple-template homology modeling in a unique and flexible way. Finally, our new MD protocol considers a series of distance restraints derived from a recently identified conserved network of helical contacts, allowing for a smoother refinement of the generated models which is particularly advised when there is low homology to the available templates. GPCR- ModSim has been tested on the GPCR Dock 2013 competition with satisfactory results. PMID:27166369

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.

Quantification issues of trace metal contaminants on silicon wafers by means of TOF-SIMS, ICP-MS, and TXRF

NASA Astrophysics Data System (ADS)

Rostam-Khani, P.; Hopstaken, M. J. P.; Vullings, P.; Noij, G.; O'Halloran, O.; Claassen, W.

2004-06-01

Measurement of surface metal contamination on silicon wafers is essential for yield enhancement in IC manufacturing. Vapor phase decomposition coupled with either inductively coupled plasma mass spectrometry (VPD-ICP-MS), or total reflection X-ray fluorescence (VPD-TXRF), TXRF and more recently time of flight secondary ion mass spectrometry (TOF-SIMS) are used to monitor surface metal contamination. These techniques complement each other in their respective strengths and weaknesses. For reliable and accurate quantification, so-called relative sensitivity factors (RSF) are required for TOF-SIMS analysis. For quantification purposes in VPD, the collection efficiency (CE) is important to ensure complete collection of contamination. A standard procedure has been developed that combines the determination of these RSFs as well as the collection efficiency using all the analytical techniques mentioned above. Therefore, sample wafers were intentionally contaminated and analyzed (by TOF-SIMS) directly after preparation. After VPD-ICP-MS, several scanned surfaces were analyzed again by TOF-SIMS. Comparing the intensities of the specific metals before and after the VPD-DC procedure on the scanned surface allows the determination of so-called removing efficiency (RE). In general, very good agreement was obtained comparing the four analytical techniques after updating the RSFs for TOF-SIMS. Progress has been achieved concerning the CE evaluation as well as determining the RSFs more precisely for TOF-SIMS.

Imaging of single liver tumor cells intoxicated by heavy metals using ToF-SIMS

NASA Astrophysics Data System (ADS)

Mai, Fu-Der; Chen, Bo-Jung; Wu, Li-Chen; Li, Feng-Yin; Chen, Wen-Kang

2006-07-01

Human liver tumor cells intoxicated with five different Cd, Cu, Cr, Hg and Zn metals were analyzed using imaging time-of-flight secondary ion mass spectrometry (ToF-SIMS) to visualize the metal distributions in a single cell basis. A protocol was developed by combining rapid freezing, freeze-fracture and imprinting for transferring the intoxicated cells to a silicon wafer. As shown in the ToF-SIMS images, the cellular morphology was preserved indicating that this protocol can be used to prepare a representative cell for ToF-SIMS imaging analysis. Among the five metal ions investigated in this study, only Cr and Cu ions show preferential diffusion into the cell after simulated intoxication while the signals of the other three ions are either too low to be detected or unable to be distinguished from background intensity.

Detection and distribution of lithium in Mg-Li-Al based alloy by ToF-SIMS

NASA Astrophysics Data System (ADS)

Kumar, Vinod

2016-12-01

Time of Flight-Secondary Ion Mass Spectrometry (ToF-SIMS) is used to investigate the surface as well as bulk microstructural features of novel Mg-Li-Al based alloy namely Mg-9Li-7Al-3Sn-1Zn (LATZ9531). ToF-SIMS study indicates that there are six multi-oxide layers present within the surface film of LATZ9531. Furthermore, The presence of Li containing phase has been qualitatively confirmed based on the high number of Li-ion counts in SIMS, and the same is verified quantitatively by using electron probe microanalysis (EPMA). The novel approach may be useful to determine the chemical composition of the phases in various alloys which has lighter alloying elements such as lithium.

Segment fusion of ToF-SIMS images.

PubMed

Milillo, Tammy M; Miller, Mary E; Fischione, Remo; Montes, Angelina; Gardella, Joseph A

2016-06-08

The imaging capabilities of time-of-flight secondary ion mass spectrometry (ToF-SIMS) have not been used to their full potential in the analysis of polymer and biological samples. Imaging has been limited by the size of the dataset and the chemical complexity of the sample being imaged. Pixel and segment based image fusion algorithms commonly used in remote sensing, ecology, geography, and geology provide a way to improve spatial resolution and classification of biological images. In this study, a sample of Arabidopsis thaliana was treated with silver nanoparticles and imaged with ToF-SIMS. These images provide insight into the uptake mechanism for the silver nanoparticles into the plant tissue, giving new understanding to the mechanism of uptake of heavy metals in the environment. The Munechika algorithm was programmed in-house and applied to achieve pixel based fusion, which improved the spatial resolution of the image obtained. Multispectral and quadtree segment or region based fusion algorithms were performed using ecognition software, a commercially available remote sensing software suite, and used to classify the images. The Munechika fusion improved the spatial resolution for the images containing silver nanoparticles, while the segment fusion allowed classification and fusion based on the tissue types in the sample, suggesting potential pathways for the uptake of the silver nanoparticles.

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.

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.

Cycloartane triterpenoid saponins from water soluble of Passiflora edulis Sims and their antidepressant-like effects.

PubMed

Wang, Cong; Xu, Feng-Qing; Shang, Jian-Hua; Xiao, Huai; Fan, Wei-Wei; Dong, Fa-Wu; Hu, Jiang-Miao; Zhou, Jun

2013-07-30

Various species of genus Passiflora have been used as traditional folk medicines owing to their sedative and anti-hypertensive properties. Passiflora edulis Sims most widely grown in the warm temperate for their fragrant fruits and their twigs and leaves are used as a folk medicine for treating both anxiety and nervousness in American countries. The present study was to evaluate the antidepressant-like effect and the active components of this plant. The alcohol extracts of the stems (PES, 10 and 2 g/kg of the plant materials) and leaves (PEL, 10 and 2 g/kg of the plant materials) of Passiflora edulis Sims were orally administered to mice for 7 day. The animals were tested in the forced swim test (FST) and tail suspension test (TST). After behavioral assay of ethanol extract, phytochemical research of the stems and leaves (5.7 kg) of Passiflora edulis Sims were developed and further bioactive verification of monomeric compounds were conducted. There are mainly cycloartane triterpenoids and their saponins isolated from this plant, including two new cycloartane triterpenoid saponins named cyclopassifloside ХII (1) and ХIII (2), together with six known cycloartane triterpenoids, cyclopassifloic acids B and E, cyclopassiflosides II, VI, IX and XI. The ethanol extract of Passiflora edulis Sims together with isolated compounds cyclopassiflosides IX and XI may possess antidepressant-like effect. Cycloartane triterpenoid was one of the main compositions of Passiflora edulis Sims and possess antidepressant-like activity. Crown Copyright © 2013. Published by Elsevier Ireland Ltd. All rights reserved.

High resolution isotopic analysis of U-bearing particles via fusion of SIMS and EDS images

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

Tarolli, Jay G.; Naes, Benjamin E.; Garcia, Benjamin J.

Image fusion of secondary ion mass spectrometry (SIMS) images and X-ray elemental maps from energy-dispersive spectroscopy (EDS) was performed to facilitate the isolation and re-analysis of isotopically unique U-bearing particles where the highest precision SIMS measurements are required. Image registration, image fusion and particle micromanipulation were performed on a subset of SIMS images obtained from a large area pre-screen of a particle distribution from a sample containing several certified reference materials (CRM) U129A, U015, U150, U500 and U850, as well as a standard reference material (SRM) 8704 (Buffalo River Sediment) to simulate particles collected on swipes during routine inspections ofmore » declared uranium enrichment facilities by the International Atomic Energy Agency (IAEA). In total, fourteen particles, ranging in size from 5 – 15 µm, were isolated and re-analyzed by SIMS in multi-collector mode identifying nine particles of CRM U129A, one of U150, one of U500 and three of U850. These identifications were made within a few percent errors from the National Institute of Standards and Technology (NIST) certified atom percent values for 234U, 235U and 238U for the corresponding CRMs. This work represents the first use of image fusion to enhance the accuracy and precision of isotope ratio measurements for isotopically unique U-bearing particles for nuclear safeguards applications. Implementation of image fusion is essential for the identification of particles of interests that fall below the spatial resolution of the SIMS images.« less

Subcellular SIMS imaging of isotopically labeled amino acids in cryogenically prepared cells

NASA Astrophysics Data System (ADS)

Chandra, Subhash

2004-06-01

Ion microscopy is a potentially powerful technique for localization of isotopically labeled molecules. In this study, L-arginine and phenylalanine amino acids labeled with stable isotopes 13C and 15N were localized in cultured cells with the ion microscope at 500 nm spatial resolution. Cells were exposed to the labeled amino acids and cryogenically prepared. SIMS analyses were made in fractured freeze-dried cells. A dynamic distribution was observed from labeled arginine-treated LLC-PK 1 kidney cells at mass 28 ( 13C15N) in negative secondaries, revealing cell-to-cell heterogeneity and preferential accumulation of the amino acid (or its metabolite) in the nucleus and nucleolus of some cells. The smaller nucleolus inside the nucleus was clearly resolved in SIMS images and confirmed by correlative light microscopy. The distribution of labeled phenylalanine contrasted with arginine as it was rather homogeneously distributed in T98G human glioblastoma cells. Images of 39K, 23Na and 40Ca were also recorded to confirm the reliability of sample preparation and authenticity of the observed amino acid distributions. These observations indicate that SIMS techniques can provide a valuable technology for subcellular localization of nitrogen-containing molecules in proteomics since nitrogen does not have a radionuclide tracer isotope. Amino acids labeled with stable isotopes can be used as tracers for studying their transport and metabolism in distinct subcellular compartments with SIMS. Further studies of phenylalanine uptake in human glioblastoma cells may have special significance in boron neutron capture therapy (BNCT) as a boron analogue of phenylalanine, boronophenylalanine is a clinically approved compound for the treatment of brain tumors.

Effect of a self-instructional module on the child rearing knowledge and practice of women with epilepsy.

PubMed

Saramma, P P; Sarma, P S; Thomas, Sanjeev V

2014-06-01

Women with epilepsy (WWE) have poorer knowledge and skill in child rearing than women without epilepsy. To evaluate the effect of a self-instructional module (SIM) on the child rearing knowledge (CRK) and practice (CRP) of WWE and developmental outcome of their babies. One hundred women in first trimester of pregnancy that were enrolled in to the Kerala Registry of Epilepsy and Pregnancy and consenting to participate were given a self instructional module (SIM) or a comparator booklet by random concealed allocation. Their child rearing knowledge (CRK) was assessed by a standardized protocol at entry (first trimester) and at 3-4 months postpartum. Their child rearing practice (CRP) was evaluated in third postpartum month. The developmental outcome of babies was assessed at 1 year of age as per registry protocol. Eighty eight women completed this 1 year study. The CRK score was significantly higher (p=.034) for the intervention group (32.91±5) when compared to the comparator group (30.61±5) However, a corresponding improvement in CRP score was not observed for the former. Developmental outcome of 68 babies showed a positive weak correlation between CRP and developmental quotient both mental and motor. The intervention group demonstrated significant increase in their CRK. Nevertheless the results did not indicate a significant improvement in the CRP. The SIM improved the CRK of WWE. Nevertheless, the child rearing practices did not show corresponding improvement. Copyright © 2014 British Epilepsy Association. Published by Elsevier Ltd. All rights reserved.

The impact of detergents on the tissue decellularization process: A ToF-SIMS study.

PubMed

White, Lisa J; Taylor, Adam J; Faulk, Denver M; Keane, Timothy J; Saldin, Lindsey T; Reing, Janet E; Swinehart, Ilea T; Turner, Neill J; Ratner, Buddy D; Badylak, Stephen F

2017-03-01

Biologic scaffolds are derived from mammalian tissues, which must be decellularized to remove cellular antigens that would otherwise incite an adverse immune response. Although widely used clinically, the optimum balance between cell removal and the disruption of matrix architecture and surface ligand landscape remains a considerable challenge. Here we describe the use of time of flight secondary ion mass spectroscopy (ToF-SIMS) to provide sensitive, molecular specific, localized analysis of detergent decellularized biologic scaffolds. We detected residual detergent fragments, specifically from Triton X-100, sodium deoxycholate and sodium dodecyl sulphate (SDS) in decellularized scaffolds; increased SDS concentrations from 0.1% to 1.0% increased both the intensity of SDS fragments and adverse cell outcomes. We also identified cellular remnants, by detecting phosphate and phosphocholine ions in PAA and CHAPS decellularized scaffolds. The present study demonstrates ToF-SIMS is not only a powerful tool for characterization of biologic scaffold surface molecular functionality, but also enables sensitive assessment of decellularization efficacy. We report here on the use of a highly sensitive analytical technique, time of flight secondary ion mass spectroscopy (ToF-SIMS) to characterize detergent decellularized scaffolds. ToF-SIMS detected cellular remnants and residual detergent fragments; increased intensity of the detergent fragments correlated with adverse cell matrix interactions. This study demonstrates the importance of maintaining a balance between cell removal and detergent disruption of matrix architecture and matrix surface ligand landscape. This study also demonstrates the power of ToF-SIMS for the characterization of decellularized scaffolds and capability for assessment of decellularization efficacy. Future use of biologic scaffolds in clinical tissue reconstruction will benefit from the fundamental results described in this work. Copyright © 2016 Acta

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.

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.

Low Power Near Field Communication Methods for RFID Applications of SIM Cards.

PubMed

Chen, Yicheng; Zheng, Zhaoxia; Gong, Mingyang; Yu, Fengqi

2017-04-14

Power consumption and communication distance have become crucial challenges for SIM card RFID (radio frequency identification) applications. The combination of long distance 2.45 GHz radio frequency (RF) technology and low power 2 kHz near distance communication is a workable scheme. In this paper, an ultra-low frequency 2 kHz near field communication (NFC) method suitable for SIM cards is proposed and verified in silicon. The low frequency transmission model based on electromagnetic induction is discussed. Different transmission modes are introduced and compared, which show that the baseband transmit mode has a better performance. The low-pass filter circuit and programmable gain amplifiers are applied for noise reduction and signal amplitude amplification. Digital-to-analog converters and comparators are used to judge the card approach and departure. A novel differential Manchester decoder is proposed to deal with the internal clock drift in range-controlled communication applications. The chip has been fully implemented in 0.18 µm complementary metal-oxide-semiconductor (CMOS) technology, with a 330 µA work current and a 45 µA idle current. The low frequency chip can be integrated into a radio frequency SIM card for near field RFID applications.

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.

The quantitative analysis of OH in vesuvianite: a polarized FTIR and SIMS study

NASA Astrophysics Data System (ADS)

Bellatreccia, Fabio; della Ventura, Giancarlo; Ottolini, Luisa; Libowitzky, Eugen; Beran, Anton

2005-05-01

A well-characterized suite of vesuvianite samples from the volcanic ejecta (skarn or syenites) from Latium (Italy) was studied by single-crystal, polarized radiation, Fourier-transform infrared (FTIR) spectroscopy and secondary-ion mass-spectrometry (SIMS). OH-stretching FTIR spectra consist of a rather well-defined triplet of broad bands at higher-frequency (3,700 3,300 cm-1) and a very broad composite absorption below 3,300 cm-1. Measurements with E//c or E⊥c show that all bands are strongly polarized with maximum absorption for E//c. They are in agreement with previous band assignments (Groat et al. Can Mineral 33:609, 1995) to the two O(11) H(1) and O(10) H(2) groups in the structure. Pleochroic measurements with changing direction of the E vector of the incident radiation show that the orientation of the O(11) H(1) dipole is OH∧c~35°, in excellent agreement with the neutron data of Lager et al. (Can Mineral 37:763, 1999). A SIMS-based calibration curve at ~10% rel. accuracy has been worked out and used as reference for the quantitative analysis of H2O in vesuvianite by FTIR. Based on previous SIMS results for silicate minerals (Ottolini and Hawthorne in J Anal At Spectrom 16:1266, 2001; Ottolini et al. in Am Mineral 87:1477, 2002) the SiO2 and FeO content of the matrix were assumed as the major factors to be considered at a first approximation in the selection of the standards for H. The lack of vesuvianite standards for quantitative SIMS analysis of H2O has been here overcome by selecting low-silica elbaite crystals (Ottolini et al. in Am Mineral 87:1477, 2002). The resulting integrated molar absorption FTIR coefficient for vesuvianite is ɛi=100.000±2.000 l mol-1 cm-2. SIMS data for Li, B, F, Sr, Y, Be, Ba REE, U and Th are also provided in the paper.

NanoSIMS opens a New Window for Deciphering Organic Matter in Terrestrial and Extraterrestrial Samples

NASA Technical Reports Server (NTRS)

Oehler, Dorothy ZS.; Robert, Francois; Mostefaoui, Smail; Meibom, Anders; Selo, Madeleine; McKay, David S.; Gibson, Everett K.

2007-01-01

Recognition of the earliest morphological or chemical evidence of terrestrial life has proved to be challenging, as organic matter in ancient rocks is commonly fragmentary and difficult to distinguish from abiotically-produced materials (Schopf, 1993; Van Zuilen et al., 2002; Altermann & Kazmierczak, 2003; Cady et al., 2003; Brasier et al., 2002, 2004, 2005; Hofmann, 2004; Skrzypczak et al., 2004, 2005). Yet, the ability to identify remnants of earliest life is critical to our understanding of the timing of life's origin on earth, the nature of earliest terrestrial life, and recognition of potential remnants of microbial life that might occur in extraterrestrial materials. The search for earliest life on Earth now extends to early Archean organic remains; these tend to be very poorly preserved and considerably more difficult to interpret than the delicately permineralized microfossils known from many Proterozoic deposits. Thus, recent efforts have been directed toward finding biosignatures that can help distinguish fragmentary remnants of ancient microbes from either pseudofossils or abiotic organic materials that may have formed hydrothermally or in extraterrestrial processes (House et al., 2000; Boyce et al., 2001; Kudryavtsev et al., 2001; Schopf, 2002; Schopf et al., 2002, 2005a,b; Cady et al., 2003; Garc a-Ruiz et al., 2003; Hofmann, 2004; Brasier et al., 2005; Rushdi and Simoneit, 2005; Skrzypczak et al., 2005). An exciting area of biosignature research involves the developing technology of NanoSIMS. NanoSIMS is secondary ion mass spectrometry (SIMS) for ultrafine feature, elemental and isotopic analysis. Its resolution approaches 0.05 micrometers for element mapping, which is 10-50 times finer than that attainable with conventional SIMS or electron microprobes. Consequently, NanoSIMS has the potential to reveal previously unknown, chemical and structural characteristics of organic matter preserved in geologic materials. Robert et al. (2005) were the first to

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.

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.

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.

Measuring modules for the research of compensators of reactive power with voltage stabilization in MATLAB

NASA Astrophysics Data System (ADS)

Vlasayevsky, Stanislav; Klimash, Stepan; Klimash, Vladimir

2017-10-01

A set of mathematical modules was developed for evaluation the energy performance in the research of electrical systems and complexes in the MatLab. In the electrotechnical library SimPowerSystems of the MatLab software, there are no measuring modules of energy coefficients characterizing the quality of electricity and the energy efficiency of electrical apparatus. Modules are designed to calculate energy coefficients characterizing the quality of electricity (current distortion and voltage distortion) and energy efficiency indicators (power factor and efficiency) are presented. There are described the methods and principles of building the modules. The detailed schemes of modules built on the elements of the Simulink Library are presented, in this connection, these modules are compatible with mathematical models of electrical systems and complexes in the MatLab. Also there are presented the results of the testing of the developed modules and the results of their verification on the schemes that have analytical expressions of energy indicators.

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.

Prevention for HIV-Seropositive Persons: Successive Approximation Toward a New Identity

ERIC Educational Resources Information Center

Lightfoot, Marguerita; Rotheram-Borus, Mary Jane; Milburn, Norweeta G.; Swendeman, Dallas

2005-01-01

This article presents a three-module intervention based on social action theory that focuses on health promotion and social identity formation for seropositive youth. The modules are designed to reduce transmission of HIV by reducing sexual and substance abuse acts, increasing healthy acts and adherence to care, and maintaining positive behavioral…

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

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.

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.

Generating optimal control simulations of musculoskeletal movement using OpenSim and MATLAB.

PubMed

Lee, Leng-Feng; Umberger, Brian R

2016-01-01

Computer modeling, simulation and optimization are powerful tools that have seen increased use in biomechanics research. Dynamic optimizations can be categorized as either data-tracking or predictive problems. The data-tracking approach has been used extensively to address human movement problems of clinical relevance. The predictive approach also holds great promise, but has seen limited use in clinical applications. Enhanced software tools would facilitate the application of predictive musculoskeletal simulations to clinically-relevant research. The open-source software OpenSim provides tools for generating tracking simulations but not predictive simulations. However, OpenSim includes an extensive application programming interface that permits extending its capabilities with scripting languages such as MATLAB. In the work presented here, we combine the computational tools provided by MATLAB with the musculoskeletal modeling capabilities of OpenSim to create a framework for generating predictive simulations of musculoskeletal movement based on direct collocation optimal control techniques. In many cases, the direct collocation approach can be used to solve optimal control problems considerably faster than traditional shooting methods. Cyclical and discrete movement problems were solved using a simple 1 degree of freedom musculoskeletal model and a model of the human lower limb, respectively. The problems could be solved in reasonable amounts of time (several seconds to 1-2 hours) using the open-source IPOPT solver. The problems could also be solved using the fmincon solver that is included with MATLAB, but the computation times were excessively long for all but the smallest of problems. The performance advantage for IPOPT was derived primarily by exploiting sparsity in the constraints Jacobian. The framework presented here provides a powerful and flexible approach for generating optimal control simulations of musculoskeletal movement using OpenSim and MATLAB. This

Generating optimal control simulations of musculoskeletal movement using OpenSim and MATLAB

PubMed Central

Lee, Leng-Feng

2016-01-01

Computer modeling, simulation and optimization are powerful tools that have seen increased use in biomechanics research. Dynamic optimizations can be categorized as either data-tracking or predictive problems. The data-tracking approach has been used extensively to address human movement problems of clinical relevance. The predictive approach also holds great promise, but has seen limited use in clinical applications. Enhanced software tools would facilitate the application of predictive musculoskeletal simulations to clinically-relevant research. The open-source software OpenSim provides tools for generating tracking simulations but not predictive simulations. However, OpenSim includes an extensive application programming interface that permits extending its capabilities with scripting languages such as MATLAB. In the work presented here, we combine the computational tools provided by MATLAB with the musculoskeletal modeling capabilities of OpenSim to create a framework for generating predictive simulations of musculoskeletal movement based on direct collocation optimal control techniques. In many cases, the direct collocation approach can be used to solve optimal control problems considerably faster than traditional shooting methods. Cyclical and discrete movement problems were solved using a simple 1 degree of freedom musculoskeletal model and a model of the human lower limb, respectively. The problems could be solved in reasonable amounts of time (several seconds to 1–2 hours) using the open-source IPOPT solver. The problems could also be solved using the fmincon solver that is included with MATLAB, but the computation times were excessively long for all but the smallest of problems. The performance advantage for IPOPT was derived primarily by exploiting sparsity in the constraints Jacobian. The framework presented here provides a powerful and flexible approach for generating optimal control simulations of musculoskeletal movement using OpenSim and MATLAB

Learning and Literacy in an Online Gaming Community: Examples of Participatory Practices in a Sims Affinity Space

ERIC Educational Resources Information Center

Lee, Yoonhee Naseef

2012-01-01

The goal of this research was to understand the different kinds of learning that take place in "Mod The Sims" (MTS), an online "Sims" gaming community. The study aimed to explore users' experiences and to understand learning practices that are not commonly observed in formal educational settings. To achieve this goal, the…

Tracing photosynthetic carbon in leaves with nanoSIMS after 13CO2 labelling

NASA Astrophysics Data System (ADS)

Dannoura, Masako; Takeuchi, Miyuki; Kominami, Yuji; Takanashi, Satoru; Kenichi, Yoshimura; Ataka, Mioko

2015-04-01

To understand the carbon allocation of the tree and forest ecosystem, it is important to consider the residence time of carbon in different pools at suitable time scales. For example the carbon used for respiration will stay a few minutes to a few days in the tree, the carbon used for storage or structure of leaves will stay months to years, and the carbon used for wood structure, it will stay over the whole lifespan of the tree. The leaves are the entrance of carbon in trees where it can be used for foliage growth and maintenance or exported to the other organs or the other forest ecosystem compartments. Tracing carbon isotope using NanoSIMS technique is one of useful methods to estimate where and how long the carbon stay in the tree organs. In this study, 13CO2 pulse labelling were conducted and 13C was measured by IRMS to see the amount of C remaining in the leaves with time.NanoSIMS was used to localize where the labelled C remained within the leaf tissue. Twice labelling were done on branches of Quercus serrata at FFPRI(Forest and Forest Products research Institute) in Kyoto, Japan. The first labelling was in 30 April 2012 when the leaves start flushing and the second one was in 29 May 2012 when the leaves were completely deployed. For both labelling experiment, one branch was selected and covered with transparent plastic bag. CO2 concentration was recorded with IRGA and air temperature inside the chamber was monitored. Then 13CO2 was injected into the bag, and after 1 hour, the bag was removed and the branch was again exposed to ambient air. Leaves were collected before and 10-12 times after labelling and their isotope compositions were measured by IRMS. The leaf collected just after labelling and 6 days after labelling were used for NanoSIMS observation. Samples for nanoSIMS were preserved in glutaraldehyde and then embed in epoxy resin. The sliced sample were placed on the silicon wafer and observed by NanoSIMS 50L(Cameca, France). The 13C was highest just

SimExTargId: A comprehensive package for real-time LC-MS data acquisition and analysis.

PubMed

Edmands, William M B; Hayes, Josie; Rappaport, Stephen M

2018-05-22

Liquid chromatography mass spectrometry (LC-MS) is the favored method for untargeted metabolomic analysis of small molecules in biofluids. Here we present SimExTargId, an open-source R package for autonomous analysis of metabolomic data and real-time observation of experimental runs. This simultaneous, fully automated and multi-threaded (optional) package is a wrapper for vendor-independent format conversion (ProteoWizard), xcms- and CAMERA- based peak-picking, MetMSLine-based pre-processing and covariate-based statistical analysis. Users are notified of detrimental instrument drift or errors by email. Also included are two shiny applications, targetId for real-time MS2 target identification, and peakMonitor to monitor targeted metabolites. SimExTargId is publicly available under GNU LGPL v3.0 license at https://github.com/JosieLHayes/simExTargId, which includes a vignette with example data. SimExTargId should be installed on a dedicated data-processing workstation or server that is networked to the LC-MS platform to facilitate MS1 profiling of metabolomic data. josie.hayes@berkeley.edu. Supplementary data are available at Bioinformatics online.

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.

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.

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

LavaSIM: the effect of heat transfer in 3D on lava flow characteristics (Invited)

NASA Astrophysics Data System (ADS)

Fujita, E.

2013-12-01

Characteristics of lava flow are governed by many parameters like lava viscosity, effusion rate, ground topography, etc. The accuracy and applicability of lava flow simulation code is evaluated whether the numerical simulation can reproduce these features quantitatively, which is important from both strategic and scientific points of views. Many lava flow simulation codes are so far proposed, and they are classified into two categories, i.e., the deterministic and the probabilistic models. LavaSIM is one of the former category models, and has a disadvantage of time consuming. But LavaSIM can solves the equations of continuity, motion, energy by step and has an advantage in the calculation of three-dimensional analysis with solid-liquid two phase flow, including the heat transfer between lava, solidified crust, air, water and ground, and three-dimensional convection in liquid lava. In other word, we can check the detailed structure of lava flow by LavaSIM. Therefore, this code can produce both channeled and fan-dispersive flows. The margin of the flow is solidified by cooling and these solidified crusts control the behavior of successive lava flow. In case of a channel flow, the solidified margin supports the stable central main flow and elongates the lava flow distance. The cross section of lava flow shows that the liquid lava flows between solidified crusts. As for the lava extrusion flow rate, LavaSIM can include the time function as well as the location of the vents. In some cases, some parts of the solidified wall may be broken by the pressure of successive flow and/or re-melting. These mechanisms could characterize complex features of the observed lava flows at many volcanoes in the world. To apply LavaSIM to the benchmark tests organized by V-hub is important to improve the lava flow evaluation technique.

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

THE INTRA- AND INTER-RATER RELIABILITY OF THE SOCCER INJURY MOVEMENT SCREEN (SIMS).

PubMed

McCunn, Robert; Aus der Fünten, Karen; Govus, Andrew; Julian, Ross; Schimpchen, Jan; Meyer, Tim

2017-02-01

The growing volume of movement screening research reveals a belief among practitioners and researchers alike that movement quality may have an association with injury risk. However, existing movement screening tools have not considered the sport-specific movement and injury patterns relevant to soccer. The present study introduces the Soccer Injury Movement Screen (SIMS), which has been designed specifically for use within soccer. Furthermore, the purpose of the present study was to assess the intra- and inter-rater reliability of the SIMS and determine its suitability for use in further research. The study utilized a test-retest design to discern reliablility. Twenty-five (11 males, 14 females) healthy, recreationally active university students (age 25.5 ± 4.0 years, height 171 ± 9 cm, weight 64.7 ± 12.6 kg) agreed to participate. The SIMS contains five sub-tests: the anterior reach, single-leg deadlift, in-line lunge, single-leg hop for distance and tuck jump. Each movement was scored out of 10 points and summed to produce a composite score out of 50. The anterior reach and single-leg hop for distance were scored in real-time while the remaining tests were filmed and scored retrospectively. Three raters conducted the SIMS with each participant on three occasions separated by an average of three and a half days (minimum one day, maximum seven days). Rater 1 re-scored the filmed movements for all participants on all occasions six months later to establish the 'pure' intra-rater (intra-occasion) reliability for those movements. Intraclass correlation coefficient (ICC) values for intra- and inter-rater composite score reliability ranged from 0.66-0.72 and 0.79-0.86 respectively. Weighted kappa values representing the intra- and inter-rater reliability of the individual sub-tests ranged from 0.35-0.91 indicating fair to almost perfect agreement. Establishing the reliability of the SIMS is a prerequisite for further research seeking to investigate

THE INTRA- AND INTER-RATER RELIABILITY OF THE SOCCER INJURY MOVEMENT SCREEN (SIMS)

PubMed Central

aus der Fünten, Karen; Govus, Andrew; Julian, Ross; Schimpchen, Jan; Meyer, Tim

2017-01-01

Background/purpose The growing volume of movement screening research reveals a belief among practitioners and researchers alike that movement quality may have an association with injury risk. However, existing movement screening tools have not considered the sport-specific movement and injury patterns relevant to soccer. The present study introduces the Soccer Injury Movement Screen (SIMS), which has been designed specifically for use within soccer. Furthermore, the purpose of the present study was to assess the intra- and inter-rater reliability of the SIMS and determine its suitability for use in further research. Methods The study utilized a test-retest design to discern reliablility. Twenty-five (11 males, 14 females) healthy, recreationally active university students (age 25.5 ± 4.0 years, height 171 ± 9 cm, weight 64.7 ± 12.6 kg) agreed to participate. The SIMS contains five sub-tests: the anterior reach, single-leg deadlift, in-line lunge, single-leg hop for distance and tuck jump. Each movement was scored out of 10 points and summed to produce a composite score out of 50. The anterior reach and single-leg hop for distance were scored in real-time while the remaining tests were filmed and scored retrospectively. Three raters conducted the SIMS with each participant on three occasions separated by an average of three and a half days (minimum one day, maximum seven days). Rater 1 re-scored the filmed movements for all participants on all occasions six months later to establish the ‘pure’ intra-rater (intra-occasion) reliability for those movements. Results Intraclass correlation coefficient (ICC) values for intra- and inter-rater composite score reliability ranged from 0.66-0.72 and 0.79-0.86 respectively. Weighted kappa values representing the intra- and inter-rater reliability of the individual sub-tests ranged from 0.35-0.91 indicating fair to almost perfect agreement. Conclusions Establishing the reliability of the SIMS is a

Molecular imaging of alkaloids in khat (Catha edulis) leaves with MeV-SIMS

NASA Astrophysics Data System (ADS)

Jenčič, Boštjan; Jeromel, Luka; Ogrinc Potočnik, Nina; Vogel-Mikuš, Katarina; Vavpetič, Primož; Rupnik, Zdravko; Bučar, Klemen; Vencelj, Matjaž; Kelemen, Mitja; Matsuo, Jiro; Kusakari, Masakazu; Siketić, Zdravko; Al-Jalali, Muhammad A.; Shaltout, Abdallah; Pelicon, Primož

2017-08-01

Imaging Mass Spectroscopy (IMS) is a unique research tool providing localization and identification of a wide range of biomolecules as essential data to understand biochemical processes in living organisms. Secondary Ion Mass Spectrometry with high-energy heavy ions (MeV-SIMS) is emerging as a promising IMS technique for chemical imaging of biological tissue. We measured the molecular mass spatial distributions in leaves of khat (Catha edulis). Khat is a natural drug plant, native to eastern Africa and the Arabian Peninsula. In these countries, fresh leaves are being chewed by significant part of population. It was reported that 80% of the adult population in Yemen chew the khat leaves. The main stimulating effects of khat are induced by a monoamine alkaloid called cathinone. During leaf ageing, cathinone is further metabolised to cathine and norephedrine. Earlier studies identified the alkaloids in khat, however little is known on their spatial distribution, reflecting the biosynthesis and accumulation in the tissue. Chemical mapping of alkaloids on cross-sections of khat leaves by MeV-SIMS was done at JSI by a pulsed 5.8 MeV 35Cl6+ beam, focused to a diameter of 15 μm, using a linear time-of-flight (TOF) spectrometer with a mass resolution of 500. In addition, measurements of MeV-SIMS mass spectra were performed at Kyoto University by a continuous broad beam of 6 MeV 63Cu4+ ions at an orthogonal TOF spectrometer with a high mass resolution of 11,000. Sections of leaves were analysed and mass spectra obtained at both MeV-SIMS setups were compared. Tissue-level distributions of detected alkaloids are presented and discussed.

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.

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

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.

The outlook of physician histories: J. Marion Sims and 'The Discovery of Anaesthesia'.

PubMed

Rosenbloom, Julia M; Schonberger, Robert B

2015-12-01

The fact that doctors have a long tradition of writing medical history to interpret and direct their profession is well established. But readers (particularly modern physician readers) can also understand physician-authored histories as offering commentary and analysis of the world beyond medicine. In this essay, we offer a reading (perhaps a modern one) of J. Marion Sims's 1877 article, 'The Discovery of Anaesthesia' which exemplifies the stance of looking both inward and outward from the medical field. We begin by discussing Sims, including the complicated legacy he left as a physician. Next, we review late 19th-century history with a focus on Reconstruction. Finally, we show how the modern reader can use Sims's article both to trace the first use of ether and nitrous oxide for surgical anaesthesia and to provide a window into the 19th-century medical profession and the post-Civil War period. Through this study, we hope to show how to read both medicine and the world around it in physician histories. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

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.

Development of nanotopography during SIMS characterization of thin films of Ge1-xSnx alloy

NASA Astrophysics Data System (ADS)

Secchi, M.; Demenev, E.; Colaux, J. L.; Giubertoni, D.; Dell'Anna, R.; Iacob, E.; Gwilliam, R. M.; Jeynes, C.; Bersani, M.

2015-11-01

This work presents a study of application of secondary ion mass spectrometry (SIMS) to measure tin concentration in Ge1-xSnx alloy with x higher than solid solubility ∼1%, i.e. well above the diluted regime where SIMS measurements usually provide the most reliable quantitative results. SIMS analysis was performed on Sn+ ion implanted Ge films, epitaxially deposited on Si, and on chemical vapor deposition deposited Ge0.93Sn0.07 alloy. Three SIMS conditions were investigated, varying primary beam ion species and secondary ion polarity keeping 1 keV impact energy. Best depth profile accuracy, best agreement with the fluences measured by Rutherford backscattering spectrometry, good detection limit (∼1 × 1017 at/cm3) and depth resolution (∼2 nm/decade) are achieved in Cs+/SnCs+ configuration. However, applied sputtering conditions (Cs+ 1 keV, 64° incidence vs. normal) induced an early formation of surface topography on the crater bottom resulting in significant variation of sputtering yield. Atomic force microscopy shows a peculiar topography developed on Ge: for oblique incidence, a topography consisting in a sequence of dots and ripples was observed on the crater bottom. This behavior is unusual for grazing incidence and has been observed to increase with the Cs+ fluence. Rotating sample during sputtering prevents this ripple formation and consequently improves the depth accuracy.

On the SIMS Ionization Probability of Organic Molecules.

PubMed

Popczun, Nicholas J; Breuer, Lars; Wucher, Andreas; Winograd, Nicholas

2017-06-01

The prospect of improved secondary ion yields for secondary ion mass spectrometry (SIMS) experiments drives innovation of new primary ion sources, instrumentation, and post-ionization techniques. The largest factor affecting secondary ion efficiency is believed to be the poor ionization probability (α + ) of sputtered material, a value rarely measured directly, but estimated to be in some cases as low as 10 -5 . Our lab has developed a method for the direct determination of α + in a SIMS experiment using laser post-ionization (LPI) to detect neutral molecular species in the sputtered plume for an organic compound. Here, we apply this method to coronene (C 24 H 12 ), a polyaromatic hydrocarbon that exhibits strong molecular signal during gas-phase photoionization. A two-dimensional spatial distribution of sputtered neutral molecules is measured and presented. It is shown that the ionization probability of molecular coronene desorbed from a clean film under bombardment with 40 keV C 60 cluster projectiles is of the order of 10 -3 , with some remaining uncertainty arising from laser-induced fragmentation and possible differences in the emission velocity distributions of neutral and ionized molecules. In general, this work establishes a method to estimate the ionization efficiency of molecular species sputtered during a single bombardment event. Graphical Abstract .

The Beginner's Guide to Wind Tunnels with TunnelSim and TunnelSys

NASA Technical Reports Server (NTRS)

Benson, Thomas J.; Galica, Carol A.; Vila, Anthony J.

2010-01-01

The Beginner's Guide to Wind Tunnels is a Web-based, on-line textbook that explains and demonstrates the history, physics, and mathematics involved with wind tunnels and wind tunnel testing. The Web site contains several interactive computer programs to demonstrate scientific principles. TunnelSim is an interactive, educational computer program that demonstrates basic wind tunnel design and operation. TunnelSim is a Java (Sun Microsystems Inc.) applet that solves the continuity and Bernoulli equations to determine the velocity and pressure throughout a tunnel design. TunnelSys is a group of Java applications that mimic wind tunnel testing techniques. Using TunnelSys, a team of students designs, tests, and post-processes the data for a virtual, low speed, and aircraft wing.

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.

Performance modeling codes for the QuakeSim problem solving environment

NASA Technical Reports Server (NTRS)

Parker, J. W.; Donnellan, A.; Lyzenga, G.; Rundle, J.; Tullis, T.

2003-01-01

The QuakeSim Problem Solving Environment uses a web-services approach to unify and deploy diverse remote data sources and processing services within a browser environment. Here we focus on the high-performance crustal modeling applications that will be included in this set of remote but interoperable applications.

Dissociating effects of stimulus identity and load on working memory attentional guidance: lengthening encoding time eliminates the effect of load but not identity.

PubMed

Tsvetanov, Kamen A; Arvanitis, Theodoros N; Humphreys, Glyn W

2012-01-01

Effects of the identity and load of items in working memory (WM) on visual attention were examined. With a short interval between the WM item and a subsequent search task, there were effects of both load (slowed overall reaction times, RTs, in a WM condition relative to a mere repetition baseline) and identity (search RTs were affected by re-presentation of the item in WM in the search display). As the time to encode the initial display increased, the effects of load decreased while the effect of identity remained. The data indicate that the identity of stimuli in WM can affect the subsequent deployment of attention even when time is allowed for consolidation of the stimuli in WM, and that the WM effects are not causally related to the presence of cognitive load. The results are consistent with the identity of stimuli in WM modulating attention post the memory consolidation stage.

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.

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

SimBOX: a scalable architecture for aggregate distributed command and control of spaceport and service constellation

NASA Astrophysics Data System (ADS)

Prasad, Guru; Jayaram, Sanjay; Ward, Jami; Gupta, Pankaj

2004-08-01

In this paper, Aximetric proposes a decentralized Command and Control (C2) architecture for a distributed control of a cluster of on-board health monitoring and software enabled control systems called SimBOX that will use some of the real-time infrastructure (RTI) functionality from the current military real-time simulation architecture. The uniqueness of the approach is to provide a "plug and play environment" for various system components that run at various data rates (Hz) and the ability to replicate or transfer C2 operations to various subsystems in a scalable manner. This is possible by providing a communication bus called "Distributed Shared Data Bus" and a distributed computing environment used to scale the control needs by providing a self-contained computing, data logging and control function module that can be rapidly reconfigured to perform different functions. This kind of software-enabled control is very much needed to meet the needs of future aerospace command and control functions.

Challenging Notions of Gendered Game Play: Teenagers Playing the Sims

ERIC Educational Resources Information Center

Beavis, Catherine; Charles, Claire

2005-01-01

This paper challenges notions of gendered game playing practice implicit in much research into young women's involvement with the computer gaming culture. It draws on a study of Australian teenagers playing "The Sims Deluxe" as part of an English curriculum unit and insights from feminist media studies to explore relationships between…

"SimChemistry" as an Active Learning Tool in Chemical Education

ERIC Educational Resources Information Center

Bolton, Kim; Saalman, Elisabeth; Christie, Michael; Ingerman, Ake; Linder, Cedric

2008-01-01

The publicly available free computer program, "SimChemistry," was used as an active learning tool in the chemical engineering curriculum at the University College of Boras, Sweden. The activity involved students writing their own simulation programs on topics in the area of molecular structure and interactions. Evaluation of the learning…

Final report on SIM Regional Key Comparison SIM.L-K1.2007: Calibration of gauge blocks by optical interferometry

NASA Astrophysics Data System (ADS)

Colín, C.; Viliesid, M.; Chaudhary, K. P.; Decker, J.; Dvorácek, F.; Franca, R.; Ilieff, S.; Rodríguez, J.; Stoup, J.

2012-01-01

This Key Comparison of gauge blocks (GB) calibration by optical interferometry was carried out to support this Calibration and Measurement Capability (CMC) of the National Measurement Institutes (NMI) from the SIM Region for this specific service and for those that rely on this kind of technique as required by the Mutual Recognition Arrangement (MRA). It provides evidence of the participant's technical competence and supports the uncertainties they state in their CMC. It is a Regional Key Comparison and should be linked to the upper level corresponding comparison CCL-K1. The comparison had nine participants, five from the SIM Region—NRC-CNRC, Canada; NIST, USA; CENAM, Mexico; INMETRO, Brazil; and INTI, Argentina— and four from other regions—CMI, Czech Rep.; CEM, Spain; NPLI, India; and NMISA South Africa. It included the circulation of fourteen GB—seven steel GB and seven ceramic GB. The circulation of the artifacts started on 2007-11-01 and ended on 2010-04-25. Some additional time was required to publish the results as the same artifacts were used thereafter for comparison SIM.L-S6, Calibration of GB by mechanical comparison, and the results could not be disclosed until the participants of the second circulation loop had sent their results. The final report of this comparison was sent out for review in May 2012 and the final version was approved in August 2012. The behavior of the artifacts throughout the circulation was good and therefore the results obtained were judged technically valid. The reference value was taken as arithmetic mean of the largest subset of consistent results. Most of participates obtained results in good agreement with the reference values with a few exceptions mentioned in the report. The corresponding NMIs are responsible for identifying the causes and taking corrective action. This makes the present comparison exercise valid to support the CMC claims of the participants in GB calibration by optical interferometry. Main text. To

Improved mass resolution and mass accuracy in TOF-SIMS spectra and images using argon gas cluster ion beams.

PubMed

Shon, Hyun Kyong; Yoon, Sohee; Moon, Jeong Hee; Lee, Tae Geol

2016-06-09

The popularity of argon gas cluster ion beams (Ar-GCIB) as primary ion beams in time-of-flight secondary ion mass spectrometry (TOF-SIMS) has increased because the molecular ions of large organic- and biomolecules can be detected with less damage to the sample surfaces. However, Ar-GCIB is limited by poor mass resolution as well as poor mass accuracy. The inferior quality of the mass resolution in a TOF-SIMS spectrum obtained by using Ar-GCIB compared to the one obtained by a bismuth liquid metal cluster ion beam and others makes it difficult to identify unknown peaks because of the mass interference from the neighboring peaks. However, in this study, the authors demonstrate improved mass resolution in TOF-SIMS using Ar-GCIB through the delayed extraction of secondary ions, a method typically used in TOF mass spectrometry to increase mass resolution. As for poor mass accuracy, although mass calibration using internal peaks with low mass such as hydrogen and carbon is a common approach in TOF-SIMS, it is unsuited to the present study because of the disappearance of the low-mass peaks in the delayed extraction mode. To resolve this issue, external mass calibration, another regularly used method in TOF-MS, was adapted to enhance mass accuracy in the spectrum and image generated by TOF-SIMS using Ar-GCIB in the delayed extraction mode. By producing spectra analyses of a peptide mixture and bovine serum albumin protein digested with trypsin, along with image analyses of rat brain samples, the authors demonstrate for the first time the enhancement of mass resolution and mass accuracy for the purpose of analyzing large biomolecules in TOF-SIMS using Ar-GCIB through the use of delayed extraction and external mass calibration.

Advantages of TOF-SIMS analysis of hydroxyapatite and fluorapatite in comparison with XRD, HR-TEM and FT-IR.

PubMed

Okazaki, Masayuki; Hirata, Isao; Matsumoto, Takuya; Takahashi, Junzo

2005-12-01

The chemical analysis of hydroxyapatite and fluorapatite was carried out using time-of-flight secondary ion mass spectrometry (TOF-SIMS). Hydroxyapatite and fluorapatite were synthesized at 80 +/- 1 degrees C and pH 7.4 +/- 0.2. Fluorapatite was better crystallized, with its (300) reflection shifted to a slightly higher angle. High-resolution transmission electron microscopy clearly revealed a typical, regular hexagonal cross section perpendicular to the c-axis for fluorapatite and a flattened hexagonal cross section for hydroxyapatite. FT-IR spectra of fluorapatite confirmed the absence of OH absorption peak--which was seen in hydroxyapatite at about 3570 cm(-1). TOF-SIMS mass spectra showed a peak at 40 amu due to calcium. In addition, a peak at 19 amu due to fluorine could be clearly seen, although the intensities of PO, PO2, and PO3 were very low. It was confirmed that TOF-SIMS clearly showed the differences between positive and negative mass spectra of hydroxyapatite and fluorapatite, especially for F-. We concluded that TOF-SIMS exhibited distinct advantages compared with other methods of analysis.

Altered self-identity and autobiographical memory in epilepsy.

PubMed

Allebone, James; Rayner, Genevieve; Siveges, Benjamin; Wilson, Sarah J

2015-12-01

Research suggests that individuals with chronic epilepsy display differences in their self-identity. The mechanisms by which self-identity is altered, however, are not well understood. Neural networks supporting autobiographical memory retrieval in the mesial temporal (MT) lobe are thought to be fundamental to self-identity processes. Thus, we examined differences in self-identity and autobiographical memory in patients with either MT or non-mesial temporal (NMT) foci with early or late age of habitual seizure onset. Participants included 102 adults: 51 healthy individuals and 51 patients with drug-resistant focal seizures (19 MT, 32 NMT). We used the Ego Identity Process Questionnaire to profile the identity development of participants, and examined how this related to memory function assessed using the Autobiographical Memory Test. Patients and controls had strikingly different self-identity profiles, with early onset MT patients showing the least identity development compared to controls and other patient groups. In contrast, late-onset NMT patients showed the highest level of identity development of the patient groups and closely resembled healthy controls (p < 0.05 for all comparisons). For all MT patients, poor autobiographical memory retrieval was correlated with altered self-identity (p < 0.001). No associations between autobiographical memory and self-identity were evident in the NMT group. Self-identity in epilepsy may be modulated by the extent to which seizure foci impinge on the autobiographical memory network and the timing of seizure onset. Early disruption to MT regions of the autobiographical memory network may constitute a neurocognitive mechanism by which self-identity is altered in chronic focal epilepsy. Wiley Periodicals, Inc. © 2015 International League Against Epilepsy.

A New Approach to Micro-arcsecond Astrometry with SIM Allowing Early Mission Narrow Angle Measurements of Compelling Astronomical Targets

NASA Technical Reports Server (NTRS)

Shaklan, Stuart; Pan, Xiaopei

2004-01-01

The Space Interferometry Mission (SIM) is capable of detecting and measuring the mass of terrestrial planets around stars other than our own. It can measure the mass of black holes and the visual orbits of radio and x-ray binary sources. SIM makes possible a new level of understanding of complex astrophysical processes. SIM achieves its high precision in the so-called narrow-angle regime. This is defined by a 1 degree diameter field in which the position of a target star is measured with respect to a set of reference stars. The observation is performed in two parts: first, SIM observes a grid of stars that spans the full sky. After a few years, repeated observations of the grid allow one to determine the orientation of the interferometer baseline. Second, throughout the mission, SIM periodically observes in the narrow-angle mode. Every narrow-angle observation is linked to the grid to determine the precise attitude and length of the baseline. The narrow angle process demands patience. It is not until five years after launch that SIM achieves its ultimate accuracy of 1 microarcsecond. The accuracy is degraded by a factor of approx. 2 at mid-mission. Our work proposes a technique for narrow angle astrometry that does not rely on the measurement of grid stars. This technique, called Gridless Narrow Angle Astrometry (GNAA) can obtain microarcsecond accuracy and can detect extra-solar planets and other exciting objects with a few days of observation. It can be applied as early as during the first six months of in-orbit calibration (IOC). The motivations for doing this are strong. First, and obviously, it is an insurance policy against a catastrophic mid-mission failure. Second, at the start of the mission, with several space-based interferometers in the planning or implementation phase, NASA will be eager to capture the public's imagination with interferometric science. Third, early results and a technique that can duplicate those results throughout the mission will

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

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

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

Action recognition is sensitive to the identity of the actor.

PubMed

Ferstl, Ylva; Bülthoff, Heinrich; de la Rosa, Stephan

2017-09-01

Recognizing who is carrying out an action is essential for successful human interaction. The cognitive mechanisms underlying this ability are little understood and have been subject of discussions in embodied approaches to action recognition. Here we examine one solution, that visual action recognition processes are at least partly sensitive to the actor's identity. We investigated the dependency between identity information and action related processes by testing the sensitivity of neural action recognition processes to clothing and facial identity information with a behavioral adaptation paradigm. Our results show that action adaptation effects are in fact modulated by both clothing information and the actor's facial identity. The finding demonstrates that neural processes underlying action recognition are sensitive to identity information (including facial identity) and thereby not exclusively tuned to actions. We suggest that such response properties are useful to help humans in knowing who carried out an action. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Opposite brain emotion-regulation patterns in identity states of dissociative identity disorder: a PET study and neurobiological model.

PubMed

Reinders, Antje A T S; Willemsen, Antoon T M; den Boer, Johan A; Vos, Herry P J; Veltman, Dick J; Loewenstein, Richard J

2014-09-30

Imaging studies in posttraumatic stress disorder (PTSD) have shown differing neural network patterns between hypo-aroused/dissociative and hyper-aroused subtypes. Since dissociative identity disorder (DID) involves different emotional states, this study tests whether DID fits aspects of the differing brain-activation patterns in PTSD. While brain activation was monitored using positron emission tomography, DID individuals (n=11) and matched DID-simulating healthy controls (n=16) underwent an autobiographic script-driven imagery paradigm in a hypo-aroused and a hyper-aroused identity state. Results were consistent with those previously found in the two PTSD subtypes for the rostral/dorsal anterior cingulate, the prefrontal cortex, and the amygdala and insula, respectively. Furthermore, the dissociative identity state uniquely activated the posterior association areas and the parahippocampal gyri, whereas the hyper-aroused identity state uniquely activated the caudate nucleus. Therefore, we proposed an extended PTSD-based neurobiological model for emotion modulation in DID: the hypo-aroused identity state activates the prefrontal cortex, cingulate, posterior association areas and parahippocampal gyri, thereby overmodulating emotion regulation; the hyper-aroused identity state activates the amygdala and insula as well as the dorsal striatum, thereby undermodulating emotion regulation. This confirms the notion that DID is related to PTSD as hypo-aroused and hyper-arousal states in DID and PTSD are similar. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

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…

Stone-age mass spectrometry: the beginnings of "SIMS" at RCA Laboratories, Princeton

NASA Astrophysics Data System (ADS)

Honig, Richard E.

1995-05-01

This paper takes you back almost half a century, to the time when mass spectrometry was young and exciting, and research was exploring new frontiers every day. Our early experiments called "sputtering of surfaces by positive ion beams", now known as "SIMS", were carried out with the simple, yet flexible instrumentation available at that time and produced many interesting results that are still valid today. Since commercial equipment did not exist in those days, just about everything had to be designed and constructed in-house - hardware as well as circuitry. Thus progress was slow, but occasional malfunctioning of a component could be readily rectified. It is gratifying to see how SIMS has developed in the interim from our early feasibility studies into a major research effort carried out worldwide in many laboratories.

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.

Investigation of the Ionization Mechanism of NAD+/NADH-Modified Gold Electrodes in ToF-SIMS Analysis.

PubMed

Hua, Xin; Zhao, Li-Jun; Long, Yi-Tao

2018-06-04

Analysis of nicotinamide adenine dinucleotide (NAD + /NADH)-modified electrodes is important for in vitro monitoring of key biological processes. In this work, time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used to analyze NAD + /NADH-modified gold electrodes. Interestingly, no obvious characteristic peaks of nicotinamide fragment could be observed in the mass spectra of NAD + /NADH in their neutral sodium pyrophosphate form. However, after acidification, the characteristic peaks for both NAD + and NADH were detected. This was due to the suppression effect of inner pyrophosphoric salts in both neutral molecules. Besides, it was proved that the suppression by inner salt was intramolecular. No obvious suppression was found between neighboring molecules. These results demonstrated the suppression effect of inner salts in ToF-SIMS analysis, providing useful evidence for the study of ToF-SIMS ionization mechanism of organic molecule-modified electrodes. Graphical Abstract ᅟ.

Image segmentation for uranium isotopic analysis by SIMS: Combined adaptive thresholding and marker controlled watershed approach

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

Willingham, David G.; Naes, Benjamin E.; Heasler, Patrick G.

A novel approach to particle identification and particle isotope ratio determination has been developed for nuclear safeguard applications. This particle search approach combines an adaptive thresholding algorithm and marker-controlled watershed segmentation (MCWS) transform, which improves the secondary ion mass spectrometry (SIMS) isotopic analysis of uranium containing particle populations for nuclear safeguards applications. The Niblack assisted MCWS approach (a.k.a. SEEKER) developed for this work has improved the identification of isotopically unique uranium particles under conditions that have historically presented significant challenges for SIMS image data processing techniques. Particles obtained from five NIST uranium certified reference materials (CRM U129A, U015, U150, U500more » and U850) were successfully identified in regions of SIMS image data 1) where a high variability in image intensity existed, 2) where particles were touching or were in close proximity to one another and/or 3) where the magnitude of ion signal for a given region was count limited. Analysis of the isotopic distributions of uranium containing particles identified by SEEKER showed four distinct, accurately identified 235U enrichment distributions, corresponding to the NIST certified 235U/238U isotope ratios for CRM U129A/U015 (not statistically differentiated), U150, U500 and U850. Additionally, comparison of the minor uranium isotope (234U, 235U and 236U) atom percent values verified that, even in the absence of high precision isotope ratio measurements, SEEKER could be used to segment isotopically unique uranium particles from SIMS image data. Although demonstrated specifically for SIMS analysis of uranium containing particles for nuclear safeguards, SEEKER has application in addressing a broad set of image processing challenges.« less

Photovoltaic module and module arrays

DOEpatents

Botkin, Jonathan; Graves, Simon; Lenox, Carl J. S.; Culligan, Matthew; Danning, Matt

2013-08-27

A photovoltaic (PV) module including a PV device and a frame, The PV device has a PV laminate defining a perimeter and a major plane. The frame is assembled to and encases the laminate perimeter, and includes leading, trailing, and side frame members, and an arm that forms a support face opposite the laminate. The support face is adapted for placement against a horizontal installation surface, to support and orient the laminate in a non-parallel or tilted arrangement. Upon final assembly, the laminate and the frame combine to define a unitary structure. The frame can orient the laminate at an angle in the range of 3.degree.-7.degree. from horizontal, and can be entirely formed of a polymeric material. Optionally, the arm incorporates integral feature(s) that facilitate interconnection with corresponding features of a second, identically formed PV module.

Photovoltaic module and module arrays

DOEpatents

Botkin, Jonathan [El Cerrito, CA; Graves, Simon [Berkeley, CA; Lenox, Carl J. S. [Oakland, CA; Culligan, Matthew [Berkeley, CA; Danning, Matt [Oakland, CA

2012-07-17

A photovoltaic (PV) module including a PV device and a frame. The PV device has a PV laminate defining a perimeter and a major plane. The frame is assembled to and encases the laminate perimeter, and includes leading, trailing, and side frame members, and an arm that forms a support face opposite the laminate. The support face is adapted for placement against a horizontal installation surface, to support and orient the laminate in a non-parallel or tilted arrangement. Upon final assembly, the laminate and the frame combine to define a unitary structure. The frame can orient the laminate at an angle in the range of 3.degree.-7.degree. from horizontal, and can be entirely formed of a polymeric material. Optionally, the arm incorporates integral feature(s) that facilitate interconnection with corresponding features of a second, identically formed PV module.

In silico predictions of gastrointestinal drug absorption in pharmaceutical product development: application of the mechanistic absorption model GI-Sim.

PubMed

Sjögren, Erik; Westergren, Jan; Grant, Iain; Hanisch, Gunilla; Lindfors, Lennart; Lennernäs, Hans; Abrahamsson, Bertil; Tannergren, Christer

2013-07-16

Oral drug delivery is the predominant administration route for a major part of the pharmaceutical products used worldwide. Further understanding and improvement of gastrointestinal drug absorption predictions is currently a highly prioritized area of research within the pharmaceutical industry. The fraction absorbed (fabs) of an oral dose after administration of a solid dosage form is a key parameter in the estimation of the in vivo performance of an orally administrated drug formulation. This study discloses an evaluation of the predictive performance of the mechanistic physiologically based absorption model GI-Sim. GI-Sim deploys a compartmental gastrointestinal absorption and transit model as well as algorithms describing permeability, dissolution rate, salt effects, partitioning into micelles, particle and micelle drifting in the aqueous boundary layer, particle growth and amorphous or crystalline precipitation. Twelve APIs with reported or expected absorption limitations in humans, due to permeability, dissolution and/or solubility, were investigated. Predictions of the intestinal absorption for different doses and formulations were performed based on physicochemical and biopharmaceutical properties, such as solubility in buffer and simulated intestinal fluid, molecular weight, pK(a), diffusivity and molecule density, measured or estimated human effective permeability and particle size distribution. The performance of GI-Sim was evaluated by comparing predicted plasma concentration-time profiles along with oral pharmacokinetic parameters originating from clinical studies in healthy individuals. The capability of GI-Sim to correctly predict impact of dose and particle size as well as the in vivo performance of nanoformulations was also investigated. The overall predictive performance of GI-Sim was good as >95% of the predicted pharmacokinetic parameters (C(max) and AUC) were within a 2-fold deviation from the clinical observations and the predicted plasma AUC

Preparation of Authigenic Pyrite from Methane-bearing Sediments for In Situ Sulfur Isotope Analysis Using SIMS.

PubMed

Lin, Zhiyong; Sun, Xiaoming; Peckmann, Jörn; Lu, Yang; Strauss, Harald; Xu, Li; Lu, Hongfeng; Teichert, Barbara M A

2017-08-31

Different sulfur isotope compositions of authigenic pyrite typically result from the sulfate-driven anaerobic oxidation of methane (SO4-AOM) and organiclastic sulfate reduction (OSR) in marine sediments. However, unravelling the complex pyritization sequence is a challenge because of the coexistence of different sequentially formed pyrite phases. This manuscript describes a sample preparation procedure that enables the use of secondary ion mass spectroscopy (SIMS) to obtain in situ δ 34 S values of various pyrite generations. This allows researchers to constrain how SO4-AOM affects pyritization in methane-bearing sediments. SIMS analysis revealed an extreme range in δ 34 S values, spanning from -41.6 to +114.8‰, which is much wider than the range of δ 34 S values obtained by the traditional bulk sulfur isotope analysis of the same samples. Pyrite in the shallow sediment mainly consists of 34 S-depleted framboids, suggesting early diagenetic formation by OSR. Deeper in the sediment, more pyrite occurs as overgrowths and euhedral crystals, which display much higher SIMS δ 34 S values than the framboids. Such 34 S-enriched pyrite is related to enhanced SO4-AOM at the sulfate-methane transition zone, postdating OSR. High-resolution in situ SIMS sulfur isotope analyses allow for the reconstruction of the pyritization processes, which cannot be resolved by bulk sulfur isotope analysis.

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.

Precision Linear Actuator for Space Interferometry Mission (SIM) Siderostat Pointing

NASA Technical Reports Server (NTRS)

Cook, Brant; Braun, David; Hankins, Steve; Koenig, John; Moore, Don

2008-01-01

'SIM PlanetQuest will exploit the classical measuring tool of astrometry (interferometry) with unprecedented precision to make dramatic advances in many areas of astronomy and astrophysics'(1). In order to obtain interferometric data two large steerable mirrors, or Siderostats, are used to direct starlight into the interferometer. A gimbaled mechanism actuated by linear actuators is chosen to meet the unprecedented pointing and angle tracking requirements of SIM. A group of JPL engineers designed, built, and tested a linear ballscrew actuator capable of performing submicron incremental steps for 10 years of continuous operation. Precise, zero backlash, closed loop pointing control requirements, lead the team to implement a ballscrew actuator with a direct drive DC motor and a precision piezo brake. Motor control commutation using feedback from a precision linear encoder on the ballscrew output produced an unexpected incremental step size of 20 nm over a range of 120 mm, yielding a dynamic range of 6,000,000:1. The results prove linear nanometer positioning requires no gears, levers, or hydraulic converters. Along the way many lessons have been learned and will subsequently be shared.

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

ToF-SIMS Parallel Imaging MS/MS of Lipid Species in Thin Tissue Sections.

PubMed

Bruinen, Anne Lisa; Fisher, Gregory L; Heeren, Ron M A

2017-01-01

Unambiguous identification of detected species is essential in complex biomedical samples. To date, there are not many mass spectrometry imaging techniques that can provide both high spatial resolution and identification capabilities. A new and patented imaging tandem mass spectrometer, exploiting the unique characteristics of the nanoTOF II (Physical Electronics, USA) TOF-SIMS TRIFT instrument, was developed to address this.Tandem mass spectrometry is based on the selection of precursor ions from the full secondary ion spectrum (MS 1 ), followed by energetic activation and fragmentation, and collection of the fragment ions to obtain a tandem MS spectrum (MS 2 ). The PHI NanoTOF II mass spectrometer is equipped with a high-energy collision induced dissociation (CID) fragmentation cell as well as a second time-of-flight analyzer developed for simultaneous ToF-SIMS and tandem MS imaging experiments.We describe here the results of a ToF-SIMS imaging experiment on a thin tissue section of an infected zebrafish as a model organism for tuberculosis. The focus is on the obtained ion distribution plot of a fatty acid as well as its identification by tandem mass spectrometry.

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.

Final report of the SIM.QM-S8 supplementary comparison, trace metals in drinking water

NASA Astrophysics Data System (ADS)

Yang, Lu; Nadeau, Kenny; Gedara Pihillagawa, Indu; Meija, Juris; Mester, Zoltan; Napoli, Romina; Pérez Zambra, Ramiro; Ferreira, Elizabeth; Alejandro Ahumada Forigua, Diego; Abella Gamba, Johanna Paola

2018-01-01

After completing a supplementary comparison SIM.QM-S7, the National Metrology Institute of Colombia (NMIC) requested to National Research Council of Canada (NRC) a subsequent bilateral comparison, because INMC considered that its results in SIM.QM-S7 unrepresentative of its standards. In this context, NRC agreed to coordinate this bilateral comparison with the aim of demonstrating the measurement capabilities of trace elements in fresh water. Participants included NMIC and LATU. No measurement method was prescribed by the coordinating laboratory. Therefore, NMIs used measurement methods of their choice. However, the majority of NMIs/DIs used ICP-MS. This SIM.QM-S8 Supplementary Comparison provides NMIs with the needed evidence for CMC claims for trace elements in fresh waters and similar matrices. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

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.

Meso-scale anisotropic hydrogen segregation near grain-boundaries in polycrystalline nickel characterized by EBSD/SIMS

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

Oudriss, A.; Le Guernic, Solenne; Wang, Zhaoying

2016-02-15

To study anisotropic hydrogen segregation and diffusion in nickel polycrystalline, Secondary Ion Mass Spectrometry (SIMS) and Electron Back Scattered Diffraction (EBSD) are integrated to investigate hydrogen distribution around grain boundaries. Hydrogen distribution in pre-charged samples were correlated with grain boundary character by integrating high-resolution grain microstructure from EBSD inverse pole figure map and low-resolution hydrogen concentration profile map from SIMS. This multimodal imaging instrumentation shows that grain boundaries in nickel can be categorized into two families based on behavior of hydrogen distribution crossing grain boundary: the first one includes random grain boundaries with fast hydrogen diffusivity, showing a sharp gapmore » for hydrogen concentration profile cross the grain boundaries. The second family are special Σ3n grain boundaries with low hydrogen diffusivity, showing a smooth gradient of hydrogen concentration cross the grain boundary. Heterogeneous hydrogen distributions due to grain boundary family revealed by SIMS/EBSD on mesoscale further validate the recent hydrogen permeation data and anisotropic ab-initio calculations in nanoscale. The results highlight the fact that grain boundaries character impacts hydrogen distribution significantly.« less

SimBox: a simulation-based scalable architecture for distributed command and control of spaceport and service constellations

NASA Astrophysics Data System (ADS)

Prasad, Guru; Jayaram, Sanjay; Ward, Jami; Gupta, Pankaj

2004-09-01

In this paper, Aximetric proposes a decentralized Command and Control (C2) architecture for a distributed control of a cluster of on-board health monitoring and software enabled control systems called SimBOX that will use some of the real-time infrastructure (RTI) functionality from the current military real-time simulation architecture. The uniqueness of the approach is to provide a "plug and play environment" for various system components that run at various data rates (Hz) and the ability to replicate or transfer C2 operations to various subsystems in a scalable manner. This is possible by providing a communication bus called "Distributed Shared Data Bus" and a distributed computing environment used to scale the control needs by providing a self-contained computing, data logging and control function module that can be rapidly reconfigured to perform different functions. This kind of software-enabled control is very much needed to meet the needs of future aerospace command and control functions.

Comparison on the calibrations of hydrometers for liquids density determination between SIM laboratories

NASA Astrophysics Data System (ADS)

Morales, Abed; Quiroga, Aldo; Daued, Arturo; Cantero, Diana; Sequeira, Francisco; Castro, Luis Carlos; Becerra, Luis Omar; Salazar, Manuel; Vega, Maria

2017-01-01

A supplementary comparison was made between SIM laboratories concerning the calibration of four hydrometers within the range of 600 kg/m3 to 2000 kg/m3. The main objectives of the comparison were to evaluate the degree of equivalences SIM NMIs in the calibration of hydrometers of high accuracy. The participant NMIs were: CENAM, IBMETRO, INEN, INDECOPI, INM, INTN and LACOMET. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

An unsupervised MVA method to compare specific regions in human breast tumor tissue samples using ToF-SIMS.

PubMed

Bluestein, Blake M; Morrish, Fionnuala; Graham, Daniel J; Guenthoer, Jamie; Hockenbery, David; Porter, Peggy L; Gamble, Lara J

2016-03-21

Imaging time-of-flight secondary ion mass spectrometry (ToF-SIMS) and principal component analysis (PCA) were used to investigate two sets of pre- and post-chemotherapy human breast tumor tissue sections to characterize lipids associated with tumor metabolic flexibility and response to treatment. The micron spatial resolution imaging capability of ToF-SIMS provides a powerful approach to attain spatially-resolved molecular and cellular data from cancerous tissues not available with conventional imaging techniques. Three ca. 1 mm(2) areas per tissue section were analyzed by stitching together 200 μm × 200 μm raster area scans. A method to isolate and analyze specific tissue regions of interest by utilizing PCA of ToF-SIMS images is presented, which allowed separation of cellularized areas from stromal areas. These PCA-generated regions of interest were then used as masks to reconstruct representative spectra from specifically stromal or cellular regions. The advantage of this unsupervised selection method is a reduction in scatter in the spectral PCA results when compared to analyzing all tissue areas or analyzing areas highlighted by a pathologist. Utilizing this method, stromal and cellular regions of breast tissue biopsies taken pre- versus post-chemotherapy demonstrate chemical separation using negatively-charged ion species. In this sample set, the cellular regions were predominantly all cancer cells. Fatty acids (i.e. palmitic, oleic, and stearic), monoacylglycerols, diacylglycerols and vitamin E profiles were distinctively different between the pre- and post-therapy tissues. These results validate a new unsupervised method to isolate and interpret biochemically distinct regions in cancer tissues using imaging ToF-SIMS data. In addition, the method developed here can provide a framework to compare a variety of tissue samples using imaging ToF-SIMS, especially where there is section-to-section variability that makes it difficult to use a serial hematoxylin

A comparative ToF-SIMS and GC—MS analysis of phototrophic communities collected from an alkaline silica-depositing hot spring

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

Siljestrom, S.; Parenteau, M. N.; Jahnke, L. L.

One of few techniques that is able to spatially resolve chemical data, including organic molecules, to morphological features in modern and ancient geological samples, is time-of-flight secondary ion mass spectrometry (ToF-SIMS). The ability to connect chemical data to morphology is key for interpreting the biogenicity of preserved remains in ancient samples. However, due to the lack of reference data for geologically relevant samples and the ease with which samples can be contaminated, ToF-SIMS data may be difficult to interpret. In this project, we aimed to build a ToF-SIMS spectral database by performing parallel ToF-SIMS and gas chromatography–mass spectrometry (GC–MS) analysesmore » of extant photosynthetic microbial communities collected from an alkaline silica-depositing hot spring in Yellowstone National Park, USA. We built the library by analyzing samples of increasing complexity: pure lipid standards commonly found in thermophilic phototrophs, solvent extracts of specific lipid fractions, total lipid extracts, pure cultures of dominant phototrophic community members, and unsilicified phototrophic streamer communities. The results showed that important lipids and pigments originating from phototrophs were detected by ToF-SIMS (e.g., wax esters, monogalactosyldiacylglycerol, digalactosyldiacylglycerol, sufloquinovosyldiaglycerol, alkanes, etc.) in the streamer lipid extracts. Many of the lipids were also detected in situ in the unsilicified streamer, and could even be spatially resolved to individual cells within the streamer community. Together with the ToF-SIMS database, this mapping ability will be used to further explore other microbial mats and their fossilized counterparts in the geological record. This is likely to expand the geochemical understanding of these types of samples.« less

A comparative ToF-SIMS and GC—MS analysis of phototrophic communities collected from an alkaline silica-depositing hot spring

DOE PAGES

Siljestrom, S.; Parenteau, M. N.; Jahnke, L. L.; ...

2017-04-03

One of few techniques that is able to spatially resolve chemical data, including organic molecules, to morphological features in modern and ancient geological samples, is time-of-flight secondary ion mass spectrometry (ToF-SIMS). The ability to connect chemical data to morphology is key for interpreting the biogenicity of preserved remains in ancient samples. However, due to the lack of reference data for geologically relevant samples and the ease with which samples can be contaminated, ToF-SIMS data may be difficult to interpret. In this project, we aimed to build a ToF-SIMS spectral database by performing parallel ToF-SIMS and gas chromatography–mass spectrometry (GC–MS) analysesmore » of extant photosynthetic microbial communities collected from an alkaline silica-depositing hot spring in Yellowstone National Park, USA. We built the library by analyzing samples of increasing complexity: pure lipid standards commonly found in thermophilic phototrophs, solvent extracts of specific lipid fractions, total lipid extracts, pure cultures of dominant phototrophic community members, and unsilicified phototrophic streamer communities. The results showed that important lipids and pigments originating from phototrophs were detected by ToF-SIMS (e.g., wax esters, monogalactosyldiacylglycerol, digalactosyldiacylglycerol, sufloquinovosyldiaglycerol, alkanes, etc.) in the streamer lipid extracts. Many of the lipids were also detected in situ in the unsilicified streamer, and could even be spatially resolved to individual cells within the streamer community. Together with the ToF-SIMS database, this mapping ability will be used to further explore other microbial mats and their fossilized counterparts in the geological record. This is likely to expand the geochemical understanding of these types of samples.« less

A comparative ToF-SIMS and GC–MS analysis of phototrophic communities collected from an alkaline silica-depositing hot spring

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

Siljeström, S.; Parenteau, M. N.; Jahnke, L. L.

One of few techniques that is able to spatially resolve chemical data, including organic molecules, to morphological features in modern and ancient geological samples, is time-of-flight secondary ion mass spectrometry (ToF-SIMS). The ability to connect chemical data to morphology is key for interpreting the biogenicity of preserved remains in ancient samples. However, due to the lack of reference data for geologically relevant samples and the ease with which samples can be contaminated, ToF-SIMS data may be difficult to interpret. In this project, we aimed to build a ToF-SIMS spectral database by performing parallel ToF-SIMS and gas chromatography–mass spectrometry (GC–MS) analysesmore » of extant photosynthetic microbial communities collected from an alkaline silica-depositing hot spring in Yellowstone National Park, USA. We built the library by analyzing samples of increasing complexity: pure lipid standards commonly found in thermophilic phototrophs, solvent extracts of specific lipid fractions, total lipid extracts, pure cultures of dominant phototrophic community members, and unsilicified phototrophic streamer communities. The results showed that important lipids and pigments originating from phototrophs were detected by ToF-SIMS (e.g., wax esters, monogalactosyldiacylglycerol, digalactosyldiacylglycerol, sufloquinovosyldiaglycerol, alkanes, etc.) in the streamer lipid extracts. Many of the lipids were also detected in situ in the unsilicified streamer, and could even be spatially resolved to individual cells within the streamer community. Together with the ToF-SIMS database, this mapping ability will be used to further explore other microbial mats and their fossilized counterparts in the geological record. This is likely to expand the geochemical understanding of these types of samples.« less

SIMS chemical and isotopic analysis of impact features from LDEF experiments AO187-1 and AO187-2

NASA Technical Reports Server (NTRS)

Stadermann, Frank J.; Amari, Sachiko; Foote, John; Swan, Pat; Walker, Robert M.; Zinner, Ernst

1995-01-01

Previous secondary ion mass spectrometry (SIMS) studies of extended impact features from LDEF capture cell experiment AO187-2 showed that it is possible to distinguish natural and man-made particle impacts based on the chemical composition of projectile residues. The same measurement technique has now been applied to specially prepared gold target impacts from experiment AO187-1 in order to identify the origins of projectiles that left deposits too thin to be analyzed by conventional energy-dispersive x-ray (EDX) spectroscopy. The results indicate that SIMS may be the method of choice for the analysis of impact deposits on a variety of sample surfaces. SIMS was also used to determine the isotopic compositions of impact residues from several natural projectiles. Within the precision of the measurements all analyzed residues show isotopically normal compositions.

Thin film characterization by laser interferometry combined with SIMS

NASA Astrophysics Data System (ADS)

Kempf, J.; Nonnenmacher, M.; Wagner, H. H.

1988-10-01

Thin film properties of technologically important materials (Si, GaAs, SiO2, WSix) have been measured by using a novel technique that combines secondary ion mass spectrometry (SIMS) and laser interferometry. The simultaneous measurement of optical phase and reflectance as well as SIMS species during ion sputtering yielded optical constants, sputtering rates and composition of thin films with high depth resolution. A model based on the principle of multiple reflection within a multilayer structure, which considered also transformation of the film composition in depth and time during sputtering, was fitted to the reflectance and phase data. This model was applied to reveal the transformation of silicon by sputtering with O{2/+} ions. Special attention was paid to the preequilibrium phase of the sputter process (amorphization, oxidation, and volume expansion). To demonstrate the analytical potential of our method the multilayer system WSix/poly-Si/SiO2/Si was investigated. The physical parameters and the stoichiometry of tungsten suicide were determined for annealed as well as deposited films. A highly sensitive technique that makes use of a Fabry-Perot etalon integrated with a Michelson type interferometer is proposed. This two-stage interferometer has the potential to profile a sample surface with subangstroem resolution.

Low loss poly-silicon for high performance capacitive silicon modulators.

PubMed

Douix, Maurin; Baudot, Charles; Marris-Morini, Delphine; Valéry, Alexia; Fowler, Daivid; Acosta-Alba, Pablo; Kerdilès, Sébastien; Euvrard, Catherine; Blanc, Romuald; Beneyton, Rémi; Souhaité, Aurélie; Crémer, Sébastien; Vulliet, Nathalie; Vivien, Laurent; Boeuf, Frédéric

2018-03-05

Optical properties of poly-silicon material are investigated to be integrated in new silicon photonics devices, such as capacitive modulators. Test structure fabrication is done on 300 mm wafer using LPCVD deposition: 300 nm thick amorphous silicon layers are deposited on thermal oxide, followed by solid phase crystallization anneal. Rib waveguides are fabricated and optical propagation losses measured at 1.31 µm. Physical analysis (TEM ASTAR, AFM and SIMS) are used to assess the origin of losses. Optimal deposition and annealing conditions have been defined, resulting in 400 nm-wide rib waveguides with only 9.2-10 dB/cm losses.

An investigation on the mechanism of sublimed DHB matrix on molecular ion yields in SIMS imaging of brain tissue.

PubMed

Dowlatshahi Pour, Masoumeh; Malmberg, Per; Ewing, Andrew

2016-05-01

We have characterized the use of sublimation to deposit matrix-assisted laser desorption/ionization (MALDI) matrices in secondary ion mass spectrometry (SIMS) analysis, i.e. matrix-enhanced SIMS (ME-SIMS), a common surface modification method to enhance sensitivity for larger molecules and to increase the production of intact molecular ions. We use sublimation to apply a thin layer of a conventional MALDI matrix, 2,5-dihydroxybenzoic acid (DHB), onto rat brain cerebellum tissue to show how this technique can be used to enhance molecular yields in SIMS while still retaining a lateral resolution around 2 μm and also to investigate the mechanism of this enhancement. The results here illustrate that cholesterol, which is a dominant lipid species in the brain, is decreased on the tissue surface after deposition of matrix, particularly in white matter. The decrease of cholesterol is followed by an increased ion yield of several other lipid species. Depth profiling of the sublimed rat brain reveals that the lipid species are de facto extracted by the DHB matrix and concentrated in the top most layers of the sublimed matrix. This extraction/concentration of lipids directly leads to an increase of higher mass lipid ion yield. It is also possible that the decrease of cholesterol decreases the potential suppression of ion yield caused by cholesterol migration to the tissue surface. This result provides us with significant insights into the possible mechanisms involved when using sublimation to deposit this matrix in ME-SIMS.

Assimilation of ASCAT near-surface soil moisture into the SIM hydrological model over France

NASA Astrophysics Data System (ADS)

Draper, C.; Mahfouf, J.-F.; Calvet, J.-C.; Martin, E.; Wagner, W.

2011-12-01

This study examines whether the assimilation of remotely sensed near-surface soil moisture observations might benefit an operational hydrological model, specifically Météo-France's SAFRAN-ISBA-MODCOU (SIM) model. Soil moisture data derived from ASCAT backscatter observations are assimilated into SIM using a Simplified Extended Kalman Filter (SEKF) over 3.5 years. The benefit of the assimilation is tested by comparison to a delayed cut-off version of SIM, in which the land surface is forced with more accurate atmospheric analyses, due to the availability of additional atmospheric observations after the near-real time data cut-off. However, comparing the near-real time and delayed cut-off SIM models revealed that the main difference between them is a dry bias in the near-real time precipitation forcing, which resulted in a dry bias in the root-zone soil moisture and associated surface moisture flux forecasts. While assimilating the ASCAT data did reduce the root-zone soil moisture dry bias (by nearly 50%), this was more likely due to a bias within the SEKF, than due to the assimilation having accurately responded to the precipitation errors. Several improvements to the assimilation are identified to address this, and a bias-aware strategy is suggested for explicitly correcting the model bias. However, in this experiment the moisture added by the SEKF was quickly lost from the model surface due to the enhanced surface fluxes (particularly drainage) induced by the wetter soil moisture states. Consequently, by the end of each winter, during which frozen conditions prevent the ASCAT data from being assimilated, the model land surface had returned to its original (dry-biased) climate. This highlights that it would be more effective to address the precipitation bias directly, than to correct it by constraining the model soil moisture through data assimilation.

Enhanced subcarrier-index modulation-based asymmetrically clipped optical OFDM using even subcarriers

NASA Astrophysics Data System (ADS)

Guan, Rui; Xu, Wei; Yang, Zhaohui; Huang, Nuo; Wang, Jin-Yuan; Chen, Ming

2017-11-01

In this paper, we propose a subcarrier-index modulation-based asymmetrically clipped optical orthogonal frequency division multiplexing (SACO-OFDM) scheme for optical wireless communication (OWC) systems, which benefits from the subcarrier-index modulation (SIM) and asymmetrically clipped optical orthogonal frequency division multiplexing (ACO-OFDM) techniques. SACO-OFDM conveys additional information via the subcarrier indexing, and the error rate of the bit transmitted by the subcarrier indexing is much lower than that of the conventional M-ary modulation scheme. On the other hand, as the signal constellation in M-ary modulation is relieved, SACO-OFDM has simple transceiver structure and low detection complexity. Moreover, considering the spectral, an enhanced SACO-OFDM (ESACO-OFDM) using even subcarriers is proposed. In this technique, the odd subcarriers are activated for SACO-OFDM, and the imaginary part of even subcarriers are activated for pulse-amplitude-modulated discrete multitone (PAM-DMT). Clearly, ESACO-OFDM achieves better spectral efficiency than the conventional optical OFDM, since all subcarriers are used for data transmission. Simulation results verify the significant bit error rate (BER) and peak-to-average power ratio (PAPR) improvement by the proposed ESACO-OFDM, especially for the medium-to-high signal-to-noise ratio (SNR) regime.

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.

nmsBuilder: Freeware to create subject-specific musculoskeletal models for OpenSim.

PubMed

Valente, Giordano; Crimi, Gianluigi; Vanella, Nicola; Schileo, Enrico; Taddei, Fulvia

2017-12-01

Musculoskeletal modeling and simulations of movement have been increasingly used in orthopedic and neurological scenarios, with increased attention to subject-specific applications. In general, musculoskeletal modeling applications have been facilitated by the development of dedicated software tools; however, subject-specific studies have been limited also by time-consuming modeling workflows and high skilled expertise required. In addition, no reference tools exist to standardize the process of musculoskeletal model creation and make it more efficient. Here we present a freely available software application, nmsBuilder 2.0, to create musculoskeletal models in the file format of OpenSim, a widely-used open-source platform for musculoskeletal modeling and simulation. nmsBuilder 2.0 is the result of a major refactoring of a previous implementation that moved a first step toward an efficient workflow for subject-specific model creation. nmsBuilder includes a graphical user interface that provides access to all functionalities, based on a framework for computer-aided medicine written in C++. The operations implemented can be used in a workflow to create OpenSim musculoskeletal models from 3D surfaces. A first step includes data processing to create supporting objects necessary to create models, e.g. surfaces, anatomical landmarks, reference systems; and a second step includes the creation of OpenSim objects, e.g. bodies, joints, muscles, and the corresponding model. We present a case study using nmsBuilder 2.0: the creation of an MRI-based musculoskeletal model of the lower limb. The model included four rigid bodies, five degrees of freedom and 43 musculotendon actuators, and was created from 3D surfaces of the segmented images of a healthy subject through the modeling workflow implemented in the software application. We have presented nmsBuilder 2.0 for the creation of musculoskeletal OpenSim models from image-based data, and made it freely available via nmsbuilder

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

Monte Carlo code G3sim for simulation of plastic scintillator detectors with wavelength shifter fiber readout.

PubMed

Mohanty, P K; Dugad, S R; Gupta, S K

2012-04-01

A detailed description of a compact Monte Carlo simulation code "G3sim" for studying the performance of a plastic scintillator detector with wavelength shifter (WLS) fiber readout is presented. G3sim was developed for optimizing the design of new scintillator detectors used in the GRAPES-3 extensive air shower experiment. Propagation of the blue photons produced by the passage of relativistic charged particles in the scintillator is treated by incorporating the absorption, total internal, and diffuse reflections. Capture of blue photons by the WLS fibers and subsequent re-emission of longer wavelength green photons is appropriately treated. The trapping and propagation of green photons inside the WLS fiber is treated using the laws of optics for meridional and skew rays. Propagation time of each photon is taken into account for the generation of the electrical signal at the photomultiplier. A comparison of the results from G3sim with the performance of a prototype scintillator detector showed an excellent agreement between the simulated and measured properties. The simulation results can be parametrized in terms of exponential functions providing a deeper insight into the functioning of these versatile detectors. G3sim can be used to aid the design and optimize the performance of scintillator detectors prior to actual fabrication that may result in a considerable saving of time, labor, and money spent. © 2012 American Institute of Physics

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

FluoroSim: A Visual Problem-Solving Environment for Fluorescence Microscopy

PubMed Central

Quammen, Cory W.; Richardson, Alvin C.; Haase, Julian; Harrison, Benjamin D.; Taylor, Russell M.; Bloom, Kerry S.

2010-01-01

Fluorescence microscopy provides a powerful method for localization of structures in biological specimens. However, aspects of the image formation process such as noise and blur from the microscope's point-spread function combine to produce an unintuitive image transformation on the true structure of the fluorescing molecules in the specimen, hindering qualitative and quantitative analysis of even simple structures in unprocessed images. We introduce FluoroSim, an interactive fluorescence microscope simulator that can be used to train scientists who use fluorescence microscopy to understand the artifacts that arise from the image formation process, to determine the appropriateness of fluorescence microscopy as an imaging modality in an experiment, and to test and refine hypotheses of model specimens by comparing the output of the simulator to experimental data. FluoroSim renders synthetic fluorescence images from arbitrary geometric models represented as triangle meshes. We describe three rendering algorithms on graphics processing units for computing the convolution of the specimen model with a microscope's point-spread function and report on their performance. We also discuss several cases where the microscope simulator has been used to solve real problems in biology. PMID:20431698

MuSim, a Graphical User Interface for Multiple Simulation Programs

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

Roberts, Thomas; Cummings, Mary Anne; Johnson, Rolland

2016-06-01

MuSim is a new user-friendly program designed to interface to many different particle simulation codes, regardless of their data formats or geometry descriptions. It presents the user with a compelling graphical user interface that includes a flexible 3-D view of the simulated world plus powerful editing and drag-and-drop capabilities. All aspects of the design can be parametrized so that parameter scans and optimizations are easy. It is simple to create plots and display events in the 3-D viewer (with a slider to vary the transparency of solids), allowing for an effortless comparison of different simulation codes. Simulation codes: G4beamline, MAD-X,more » and MCNP; more coming. Many accelerator design tools and beam optics codes were written long ago, with primitive user interfaces by today's standards. MuSim is specifically designed to make it easy to interface to such codes, providing a common user experience for all, and permitting the construction and exploration of models with very little overhead. For today's technology-driven students, graphical interfaces meet their expectations far better than text-based tools, and education in accelerator physics is one of our primary goals.« less

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.

Sim1 Neurons Are Sufficient for MC4R-Mediated Sexual Function in Male Mice.

PubMed

Semple, Erin; Hill, Jennifer W

2018-01-01

Sexual dysfunction is a poorly understood condition that affects up to one-third of men around the world. Existing treatments that target the periphery do not work for all men. Previous studies have shown that central melanocortins, which are released by pro-opiomelanocortin neurons in the arcuate nucleus of the hypothalamus, can lead to male erection and increased libido. Several studies specifically implicate the melanocortin 4 receptor (MC4R) in the central control of sexual function, but the specific neural circuitry involved is unknown. We hypothesized that single-minded homolog 1 (Sim1) neurons play an important role in the melanocortin-mediated regulation of male sexual behavior. To test this hypothesis, we examined the sexual behavior of mice expressing MC4R only on Sim1-positive neurons (tbMC4Rsim1 mice) in comparison with tbMC4R null mice and wild-type controls. In tbMC4Rsim1 mice, MC4R reexpression was found in the medial amygdala and paraventricular nucleus of the hypothalamus. These mice were paired with sexually experienced females, and their sexual function and behavior was scored based on mounting, intromission, and ejaculation. tbMC4R null mice showed a longer latency to mount, a reduced intromission efficiency, and an inability to reach ejaculation. Expression of MC4R only on Sim1 neurons reversed the sexual deficits seen in tbMC4R null mice. This study implicates melanocortin signaling via the MC4R on Sim1 neurons in the central control of male sexual behavior. Copyright © 2018 Endocrine Society.

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.

Nanoscale imaging of alteration layers of corroded international simple glass particles using ToF-SIMS

DOE PAGES

Zhang, Jiandong; Neeway, James J.; Zhang, Yanyan; ...

2017-02-24

Glass particles with dimensions typically ranging from tens to hundreds of microns are often used in glass corrosion research in order to accelerate testing. Two-dimensional and three-dimensional nanoscale imaging techniques are badly needed to characterize the alteration layers at the surfaces of these corroded glass particles. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) can provide a lateral resolution as low as ~100 nm, and, compared to other imaging techniques, is sensitive to elements lighter than carbon. Here, we used ToF-SIMS to characterize the alteration layers of corroded international simple glass (ISG) particles. At most particle surfaces, we observed inhomogeneous or nomore » alteration layers, indicating that the thickness of the alterations layers may be too thin to be observable by ToF-SIMS imaging. Relatively thick (e.g., 1–10 µm) alteration layers were inhomogeneously distributed at a small portion of surfaces.Interestingly, some large-size (tens of microns) glass particles were fully altered. Above observations suggest that weak attachment and the defects on ISG particle surfaces play an important role in ISG glass corrosion.« less

Final report of the SIM.QM-S7 supplementary comparison, trace metals in drinking water

NASA Astrophysics Data System (ADS)

Yang, Lu; Nadeau, Kenny; Gedara Pihillagawa, Indu; Meija, Juris; Grinberg, Patricia; Mester, Zoltan; Valle Moya, Edith; Solís González, Faviola Alejandra; del Rocio Arvizu Torres, María; Yañez Muñoz, Oscar; Velina Lara-Manzano, Judith; Mazzitello, Gisela; Prina, Pedro; Acosta, Osvaldo; Napoli, Romina; Pérez Zambra, Ramiro; Ferreira, Elizabeth; Dobrovolskiy, Vladimir; Aprelev, Aleksei; Stakheev, Aleksei; Frolov, Dmitriy; Gusev, Leonid; Ivanova, Veronika; Näykki, Teemu; Sara-Aho, Timo; Venegas Padilla, Jimmy; Acuña Cubillo, Carlos; Bremmer, Dwyte; Freemantle, Ruel; Taebunpakul, Sutthinun; Tangpaisarnkul, Nongluck; Rodruangthum, Patumporn; Kaewkhomdee, Nattikarn; Thiengmanee, Usana; Tangjit, Tararat; Buzoianu, Mirella; Alejandro Ahumada Forigua, Diego; Abella Gamba, Johanna Paola; Alfredo Chavarro Medina, Luis; Sobina, Egor; Tabatchikova, Tatyana; Alexopoulos, Charalambos; Kakoulides, Elias; Delgado, Mabel; Flores, Liliana; Knox, Saira; Siewlal, Kester; Maharaj, Avinash

2018-01-01

SIM.QM-S7 was performed to assess the analytical capabilities of National Metrology Institutes (NMIs) and Designated Institutes (DIs) of SIM members (or other regions) for the accurate determination of trace metals in drinking water. The study was proposed by the coordinating laboratories National Research Council Canada (NRC) and Centro Nacional de Metrologia (CENAM) as an activity of Inorganic Analysis Working Group (IAWG) of Consultative Committee for Amount of Substance - Metrology in Chemistry and Biology (CCQM). Participants included 16 NMIs/DIs from 15 countries. No measurement method was prescribed by the coordinating laboratories. Therefore, NMIs used measurement methods of their choice. However, the majority of NMIs/DIs used ICP-MS. This SIM.QM-S7 Supplementary Comparison provides NMIs/DIs with the needed evidence for CMC claims for trace elements in fresh waters and similar matrices. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Nanoscale imaging of alteration layers of corroded international simple glass particles using ToF-SIMS

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

Zhang, Jiandong; Neeway, James J.; Zhang, Yanyan

Glass particles with dimensions typically ranging from tens to hundreds of microns are often used in glass corrosion research in order to accelerate testing. Two-dimensional and three-dimensional nanoscale imaging techniques are badly needed to characterize the alteration layers at the surfaces of these corroded glass particles. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) can provide a lateral resolution as low as ~100 nm, and, compared to other imaging techniques, is sensitive to elements lighter than carbon. In this work, we used ToF-SIMS to characterize the alteration layers of corroded international simple glass (ISG) particles. At most particle surfaces, inhomogeneous or nomore » alteration layers were observed, indicating that the thickness of the alterations layers may be too thin to be observable by ToF-SIMS imaging. Relatively thick (e.g., 1-10 microns) alteration layers were inhomogeneously distributed at a small portion of surfaces. More interestingly, some large-size (tens of microns) glass particles were fully altered. Above observations suggest that weak attachment and the defects on ISG particle surfaces play an important role in ISG glass corrosion.« less

SIM(1)-VSR Maxwell-Chern-Simons electrodynamics

NASA Astrophysics Data System (ADS)

Bufalo, R.

2016-06-01

In this paper we propose a very special relativity (VSR)-inspired generalization of the Maxwell-Chern-Simons (MCS) electrodynamics. This proposal is based upon the construction of a proper study of the SIM (1)-VSR gauge-symmetry. It is shown that the VSR nonlocal effects present a significant and healthy departure from the usual MCS theory. The classical dynamics is analysed in full detail, by studying the solution for the electric field and static energy for this configuration. Afterwards, the interaction energy between opposite charges is derived and we show that the VSR effects play an important part in obtaining a (novel) finite expression for the static potential.

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

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

GUM Analysis for TIMS and SIMS Isotopic Ratios in Graphite

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

Heasler, Patrick G.; Gerlach, David C.; Cliff, John B.

2007-04-01

This report describes GUM calculations for TIMS and SIMS isotopic ratio measurements of reactor graphite samples. These isotopic ratios are used to estimate reactor burn-up, and currently consist of various ratios of U, Pu, and Boron impurities in the graphite samples. The GUM calculation is a propagation of error methodology that assigns uncertainties (in the form of standard error and confidence bound) to the final estimates.

Recent Status of SIM Lite Astrometric Observatory Mission: Flight Engineering Risk Reduction Activities

NASA Technical Reports Server (NTRS)

Goullioud, Renaud; Dekens, Frank; Nemati, Bijan; An, Xin; Carson, Johnathan

2010-01-01

The SIM Lite Astrometric Observatory is a mission concept for a space-borne instrument to perform micro-arc-second narrow-angle astrometry to search 60 to 100 nearby stars for Earth-like planets, and to perform global astrometry for a broad astrophysics program. The instrument consists of two Michelson stellar interferometers and a telescope. The first interferometer chops between the target star and a set of reference stars. The second interferometer monitors the attitude of the instrument in the direction of the target star. The telescope monitors the attitude of the instrument in the other two directions. The main enabling technology development for the mission was completed during phases A & B. The project is currently implementing the developed technology onto flight-ready engineering models. These key engineering tasks will significantly reduce the implementation risks during the flight phases C & D of the mission. The main optical interferometer components, including the astrometric beam combiner, the fine steering optical mechanism, the path-length-control and modulation optical mechanisms, focal-plane camera electronics and cooling heat pipe, are currently under development. Main assemblies are built to meet flight requirements and will be subjected to flight qualification level environmental testing (random vibration and thermal cycling) and performance testing. This paper summarizes recent progress in engineering risk reduction activities.

SIMS analyses of the oldest known assemblage of microfossils document their taxon-correlated carbon isotope compositions

NASA Astrophysics Data System (ADS)

Schopf, J. William; Kitajima, Kouki; Spicuzza, Michael J.; Kudryavtsev, Anatoliy B.; Valley, John W.

2018-01-01

Analyses by secondary ion mass spectroscopy (SIMS) of 11 specimens of five taxa of prokaryotic filamentous kerogenous cellular microfossils permineralized in a petrographic thin section of the ˜3,465 Ma Apex chert of northwestern Western Australia, prepared from the same rock sample from which this earliest known assemblage of cellular fossils was described more than two decades ago, show their δ13C compositions to vary systematically taxon to taxon from ‑31‰ to ‑39‰. These morphospecies-correlated carbon isotope compositions confirm the biogenicity of the Apex fossils and validate their morphology-based taxonomic assignments. Perhaps most significantly, the δ13C values of each of the five taxa are lower than those of bulk samples of Apex kerogen (‑27‰), those of SIMS-measured fossil-associated dispersed particulate kerogen (‑27.6‰), and those typical of modern prokaryotic phototrophs (‑25 ± 10‰). The SIMS data for the two highest δ13C Apex taxa are consistent with those of extant phototrophic bacteria; those for a somewhat lower δ13C taxon, with nonbacterial methane-producing Archaea; and those for the two lowest δ13C taxa, with methane-metabolizing γ-proteobacteria. Although the existence of both methanogens and methanotrophs has been inferred from bulk analyses of the carbon isotopic compositions of pre-2,500 Ma kerogens, these in situ SIMS analyses of individual microfossils present data interpretable as evidencing the cellular preservation of such microorganisms and are consistent with the near-basal position of the Archaea in rRNA phylogenies.

SIMS analyses of the oldest known assemblage of microfossils document their taxon-correlated carbon isotope compositions.

PubMed

Schopf, J William; Kitajima, Kouki; Spicuzza, Michael J; Kudryavtsev, Anatoliy B; Valley, John W

2018-01-02

Analyses by secondary ion mass spectroscopy (SIMS) of 11 specimens of five taxa of prokaryotic filamentous kerogenous cellular microfossils permineralized in a petrographic thin section of the ∼3,465 Ma Apex chert of northwestern Western Australia, prepared from the same rock sample from which this earliest known assemblage of cellular fossils was described more than two decades ago, show their δ 13 C compositions to vary systematically taxon to taxon from -31‰ to -39‰. These morphospecies-correlated carbon isotope compositions confirm the biogenicity of the Apex fossils and validate their morphology-based taxonomic assignments. Perhaps most significantly, the δ 13 C values of each of the five taxa are lower than those of bulk samples of Apex kerogen (-27‰), those of SIMS-measured fossil-associated dispersed particulate kerogen (-27.6‰), and those typical of modern prokaryotic phototrophs (-25 ± 10‰). The SIMS data for the two highest δ 13 C Apex taxa are consistent with those of extant phototrophic bacteria; those for a somewhat lower δ 13 C taxon, with nonbacterial methane-producing Archaea; and those for the two lowest δ 13 C taxa, with methane-metabolizing γ-proteobacteria. Although the existence of both methanogens and methanotrophs has been inferred from bulk analyses of the carbon isotopic compositions of pre-2,500 Ma kerogens, these in situ SIMS analyses of individual microfossils present data interpretable as evidencing the cellular preservation of such microorganisms and are consistent with the near-basal position of the Archaea in rRNA phylogenies.

Optimized conditions for selective gold flotation by ToF-SIMS and ToF-LIMS

NASA Astrophysics Data System (ADS)

Chryssoulis, S. L.; Dimov, S. S.

2004-06-01

This work describes a comprehensive characterization of the factors controlling the floatability of free gold from flotation test using reagents (collectors) at plant concentration levels. A relationship between the collectors loadings on gold particles and their surface composition has been established. The findings of this study show that silver activates gold flotation and there is a strong correlation between the surface concentration of silver and the loading of certain collectors. The organic surface analysis was done by ToF-SIMS while the inorganic surface analysis was carried out by time-of-flight laser ionization mass spectrometry (ToF-LIMS). The developed testing protocol based on ToF-LIMS and ToF-SIMS complementary surface analysis allows for optimization of the flotation scheme and hence improved gold recovery.

Modulated CMOS camera for fluorescence lifetime microscopy.

PubMed

Chen, Hongtao; Holst, Gerhard; Gratton, Enrico

2015-12-01

Widefield frequency-domain fluorescence lifetime imaging microscopy (FD-FLIM) is a fast and accurate method to measure the fluorescence lifetime of entire images. However, the complexity and high costs involved in construction of such a system limit the extensive use of this technique. PCO AG recently released the first luminescence lifetime imaging camera based on a high frequency modulated CMOS image sensor, QMFLIM2. Here we tested and provide operational procedures to calibrate the camera and to improve the accuracy using corrections necessary for image analysis. With its flexible input/output options, we are able to use a modulated laser diode or a 20 MHz pulsed white supercontinuum laser as the light source. The output of the camera consists of a stack of modulated images that can be analyzed by the SimFCS software using the phasor approach. The nonuniform system response across the image sensor must be calibrated at the pixel level. This pixel calibration is crucial and needed for every camera settings, e.g. modulation frequency and exposure time. A significant dependency of the modulation signal on the intensity was also observed and hence an additional calibration is needed for each pixel depending on the pixel intensity level. These corrections are important not only for the fundamental frequency, but also for the higher harmonics when using the pulsed supercontinuum laser. With these post data acquisition corrections, the PCO CMOS-FLIM camera can be used for various biomedical applications requiring a large frame and high speed acquisition. © 2015 Wiley Periodicals, Inc.

Cyclic Voltammetry Simulations with DigiSim Software: An Upper-Level Undergraduate Experiment

ERIC Educational Resources Information Center

Messersmith, Stephania J.

2014-01-01

An upper-division undergraduate chemistry experiment is described which utilizes DigiSim software to simulate cyclic voltammetry (CV). Four mechanisms were studied: a reversible electron transfer with no subsequent or proceeding chemical reactions, a reversible electron transfer followed by a reversible chemical reaction, a reversible chemical…

55 'Mini Sim' - innovative bite sized simulation teaching in a busy children's emergency department.

PubMed

Sunley, Rachel; Moloney, Karen; Parker, Jessica; Arrowsmith, Christopher; Brown, Kirsty; Wilson, Alex

2017-12-01

: Emergency Medicine requires a highly skilled workforce who are passionate about delivering excellent patient care. Shift patterns linked with the ever increasing numbers of patients who attend Emergency Departments puts strain on educating the workforce and fostering team togetherness.Our objective in devising and instigating the 'Mini Sim' programme was to embed regular in-situ simulation training to enhance the learning of all staff within our Emergency Department team, building a highly trained workforce to deliver excellent care within the remit of our busy department. The whole team is involved including junior nurses, senior nurses and all tiers of junior doctors including foundation, general practice and senior ED trainees (including Grid).'Mini Sim' takes place on a weekly basis, every Tuesday morning from 0930-1000. This timing is to ensure maximum participation from all staff. The setup is a fifteen minute simulation (one nurse, one junior doctor, one senior doctor) followed by fifteen minutes of debrief. The format includes an assessment of the participants confidence prior to 'Mini Sim' in the subject being practiced. This is rated on a numerical scale from 1 (being not confident at all) to 5 (being completely confident). The topics chosen are based on feedback from trainees and nurses on clinical skills they feel under confident in, (e.g., pelvic binder application, rapid sequence induction, sickle cell crisis), clinical incidents which have occurred around the Trust (e.g., seizures and access to benzodiazepines), National Patient Safety Alerts (e.g., phenytoin toxicity), protocols (e.g., abducted child, rapid tranquilisation for the acutely disturbed adolescent) , governance issues (e.g., blocked tracheostomy, resuscitation room rebuild) and competencies linked to RCEM objectives. The 'Mini Sim' then takes place in situ within the ED resus, ED main department or our short stay observation ward which is under the auspices of the Children's Emergency

On the power spectral density of quadrature modulated signals. [satellite communication

NASA Technical Reports Server (NTRS)

Yan, T. Y.

1981-01-01

The conventional (no-offset) quadriphase modulation technique suffers from the fact that hardlimiting will restore the frequency sidelobes removed by proper filtering. Thus, offset keyed quadriphase modulation techniques are often proposed for satellite communication with bandpass hardlimiting. A unified theory is developed which is capable of describing the power spectral density before and after the hardlimiting process. Using the in-phase and the quadrature phase channel with arbitrary pulse shaping, analytical results are established for generalized quadriphase modulation. In particular MSK, OPSK or the recently introduced overlapped raised cosine keying all fall into this general category. It is shown that for a linear communication channel, the power spectral density of the modulated signal remains unchanged regardless of the offset delay. Furthermore, if the in phase and the quadrature phase channel have identical pulse shapes without offset, the spectrum after bandpass hardlimiting will be identical to that of the conventional QPSK modulation. Numerical examples are given for various modulation techniques. A case of different pulse shapes in the in phase and the quadrature phase channel is also considered.

A collaborative filtering recommendation algorithm based on weighted SimRank and social trust

NASA Astrophysics Data System (ADS)

Su, Chang; Zhang, Butao

2017-05-01

Collaborative filtering is one of the most widely used recommendation technologies, but the data sparsity and cold start problem of collaborative filtering algorithms are difficult to solve effectively. In order to alleviate the problem of data sparsity in collaborative filtering algorithm, firstly, a weighted improved SimRank algorithm is proposed to compute the rating similarity between users in rating data set. The improved SimRank can find more nearest neighbors for target users according to the transmissibility of rating similarity. Then, we build trust network and introduce the calculation of trust degree in the trust relationship data set. Finally, we combine rating similarity and trust to build a comprehensive similarity in order to find more appropriate nearest neighbors for target user. Experimental results show that the algorithm proposed in this paper improves the recommendation precision of the Collaborative algorithm effectively.

Climate responses to SATIRE and SIM-based spectral solar forcing in a 3D atmosphere-ocean coupled GCM

NASA Astrophysics Data System (ADS)

Wen, Guoyong; Cahalan, Robert F.; Rind, David; Jonas, Jeffrey; Pilewskie, Peter; Wu, Dong L.; Krivova, Natalie A.

2017-03-01

We apply two reconstructed spectral solar forcing scenarios, one SIM (Spectral Irradiance Monitor) based, the other the SATIRE (Spectral And Total Irradiance REconstruction) modeled, as inputs to the GISS (Goddard Institute for Space Studies) GCMAM (Global Climate Middle Atmosphere Model) to examine climate responses on decadal to centennial time scales, focusing on quantifying the difference of climate response between the two solar forcing scenarios. We run the GCMAM for about 400 years with present day trace gas and aerosol for the two solar forcing inputs. We find that the SIM-based solar forcing induces much larger long-term response and 11-year variation in global averaged stratospheric temperature and column ozone. We find significant decreasing trends of planetary albedo for both forcing scenarios in the 400-year model runs. However the mechanisms for the decrease are very different. For SATIRE solar forcing, the decreasing trend of planetary albedo is associated with changes in cloud cover. For SIM-based solar forcing, without significant change in cloud cover on centennial and longer time scales, the apparent decreasing trend of planetary albedo is mainly due to out-of-phase variation in shortwave radiative forcing proxy (downwelling flux for wavelength >330 nm) and total solar irradiance (TSI). From the Maunder Minimum to present, global averaged annual mean surface air temperature has a response of 0.1 °C to SATIRE solar forcing compared to 0.04 °C to SIM-based solar forcing. For 11-year solar cycle, the global surface air temperature response has 3-year lagged response to either forcing scenario. The global surface air 11-year temperature response to SATIRE forcing is about 0.12 °C, similar to recent multi-model estimates, and comparable to the observational-based evidence. However, the global surface air temperature response to 11-year SIM-based solar forcing is insignificant and inconsistent with observation-based evidence.

simDEF: definition-based semantic similarity measure of gene ontology terms for functional similarity analysis of genes.

PubMed

Pesaranghader, Ahmad; Matwin, Stan; Sokolova, Marina; Beiko, Robert G

2016-05-01

Measures of protein functional similarity are essential tools for function prediction, evaluation of protein-protein interactions (PPIs) and other applications. Several existing methods perform comparisons between proteins based on the semantic similarity of their GO terms; however, these measures are highly sensitive to modifications in the topological structure of GO, tend to be focused on specific analytical tasks and concentrate on the GO terms themselves rather than considering their textual definitions. We introduce simDEF, an efficient method for measuring semantic similarity of GO terms using their GO definitions, which is based on the Gloss Vector measure commonly used in natural language processing. The simDEF approach builds optimized definition vectors for all relevant GO terms, and expresses the similarity of a pair of proteins as the cosine of the angle between their definition vectors. Relative to existing similarity measures, when validated on a yeast reference database, simDEF improves correlation with sequence homology by up to 50%, shows a correlation improvement >4% with gene expression in the biological process hierarchy of GO and increases PPI predictability by > 2.5% in F1 score for molecular function hierarchy. Datasets, results and source code are available at http://kiwi.cs.dal.ca/Software/simDEF CONTACT: ahmad.pgh@dal.ca or beiko@cs.dal.ca 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.

Investigating Representations of Facial Identity in Human Ventral Visual Cortex with Transcranial Magnetic Stimulation

PubMed Central

Gilaie-Dotan, Sharon; Silvanto, Juha; Schwarzkopf, Dietrich S.; Rees, Geraint

2010-01-01

The occipital face area (OFA) is face-selective. This enhanced activation to faces could reflect either generic face and shape-related processing or high-level conceptual processing of identity. Here we examined these two possibilities using a state-dependent transcranial magnetic stimulation (TMS) paradigm. The lateral occipital (LO) cortex which is activated non-selectively by various types of objects served as a control site. We localized OFA and LO on a per-participant basis using functional MRI. We then examined whether TMS applied to either of these regions affected the ability of participants to decide whether two successively presented and physically different face images were of the same famous person or different famous people. TMS was applied during the delay between first and second face presentations to investigate whether neuronal populations in these regions played a causal role in mediating the behavioral effects of identity repetition. Behaviorally we found a robust identity repetition effect, with shorter reaction times (RTs) when identity was repeated, regardless of the fact that the pictures were physically different. Surprisingly, TMS applied over LO (but not OFA) modulated overall RTs, compared to the No-TMS condition. But critically, we found no effects of TMS to either area that were modulated by identity repetition. Thus, we found no evidence to suggest that OFA or LO contain neuronal representations selective for the identity of famous faces which play a causal role in identity processing. Instead, these brain regions may be involved in the processing of more generic features of their preferred stimulus categories. PMID:20631842

Quantification of Lignin and Its Structural Features in Plant Biomass Using 13C Lignin as Internal Standard for Pyrolysis-GC-SIM-MS.

PubMed

van Erven, Gijs; de Visser, Ries; Merkx, Donny W H; Strolenberg, Willem; de Gijsel, Peter; Gruppen, Harry; Kabel, Mirjam A

2017-10-17

Understanding the mechanisms underlying plant biomass recalcitrance at the molecular level can only be achieved by accurate analyses of both the content and structural features of the molecules involved. Current quantification of lignin is, however, majorly based on unspecific gravimetric analysis after sulfuric acid hydrolysis. Hence, our research aimed at specific lignin quantification with concurrent characterization of its structural features. Hereto, for the first time, a polymeric 13 C lignin was used as internal standard (IS) for lignin quantification via analytical pyrolysis coupled to gas chromatography with mass-spectrometric detection in selected ion monitoring mode (py-GC-SIM-MS). In addition, relative response factors (RRFs) for the various pyrolysis products obtained were determined and applied. First, 12 C and 13 C lignin were isolated from nonlabeled and uniformly 13 C labeled wheat straw, respectively, and characterized by heteronuclear single quantum coherence (HSQC), nuclear magnetic resonance (NMR), and py-GC/MS. The two lignin isolates were found to have identical structures. Second, 13 C-IS based lignin quantification by py-GC-SIM-MS was validated in reconstituted biomass model systems with known contents of the 12 C lignin analogue and was shown to be extremely accurate (>99.9%, R 2 > 0.999) and precise (RSD < 1.5%). Third, 13 C-IS based lignin quantification was applied to four common poaceous biomass sources (wheat straw, barley straw, corn stover, and sugar cane bagasse), and lignin contents were in good agreement with the total gravimetrically determined lignin contents. Our robust method proves to be a promising alternative for the high-throughput quantification of lignin in milled biomass samples directly and simultaneously provides a direct insight into the structural features of lignin.

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

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

Foraminiferal Metabolism Under Hypoxia: Sub-Cellular NanoSIMS Imaging of Intertidal Ammonia tepida Feeding Behavior

NASA Astrophysics Data System (ADS)

LeKieffre, C.; Spangenberg, J.; Geslin, E.; Meibom, A.

2016-02-01

Hypoxic events particularly affect benthic ecosystems on continental shelves and in coastal areas where renewal of bottom waters slow. Foraminifera living in such environments are among the most tolerant to hypoxia in the meiofauna. Some foraminifera species are able to survive hypoxia, and even anoxia, for weeks to months. Different species must have developed different mechanisms for survival - hypotheses include reduction of the metabolism, symbiosis with bacteria, or denitrification. NanoSIMS (Secondary Ion Mass Spectrometry) imaging is a powerful analytical technique to visualize and quantify the incorporation and transfer of isotopically labeled compounds in organisms with subcellular resolution. We used NanoSIMS imaging, correlated with TEM ultrastructural observations of individual foraminifera, to study the metabolism of intertidal Ammonia tepida, which has shown strongly reduced metabolism under anoxia. Individuals were fed with a 13C-labeled microalgal biofilm and incubated for 4 weeks in oxic and anoxic conditions, respectively. NanoSIMS imaging reveal strongly contrasting cellular-level dynamics of integration and transfer of the ingested biofilm components under the two conditions. In oxic conditions, ingested biofilm components are internalized, metabolized, and used for biosynthesis of different cellular components on a time scale of 24 hours: Lipid droplets are formed, then consumed through respiration. In contrast, upon the onset of anoxia, individual internalized biofilm components remain visible within the cytoplasm after 4 weeks. Lipids of different compositions are initially formed but then not respired. These observations indicate that foraminifera do initially have an active heterotrophic metabolism in the absence of oxygen, but this it is strongly reduced when oxygen is no longer available. Isotopic labeling experiments, NanoSIMS and TEM imaging, and GC-MS will be key to study metabolic mechanisms under anoxic conditions in marine

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.

Parallelization of interpolation, solar radiation and water flow simulation modules in GRASS GIS using OpenMP

NASA Astrophysics Data System (ADS)

Hofierka, Jaroslav; Lacko, Michal; Zubal, Stanislav

2017-10-01

In this paper, we describe the parallelization of three complex and computationally intensive modules of GRASS GIS using the OpenMP application programming interface for multi-core computers. These include the v.surf.rst module for spatial interpolation, the r.sun module for solar radiation modeling and the r.sim.water module for water flow simulation. We briefly describe the functionality of the modules and parallelization approaches used in the modules. Our approach includes the analysis of the module's functionality, identification of source code segments suitable for parallelization and proper application of OpenMP parallelization code to create efficient threads processing the subtasks. We document the efficiency of the solutions using the airborne laser scanning data representing land surface in the test area and derived high-resolution digital terrain model grids. We discuss the performance speed-up and parallelization efficiency depending on the number of processor threads. The study showed a substantial increase in computation speeds on a standard multi-core computer while maintaining the accuracy of results in comparison to the output from original modules. The presented parallelization approach showed the simplicity and efficiency of the parallelization of open-source GRASS GIS modules using OpenMP, leading to an increased performance of this geospatial software on standard multi-core computers.

Social Impacts Module (SIM) Transition

DTIC Science & Technology

2012-09-28

User String The authorized user’s name to access the PAVE database. Applies only to Microsoft SQL Server; leave blank, otherwise. passwd String The...otherwise. passwd String The password if an authorized user’s name is required; otherwise, leave blank driver String The class name for the driver to

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.

Micro-Vibration Performance Prediction of SEPTA24 Using SMeSim (RUAG Space Mechanism Simulator Tool)

NASA Astrophysics Data System (ADS)

Omiciuolo, Manolo; Lang, Andreas; Wismer, Stefan; Barth, Stephan; Szekely, Gerhard

2013-09-01

Scientific space missions are currently challenging the performances of their payloads. The performances can be dramatically restricted by micro-vibration loads generated by any moving parts of the satellites, thus by Solar Array Drive Assemblies too. Micro-vibration prediction of SADAs is therefore very important to support their design and optimization in the early stages of a programme. The Space Mechanism Simulator (SMeSim) tool, developed by RUAG, enhances the capability of analysing the micro-vibration emissivity of a Solar Array Drive Assembly (SADA) under a specified set of boundary conditions. The tool is developed in the Matlab/Simulink® environment throughout a library of blocks simulating the different components a SADA is made of. The modular architecture of the blocks, assembled by the user, and the set up of the boundary conditions allow time-domain and frequency-domain analyses of a rigid multi-body model with concentrated flexibilities and coupled- electronic control of the mechanism. SMeSim is used to model the SEPTA24 Solar Array Drive Mechanism and predict its micro-vibration emissivity. SMeSim and the return of experience earned throughout its development and use can now support activities like verification by analysis of micro-vibration emissivity requirements and/or design optimization to minimize the micro- vibration emissivity of a SADA.

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…

Force supplementary comparison at SIM (SIM.M.F-S5), compression testing machines calibration, up to 200 kN

NASA Astrophysics Data System (ADS)

Cárdenas Moctezuma, A.; Torres Guzmán, J. C.

2016-01-01

CENAM, through the Force and Pressure Division, organized a comparison on testing machines calibration, in compression mode. The participating laboratories were SIM National Institutes of Metrology from Colombia, Peru and Costa Rica, where CENAM, Mexico was the pilot and reference laboratory. The results obtained by the laboratories are presented in this paper as well as the analysis of compatibility. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Correlating microscopy techniques and ToF-SIMS analysis of fully grown mammalian oocytes.

PubMed

Gulin, Alexander; Nadtochenko, Victor; Astafiev, Artyom; Pogorelova, Valentina; Rtimi, Sami; Pogorelov, Alexander

2016-06-20

The 2D-molecular thin film analysis protocol for fully grown mice oocytes is described using an innovative approach. Time-of-flight secondary ion mass spectrometry (ToF-SIMS), scanning electron microscopy (SEM), atomic force microscopy (AFM) and optical microscopy imaging were applied to the same mice oocyte section on the same sample holder. A freeze-dried mice oocyte was infiltrated into embedding media, e.g. Epon, and then was cut with a microtome and 2 μm thick sections were transferred onto an ITO coated conductive glass. Mammalian oocytes can contain "nucleolus-like body" (NLB) units and ToF-SIMS analysis was used to investigate the NLB composition. The ion-spatial distribution in the cell components was identified and compared with the images acquired by SEM, AFM and optical microscopy. This study presents a significant advancement in cell embryology, cell physiology and cancer-cell biochemistry.

The SIMS Screen for feigned mental disorders: the development of detection-based scales.

PubMed

Rogers, Richard; Robinson, Emily V; Gillard, Nathan D

2014-01-01

Time-efficient screens for feigned mental disorders (FMDs) constitute important tools in forensic assessments. The Structured Inventory of Malingered Symptomatology (SIMS) is a 75-item true-false questionnaire that has been extensively studied as an FMD screen. However, the SIMS scales are not based on established detection strategies, and only its total score is utilized as a feigning screen. This investigation develops two new feigning scales based on well-established detection-strategies: rare symptoms (RS) and symptom combinations (SC). They are studied in a between-subjects simulation design using inpatients with partial-malingering (i.e., patients with genuine disorders asked to feign greater disabilities) conditions. Subject to future cross-validation, the SC scale evidenced the highest effect size (d=2.01) and appeared the most effective at ruling out examinees, who have a high likelihood of genuine responding. Copyright © 2014 John Wiley & Sons, Ltd.

Efficiency of the modified Sims maternal position in the rotation of persistent occiput posterior position during labor: A randomized clinical trial.

PubMed

Bueno-Lopez, Vanessa; Fuentelsaz-Gallego, Carmen; Casellas-Caro, Manel; Falgueras-Serrano, Ana Maria; Crespo-Berros, Silvia; Silvano-Cocinero, Ana Maria; Alcaine-Guisado, Carolina; Zamoro Fuentes, Manuela; Carreras, Elena; Terré-Rull, Carmen

2018-03-14

Fetal occiput posterior position in labor is associated with more painful and prolonged labor, and an increase in both maternal and fetal morbidity. The aim of this study is to assess whether the modified Sims position on the side of the fetal spine increases the rotation to occiput anterior position in women with epidural analgesia and a fetus in persistent occiput posterior (POP) position. This is an open, randomized controlled, clinical trial. One hundred and twenty women in labor with fetuses in POP position were included. The diagnosis was performed through digital vaginal examination and confirmed with an ultrasound scan. Women were randomized into the free position group or the modified Sims on the side of the fetal spine. The primary outcome was rotation to occiput anterior, and secondary outcomes were type of delivery, postpartum perineal condition, perinatal results, and maternal satisfaction. In pregnant women undergoing labor in the Sims position, fetuses in POP rotated to occiput anterior in 50.8% of cases, whilst in the free position group, the rotation occurred in 21.7% (P = .001). The rate of vaginal deliveries was higher in the Sims group compared with the free position group (84.7% vs 68.3%, P = .035). The modified Sims position is a maternal posture intervention efficient in POP rotation, which decreases cesarean delivery rate. It is a simple and noninvasive intervention, reproducible, and well tolerated by pregnant women. © 2018 Wiley Periodicals, Inc.

Quantitative SIMS depth profiling of diffusion barrier gate-oxynitride structures in TFT-LCDs.

PubMed

Dreer, Sabine; Wilhartitz, Peter; Piplits, Kurt; Mayerhofer, Karl; Foisner, Johann; Hutter, Herbert

2004-06-01

Gate oxynitride structures of TFT-LCDs were investigated by SIMS, and successful solutions are demonstrated to overcome difficulties arising due to the charging effects of the multilayer systems, the matrix effect of the method, and the small pattern sizes of the samples. Because of the excellent reproducibility achieved by applying exponential relative sensitivity functions for quantitative analysis, minor differences in the barrier gate-oxynitride composition deposited on molybdenum capped aluminium-neodymium metallisation electrodes were determined between the centre and the edge of the TFT-LCD substrates. No differences were found for molybdenum-tungsten metallisations. Furthermore, at the edge of the glass substrates, aluminium, neodymium, and molybdenum SIMS depth profiles show an exponential trend. With TEM micrographs an inhomogeneous thickness of the molybdenum capping is revealed as the source of this effect, which influences the electrical behaviour of the device. The production process was improved after these results and the aging behaviour of TFT-LCDs was investigated in order to explain the change in control voltage occurring during the lifetime of the displays. SIMS and TEM show an enrichment of neodymium at the interface to the molybdenum layer, confirming good diffusion protection of the molybdenum barrier during accelerated aging. The reason for the shift of the control voltage was finally located by semi-quantitative depth profiling of the sodium diffusion originating from the glass substrate. Molybdenum-tungsten was a much better buffer for the highly-mobile charge carriers than aluminium-neodymium. Best results were achieved with PVD silicon oxynitride as diffusion barrier and gate insulator deposited on aluminium-neodymium metallisation layers.

No Selling the Genie Lamp: A Game Literacy Practice in "The Sims"

ERIC Educational Resources Information Center

Hayes, Elisabeth R.; Gee, James Paul

2010-01-01

Drawing on the New Literacy Studies, the authors argue that game literacy takes multiple forms and is embedded in different practices associated with particular games and gaming communities. They examine one specific game literacy practice that involves players of "The Sims" creating challenges for other players, and they identify how playing and…

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.

Imaging cellular structures in super-resolution with SIM, STED and Localisation Microscopy: A practical comparison.

PubMed

Wegel, Eva; Göhler, Antonia; Lagerholm, B Christoffer; Wainman, Alan; Uphoff, Stephan; Kaufmann, Rainer; Dobbie, Ian M

2016-06-06

Many biological questions require fluorescence microscopy with a resolution beyond the diffraction limit of light. Super-resolution methods such as Structured Illumination Microscopy (SIM), STimulated Emission Depletion (STED) microscopy and Single Molecule Localisation Microscopy (SMLM) enable an increase in image resolution beyond the classical diffraction-limit. Here, we compare the individual strengths and weaknesses of each technique by imaging a variety of different subcellular structures in fixed cells. We chose examples ranging from well separated vesicles to densely packed three dimensional filaments. We used quantitative and correlative analyses to assess the performance of SIM, STED and SMLM with the aim of establishing a rough guideline regarding the suitability for typical applications and to highlight pitfalls associated with the different techniques.

Intervertebral reaction force prediction using an enhanced assembly of OpenSim models.

PubMed

Senteler, Marco; Weisse, Bernhard; Rothenfluh, Dominique A; Snedeker, Jess G

2016-01-01

OpenSim offers a valuable approach to investigating otherwise difficult to assess yet important biomechanical parameters such as joint reaction forces. Although the range of available models in the public repository is continually increasing, there currently exists no OpenSim model for the computation of intervertebral joint reactions during flexion and lifting tasks. The current work combines and improves elements of existing models to develop an enhanced model of the upper body and lumbar spine. Models of the upper body with extremities, neck and head were combined with an improved version of a lumbar spine from the model repository. Translational motion was enabled for each lumbar vertebrae with six controllable degrees of freedom. Motion segment stiffness was implemented at lumbar levels and mass properties were assigned throughout the model. Moreover, body coordinate frames of the spine were modified to allow straightforward variation of sagittal alignment and to simplify interpretation of results. Evaluation of model predictions for level L1-L2, L3-L4 and L4-L5 in various postures of forward flexion and moderate lifting (8 kg) revealed an agreement within 10% to experimental studies and model-based computational analyses. However, in an extended posture or during lifting of heavier loads (20 kg), computed joint reactions differed substantially from reported in vivo measures using instrumented implants. We conclude that agreement between the model and available experimental data was good in view of limitations of both the model and the validation datasets. The presented model is useful in that it permits computation of realistic lumbar spine joint reaction forces during flexion and moderate lifting tasks. The model and corresponding documentation are now available in the online OpenSim repository.

Adolescents Media Experiences in the Classroom: SimCity as a Cultural Model

ERIC Educational Resources Information Center

Lacasa, Pilar; García-Pernía, María-Ruth; Núñez, Patricia

2014-01-01

The main goal of this paper is to analyze adolescents' experiences when they play SimCity (EA, 2008), a commercial videogame, in an innovative learning environment designed around the concept of participatory culture. By using this video game in the classroom and machinima productions created in relation to the game, we sought to generate a…

SIM PlanetQuest: The TOM-3 (Thermo-Optical-Mechanical) Siderostat Mirror Test

NASA Technical Reports Server (NTRS)

Phillips, Charles J.

2006-01-01

This slide presentation reviews the Space Interferometry Mission (SIM) PlanetQuest mission. It describes the mission, shows diagrams of the instrument, the collector bays, the Siderostat mirrors, the COL bay thermal environment, the TOM-3 replicating COL Bay Environment, the thermal hardware for the SID heater control, and the results of the test are shown

A challenging dissociation in masked identity priming with the lexical decision task.

PubMed

Perea, Manuel; Jiménez, María; Gómez, Pablo

2014-05-01

The masked priming technique has been used extensively to explore the early stages of visual-word recognition. One key phenomenon in masked priming lexical decision is that identity priming is robust for words, whereas it is small/unreliable for nonwords. This dissociation has usually been explained on the basis that masked priming effects are lexical in nature, and hence there should not be an identity prime facilitation for nonwords. We present two experiments whose results are at odds with the assumption made by models that postulate that identity priming is purely lexical, and also challenge the assumption that word and nonword responses are based on the same information. Our experiments revealed that for nonwords, but not for words, matched-case identity PRIME-TARGET pairs were responded to faster than mismatched-case identity prime-TARGET pairs, and this phenomenon was not modulated by the lowercase/uppercase feature similarity of the stimuli. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

SimTrack: A compact c++ code for particle orbit and spin tracking in accelerators

DOE PAGES

Luo, Yun

2015-08-29

SimTrack is a compact c++ code of 6-d symplectic element-by-element particle tracking in accelerators originally designed for head-on beam–beam compensation simulation studies in the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory. It provides a 6-d symplectic orbit tracking with the 4th order symplectic integration for magnet elements and the 6-d symplectic synchro-beam map for beam–beam interaction. Since its inception in 2009, SimTrack has been intensively used for dynamic aperture calculations with beam–beam interaction for RHIC. Recently, proton spin tracking and electron energy loss due to synchrotron radiation were added. In this article, I will present the code architecture,more » physics models, and some selected examples of its applications to RHIC and a future electron-ion collider design eRHIC.« less

SimTrack: A compact c++ library for particle orbit and spin tracking in accelerators

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

Luo, Yun

2015-06-24

SimTrack is a compact c++ library of 6-d symplectic element-by-element particle tracking in accelerators originally designed for head-on beam-beam compensation simulation studies in the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory. It provides a 6-d symplectic orbit tracking with the 4th order symplectic integration for magnet elements and the 6-d symplectic synchro-beam map for beam-beam interaction. Since its inception in 2009, SimTrack has been intensively used for dynamic aperture calculations with beam-beam interaction for RHIC. Recently, proton spin tracking and electron energy loss due to synchrotron radiation were added. In this article, I will present the code architecture,more » physics models, and some selected examples of its applications to RHIC and a future electron-ion collider design eRHIC.« less

Decomposition of ultrathin LiF cathode underlayer in organic-based devices evidenced by ToF-SIMS depth profiling

NASA Astrophysics Data System (ADS)

Pakhomov, Georgy L.; Drozdov, Mikhail N.; Travkin, Vlad V.; Bochkarev, Mikhail N.

2017-11-01

In this work we investigate the chemical composition of an archetypal thin-film organic device with the Ag/LiF cathode using the time-of-flight secondary ion mass spectrometry (ToF-SIMS) with depth profiling. The LiF cathode underlayer is partly decomposed because a significant amount of lithium is released into the bulk of the multilayer device. The released lithium diffuses all the way to the substrate, accumulating, as revealed by ToF-SIMS depth profiles, at the interfaces rather than uniformly doping the underlying layers. Particularly, the bottom anode becomes chemically modified.

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.

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.

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

Unexpected materials in a Rembrandt painting characterized by high spatial resolution cluster-TOF-SIMS imaging.

PubMed

Sanyova, Jana; Cersoy, Sophie; Richardin, Pascale; Laprévote, Olivier; Walter, Philippe; Brunelle, Alain

2011-02-01

The painting materials of the Portrait of Nicolaes van Bambeeck (Royal Museums of Fine Arts of Belgium, Brussels, inv. 155) painted by Rembrandt van Rijn in 1641 has been studied using high resolution cluster-TOF-SIMS imaging. In the first step, a moderate spatial resolution (2 μm) was used to characterize the layer structure and the chemical composition of each layer on account of a high mass resolution. Then, in the second step, and despite a low mass resolution, the cluster primary ion beam was focused well below 1 μm in order to reveal smaller structures in the painting sample. The study confirmed the presence of starch in the second ground layer, which is quite surprising and, at least for Rembrandt paintings, has never been reported before. TOF-SIMS also indicated the presence of proteins, which, added to the size and shape of lake particles, suggests that it was manufactured from shearings (waste of textile manufacturing) of dyed wool, used as the source of the dyestuff. The analyses have also shown various lead carboxylates, being the products of the interaction between lead white and the oil of the binding medium. These findings considerably contribute to the understanding of Rembrandt's studio practice and thus demonstrate the importance and potential of cluster-TOF-SIMS imaging in the characterization on a submicrometer scale of artist painting materials.

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

[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

Quantitative analysis of Si1-xGex alloy films by SIMS and XPS depth profiling using a reference material

NASA Astrophysics Data System (ADS)

Oh, Won Jin; Jang, Jong Shik; Lee, Youn Seoung; Kim, Ansoon; Kim, Kyung Joong

2018-02-01

Quantitative analysis methods of multi-element alloy films were compared. The atomic fractions of Si1-xGex alloy films were measured by depth profiling analysis with secondary ion mass spectrometry (SIMS) and X-ray Photoelectron Spectroscopy (XPS). Intensity-to-composition conversion factor (ICF) was used as a mean to convert the intensities to compositions instead of the relative sensitivity factors. The ICFs were determined from a reference Si1-xGex alloy film by the conventional method, average intensity (AI) method and total number counting (TNC) method. In the case of SIMS, although the atomic fractions measured by oxygen ion beams were not quantitative due to severe matrix effect, the results by cesium ion beam were very quantitative. The quantitative analysis results by SIMS using MCs2+ ions are comparable to the results by XPS. In the case of XPS, the measurement uncertainty was highly improved by the AI method and TNC method.

Identity Orientations: Definition, Assessment, and Personal Correlates. A Teaching Module.

ERIC Educational Resources Information Center

Carducci, Bernardo J.

Probably no other concept comes closer to encompassing the core of personality psychology than the concept of the self. This teaching activity provides instructors with a self-contained teaching module--including lecture material, an in-class activity, suggestions for in-class discussion, and supporting references--on the topic of identity…

Quantification of Lignin and Its Structural Features in Plant Biomass Using 13C Lignin as Internal Standard for Pyrolysis-GC-SIM-MS

PubMed Central

2017-01-01

Understanding the mechanisms underlying plant biomass recalcitrance at the molecular level can only be achieved by accurate analyses of both the content and structural features of the molecules involved. Current quantification of lignin is, however, majorly based on unspecific gravimetric analysis after sulfuric acid hydrolysis. Hence, our research aimed at specific lignin quantification with concurrent characterization of its structural features. Hereto, for the first time, a polymeric 13C lignin was used as internal standard (IS) for lignin quantification via analytical pyrolysis coupled to gas chromatography with mass-spectrometric detection in selected ion monitoring mode (py-GC-SIM-MS). In addition, relative response factors (RRFs) for the various pyrolysis products obtained were determined and applied. First, 12C and 13C lignin were isolated from nonlabeled and uniformly 13C labeled wheat straw, respectively, and characterized by heteronuclear single quantum coherence (HSQC), nuclear magnetic resonance (NMR), and py-GC/MS. The two lignin isolates were found to have identical structures. Second, 13C-IS based lignin quantification by py-GC-SIM-MS was validated in reconstituted biomass model systems with known contents of the 12C lignin analogue and was shown to be extremely accurate (>99.9%, R2 > 0.999) and precise (RSD < 1.5%). Third, 13C-IS based lignin quantification was applied to four common poaceous biomass sources (wheat straw, barley straw, corn stover, and sugar cane bagasse), and lignin contents were in good agreement with the total gravimetrically determined lignin contents. Our robust method proves to be a promising alternative for the high-throughput quantification of lignin in milled biomass samples directly and simultaneously provides a direct insight into the structural features of lignin. PMID:28926698

ToF-SIMS applied to historical archaeology in the Alps

NASA Astrophysics Data System (ADS)

Sodhi, R. N. S.; Mahaney, W. C.; Milner, M. W.

2006-07-01

The actual route Hannibal followed during the invasion of Italia in the Second Punic War is one of the major questions of antiquity, one that historians/archaeologists have long studied. There are six possible passes Hannibal could have used and one of the many bits of evidence in the ancient literature that might help answer this question is the location of fired rock, the result of a conflagration Hannibal is reputed to have employed to reduce the size of boulders in a two-tier blocking rockslide on the lee side (e.g. Italian) some distance down from the high col. The only route with fired rock along the roadway leading to the Po River Valley or the Dora Riparia is below the Col du Clapier, one of the possible northern routes. ToF-SIMS investigation of the 100-μm thick burned crust in hornblende schist interlaced with veins of quartz-feldspathic minerals yields various elements C, Mg, Na, Ca, Si, Ti, P, Al, Fe and their associated fragments. Hydrocarbon fragments are thought to be products of combustion whereas Ca and Na along with Mg-Fe silicates are derived from the country rock. Aeolian components along with clay minerals settled onto rock surfaces following firing. While the SIMS data clearly would not provide an age for the burnt rock, compositional evidence of the conflagration may relate to Hannibal's actual route.

Investigation of Ion-Solvent Interactions in Nonaqueous Electrolytes Using in Situ Liquid SIMS.

PubMed

Zhang, Yanyan; Su, Mao; Yu, Xiaofei; Zhou, Yufan; Wang, Jungang; Cao, Ruiguo; Xu, Wu; Wang, Chongmin; Baer, Donald R; Borodin, Oleg; Xu, Kang; Wang, Yanting; Wang, Xue-Lin; Xu, Zhijie; Wang, Fuyi; Zhu, Zihua

2018-03-06

Ion-solvent interactions in nonaqueous electrolytes are of fundamental interest and practical importance, yet debates regarding ion preferential solvation and coordination numbers persist. In this work, in situ liquid SIMS was used to examine ion-solvent interactions in three representative electrolytes, i.e., lithium hexafluorophosphate (LiPF 6 ) at 1.0 M in ethylene carbonate (EC)-dimethyl carbonate (DMC) and lithium bis(fluorosulfonyl)imide (LiFSI) at both low (1.0 M) and high (4.0 M) concentrations in 1,2-dimethoxyethane (DME). In the positive ion mode, solid molecular evidence strongly supports the preferential solvation of Li + by EC. Besides, from the negative spectra, we also found that PF 6 - forms association with EC, which has been neglected by previous studies due to the relatively weak interaction. In both LiFSI in DME electrolytes, however, no evidence shows that FSI - is associated with DME. Furthermore, strong salt ion cluster signals were observed in the 1.0 M LiPF 6 in EC-DMC electrolyte, suggesting that a significant amount of Li + ions stay in the vicinity of anions. In sharp comparison, weak ion cluster signals were detected in dilute LiFSI in DME electrolyte, suggesting most ions are well separated, in agreement with our molecular dynamics simulation results. These findings indicate that with virtues of little bias on detecting positive and negative ions and the capability of directly analyzing concentrated electrolytes, in situ liquid SIMS is a powerful tool that can provide key evidence for improved understanding on the ion-solvent interactions in nonaqueous electrolytes. Therefore, we anticipate wide applications of in situ liquid SIMS on investigations of various ion-solvent interactions in the near future.

As We Teach and Learn: Recognizing Our Catholic Identity. Module 4: Service Learning.

ERIC Educational Resources Information Center

Grace, Bill; Ristau, Karen, Ed.; Haney, Regina, Ed.

The As We Teach and Learn program consists of an instrument to assess the Catholic dimension of a school and is designed to be used with study modules in a faculty-meeting format. Module topics include: "Faith Community"; "Faith Development"; "Religion Curriculum Articulation: Faith as the Root of all Instruction";…

As We Teach and Learn: Recognizing Our Catholic Identity. Module 2: Faith Development.

ERIC Educational Resources Information Center

Zukowski, Angela Ann; Ristau, Karen, Ed.; Haney, Regina, Ed.

The As We Teach and Learn program consists of an instrument to assess the Catholic dimension of a school and is designed to be used with study modules in a faculty-meeting format. Module topics include: "Faith Community"; "Faith Development"; "Religion Curriculum Articulation: Faith as the Root of all Instruction";…

As We Teach and Learn: Recognizing Our Catholic Identity. Module 6: Social Justice.

ERIC Educational Resources Information Center

McGinnis, James; McGinnis, Kathleen; Ristau, Karen, Ed.; Haney, Regina, Ed.

The As We Teach and Learn program consists of an instrument to assess the Catholic dimension of a school and is designed to be used with study modules in a faculty-meeting format. Module topics include: "Faith Community"; "Faith Development"; "Religion Curriculum Articulation: Faith as the Root of all Instruction";…

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

Matrix Effects in SIMS Analysis of Hydrogen in Nominally Anhydrous Minerals (NAMs)

NASA Astrophysics Data System (ADS)

Mosenfelder, J. L.; Rossman, G. R.

2014-12-01

Accurate analysis of trace H in NAMs has become important with recognition that even small amounts of H influence geochemical and geophysical processes. FTIR and SIMS can measure concentrations down to ~1 ppmw H2O. However, a major limitation is that they rely on standards calibrated with other methods. SIMS matrix effects for H in NAMs are poorly constrained, but are likely dominated by differences in mean atomic mass. Here we use volatile-free molar weight (VFMW) normalized to one O/mol as a proxy for this parameter [cf. 1]. Our goal is to constrain SIMS matrix effects by combining our work on olivine [2], pyroxene [3], and feldspar [4] with new data on kyanite, zircon, and 37 garnets (pyropes, grossulars, spessartines, and andradites), while critically evaluating absolute calibrations of IR absorption coefficients (ɛi) for H in NAMs. All of these NAMs taken together span a wider range in VFMW (~32-45) than in previous comparisons [5, 6] concentrating only on olivine, pyroxene, and pyrope-rich garnet (VFMW ~ 34-37). Our results and conclusions include the following: 1) SIMS-FTIR comparisons demonstrate that ɛi is wavenumber dependent for feldspar, zircon, grossular, and clinopyroxene, in accord with theory and empirical calibrations on hydrous materials. On the other hand, a factor of 3 difference in ɛi for H defects in olivine [7] is unsupported by our data [2]. 2) Calibration slopes (for plots of ppmw H2O vs. 16OH/30Si × SiO2) correlate positively with VFMW, an effect not discerned in previous work [6]. This result is also opposite to a study demonstrating a negative correlation for hydrous phases and glasses [1]. This discrepancy may be related to differences in analytical methods (e.g., Cs+ vs. O- primary beam, collection of OH- versus H+). 3) Scatter in the trend of calibration slopes vs. VFMW is likely due to uncertainties in ɛi. Another possible factor is the structure of the matrix, which can affect the kinetic energy of cascade collisions leading to

System and method for simultaneously collecting serial number information from numerous identity tags

DOEpatents

Doty, Michael A.

1997-01-01

A system and method for simultaneously collecting serial number information reports from numerous colliding coded-radio-frequency identity tags. Each tag has a unique multi-digit serial number that is stored in non-volatile RAM. A reader transmits an ASCII coded "D" character on a carrier of about 900 MHz and a power illumination field having a frequency of about 1.6 Ghz. A one MHz tone is modulated on the 1.6 Ghz carrier as a timing clock for a microprocessor in each of the identity tags. Over a thousand such tags may be in the vicinity and each is powered-up and clocked by the 1.6 Ghz power illumination field. Each identity tag looks for the "D" interrogator modulated on the 900 MHz carrier, and each uses a digit of its serial number to time a response. Clear responses received by the reader are repeated for verification. If no verification or a wrong number is received by any identity tag, it uses a second digital together with the first to time out a more extended period for response. Ultimately, the entire serial number will be used in the worst case collision environments; and since the serial numbers are defined as being unique, the final possibility will be successful because a clear time-slot channel will be available.

System and method for simultaneously collecting serial number information from numerous identity tags

DOEpatents

Doty, M.A.

1997-01-07

A system and method are disclosed for simultaneously collecting serial number information reports from numerous colliding coded-radio-frequency identity tags. Each tag has a unique multi-digit serial number that is stored in non-volatile RAM. A reader transmits an ASCII coded ``D`` character on a carrier of about 900 MHz and a power illumination field having a frequency of about 1.6 Ghz. A one MHz tone is modulated on the 1.6 Ghz carrier as a timing clock for a microprocessor in each of the identity tags. Over a thousand such tags may be in the vicinity and each is powered-up and clocked by the 1.6 Ghz power illumination field. Each identity tag looks for the ``D`` interrogator modulated on the 900 MHz carrier, and each uses a digit of its serial number to time a response. Clear responses received by the reader are repeated for verification. If no verification or a wrong number is received by any identity tag, it uses a second digital together with the first to time out a more extended period for response. Ultimately, the entire serial number will be used in the worst case collision environments; and since the serial numbers are defined as being unique, the final possibility will be successful because a clear time-slot channel will be available. 5 figs.

Sweden SimSmoke: the effect of tobacco control policies on smoking and snus prevalence and attributable deaths

PubMed Central

Near, Aimee M.; Blackman, Kenneth; Currie, Laura M.

2014-01-01

Background: This study examines the effect of past tobacco control policies and projects the effect of future policies on smoking and snus use prevalence and associated premature mortality in Sweden. Methods: The established SimSmoke model was adapted with population, smoking rates and tobacco control policy data from Sweden. SimSmoke evaluates the effect of taxes, smoke-free air, mass media, marketing bans, warning labels, cessation treatment and youth access policies on smoking and snus prevalence and the number of deaths attributable to smoking and snus use by gender from 2010 to 2040. Results: Sweden SimSmoke estimates that significant inroads to reducing smoking and snus prevalence and premature mortality can be achieved through tax increases, especially when combined with other policies. Smoking prevalence can be decreased by as much as 26% in the first few years, reaching a 37% reduction within 30 years. Without effective tobacco control policies, almost 54 500 lives will be lost in Sweden due to tobacco use by the year 2040. Conclusion: Besides presenting the benefits of a comprehensive tobacco control strategy, the model identifies gaps in surveillance and evaluation that can help better focus tobacco control policy in Sweden. PMID:24287030

Real time wind farm emulation using SimWindFarm toolbox

NASA Astrophysics Data System (ADS)

Topor, Marcel

2016-06-01

This paper presents a wind farm emulation solution using an open source Matlab/Simulink toolbox and the National Instruments cRIO platform. This work is based on the Aeolus SimWindFarm (SWF) toolbox models developed at Aalborg university, Denmark. Using the Matlab Simulink models developed in SWF, the modeling code can be exported to a real time model using the NI Veristand model framework and the resulting code is integrated as a hardware in the loop control on the NI 9068 platform.

Rosmarinic acid content in antidiabetic aqueous extract from ocimum canum sims in Ghana

USDA-ARS?s Scientific Manuscript database

Rosmarinic acid (RA) is an important polyphenol that is found in a variety of herbs including Ocimum canum sims (locally called eme or akokobesa in Ghana). Aqueous extracts from the leaves of O. canum are used as an antidiabetic herbal medicine in Ghana. Analytical TLC was used to examine the compos...

Distribution and visualisation of chlorhexidine within the skin using ToF-SIMS: a potential platform for the design of more efficacious skin antiseptic formulations.

PubMed

Judd, Amy M; Scurr, David J; Heylings, Jon R; Wan, Ka-Wai; Moss, Gary P

2013-07-01

In order to increase the efficacy of a topically applied antimicrobial compound the permeation profile, localisation and mechanism of action within the skin must first be investigated. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used to visualise the distribution of a conventional antimicrobial compound, chlorhexidine digluconate, within porcine skin without the need for laborious preparation, radio-labels or fluorescent tags. High mass resolution and high spatial resolution mass spectra and chemical images were achieved when analysing chlorhexidine digluconate treated cryo-sectioned porcine skin sections by ToF-SIMS. The distribution of chlorhexidine digluconate was mapped throughout the skin sections and our studies indicate that the compound appears to be localised within the stratum corneum. In parallel, tape strips taken from chlorhexidine digluconate treated porcine skin were analysed by ToF-SIMS to support the distribution profile obtained from the skin sections. ToF-SIMS can act as a powerful complementary technique to map the distribution of topically applied compounds within the skin.

Structure and function of Per-ARNT-Sim domains and their possible role in the life-cycle biology of Trypanosoma cruzi.

PubMed

Rojas-Pirela, Maura; Rigden, Daniel J; Michels, Paul A; Cáceres, Ana J; Concepción, Juan Luis; Quiñones, Wilfredo

2018-01-01

Per-ARNT-Sim (PAS) domains of proteins play important roles as modules for signalling and cellular regulation processes in widely diverse organisms such as Archaea, Bacteria, protists, plants, yeasts, insects and vertebrates. These domains are present in many proteins where they are used as sensors of stimuli and modules for protein interactions. Characteristically, they can bind a broad spectrum of molecules. Such binding causes the domain to trigger a specific cellular response or to make the protein containing the domain susceptible to responding to additional physical or chemical signals. Different PAS proteins have the ability to sense redox potential, light, oxygen, energy levels, carboxylic acids, fatty acids and several other stimuli. Such proteins have been found to be involved in cellular processes such as development, virulence, sporulation, adaptation to hypoxia, circadian cycle, metabolism and gene regulation and expression. Our analysis of the genome of different kinetoplastid species revealed the presence of PAS domains also in different predicted kinases from these protists. Open-reading frames coding for these PAS-kinases are unusually large. In addition, the products of these genes appear to contain in their structure combinations of domains uncommon in other eukaryotes. The physiological significance of PAS domains in these parasites, specifically in Trypanosoma cruzi, is discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

Temperature Effects on Olive Fruit Fly Infestation in the FlySim Cellular Automata Model

NASA Astrophysics Data System (ADS)

Bruno, Vincenzo; Baldacchini, Valerio; di Gregorio, Salvatore

FlySim is a Cellular Automata model developed for simulating infestation of olive fruit flies (Bactrocera Oleae) on olive (Olea europaea) groves. The flies move into the groves looking for mature olives where eggs are spawn. This serious agricultural problem is mainly tackled by using chemical agents at the first signs of the infestation, but organic productions with no or few chemicals are strongly requested by the market. Oil made with infested olives is poor in quality, nor olives are suitable for selling in stores. The FlySim model simulates the diffusion of flies looking for mature olives and the growing of flies due to atmospheric conditions. Foreseeing an infestation is the best way to prevent it and to reduce the need of chemicals in agriculture. In this work we investigated the effects of temperature on olive fruit flies and resulting infestation during late spring and summer.

Correlated NanoSIMS, TEM, and XANES Studies of Presolar Grains

NASA Astrophysics Data System (ADS)

Groopman, Evan Edward

The objective of this thesis is to describe the correlated study of individual presolar grains via Nano-scale Secondary Ion Mass Spectrometry (NanoSIMS), Transmission Electron Microscopy (TEM), and Scanning Transmission X-ray Microscopy (STXM) utilizing X-ray Absorption Near Edge Structure (XANES), with a focus on connecting these correlated laboratory studies to astrophysical phenomena. The correlated isotopic, chemical, and microstructural studies of individual presolar grains provide the most detailed description of their formation environments, and help to inform astrophysical models and observations of stellar objects. As a part of this thesis I have developed and improved upon laboratory techniques for micromanipulating presolar grains and embedding them in resin for ultramicrotomy after NanoSIMS analyses and prior to TEM characterization. The new methods have yielded a 100% success rate and allow for the specific correlation of microstructural and isotopic properties of individual grains. Knowing these properties allows for inferences to be made regarding the condensation sequences and the origins of the stellar material that condensed to form these grains. NanoSIMS studies of ultramicrotomed sections of presolar graphite grains have revealed complex isotopic heterogeneities that appear to be primary products of the grains' formation environments and not secondary processing during the grains' lifetimes. Correlated excesses in 15N and 18O were identified as being carried by TiC subgrains within presolar graphite grains from supernovae (SNe). These spatially-correlated isotopic anomalies pinpoint the origin of the material that formed these grains: the inner He/C zone. Complex microstructures and isotopic heterogeneities also provide evidence for mixing in globular SN ejecta, which is corroborated by models and telescopic observations. In addition to these significant isotopic discoveries, I have also observed the first reported nanocrystalline core

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

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.

Memory-Modulation: Self-Improvement or Self-Depletion?

PubMed

Lavazza, Andrea

2018-01-01

Autobiographical memory is fundamental to the process of self-construction. Therefore, the possibility of modifying autobiographical memories, in particular with memory-modulation and memory-erasing, is a very important topic both from the theoretical and from the practical point of view. The aim of this paper is to illustrate the state of the art of some of the most promising areas of memory-modulation and memory-erasing, considering how they can affect the self and the overall balance of the "self and autobiographical memory" system. Indeed, different conceptualizations of the self and of personal identity in relation to autobiographical memory are what makes memory-modulation and memory-erasing more or less desirable. Because of the current limitations (both practical and ethical) to interventions on memory, I can only sketch some hypotheses. However, it can be argued that the choice to mitigate painful memories (or edit memories for other reasons) is somehow problematic, from an ethical point of view, according to some of the theories of the self and personal identity in relation to autobiographical memory, in particular for the so-called narrative theories of personal identity, chosen here as the main case of study. Other conceptualizations of the "self and autobiographical memory" system, namely the constructivist theories, do not have this sort of critical concerns. However, many theories rely on normative (and not empirical) conceptions of the self: for them, the actions aimed at mitigating or removing specific (negative) memories can be seen either as an improvement or as a depletion or impairment of the self.

Memory-Modulation: Self-Improvement or Self-Depletion?

PubMed Central

Lavazza, Andrea

2018-01-01

Autobiographical memory is fundamental to the process of self-construction. Therefore, the possibility of modifying autobiographical memories, in particular with memory-modulation and memory-erasing, is a very important topic both from the theoretical and from the practical point of view. The aim of this paper is to illustrate the state of the art of some of the most promising areas of memory-modulation and memory-erasing, considering how they can affect the self and the overall balance of the “self and autobiographical memory” system. Indeed, different conceptualizations of the self and of personal identity in relation to autobiographical memory are what makes memory-modulation and memory-erasing more or less desirable. Because of the current limitations (both practical and ethical) to interventions on memory, I can only sketch some hypotheses. However, it can be argued that the choice to mitigate painful memories (or edit memories for other reasons) is somehow problematic, from an ethical point of view, according to some of the theories of the self and personal identity in relation to autobiographical memory, in particular for the so-called narrative theories of personal identity, chosen here as the main case of study. Other conceptualizations of the “self and autobiographical memory” system, namely the constructivist theories, do not have this sort of critical concerns. However, many theories rely on normative (and not empirical) conceptions of the self: for them, the actions aimed at mitigating or removing specific (negative) memories can be seen either as an improvement or as a depletion or impairment of the self. PMID:29674992

Combined TEM and NanoSIMS Analysis of Subgrains in a SiC AB Grain

NASA Astrophysics Data System (ADS)

Hynes, K. M.; Amari, S.; Bernatowicz, T. J.; Lebsack, E.; Gyngard, F.; Nittler, L. R.

2011-03-01

We report the results of NanoSIMS and TEM analysis, including isotopic, structural, chemical, and subgrain data, on a SiC AB grain. This grain contains the first oldhamite subgrains observed in a presolar grain, as well as TiC- and Fe-rich subgrains.

HexSim: A flexible simulation model for forecasting wildlife responses to multiple interacting stressors

EPA Science Inventory

With SERDP funding, we have improved upon a popular life history simulator (PATCH), and in doing so produced a powerful new forecasting tool (HexSim). PATCH, our starting point, was spatially explicit and individual-based, and was useful for evaluating a range of terrestrial lif...

SIM PlanetQuest Spectral Calibration Development Unit Beam Combiner

NASA Technical Reports Server (NTRS)

Tang, Hong

2008-01-01

The beam combiner of an astronomical long-baseline interferometer combines the two beams of starlight to form white-light fringes. We describe beam combiner in the SIM PlanetQuest Spectral Calibration Development Unit (SCDU). In addition to forming white light fringes, the beam combiner provides other functions such as separating the light for guiding, fringe tracking, and science measurement. It is designed to function over the optical bandpass 450-950 nm. Coating design is critical to beam combiner as residual dispersion and mismatches affect the ability to accurately measure the position of stars of varying spectral types.

Securing electronic health records with novel mobile encryption schemes.

PubMed

Weerasinghe, Dasun; Elmufti, Kalid; Rajarajan, Muttukrishnan; Rakocevic, Veselin

2007-01-01

Mobile devices have penetrated the healthcare sector due to their increased functionality, low cost, high reliability and easy-to-use nature. However, in healthcare applications the privacy and security of the transmitted information must be preserved. Therefore applications require a concrete security framework based on long-term security keys, such as the security key that can be found in a mobile Subscriber Identity Module (SIM). The wireless nature of communication links in mobile networks presents a major challenge in this respect. This paper presents a novel protocol that will send the information securely while including the access privileges to the authorized recipient.

Imaging of Crystalline and Amorphous Surface Regions Using Time-of-Flight Secondary-Ion Mass Spectrometry (ToF-SIMS): Application to Pharmaceutical Materials.

PubMed

Iuraş, Andreea; Scurr, David J; Boissier, Catherine; Nicholas, Mark L; Roberts, Clive J; Alexander, Morgan R

2016-04-05

The structure of a material, in particular the extremes of crystalline and amorphous forms, significantly impacts material performance in numerous sectors such as semiconductors, energy storage, and pharmaceutical products, which are investigated in this paper. To characterize the spatial distribution for crystalline-amorphous forms at the uppermost molecular surface layer, we performed time-of-flight secondary-ion mass spectroscopy (ToF-SIMS) measurements for quench-cooled amorphous and recrystallized samples of the drugs indomethacin, felodipine, and acetaminophen. Polarized light microscopy was used to localize crystallinity induced in the samples under controlled conditions. Principal component analysis was used to identify the subtle changes in the ToF-SIMS spectra indicative of the amorphous and crystalline forms for each drug. The indicators of amorphous and crystalline surfaces were common in type across the three drugs, and could be explained in general terms of crystal packing and intermolecular bonding, leading to intramolecular bond scission in the formation of secondary ions. Less intramolecular scission occurred in the amorphous form, resulting in a greater intensity of molecular and dimer secondary ions. To test the generality of amorphous-crystalline differentiation using ToF-SIMS, a different recrystallization method was investigated where acetaminophen single crystals were recrystallized from supersaturated solutions. The findings indicated that the ability to assign the crystalline/amorphous state of the sample using ToF-SIMS was insensitive to the recrystallization method. This demonstrates that ToF-SIMS is capable of detecting and mapping ordered crystalline and disordered amorphous molecular materials forms at micron spatial resolution in the uppermost surface of a material.

Ultrasound-Assisted Extraction and Identification of Natural Antioxidants from the Fruit of Melastoma sanguineum Sims.

PubMed

Zhou, Tong; Xu, Dong-Ping; Lin, Sheng-Jun; Li, Ya; Zheng, Jie; Zhou, Yue; Zhang, Jiao-Jiao; Li, Hua-Bin

2017-02-18

The fruit of Melastoma sanguineum Sims is an edible and sweet wild fruit. In our previous study, the fruit was found to have a strong antioxidant property. In this study, an ultrasound-assisted extraction (UAE) method was developed to extract natural antioxidants from the fruit of Melastoma sanguineum Sims, and a response surface methodology was used to optimize the conditions of UAE to maximize the extraction efficiency. The influence of five independent extraction parameters (ethanol concentration, solvent/material ratio, extracting time, temperature, and ultrasound power) on the extraction efficiency were investigated using a single factor experiment, and then a central composite rotatable design was used to investigate the interaction of three key parameters. The results showed that the optimal extraction conditions were 42.98% ethanol, 28.29 mL/g solvent/material ratio, 34.29 min extracting time, 60 °C temperature, and 600 W ultrasound power. Under these conditions, the Trolox equivalent antioxidant capacity (TEAC) value of the extracts was 1074.61 ± 32.56 μmol Trolox/g dry weight (DW). Compared with conventional maceration (723.27 ± 11.61 μmol Trolox/g DW) and Soxhlet extraction methods (518.37 ± 23.23 μmol Trolox/g DW), the UAE method improved the extraction efficiency, in a shorter period of time. In addition, epicatechin gallate, epicatechin, rutin, epigallocatechin, protocatechuic acid, chlorogenic acid, and quercetin, were identified and quantified in the fruit extracts of Melastoma sanguineum Sims by UPLC-MS/MS.

SIM PlanetQuest Key Project Precursor Observations to Detect Gas Giant Planets Around Young Stars

NASA Technical Reports Server (NTRS)

Tanner, Angelle; Beichman, Charles; Akeson, Rachel; Ghez, Andrea; Grankin, Konstantin N.; Herbst, William; Hillenbrand, Lynne; Huerta, Marcos; Konopacky, Quinn; Metchev, Stanimir;