Mena/VASP and αII-Spectrin complexes regulate cytoplasmic actin networks in cardiomyocytes and protect from conduction abnormalities and dilated cardiomyopathy.

PubMed

Benz, Peter M; Merkel, Carla J; Offner, Kristin; Abeßer, Marco; Ullrich, Melanie; Fischer, Tobias; Bayer, Barbara; Wagner, Helga; Gambaryan, Stepan; Ursitti, Jeanine A; Adham, Ibrahim M; Linke, Wolfgang A; Feller, Stephan M; Fleming, Ingrid; Renné, Thomas; Frantz, Stefan; Unger, Andreas; Schuh, Kai

2013-08-12

In the heart, cytoplasmic actin networks are thought to have important roles in mechanical support, myofibrillogenesis, and ion channel function. However, subcellular localization of cytoplasmic actin isoforms and proteins involved in the modulation of the cytoplasmic actin networks are elusive. Mena and VASP are important regulators of actin dynamics. Due to the lethal phenotype of mice with combined deficiency in Mena and VASP, however, distinct cardiac roles of the proteins remain speculative. In the present study, we analyzed the physiological functions of Mena and VASP in the heart and also investigated the role of the proteins in the organization of cytoplasmic actin networks. We generated a mouse model, which simultaneously lacks Mena and VASP in the heart. Mena/VASP double-deficiency induced dilated cardiomyopathy and conduction abnormalities. In wild-type mice, Mena and VASP specifically interacted with a distinct αII-Spectrin splice variant (SH3i), which is in cardiomyocytes exclusively localized at Z- and intercalated discs. At Z- and intercalated discs, Mena and β-actin localized to the edges of the sarcomeres, where the thin filaments are anchored. In Mena/VASP double-deficient mice, β-actin networks were disrupted and the integrity of Z- and intercalated discs was markedly impaired. Together, our data suggest that Mena, VASP, and αII-Spectrin assemble cardiac multi-protein complexes, which regulate cytoplasmic actin networks. Conversely, Mena/VASP deficiency results in disrupted β-actin assembly, Z- and intercalated disc malformation, and induces dilated cardiomyopathy and conduction abnormalities.

Bacterial communities and enzymatic activities in the vegetation-activated sludge process (V-ASP) and related advantages by comparison with conventional constructed wetland.

PubMed

Yuan, Jiajia; Dong, Wenyi; Sun, Feiyun; Zhao, Ke; Du, Changhang; Shao, Yunxian

2016-11-01

A new-developed vegetation-activated sludge process (V-ASP) was implemented for decentralized domestic wastewater treatment, and studied in lab-scale and full-scale. The main purpose of this work was the investigation of biomass activities and microbial communities in V-ASP by comparison with conventional constructed wetland (CW), to unveil the causations of its consistently higher pollutants removal efficiencies. Compared with CWs, V-ASP has greater vegetation nitrogen and phosphorus uptake rates, higher biomass and enzymatic activities, and more bacteria community diversity. The microbial community structure was comprehensively analyzed by using high-throughput sequencing. It was observed that Proteobacteria was dominated in both CWs and V-ASPs, while their subdivisions distribution was rather different. V-ASPs contained a higher nitrite-oxidizing bacteria (Nitrospira) abundances that resulted in a consistently better nitrogen removal efficiency. Hence, a long-term experiment of full-scale V-ASP displayed stably excellent capability in resistance of influent loading shocks and seasonal temperature effect. Copyright © 2016 Elsevier Ltd. All rights reserved.

WAVE binds Ena/VASP for enhanced Arp2/3 complex–based actin assembly

PubMed Central

Havrylenko, Svitlana; Noguera, Philippe; Abou-Ghali, Majdouline; Manzi, John; Faqir, Fahima; Lamora, Audrey; Guérin, Christophe; Blanchoin, Laurent; Plastino, Julie

2015-01-01

The WAVE complex is the main activator of the Arp2/3 complex for actin filament nucleation and assembly in the lamellipodia of moving cells. Other important players in lamellipodial protrusion are Ena/VASP proteins, which enhance actin filament elongation. Here we examine the molecular coordination between the nucleating activity of the Arp2/3 complex and the elongating activity of Ena/VASP proteins for the formation of actin networks. Using an in vitro bead motility assay, we show that WAVE directly binds VASP, resulting in an increase in Arp2/3 complex–based actin assembly. We show that this interaction is important in vivo as well, for the formation of lamellipodia during the ventral enclosure event of Caenorhabditis elegans embryogenesis. Ena/VASP's ability to bind F-actin and profilin-complexed G-actin are important for its effect, whereas Ena/VASP tetramerization is not necessary. Our data are consistent with the idea that binding of Ena/VASP to WAVE potentiates Arp2/3 complex activity and lamellipodial actin assembly. PMID:25355952

Ternary alloy material prediction using genetic algorithm and cluster expansion

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

Chen, Chong

2015-12-01

This thesis summarizes our study on the crystal structures prediction of Fe-V-Si system using genetic algorithm and cluster expansion. Our goal is to explore and look for new stable compounds. We started from the current ten known experimental phases, and calculated formation energies of those compounds using density functional theory (DFT) package, namely, VASP. The convex hull was generated based on the DFT calculations of the experimental known phases. Then we did random search on some metal rich (Fe and V) compositions and found that the lowest energy structures were body centered cube (bcc) underlying lattice, under which we didmore » our computational systematic searches using genetic algorithm and cluster expansion. Among hundreds of the searched compositions, thirteen were selected and DFT formation energies were obtained by VASP. The stability checking of those thirteen compounds was done in reference to the experimental convex hull. We found that the composition, 24-8-16, i.e., Fe 3VSi 2 is a new stable phase and it can be very inspiring to the future experiments.« less

Computational Thermodynamics of Materials Zi-Kui Liu and Yi Wang

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

Devanathan, Ram

This authoritative volume introduces the reader to computational thermodynamics and the use of this approach to the design of material properties by tailoring the chemical composition. The text covers applications of this approach, introduces the relevant computational codes, and offers exercises at the end of each chapter. The book has nine chapters and two appendices that provide background material on computer codes. Chapter 1 covers the first and second laws of thermodynamics, introduces the spinodal as the limit of stability, and presents the Gibbs-Duhem equation. Chapter 2 focuses on the Gibbs energy function. Starting with a homogeneous system with amore » single phase, the authors proceed to phases with variable compositions, and polymer blends. The discussion includes the contributions of external electric and magnetic fields to the Gibbs energy. Chapter 3 deals with phase equilibria in heterogeneous systems, the Gibbs phase rule, and phase diagrams. Chapter 4 briefly covers experimental measurements of thermodynamic properties used as input for thermodynamic modeling by Calculation of Phase Diagrams (CALPHAD). Chapter 5 discusses the use of density functional theory to obtain thermochemical data and fill gaps where experimental data is missing. The reader is introduced to the Vienna Ab Initio Simulation Package (VASP) for density functional theory and the YPHON code for phonon calculations. Chapter 6 introduces the modeling of Gibbs energy of phases with the CALPHAD method. Chapter 7 deals with chemical reactions and the Ellingham diagram for metal-oxide systems and presents the calculation of the maximum reaction rate from equilibrium thermodynamics. Chapter 8 is devoted to electrochemical reactions and Pourbaix diagrams with application examples. Chapter 9 concludes this volume with the application of a model of multiple microstates to Ce and Fe3Pt. CALPHAD modeling is briefly discussed in the context of genomics of materials. The book introduces basic thermodynamic concepts clearly and directs readers to appropriate references for advanced concepts and details of software implementation. The list of references is quite comprehensive. The authors make liberal use of diagrams to illustrate key concepts. The two Appendices at the end discuss software requirements and the file structure, and present templates for special quasi-random structures. There is also a link to download pre-compiled binary files of the YPHON code for Linux or Microsoft Windows systems. The exercises at the end of the chapters assume that the reader has access to VASP, which is not freeware. Readers without access to this code can work on a limited number of exercises. However, results from other first principles codes can be organized in the YPHON format as explained in the Appendix. This book will serve as an excellent reference on computational thermodynamics and the exercises provided at the end of each chapter make it valuable as a graduate level textbook. Reviewer: Ram Devanathan is Acting Director of Earth Systems Science Division, Pacific Northwest National Laboratory, USA.« less

Low temperature effects on nitrification and nitrifier community structure in V-ASP for decentralized wastewater treatment and its improvement by bio-augmentation.

PubMed

Yuan, Jiajia; Dong, Wenyi; Sun, Feiyun; Zhao, Ke

2018-03-01

The vegetation-activated sludge process (V-ASP) has been proved to be an environment-friendly decentralized wastewater treatment system with extra esthetic function and less footprint. However, the effects of low temperature on the treatment performance of V-ASP and related improvement methods are rarely investigated, up to now. In this work, the effect of low temperature on nitrification in V-ASP was comprehensively investigated from overall nitrification performance, substrate utilization kinetics, functional enzymatic activities, and microbial community structure shift by comparison with conventional ASP. Bio-augmentation methods in terms of single-time nitrifier-enriched biomass dosage were employed to improve nitrification efficiency in bench- and full-scale systems. The experiment results demonstrated that the NH 4 + -N removal efficiency in V-ASP system decreased when the operational temperature decreased from 30 to 15 °C, and the decreasing extent was rather smaller compared to ASP, as well as ammonium and nitrite oxidation rates and enzymatic activities, which indicated the V-ASP system possesses high resistance to low temperature. With direct dosage of 1.6 mg nitrifier/gSS sludge, the nitrification efficiency in V-ASP was enhanced dramatically from below 50% to above 90%, implying that bio-augmentation was effective for V-ASP whose enzymatic activities and microbial communities were both also improved. The feasibility and effectiveness of bio-augmentation was further confirmed in a full-scale V-ASP system after a long-term experiment which is instructive for the practical application.

A WASp–VASP complex regulates actin polymerization at the plasma membrane

PubMed Central

Castellano, Flavia; Le Clainche, Christophe; Patin, Delphine; Carlier, Marie-France; Chavrier, Philippe

2001-01-01

Proteins of the Wiskott–Aldrich syndrome and Ena/VASP families both play essential functions in the regulation of actin dynamics at the cell leading edge. However, possibilities of functional interplay between members of these two families have not been addressed. Here we show that, in hemopoietic cells, recruitment of the C-terminal VCA (Verprolin homology, Cofilin homology, Acidic) domain of WASp at the plasma membrane by a ligand technique using rapamycin as an intermediate is not sufficient to elicit efficient Arp2/3 complex-mediated actin polymerization. Other domains of WASp, in particular the proline-rich domain, are required for the formation of actin-rich structures. An in vitro analysis demonstrates that the proline-rich domain of WASp binds VASP with an affinity of ∼106 M–1. In addition, WASp and VASP both accumulate in actin-rich phagocytic cups. Finally, in a reconstituted motility medium, VASP enhances actin-based propulsion of WASp-coated beads in a fashion reminiscent of its effect on Listeria movement. We propose that VASP and WASp cooperation is essential in stimulating actin assembly and membrane protrusion at the leading edge. PMID:11598004

Users manual for the Variable dimension Automatic Synthesis Program (VASP)

NASA Technical Reports Server (NTRS)

White, J. S.; Lee, H. Q.

1971-01-01

A dictionary and some problems for the Variable Automatic Synthesis Program VASP are submitted. The dictionary contains a description of each subroutine and instructions on its use. The example problems give the user a better perspective on the use of VASP for solving problems in modern control theory. These example problems include dynamic response, optimal control gain, solution of the sampled data matrix Ricatti equation, matrix decomposition, and pseudo inverse of a matrix. Listings of all subroutines are also included. The VASP program has been adapted to run in the conversational mode on the Ames 360/67 computer.

Tributyltin induces disruption of microfilament in HL7702 cells via MAPK-mediated hyperphosphorylation of VASP.

PubMed

Tu, Wei-Wei; Ji, Lin-Dan; Qian, Hai-Xia; Zhou, Mi; Zhao, Jin-Shun; Xu, Jin

2016-11-01

Tributyltin (TBT) has been widely used for various industrial purposes, and it has toxic effects on multiple organs and tissues. Previous studies have found that TBT could induce cytoskeletal disruption, especially of the actin filaments. However, the underlying mechanisms remain unclear. The aim of the present study was to determine whether TBT could induce microfilament disruption using HL7702 cells and then to assess for the total levels of various microfilament-associated proteins; finally, the involvement of the MAPK pathway was investigated. The results showed that after TBT treatment, F-actin began to depolymerize and lost its characteristic filamentous structure. The protein levels of Ezrin and Cofilin remained unchanged, the actin-related protein (ARP) 2/3 levels decreased slightly, and the vasodilator-stimulated phosphoprotein (VASP) decreased dramatically. However, the phosphorylation levels of VASP increased 2.5-fold, and the ratio of phosphorylated-VASP/unphosphorylated-VASP increased 31-fold. The mitogen-activated protein kinases (MAPKs) ERK and JNK were discovered to be activated. Inhibition of ERK and JNK not only largely diminished the TBT-induced hyperphosphorylation of VASP but also recovered the cellular morphology and rescued the cells from death. In summary, this study demonstrates that TBT-induced disruption of actin filaments is caused by the hyperphosphorylation of VASP through MAPK pathways. © 2015 Wiley Periodicals, Inc. Environ Toxicol 31: 1530-1538, 2016. © 2015 Wiley Periodicals, Inc.

Tumor suppressor berberine binds VASP to inhibit cell migration in basal-like breast cancer.

PubMed

Su, Ke; Hu, Pengchao; Wang, Xiaolan; Kuang, Changchun; Xiang, Qingmin; Yang, Fang; Xiang, Jin; Zhu, Shan; Wei, Lei; Zhang, Jingwei

2016-07-19

Berberine is a plant-derived compound used in traditional Chinese medicine, which has been shown to inhibit cell proliferation and migration in breast cancer. On the other hand, vasodilator-stimulated phosphoprotein (VASP) promotes actin filament elongation and cell migration. We previously showed that VASP is overexpressed in high-motility breast cancer cells. Here we investigated whether the anti-tumorigenic effects of berberine are mediated by binding VASP in basal-like breast cancer. Our results show that berberine suppresses proliferation and migration of MDA-MB-231 cells as well as tumor growth in MDA-MB-231 nude mouse xenografts. We also show that berberine binds to VASP, inducing changes in its secondary structure and inhibits actin polymerization. Our study reveals the mechanism underlying berberine's inhibition of cell proliferation and migration in basal-like breast cancer, highlighting the use of berberine as a potential adjuvant therapeutic agent.

Tumor suppressor berberine binds VASP to inhibit cell migration in basal-like breast cancer

PubMed Central

Wang, Xiaolan; Kuang, Changchun; Xiang, Qingmin; Yang, Fang; Xiang, Jin; Zhu, Shan; Wei, Lei; Zhang, Jingwei

2016-01-01

Berberine is a plant-derived compound used in traditional Chinese medicine, which has been shown to inhibit cell proliferation and migration in breast cancer. On the other hand, vasodilator-stimulated phosphoprotein (VASP) promotes actin filament elongation and cell migration. We previously showed that VASP is overexpressed in high-motility breast cancer cells. Here we investigated whether the anti-tumorigenic effects of berberine are mediated by binding VASP in basal-like breast cancer. Our results show that berberine suppresses proliferation and migration of MDA-MB-231 cells as well as tumor growth in MDA-MB-231 nude mouse xenografts. We also show that berberine binds to VASP, inducing changes in its secondary structure and inhibits actin polymerization. Our study reveals the mechanism underlying berberine's inhibition of cell proliferation and migration in basal-like breast cancer, highlighting the use of berberine as a potential adjuvant therapeutic agent. PMID:27322681

Ab initio MD simulations of Mg2SiO4 liquid at high pressures and temperatures relevant to the Earth's mantle

NASA Astrophysics Data System (ADS)

Martin, G. B.; Kirtman, B.; Spera, F. J.

2010-12-01

Computational studies implementing Density Functional Theory (DFT) methods have become very popular in the Materials Sciences in recent years. DFT codes are now used routinely to simulate properties of geomaterials—mainly silicates and geochemically important metals such as Fe. These materials are ubiquitous in the Earth’s mantle and core and in terrestrial exoplanets. Because of computational limitations, most First Principles Molecular Dynamics (FPMD) calculations are done on systems of only 100 atoms for a few picoseconds. While this approach can be useful for calculating physical quantities related to crystal structure, vibrational frequency, and other lattice-scale properties (especially in crystals), it would be useful to be able to compute larger systems especially for extracting transport properties and coordination statistics. Previous studies have used codes such as VASP where CPU time increases as N2, making calculations on systems of more than 100 atoms computationally very taxing. SIESTA (Soler, et al. 2002) is a an order-N (linear-scaling) DFT code that enables electronic structure and MD computations on larger systems (N 1000) by making approximations such as localized numerical orbitals. Here we test the applicability of SIESTA to simulate geosilicates in the liquid and glass state. We have used SIESTA for MD simulations of liquid Mg2SiO4 at various state points pertinent to the Earth’s mantle and congruous with those calculated in a previous DFT study using the VASP code (DeKoker, et al. 2008). The core electronic wave functions of Mg, Si, and O were approximated using pseudopotentials with a core cutoff radius of 1.38, 1.0, and 0.61 Angstroms respectively. The Ceperly-Alder parameterization of the Local Density Approximation (LDA) was used as the exchange-correlation functional. Known systematic overbinding of LDA was corrected with the addition of a pressure term, P 1.6 GPa, which is the pressure calculated by SIESTA at the experimental zero-pressure volume of forsterite under static conditions (Stixrude and Lithgow-Bertollini 2005). Results are reported here that show SIESTA calculations of T and P on densities in the range of 2.7 - 5.0 g/cc of liquid Mg2SiO4 are similar to the VASP calculations of DeKoker et al. (2008), which used the same functional. This opens the possibility of conducting fast /emph{ab initio} MD simulations of geomaterials with a hundreds of atoms.

VASP-4096: a very high performance programmable device for digital media processing applications

NASA Astrophysics Data System (ADS)

Krikelis, Argy

2001-03-01

Over the past few years, technology drivers for microprocessors have changed significantly. Media data delivery and processing--such as telecommunications, networking, video processing, speech recognition and 3D graphics--is increasing in importance and will soon dominate the processing cycles consumed in computer-based systems. This paper presents the architecture of the VASP-4096 processor. VASP-4096 provides high media performance with low energy consumption by integrating associative SIMD parallel processing with embedded microprocessor technology. The major innovations in the VASP-4096 is the integration of thousands of processing units in a single chip that are capable of support software programmable high-performance mathematical functions as well as abstract data processing. In addition to 4096 processing units, VASP-4096 integrates on a single chip a RISC controller that is an implementation of the SPARC architecture, 128 Kbytes of Data Memory, and I/O interfaces. The SIMD processing in VASP-4096 implements the ASProCore architecture, which is a proprietary implementation of SIMD processing, operates at 266 MHz with program instructions issued by the RISC controller. The device also integrates a 64-bit synchronous main memory interface operating at 133 MHz (double-data rate), and a 64- bit 66 MHz PCI interface. VASP-4096, compared with other processors architectures that support media processing, offers true performance scalability, support for deterministic and non-deterministic data processing on a single device, and software programmability that can be re- used in future chip generations.

Vasodilator-stimulated phosphoprotein promotes activation of hepatic stellate cells by regulating Rab11-dependent plasma membrane targeting of transforming growth factor beta receptors.

PubMed

Tu, Kangsheng; Li, Jiachu; Verma, Vikas K; Liu, Chunsheng; Billadeau, Daniel D; Lamprecht, Georg; Xiang, Xiaoyu; Guo, Luyang; Dhanasekaran, Renumathy; Roberts, Lewis R; Shah, Vijay H; Kang, Ningling

2015-01-01

Liver microenvironment is a critical determinant for development and progression of liver metastasis. Under transforming growth factor beta (TGF-β) stimulation, hepatic stellate cells (HSCs), which are liver-specific pericytes, transdifferentiate into tumor-associated myofibroblasts that promote tumor implantation (TI) and growth in the liver. However, the regulation of this HSC activation process remains poorly understood. In this study, we tested whether vasodilator-stimulated phosphoprotein (VASP) of HSCs regulated the TGF-β-mediated HSC activation process and tumor growth. In both an experimental liver metastasis mouse model and cancer patients, colorectal cancer cells reaching liver sinusoids induced up-regulation of VASP and alpha-smooth muscle actin (α-SMA) in adjacent HSCs. VASP knockdown in HSCs inhibited TGF-β-mediated myofibroblastic activation of HSCs, TI, and growth in mice. Mechanistically, VASP formed protein complexes with TGF-β receptor II (TβRII) and Rab11, a Ras-like small GTPase and key regulator of recycling endosomes. VASP knockdown impaired Rab11 activity and Rab11-dependent targeting of TβRII to the plasma membrane, thereby desensitizing HSCs to TGF-β1 stimulation. Our study demonstrates a requirement of VASP for TGF-β-mediated HSC activation in the tumor microenvironment by regulating Rab11-dependent recycling of TβRII to the plasma membrane. VASP and its effector, Rab11, in the tumor microenvironment thus present therapeutic targets for reducing TI and metastatic growth in the liver. © 2014 by the American Association for the Study of Liver Diseases.

Study of salivary and serum vaspin and total antioxidants in anorexia nervosa.

PubMed

Paszynska, Elzbieta; Tyszkiewicz-Nwafor, Marta; Slopien, Agnieszka; Dmitrzak-Weglarz, Monika; Dutkiewicz, Agata; Grzelak, Teresa

2018-02-14

Patients with anorexia nervosa (AN) are primarily at high risk of multiple somatic complications, including oral diseases. In recent years, a number of new molecules that may play a potentially important role in AN progress and prognosis have been identified in saliva, but their exact roles are still poorly understood. Two such group of substances are antioxidants and vaspin. The purpose of this observational, cross-sectional study was to measure both the salivary and serum total antioxidant status (TAS), and vaspin (VASP) concentrations of patients with AN in comparison to an average population. Ninety subjects participated (30 patients with AN, 60 matched healthy control subjects). A clinical examination was made, and blood and salivary samples were taken during the acute stage of AN (BMI < 15 kg/m 2 ) in the first week of hospitalization. Enzyme immunoassay (ELISA) suitable for measuring VASP and colorimetric assay for TAS were used. Anorexic patients had significant reductions in salivary flow, TAS, and an elevation in VASP levels in their saliva and serum. Significant correlations between TAS, VASP, salivary flow, and nutritional status were detected. Determination of TAS and VASP in combined biological material confirmed that saliva might be a reliable non-invasive source of information for potent nutritional biomarkers. Our findings suggest that VASP cannot be excluded, as its increased concentration in saliva is an adaptive mechanism in reduced TAS, one resulting from diminished salivary secretion. It is therefore worth conducting further research aimed at recognizing the role of TAS and VASP in the saliva of underweight patients.

VASP- VARIABLE DIMENSION AUTOMATIC SYNTHESIS PROGRAM

NASA Technical Reports Server (NTRS)

White, J. S.

1994-01-01

VASP is a variable dimension Fortran version of the Automatic Synthesis Program, ASP. The program is used to implement Kalman filtering and control theory. Basically, it consists of 31 subprograms for solving most modern control problems in linear, time-variant (or time-invariant) control systems. These subprograms include operations of matrix algebra, computation of the exponential of a matrix and its convolution integral, and the solution of the matrix Riccati equation. The user calls these subprograms by means of a FORTRAN main program, and so can easily obtain solutions to most general problems of extremization of a quadratic functional of the state of the linear dynamical system. Particularly, these problems include the synthesis of the Kalman filter gains and the optimal feedback gains for minimization of a quadratic performance index. VASP, as an outgrowth of the Automatic Synthesis Program, has the following improvements: more versatile programming language; more convenient input/output format; some new subprograms which consolidate certain groups of statements that are often repeated; and variable dimensioning. The pertinent difference between the two programs is that VASP has variable dimensioning and more efficient storage. The documentation for the VASP program contains a VASP dictionary and example problems. The dictionary contains a description of each subroutine and instructions on its use. The example problems include dynamic response, optimal control gain, solution of the sampled data matrix Riccati equation, matrix decomposition, and a pseudo-inverse of a matrix. This program is written in FORTRAN IV and has been implemented on the IBM 360. The VASP program was developed in 1971.

Nexus: A modular workflow management system for quantum simulation codes

NASA Astrophysics Data System (ADS)

Krogel, Jaron T.

2016-01-01

The management of simulation workflows represents a significant task for the individual computational researcher. Automation of the required tasks involved in simulation work can decrease the overall time to solution and reduce sources of human error. A new simulation workflow management system, Nexus, is presented to address these issues. Nexus is capable of automated job management on workstations and resources at several major supercomputing centers. Its modular design allows many quantum simulation codes to be supported within the same framework. Current support includes quantum Monte Carlo calculations with QMCPACK, density functional theory calculations with Quantum Espresso or VASP, and quantum chemical calculations with GAMESS. Users can compose workflows through a transparent, text-based interface, resembling the input file of a typical simulation code. A usage example is provided to illustrate the process.

Investigation of structural stability and elastic properties of CrH and MnH: A first principles study

NASA Astrophysics Data System (ADS)

Kanagaprabha, S.; Rajeswarapalanichamy, R.; Sudhapriyanga, G.; Murugan, A.; Santhosh, M.; Iyakutti, K.

2015-06-01

The structural and mechanical properties of CrH and MnH are investigated using first principles calculation based on density functional theory as implemented in VASP code with generalized gradient approximation. The calculated ground state properties are in good agreement with previous experimental and other theoretical results. A structural phase transition from NaCl to NiAs phase at a pressure of 76 GPa is predicted for both CrH and MnH.

PKA-regulated VASP phosphorylation promotes extrusion of transformed cells from the epithelium

PubMed Central

Anton, Katarzyna A.; Sinclair, John; Ohoka, Atsuko; Kajita, Mihoko; Ishikawa, Susumu; Benz, Peter M.; Renne, Thomas; Balda, Maria; Matter, Karl; Fujita, Yasuyuki

2014-01-01

ABSTRACT At the early stages of carcinogenesis, transformation occurs in single cells within tissues. In an epithelial monolayer, such mutated cells are recognized by their normal neighbors and are often apically extruded. The apical extrusion requires cytoskeletal reorganization and changes in cell shape, but the molecular switches involved in the regulation of these processes are poorly understood. Here, using stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative mass spectrometry, we have identified proteins that are modulated in transformed cells upon their interaction with normal cells. Phosphorylation of VASP at serine 239 is specifically upregulated in RasV12-transformed cells when they are surrounded by normal cells. VASP phosphorylation is required for the cell shape changes and apical extrusion of Ras-transformed cells. Furthermore, PKA is activated in Ras-transformed cells that are surrounded by normal cells, leading to VASP phosphorylation. These results indicate that the PKA–VASP pathway is a crucial regulator of tumor cell extrusion from the epithelium, and they shed light on the events occurring at the early stage of carcinogenesis. PMID:24963131

Interplay of electronic, structural and magnetic properties as the driving feature of high-entropy CoCrFeNiPd alloys

NASA Astrophysics Data System (ADS)

Calvo-Dahlborg, M.; Cornide, J.; Tobola, J.; Nguyen-Manh, D.; Wróbel, J. S.; Juraszek, J.; Jouen, S.; Dahlborg, U.

2017-05-01

The structural and magnetic properties of CoCrFe y Ni and CoCrFeNi-Pd x alloys earlier investigated experimentally by x-ray and neutron diffraction techniques and magnetometry have been theoretically reproduced using two complementary approaches for electronic structure calculations, i.e. the Korringa-Kohn-Rostoker method with the coherent potential approximation (KKR-CPA) and implemented in the ab initio framework of density functional theory and the Vienna ab initio simulation package (VASP) for supercell models of high-entropy alloy (HEA) structures. The comparison between experimental results and calculations of the lattice constants by both calculation methods indicate that the structure of CoCrFe y Ni is well described by ordered fcc configurations. The values of local magnetic moments on Fe, Co, Cr, and Ni atoms depend not only on the Pd concentration but on chemical disordering. In the case of the CoCrFeNi-Pd x alloys, the KKR-CPA and the VASP calculations of disordered configurations reproduce the experimental values at 5 K up to equimolar composition and at 300 K above. The experimental values above the equimolar composition at 5 K are not satisfactorily reproduced by any of the calculations. The divergence between the experimental and calculated values is related to the variation of the ferromagnetic to paramagnetic transition temperature as a function of palladium content and to the existence of several phases, FeCoCr-rich above room temperature and FeCrPd-rich below, observed by diffraction and detected by microscopy and atom probe investigations. VASP calculations of a FeCrPd-rich phase effectively reproduced both the lattice constant and magnetization of the alloy above equimolar composition. An important conclusion of this work is that the combined analysis of the electronic, structural, and magnetic properties plays an important role in understanding the complexity of magnetic HEAs.

Miniature protein ligands for EVH1 domains: Interplay between affinity, specificity, and cell motility⊥

PubMed Central

Holtzman, Jennifer H.; Woronowicz, Kamil; Golemi-Kotra, Dasantila; Schepartz, Alanna

2008-01-01

Dynamic rearrangements of the actin cytoskeleton power cell motility in contexts ranging from intracellular microbial pathogenesis to axon guidance. The Ena/VASP family proteins--Mena, VASP, and Evl--are believed to control cell motility by serving as a direct link between signaling events and the actin cytoskeleton. Our lab has previously reported a novel miniature protein, pGolemi, which binds with high affinity to the EVH1 domain of Mena (Mena1-112) but not to those of VASP (VASP1-115) or Evl (Evl1-115) and also causes an unusual defect in actin-driven L. monocytogenes motility. Here, we use scanning mutagenesis to examine the effects of single amino acid changes within pGolemi on EVH1 domain affinity and specificity, miniature protein secondary structure, and L. monocytogenes motility. The data suggest that pGolemi contains the expected aPP-like fold and binds Mena1-112 in a manner highly analogous to the proline-rich repeat region of L. monocytogenes ActA protein. Residues throughout pGolemi contribute to both EVH1 domain affinity and paralog specificity. Moreover, the affinities of pGolemi variants for Mena1-112 correlate with selectivity against the EVH1 domains of VASP and Evl. In L. monocytogenes motility assays, speed and speed variability correlate strongly with EVH1 paralog specificity, suggesting that the Ena/VASP paralogs do not play equivalent roles in the process of L. monocytogenes actin tail maturation. PMID:17973491

LiquidLib: A comprehensive toolbox for analyzing classical and ab initio molecular dynamics simulations of liquids and liquid-like matter with applications to neutron scattering experiments

NASA Astrophysics Data System (ADS)

Walter, Nathan P.; Jaiswal, Abhishek; Cai, Zhikun; Zhang, Yang

2018-07-01

Neutron scattering is a powerful experimental technique for characterizing the structure and dynamics of materials on the atomic or molecular scale. However, the interpretation of experimental data from neutron scattering is oftentimes not trivial, partly because scattering methods probe ensemble-averaged information in the reciprocal space. Therefore, computer simulations, such as classical and ab initio molecular dynamics, are frequently used to unravel the time-dependent atomistic configurations that can reproduce the scattering patterns and thus assist in the understanding of the microscopic origin of certain properties of materials. LiquidLib is a post-processing package for analyzing the trajectory of atomistic simulations of liquids and liquid-like matter with application to neutron scattering experiments. From an atomistic simulation, LiquidLib provides the computation of various statistical quantities including the pair distribution function, the weighted and unweighted structure factors, the mean squared displacement, the non-Gaussian parameter, the four-point correlation function, the velocity auto correlation function, the self and collective van Hove correlation functions, the self and collective intermediate scattering functions, and the bond orientational order parameter. LiquidLib analyzes atomistic trajectories generated from packages such as LAMMPS, GROMACS, and VASP. It also offers an extendable platform to conveniently integrate new quantities into the library and integrate simulation trajectories of other file formats for analysis. Weighting the quantities by element-specific neutron-scattering lengths provides results directly comparable to neutron scattering measurements. Lastly, LiquidLib is independent of dimensionality, which allows analysis of trajectories in two, three, and higher dimensions. The code is beginning to find worldwide use.

Nexus: a modular workflow management system for quantum simulation codes

DOE PAGES

Krogel, Jaron T.

2015-08-24

The management of simulation workflows is a significant task for the individual computational researcher. Automation of the required tasks involved in simulation work can decrease the overall time to solution and reduce sources of human error. A new simulation workflow management system, Nexus, is presented to address these issues. Nexus is capable of automated job management on workstations and resources at several major supercomputing centers. Its modular design allows many quantum simulation codes to be supported within the same framework. Current support includes quantum Monte Carlo calculations with QMCPACK, density functional theory calculations with Quantum Espresso or VASP, and quantummore » chemical calculations with GAMESS. Users can compose workflows through a transparent, text-based interface, resembling the input file of a typical simulation code. A usage example is provided to illustrate the process.« less

Structural electronic and mechanical properties of YM2 (M=Mn, Fe, Co) laves phase compounds: First principle calculations analyzed with datamining approach

NASA Astrophysics Data System (ADS)

Saidi, F.; Sebaa, N.; Mahmoudi, A.; Aourag, H.; Merad, G.; Dergal, M.

2018-06-01

We performed first-principle calculations to investigate structural, phase stability, electronic and mechanical properties for the Laves phases YM2 (M = Mn, Fe, Co) with C15, C14 and C36 structures. We used the density functional theory within the framework of both pseudo-potentials and plane wave basis using VASP (Vienna Ab Initio Software Package). The calculated equilibrium structural parameters are in accordance with available theoretical values. Mechanical properties were calculated, discussed, and analyzed with data mining approach in terms of structure stability. The results reveal that YCo2 is harder than YFe2 and YMn2.

Unexpected carboxylate like CO adsorption at the Sr3Ru2O7 (001) surface

NASA Astrophysics Data System (ADS)

Hieckel, Marcel; Mittendorfer, Florian; Redinger, Josef; Stoeger, Bernhard; Wang, Zhiming; Schmid, Michael; Diebold, Ulrike

2014-03-01

Oxide perovskite materials have attracted enormous attention because of a variety of intriguing physical properties ranging from catalysis to multiferroicity. We present a combined experimental and ab-initio (DFT) study with the Vienna Ab initio Simulation Package (VASP) on the adsorption of CO at the Sr3Ru2O7 (001) surface. We identify both a physisorbed and a chemisorbed CO configuraton. Unexpectedly, in the latter case adsorption occurs in a carboxylate (COO) like state. Both configurations have been confirmed by detailed STM experiments and simulations. In addition we find only a small barrier for the carboxylate formation on the surface. Work supported by the Austrian FWF, SFB F45 (FOXSI).

Elastic constants of random solid solutions by SQS and CPA approaches: the case of fcc Ti-Al.

PubMed

Tian, Li-Yun; Hu, Qing-Miao; Yang, Rui; Zhao, Jijun; Johansson, Börje; Vitos, Levente

2015-08-12

Special quasi-random structure (SQS) and coherent potential approximation (CPA) are techniques widely employed in the first-principles calculations of random alloys. Here we scrutinize these approaches by focusing on the local lattice distortion (LLD) and the crystal symmetry effects. We compare the elastic parameters obtained from SQS and CPA calculations, taking the random face-centered cubic (fcc) Ti(1-x)Al(x) (0 ≤ x ≤ 1) alloy as an example of systems with components showing different electronic structures and bonding characteristics. For the CPA and SQS calculations, we employ the Exact Muffin-Tin Orbitals (EMTO) method and the pseudopotential method as implemented in the Vienna Ab initio Simulation Package (VASP), respectively. We show that the predicted trends of the VASP-SQS and EMTO-CPA parameters against composition are in good agreement with each other. The energy associated with the LLD increases with x up to x = 0.625 ~ 0.750 and drops drastically thereafter. The influence of the LLD on the lattice constants and C12 elastic constant is negligible. C11 and C44 decrease after atomic relaxation for alloys with large LLD, however, the trends of C11 and C44 are not significantly affected. In general, the uncertainties in the elastic parameters associated with the symmetry lowering turn out to be superior to the differences between the two techniques including the effect of LLD.

49 CFR 178.905 - Large Packaging identification codes.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Large Packaging identification codes. 178.905... FOR PACKAGINGS Large Packagings Standards § 178.905 Large Packaging identification codes. Large packaging code designations consist of: two numerals specified in paragraph (a) of this section; followed by...

Carbon Monoxide and Nitric Oxide Mediate Cytoskeletal Reorganization in Microvascular Cells via Vasodilator-Stimulated Phosphoprotein Phosphorylation

PubMed Central

Li Calzi, Sergio; Purich, Daniel L.; Chang, Kyung Hee; Afzal, Aqeela; Nakagawa, Takahiko; Busik, Julia V.; Agarwal, Anupam; Segal, Mark S.; Grant, Maria B.

2008-01-01

OBJECTIVE— We examined the effect of the vasoactive agents carbon monoxide (CO) and nitric oxide (NO) on the phosphorylation and intracellular redistribution of vasodilator-stimulated phosphoprotein (VASP), a critical actin motor protein required for cell migration that also controls vasodilation and platelet aggregation. RESEARCH DESIGN AND METHODS— We examined the effect of donor-released CO and NO in endothelial progenitor cells (EPCs) and platelets from nondiabetic and diabetic subjects and in human microvascular endothelial cells (HMECs) cultured under low (5.5 mmol/l) or high (25 mmol/l) glucose conditions. VASP phosphorylation was evaluated using phosphorylation site-specific antibodies. RESULTS— In control platelets, CO selectively promotes phosphorylation at VASP Ser-157, whereas NO promotes phosphorylation primarily at Ser-157 and also at Ser-239, with maximal responses at 1 min with both agents on Ser-157 and at 15 min on Ser-239 with NO treatment. In diabetic platelets, neither agent resulted in VASP phosphorylation. In nondiabetic EPCs, NO and CO increased phosphorylation at Ser-239 and Ser-157, respectively, but this response was markedly reduced in diabetic EPCs. In endothelial cells cultured under low glucose conditions, both CO and NO induced phosphorylation at Ser-157 and Ser-239; however, this response was completely lost when cells were cultured under high glucose conditions. In control EPCs and in HMECs exposed to low glucose, VASP was redistributed to filopodia-like structures following CO or NO exposure; however, redistribution was dramatically attenuated under high glucose conditions. CONCLUSIONS— Vasoactive gases CO and NO promote cytoskeletal changes through site- and cell type–specific VASP phosphorylation, and in diabetes, blunted responses to these agents may lead to reduced vascular repair and tissue perfusion. PMID:18559661

The Mediation of Platelet Quiescence by NO-Releasing Polymers via cGMP-Induced Serine 239 Phosphorylation of Vasodilator-Stimulated Phosphoprotein

PubMed Central

Major, Terry C; Handa, Hitesh; Brisbois, Elizabeth J; Reynolds, Melissa M; Annich, Gail M; Meyerhoff, Mark E; Bartlett, Robert H

2013-01-01

Nitric oxide (NO) releasing (NORel) materials have been shown to create localized increases in NO concentration by the release of NO from a diazeniumdiaolate-containing or S-nitrosothiol-containing polymer coating and the improvement of extracorporeal circulation (ECC) hemocompatibility. However, the mechanism and, in particular, the platelet upregulation of the NO/cGMP signaling protein, vasodilator-stimulated phosphoprotein phosphorylated at serine 239 (P-VASP (ser 239), for the improved ECC hemocompatibility via NO release still needs elucidation. In this work, two NORel polymeric coatings were evaluated in a 4 h rabbit thrombogenicity (RT) model and the anti-thrombotic mechanism investigated for rabbit platelet P-VASP upregulation. Polymer films containing 25 wt% diazeniumdiolated dibutylhexansdiamine (DBHD) or 5 wt% S-nitroso-N-acetylpenicillamine (SNAP) coated on the inner walls of ECC circuits yielded significantly reduced ECC thrombus formation and maintained normal platelet aggregation compared to polymer controls after 4 h of blood exposure. Platelet P-VASP (ser 239), a useful tool to monitor NO/cGMP signaling, was upregulated after 4 h on ECC and markedly increased after ex vivo sodium nitroprusside (SNP) stimulation. Interestingly, in the rabbit platelet, NO did not upregulate the cAMP P-VASP phosphoprotein P-VASP (ser 157) as previously shown in human platelets. These results suggest that NORel polymers preserve rabbit platelet quiescence by sustainng a level of cGMP signaling as monitored by P-VASP (ser 239) upregulation. The upregulation of this NO-mediated platelet signaling mechanism in this RT model indicates the potential for improved thromboresistance of any NORel-coated medical device. PMID:23906514

Tes, a specific Mena interacting partner, breaks the rules for EVH1 binding.

PubMed

Boëda, Batiste; Briggs, David C; Higgins, Theresa; Garvalov, Boyan K; Fadden, Andrew J; McDonald, Neil Q; Way, Michael

2007-12-28

The intracellular targeting of Ena/VASP family members is achieved via the interaction of their EVH1 domain with FPPPP sequence motifs found in a variety of cytoskeletal proteins, including lamellipodin, vinculin, and zyxin. Here we show that the LIM3 domain of Tes, which lacks the FPPPP motif, binds to the EVH1 domain of Mena, but not to those of VASP or Evl. The structure of the LIM3:EVH1 complex reveals that Tes occludes the FPPPP-binding site and competes with FPPPP-containing proteins for EVH1 binding. Structure-based gain-of-function experiments define the molecular basis for the specificity of the Tes-Mena interaction. Consistent with in vitro observations, the LIM3 domain displaces Mena, but not VASP, from the leading edge and focal adhesions. It also regulates cell migration through a Mena-dependent mechanism. Our observations identify Tes as an atypical EVH1 binding partner and a regulator specific to a single Ena/VASP family member.

Nobiletin, a citrus flavonoid, activates vasodilator-stimulated phosphoprotein in human platelets through non-cyclic nucleotide-related mechanisms.

PubMed

Jayakumar, Thanasekaran; Lin, Kao-Chang; Lu, Wan-Jung; Lin, Chia-Ying; Pitchairaj, Geraldine; Li, Jiun-Yi; Sheu, Joen-Rong

2017-01-01

Nobiletin, a bioactive polymethoxylated flavone, has been described to possess a diversity of biological effects through its antioxidant and anti-inflammatory properties. Vasodilator-stimulated phosphoprotein (VASP) is a common substrate for cyclic AMP and cyclic GMP-regulated protein kinases [i.e., cyclic AMP-dependent protein kinase (PKA; also known as protein kinase A) and cyclic GMP-dependent protein kinase (PKG; also known as protein kinase G)] and it has been shown to be directly phosphorylated by protein kinase C (PKC). In the present study, we demonstrate that VASP is phosphorylated by nobiletin in human platelets via a non-cyclic nucleotide-related mechanism. This was confirmed by the use of inhibitors of adenylate cyclase (SQ22536) and guanylate cyclase [1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one (ODQ)], since they prevented VASP phosphorylation induced by nobiletin. Furthormore, this event was also not affected by specific inhibitors of PKA (H-89), PKG (KT5823) and PKC (Ro318220), representing cyclic nucleotide-dependent pathways upon nobiletin-induced VASP phosphorylation. Similarly, inhibitors of p38 mitogen-activated protein kinase (MAPK; SB203580), extracellular signal-regulated kinase 2 (ERK2; PD98059), c-Jun N-terminal kinase 1 (JNK1; SP600125), Akt (LY294002) and nuclear factor-κB (NF-κB; Bay11-7082) did not affect nobiletin‑induced VASP phosphorylation. Moreover, electron spin resonance, dichlorofluorescein fluorescence and western blotting techniques revealed that nobiletin did not affect hydroxyl radicals (OH•), intracellular reactive oxygen species (ROS) and on protein carbonylation, respectively. Furthermore, the nobiletin‑induced VASP phosphorylation was surprisingly reversed by the intracellular antioxidant, N-acetylcysteine (NAC), but not by the inhibitor of NADPH oxidase, diphenyleneiodonium chloride (DPI). It was surprising to observe the differential effects of nobiletin and NAC on VASP phosphorylation in human platelets, since they both have been reported to have antioxidant properties. The likely explanation for this discrepancy is that NAC may bind to allosteric sites on the receptor different from those that nobiletin binds to in human platelets. Taken together, our findings suggest that nobiletin induces VASP phosphorylation in human platelets through non-cyclic nucleotide-related mechanisms. Nevertheless, the exact mechanisms responsible for these effects need to be further confirmed in future studies.

ENA/VASP downregulation triggers cell death by impairing axonal maintenance in hippocampal neurons.

PubMed

Franco, D Lorena; Rezával, Carolina; Cáceres, Alfredo; Schinder, Alejandro F; Ceriani, M Fernanda

2010-06-01

Neurodegenerative diseases encompass a broad variety of motor and cognitive disorders that are accompanied by death of specific neuronal populations or brain regions. Cellular and molecular mechanisms underlying these complex disorders remain largely unknown. In a previous work we searched for novel Drosophila genes relevant for neurodegeneration and singled out enabled (ena), which encodes a protein involved in cytoskeleton remodeling. To extend our understanding on the mechanisms of ENA-triggered degeneration we now investigated the effect of silencing ena ortholog genes in mouse hippocampal neurons. We found that ENA/VASP downregulation led to neurite retraction and concomitant neuronal cell death through an apoptotic pathway. Remarkably, this retraction initially affected the axonal structure, showing no effect on dendrites. Reduction in ENA/VASP levels blocked the neuritogenic effect of a specific RhoA kinase (ROCK) inhibitor, thus suggesting that these proteins could participate in the Rho-signaling pathway. Altogether these observations demonstrate that ENA/VASP proteins are implicated in the establishment and maintenance of the axonal structure and that a change on their expression levels triggers neuronal degeneration. 2010 Elsevier Inc. All rights reserved.

Alterative Expression and Localization of Profilin 1/VASPpS157 and Cofilin 1/VASPpS239 Regulates Metastatic Growth and Is Modified by DHA Supplementation.

PubMed

Ali, Mehboob; Heyob, Kathryn; Jacob, Naduparambil K; Rogers, Lynette K

2016-09-01

Profilin 1, cofilin 1, and vasodialator-stimulated phosphoprotein (VASP) are actin-binding proteins (ABP) that regulate actin remodeling and facilitate cancer cell metastases. miR-17-92 is highly expressed in metastatic tumors and profilin1 and cofilin1 are predicted targets. Docosahexaenoic acid (DHA) inhibits cancer cell proliferation and adhesion. These studies tested the hypothesis that the metastatic phenotype is driven by changes in ABPs including alternative phosphorylation and/or changes in subcellular localization. In addition, we tested the efficacy of DHA supplementation to attenuate or inhibit these changes. Human lung cancer tissue sections were analyzed for F-actin content and expression and cellular localization of profilin1, cofilin1, and VASP (S157 or S239 phosphorylation). The metastatic phenotype was investigated in A549 and MLE12 cells lines using 8 Br-cAMP as a metastasis inducer and DHA as a therapeutic agent. Migration was assessed by wound assay and expression measured by Western blot and confocal analysis. miR-17-92 expression was measured by qRT-PCR. Results indicated increased expression and altered cellular distribution of profilin1/VASP(pS157), but no changes in cofilin1/VASP(pS239) in the human malignant tissues compared with normal tissues. In A549 and MLE12 cells, the expression patterns of profilin1/VASP(pS157) or cofilin1/VASP(pS239) suggested an interaction in regulation of actin dynamics. Furthermore, DHA inhibited cancer cell migration and viability, ABP expression and cellular localization, and modulated expression of miR-17-92 in A549 cells with minimal effects in MLE12 cells. Further investigations are warranted to understand ABP interactions, changes in cellular localization, regulation by miR-17-92, and DHA as a novel therapeutic. Mol Cancer Ther; 15(9); 2220-31. ©2016 AACR. ©2016 American Association for Cancer Research.

Differential display cloning of a novel rat cDNA (RNB6) that shows high expression in the neonatal brain revealed a member of Ena/VASP family.

PubMed

Ohta, S; Mineta, T; Kimoto, M; Tabuchi, K

1997-08-18

We have used the differential display method to identify genes that control the neural cell development in CNS. Screening of the differential display bands that showed higher expression at neonate than at adult age enabled us to identify a novel rat cDNA (RNB6) coding for a protein of 393 amino acid residues. Database search revealed this gene as a rat homologue of the murine EVL, a member of Ena/VASP protein family that is implicated to be involved in the control of cell motility through actin filament assembly by their GP5 motifs. Although the precise characterization of EVL was not reported, our Northern blot and immunoblot analyses demonstrated that RNB6 expression in the brain gradually increases during embryonic development, reaches maximum at postnatal day 1 and decreases thereafter. Studies of tissue distribution revealed the expression of RNB6 not only in the brain but also in the spleen, thymus and testis. Histochemical analyses showed that RNB6 protein is mainly expressed in neurons and may be expressed in neural fibers. Our analyses suggest that RNB6 is critically involved in the development of CNS probably through the control of neural cell motility and/or including neuronal fiber extension.

Charge Transfer in Saturation Doping of Double-Wall Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Tchernatinsky, Alexander; Jayanthi, Chakram; Sumanasekera, Gamini; Wu, Shi-Yu

2004-03-01

Recent experimental evidences suggest that the outer tube of a double-wall carbon nanotube (DWCNT) may serve as a 'Faraday' cage (G. Chen, et al., Phys. Rev. Lett., 90, 257403 (2003)). In this presentation, we report the result of our systematic study of the effect of saturation doping of a (10,10) single-wall carbon nanotube, a (5,5)@(10,10) DWCNT, and a C_60@(10,10) peapod using DFT-based VASP computational package (G. Kresse and J. Hafner, Phys. Rev. B, 47, 558 (1993)). By comparing the resulting charge transfer of the above mentioned cases we shall provide the physics underlying the Faraday cage behavior of DWCNTs. Acknowledgments: This work was supported by the NSF (DMR-0112824) and the U.S.DOE (DE-FG02-00ER45832).

Arp2/3 and VASP Are Essential for Fear Memory Formation in Lateral Amygdala.

PubMed

Basu, Sreetama; Kustanovich, Irina; Lamprecht, Raphael

2016-01-01

The actin cytoskeleton is involved in key neuronal functions such as synaptic transmission and morphogenesis. However, the roles and regulation of actin cytoskeleton in memory formation remain to be clarified. In this study, we unveil the mechanism whereby actin cytoskeleton is regulated to form memory by exploring the roles of the major actin-regulatory proteins Arp2/3, VASP, and formins in long-term memory formation. Inhibition of Arp2/3, involved in actin filament branching and neuronal morphogenesis, in lateral amygdala (LA) with the specific inhibitor CK-666 during fear conditioning impaired long-term, but not short-term, fear memory. The inactive isomer CK-689 had no effect on memory formation. We observed that Arp2/3 is colocalized with the actin-regulatory protein profilin in LA neurons of fear-conditioned rats. VASP binding to profilin is needed for profilin-mediated stabilization of actin cytoskeleton and dendritic spine morphology. Microinjection of poly-proline peptide [G(GP 5 ) 3 ] into LA, to interfere with VASP binding to profilin, impaired long-term but not short-term fear memory formation. Control peptide [G(GA 5 ) 3 ] had no effect. Inhibiting formins, which regulate linear actin elongation, in LA during fear conditioning by microinjecting the formin-specific inhibitor SMIFH2 into LA had no effect on long-term fear memory formation. We conclude that Arp2/3 and VASP, through the profilin binding site, are essential for the formation of long-term fear memory in LA and propose a model whereby these proteins subserve cellular events, leading to memory consolidation.

Motility Determinants in WASP Family ProteinsD⃞

PubMed Central

Yarar, Defne; D'Alessio, Joseph A.; Jeng, Robert L.; Welch, Matthew D.

2002-01-01

In response to upstream signals, proteins in the Wiskott-Aldrich Syndrome protein (WASP) family regulate actin nucleation via the Arp2/3 complex. Despite intensive study of the function of WASP family proteins in nucleation, it is not yet understood how their distinct structural organization contributes to actin-based motility. Herein, we analyzed the activities of WASP and Scar1 truncation derivatives by using a bead-based motility assay. The minimal region of WASP sufficient to direct movement was the C-terminal WCA fragment, whereas the corresponding region of Scar1 was insufficient. In addition, the proline-rich regions of WASP and Scar1 and the Ena/VASP homology 1 (EVH1) domain of WASP independently enhanced motility rates. The contributions of these regions to motility could not be accounted for by their direct effects on actin nucleation with the Arp2/3 complex, suggesting that they stimulate motility by recruiting additional factors. We have identified profilin as one such factor. WASP- and Scar1-coated bead motility rates were significantly reduced by depletion of profilin and VASP and could be more efficiently rescued by a combination of VASP and wild-type profilin than by VASP and a mutant profilin that cannot bind proline-rich sequences. Moreover, motility of WASP WCA beads was not affected by the depletion or addback of VASP and profilin. Our results suggest that recruitment of factors, including profilin, by the proline-rich regions of WASP and Scar1 and the EVH1 domain of WASP stimulates cellular actin-based motility. PMID:12429845

The conformational state of Tes regulates its zyxin-dependent recruitment to focal adhesions.

PubMed

Garvalov, Boyan K; Higgins, Theresa E; Sutherland, James D; Zettl, Markus; Scaplehorn, Niki; Köcher, Thomas; Piddini, Eugenia; Griffiths, Gareth; Way, Michael

2003-04-14

The function of the human Tes protein, which has extensive similarity to zyxin in both sequence and domain organization, is currently unknown. We now show that Tes is a component of focal adhesions that, when expressed, negatively regulates proliferation of T47D breast carcinoma cells. Coimmunoprecipitations demonstrate that in vivo Tes is complexed with actin, Mena, and vasodilator-stimulated phosphoprotein (VASP). Interestingly, the isolated NH2-terminal half of Tes pulls out alpha-actinin and paxillin from cell extracts in addition to actin. The COOH-terminal half recruits zyxin as well as Mena and VASP from cell extracts. These differences suggest that the ability of Tes to associate with alpha-actinin, paxillin, and zyxin is dependent on the conformational state of the molecule. Consistent with this hypothesis, we demonstrate that the two halves of Tes interact with each other in vitro and in vivo. Using fibroblasts lacking Mena and VASP, we show that these proteins are not required to recruit Tes to focal adhesions. However, using RNAi ablation, we demonstrate that zyxin is required to recruit Tes, as well as Mena and VASP, but not vinculin or paxillin, to focal adhesions.

Investigation of the interface in silica-encapsulated liposomes by combining solid state NMR and first principles calculations.

PubMed

Folliet, Nicolas; Roiland, Claire; Bégu, Sylvie; Aubert, Anne; Mineva, Tzonka; Goursot, Annick; Selvaraj, Kaliaperumal; Duma, Luminita; Tielens, Frederik; Mauri, Francesco; Laurent, Guillaume; Bonhomme, Christian; Gervais, Christel; Babonneau, Florence; Azaïs, Thierry

2011-10-26

In the context of nanomedicine, liposils (liposomes and silica) have a strong potential for drug storage and release schemes: such materials combine the intrinsic properties of liposome (encapsulation) and silica (increased rigidity, protective coating, pH degradability). In this work, an original approach combining solid state NMR, molecular dynamics, first principles geometry optimization, and NMR parameters calculation allows the building of a precise representation of the organic/inorganic interface in liposils. {(1)H-(29)Si}(1)H and {(1)H-(31)P}(1)H Double Cross-Polarization (CP) MAS NMR experiments were implemented in order to explore the proton chemical environments around the silica and the phospholipids, respectively. Using VASP (Vienna Ab Initio Simulation Package), DFT calculations including molecular dynamics, and geometry optimization lead to the determination of energetically favorable configurations of a DPPC (dipalmitoylphosphatidylcholine) headgroup adsorbed onto a hydroxylated silica surface that corresponds to a realistic model of an amorphous silica slab. These data combined with first principles NMR parameters calculations by GIPAW (Gauge Included Projected Augmented Wave) show that the phosphate moieties are not directly interacting with silanols. The stabilization of the interface is achieved through the presence of water molecules located in-between the head groups of the phospholipids and the silica surface forming an interfacial H-bonded water layer. A detailed study of the (31)P chemical shift anisotropy (CSA) parameters allows us to interpret the local dynamics of DPPC in liposils. Finally, the VASP/solid state NMR/GIPAW combined approach can be extended to a large variety of organic-inorganic hybrid interfaces.

Comparing contribution of flexural and planar modes to thermodynamic properties

NASA Astrophysics Data System (ADS)

Mann, Sarita; Rani, Pooja; Jindal, V. K.

2017-05-01

Graphene, the most studied and explored 2D structure has unusual thermal properties such as negative thermal expansion, high thermal conductivity etc. We have already studied the thermal expansion behavior and various thermodynamic properties of pure graphene like heat capacity, entropy and free energy. The results of thermal expansion and various thermodynamic properties match well with available theoretical studies. For a deeper understanding of these properties, we analyzed the contribution of each phonon branch towards the total value of the individual property. To compute these properties, the dynamical matrix was calculated using VASP code where the density functional perturbation theory (DFPT) is employed under quasi-harmonic approximation in interface with phonopy code. It is noticed that transverse mode has major contribution to negative thermal expansion and all branches have almost same contribution towards the various thermodynamic properties with the contribution of ZA mode being the highest.

Optical properties of an indium doped CdSe nanocrystal: A density functional approach

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

Salini, K.; Mathew, Vincent, E-mail: vincent@cukerala.ac.in; Mathew, Thomas

2016-05-06

We have studied the electronic and optical properties of a CdSe nanocrystal doped with n-type impurity atom. First principle calculations of the CdSe nanocrystal based on the density functional theory (DFT), as implemented in the Vienna Ab Initio Simulation Package (VASP) was used in the calculations. We have introduced a single Indium impurity atom into CdSe nanocrystal with 1.3 nm diameter. Nanocrystal surface dangling bonds are passivated with hydrogen atom. The band-structure, density of states and absorption spectra of the doped and undopted nanocrystals were discussed. Inclusion of the n-type impurity atom introduces an additional electron in conduction band, and significantlymore » alters the electronic and optical properties of undoped CdSe nanocrystal. Indium doped CdSe nannocrystal have potential applications in optoelectronic devices.« less

Implementation of radiation shielding calculation methods. Volume 1: Synopsis of methods and summary of results

NASA Technical Reports Server (NTRS)

Capo, M. A.; Disney, R. K.

1971-01-01

The work performed in the following areas is summarized: (1) Analysis of Realistic nuclear-propelled vehicle was analyzed using the Marshall Space Flight Center computer code package. This code package includes one and two dimensional discrete ordinate transport, point kernel, and single scatter techniques, as well as cross section preparation and data processing codes, (2) Techniques were developed to improve the automated data transfer in the coupled computation method of the computer code package and improve the utilization of this code package on the Univac-1108 computer system. (3) The MSFC master data libraries were updated.

A QR code identification technology in package auto-sorting system

NASA Astrophysics Data System (ADS)

di, Yi-Juan; Shi, Jian-Ping; Mao, Guo-Yong

2017-07-01

Traditional manual sorting operation is not suitable for the development of Chinese logistics. For better sorting packages, a QR code recognition technology is proposed to identify the QR code label on the packages in package auto-sorting system. The experimental results compared with other algorithms in literatures demonstrate that the proposed method is valid and its performance is superior to other algorithms.

Targeting Epithelial Cell Migration to Accelerate Wound Healing

DTIC Science & Technology

2012-02-01

the presence and absence of forskolin to stimulate PKA. As seen in figure 10 cells depleted of Rsu1 and PINCH1 exhibit elevated phospho-VASP(ser157)at...a site of PKA and PKC phosphorylation even in the absence of cAMP increase and PKA activation by forskolin treatment. This indicates that RIPP...transfection were harvested with or without a 15 minutes exposure to forskolin (20 M). Blots were reacted with anti- phosphoVASP specific for serine 157

Triiodothyronine Potentiates Vasorelaxation via PKG/VASP Signaling in Vascular Smooth Muscle Cells.

PubMed

Samuel, Sherin; Zhang, Kuo; Tang, Yi-Da; Gerdes, A Martin; Carrillo-Sepulveda, Maria Alicia

2017-01-01

Vascular relaxation caused by Triiodothyronine (T3) involves direct activation of endothelial cells (EC) and vascular smooth muscle cells (VSMC). Activation of protein kinase G (PKG) has risen as a novel contributor to the vasorelaxation mechanism triggered by numerous stimuli. We hypothesize that T3-induced vasorelaxation involves PKG/vasodilator-stimulated phosphoprotein (VASP) signaling pathway in VSMC. Human aortic endothelial cells (HAEC) and VSMC were treated with T3 for short (2 to 60 minutes) and long term (24 hours). Nitric oxide (NO) production was measured using DAF-FM. Expression of protein targets was determined using western blot. For functional studies, rat aortas were isolated and treated with T3 for 20 minutes and mounted in a wire myograph. Relaxation was measured by a concentration-dependent response to acetylcholine (ACh) and sodium nitroprusside (SNP). Aortas stimulated with T3 exhibited augmented sensitivity to ACh and SNP-induced relaxation, endothelium-dependent and endothelium-independent responses, respectively. T3 directly increased vasorelaxation, which was abolished in the presence of a PKG inhibitor. T3 markedly induced phosphorylation of Akt, eNOS and consequently increased NO production in EC. Likewise, T3 induced phosphorylation of VASP at serine 239 via the PKG pathway in VSMC. Our findings have uncovered a PKG/VASP signaling pathway in VSMC as a key molecular mechanism underlying T3-induced vascular relaxation. © 2017 The Author(s)Published by S. Karger AG, Basel.

Electronic structure and bonding of intergranular glassy films in polycrystalline Si3 N4 : Ab initio studies and classical molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Rulis, P.; Chen, J.; Ouyang, L.; Ching, W.-Y.; Su, X.; Garofalini, S. H.

2005-06-01

The electronic structure and bonding of a realistic model of an intergranular glassy film (IGF) was studied with multiple computational methods. The model has a Si-O-N glassy region sandwiched between crystalline basal planes of β-Si3N4 and contains a total of 798 atoms. It was constructed with periodic boundary conditions via classical molecular dynamics (MD) techniques using an accurate multibody atomic potential. The model was then further relaxed by the VASP (Vienna ab initio simulation package) program. It is shown that the VASP-relaxed structure reduces the total energy from the MD-relaxed structure by only 47.38eV , validating the accuracy of the multiatom potential used. The calculated electronic structure shows the IGF model to be an insulator with a sizable gap of almost 3eV . Quasidefectlike states can be identified near the band edges arising from the more strained Si-N and Si-O bonds at the interface. Calculation of the Mulliken effective charge and bond order values indicates that the bonds in the glassy region and at the interface can be enhanced and weakened by distortions in the bond length and bond angle. The states at the top of the valence band are derived mostly from the crystalline part of the Si-N bonding while the states at the bottom of the conduction band are dominated by the Si-O bonding in the glassy region. Calculation of the electrostatic potential across the interface shows an average band offset of about 1.5eV between the crystalline β-Si3N4 and the glassy Si-O-N region which could be related to the space charge model for IGF.

Influence of de qi on the immediate analgesic effect of SP6 acupuncture in patients with primary dysmenorrhoea and cold and dampness stagnation: a multicentre randomised controlled trial.

PubMed

Zhao, Min-Yi; Zhang, Peng; Li, Jing; Wang, Lin-Peng; Zhou, Wei; Wang, Yan-Xia; She, Yan-Fen; Ma, Liang-Xiao; Wang, Pei; Hu, Ni-Juan; Lin, Chi; Hu, Shang-Qin; Wu, Gui-Wen; Wang, Ya-Feng; Sun, Jun-Jun; Jiang, Si-Zhu; Zhu, Jiang

2017-10-01

The aim of this multicentre randomised controlled trial was to investigate the contribution of de qi to the immediate analgesic effect of acupuncture in patients with primary dysmenorrhoea and the specific traditional Chinese medicine diagnosis cold and dampness stagnation . Eighty-eight patients with primary dysmenorrhoea and cold and dampness stagnation were randomly assigned to de qi (n=43) or no de qi (n=45) groups and underwent 30 min of SP6 acupuncture. The de qi group received deep needling at SP6 with manipulation using thick needles; the no de qi group received shallow needling with no manipulation using thin needles. In both groups the pain scores and actual de qi sensation were evaluated using a visual analogue scale for pain (VAS-P) and the acupuncture de qi clinical assessment scale (ADCAS), respectively. Both groups showed reductions in VAS-P, with no signficant differences between groups. ADCAS scores showed 43/43 and 25/45 patients in de qi and no de qi groups, respectively, actually experienced de qi sensation. Independent of original group allocation, VAS-P reductions associated with actual de qi (n=68) were greater than those without (28.4±18.19 mm vs 14.6±12.28 mm, p=0.008). This study showed no significant difference in VAS-P scores in patients with primary dysmenorrhoea and cold and dampness stagnation immediately after SP6 acupuncture designed to induce or avoid de qi sensation. Both treatments significantly reduced VAS-P relative to baseline. Irrespective of group allocation, patients experiencing actual de qi sensation demonstrated larger reductions in pain score relative to those without, suggesting greater analgesic effects. Chinese Clinical Trial Registry (ChiCTR-TRC-13003086); Results. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Optimization and Control of Burning Plasmas Through High Performance Computing

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

Pankin, Alexei

This project has revived the FACETS code, that has been developed under SciDAC fund- ing in 2008-2012. The code has been dormant for a number of years after the SciDAC funding stopped. FACETS depends on external packages. The external packages and libraries such as PETSc, FFTW, HDF5 and NETCDF that are included in FACETS have evolved during these years. Some packages in FACETS are also parts of other codes such as PlasmaState, NUBEAM, GACODES, and UEDGE. These packages have been also evolved together with their host codes which include TRANSP, TGYRO and XPTOR. Finally, there is also a set ofmore » packages in FACETS that are being developed and maintained by Tech-X. These packages include BILDER, SciMake, and FcioWrappers. Many of these packages evolved significantly during the last several years and FACETS had to be updated to synchronize with the re- cent progress in the external packages. The PI has introduced new changes to the BILDER package to support the updated interfaces to the external modules. During the last year of the project, the FACETS version of the UEDGE code has been extracted from FACETS as a standalone package. The PI collaborates with the scientists from LLNL on the updated UEDGE model in FACETS. Drs. T. Rognlien, M. Umansky and A. Dimits from LLNL are contributing to this task.« less

Radio controlled release apparatus for animal data acquisition devices

DOEpatents

Stamps, James Frederick

2000-01-01

A novel apparatus for reliably and selectively releasing a data acquisition package from an animal for recovery. The data package comprises two parts: 1) an animal data acquisition device and 2) a co-located release apparatus. One embodiment, which is useful for land animals, the release apparatus includes two major components: 1) an electronics package, comprising a receiver; a decoder comparator, having at plurality of individually selectable codes; and an actuator circuit and 2) a release device, which can be a mechanical device, which acts to release the data package from the animal. To release a data package from a particular animal, a radio transmitter sends a coded signal which is decoded to determine if the code is valid for that animal data package. Having received a valid code, the release device is activated to release the data package from the animal for subsequent recovery. A second embodiment includes floatation means and is useful for releasing animal data acquisition devices attached to sea animals. This embodiment further provides for releasing a data package underwater by employing an acoustic signal.

An ecological vegetation-activated sludge process (V-ASP) for decentralized wastewater treatment: system development, treatment performance, and mathematical modeling.

PubMed

Yuan, Jiajia; Dong, Wenyi; Sun, Feiyun; Li, Pu; Zhao, Ke

2016-05-01

An environment-friendly decentralized wastewater treatment process that is comprised of activated sludge process (ASP) and wetland vegetation, named as vegetation-activated sludge process (V-ASP), was developed for decentralized wastewater treatment. The long-term experimental results evidenced that the vegetation sequencing batch reactor (V-SBR) process had consistently stable higher removal efficiencies of organic substances and nutrients from domestic wastewater compared with traditional sequencing batch reactor (SBR). The vegetation allocated into V-SBR system could not only remove nutrients through its vegetation transpiration ratio but also provide great surface area for microorganism activity enhancement. This high vegetation transpiration ratio enhanced nutrients removal effectiveness from wastewater mainly by flux enhancement, oxygen and substrate transportation acceleration, and vegetation respiration stimulation. A mathematical model based on ASM2d was successfully established by involving the specific function of vegetation to simulate system performance. The simulation results on the influence of operational parameters on V-ASP treatment effectiveness demonstrated that V-SBR had a high resistance to seasonal temperature fluctuations and influent loading shocking.

Genetic ablation of zyxin causes Mena/VASP mislocalization, increased motility, and deficits in actin remodeling

PubMed Central

Hoffman, Laura M.; Jensen, Christopher C.; Kloeker, Susanne; Wang, C.-L. Albert; Yoshigi, Masaaki; Beckerle, Mary C.

2006-01-01

Focal adhesions are specialized regions of the cell surface where integrin receptors and associated proteins link the extracellular matrix to the actin cytoskeleton. To define the cellular role of the focal adhesion protein zyxin, we characterized the phenotype of fibroblasts in which the zyxin gene was deleted by homologous recombination. Zyxin-null fibroblasts display enhanced integrin-dependent adhesion and are more migratory than wild-type fibroblasts, displaying reduced dependence on extracellular matrix cues. We identified differences in the profiles of 75- and 80-kD tyrosine-phosphorylated proteins in the zyxin-null cells. Tandem array mass spectrometry identified both modified proteins as isoforms of the actomyosin regulator caldesmon, a protein known to influence contractility, stress fiber formation, and motility. Zyxin-null fibroblasts also show deficits in actin stress fiber remodeling and exhibit changes in the molecular composition of focal adhesions, most notably by severely reduced accumulation of Ena/VASP proteins. We postulate that zyxin cooperates with Ena/VASP proteins and caldesmon to influence integrin-dependent cell motility and actin stress fiber remodeling. PMID:16505170

Density functional theory study of nitrogen atoms and molecules interacting with Fe(1 1 1) surfaces

NASA Astrophysics Data System (ADS)

Nosir, M. A.; Martin-Gondre, L.; Bocan, G. A.; Díez Muiño, R.

2016-09-01

We present Density functional theory (DFT) calculations for the investigation of the structural relaxation of Fe(1 1 1), as well as for the study of the interaction of nitrogen atoms and molecules with this surface. We perform spin polarized DFT calculations using VASP (Vienna Ab-initio Simulation Package) code. We use the supercell approach and up to 19 slab layers for the relaxation of the Fe(1 1 1) surface. We find a contraction of the first two interlayer distances with a relative value of Δ12 = - 7.8 % and Δ23 = - 21.7 % with respect to the bulk reference. The third interlayer distance is however expanded with a relative change of Δ34 = 9.7 % . Early experimental studies of the surface relaxation using Low Energy Electron Diffraction (LEED) and Medium Energy Ion Scattering (MEIS) showed contradictory results, even on the relaxation general trend. Our current theoretical results support the LEED conclusions and are consistent qualitatively with other recent theoretical calculations. In addition, we study the interaction energy of nitrogen atoms and molecules on the Fe(1 1 1) surface. The nitrogen atoms are adsorbed in the hollow site of the unit cell, with an adsorption energy consistent with the one found in previous studies. In addition, we find the three molecularly adsorbed states that are observed experimentally. Two of them correspond to the adsorbed molecule oriented normal to the surface and a third one corresponds to the molecule adsorbed parallel to the surface. We conclude that our results are accurate enough to be used to build a full six-dimensional potential energy surface for the N2 system.

NORTICA—a new code for cyclotron analysis

NASA Astrophysics Data System (ADS)

Gorelov, D.; Johnson, D.; Marti, F.

2001-12-01

The new package NORTICA (Numerical ORbit Tracking In Cyclotrons with Analysis) of computer codes for beam dynamics simulations is under development at NSCL. The package was started as a replacement for the code MONSTER [1] developed in the laboratory in the past. The new codes are capable of beam dynamics simulations in both CCF (Coupled Cyclotron Facility) accelerators, the K500 and K1200 superconducting cyclotrons. The general purpose of this package is assisting in setting and tuning the cyclotrons taking into account the main field and extraction channel imperfections. The computer platform for the package is Alpha Station with UNIX operating system and X-Windows graphic interface. A multiple programming language approach was used in order to combine the reliability of the numerical algorithms developed over the long period of time in the laboratory and the friendliness of modern style user interface. This paper describes the capability and features of the codes in the present state.

Effects of abacavir administration on structural and functional markers of platelet activation.

PubMed

Trevillyan, Janine M; Arthur, Jane F; Jing, Jing; Andrews, Robert K; Gardiner, Elizabeth E; Hoy, Jennifer F

2015-11-01

Current abacavir exposure has been reported to be associated with cardiovascular disease. Changes in platelet reactivity could plausibly explain the clinically observed pattern of association. To determine if platelet reactivity changed following abacavir exposure and whether this effect was reversible on cessation of the drug. In an open-label, interventional study abacavir, 600 mg daily, was added to a suppressive antiretroviral regimen in 20 adult HIV-positive men. Platelet function, estimated by the phosphorylated vasodilator-stimulated phosphoprotein (P-VASP) assay and through measurement of the expression and shedding of platelet-specific receptors, was assessed at baseline, following 15 days of abacavir and at completion of a 28-day washout period. The VASP-index decreased significantly from 79.1% [interquartile range (IQR) 47.8-87.6] to 32.6% (IQR -11.5-51.0) following 15 days of abacavir administration (P = 0.010), and returned to baseline levels following the washout period (day 43 =76.3%; IQR 40.7-92.3). There was no change in resting (prostaglandin E1 alone) P-VASP but a slight increase in P-VASP within stimulated platelets (prostaglandin E1 and adenosine diphosphate). Integrin β3 levels decreased significantly [208.5 ng/ml (IQR 177.0-231.1) to 177.5 ng/ml (IQR 151.7-205) P < 0.001] and there was a nonsignificant trend towards decreased soluble glycoprotein VI levels [baseline; 72.5 ng/ml (95% CI 58.3-81.5) vs. day 15; 45.0 ng/ml (95% CI 33.0-98.2) P = 0.79]. Abacavir led to reversible changes in platelet function and structure. The clinical implications of these changes are uncertain; they may represent negative feedback mechanisms in response to an abacavir-associated prothrombotic state.

ON UPGRADING THE NUMERICS IN COMBUSTION CHEMISTRY CODES. (R824970)

EPA Science Inventory

A method of updating and reusing legacy FORTRAN codes for combustion simulations is presented using the DAEPACK software package. The procedure is demonstrated on two codes that come with the CHEMKIN-II package, CONP and SENKIN, for the constant-pressure batch reactor simulati...

Analysis of the structural, electronic and optic properties of Ni doped MgSiP{sub 2} semiconductor chalcopyrite compound

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

Kocak, Belgin, E-mail: koakbelgin@gmail.com; Ciftci, Yasemin Oztekin, E-mail: yasemin@gazi.edu.tr

2016-03-25

The structural, electronic band structure and optic properties of the Ni doped MgSiP{sub 2} chalcopyrite compound have been performed by using first-principles method in the density functional theory (DFT) as implemented in Vienna Ab-initio Simulation Package (VASP). The generalized gradient approximation (GGA) in the scheme of Perdew, Burke and Ernzerhof (PBE) is used for the exchange and correlation functional. The present lattice constant (a) follows generally the Vegard’s law. The electronic band structure, total and partial density of states (DOS and PDOS) are calculated. We present data for the frequency dependence of imaginary and real parts of dielectric functions ofmore » Ni doped MgSiP{sub 2}. For further investigation of the optical properties the reflectivity, refractive index, extinction coefficient and electron energy loss function are also predicted. Our obtained results indicate that the lattice constants, electronic band structure and optical properties of this compound are dependent on the substitution concentration of Ni.« less

Ab-initio study of thermal expansion in pure graphene

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

Mann, Sarita; Kumar, Ranjan; Jindal, V. K., E-mail: jindal@pu.ac.in

Graphene is a zero band gap semiconductor with exceptionally high thermal conductivity. The electronic properties having been studied, therole of phonon in contributing to thermal expansion, thermal conductivity and other thermodynamic properties, is required to be investigated. This paper focuses more on thermal expansion. Some others results like phonon dispersion, Grüneisenparameters and bulk modulus,which are essential to estimation of thermal expansion, are also presented. The dynamical matrix was calculated using VASP code using both DFT and DFPT and the phonon frequencies were calculated using phonopy code under harmonic approximation. The linear thermal expansion coefficient of graphene is found to bemore » strongly dependent on temperature but remains negative upto 470 K and positive thereafter, with a room temperature value of −1.44×10{sup −6}. The negative expansion coefficient is very interesting and is found to be in conformity with experimental as well as with recent theoretical estimates. There is only qualitative agreement of our results with experimental data and motivates further investigation, primarily on the high negative values of Grüneisen parameters.« less

A predictive transport modeling code for ICRF-heated tokamaks

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

Phillips, C.K.; Hwang, D.Q.; Houlberg, W.

In this report, a detailed description of the physic included in the WHIST/RAZE package as well as a few illustrative examples of the capabilities of the package will be presented. An in depth analysis of ICRF heating experiments using WHIST/RAZE will be discussed in a forthcoming report. A general overview of philosophy behind the structure of the WHIST/RAZE package, a summary of the features of the WHIST code, and a description of the interface to the RAZE subroutines are presented in section 2 of this report. Details of the physics contained in the RAZE code are examined in section 3.more » Sample results from the package follow in section 4, with concluding remarks and a discussion of possible improvements to the package discussed in section 5.« less

A predictive transport modeling code for ICRF-heated tokamaks

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

Phillips, C.K.; Hwang, D.Q.; Houlberg, W.

1992-02-01

In this report, a detailed description of the physic included in the WHIST/RAZE package as well as a few illustrative examples of the capabilities of the package will be presented. An in depth analysis of ICRF heating experiments using WHIST/RAZE will be discussed in a forthcoming report. A general overview of philosophy behind the structure of the WHIST/RAZE package, a summary of the features of the WHIST code, and a description of the interface to the RAZE subroutines are presented in section 2 of this report. Details of the physics contained in the RAZE code are examined in section 3.more » Sample results from the package follow in section 4, with concluding remarks and a discussion of possible improvements to the package discussed in section 5.« less

Overcoming Short-Circuit in Lead-Free CH3NH3SnI3 Perovskite Solar Cells via Kinetically Controlled Gas-Solid Reaction Film Fabrication Process.

PubMed

Yokoyama, Takamichi; Cao, Duyen H; Stoumpos, Constantinos C; Song, Tze-Bin; Sato, Yoshiharu; Aramaki, Shinji; Kanatzidis, Mercouri G

2016-03-03

The development of Sn-based perovskite solar cells has been challenging because devices often show short-circuit behavior due to poor morphologies and undesired electrical properties of the thin films. A low-temperature vapor-assisted solution process (LT-VASP) has been employed as a novel kinetically controlled gas-solid reaction film fabrication method to prepare lead-free CH3NH3SnI3 thin films. We show that the solid SnI2 substrate temperature is the key parameter in achieving perovskite films with high surface coverage and excellent uniformity. The resulting high-quality CH3NH3SnI3 films allow the successful fabrication of solar cells with drastically improved reproducibility, reaching an efficiency of 1.86%. Furthermore, our Kelvin probe studies show the VASP films have a doping level lower than that of films prepared from the conventional one-step method, effectively lowering the film conductivity. Above all, with (LT)-VASP, the short-circuit behavior often obtained from the conventional one-step-fabricated Sn-based perovskite devices has been overcome. This study facilitates the path to more successful Sn-perovskite photovoltaic research.

The possible role of Mena protein and its splicing-derived variants in embryogenesis, carcinogenesis, and tumor invasion: a systematic review of the literature.

PubMed

Gurzu, Simona; Ciortea, Diana; Ember, Istvan; Jung, Ioan

2013-01-01

The Ena/VASP (enabled/vasodilator stimulated phosphoprotein) family includes the binding actin proteins such as mammalian Ena (Mena), VASP, and Ena-VASP-like. It is known that the perturbation of actin cycle could determine alteration in the mobility of cells and in consequence of organogenesis. Few recent studies have revealed that Mena protein could play a role in breast or pancreatic carcinogenesis. Based on our researches, we observed that the intensity of Mena expression increased from premalignant to malignant lesions in some organs such as large bowel, stomach, cervix, and salivary glands. These findings prove that Mena could be a marker of premalignant epithelial lesions. In premalignant lesions, it could be helpful to define more accurately the risk for malignant transformation. In malignant tumors, correlation of expression of its splice variants could indicate metastatic behavior. In conclusion, we consider that it is necessary to analyze the expression of Mena splice variants in a higher number of cases, in different epithelial lesions, and also in experimental studies to define its exact role in carcinogenesis and also its possible prognostic and predictive values.

Low-Pressure Vapor-Assisted Solution Process for Thiocyanate-Based Pseudohalide Perovskite Solar Cells.

PubMed

Chiang, Yu-Hsien; Cheng, Hsin-Min; Li, Ming-Hsien; Guo, Tzung-Fang; Chen, Peter

2016-09-22

In this report, we fabricated thiocyanate-based perovskite solar cells with low-pressure vapor-assisted solution process (LP-VASP) method. Photovoltaic performances are evaluated with detailed materials characterizations. Scanning electron microscopy images show that SCN-based perovskite films fabricated using LP-VASP have long-range uniform morphology and large grain sizes up to 1 μm. The XRD and Raman spectra were employed to observe the characteristic peaks for both SCN-based and pure CH 3 NH 3 PbI 3 perovskite. We observed that the Pb(SCN) 2 film transformed to PbI 2 before the formation of perovskite film. X-ray photoemission spectra (XPS) show that only a small amount of S remained in the film. Using LP-VASP method, we fabricated SCN-based perovskite solar cells and achieved a power conversion efficiency of 12.72 %. It is worth noting that the price of Pb(SCN) 2 is only 4 % of PbI 2 . These results demonstrate that pseudo-halide perovskites are promising materials for fabricating low-cost perovskite solar cells. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ab-initio study of electronic and magnetic properties of Co-doped Mo2C monolayer

NASA Astrophysics Data System (ADS)

Mehta, Veenu; Tankeshwar, K.; Saini, Hardev S.

2018-05-01

The spin polarized density functional theory (DFT) based calculations has been performed to investigate the electronic and magnetic properties of pristine and Co-doped Mo2C using VASP code. The calculated results show that the pristine Mo2C is found to be non-magnetic whereas the Co dopant at Mo-site in the Mo2C monolayer generates the ferromagnetism in the resultant compound. The total magnetic moment of the system has been found to be 1.2µB which increases to 2.03µB as the concentration of Co increase from 3% to 8%, respectively. The electronic structure calculations of the pristine and Co-doped Mo2C show its metallic behavior which may found its application in magnetic energy storage devices, magnetic tape etc.

A Case Study Of Organic Dirac Materials -

NASA Astrophysics Data System (ADS)

Commeau, Benjamin; Geilhufe, Matthias; Fernando, Gayanath; Balatsky, Alexander

Dirac Materials are characterized by linear band crossings within the electronic band structure. Most research of Dirac materials has been dedicated towards inorganic materials, e.g., binary chalcogenides as toplogical insulators, the Weyl semimetal TaAs or graphene. The purpose of this study is to investigate the formation of Dirac points in organic materials under pressure and mechanical strain. We study multiple structural phases of the organic charge-transfer salt (BEDT-TTF)2I3. We numerically calculate the relaxed band structure near the Fermi level along different k-space directions. Once the relaxed ion structure is obtained, we pick different cell parameters to shrink and investigate the changes in the band structure. We discuss band structure degeneracies protected by crystalline and other symmetries, if any. Quantum Espresso and VASP codes were used to calculate and validate our results.

MIFT: GIFT Combinatorial Geometry Input to VCS Code

DTIC Science & Technology

1977-03-01

r-w w-^ H ^ß0318is CQ BRL °RCUMr REPORT NO. 1967 —-S: ... MIFT: GIFT COMBINATORIAL GEOMETRY INPUT TO VCS CODE Albert E...TITLE (and Subtitle) MIFT: GIFT Combinatorial Geometry Input to VCS Code S. TYPE OF REPORT & PERIOD COVERED FINAL 6. PERFORMING ORG. REPORT NUMBER...Vehicle Code System (VCS) called MORSE was modified to accept the GIFT combinatorial geometry package. GIFT , as opposed to the geometry package

The Model 9977 Radioactive Material Packaging Primer

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

Abramczyk, G.

2015-10-09

The Model 9977 Packaging is a single containment drum style radioactive material (RAM) shipping container designed, tested and analyzed to meet the performance requirements of Title 10 the Code of Federal Regulations Part 71. A radioactive material shipping package, in combination with its contents, must perform three functions (please note that the performance criteria specified in the Code of Federal Regulations have alternate limits for normal operations and after accident conditions): Containment, the package must “contain” the radioactive material within it; Shielding, the packaging must limit its users and the public to radiation doses within specified limits; and Subcriticality, themore » package must maintain its radioactive material as subcritical« less

Increasing Flexibility in Energy Code Compliance: Performance Packages

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

Hart, Philip R.; Rosenberg, Michael I.

Energy codes and standards have provided significant increases in building efficiency over the last 38 years, since the first national energy code was published in late 1975. The most commonly used path in energy codes, the prescriptive path, appears to be reaching a point of diminishing returns. As the code matures, the prescriptive path becomes more complicated, and also more restrictive. It is likely that an approach that considers the building as an integrated system will be necessary to achieve the next real gains in building efficiency. Performance code paths are increasing in popularity; however, there remains a significant designmore » team overhead in following the performance path, especially for smaller buildings. This paper focuses on development of one alternative format, prescriptive packages. A method to develop building-specific prescriptive packages is reviewed based on a multiple runs of prototypical building models that are used to develop parametric decision analysis to determines a set of packages with equivalent energy performance. The approach is designed to be cost-effective and flexible for the design team while achieving a desired level of energy efficiency performance. A demonstration of the approach based on mid-sized office buildings with two HVAC system types is shown along with a discussion of potential applicability in the energy code process.« less

Overcoming Short-Circuit in Lead-Free CH 3 NH 3 SnI 3 Perovskite Solar Cells via Kinetically Controlled Gas–Solid Reaction Film Fabrication Process

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

Yokoyama, Takamichi; Cao, Duyen H.; Stoumpos, Constantinos C.

2016-02-17

The development of Sn-based perovskite solar cells has been challenging because devices often show short-circuit behavior due to poor morphologies and undesired electrical properties of the thin films. A low-temperature vapor-assisted solution process (LT-VASP) has been employed as a novel kinetically controlled gas–solid reaction film fabrication method to prepare lead-free CH3NH3SnI3 thin films. We show that the solid SnI2 substrate temperature is the key parameter in achieving perovskite films with high surface coverage and excellent uniformity. The resulting high-quality CH3NH3SnI3 films allow the successful fabrication of solar cells with drastically improved reproducibility, reaching an efficiency of 1.86%. Furthermore, our Kelvinmore » probe studies show the VASP films have a doping level lower than that of films prepared from the conventional one-step method, effectively lowering the film conductivity. Above all, with (LT)-VASP, the short-circuit behavior often obtained from the conventional one-step-fabricated Sn-based perovskite devices has been overcome. This study facilitates the path to more successful Sn-perovskite photovoltaic research.« less

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.

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

Influence of cytochrome 2C19 allelic variants on on-treatment platelet reactivity evaluated by five different platelet function tests.

PubMed

Gremmel, Thomas; Kopp, Christoph W; Moertl, Deddo; Seidinger, Daniela; Koppensteiner, Renate; Panzer, Simon; Mannhalter, Christine; Steiner, Sabine

2012-05-01

The antiplatelet effect of clopidogrel has been linked to cytochrome P450 2C19 (CYP2C19) carrier status. The presence of loss of function and gain of function variants were found to have a gene-dose effect on clopidogrel metabolism. However, genotyping is only one aspect of predicting response to clopidogrel and several platelet function tests are available to measure platelet response. Patients and methods We studied the influence of CYP2C19 allelic variants on on-treatment platelet reactivity as assessed by light transmission aggregometry (LTA), the VerifyNow P2Y12 assay, the VASP assay, multiple electrode aggregometry (MEA), and the Impact-R in 288 patients after stenting for cardiovascular disease. Allelic variants of CYP2C19 were determined with the Infiniti® CYP450 2C19+ assay and categorized into four metabolizer states (ultrarapid, extensive, intermediate, poor). Platelet reactivity increased linearly from ultrarapid to poor metabolizers using the VerifyNow P2Y12 assay (P = 0.04), the VASP assay (P = 0.02) and the Impact-R (P = 0.04). The proportion of patients with high on-treatment residual platelet reactivity (HRPR) identified by LTA, the VerifyNow P2Y12 assay and the VASP assay increased when the metabolizer status decreased, while no such relationship could be identified for results of MEA and Impact-R. The presence of loss of function variants (*2/*2, *2-8*/wt, *2/*17) was an independent predictor of HRPR in LTA and the VASP assay while it did not reach statistical significance in the VerifyNow P2Y12 assay, MEA, and the Impact-R. Depending on the type of platelet function test differences in the association of on-treatment platelet reactivity with CYP2C19 carrier status are observed. Copyright © 2011 Elsevier Ltd. All rights reserved.

Hybrid density-functional calculations of phonons in LaCoO3

NASA Astrophysics Data System (ADS)

Gryaznov, Denis; Evarestov, Robert A.; Maier, Joachim

2010-12-01

Phonon frequencies at Γ point in nonmagnetic rhombohedral phase of LaCoO3 were calculated using density-functional theory with hybrid exchange correlation functional PBE0. The calculations involved a comparison of results for two types of basis functions commonly used in ab initio calculations, namely, the plane-wave approach and linear combination of atomic orbitals, as implemented in VASP and CRYSTAL computer codes, respectively. A good qualitative, but also within an error margin of less than 30%, a quantitative agreement was observed not only between the two formalisms but also between theoretical and experimental phonon frequency predictions. Moreover, the correlation between the phonon symmetries in cubic and rhombohedral phases is discussed in detail on the basis of group-theoretical analysis. It is concluded that the hybrid PBE0 functional is able to predict correctly the phonon properties in LaCoO3 .

The ENSDF Java Package

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

Sonzogni, A.A.

2005-05-24

A package of computer codes has been developed to process and display nuclear structure and decay data stored in the ENSDF (Evaluated Nuclear Structure Data File) library. The codes were written in an object-oriented fashion using the java language. This allows for an easy implementation across multiple platforms as well as deployment on web pages. The structure of the different java classes that make up the package is discussed as well as several different implementations.

RNAi-dependent and -independent antiviral phenotypes of chromosomally integrated shRNA clones: role of VASP in respiratory syncytial virus growth.

PubMed

Musiyenko, Alla; Bitko, Vira; Barik, Sailen

2007-07-01

Stable RNA interference (RNAi) is commonly achieved by recombinant expression of short hairpin RNA (shRNA). To generate virus-resistant cell lines, we cloned a shRNA cassette against the phosphoprotein gene of respiratory syncytial virus (RSV) into a polIII-driven plasmid vector. Analysis of individual stable transfectants showed a spectrum of RSV resistance correlating with the levels of shRNA expressed from different chromosomal locations. Interestingly, resistance in a minority of clones was due to mono-allelic disruption of the cellular gene for vasodilator-stimulated phosphoprotein (VASP). Thus, pure clones of chromosomally integrated DNA-directed RNAi can exhibit gene disruption phenotypes resembling but unrelated to RNAi.

Extending R packages to support 64-bit compiled code: An illustration with spam64 and GIMMS NDVI3g data

NASA Astrophysics Data System (ADS)

Gerber, Florian; Mösinger, Kaspar; Furrer, Reinhard

2017-07-01

Software packages for spatial data often implement a hybrid approach of interpreted and compiled programming languages. The compiled parts are usually written in C, C++, or Fortran, and are efficient in terms of computational speed and memory usage. Conversely, the interpreted part serves as a convenient user-interface and calls the compiled code for computationally demanding operations. The price paid for the user friendliness of the interpreted component is-besides performance-the limited access to low level and optimized code. An example of such a restriction is the 64-bit vector support of the widely used statistical language R. On the R side, users do not need to change existing code and may not even notice the extension. On the other hand, interfacing 64-bit compiled code efficiently is challenging. Since many R packages for spatial data could benefit from 64-bit vectors, we investigate strategies to efficiently pass 64-bit vectors to compiled languages. More precisely, we show how to simply extend existing R packages using the foreign function interface to seamlessly support 64-bit vectors. This extension is shown with the sparse matrix algebra R package spam. The new capabilities are illustrated with an example of GIMMS NDVI3g data featuring a parametric modeling approach for a non-stationary covariance matrix.

Density functional calculations on structural materials for nuclear energy applications and functional materials for photovoltaic energy applications (abstract only).

PubMed

Domain, C; Olsson, P; Becquart, C S; Legris, A; Guillemoles, J F

2008-02-13

Ab initio density functional theory calculations are carried out in order to predict the evolution of structural materials under aggressive working conditions such as cases with exposure to corrosion and irradiation, as well as to predict and investigate the properties of functional materials for photovoltaic energy applications. Structural metallic materials used in nuclear facilities are subjected to irradiation which induces the creation of large amounts of point defects. These defects interact with each other as well as with the different elements constituting the alloys, which leads to modifications of the microstructure and the mechanical properties. VASP (Vienna Ab initio Simulation Package) has been used to determine the properties of point defect clusters and also those of extended defects such as dislocations. The resulting quantities, such as interaction energies and migration energies, are used in larger scale simulation methods in order to build predictive tools. For photovoltaic energy applications, ab initio calculations are used in order to search for new semiconductors and possible element substitutions for existing ones in order to improve their efficiency.

49 CFR 178.523 - Standards for composite packagings with inner glass, porcelain, or stoneware receptacles.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Standards for composite packagings with inner... Packaging Standards § 178.523 Standards for composite packagings with inner glass, porcelain, or stoneware receptacles. (a) The following are identification codes for composite packagings with inner receptacles of...

Esomeprazole and rabeprazole did not reduce antiplatelet effects of aspirin/clopidogrel dual therapy in patients undergoing percutaneous coronary intervention: a prospective, randomized, case-control study.

PubMed

Liu, Li-Peng; Wang, Yan; Si, Rui; Yuan, Ming; Cheng, Kang; Guo, Wen-Yi

2016-01-01

Controversy has been prompted based on drug interaction between proton pump inhibitors (PPIs) and aspirin/clopidogrel leading to weakened effects. However, whether such interaction was drug-specific or class effect remains controversial. This study predicted the impact of esomeprazole and rabeprazole on efficacy of dual antiplatelet therapy (DAPT). This study, involving 150 patients, evaluated the efficacy of DAPT upon concomitant use of esomeprazole (40 mg/d) or rabeprazole (20 mg/d). Platelet reactivity was assessed by value of ADP-induced light transmittance aggregometry (LTA) and vasodilator-stimulated phosphoprotein phosphorylation-platelet reactivity index (VASP-PRI) at day 1, day 3 and day 30 end points after initiation of DAPT. No significance were observed by post-hoc analysis of treatment-by-period interaction in LTA value and VASP-PRI value when compared with non-PPI users, which suggests no carryover effect in both PPIs over the 30-day treatment period. Moreover, no statistical differences was in LTA or VASP-PRI value in esomeprazole group while rabeprazole group showed decreased in antiplatelet function of DAPT at the day 3 and day 30 end points. Although antiplatelet effect of DAPT were not affected upon concomitant use of both PPIs over the 30-day treatment period, esomeprazole exerts much more stable impact on antiplatelet effect than rabeprazole among respective end points.

An Object-Oriented Serial DSMC Simulation Package

NASA Astrophysics Data System (ADS)

Liu, Hongli; Cai, Chunpei

2011-05-01

A newly developed three-dimensional direct simulation Monte Carlo (DSMC) simulation package, named GRASP ("Generalized Rarefied gAs Simulation Package"), is reported in this paper. This package utilizes the concept of simulation engine, many C++ features and software design patterns. The package has an open architecture which can benefit further development and maintenance of the code. In order to reduce the engineering time for three-dimensional models, a hybrid grid scheme, combined with a flexible data structure compiled by C++ language, are implemented in this package. This scheme utilizes a local data structure based on the computational cell to achieve high performance on workstation processors. This data structure allows the DSMC algorithm to be very efficiently parallelized with domain decomposition and it provides much flexibility in terms of grid types. This package can utilize traditional structured, unstructured or hybrid grids within the framework of a single code to model arbitrarily complex geometries and to simulate rarefied gas flows. Benchmark test cases indicate that this package has satisfactory accuracy for complex rarefied gas flows.

PlasmaPy: beginning a community developed Python package for plasma physics

NASA Astrophysics Data System (ADS)

Murphy, Nicholas A.; Huang, Yi-Min; PlasmaPy Collaboration

2016-10-01

In recent years, researchers in several disciplines have collaborated on community-developed open source Python packages such as Astropy, SunPy, and SpacePy. These packages provide core functionality, common frameworks for data analysis and visualization, and educational tools. We propose that our community begins the development of PlasmaPy: a new open source core Python package for plasma physics. PlasmaPy could include commonly used functions in plasma physics, easy-to-use plasma simulation codes, Grad-Shafranov solvers, eigenmode solvers, and tools to analyze both simulations and experiments. The development will include modern programming practices such as version control, embedding documentation in the code, unit tests, and avoiding premature optimization. We will describe early code development on PlasmaPy, and discuss plans moving forward. The success of PlasmaPy depends on active community involvement and a welcoming and inclusive environment, so anyone interested in joining this collaboration should contact the authors.

76 FR 30551 - Specifications for Packagings

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-26

... 178 Specifications for Packagings CFR Correction In Title 49 of the Code of Federal Regulations, Parts... design qualification test and each periodic retest on a packaging, a test report must be prepared. The test report must be maintained at each location where the packaging is manufactured and each location...

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

Grote, D. P.

Forthon generates links between Fortran and Python. Python is a high level, object oriented, interactive and scripting language that allows a flexible and versatile interface to computational tools. The Forthon package generates the necessary wrapping code which allows access to the Fortran database and to the Fortran subroutines and functions. This provides a development package where the computationally intensive parts of a code can be written in efficient Fortran, and the high level controlling code can be written in the much more versatile Python language.

49 CFR 178.522 - Standards for composite packagings with inner plastic receptacles.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Standards for composite packagings with inner... Standards for composite packagings with inner plastic receptacles. (a) The following are the identification codes for composite packagings with inner plastic receptacles: (1) 6HA1 for a plastic receptacle within...

Enhancement of the CAVE computer code. [aerodynamic heating package for nose cones and scramjet engine sidewalls

NASA Technical Reports Server (NTRS)

Rathjen, K. A.; Burk, H. O.

1983-01-01

The computer code CAVE (Conduction Analysis via Eigenvalues) is a convenient and efficient computer code for predicting two dimensional temperature histories within thermal protection systems for hypersonic vehicles. The capabilities of CAVE were enhanced by incorporation of the following features into the code: real gas effects in the aerodynamic heating predictions, geometry and aerodynamic heating package for analyses of cone shaped bodies, input option to change from laminar to turbulent heating predictions on leading edges, modification to account for reduction in adiabatic wall temperature with increase in leading sweep, geometry package for two dimensional scramjet engine sidewall, with an option for heat transfer to external and internal surfaces, print out modification to provide tables of select temperatures for plotting and storage, and modifications to the radiation calculation procedure to eliminate temperature oscillations induced by high heating rates. These new features are described.

The Composite Analytic and Simulation Package or RFI (CASPR) on a coded channel

NASA Technical Reports Server (NTRS)

Freedman, Jeff; Berman, Ted

1993-01-01

CASPR is an analysis package which determines the performance of a coded signal in the presence of Radio Frequency Interference (RFI) and Additive White Gaussian Noise (AWGN). It can analyze a system with convolutional coding, Reed-Solomon (RS) coding, or a concatenation of the two. The signals can either be interleaved or non-interleaved. The model measures the system performance in terms of either the E(sub b)/N(sub 0) required to achieve a given Bit Error Rate (BER) or the BER needed for a constant E(sub b)/N(sub 0).

Quality of life and functional capacity in patients with rheumatoid arthritis - Cross-sectional study.

PubMed

Rosa-Gonçalves, Diana; Bernardes, Miguel; Costa, Lúcia

2017-04-08

To analyze the Health related Quality of Life (HRQoL) and physical function in rheumatoid arthritis (RA) patients and compare it with the general population. We also intended to analyze about disease activity influence in HRQoL and functional capacity, as well as determine potential determinants for these outcomes. A cross-sectional study was conducted in RA patients from a university hospital of Portugal. We obtained Short Form 36, EuroQoL 5D, health assessment questionnaire, visual analog scale for pain and patient's assessment of disease activity. Comparisons between SF-36 and EQ-5D values with our population reference values were conducted using the Mann-Whitney test. Data were compared in different levels of disease activity, using Kruskal Wallis test and Fisher's exact test. A multiple regression analysis was conducted to identify the potential determinants of outcomes. RA sample showed significantly lower values than the portuguese general population on physical summary measure of SF-36 (median=32 vs. 50, p<0.001) and EQ-5D (median=0.620 vs. 0.758 respectively; p<0.001). Lower disease activity levels had better PROs and this was true even when compared patients achieving remission with those in low disease activity. The HAQ (r 2 =67%), VAS-P (r 2 =62%) and VAS-DA (r 2 =58%) were the variables that strongly related to SF-36. Considering HAQ, the strongest relation was found with VAS-P, VAS-DA and age (r 2 =60%, 61% and 33%, respectively). Multiple regression analysis identified HAQ, VAS-P and educational status as determinants of the HRQoL; age, female gender, employment, VAS-P and VAS-DA as determinants of physical function. Impairment of HRQoL in RA patients is enormous. We found significant differences between different levels of disease activity, showing higher HRQoL and functional capacity at lower disease activity levels. Copyright © 2017 Elsevier España, S.L.U. and Sociedad Española de Reumatología y Colegio Mexicano de Reumatología. All rights reserved.

Low Pressure Vapor-assisted Solution Process for Tunable Band Gap Pinhole-free Methylammonium Lead Halide Perovskite Films

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

Sutter-Fella, Carolin M.; Li, Yanbo; Cefarin, Nicola

Organo-lead halide perovskites have recently attracted great interest for potential applications in thin-film photovoltaics and optoelectronics. Herein, we present a protocol for the fabrication of this material via the low-pressure vapor assisted solution process (LP-VASP) method, which yields ~19% power conversion efficiency in planar heterojunction perovskite solar cells. First, we report the synthesis of methylammonium iodide (CH 3NH 3I) and methylammonium bromide (CH 3NH 3Br) from methylamine and the corresponding halide acid (HI or HBr). Then, we describe the fabrication of pinhole-free, continuous methylammonium-lead halide perovskite (CH 3NH 3PbX 3 with X = I, Br, Cl and their mixture) filmsmore » with the LP-VASP. This process is based on two steps: i) spin-coating of a homogenous layer of lead halide precursor onto a substrate, and ii) conversion of this layer to CH 3NH 3PbI 3-xBr x by exposing the substrate to vapors of a mixture of CH 3NH 3I and CH 3NH 3Br at reduced pressure and 120 °C. Through slow diffusion of the methylammonium halide vapor into the lead halide precursor, we achieve slow and controlled growth of a continuous, pinhole-free perovskite film. The LP-VASP allows synthetic access to the full halide composition space in CH 3NH 3PbI 3-xBr x with 0 ≤ x ≤ 3. Depending on the composition of the vapor phase, the bandgap can be tuned between 1.6 eV ≤ E g ≤ 2.3 eV. In addition, by varying the composition of the halide precursor and of the vapor phase, we can also obtain CH 3NH 3PbI 3-xCl x. Films obtained from the LP-VASP are reproducible, phase pure as confirmed by X-ray diffraction measurements, and show high photoluminescence quantum yield. The process does not require the use of a glovebox.« less

Low Pressure Vapor-assisted Solution Process for Tunable Band Gap Pinhole-free Methylammonium Lead Halide Perovskite Films

DOE PAGES

Sutter-Fella, Carolin M.; Li, Yanbo; Cefarin, Nicola; ...

2017-09-08

Organo-lead halide perovskites have recently attracted great interest for potential applications in thin-film photovoltaics and optoelectronics. Herein, we present a protocol for the fabrication of this material via the low-pressure vapor assisted solution process (LP-VASP) method, which yields ~19% power conversion efficiency in planar heterojunction perovskite solar cells. First, we report the synthesis of methylammonium iodide (CH 3NH 3I) and methylammonium bromide (CH 3NH 3Br) from methylamine and the corresponding halide acid (HI or HBr). Then, we describe the fabrication of pinhole-free, continuous methylammonium-lead halide perovskite (CH 3NH 3PbX 3 with X = I, Br, Cl and their mixture) filmsmore » with the LP-VASP. This process is based on two steps: i) spin-coating of a homogenous layer of lead halide precursor onto a substrate, and ii) conversion of this layer to CH 3NH 3PbI 3-xBr x by exposing the substrate to vapors of a mixture of CH 3NH 3I and CH 3NH 3Br at reduced pressure and 120 °C. Through slow diffusion of the methylammonium halide vapor into the lead halide precursor, we achieve slow and controlled growth of a continuous, pinhole-free perovskite film. The LP-VASP allows synthetic access to the full halide composition space in CH 3NH 3PbI 3-xBr x with 0 ≤ x ≤ 3. Depending on the composition of the vapor phase, the bandgap can be tuned between 1.6 eV ≤ E g ≤ 2.3 eV. In addition, by varying the composition of the halide precursor and of the vapor phase, we can also obtain CH 3NH 3PbI 3-xCl x. Films obtained from the LP-VASP are reproducible, phase pure as confirmed by X-ray diffraction measurements, and show high photoluminescence quantum yield. The process does not require the use of a glovebox.« less

BEARCLAW: Boundary Embedded Adaptive Refinement Conservation LAW package

NASA Astrophysics Data System (ADS)

Mitran, Sorin

2011-04-01

The BEARCLAW package is a multidimensional, Eulerian AMR-capable computational code written in Fortran to solve hyperbolic systems for astrophysical applications. It is part of AstroBEAR, a hydrodynamic & magnetohydrodynamic code environment designed for a variety of astrophysical applications which allows simulations in 2, 2.5 (i.e., cylindrical), and 3 dimensions, in either cartesian or curvilinear coordinates.

78 FR 29016 - Establishing Quality Assurance Programs for Packaging Used in Transport of Radioactive Material

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-16

... Establishing Quality Assurance Programs for Packaging Used in Transport of Radioactive Material AGENCY: Nuclear..., ``Establishing Quality Assurance Programs for Packaging Used in Transport of Radioactive Material.'' This draft... regulations for the packaging and transportation of radioactive material in Part 71 of Title 10 of the Code of...

76 FR 5215 - Draft Regulatory Guide: Issuance, Availability

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-28

... Compliance with Packaging Requirements for Shipment and Receipt of Radioactive Material,'' is temporarily... Code of Federal Regulations, Part 71, ``Packaging and Transportation of Radioactive Material'' (10 CFR... Compliance with Packaging Requirements for Shipments of Radioactive Materials,'' as an acceptable process for...

ATLAS software configuration and build tool optimisation

NASA Astrophysics Data System (ADS)

Rybkin, Grigory; Atlas Collaboration

2014-06-01

ATLAS software code base is over 6 million lines organised in about 2000 packages. It makes use of some 100 external software packages, is developed by more than 400 developers and used by more than 2500 physicists from over 200 universities and laboratories in 6 continents. To meet the challenge of configuration and building of this software, the Configuration Management Tool (CMT) is used. CMT expects each package to describe its build targets, build and environment setup parameters, dependencies on other packages in a text file called requirements, and each project (group of packages) to describe its policies and dependencies on other projects in a text project file. Based on the effective set of configuration parameters read from the requirements files of dependent packages and project files, CMT commands build the packages, generate the environment for their use, or query the packages. The main focus was on build time performance that was optimised within several approaches: reduction of the number of reads of requirements files that are now read once per package by a CMT build command that generates cached requirements files for subsequent CMT build commands; introduction of more fine-grained build parallelism at package task level, i.e., dependent applications and libraries are compiled in parallel; code optimisation of CMT commands used for build; introduction of package level build parallelism, i. e., parallelise the build of independent packages. By default, CMT launches NUMBER-OF-PROCESSORS build commands in parallel. The other focus was on CMT commands optimisation in general that made them approximately 2 times faster. CMT can generate a cached requirements file for the environment setup command, which is especially useful for deployment on distributed file systems like AFS or CERN VMFS. The use of parallelism, caching and code optimisation significantly-by several times-reduced software build time, environment setup time, increased the efficiency of multi-core computing resources utilisation, and considerably improved software developer and user experience.

HZETRN: A heavy ion/nucleon transport code for space radiations

NASA Technical Reports Server (NTRS)

Wilson, John W.; Chun, Sang Y.; Badavi, Forooz F.; Townsend, Lawrence W.; Lamkin, Stanley L.

1991-01-01

The galactic heavy ion transport code (GCRTRN) and the nucleon transport code (BRYNTRN) are integrated into a code package (HZETRN). The code package is computer efficient and capable of operating in an engineering design environment for manned deep space mission studies. The nuclear data set used by the code is discussed including current limitations. Although the heavy ion nuclear cross sections are assumed constant, the nucleon-nuclear cross sections of BRYNTRN with full energy dependence are used. The relation of the final code to the Boltzmann equation is discussed in the context of simplifying assumptions. Error generation and propagation is discussed, and comparison is made with simplified analytic solutions to test numerical accuracy of the final results. A brief discussion of biological issues and their impact on fundamental developments in shielding technology is given.

Code Development in Coupled PARCS/RELAP5 for Supercritical Water Reactor

DOE PAGES

Hu, Po; Wilson, Paul

2014-01-01

The new capability is added to the existing coupled code package PARCS/RELAP5, in order to analyze SCWR design under supercritical pressure with the separated water coolant and moderator channels. This expansion is carried out on both codes. In PARCS, modification is focused on extending the water property tables to supercritical pressure, modifying the variable mapping input file and related code module for processing thermal-hydraulic information from separated coolant/moderator channels, and modifying neutronics feedback module to deal with the separated coolant/moderator channels. In RELAP5, modification is focused on incorporating more accurate water properties near SCWR operation/transient pressure and temperature in themore » code. Confirming tests of the modifications is presented and the major analyzing results from the extended codes package are summarized.« less

9 CFR 381.144 - Packaging materials.

Code of Federal Regulations, 2010 CFR

2010-01-01

..., from the packaging supplier under whose brand name and firm name the material is marketed to the... distinguishing brand name or code designation appearing on the packaging material shipping container; must....13) will be acceptable. The management of the establishment must maintain a file containing...

ANITA-2000 activation code package - updating of the decay data libraries and validation on the experimental data of the 14 MeV Frascati Neutron Generator

NASA Astrophysics Data System (ADS)

Frisoni, Manuela

2016-03-01

ANITA-2000 is a code package for the activation characterization of materials exposed to neutron irradiation released by ENEA to OECD-NEADB and ORNL-RSICC. The main component of the package is the activation code ANITA-4M that computes the radioactive inventory of a material exposed to neutron irradiation. The code requires the decay data library (file fl1) containing the quantities describing the decay properties of the unstable nuclides and the library (file fl2) containing the gamma ray spectra emitted by the radioactive nuclei. The fl1 and fl2 files of the ANITA-2000 code package, originally based on the evaluated nuclear data library FENDL/D-2.0, were recently updated on the basis of the JEFF-3.1.1 Radioactive Decay Data Library. This paper presents the results of the validation of the new fl1 decay data library through the comparison of the ANITA-4M calculated values with the measured electron and photon decay heats and activities of fusion material samples irradiated at the 14 MeV Frascati Neutron Generator (FNG) of the NEA-Frascati Research Centre. Twelve material samples were considered, namely: Mo, Cu, Hf, Mg, Ni, Cd, Sn, Re, Ti, W, Ag and Al. The ratios between calculated and experimental values (C/E) are shown and discussed in this paper.

Watermarking spot colors in packaging

NASA Astrophysics Data System (ADS)

Reed, Alastair; Filler, TomáÅ.¡; Falkenstern, Kristyn; Bai, Yang

2015-03-01

In January 2014, Digimarc announced Digimarc® Barcode for the packaging industry to improve the check-out efficiency and customer experience for retailers. Digimarc Barcode is a machine readable code that carries the same information as a traditional Universal Product Code (UPC) and is introduced by adding a robust digital watermark to the package design. It is imperceptible to the human eye but can be read by a modern barcode scanner at the Point of Sale (POS) station. Compared to a traditional linear barcode, Digimarc Barcode covers the whole package with minimal impact on the graphic design. This significantly improves the Items per Minute (IPM) metric, which retailers use to track the checkout efficiency since it closely relates to their profitability. Increasing IPM by a few percent could lead to potential savings of millions of dollars for retailers, giving them a strong incentive to add the Digimarc Barcode to their packages. Testing performed by Digimarc showed increases in IPM of at least 33% using the Digimarc Barcode, compared to using a traditional barcode. A method of watermarking print ready image data used in the commercial packaging industry is described. A significant proportion of packages are printed using spot colors, therefore spot colors needs to be supported by an embedder for Digimarc Barcode. Digimarc Barcode supports the PANTONE spot color system, which is commonly used in the packaging industry. The Digimarc Barcode embedder allows a user to insert the UPC code in an image while minimizing perceptibility to the Human Visual System (HVS). The Digimarc Barcode is inserted in the printing ink domain, using an Adobe Photoshop plug-in as the last step before printing. Since Photoshop is an industry standard widely used by pre-press shops in the packaging industry, a Digimarc Barcode can be easily inserted and proofed.

Corrosion Thermodynamics of Magnesium and Alloys from First Principles as a Function of Solvation

NASA Astrophysics Data System (ADS)

Limmer, Krista; Williams, Kristen; Andzelm, Jan

Thermodynamics of corrosion processes occurring on magnesium surfaces, such as hydrogen evolution and water dissociation, have been examined with density functional theory (DFT) to evaluate the effect of impurities and dilute alloying additions. The modeling of corrosion thermodynamics requires examination of species in a variety of chemical and electronic states in order to accurately represent the complex electrochemical corrosion process. In this study, DFT calculations for magnesium corrosion thermodynamics were performed with two DFT codes (VASP and DMol3), with multiple exchange-correlation functionals for chemical accuracy, as well as with various levels of implicit and explicit solvation for surfaces and solvated ions. The accuracy of the first principles calculations has been validated against Pourbaix diagrams constructed from solid, gas and solvated charged ion calculations. For aqueous corrosion, it is shown that a well parameterized implicit solvent is capable of accurately representing all but the first coordinating layer of explicit water for charged ions.

Nb2OsB2, with a new twofold superstructure of the U3Si2 type: Synthesis, crystal chemistry and chemical bonding

NASA Astrophysics Data System (ADS)

Mbarki, Mohammed; Touzani, Rachid St.; Fokwa, Boniface P. T.

2013-07-01

The new ternary metal-rich boride, Nb2OsB2, was synthesized by arc-melting the elements in a water-cooled copper crucible under an argon atmosphere. The compound was characterized from single-crystal X-ray data and EDX measurements. It crystallizes as a new superstructure (space group P4/mnc, no. 128) of the tetragonal U3Si2-structure type with lattice parameters a=5.922(1) Å and c=6.879(2) Å. All of the B atoms are involved in B2 dumbbells with B-B distances of 1.89(4) Å. Structure relaxation using VASP (Vienna ab intio Simulation Package) has confirmed the space group and the lattice parameters. According to electronic structure calculations (TB-LMTO-ASA), the homoatomic B-B interactions are optimized and very strong, but relatively strong heteroatomic Os-B, Nb-B and Nb-Os bonds are also found: These interactions, which together build a three-dimensional network, are mainly responsible for the structural stability of this new phase. The density of state at the Fermi level predicts metallic behavior, as expected, from this metal-rich boride.

Magnetic properties and stability of Cu3V2O8 compound in the different phases

NASA Astrophysics Data System (ADS)

Jezierski, Andrzej

2016-11-01

The magnetic and thermodynamic properties of Cu3V2O8 compound in four structures (P-1, P21/c, P21/m and Cmca) are reported. The calculations are performed by using the Full-Potential Local Orbital Minimum Basis (FPLO) and Vienna ab initio Simulation Package (VASP) methods. We have applied the local density approximation (LDA) with the generalized gradient corrections (GGA). The effect of electron correlations was also included in GGA+U approximation. The thermodynamic properties were obtained in the quasi-harmonic Debye-Grüneisen model using the equation of states (EOS) in the form of Poirier-Tarantola. Our ab-intio results indicate that α (P-1) phase is stable below 1.87 GPa, β (P21/c) exists in the region 1.87

Unexpected Competition between Antiferromagnetic and Ferromagnetic States in Hf2MnRu5B2: Predicted and Realized.

PubMed

Shankhari, Pritam; Zhang, Yuemei; Stekovic, Dejan; Itkis, Mikhail E; Fokwa, Boniface P T

2017-11-06

Materials "design" is increasingly gaining importance in the solid-state materials community in general and in the field of magnetic materials in particular. Density functional theory (DFT) predicted the competition between ferromagnetic (FM) and antiferromagnetic (AFM) ground states in a ruthenium-rich Ti 3 Co 5 B 2 -type boride (Hf 2 MnRu 5 B 2 ) for the first time. Vienna ab initio simulation package (VASP) total energy calculations indicated that the FM model was marginally more stable than one of the AFM models (AFM1), indicating very weak interactions between magnetic 1D Mn chains that can be easily perturbated by external means (magnetic field or composition). The predicted phase was then synthesized by arc-melting and characterized as Hf 2 Mn 1-x Ru 5+x B 2 (x = 0.27). Vibrating-scanning magnetometry shows an AFM ground state with T N ≈ 20 K under low magnetic field (0.005 T). At moderate-to-higher fields, AFM ordering vanishes while FM ordering emerges with a Curie temperature of 115 K. These experimental outcomes confirm the weak nature of the interchain interactions, as predicted by DFT calculations.

C2x: A tool for visualisation and input preparation for CASTEP and other electronic structure codes

NASA Astrophysics Data System (ADS)

Rutter, M. J.

2018-04-01

The c2x code fills two distinct roles. Its first role is in acting as a converter between the binary format .check files from the widely-used CASTEP [1] electronic structure code and various visualisation programs. Its second role is to manipulate and analyse the input and output files from a variety of electronic structure codes, including CASTEP, ONETEP and VASP, as well as the widely-used 'Gaussian cube' file format. Analysis includes symmetry analysis, and manipulation arbitrary cell transformations. It continues to be under development, with growing functionality, and is written in a form which would make it easy to extend it to working directly with files from other electronic structure codes. Data which c2x is capable of extracting from CASTEP's binary checkpoint files include charge densities, spin densities, wavefunctions, relaxed atomic positions, forces, the Fermi level, the total energy, and symmetry operations. It can recreate .cell input files from checkpoint files. Volumetric data can be output in formats useable by many common visualisation programs, and c2x will itself calculate integrals, expand data into supercells, and interpolate data via combinations of Fourier and trilinear interpolation. It can extract data along arbitrary lines (such as lines between atoms) as 1D output. C2x is able to convert between several common formats for describing molecules and crystals, including the .cell format of CASTEP. It can construct supercells, reduce cells to their primitive form, and add specified k-point meshes. It uses the spglib library [2] to report symmetry information, which it can add to .cell files. C2x is a command-line utility, so is readily included in scripts. It is available under the GPL and can be obtained from http://www.c2x.org.uk. It is believed to be the only open-source code which can read CASTEP's .check files, so it will have utility in other projects.

Deconvolution of subcellular protrusion heterogeneity and the underlying actin regulator dynamics from live cell imaging.

PubMed

Wang, Chuangqi; Choi, Hee June; Kim, Sung-Jin; Desai, Aesha; Lee, Namgyu; Kim, Dohoon; Bae, Yongho; Lee, Kwonmoo

2018-04-27

Cell protrusion is morphodynamically heterogeneous at the subcellular level. However, the mechanism of cell protrusion has been understood based on the ensemble average of actin regulator dynamics. Here, we establish a computational framework called HACKS (deconvolution of heterogeneous activity in coordination of cytoskeleton at the subcellular level) to deconvolve the subcellular heterogeneity of lamellipodial protrusion from live cell imaging. HACKS identifies distinct subcellular protrusion phenotypes based on machine-learning algorithms and reveals their underlying actin regulator dynamics at the leading edge. Using our method, we discover "accelerating protrusion", which is driven by the temporally ordered coordination of Arp2/3 and VASP activities. We validate our finding by pharmacological perturbations and further identify the fine regulation of Arp2/3 and VASP recruitment associated with accelerating protrusion. Our study suggests HACKS can identify specific subcellular protrusion phenotypes susceptible to pharmacological perturbation and reveal how actin regulator dynamics are changed by the perturbation.

Data Packages for the Hanford Immobilized Low Activity Tank Waste Performance Assessment 2001 Version [SEC 1 THRU 5

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

MANN, F.M.

Data package supporting the 2001 Immobilized Low-Activity Waste Performance Analysis. Geology, hydrology, geochemistry, facility, waste form, and dosimetry data based on recent investigation are provided. Verification and benchmarking packages for selected software codes are provided.

HEPMath 1.4: A mathematica package for semi-automatic computations in high energy physics

NASA Astrophysics Data System (ADS)

Wiebusch, Martin

2015-10-01

This article introduces the Mathematica package HEPMath which provides a number of utilities and algorithms for High Energy Physics computations in Mathematica. Its functionality is similar to packages like FormCalc or FeynCalc, but it takes a more complete and extensible approach to implementing common High Energy Physics notations in the Mathematica language, in particular those related to tensors and index contractions. It also provides a more flexible method for the generation of numerical code which is based on new features for C code generation in Mathematica. In particular it can automatically generate Python extension modules which make the compiled functions callable from Python, thus eliminating the need to write any code in a low-level language like C or Fortran. It also contains seamless interfaces to LHAPDF, FeynArts, and LoopTools.

An analysis of options available for developing a common laser ray tracing package for Ares and Kull code frameworks

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

Weeratunga, S K

Ares and Kull are mature code frameworks that support ALE hydrodynamics for a variety of HEDP applications at LLNL, using two widely different meshing approaches. While Ares is based on a 2-D/3-D block-structured mesh data base, Kull is designed to support unstructured, arbitrary polygonal/polyhedral meshes. In addition, both frameworks are capable of running applications on large, distributed-memory parallel machines. Currently, both these frameworks separately support assorted collections of physics packages related to HEDP, including one for the energy deposition by laser/ion-beam ray tracing. This study analyzes the options available for developing a common laser/ion-beam ray tracing package that can bemore » easily shared between these two code frameworks and concludes with a set of recommendations for its development.« less

49 CFR 173.242 - Bulk packagings for certain medium hazard liquids and solids, including solids with dual hazards.

Code of Federal Regulations, 2012 CFR

2012-10-01

... provisions specified in column 7 of the § 172.101 table. (a) Rail cars: Class DOT 103, 104, 105, 109, 111... IM 101, IM 102, and UN portable tanks when a T Code is specified in Column (7) of the § 172.101... authorized according to the IBC packaging code specified for the specific hazardous material in Column (7) of...

49 CFR 173.242 - Bulk packagings for certain medium hazard liquids and solids, including solids with dual hazards.

Code of Federal Regulations, 2010 CFR

2010-10-01

... provisions specified in column 7 of the § 172.101 table. (a) Rail cars: Class DOT 103, 104, 105, 109, 111...; Specification IM 101, IM 102, and UN portable tanks when a T Code is specified in Column (7) of the § 172.101... authorized according to the IBC packaging code specified for the specific hazardous material in Column (7) of...

49 CFR 173.242 - Bulk packagings for certain medium hazard liquids and solids, including solids with dual hazards.

Code of Federal Regulations, 2013 CFR

2013-10-01

... provisions specified in column 7 of the § 172.101 table. (a) Rail cars: Class DOT 103, 104, 105, 109, 111... IM 101, IM 102, and UN portable tanks when a T Code is specified in Column (7) of the § 172.101... authorized according to the IBC packaging code specified for the specific hazardous material in Column (7) of...

49 CFR 173.242 - Bulk packagings for certain medium hazard liquids and solids, including solids with dual hazards.

Code of Federal Regulations, 2011 CFR

2011-10-01

... provisions specified in column 7 of the § 172.101 table. (a) Rail cars: Class DOT 103, 104, 105, 109, 111... IM 101, IM 102, and UN portable tanks when a T Code is specified in Column (7) of the § 172.101... authorized according to the IBC packaging code specified for the specific hazardous material in Column (7) of...

49 CFR 173.242 - Bulk packagings for certain medium hazard liquids and solids, including solids with dual hazards.

Code of Federal Regulations, 2014 CFR

2014-10-01

... provisions specified in column 7 of the § 172.101 table. (a) Rail cars: Class DOT 103, 104, 105, 109, 111... IM 101, IM 102, and UN portable tanks when a T Code is specified in Column (7) of the § 172.101... authorized according to the IBC packaging code specified for the specific hazardous material in Column (7) of...

MELCOR computer code manuals

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

Summers, R.M.; Cole, R.K. Jr.; Smith, R.C.

1995-03-01

MELCOR is a fully integrated, engineering-level computer code that models the progression of severe accidents in light water reactor nuclear power plants. MELCOR is being developed at Sandia National Laboratories for the U.S. Nuclear Regulatory Commission as a second-generation plant risk assessment tool and the successor to the Source Term Code Package. A broad spectrum of severe accident phenomena in both boiling and pressurized water reactors is treated in MELCOR in a unified framework. These include: thermal-hydraulic response in the reactor coolant system, reactor cavity, containment, and confinement buildings; core heatup, degradation, and relocation; core-concrete attack; hydrogen production, transport, andmore » combustion; fission product release and transport; and the impact of engineered safety features on thermal-hydraulic and radionuclide behavior. Current uses of MELCOR include estimation of severe accident source terms and their sensitivities and uncertainties in a variety of applications. This publication of the MELCOR computer code manuals corresponds to MELCOR 1.8.3, released to users in August, 1994. Volume 1 contains a primer that describes MELCOR`s phenomenological scope, organization (by package), and documentation. The remainder of Volume 1 contains the MELCOR Users Guides, which provide the input instructions and guidelines for each package. Volume 2 contains the MELCOR Reference Manuals, which describe the phenomenological models that have been implemented in each package.« less

49 CFR 178.523 - Standards for composite packagings with inner glass, porcelain, or stoneware receptacles.

Code of Federal Regulations, 2011 CFR

2011-10-01

... glass, porcelain, or stoneware receptacles. 178.523 Section 178.523 Transportation Other Regulations... Standards § 178.523 Standards for composite packagings with inner glass, porcelain, or stoneware receptacles. (a) The following are identification codes for composite packagings with inner receptacles of glass...

49 CFR 178.522 - Standards for composite packagings with inner plastic receptacles.

Code of Federal Regulations, 2011 CFR

2011-10-01

... plastic receptacles. 178.522 Section 178.522 Transportation Other Regulations Relating to Transportation... packagings with inner plastic receptacles. (a) The following are the identification codes for composite packagings with inner plastic receptacles: (1) 6HA1 for a plastic receptacle within a protective steel drum...

49 CFR 178.522 - Standards for composite packagings with inner plastic receptacles.

Code of Federal Regulations, 2012 CFR

2012-10-01

... plastic receptacles. 178.522 Section 178.522 Transportation Other Regulations Relating to Transportation... packagings with inner plastic receptacles. (a) The following are the identification codes for composite packagings with inner plastic receptacles: (1) 6HA1 for a plastic receptacle within a protective steel drum...

49 CFR 178.522 - Standards for composite packagings with inner plastic receptacles.

Code of Federal Regulations, 2014 CFR

2014-10-01

... plastic receptacles. 178.522 Section 178.522 Transportation Other Regulations Relating to Transportation... packagings with inner plastic receptacles. (a) The following are the identification codes for composite packagings with inner plastic receptacles: (1) 6HA1 for a plastic receptacle within a protective steel drum...

49 CFR 178.522 - Standards for composite packagings with inner plastic receptacles.

Code of Federal Regulations, 2013 CFR

2013-10-01

... plastic receptacles. 178.522 Section 178.522 Transportation Other Regulations Relating to Transportation... packagings with inner plastic receptacles. (a) The following are the identification codes for composite packagings with inner plastic receptacles: (1) 6HA1 for a plastic receptacle within a protective steel drum...

High Resolution Aerospace Applications using the NASA Columbia Supercomputer

NASA Technical Reports Server (NTRS)

Mavriplis, Dimitri J.; Aftosmis, Michael J.; Berger, Marsha

2005-01-01

This paper focuses on the parallel performance of two high-performance aerodynamic simulation packages on the newly installed NASA Columbia supercomputer. These packages include both a high-fidelity, unstructured, Reynolds-averaged Navier-Stokes solver, and a fully-automated inviscid flow package for cut-cell Cartesian grids. The complementary combination of these two simulation codes enables high-fidelity characterization of aerospace vehicle design performance over the entire flight envelope through extensive parametric analysis and detailed simulation of critical regions of the flight envelope. Both packages. are industrial-level codes designed for complex geometry and incorpor.ats. CuStomized multigrid solution algorithms. The performance of these codes on Columbia is examined using both MPI and OpenMP and using both the NUMAlink and InfiniBand interconnect fabrics. Numerical results demonstrate good scalability on up to 2016 CPUs using the NUMAIink4 interconnect, with measured computational rates in the vicinity of 3 TFLOP/s, while InfiniBand showed some performance degradation at high CPU counts, particularly with multigrid. Nonetheless, the results are encouraging enough to indicate that larger test cases using combined MPI/OpenMP communication should scale well on even more processors.

Treatment of myofascial trigger points in patients with chronic shoulder pain: a randomized, controlled trial

PubMed Central

2011-01-01

Background Shoulder pain is a common musculoskeletal problem that is often chronic or recurrent. Myofascial trigger points (MTrPs) cause shoulder pain and are prevalent in patients with shoulder pain. However, few studies have focused on MTrP therapy. The aim of this study was to assess the effectiveness of multimodal treatment of MTrPs in patients with chronic shoulder pain. Methods A single-assessor, blinded, randomized, controlled trial was conducted. The intervention group received comprehensive treatment once weekly consisting of manual compression of the MTrPs, manual stretching of the muscles and intermittent cold application with stretching. Patients were instructed to perform muscle-stretching and relaxation exercises at home and received ergonomic recommendations and advice to assume and maintain good posture. The control group remained on the waiting list for 3 months. The Disabilities of Arm, Shoulder and Hand (DASH) questionnaire score (primary outcome), Visual Analogue Scale for Pain (VAS-P), Global Perceived Effect (GPE) scale and the number of muscles with MTrPs were assessed at 6 and 12 weeks in the intervention group and compared with those of a control group. Results Compared with the control group, the intervention group showed significant improvement (P < 0.05) on the DASH after 12 weeks (mean difference, 7.7; 95% confidence interval (95% CI), 1.2 to 14.2), on the VAS-P1 for current pain (mean difference, 13.8; 95% CI, 2.6 to 25.0), on the VAS-P2 for pain in the past 7 days (mean difference, 10.2; 95% CI, 0.7 to 19.7) and VAS-P3 most severe pain in the past 7 days (mean difference, 13.8; 95% CI, 0.8 to 28.4). After 12 weeks, 55% of the patients in the intervention group reported improvement (from slightly improved to completely recovered) versus 14% in the control group. The mean number of muscles with active MTrPs decreased in the intervention group compared with the control group (mean difference, 2.7; 95% CI, 1.2 to 4.2). Conclusions The results of this study show that 12-week comprehensive treatment of MTrPs in shoulder muscles reduces the number of muscles with active MTrPs and is effective in reducing symptoms and improving shoulder function in patients with chronic shoulder pain. Trial registration number ISRCTN: ISRCTN75722066 PMID:21261971

Moving from Batch to Field Using the RT3D Reactive Transport Modeling System

NASA Astrophysics Data System (ADS)

Clement, T. P.; Gautam, T. R.

2002-12-01

The public domain reactive transport code RT3D (Clement, 1997) is a general-purpose numerical code for solving coupled, multi-species reactive transport in saturated groundwater systems. The code uses MODFLOW to simulate flow and several modules of MT3DMS to simulate the advection and dispersion processes. RT3D employs the operator-split strategy which allows the code solve the coupled reactive transport problem in a modular fashion. The coupling between reaction and transport is defined through a separate module where the reaction equations are specified. The code supports a versatile user-defined reaction option that allows users to define their own reaction system through a Fortran-90 subroutine, known as the RT3D-reaction package. Further a utility code, known as BATCHRXN, allows the users to independently test and debug their reaction package. To analyze a new reaction system at a batch scale, users should first run BATCHRXN to test the ability of their reaction package to model the batch data. After testing, the reaction package can simply be ported to the RT3D environment to study the model response under 1-, 2-, or 3-dimensional transport conditions. This paper presents example problems that demonstrate the methods for moving from batch to field-scale simulations using BATCHRXN and RT3D codes. The first example describes a simple first-order reaction system for simulating the sequential degradation of Tetrachloroethene (PCE) and its daughter products. The second example uses a relatively complex reaction system for describing the multiple degradation pathways of Tetrachloroethane (PCA) and its daughter products. References 1) Clement, T.P, RT3D - A modular computer code for simulating reactive multi-species transport in 3-Dimensional groundwater aquifers, Battelle Pacific Northwest National Laboratory Research Report, PNNL-SA-28967, September, 1997. Available at: http://bioprocess.pnl.gov/rt3d.htm.

Basic Business and Economics: Understanding the Uses of the Universal Product Code

ERIC Educational Resources Information Center

Blockhus, Wanda

1977-01-01

Describes the Universal Product Code (UPC), the two-part food labeling and packaging code which is both human- and electronic scanner-readable. Discusses how it affects both consumer and business, and suggests how to teach the UPC code to business education students. (HD)

Parallel Adaptive Mesh Refinement Library

NASA Technical Reports Server (NTRS)

Mac-Neice, Peter; Olson, Kevin

2005-01-01

Parallel Adaptive Mesh Refinement Library (PARAMESH) is a package of Fortran 90 subroutines designed to provide a computer programmer with an easy route to extension of (1) a previously written serial code that uses a logically Cartesian structured mesh into (2) a parallel code with adaptive mesh refinement (AMR). Alternatively, in its simplest use, and with minimal effort, PARAMESH can operate as a domain-decomposition tool for users who want to parallelize their serial codes but who do not wish to utilize adaptivity. The package builds a hierarchy of sub-grids to cover the computational domain of a given application program, with spatial resolution varying to satisfy the demands of the application. The sub-grid blocks form the nodes of a tree data structure (a quad-tree in two or an oct-tree in three dimensions). Each grid block has a logically Cartesian mesh. The package supports one-, two- and three-dimensional models.

49 CFR 178.503 - Marking of packagings.

Code of Federal Regulations, 2011 CFR

2011-10-01

... that is represented as manufactured to meet a UN standard with the marks specified in this section. The... marks should be used to separate this information. A packaging conforming to a UN standard must be... “UN”) may be applied in place of the symbol;; (2) A packaging identification code designating the type...

49 CFR 178.503 - Marking of packagings.

Code of Federal Regulations, 2012 CFR

2012-10-01

... that is represented as manufactured to meet a UN standard with the marks specified in this section. The... marks should be used to separate this information. A packaging conforming to a UN standard must be... “UN”) may be applied in place of the symbol;; (2) A packaging identification code designating the type...

49 CFR 178.503 - Marking of packagings.

Code of Federal Regulations, 2013 CFR

2013-10-01

... that is represented as manufactured to meet a UN standard with the marks specified in this section. The... marks should be used to separate this information. A packaging conforming to a UN standard must be... “UN” may be applied in place of the symbol); (2) A packaging identification code designating the type...

49 CFR 178.503 - Marking of packagings.

Code of Federal Regulations, 2014 CFR

2014-10-01

... that is represented as manufactured to meet a UN standard with the marks specified in this section. The... marks should be used to separate this information. A packaging conforming to a UN standard must be... “UN” may be applied in place of the symbol); (2) A packaging identification code designating the type...

PARAMESH: A Parallel Adaptive Mesh Refinement Community Toolkit

NASA Technical Reports Server (NTRS)

MacNeice, Peter; Olson, Kevin M.; Mobarry, Clark; deFainchtein, Rosalinda; Packer, Charles

1999-01-01

In this paper, we describe a community toolkit which is designed to provide parallel support with adaptive mesh capability for a large and important class of computational models, those using structured, logically cartesian meshes. The package of Fortran 90 subroutines, called PARAMESH, is designed to provide an application developer with an easy route to extend an existing serial code which uses a logically cartesian structured mesh into a parallel code with adaptive mesh refinement. Alternatively, in its simplest use, and with minimal effort, it can operate as a domain decomposition tool for users who want to parallelize their serial codes, but who do not wish to use adaptivity. The package can provide them with an incremental evolutionary path for their code, converting it first to uniformly refined parallel code, and then later if they so desire, adding adaptivity.

An electron-beam dose deposition experiment: TIGER 1-D simulation code versus thermoluminescent dosimetry

NASA Astrophysics Data System (ADS)

Murrill, Steven R.; Tipton, Charles W.; Self, Charles T.

1991-03-01

The dose absorbed in an integrated circuit (IC) die exposed to a pulse of low-energy electrons is a strong function of both electron energy and surrounding packaging materials. This report describes an experiment designed to measure how well the Integrated TIGER Series one-dimensional (1-D) electron transport simulation program predicts dose correction factors for a state-of-the-art IC package and package/printed circuit board (PCB) combination. These derived factors are compared with data obtained experimentally using thermoluminescent dosimeters (TLD's) and the FX-45 flash x-ray machine (operated in electron-beam (e-beam) mode). The results of this experiment show that the TIGER 1-D simulation code can be used to accurately predict FX-45 e-beam dose deposition correction factors for reasonably complex IC packaging configurations.

SpecBit, DecayBit and PrecisionBit: GAMBIT modules for computing mass spectra, particle decay rates and precision observables

NASA Astrophysics Data System (ADS)

Athron, Peter; Balázs, Csaba; Dal, Lars A.; Edsjö, Joakim; Farmer, Ben; Gonzalo, Tomás E.; Kvellestad, Anders; McKay, James; Putze, Antje; Rogan, Chris; Scott, Pat; Weniger, Christoph; White, Martin

2018-01-01

We present the GAMBIT modules SpecBit, DecayBit and PrecisionBit. Together they provide a new framework for linking publicly available spectrum generators, decay codes and other precision observable calculations in a physically and statistically consistent manner. This allows users to automatically run various combinations of existing codes as if they are a single package. The modular design allows software packages fulfilling the same role to be exchanged freely at runtime, with the results presented in a common format that can easily be passed to downstream dark matter, collider and flavour codes. These modules constitute an essential part of the broader GAMBIT framework, a major new software package for performing global fits. In this paper we present the observable calculations, data, and likelihood functions implemented in the three modules, as well as the conventions and assumptions used in interfacing them with external codes. We also present 3-BIT-HIT, a command-line utility for computing mass spectra, couplings, decays and precision observables in the MSSM, which shows how the three modules can easily be used independently of GAMBIT.

Computational models for the viscous/inviscid analysis of jet aircraft exhaust plumes

NASA Astrophysics Data System (ADS)

Dash, S. M.; Pergament, H. S.; Thorpe, R. D.

1980-05-01

Computational models which analyze viscous/inviscid flow processes in jet aircraft exhaust plumes are discussed. These models are component parts of an NASA-LaRC method for the prediction of nozzle afterbody drag. Inviscid/shock processes are analyzed by the SCIPAC code which is a compact version of a generalized shock capturing, inviscid plume code (SCIPPY). The SCIPAC code analyzes underexpanded jet exhaust gas mixtures with a self-contained thermodynamic package for hydrocarbon exhaust products and air. A detailed and automated treatment of the embedded subsonic zones behind Mach discs is provided in this analysis. Mixing processes along the plume interface are analyzed by two upgraded versions of an overlaid, turbulent mixing code (BOAT) developed previously for calculating nearfield jet entrainment. The BOATAC program is a frozen chemistry version of BOAT containing the aircraft thermodynamic package as SCIPAC; BOATAB is an afterburning version with a self-contained aircraft (hydrocarbon/air) finite-rate chemistry package. The coupling of viscous and inviscid flow processes is achieved by an overlaid procedure with interactive effects accounted for by a displacement thickness type correction to the inviscid plume interface.

Computational models for the viscous/inviscid analysis of jet aircraft exhaust plumes. [predicting afterbody drag

NASA Technical Reports Server (NTRS)

Dash, S. M.; Pergament, H. S.; Thorpe, R. D.

1980-01-01

Computational models which analyze viscous/inviscid flow processes in jet aircraft exhaust plumes are discussed. These models are component parts of an NASA-LaRC method for the prediction of nozzle afterbody drag. Inviscid/shock processes are analyzed by the SCIPAC code which is a compact version of a generalized shock capturing, inviscid plume code (SCIPPY). The SCIPAC code analyzes underexpanded jet exhaust gas mixtures with a self-contained thermodynamic package for hydrocarbon exhaust products and air. A detailed and automated treatment of the embedded subsonic zones behind Mach discs is provided in this analysis. Mixing processes along the plume interface are analyzed by two upgraded versions of an overlaid, turbulent mixing code (BOAT) developed previously for calculating nearfield jet entrainment. The BOATAC program is a frozen chemistry version of BOAT containing the aircraft thermodynamic package as SCIPAC; BOATAB is an afterburning version with a self-contained aircraft (hydrocarbon/air) finite-rate chemistry package. The coupling of viscous and inviscid flow processes is achieved by an overlaid procedure with interactive effects accounted for by a displacement thickness type correction to the inviscid plume interface.

MELCOR computer code manuals: Primer and user`s guides, Version 1.8.3 September 1994. Volume 1

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

Summers, R.M.; Cole, R.K. Jr.; Smith, R.C.

1995-03-01

MELCOR is a fully integrated, engineering-level computer code that models the progression of severe accidents in light water reactor nuclear power plants. MELCOR is being developed at Sandia National Laboratories for the US Nuclear Regulatory Commission as a second-generation plant risk assessment tool and the successor to the Source Term Code Package. A broad spectrum of severe accident phenomena in both boiling and pressurized water reactors is treated in MELCOR in a unified framework. These include: thermal-hydraulic response in the reactor coolant system, reactor cavity, containment, and confinement buildings; core heatup, degradation, and relocation; core-concrete attack; hydrogen production, transport, andmore » combustion; fission product release and transport; and the impact of engineered safety features on thermal-hydraulic and radionuclide behavior. Current uses of MELCOR include estimation of severe accident source terms and their sensitivities and uncertainties in a variety of applications. This publication of the MELCOR computer code manuals corresponds to MELCOR 1.8.3, released to users in August, 1994. Volume 1 contains a primer that describes MELCOR`s phenomenological scope, organization (by package), and documentation. The remainder of Volume 1 contains the MELCOR Users` Guides, which provide the input instructions and guidelines for each package. Volume 2 contains the MELCOR Reference Manuals, which describe the phenomenological models that have been implemented in each package.« less

The R package 'Luminescence': a history of unexpected complexity and concepts to deal with it

NASA Astrophysics Data System (ADS)

Kreutzer, Sebastian; Burow, Christoph; Dietze, Michael; Fuchs, Margret C.; Friedrich, Johannes; Fischer, Manfred; Schmidt, Christoph

2017-04-01

Overcoming limitations in the so far used standard software, developing an efficient solution of low weight for a very specific task or creating graphs of high quality: the reasons that may had initially lead a scientist to work with R are manifold. And as long as developed solutions, e.g., R scripts, are needed for personal use only, code can remain unstructured and a documentation is not compulsory. However, this changes with the first friendly request for help after the code has been reused by others. In contrast to single scripts, written without intention to ever get published, for R packages the CRAN policy demands a more structured and elaborated approach including a minimum of documentation. Nevertheless, growing projects with thousands of lines of code that need to be maintained can become overwhelming, in particular as researchers are not by definition experts on managing software projects. The R package 'Luminescence' (Kreutzer et al., 2017), a collection of tools dealing with the analysis of luminescence data in a geoscientific, geochronological context, started as one single R script, but quickly evolved into a comprehensive solution connected with various other R packages. We present (1) a very brief development history of the package 'Luminescence', before we (2) sketch technical challenges encountered over time and solutions that have been found to deal with it by using various open source tools. Our presentation is considered as a collection of concepts and approaches to set up R projects in geosciences. References. Kreutzer, S., Dietze, M., Burow, C., Fuchs, M. C., Schmidt, C., Fischer, M., Friedrich, J., 2017. Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.6.4. https://CRAN.R-project.org/package=Luminescence

Cordycepin-enriched WIB801C from Cordyceps militaris inhibits ADP-induced [Ca(2+)] i mobilization and fibrinogen binding via phosphorylation of IP 3R and VASP.

PubMed

Lee, Dong-Ha; Kwon, Hyuk-Woo; Kim, Hyun-Hong; Lim, Deok Hwi; Nam, Gi Suk; Shin, Jung-Hae; Kim, Yun-Yi; Kim, Jong-Lae; Lee, Jong-Jin; Kwon, Ho-Kyun; Park, Hwa-Jin

2015-01-01

In this study, we investigated the effect of cordycepin-enriched (CE)-WIB801C from Cordyceps militaris on ADP (20 µM)-stimulated platelet aggregation. CE-WIB801C dose-dependently inhibited ADP-induced platelet aggregation, and its IC50 value was 18.5 μg/mL. CE-WIB801C decreased TXA2 production, but did not inhibit the activities of COX-1 and thromboxane synthase (TXAS) in ADP-activated platelets, which suggests that the inhibition of TXA2 production by CE-WIB801C is not resulted from the direct inhibition of COX-1 and TXAS. CE-WIB801C inhibited ATP release and [Ca(2+)]i mobilization, and increased cAMP level and IP3RI (Ser(1756)) phosphorylation in ADP-activated platelets. cAMP-dependent protein kinase (A-kinase) inhibitor Rp-8-Br-cAMPS increased CE-WIB801C-inhibited [Ca(2+)]i mobilization, and strongly inhibited CE-WIB801C-increased IP3RI (Ser(1756)) phosphorylation. CE-WIB801C elevated the phosphorylation of VASP (Ser(157)), an A-kinase substrate, but inhibited fibrinogen binding to αIIb/β3. These results suggest that CE-WIB801C-elevated cAMP involved in IP3RI (Ser(1756)) phosphorylation to inhibit [Ca(2+)]i mobilization and, VASP (Ser(157)) phosphorylation to inhibit αIIb/β3 activation. Therefore, in this study, we demonstrate that CE-WIB801C may have a preventive or therapeutic potential for platelet aggregation-mediated diseases, such as thrombosis, myocardial infarction, atherosclerosis, and ischemic cerebrovascular disease.

Experimental evidence of Migfilin as a new therapeutic target of hepatocellular carcinoma metastasis

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

Gkretsi, Vasiliki, E-mail: vasso.gkretsi@gmail.com; Bogdanos, Dimitrios P.; Department of Rheumatology, School of Medicine, University of Thessaly, University Hospital of Larissa, 41110 Larissa

Migfilin is a novel cell–matrix adhesion protein known to interact with Vasodilator Stimulated Phosphoprotein (VASP) and be localized both at cell–matrix and cell–cell adhesions. To date there is nothing known about its role in hepatocellular carcinoma (HCC). As matrix is important in metastasis, we aimed to investigate the Migfilin's role in HCC metastasis using two human HCC cell lines that differ in their metastatic potential; non-invasive Alexander cells and the highly invasive HepG2 cells. We silenced Migfilin by siRNA and studied its effect on signaling and metastasis-related cellular properties. We show that Migfilin's expression is elevated in HepG2 cells andmore » its silencing leads to upregulation of actin reorganization-related proteins, namely phosphor-VASP (Ser157 and Ser239), Fascin-1 and Rho-kinase-1, promoting actin polymerization and inhibiting cell invasion. Phosphor-Akt (Ser473) is decreased contributing to the upregulation of free and phosphor-β-catenin (Ser33/37Thr41) and inducing proliferation. Migfilin elimination upregulates Extracellular Signal–regulated kinase, which increases cell adhesion in HepG2 and reduces invasiveness. This is the first study to reveal that Migfilin inhibition can halt HCC metastasis in vitro, providing the molecular mechanism involved and presenting Migfilin as potential therapeutic target against HCC metastasis. - Highlights: • Migfilin is a cell–matrix and cell–cell adhesion protein known to interact with VASP. • Nothing is known about Migfilin's role in hepatocellular carcinoma (HCC). • We eliminated Migfilin from 2 HCC cell lines and studied in vitro metastasis. • Its silencing inhibits cell invasion and promotes adhesion in HepG2 invasive cells. • We provide molecular mechanism by which Migfilin elimination halts HCC metastasis.« less

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

Topkan, Erkan, E-mail: docdretopkan@gmail.com; Yildirim, Berna Akkus; Guler, Ozan Cem

Purpose: To investigate the safety and efficacy of single-dose 8-Gy palliative chest reirradiation (CRI) in metastatic non-small cell lung cancer (M-NSCLC) patients with painful thoracic failures (TF) within the previous radiation portal. Patients and Methods: We retrospectively analyzed the clinical data of 78 M-NSCLC patients who received single-dose 8-Gy CRI for painful TF after concurrent chemoradiation therapy to a total radiation dose of 52 to 66 Gy between 2007 and 2012. Primary endpoints included significant pain relief (SPR) defined as a ≥2 point decrement in the Visual Analogue Scale for Pain inventory (VAS-P), time to pain relief, and duration of painmore » control. Secondary objectives were survival and prognostic factors. Results: Treatment was well tolerated, with only 5.1% grade 3 pneumonitis and 1.3% grade 2 esophagitis. Pre-CRI median and post-CRI minimum VAS-P were 7 and 3 (P<.001), respectively. SPR was noted in 67 (85.9%) patients, and only 3 (3.9%) scored progressive pain. Median time to lowest VAS-P and duration of pain control were 27 days and 6.1 months, respectively. Median overall survival (OS) was 7.7 months, and the 1-year OS rate was 26.5%. On multivariate analyses, lower Eastern Cooperative Oncology group score (1-2; P<.001), absence of anemia (P=.001), and fewer metastatic sites (1-2; P<.001) were found to be associated with longer OS. Conclusions: Single-dose 8-Gy CRI provides safe, effective, and durable pain palliation for TF in radically irradiated M-NSCLC patients. Because of its convenience, lower cost, and higher comfort, the present protocol can be considered an appropriate option for patients with limited life spans.« less

Theobromine up-regulates cerebral brain-derived neurotrophic factor and facilitates motor learning in mice.

PubMed

Yoneda, Mitsugu; Sugimoto, Naotoshi; Katakura, Masanori; Matsuzaki, Kentaro; Tanigami, Hayate; Yachie, Akihiro; Ohno-Shosaku, Takako; Shido, Osamu

2017-01-01

Theobromine, which is a caffeine derivative, is the primary methylxanthine produced by Theobroma cacao. Theobromine works as a phosphodiesterase (PDE) inhibitor to increase intracellular cyclic adenosine monophosphate (cAMP). cAMP activates the cAMP-response element-binding protein (CREB), which is involved in a large variety of brain processes, including the induction of the brain-derived neurotrophic factor (BDNF). BDNF supports cell survival and neuronal functions, including learning and memory. Thus, cAMP/CREB/BDNF pathways play an important role in learning and memory. Here, we investigated whether orally administered theobromine could act as a PDE inhibitor centrally and affect cAMP/CREB/BDNF pathways and learning behavior in mice. The mice were divided into two groups. The control group (CN) was fed a normal diet, whereas the theobromine group (TB) was fed a diet supplemented with 0.05% theobromine for 30 days. We measured the levels of theobromine, phosphorylated vasodilator-stimulated phosphoprotein (p-VASP), phosphorylated CREB (p-CREB), and BDNF in the brain. p-VASP was used as an index of cAMP increases. Moreover, we analyzed the performance of the mice on a three-lever motor learning task. Theobromine was detectable in the brains of TB mice. The brain levels of p-VASP, p-CREB, and BDNF were higher in the TB mice compared with those in the CN mice. In addition, the TB mice performed better on the three-lever task than the CN mice did. These results strongly suggested that orally administered theobromine acted as a PDE inhibitor in the brain, and it augmented the cAMP/CREB/BDNF pathways and motor learning in mice. Copyright © 2016 Elsevier Inc. All rights reserved.

ARES: automated response function code. Users manual. [HPGAM and LSQVM

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

Maung, T.; Reynolds, G.M.

This ARES user's manual provides detailed instructions for a general understanding of the Automated Response Function Code and gives step by step instructions for using the complete code package on a HP-1000 system. This code is designed to calculate response functions of NaI gamma-ray detectors, with cylindrical or rectangular geometries.

Universal Noiseless Coding Subroutines

NASA Technical Reports Server (NTRS)

Schlutsmeyer, A. P.; Rice, R. F.

1986-01-01

Software package consists of FORTRAN subroutines that perform universal noiseless coding and decoding of integer and binary data strings. Purpose of this type of coding to achieve data compression in sense that coded data represents original data perfectly (noiselessly) while taking fewer bits to do so. Routines universal because they apply to virtually any "real-world" data source.

Characterization of open-cycle coal-fired MHD generators. Quarterly technical summary report No. 6, October 1--December 31, 1977. [PACKAGE code

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

Kolb, C.E.; Yousefian, V.; Wormhoudt, J.

1978-01-30

Research has included theoretical modeling of important plasma chemical effects such as: conductivity reductions due to condensed slag/electron interactions; conductivity and generator efficiency reductions due to the formation of slag-related negative ion species; and the loss of alkali seed due to chemical combination with condensed slag. A summary of the major conclusions in each of these areas is presented. A major output of the modeling effort has been the development of an MHD plasma chemistry core flow model. This model has been formulated into a computer program designated the PACKAGE code (Plasma Analysis, Chemical Kinetics, And Generator Efficiency). The PACKAGEmore » code is designed to calculate the effect of coal rank, ash percentage, ash composition, air preheat temperatures, equivalence ratio, and various generator channel parameters on the overall efficiency of open-cycle, coal-fired MHD generators. A complete description of the PACKAGE code and a preliminary version of the PACKAGE user's manual are included. A laboratory measurements program involving direct, mass spectrometric sampling of the positive and negative ions formed in a one atmosphere coal combustion plasma was also completed during the contract's initial phase. The relative ion concentrations formed in a plasma due to the methane augmented combustion of pulverized Montana Rosebud coal with potassium carbonate seed and preheated air are summarized. Positive ions measured include K/sup +/, KO/sup +/, Na/sup +/, Rb/sup +/, Cs/sup +/, and CsO/sup +/, while negative ions identified include PO/sub 3//sup -/, PO/sub 2//sup -/, BO/sub 2//sup -/, OH/sup -/, SH/sup -/, and probably HCrO/sub 3/, HMoO/sub 4//sup -/, and HWO/sub 3//sup -/. Comparison of the measurements with PACKAGE code predictions are presented. Preliminary design considerations for a mass spectrometric sampling probe capable of characterizing coal combustion plasmas from full scale combustors and flow trains are presented and discussed.« less

SPEXTRA: Optimal extraction code for long-slit spectra in crowded fields

NASA Astrophysics Data System (ADS)

Sarkisyan, A. N.; Vinokurov, A. S.; Solovieva, Yu. N.; Sholukhova, O. N.; Kostenkov, A. E.; Fabrika, S. N.

2017-10-01

We present a code for the optimal extraction of long-slit 2D spectra in crowded stellar fields. Its main advantage and difference from the existing spectrum extraction codes is the presence of a graphical user interface (GUI) and a convenient visualization system of data and extraction parameters. On the whole, the package is designed to study stars in crowded fields of nearby galaxies and star clusters in galaxies. Apart from the spectrum extraction for several stars which are closely located or superimposed, it allows the spectra of objects to be extracted with subtraction of superimposed nebulae of different shapes and different degrees of ionization. The package can also be used to study single stars in the case of a strong background. In the current version, the optimal extraction of 2D spectra with an aperture and the Gaussian function as PSF (point spread function) is proposed. In the future, the package will be supplemented with the possibility to build a PSF based on a Moffat function. We present the details of GUI, illustrate main features of the package, and show results of extraction of the several interesting spectra of objects from different telescopes.

The equation of state package FEOS for high energy density matter

NASA Astrophysics Data System (ADS)

Faik, Steffen; Tauschwitz, Anna; Iosilevskiy, Igor

2018-06-01

Adequate equation of state (EOS) data is of high interest in the growing field of high energy density physics and especially essential for hydrodynamic simulation codes. The semi-analytical method used in the newly developed Frankfurt equation of state (FEOS) package provides an easy and fast access to the EOS of - in principle - arbitrary materials. The code is based on the well known QEOS model (More et al., 1988; Young and Corey, 1995) and is a further development of the MPQeos code (Kemp and Meyer-ter Vehn, 1988; Kemp and Meyer-ter Vehn, 1998) from Max-Planck-Institut für Quantenoptik (MPQ) in Garching Germany. The list of features contains the calculation of homogeneous mixtures of chemical elements and the description of the liquid-vapor two-phase region with or without a Maxwell construction. Full flexibility of the package is assured by its structure: A program library provides the EOS with an interface designed for Fortran or C/C++ codes. Two additional software tools allow for the generation of EOS tables in different file output formats and for the calculation and visualization of isolines and Hugoniot shock adiabats. As an example the EOS of fused silica (SiO2) is calculated and compared to experimental data and other EOS codes.

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

Carpenter, John H.; Belcourt, Kenneth Noel

Completion of the CASL L3 milestone THM.CFD.P6.03 provides a tabular material properties capability to the Hydra code. A tabular interpolation package used in Sandia codes was modified to support the needs of multi-phase solvers in Hydra. Use of the interface is described. The package was released to Hydra under a government use license. A dummy physics was created in Hydra to prototype use of the interpolation routines. Finally, a test using the dummy physics verifies the correct behavior of the interpolation for a test water table. 3

A Mena invasion isoform potentiates EGF-induced carcinoma cell invasion and metastasis.

PubMed

Philippar, Ulrike; Roussos, Evanthia T; Oser, Matthew; Yamaguchi, Hideki; Kim, Hyung-Do; Giampieri, Silvia; Wang, Yarong; Goswami, Sumanta; Wyckoff, Jeffrey B; Lauffenburger, Douglas A; Sahai, Erik; Condeelis, John S; Gertler, Frank B

2008-12-01

The spread of cancer during metastatic disease requires that tumor cells subvert normal regulatory networks governing cell motility to invade surrounding tissues and migrate toward blood and lymphatic vessels. Enabled (Ena)/vasodilator-stimulated phosphoprotein (VASP) proteins regulate cell motility by controlling the geometry of assembling actin networks. Mena, an Ena/VASP protein, is upregulated in the invasive subpopulation of breast cancer cells. In addition, Mena is alternately spliced to produce an invasion isoform, Mena(INV). Here we show that Mena and Mena(INV) promote carcinoma cell motility and invasiveness in vivo and in vitro, and increase lung metastasis. Mena and Mena(INV) potentiate epidermal growth factor (EGF)-induced membrane protrusion and increase the matrix degradation activity of tumor cells. Interestingly, Mena(INV) is significantly more effective than Mena in driving metastases and sensitizing cells to EGF-dependent invasion and protrusion. Upregulation of Mena(INV) could therefore enable tumor cells to invade in response to otherwise benign EGF stimulus levels.

The VENUS/NWChem software package. Tight coupling between chemical dynamics simulations and electronic structure theory

NASA Astrophysics Data System (ADS)

Lourderaj, Upakarasamy; Sun, Rui; Kohale, Swapnil C.; Barnes, George L.; de Jong, Wibe A.; Windus, Theresa L.; Hase, William L.

2014-03-01

The interface for VENUS and NWChem, and the resulting software package for direct dynamics simulations are described. The coupling of the two codes is considered to be a tight coupling since the two codes are compiled and linked together and act as one executable with data being passed between the two codes through routine calls. The advantages of this type of coupling are discussed. The interface has been designed to have as little interference as possible with the core codes of both VENUS and NWChem. VENUS is the code that propagates the direct dynamics trajectories and, therefore, is the program that drives the overall execution of VENUS/NWChem. VENUS has remained an essentially sequential code, which uses the highly parallel structure of NWChem. Subroutines of the interface that accomplish the data transmission and communication between the two computer programs are described. Recent examples of the use of VENUS/NWChem for direct dynamics simulations are summarized.

The 9th international symposium on the packaging and transportation of radioactive materials

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

None

1989-06-01

This three-volume document contains the papers and poster sessions presented at the symposium. Volume 3 contains 87 papers on topics such as structural codes and benchmarking, shipment of plutonium by air, spent fuel shipping, planning, package design and risk assessment, package testing, OCRWN operations experience and regulations. Individual papers were processed separately for the data base. (TEM)

AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms.

PubMed

Hosny, Abdelrahman; Vera-Licona, Paola; Laubenbacher, Reinhard; Favre, Thibauld

2016-08-01

There is a growing need in bioinformatics for easy-to-use software implementations of algorithms that are usable across platforms. At the same time, reproducibility of computational results is critical and often a challenge due to source code changes over time and dependencies. The approach introduced in this paper addresses both of these needs with AlgoRun, a dedicated packaging system for implemented algorithms, using Docker technology. Implemented algorithms, packaged with AlgoRun, can be executed through a user-friendly interface directly from a web browser or via a standardized RESTful web API to allow easy integration into more complex workflows. The packaged algorithm includes the entire software execution environment, thereby eliminating the common problem of software dependencies and the irreproducibility of computations over time. AlgoRun-packaged algorithms can be published on http://algorun.org, a centralized searchable directory to find existing AlgoRun-packaged algorithms. AlgoRun is available at http://algorun.org and the source code under GPL license is available at https://github.com/algorun laubenbacher@uchc.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Structural, electronic and optical properties of CO adsorbed on the defective anatase TiO2 (101) surface; a DFT study

NASA Astrophysics Data System (ADS)

Rafique, Muhammad; Shuai, Yong; Hassan, Muhammad

2017-08-01

This paper illustrates the study of stable structural, electronic and optical properties of carbon mono oxide (CO) molecule adsorbed on pure anatase TiO2 (101) surface and CO molecule adsorbed on defective anatase TiO2 (101) surface containing oxygen (O) atom subsurface vacancy using first-principles study calculations based on density functional theory (DFT) method. A foreign molecule CO was added in the interstitial space of anatase TiO2 (101) surface. It was observed that, adsorption of CO molecule is not favorable on pure anatase TiO2 (101) surface, however adsorption process is improved when subsurface contains O atom vacancy defect. In case of anatase TiO2 (101) surface containing subsurface vacancy, adsorption process is exothermic, resulting in stable structures. The adsorption energies calculated for CO molecules adsorbed at O2c site, at defect site and at Ti5c site of anatase surface containing subsurface O vacancy are 0.16 eV (at O2c), 0.32 eV (at defect site) and 0.43 eV (at Ti5c) site. DOS and PDOS plots are calculated for all the structures. Results indicated that CO molecule adsorption introduces surface states at the Fermi energy level (EF) as shown in partial density of states (PDOS) plots. The dielectric matrix and absorption coefficient (α) for defective anatase TiO2 (101) surface, CO adsorbed at O2c site, at defect site and at Ti5C site of anatase TiO2 (101) surface containing O atom subsurface vacancy has been calculated within the random phase approximation (RPA) using VASP (Vienna ab-initio simulation package) code. It was observed that upon CO adsorption at defective anatase surface, real and imaginary dielectric function peaks were shifted towards lower energy level and a small absorption peak was observed at 1.1 eV energy level which is not present in case of defective anatase (101) surface. CO adsorption produces a red shift in the absorption spectrum of anatase TiO2 (101) surface containing subsurface O atom vacancy.

Platelet reactivity in human immunodeficiency virus infected patients on dual antiplatelet therapy for an acute coronary syndrome: the EVERE2ST-HIV study.

PubMed

Hauguel-Moreau, Marie; Boccara, Franck; Boyd, Anders; Salem, Joe-Elie; Brugier, Delphine; Curjol, Angélique; Hulot, Jean-Sébastien; Kerneis, Mathieu; Galier, Sophie; Cohen, Ariel; Montalescot, Gilles; Collet, Jean-Philippe; Silvain, Johanne

2017-06-01

To explore platelet reactivity on dual antiplatelet therapy (DAPT) of acute coronary syndrome (ACS) patients infected with HIV. Acute coronary syndrome patients infected with HIV (n = 80) were matched to ACS patients without HIV (n = 160) on age, sex, diabetes, and DAPT (aspirin 100%, clopidogrel 68%, prasugrel 31%, ticagrelor 1%). Platelet reactivity was evaluated after ACS (>30 days) by measuring residual platelet aggregation (RPA) to aspirin and to P2Y12 inhibitors with light transmission aggregometry (LTA), VerifyNow aspirin assay (ARU), and P2Y12 assay (PRU) and with the VASP platelet reactivity index (VASP-PRI). Proportion of patients with high residual platelet reactivity (HPR) was evaluated. HIV-infected ACS patients had higher levels of platelet reactivity in response to P2Y12 inhibitors (RPA: 23.8 ± 2.7% vs. 15.3 ± 1.3%; P = 0.001; PRU: 132 ± 10 vs. 107.4 ± 6.6; P = 0.04; and VASP-PRI: 45.2 ± 2.6% vs. 32.0 ± 2.0%; P < 0.001) and to aspirin (RPA: 3.6 ± 1.5% vs. 0.4 ± 0.1%; P = 0.004 and ARU: 442 ± 11 vs. 407 ± 5; P = 0.002) compared with non-HIV. HIV-infection was independently associated with increased platelet reactivity regardless of the test used (RPA: P = 0.005; PRU: P < 0.001 and VASP-PRI: P < 0.001) and a higher proportion of HPR (OR = 7.6; P < 0.001; OR = 2.06; P = 0.06; OR = 2.91; P = 0.004, respectively) in response to P2Y12 inhibitors. Similar results were found with aspirin. Protease inhibitors use was associated with increased platelet reactivity and higher rate of HPR. Acute coronary syndrome patients infected with HIV have increased levels of platelet reactivity and higher prevalence of HPR to P2Y12 inhibitors and aspirin than non-HIV patients. These results could provide potential explanations for the observed increase risk of recurrent ischemic events in the HIV-infected population. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2017. For permissions, please email: journals.permissions@oup.com.

Ab initio studies of Th3N4, Th2N3 and Th2N2(NH)

NASA Astrophysics Data System (ADS)

Obodo, K. O.; Chetty, N.

2014-09-01

Using density functional theory within the Perdew-Burke-Ernzerhof generalized gradient approximation [GGA (PBE)] implemented in the VASP codes, we investigate the structural, elastic and electronic properties of Th3N4, Th2N3 and Th2N2(NH). The calculated structural properties of these thorium-based nitrides are in good agreement with experimental data. We observe that all the Th-N based compounds that we considered are energetically favorable and elastically stable. We find that Th3N4 is semiconducting with a band gap of 1.59 eV, which compares well with the experimental band gap of 1.7 eV and we find Th2N3 to be metallic. Th2N2(NH), which is crystallographically equivalent to Th2N3, is insulating with a band gap of 2.12 eV. This is due to the -(NH) group that effects a shifting of the energy bands that results in the opening of a gap at the Fermi-level. The Th-N based compounds that we considered are predominantly ionic.

Blue and red shifted temperature dependence of implicit phonon shifts in graphene

NASA Astrophysics Data System (ADS)

Mann, Sarita; Jindal, V. K.

2017-07-01

We have calculated the implicit shift for various modes of frequency in a pure graphene sheet. Thermal expansion and Grüneisen parameter which are required for implicit shift calculation have already been studied and reported. For this calculation, phonon frequencies are obtained using force constants derived from dynamical matrix calculated using VASP code where the density functional perturbation theory (DFPT) is used in interface with phonopy software. The implicit phonon shift shows an unusual behavior as compared to the bulk materials. The frequency shift is large negative (red shift) for ZA and ZO modes and the value of negative shift increases with increase in temperature. On the other hand, blue shift arises for all other longitudinal and transverse modes with a similar trend of increase with increase in temperature. The q dependence of phonon shifts has also been studied. Such simultaneous red and blue shifts in transverse or out plane modes and surface modes, respectively leads to speculation of surface softening in out of plane direction in preference to surface melting.

Size-induced chemical and magnetic ordering in individual Fe-Au nanoparticles.

PubMed

Mukherjee, Pinaki; Manchanda, Priyanka; Kumar, Pankaj; Zhou, Lin; Kramer, Matthew J; Kashyap, Arti; Skomski, Ralph; Sellmyer, David; Shield, Jeffrey E

2014-08-26

Formation of chemically ordered compounds of Fe and Au is inhibited in bulk materials due to their limited mutual solubility. However, here we report the formation of chemically ordered L12-type Fe3Au and FeAu3 compounds in Fe-Au sub-10 nm nanoparticles, suggesting that they are equilibrium structures in size-constrained systems. The stability of these L12-ordered Fe3Au and FeAu3 compounds along with a previously discovered L10-ordered FeAu has been explained by a size-dependent equilibrium thermodynamic model. Furthermore, the spin ordering of these three compounds has been computed using ab initio first-principle calculations. All ordered compounds exhibit a substantial magnetization at room temperature. The Fe3Au had a high saturation magnetization of about 143.6 emu/g with a ferromagnetic spin structure. The FeAu3 nanoparticles displayed a low saturation magnetization of about 11 emu/g. This suggests a antiferromagnetic spin structure, with the net magnetization arising from uncompensated surface spins. First-principle calculations using the Vienna ab initio simulation package (VASP) indicate that ferromagnetic ordering is energetically most stable in Fe3Au, while antiferromagnetic order is predicted in FeAu and FeAu3, consistent with the experimental results.

Comparative study of elastic constantd of α-, β- and Cubic- silicon nitride

NASA Astrophysics Data System (ADS)

Yao, Hongzhi; Ouyang, Lizhi; Ching, Wai-Yim

2003-03-01

Silicon nitride is an important structural ceramic and dielectric insulator. Recently, the new high pressure cubic phase of silicon nitride in spinel structure has attracted a lot of attention.^[1] We have carried out a detailed ab-initio calculation of all independent elastic constants for all three phases of Si_3N4 by using the Vienna Ab-initio Simulation Package (VASP) in both LDA and GGA approxmations. The results for β-Si_3N4 are in reasonable agreement with a experimental measurement on single crystal samples.^[2] For cubic-Si_3N4 , The three independent elastic constants are predicted to be C_11 = 504.16 GPa, C_12 = 176.66 GPa, C_44 = 326.65 GPa and a bulk modulus B = 286 GPa. This value is very close to the experimental value of 300 GPa.^[1] All these results will be compared with those obtained by using the OLCAO method based on localized orbital approach.^[3] [1]. Wai-Yim Ching, Yong-Nian Xu, Jukian D. Gale, and Manfred Ruhle, J. Am. Ceram. Soc. 81, 3189 (1998) [2]. R. Vogelgesang, M. Grimsditch, and J. S. Wallace, Appl. Phys. Lett. 76, 8 (2000) [3]. W.Y.Ching, Lizhi Ouyang, and Julian D. Gale, Phys. Rev. B61, 13, (2000)

Perpendicular magnetic anisotropy in Mn2VIn (001) films: An ab initio study

NASA Astrophysics Data System (ADS)

Zipporah, Muthui; Robinson, Musembi; Julius, Mwabora; Arti, Kashyap

2018-05-01

First principles study of the magnetic anisotropy of Mn2VIn (001) films show perpendicular magnetic anisotropy (PMA), which increases as a function of the thickness of the film. Density functional theory (DFT) as implemented in the Vienna Ab initio simulation package (VASP) is employed here to perform a comprehensive theoretical investigation of the structural, electronic and magnetic properties of the Mn2VIn(001) films of varying thickness. Our calculations were performed on fully relaxed structures, with five to seventeen mono layers (ML). The degree of spin polarization is higher in the (001) Mn2VIn thin films as compared to the bulk in contrast to what is usually the case and as in Mn2VAl, which is isoelectronic to Mn2VIn as well as inCo2VIn (001) films studied for comparison. Tetragonal distortions are found in all the systems after relaxation. The distortion in the Mn2VIn system persists even for the 17ML thin film, resulting in PMA in the Mn2VIn system. This significant finding has potential to contribute to spin transfer torque (STT) and magnetic random access memory MRAM applications, as materials with PMA derived from volume magnetocrystalline anisotropy are being proposed as ideal magnetic electrodes.

Ferromagnetic properties of manganese doped iron silicide

NASA Astrophysics Data System (ADS)

Ruiz-Reyes, Angel; Fonseca, Luis F.; Sabirianov, Renat

We report the synthesis of high quality Iron silicide (FeSi) nanowires via Chemical Vapor Deposition (CVD). The materials exhibits excellent magnetic response at room temperature, especially when doped with manganese showing values of 2.0 X 10-04 emu for the FexMnySi nanowires. SEM and TEM characterization indicates that the synthesized nanowires have a diameter of approximately 80nm. MFM measurements present a clear description of the magnetic domains when the nanowires are doped with manganese. Electron Diffraction and XRD measurements confirms that the nanowires are single crystal forming a simple cubic structure with space group P213. First-principle calculations were performed on (111) FeSi surface using the Vienna ab initio simulation package (VASP). The exchange correlations were treated under the Ceperley-Alder (CA) local density approximation (LDA). The Brillouin Zone was sampled with 8x8x1 k-point grid. A total magnetic moment of about 10 μB was obtained for three different surface configuration in which the Iron atom nearest to the surface present the higher magnetization. To study the effect of Mn doping, Fe atom was replaced for a Mn. Stronger magnetization is presented when the Mn atom is close to the surface. The exchange coupling constant have been evaluated calculating the energy difference between the ferromagnetic and anti-ferromagnetic configurations.

Atomic structures of B20 FeGe thin films grown on the Si(111) surface

NASA Astrophysics Data System (ADS)

Kim, Wondong; Noh, Seungkyun; Yoon, Jisoo; Kim, Young Heon; Lee, Inho; Kim, Jae-Sung; Hwang, Chanyong

We investigated the growth and atomic structures of FeGe thin films on the Si (111) surface by using scanning tunneling microscopy (STM) and transmission electron microscopy (TEM). The 2 5nm- thick FeGe thin films were prepared on the clean Si(111) 7x7 surface by co-deposition of Fe and Ge from separated electron-beam evaporators. With direct deposition on the substrate at the temperature above 550 K, the surface of FeGe films was not smooth and consisted of coarse grains. By the combination of room-temperature annealing and post-annealing process around 800 K, the structure of FeGe thin films evolved into the well crystalized structures. Atom-resolved STM images revealed that there are at least four different surface terminations. We constructed atomic models for each surface terminations based on the bulk atomic arrangement of a B20 chiral structure and confirmed that the observed STM images are successfully reproduced by using computational simulations employing Vienna Ab Initio Simulation package (VASP) with a B20 chiral structure model. TEM cross-sectional images also support our atomic models by revealing clearly the characteristic zigzag features of B20 structures of FeGe(111) thin films.

Enhancement of the CAVE computer code

NASA Astrophysics Data System (ADS)

Rathjen, K. A.; Burk, H. O.

1983-12-01

The computer code CAVE (Conduction Analysis via Eigenvalues) is a convenient and efficient computer code for predicting two dimensional temperature histories within thermal protection systems for hypersonic vehicles. The capabilities of CAVE were enhanced by incorporation of the following features into the code: real gas effects in the aerodynamic heating predictions, geometry and aerodynamic heating package for analyses of cone shaped bodies, input option to change from laminar to turbulent heating predictions on leading edges, modification to account for reduction in adiabatic wall temperature with increase in leading sweep, geometry package for two dimensional scramjet engine sidewall, with an option for heat transfer to external and internal surfaces, print out modification to provide tables of select temperatures for plotting and storage, and modifications to the radiation calculation procedure to eliminate temperature oscillations induced by high heating rates. These new features are described.

A multicenter collaborative approach to reducing pediatric codes outside the ICU.

PubMed

Hayes, Leslie W; Dobyns, Emily L; DiGiovine, Bruno; Brown, Ann-Marie; Jacobson, Sharon; Randall, Kelly H; Wathen, Beth; Richard, Heather; Schwab, Carolyn; Duncan, Kathy D; Thrasher, Jodi; Logsdon, Tina R; Hall, Matthew; Markovitz, Barry

2012-03-01

The Child Health Corporation of America formed a multicenter collaborative to decrease the rate of pediatric codes outside the ICU by 50%, double the days between these events, and improve the patient safety culture scores by 5 percentage points. A multidisciplinary pediatric advisory panel developed a comprehensive change package of process improvement strategies and measures for tracking progress. Learning sessions, conference calls, and data submission facilitated collaborative group learning and implementation. Twenty Child Health Corporation of America hospitals participated in this 12-month improvement project. Each hospital identified at least 1 noncritical care target unit in which to implement selected elements of the change package. Strategies to improve prevention, detection, and correction of the deteriorating patient ranged from relatively simple, foundational changes to more complex, advanced changes. Each hospital selected a broad range of change package elements for implementation using rapid-cycle methodologies. The primary outcome measure was reduction in codes per 1000 patient days. Secondary outcomes were days between codes and change in patient safety culture scores. Code rate for the collaborative did not decrease significantly (3% decrease). Twelve hospitals reported additional data after the collaborative and saw significant improvement in code rates (24% decrease). Patient safety culture scores improved by 4.5% to 8.5%. A complex process, such as patient deterioration, requires sufficient time and effort to achieve improved outcomes and create a deeply embedded culture of patient safety. The collaborative model can accelerate improvements achieved by individual institutions.

MT3D-USGS version 1: A U.S. Geological Survey release of MT3DMS updated with new and expanded transport capabilities for use with MODFLOW

USGS Publications Warehouse

Bedekar, Vivek; Morway, Eric D.; Langevin, Christian D.; Tonkin, Matthew J.

2016-09-30

MT3D-USGS, a U.S. Geological Survey updated release of the groundwater solute transport code MT3DMS, includes new transport modeling capabilities to accommodate flow terms calculated by MODFLOW packages that were previously unsupported by MT3DMS and to provide greater flexibility in the simulation of solute transport and reactive solute transport. Unsaturated-zone transport and transport within streams and lakes, including solute exchange with connected groundwater, are among the new capabilities included in the MT3D-USGS code. MT3D-USGS also includes the capability to route a solute through dry cells that may occur in the Newton-Raphson formulation of MODFLOW (that is, MODFLOW-NWT). New chemical reaction Package options include the ability to simulate inter-species reactions and parent-daughter chain reactions. A new pump-and-treat recirculation package enables the simulation of dynamic recirculation with or without treatment for combinations of wells that are represented in the flow model, mimicking the above-ground treatment of extracted water. A reformulation of the treatment of transient mass storage improves conservation of mass and yields solutions for better agreement with analytical benchmarks. Several additional features of MT3D-USGS are (1) the separate specification of the partitioning coefficient (Kd) within mobile and immobile domains; (2) the capability to assign prescribed concentrations to the top-most active layer; (3) the change in mass storage owing to the change in water volume now appears as its own budget item in the global mass balance summary; (4) the ability to ignore cross-dispersion terms; (5) the definition of Hydrocarbon Spill-Source Package (HSS) mass loading zones using regular and irregular polygons, in addition to the currently supported circular zones; and (6) the ability to specify an absolute minimum thickness rather than the default percent minimum thickness in dry-cell circumstances.Benchmark problems that implement the new features and packages test the accuracy of new code through comparison to analytical benchmarks, as well as to solutions from other published codes. The input file structure for MT3D-USGS adheres to MT3DMS conventions for backward compatibility: the new capabilities and packages described herein are readily invoked by adding three-letter package name acronyms to the name file or by setting input flags as needed. Memory is managed in MT3D-USGS using FORTRAN modules in order to simplify code development and expansion.

ALICE: A non-LTE plasma atomic physics, kinetics and lineshape package

NASA Astrophysics Data System (ADS)

Hill, E. G.; Pérez-Callejo, G.; Rose, S. J.

2018-03-01

All three parts of an atomic physics, atomic kinetics and lineshape code, ALICE, are described. Examples of the code being used to model the emissivity and opacity of plasmas are discussed and interesting features of the code which build on the existing corpus of models are shown throughout.

Development of an integrated thermal-hydraulics capability incorporating RELAP5 and PANTHER neutronics code

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

Page, R.; Jones, J.R.

1997-07-01

Ensuring that safety analysis needs are met in the future is likely to lead to the development of new codes and the further development of existing codes. It is therefore advantageous to define standards for data interfaces and to develop software interfacing techniques which can readily accommodate changes when they are made. Defining interface standards is beneficial but is necessarily restricted in application if future requirements are not known in detail. Code interfacing methods are of particular relevance with the move towards automatic grid frequency response operation where the integration of plant dynamic, core follow and fault study calculation toolsmore » is considered advantageous. This paper describes the background and features of a new code TALINK (Transient Analysis code LINKage program) used to provide a flexible interface to link the RELAP5 thermal hydraulics code with the PANTHER neutron kinetics and the SIBDYM whole plant dynamic modelling codes used by Nuclear Electric. The complete package enables the codes to be executed in parallel and provides an integrated whole plant thermal-hydraulics and neutron kinetics model. In addition the paper discusses the capabilities and pedigree of the component codes used to form the integrated transient analysis package and the details of the calculation of a postulated Sizewell `B` Loss of offsite power fault transient.« less

OPAL: An Open-Source MPI-IO Library over Cray XT

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

Yu, Weikuan; Vetter, Jeffrey S; Canon, Richard Shane

Parallel IO over Cray XT is supported by a vendor-supplied MPI-IO package. This package contains a proprietary ADIO implementation built on top of the sysio library. While it is reasonable to maintain a stable code base for application scientists' convenience, it is also very important to the system developers and researchers to analyze and assess the effectiveness of parallel IO software, and accordingly, tune and optimize the MPI-IO implementation. A proprietary parallel IO code base relinquishes such flexibilities. On the other hand, a generic UFS-based MPI-IO implementation is typically used on many Linux-based platforms. We have developed an open-source MPI-IOmore » package over Lustre, referred to as OPAL (OPportunistic and Adaptive MPI-IO Library over Lustre). OPAL provides a single source-code base for MPI-IO over Lustre on Cray XT and Linux platforms. Compared to Cray implementation, OPAL provides a number of good features, including arbitrary specification of striping patterns and Lustre-stripe aligned file domain partitioning. This paper presents the performance comparisons between OPAL and Cray's proprietary implementation. Our evaluation demonstrates that OPAL achieves the performance comparable to the Cray implementation. We also exemplify the benefits of an open source package in revealing the underpinning of the parallel IO performance.« less

What's New in GSAS-II

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

Toby, Brian H.; Von Dreele, Robert B.

The General Structure and Analysis Software II (GSAS-II) package is an all-new crystallographic analysis package written to replace and extend the capabilities of the universal and widely used GSAS and EXPGUI packages. GSAS-II was described in a 2013 article, but considerable work has been completed since then. This paper describes the advances, which include: rigid body fitting and structure solution modules; improved treatment for parametric refinements and equation of state fitting; and small-angle scattering data reduction and analysis. GSAS-II offers versatile and extensible modules for import and export of data and results. Capabilities are provided for users to select anymore » version of the code. Code documentation has reached 150 pages and 17 web-tutorials are offered. © 2014 International Centre for Diffraction Data.« less

GenomeDiagram: a python package for the visualization of large-scale genomic data.

PubMed

Pritchard, Leighton; White, Jennifer A; Birch, Paul R J; Toth, Ian K

2006-03-01

We present GenomeDiagram, a flexible, open-source Python module for the visualization of large-scale genomic, comparative genomic and other data with reference to a single chromosome or other biological sequence. GenomeDiagram may be used to generate publication-quality vector graphics, rastered images and in-line streamed graphics for webpages. The package integrates with datatypes from the BioPython project, and is available for Windows, Linux and Mac OS X systems. GenomeDiagram is freely available as source code (under GNU Public License) at http://bioinf.scri.ac.uk/lp/programs.html, and requires Python 2.3 or higher, and recent versions of the ReportLab and BioPython packages. A user manual, example code and images are available at http://bioinf.scri.ac.uk/lp/programs.html.

Tough2{_}MP: A parallel version of TOUGH2

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

Zhang, Keni; Wu, Yu-Shu; Ding, Chris

2003-04-09

TOUGH2{_}MP is a massively parallel version of TOUGH2. It was developed for running on distributed-memory parallel computers to simulate large simulation problems that may not be solved by the standard, single-CPU TOUGH2 code. The new code implements an efficient massively parallel scheme, while preserving the full capacity and flexibility of the original TOUGH2 code. The new software uses the METIS software package for grid partitioning and AZTEC software package for linear-equation solving. The standard message-passing interface is adopted for communication among processors. Numerical performance of the current version code has been tested on CRAY-T3E and IBM RS/6000 SP platforms. Inmore » addition, the parallel code has been successfully applied to real field problems of multi-million-cell simulations for three-dimensional multiphase and multicomponent fluid and heat flow, as well as solute transport. In this paper, we will review the development of the TOUGH2{_}MP, and discuss the basic features, modules, and their applications.« less

Optical Excitations and Energy Transfer in Nanoparticle Waveguides

DTIC Science & Technology

2009-03-01

All calculations were performed using our own codes given in the Appendix section. The calculations were performed using Scilab programming package...January 2007, invited Speaker) 12. Scilab is a free software compatible to the famous Matlab package. It can be found at their webpage http

Development of a MELCOR Sodium Chemistry (NAC) Package - FY17 Progress.

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

Louie, David; Humphries, Larry L.

This report describes the status of the development of MELCOR Sodium Chemistry (NAC) package. This development is based on the CONTAIN-LMR sodium physics and chemistry models to be implemented in MELCOR. In the past three years, the sodium equation of state as a working fluid from the nuclear fusion safety research and from the SIMMER code has been implemented into MELCOR. The chemistry models from the CONTAIN-LMR code, such as the spray and pool fire mode ls, have also been implemented into MELCOR. This report describes the implemented models and the issues encountered. Model descriptions and input descriptions are provided.more » Development testing of the spray and pool fire models is described, including the code-to-code comparison with CONTAIN-LMR. The report ends with an expected timeline for the remaining models to be implemented, such as the atmosphere chemistry, sodium-concrete interactions, and experimental validation tests .« less

Next-generation acceleration and code optimization for light transport in turbid media using GPUs

PubMed Central

Alerstam, Erik; Lo, William Chun Yip; Han, Tianyi David; Rose, Jonathan; Andersson-Engels, Stefan; Lilge, Lothar

2010-01-01

A highly optimized Monte Carlo (MC) code package for simulating light transport is developed on the latest graphics processing unit (GPU) built for general-purpose computing from NVIDIA - the Fermi GPU. In biomedical optics, the MC method is the gold standard approach for simulating light transport in biological tissue, both due to its accuracy and its flexibility in modelling realistic, heterogeneous tissue geometry in 3-D. However, the widespread use of MC simulations in inverse problems, such as treatment planning for PDT, is limited by their long computation time. Despite its parallel nature, optimizing MC code on the GPU has been shown to be a challenge, particularly when the sharing of simulation result matrices among many parallel threads demands the frequent use of atomic instructions to access the slow GPU global memory. This paper proposes an optimization scheme that utilizes the fast shared memory to resolve the performance bottleneck caused by atomic access, and discusses numerous other optimization techniques needed to harness the full potential of the GPU. Using these techniques, a widely accepted MC code package in biophotonics, called MCML, was successfully accelerated on a Fermi GPU by approximately 600x compared to a state-of-the-art Intel Core i7 CPU. A skin model consisting of 7 layers was used as the standard simulation geometry. To demonstrate the possibility of GPU cluster computing, the same GPU code was executed on four GPUs, showing a linear improvement in performance with an increasing number of GPUs. The GPU-based MCML code package, named GPU-MCML, is compatible with a wide range of graphics cards and is released as an open-source software in two versions: an optimized version tuned for high performance and a simplified version for beginners (http://code.google.com/p/gpumcml). PMID:21258498

78 FR 41721 - New Standards to Enhance Package Visibility

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-11

... supporting electronic documentation including piece-level address or ZIP+4[supreg] Code information effective... package strategy relies on the availability of piece- level information provided through the widespread use of IMpb. IMpb can offer a number of benefits to mailers by providing piece- level visibility...

ULFEM time series analysis package

USGS Publications Warehouse

Karl, Susan M.; McPhee, Darcy K.; Glen, Jonathan M. G.; Klemperer, Simon L.

2013-01-01

This manual describes how to use the Ultra-Low-Frequency ElectroMagnetic (ULFEM) software package. Casual users can read the quick-start guide and will probably not need any more information than this. For users who may wish to modify the code, we provide further description of the routines.

78 FR 44894 - Specifications for Packagings

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-25

... DEPARTMENT OF TRANSPORTATION Pipeline and Hazardous Materials Safety Administration 49 CFR Part 178 Specifications for Packagings CFR Correction 0 In Title 49 of the Code of Federal Regulations, Parts 178 to 199, revised as of October 1, 2012, in Sec. 178.68, on page 80, paragraph (i)(2) is...

NPTFit: A Code Package for Non-Poissonian Template Fitting

NASA Astrophysics Data System (ADS)

Mishra-Sharma, Siddharth; Rodd, Nicholas L.; Safdi, Benjamin R.

2017-06-01

We present NPTFit, an open-source code package, written in Python and Cython, for performing non-Poissonian template fits (NPTFs). The NPTF is a recently developed statistical procedure for characterizing the contribution of unresolved point sources (PSs) to astrophysical data sets. The NPTF was first applied to Fermi gamma-ray data to provide evidence that the excess of ˜GeV gamma-rays observed in the inner regions of the Milky Way likely arises from a population of sub-threshold point sources, and the NPTF has since found additional applications studying sub-threshold extragalactic sources at high Galactic latitudes. The NPTF generalizes traditional astrophysical template fits to allow for the ability to search for populations of unresolved PSs that may follow a given spatial distribution. NPTFit builds upon the framework of the fluctuation analyses developed in X-ray astronomy, thus it likely has applications beyond those demonstrated with gamma-ray data. The NPTFit package utilizes novel computational methods to perform the NPTF efficiently. The code is available at http://github.com/bsafdi/NPTFit and up-to-date and extensive documentation may be found at http://nptfit.readthedocs.io.

User’s guide for MapMark4—An R package for the probability calculations in three-part mineral resource assessments

USGS Publications Warehouse

Ellefsen, Karl J.

2017-06-27

MapMark4 is a software package that implements the probability calculations in three-part mineral resource assessments. Functions within the software package are written in the R statistical programming language. These functions, their documentation, and a copy of this user’s guide are bundled together in R’s unit of shareable code, which is called a “package.” This user’s guide includes step-by-step instructions showing how the functions are used to carry out the probability calculations. The calculations are demonstrated using test data, which are included in the package.

clusterProfiler: an R package for comparing biological themes among gene clusters.

PubMed

Yu, Guangchuang; Wang, Li-Gen; Han, Yanyan; He, Qing-Yu

2012-05-01

Increasing quantitative data generated from transcriptomics and proteomics require integrative strategies for analysis. Here, we present an R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters. The analysis module and visualization module were combined into a reusable workflow. Currently, clusterProfiler supports three species, including humans, mice, and yeast. Methods provided in this package can be easily extended to other species and ontologies. The clusterProfiler package is released under Artistic-2.0 License within Bioconductor project. The source code and vignette are freely available at http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html.

Vector-matrix-quaternion, array and arithmetic packages: All HAL/S functions implemented in Ada

NASA Technical Reports Server (NTRS)

Klumpp, Allan R.; Kwong, David D.

1986-01-01

The HAL/S avionics programmers have enjoyed a variety of tools built into a language tailored to their special requirements. Ada is designed for a broader group of applications. Rather than providing built-in tools, Ada provides the elements with which users can build their own. Standard avionic packages remain to be developed. These must enable programmers to code in Ada as they have coded in HAL/S. The packages under development at JPL will provide all of the vector-matrix, array, and arithmetic functions described in the HAL/S manuals. In addition, the linear algebra package will provide all of the quaternion functions used in Shuttle steering and Galileo attitude control. Furthermore, using Ada's extensibility, many quaternion functions are being implemented as infix operations; equivalent capabilities were never implemented in HAL/S because doing so would entail modifying the compiler and expanding the language. With these packages, many HAL/S expressions will compile and execute in Ada, unchanged. Others can be converted simply by replacing the implicit HAL/S multiply operator with the Ada *. Errors will be trapped and identified. Input/output will be convenient and readable.

5′-Inositol phosphatase SHIP2 recruits Mena to stabilize invadopodia for cancer cell invasion

PubMed Central

Zaoui, Kossay; Huang, Bruce H.; Sangwan, Veena; Gertler, Frank B.

2016-01-01

Invadopodia are specialized membrane protrusions that support degradation of extracellular matrix (ECM) by cancer cells, allowing invasion and metastatic spread. Although early stages of invadopodia assembly have been elucidated, little is known about maturation of invadopodia into structures competent for ECM proteolysis. The localized conversion of phosphatidylinositol(3,4,5)-triphosphate and accumulation of phosphatidylinositol(3,4)-bisphosphate at invadopodia is a key determinant for invadopodia maturation. Here we investigate the role of the 5′-inositol phosphatase, SHIP2, and reveal an unexpected scaffold function of SHIP2 as a prerequisite for invadopodia-mediated ECM degradation. Through biochemical and structure-function analyses, we identify specific interactions between SHIP2 and Mena, an Ena/VASP-family actin regulatory protein. We demonstrate that SHIP2 recruits Mena, but not VASP, to invadopodia and that disruption of SHIP2–Mena interaction in cancer cells leads to attenuated capacity for ECM degradation and invasion in vitro, as well as reduced metastasis in vivo. Together, these findings identify SHIP2 as a key modulator of carcinoma invasiveness and a target for metastatic disease. PMID:27597754

5'-Inositol phosphatase SHIP2 recruits Mena to stabilize invadopodia for cancer cell invasion.

PubMed

Rajadurai, Charles V; Havrylov, Serhiy; Coelho, Paula P; Ratcliffe, Colin D H; Zaoui, Kossay; Huang, Bruce H; Monast, Anie; Chughtai, Naila; Sangwan, Veena; Gertler, Frank B; Siegel, Peter M; Park, Morag

2016-09-12

Invadopodia are specialized membrane protrusions that support degradation of extracellular matrix (ECM) by cancer cells, allowing invasion and metastatic spread. Although early stages of invadopodia assembly have been elucidated, little is known about maturation of invadopodia into structures competent for ECM proteolysis. The localized conversion of phosphatidylinositol(3,4,5)-triphosphate and accumulation of phosphatidylinositol(3,4)-bisphosphate at invadopodia is a key determinant for invadopodia maturation. Here we investigate the role of the 5'-inositol phosphatase, SHIP2, and reveal an unexpected scaffold function of SHIP2 as a prerequisite for invadopodia-mediated ECM degradation. Through biochemical and structure-function analyses, we identify specific interactions between SHIP2 and Mena, an Ena/VASP-family actin regulatory protein. We demonstrate that SHIP2 recruits Mena, but not VASP, to invadopodia and that disruption of SHIP2-Mena interaction in cancer cells leads to attenuated capacity for ECM degradation and invasion in vitro, as well as reduced metastasis in vivo. Together, these findings identify SHIP2 as a key modulator of carcinoma invasiveness and a target for metastatic disease. © 2016 Rajadurai et al.

Achieving accuracy in first-principles calculations at extreme temperature and pressure

NASA Astrophysics Data System (ADS)

Mattsson, Ann; Wills, John

2013-06-01

First-principles calculations are increasingly used to provide EOS data at pressures and temperatures where experimental data is difficult or impossible to obtain. The lack of experimental data, however, also precludes validation of the calculations in those regimes. Factors influencing the accuracy of first-principles data include theoretical approximations, and computational approximations used in implementing and solving the underlying equations. The first category includes approximate exchange-correlation functionals and wave equations simplifying the Dirac equation. In the second category are, e.g., basis completeness and pseudo-potentials. While the first category is extremely hard to assess without experimental data, inaccuracies of the second type should be well controlled. We are using two rather different electronic structure methods (VASP and RSPt) to make explicit the requirements for accuracy of the second type. We will discuss the VASP Projector Augmented Wave potentials, with examples for Li and Mo. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Nanotechnology for the Solid Waste Reduction of Military Food Packaging

DTIC Science & Technology

2016-06-01

WP-200816) Nanotechnology for the Solid Waste Reduction of Military Food Packaging June 2016 This document has been cleared for public release...NAME OF RESPONSIBLE PERSON 19b. TELEPHONE NUMBER (Include area code) 01/06/2016 Cost and Performance Report 04/01/2008 - 01/01/2015 Nanotechnology for... nanotechnology packaging. The PIs have been dedicated to these efforts, and it is anticipated that this technology will be used someday by the Warfighter

The Islamic State Battle Plan: Press Release Natural Language Processing

DTIC Science & Technology

2016-06-01

Processing, text mining , corpus, generalized linear model, cascade, R Shiny, leaflet, data visualization 15. NUMBER OF PAGES 83 16. PRICE CODE...Terrorism and Responses to Terrorism TDM Term Document Matrix TF Term Frequency TF-IDF Term Frequency-Inverse Document Frequency tm text mining (R...package=leaflet. Feinerer I, Hornik K (2015) Text Mining Package “tm,” Version 0.6-2. (Jul 3) https://cran.r-project.org/web/packages/tm/tm.pdf

Assessment of the prevailing physics codes: LEOPARD, LASER, and EPRI-CELL

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

Lan, J.S.

1981-01-01

In order to analyze core performance and fuel management, it is necessary to verify reactor physics codes in great detail. This kind of work not only serves the purpose of understanding and controlling the characteristics of each code, but also ensures the reliability as codes continually change due to constant modifications and machine transfers. This paper will present the results of a comprehensive verification of three code packages - LEOPARD, LASER, and EPRI-CELL.

49 CFR 178.515 - Standards for reconstituted wood boxes.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 3 2012-10-01 2012-10-01 false Standards for reconstituted wood boxes. 178.515... PACKAGINGS Non-bulk Performance-Oriented Packaging Standards § 178.515 Standards for reconstituted wood boxes. (a) The identification code for a reconstituted wood box is 4F. (b) Construction requirements for...

49 CFR 178.515 - Standards for reconstituted wood boxes.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 3 2013-10-01 2013-10-01 false Standards for reconstituted wood boxes. 178.515... PACKAGINGS Non-bulk Performance-Oriented Packaging Standards § 178.515 Standards for reconstituted wood boxes. (a) The identification code for a reconstituted wood box is 4F. (b) Construction requirements for...

49 CFR 178.515 - Standards for reconstituted wood boxes.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 3 2014-10-01 2014-10-01 false Standards for reconstituted wood boxes. 178.515... PACKAGINGS Non-bulk Performance-Oriented Packaging Standards § 178.515 Standards for reconstituted wood boxes. (a) The identification code for a reconstituted wood box is 4F. (b) Construction requirements for...

78 FR 19007 - Certain Products Having Laminated Packaging, Laminated Packaging, and Components Thereof...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-28

... INTERNATIONAL TRADE COMMISSION [Investigation No. 337-TA-874] Certain Products Having Laminated... States Code AGENCY: U.S. International Trade Commission. ACTION: Notice. SUMMARY: Notice is hereby given that a complaint was filed with the U.S. International Trade Commission on February 20, 2013, under...

49 CFR 178.515 - Standards for reconstituted wood boxes.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 3 2011-10-01 2011-10-01 false Standards for reconstituted wood boxes. 178.515... PACKAGINGS Non-bulk Performance-Oriented Packaging Standards § 178.515 Standards for reconstituted wood boxes. (a) The identification code for a reconstituted wood box is 4F. (b) Construction requirements for...

Learn by Yourself: The Self-Learning Tools for Qualitative Analysis Software Packages

ERIC Educational Resources Information Center

Freitas, Fábio; Ribeiro, Jaime; Brandão, Catarina; Reis, Luís Paulo; de Souza, Francislê Neri; Costa, António Pedro

2017-01-01

Computer Assisted Qualitative Data Analysis Software (CAQDAS) are tools that help researchers to develop qualitative research projects. These software packages help the users with tasks such as transcription analysis, coding and text interpretation, writing and annotation, content search and analysis, recursive abstraction, grounded theory…

EEE Links. Volume 5

NASA Technical Reports Server (NTRS)

Humphrey, Robert (Editor)

1999-01-01

The EEE Links Newsletter is a quarterly publication produced by Code 562 in support of the NASA HQ funded NASA Electronic Parts and Packaging (NEPP) Program. The newsletter is produced as an electronic format deliverable made available via the referenced www site administered by Code 562, The newsletter publishes brief articles on topics of interest to NASA programs and projects in the area of electronic parts and packaging. The newsletter does not provide information pertaining to patented or proprietary information. The information provided is at the level of that produced by industry and university researchers and is published at national and international conferences.

Medicare's "Global" terrorism: where is the pay for performance?

PubMed

Reed, R Lawrence; Luchette, Fred A; Esposito, Thomas J; Pyrz, Karen; Gamelli, Richard L

2008-02-01

Medicare and Medicaid Services (CMS) payment policies for surgical operations are based on a global package concept. CMS' physician fee schedule splits the global package into preoperative, intraoperative, and postoperative components of each procedure. We hypothesized that these global package component valuations were often lower than comparable evaluation and management (E&M) services and that billing for E&M services instead of the operation could often be more profitable. Our billing database and Trauma Registry were queried for the operative procedures and hospital lengths of stay for trauma patients during the past 5 years. Determinations of preoperative, intraoperative, and postoperative payments were calculated for 10-day and 90-day global packages, comparing them to CMS payments for comparable E&M codes. Of 90-day and 10-day Current Procedural Terminology codes, 88% and 100%, respectively, do not pay for the comprehensive history and physical that trauma patients usually receive, whereas 41% and 98%, respectively, do not even meet payment levels for a simple history and physical. Of 90-day global package procedures, 70% would have generated more revenue had comprehensive daily visits been billed instead of the operation ($3,057,500 vs. $1,658,058). For 10-day global package procedures, 56% would have generated more revenue with merely problem-focused daily visits instead of the operation ($161,855 vs. $156,318). Medicare's global surgical package underpays E&M services in trauma patients. In most cases, trauma surgeons would fare better by not billing for operations to receive higher reimbursement for E&M services that are considered "bundled" in the global package payment.

Mixed-Organic-Cation (FA)x(MA)1-xPbI3 Planar Perovskite Solar Cells with 16.48% Efficiency via a Low-Pressure Vapor-Assisted Solution Process.

PubMed

Chen, Jing; Xu, Jia; Xiao, Li; Zhang, Bing; Dai, Songyuan; Yao, Jianxi

2017-01-25

Compared to that of methylammonium lead iodide perovskite (MAPbI 3 ), formamidinium lead iodide perovskite (FAPbI 3 ) has a smaller energy band gap and greater potential efficiency. To prevent the transformation of α-FAPbI 3 to δ-FAPbI 3 , preparation of (FA) x (MA) 1-x PbI 3 was regarded as an effective route. Usually, the planar (FA) x (MA) 1-x PbI 3 perovskite solar cells are fabricated by a solution process. Herein, we report a low-pressure vapor-assisted solution process (LP-VASP) for the growth of (FA) x (MA) 1-x PbI 3 perovskite solar cells that features improved electron transportation, uniform morphology, high power conversion efficiency (PCE), and better crystal stability. In LP-VASP, the (FA) x (MA) 1-x PbI 3 films were formed by the reaction between the PbI 2 film with FAI and MAI vapor in a very simple vacuum oven. LP-VASP is an inexpensive way to batch-process solar cells, avoiding the repeated deposition solution process for PbI 2 films, and the device had a low cost. We demonstrate that, with an increase in the MAI content, the (101) peak position of FAPbI 3 shifts toward the (110) peak position of MAPbI 3 , the (FA) x (MA) 1-x PbI 3 perovskites are stable, and no decomposition or phase transition is observed after 14 days. The photovoltaic performance was effectively improved by the introduction of MA + with the highest efficiency being 16.48% under conditions of 40 wt % MAI. The carrier lifetime of (FA) x (MA) 1-x PbI 3 perovskite films is approximately three times longer than that of pure FAPbI 3 . Using this process, solar cells with a large area of 1.00 cm 2 were fabricated with the PCE of 8.0%.

Ginsenoside-Rp3 inhibits platelet activation and thrombus formation by regulating MAPK and cyclic nucleotide signaling.

PubMed

Irfan, Muhammad; Jeong, Da Hye; Kwon, Hyuk-Woo; Shin, Jung-Hae; Park, Sang-Joon; Kwak, Dongmi; Kim, Tae-Hwan; Lee, Dong-Ha; Park, Hwa-Jin; Rhee, Man Hee

2018-06-08

Ginseng (Panax ginseng C.A. Mayer) contains saponin fractions called ginsenosides, which are thought to be the main components responsible for its various pharmacological activities. Ginsenosides have cardioprotective and antiplatelet effects. In the present study, we evaluated the effects of ginsenoside Rp3 (G-Rp3) on platelet function. The in vitro effects of G-Rp3 were evaluated on agonist-induced human and rat platelet aggregation, while [Ca 2+ ] i mobilization, granule secretion, integrin α IIb β 3 activation, and clot retraction were assessed in rat platelets. Its effects on vasodilator-stimulated phosphoprotein (VASP) expression, phosphorylation of MAPK signaling molecules, and PI3K/Akt activation were also studied. Moreover, the tyrosine phosphorylation of components of the P 2 Y 12 receptor downstream signaling pathway was also examined. The in vivo effects of G-Rp3 were studied using an acute pulmonary thromboembolism model and lung histopathology. G-Rp3 significantly inhibited collagen, ADP, and thrombin-induced platelet aggregation. G-Rp3 elevated cAMP levels and VASP phosphorylation and suppressed agonist-induced [Ca 2+ ] i mobilization, ATP release, and P-selectin expression along with fibrinogen binding to integrin α IIb β 3 , fibronectin adhesion, and clot retraction. G-Rp3 also attenuated the phosphorylation of MAPK, Src, and PLCγ2 as well as PI3K/Akt activation. Furthermore, it inhibited tyrosine phosphorylation of the Src family kinases (Src, Fyn, and Lyn) and PLCγ2 and protected mice from thrombosis. G-Rp3 modulates agonist-induced platelet activation and thrombus formation by inhibiting granule secretion, integrin α IIb β 3 activation, MAPK signaling, and Src, PLCγ2, and PI3K/Akt activation, and VASP stimulation. Our data suggest that G-Rp3 has therapeutic potential as a treatment for platelet-related cardiovascular disorders. Copyright © 2017. Published by Elsevier Inc.

beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types

PubMed Central

Pagès, Hervé

2018-01-01

Biological experiments involving genomics or other high-throughput assays typically yield a data matrix that can be explored and analyzed using the R programming language with packages from the Bioconductor project. Improvements in the throughput of these assays have resulted in an explosion of data even from routine experiments, which poses a challenge to the existing computational infrastructure for statistical data analysis. For example, single-cell RNA sequencing (scRNA-seq) experiments frequently generate large matrices containing expression values for each gene in each cell, requiring sparse or file-backed representations for memory-efficient manipulation in R. These alternative representations are not easily compatible with high-performance C++ code used for computationally intensive tasks in existing R/Bioconductor packages. Here, we describe a C++ interface named beachmat, which enables agnostic data access from various matrix representations. This allows package developers to write efficient C++ code that is interoperable with dense, sparse and file-backed matrices, amongst others. We evaluated the performance of beachmat for accessing data from each matrix representation using both simulated and real scRNA-seq data, and defined a clear memory/speed trade-off to motivate the choice of an appropriate representation. We also demonstrate how beachmat can be incorporated into the code of other packages to drive analyses of a very large scRNA-seq data set. PMID:29723188

beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types.

PubMed

Lun, Aaron T L; Pagès, Hervé; Smith, Mike L

2018-05-01

Biological experiments involving genomics or other high-throughput assays typically yield a data matrix that can be explored and analyzed using the R programming language with packages from the Bioconductor project. Improvements in the throughput of these assays have resulted in an explosion of data even from routine experiments, which poses a challenge to the existing computational infrastructure for statistical data analysis. For example, single-cell RNA sequencing (scRNA-seq) experiments frequently generate large matrices containing expression values for each gene in each cell, requiring sparse or file-backed representations for memory-efficient manipulation in R. These alternative representations are not easily compatible with high-performance C++ code used for computationally intensive tasks in existing R/Bioconductor packages. Here, we describe a C++ interface named beachmat, which enables agnostic data access from various matrix representations. This allows package developers to write efficient C++ code that is interoperable with dense, sparse and file-backed matrices, amongst others. We evaluated the performance of beachmat for accessing data from each matrix representation using both simulated and real scRNA-seq data, and defined a clear memory/speed trade-off to motivate the choice of an appropriate representation. We also demonstrate how beachmat can be incorporated into the code of other packages to drive analyses of a very large scRNA-seq data set.

39 CFR Appendix A to Part 121 - Tables Depicting Service Standard Day Ranges

Code of Federal Regulations, 2011 CFR

2011-07-01

... 1-3 (AK)7 (JNU) 7 (KTN) 1 (HI)7 (GU) 1-2 1-2 6-7 5-6 Standard Mail 2 3 3 3-4 10 10 9 Package Services 1 2 2 2-3 8 8 7 AK = Alaska 3-digit ZIP Codes 995-997; JNU = Juneau AK 3-digit ZIP Code 998; KTN = Ketchikan AK 3-digit ZIP Code 999; HI = Hawaii 3-digit ZIP Codes 967 and 968; GU = Guam 3-digit ZIP Code 969...

39 CFR Appendix A to Part 121 - Tables Depicting Service Standard Day Ranges

Code of Federal Regulations, 2010 CFR

2010-07-01

... 1-3 (AK)7 (JNU) 7 (KTN) 1 (HI)7 (GU) 1-2 1-2 6-7 5-6 Standard Mail 2 3 3 3-4 10 10 9 Package Services 1 2 2 2-3 8 8 7 AK = Alaska 3-digit ZIP Codes 995-997; JNU = Juneau AK 3-digit ZIP Code 998; KTN = Ketchikan AK 3-digit ZIP Code 999; HI = Hawaii 3-digit ZIP Codes 967 and 968; GU = Guam 3-digit ZIP Code 969...

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

Hart, David; Klise, Katherine A.

The PyEPANET package is a set of commands for the Python programming language that are built to wrap the EPANET toolkit library commands, without requiring the end user to program using the ctypes package. This package does not contain the EPANET code, nor does it implement the functions within the EPANET software, and it requires the separately downloaded or compiled EPANET2 toolkit dynamic library (epanet.dll, libepanent.so, or epanet.dylib) and/or the EPANET-MSX dynamic library in order to function.

User’s guide for GcClust—An R package for clustering of regional geochemical data

USGS Publications Warehouse

Ellefsen, Karl J.; Smith, David B.

2016-04-08

GcClust is a software package developed by the U.S. Geological Survey for statistical clustering of regional geochemical data, and similar data such as regional mineralogical data. Functions within the software package are written in the R statistical programming language. These functions, their documentation, and a copy of the user’s guide are bundled together in R’s unit of sharable code, which is called a “package.” The user’s guide includes step-by-step instructions showing how the functions are used to cluster data and to evaluate the clustering results. These functions are demonstrated in this report using test data, which are included in the package.

A VHDL Interface for Altera Design Files

DTIC Science & Technology

1990-01-01

this requirement dictated that all prototype products developed during this research would have to mirror standard VHDL code . In fact, the final... product would have to meet the 20 syntactic and semantic requirements of standard VHDL . The coding style used to create the transformation program was the...Transformed Decoder File ....................... 47 C. Supplemental VHDL Package Source Code ........... 54 Altpk.vhd .................................... 54 D

49 CFR 178.505 - Standards for aluminum drums.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Standards for aluminum drums. 178.505 Section 178... PACKAGINGS Non-bulk Performance-Oriented Packaging Standards § 178.505 Standards for aluminum drums. (a) The following are the identification codes for aluminum drums: (1) 1B1 for a non-removable head aluminum drum...

49 CFR 178.519 - Standards for plastic film bags.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Standards for plastic film bags. 178.519 Section... PACKAGINGS Non-bulk Performance-Oriented Packaging Standards § 178.519 Standards for plastic film bags. (a) The identification code for a plastic film bag is 5H4. (b) Construction requirements for plastic film...

49 CFR 178.509 - Standards for plastic drums and jerricans.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 3 2011-10-01 2011-10-01 false Standards for plastic drums and jerricans. 178.509... PACKAGINGS Non-bulk Performance-Oriented Packaging Standards § 178.509 Standards for plastic drums and jerricans. (a) The following are identification codes for plastic drums and jerricans: (1) 1H1 for a non...

49 CFR 178.518 - Standards for woven plastic bags.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Standards for woven plastic bags. 178.518 Section... PACKAGINGS Non-bulk Performance-Oriented Packaging Standards § 178.518 Standards for woven plastic bags. (a) The following are identification codes for woven plastic bags: (1) 5H1 for an unlined or non-coated...

49 CFR 178.509 - Standards for plastic drums and jerricans.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 3 2014-10-01 2014-10-01 false Standards for plastic drums and jerricans. 178.509... PACKAGINGS Non-bulk Performance-Oriented Packaging Standards § 178.509 Standards for plastic drums and jerricans. (a) The following are identification codes for plastic drums and jerricans: (1) 1H1 for a non...

49 CFR 178.509 - Standards for plastic drums and jerricans.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 3 2012-10-01 2012-10-01 false Standards for plastic drums and jerricans. 178.509... PACKAGINGS Non-bulk Performance-Oriented Packaging Standards § 178.509 Standards for plastic drums and jerricans. (a) The following are identification codes for plastic drums and jerricans: (1) 1H1 for a non...

49 CFR 178.509 - Standards for plastic drums and jerricans.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 3 2013-10-01 2013-10-01 false Standards for plastic drums and jerricans. 178.509... PACKAGINGS Non-bulk Performance-Oriented Packaging Standards § 178.509 Standards for plastic drums and jerricans. (a) The following are identification codes for plastic drums and jerricans: (1) 1H1 for a non...

49 CFR 178.512 - Standards for steel, aluminum or other metal boxes.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 3 2013-10-01 2013-10-01 false Standards for steel, aluminum or other metal boxes...) SPECIFICATIONS FOR PACKAGINGS Non-bulk Performance-Oriented Packaging Standards § 178.512 Standards for steel, aluminum or other metal boxes. (a) The following are identification codes for steel, aluminum, or other...

49 CFR 178.512 - Standards for steel or aluminum boxes.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 3 2012-10-01 2012-10-01 false Standards for steel or aluminum boxes. 178.512... PACKAGINGS Non-bulk Performance-Oriented Packaging Standards § 178.512 Standards for steel or aluminum boxes. (a) The following are identification codes for steel or aluminum boxes: (1) 4A for a steel box; and...

49 CFR 178.512 - Standards for steel, aluminum or other metal boxes.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 3 2014-10-01 2014-10-01 false Standards for steel, aluminum or other metal boxes...) SPECIFICATIONS FOR PACKAGINGS Non-bulk Performance-Oriented Packaging Standards § 178.512 Standards for steel, aluminum or other metal boxes. (a) The following are identification codes for steel, aluminum, or other...

49 CFR 178.512 - Standards for steel or aluminum boxes.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Standards for steel or aluminum boxes. 178.512... FOR PACKAGINGS Non-bulk Performance-Oriented Packaging Standards § 178.512 Standards for steel or aluminum boxes. (a) The following are identification codes for steel or aluminum boxes: (1) 4A for a steel...

49 CFR 178.512 - Standards for steel or aluminum boxes.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 3 2011-10-01 2011-10-01 false Standards for steel or aluminum boxes. 178.512... PACKAGINGS Non-bulk Performance-Oriented Packaging Standards § 178.512 Standards for steel or aluminum boxes. (a) The following are identification codes for steel or aluminum boxes: (1) 4A for a steel box; and...

The Effects of Prohibiting Gestures on Children's Lexical Retrieval Ability

ERIC Educational Resources Information Center

Pine, Karen J.; Bird, Hannah; Kirk, Elizabeth

2007-01-01

Two alternative accounts have been proposed to explain the role of gestures in thinking and speaking. The Information Packaging Hypothesis (Kita, 2000) claims that gestures are important for the conceptual packaging of information before it is coded into a linguistic form for speech. The Lexical Retrieval Hypothesis (Rauscher, Krauss & Chen, 1996)…

Nmrglue: an open source Python package for the analysis of multidimensional NMR data.

PubMed

Helmus, Jonathan J; Jaroniec, Christopher P

2013-04-01

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license.

Nmrglue: An Open Source Python Package for the Analysis of Multidimensional NMR Data

PubMed Central

Helmus, Jonathan J.; Jaroniec, Christopher P.

2013-01-01

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license. PMID:23456039

Translation of one high-level language to another: COBOL to ADA, an example

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

Hill, J.A.

1986-01-01

This dissertation discusses the difficulties encountered in, and explores possible solutions to, the task of automatically converting programs written in one HLL, COBOL, into programs written in another HLL, Ada, and still maintain readability. This paper presents at least one set of techniques and algorithms to solve many of the problems that were encountered. The differing view of records is solved by isolating those instances where it is a problem, then using the RENAMES option of Ada. Several solutions to doing the decimal-arithmetic translation are discussed. One method used is to emulate COBOL arithmetic in an arithmetic package. Another partialmore » solution suggested is to convert the values to decimal-scaled integers and use modular arithmetic. Conversion to fixed-point type and floating-point type are the third and fourth methods. The work of another researcher, Bobby Othmer, is utilized to correct any unstructured code, to remap statements not directly translatable such as ALTER, and to pull together isolated code sections. Algorithms are then presented to convert this restructured COBOL code into Ada code with local variables, parameters, and packages. The input/output requirements are partially met by mapping them to a series of procedure calls that interface with Ada's standard input-output package. Several examples are given of hand translations of COBOL programs. In addition, a possibly new method is shown for measuring the readability of programs.« less

ANITA-IEAF activation code package - updating of the decay and cross section data libraries and validation on the experimental data from the Karlsruhe Isochronous Cyclotron

NASA Astrophysics Data System (ADS)

Frisoni, Manuela

2017-09-01

ANITA-IEAF is an activation package (code and libraries) developed in the past in ENEA-Bologna in order to assess the activation of materials exposed to neutrons with energies greater than 20 MeV. An updated version of the ANITA-IEAF activation code package has been developed. It is suitable to be applied to the study of the irradiation effects on materials in facilities like the International Fusion Materials Irradiation Facility (IFMIF) and the DEMO Oriented Neutron Source (DONES), in which a considerable amount of neutrons with energies above 20 MeV is produced. The present paper summarizes the main characteristics of the updated version of ANITA-IEAF, able to use decay and cross section data based on more recent evaluated nuclear data libraries, i.e. the JEFF-3.1.1 Radioactive Decay Data Library and the EAF-2010 neutron activation cross section library. In this paper the validation effort related to the comparison between the code predictions and the activity measurements obtained from the Karlsruhe Isochronous Cyclotron is presented. In this integral experiment samples of two different steels, SS-316 and F82H, pure vanadium and a vanadium alloy, structural materials of interest in fusion technology, were activated in a neutron spectrum similar to the IFMIF neutron field.

Radio Astronomy Tools in Python: Spectral-cube, pvextractor, and more

NASA Astrophysics Data System (ADS)

Ginsburg, A.; Robitaille, T.; Beaumont, C.; Rosolowsky, E.; Leroy, A.; Brogan, C.; Hunter, T.; Teuben, P.; Brisbin, D.

2015-12-01

The radio-astro-tools organization has been established to facilitate development of radio and millimeter analysis tools by the scientific community. The first packages developed under its umbrella are: • The spectral-cube package, for reading, writing, and analyzing spectral data cubes • The pvextractor package for extracting position-velocity slices from position-position-velocity cubes along aribitrary paths • The radio-beam package to handle gaussian beams in the context of the astropy quantity and unit framework • casa-python to enable installation of these packages - and any other - into users' CASA environments without conflicting with the underlying CASA package. Community input in the form of code contributions, suggestions, questions and commments is welcome on all of these tools. They can all be found at http://radio-astro-tools.github.io.

A tactile-output paging communication system for the deaf-blind

NASA Technical Reports Server (NTRS)

Baer, J. A.

1979-01-01

A radio frequency paging communication system that has coded vibrotactile outputs suitable for use by deaf-blind people was developed. In concept, the system consists of a base station transmitting and receiving unit and many on-body transmitting and receiving units. The completed system has seven operating modes: fire alarm; time signal; repeated single character Morse code; manual Morse code; emergency aid request; operational status test; and message acknowledge. The on-body units can be addressed in three ways: all units; a group of units; or an individual unit. All the functions developed were integrated into a single package that can be worn on the user's wrist. The control portion of the on-body unit is implemented by a microcomputer. The microcomputer is packaged in a custom-designed hybrid circuit to reduce its physical size.

Simulations of neutron transport at low energy: a comparison between GEANT and MCNP.

PubMed

Colonna, N; Altieri, S

2002-06-01

The use of the simulation tool GEANT for neutron transport at energies below 20 MeV is discussed, in particular with regard to shielding and dose calculations. The reliability of the GEANT/MICAP package for neutron transport in a wide energy range has been verified by comparing the results of simulations performed with this package in a wide energy range with the prediction of MCNP-4B, a code commonly used for neutron transport at low energy. A reasonable agreement between the results of the two codes is found for the neutron flux through a slab of material (iron and ordinary concrete), as well as for the dose released in soft tissue by neutrons. These results justify the use of the GEANT/MICAP code for neutron transport in a wide range of applications, including health physics problems.

WOLF: a computer code package for the calculation of ion beam trajectories

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

Vogel, D.L.

1985-10-01

The WOLF code solves POISSON'S equation within a user-defined problem boundary of arbitrary shape. The code is compatible with ANSI FORTRAN and uses a two-dimensional Cartesian coordinate geometry represented on a triangular lattice. The vacuum electric fields and equipotential lines are calculated for the input problem. The use may then introduce a series of emitters from which particles of different charge-to-mass ratios and initial energies can originate. These non-relativistic particles will then be traced by WOLF through the user-defined region. Effects of ion and electron space charge are included in the calculation. A subprogram PISA forms part of this codemore » and enables optimization of various aspects of the problem. The WOLF package also allows detailed graphics analysis of the computed results to be performed.« less

DFT +U Modeling of Hole Polarons in Organic Lead Halide Perovskites

NASA Astrophysics Data System (ADS)

Welch, Eric; Erhart, Paul; Scolfaro, Luisa; Zakhidov, Alex

Due to the ever present drive towards improved efficiencies in solar cell technology, new and improved materials are emerging rapidly. Organic halide perovskites are a promising prospect, yet a fundamental understanding of the organic perovskite structure and electronic properties is missing. Particularly, explanations of certain physical phenomena, specifically a low recombination rate and high mobility of charge carriers still remain controversial. We theoretically investigate possible formation of hole polarons adopting methodology used for oxide perovskites. The perovskite studied here is the ABX3structure, with A being an organic cation, B lead and C a halogen; the combinations studied allow for A1,xA2 , 1 - xBX1,xX2 , 3 - xwhere the alloy convention is used to show mixtures of the organic cations and/or the halogens. Two organic cations, methylammonium and formamidinium, and three halogens, iodine, chlorine and bromine are studied. Electronic structures and polaron behavior is studied through first principle density functional theory (DFT) calculations using the Vienna Ab Initio Simulation Package (VASP). Local density approximation (LDA) pseudopotentials are used and a +U Hubbard correction of 8 eV is added; this method was shown to work with oxide perovskites. It is shown that a localized state is realized with the Hubbard correction in systems with an electron removed, residing in the band gap of each different structure. Thus, hole polarons are expected to be seen in these perovskites.

Eddylicious: A Python package for turbulent inflow generation

NASA Astrophysics Data System (ADS)

Mukha, Timofey; Liefvendahl, Mattias

2018-01-01

A Python package for generating inflow for scale-resolving computer simulations of turbulent flow is presented. The purpose of the package is to unite existing inflow generation methods in a single code-base and make them accessible to users of various Computational Fluid Dynamics (CFD) solvers. The currently existing functionality consists of an accurate inflow generation method suitable for flows with a turbulent boundary layer inflow and input/output routines for coupling with the open-source CFD solver OpenFOAM.

An Interactive Computer Aided Design and Analysis Package.

DTIC Science & Technology

1986-03-01

Al-A167 114 AN INTERACTIVE COMPUTER AIDED DESIGN MUD ANAILYSIS 1/𔃼 PACKAGE(U) NAVAL POSTGRADUATE SCHOOL NONTEREY CA T L EUALD "AR 86 UNCLSSIFIED F... SCHOOL Monterey, California DTIC .LECTE MAYOS THESIS AN INTERACTIVE COMPUTER AIDED DESIGN AND ANALYSIS PACKAGE by Terrence L. Ewald March 1986 jThesis...ORGANIZATION Naval Postgraduate School (if dAp90h81111) Naval Postgraduate School . 62A 6C. ADDRESS (0ty. State, and ZIP Code) 7b. ADDRESS (City State. and

Community-based benchmarking of the CMIP DECK experiments

NASA Astrophysics Data System (ADS)

Gleckler, P. J.

2015-12-01

A diversity of community-based efforts are independently developing "diagnostic packages" with little or no coordination between them. A short list of examples include NCAR's Climate Variability Diagnostics Package (CVDP), ORNL's International Land Model Benchmarking (ILAMB), LBNL's Toolkit for Extreme Climate Analysis (TECA), PCMDI's Metrics Package (PMP), the EU EMBRACE ESMValTool, the WGNE MJO diagnostics package, and CFMIP diagnostics. The full value of these efforts cannot be realized without some coordination. As a first step, a WCRP effort has initiated a catalog to document candidate packages that could potentially be applied in a "repeat-use" fashion to all simulations contributed to the CMIP DECK (Diagnostic, Evaluation and Characterization of Klima) experiments. Some coordination of community-based diagnostics has the additional potential to improve how CMIP modeling groups analyze their simulations during model-development. The fact that most modeling groups now maintain a "CMIP compliant" data stream means that in principal without much effort they could readily adopt a set of well organized diagnostic capabilities specifically designed to operate on CMIP DECK experiments. Ultimately, a detailed listing of and access to analysis codes that are demonstrated to work "out of the box" with CMIP data could enable model developers (and others) to select those codes they wish to implement in-house, potentially enabling more systematic evaluation during the model development process.

Determinant Computation on the GPU using the Condensation Method

NASA Astrophysics Data System (ADS)

Anisul Haque, Sardar; Moreno Maza, Marc

2012-02-01

We report on a GPU implementation of the condensation method designed by Abdelmalek Salem and Kouachi Said for computing the determinant of a matrix. We consider two types of coefficients: modular integers and floating point numbers. We evaluate the performance of our code by measuring its effective bandwidth and argue that it is numerical stable in the floating point number case. In addition, we compare our code with serial implementation of determinant computation from well-known mathematical packages. Our results suggest that a GPU implementation of the condensation method has a large potential for improving those packages in terms of running time and numerical stability.

magnum.fe: A micromagnetic finite-element simulation code based on FEniCS

NASA Astrophysics Data System (ADS)

Abert, Claas; Exl, Lukas; Bruckner, Florian; Drews, André; Suess, Dieter

2013-11-01

We have developed a finite-element micromagnetic simulation code based on the FEniCS package called magnum.fe. Here we describe the numerical methods that are applied as well as their implementation with FEniCS. We apply a transformation method for the solution of the demagnetization-field problem. A semi-implicit weak formulation is used for the integration of the Landau-Lifshitz-Gilbert equation. Numerical experiments show the validity of simulation results. magnum.fe is open source and well documented. The broad feature range of the FEniCS package makes magnum.fe a good choice for the implementation of novel micromagnetic finite-element algorithms.

Use of the MATRIXx Integrated Toolkit on the Microwave Anisotropy Probe Attitude Control System

NASA Technical Reports Server (NTRS)

Ward, David K.; Andrews, Stephen F.; McComas, David C.; ODonnell, James R., Jr.

1999-01-01

Recent advances in analytical software tools allow the analysis, simulation, flight code, and documentation of an algorithm to be generated from a single source, all within one integrated analytical design package. NASA's Microwave Anisotropy Probe project has used one such package, Integrated Systems' MATRIXx suite, in the design of the spacecraft's Attitude Control System. The project's experience with the linear analysis, simulation, code generation, and documentation tools will be presented and compared with more traditional development tools. In particular, the quality of the flight software generated will be examined in detail. Finally, lessons learned on each of the tools will be shared.

NPTFit: A Code Package for Non-Poissonian Template Fitting

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

Mishra-Sharma, Siddharth; Rodd, Nicholas L.; Safdi, Benjamin R., E-mail: smsharma@princeton.edu, E-mail: nrodd@mit.edu, E-mail: bsafdi@mit.edu

We present NPTFit, an open-source code package, written in Python and Cython, for performing non-Poissonian template fits (NPTFs). The NPTF is a recently developed statistical procedure for characterizing the contribution of unresolved point sources (PSs) to astrophysical data sets. The NPTF was first applied to Fermi gamma-ray data to provide evidence that the excess of ∼GeV gamma-rays observed in the inner regions of the Milky Way likely arises from a population of sub-threshold point sources, and the NPTF has since found additional applications studying sub-threshold extragalactic sources at high Galactic latitudes. The NPTF generalizes traditional astrophysical template fits to allowmore » for the ability to search for populations of unresolved PSs that may follow a given spatial distribution. NPTFit builds upon the framework of the fluctuation analyses developed in X-ray astronomy, thus it likely has applications beyond those demonstrated with gamma-ray data. The NPTFit package utilizes novel computational methods to perform the NPTF efficiently. The code is available at http://github.com/bsafdi/NPTFit and up-to-date and extensive documentation may be found at http://nptfit.readthedocs.io.« less

Electronic structure, defect formation energy, and photovoltaic properties of wurtzite-derived CuGaO2

NASA Astrophysics Data System (ADS)

Okumura, H.; Sato, K.; Kakeshita, T.

2018-04-01

Wurtzite-derived CuGaO2 (β-CuGaO2) is a recently synthesized oxide and expected as a candidate material for photovoltaic solar cells. In this paper, we propose computational material design concerning β-CuGaO2 based on the first-principles calculations. We perform hybrid calculations by using the VASP code. It is predicted that β-CuGaO2 has a direct bandgap (Eg = 1.56 eV), which is nearly optimal for high efficiency solar cells. The calculated formation energy of Cu vacancy (VCu) is very small and can be negative depending on the Fermi level. This result reasonably explains the observed p-type conduction in this material. As for the n-type doping, Cd doping could be suitable; however, VCu formation needs to be repressed in order to realize n-type β-CuGaO2. It is also shown that halogen impurities are not suitable for n-type β-CuGaO2 because of their large formation energy. Band alignment between β-CuGaO2 and ZnO is predicted to be type-II, leading to a suggestion of photovoltaic device based on the heterojunction.

Bayesian Atmospheric Radiative Transfer (BART): Model, Statistics Driver, and Application to HD 209458b

NASA Astrophysics Data System (ADS)

Cubillos, Patricio; Harrington, Joseph; Blecic, Jasmina; Stemm, Madison M.; Lust, Nate B.; Foster, Andrew S.; Rojo, Patricio M.; Loredo, Thomas J.

2014-11-01

Multi-wavelength secondary-eclipse and transit depths probe the thermo-chemical properties of exoplanets. In recent years, several research groups have developed retrieval codes to analyze the existing data and study the prospects of future facilities. However, the scientific community has limited access to these packages. Here we premiere the open-source Bayesian Atmospheric Radiative Transfer (BART) code. We discuss the key aspects of the radiative-transfer algorithm and the statistical package. The radiation code includes line databases for all HITRAN molecules, high-temperature H2O, TiO, and VO, and includes a preprocessor for adding additional line databases without recompiling the radiation code. Collision-induced absorption lines are available for H2-H2 and H2-He. The parameterized thermal and molecular abundance profiles can be modified arbitrarily without recompilation. The generated spectra are integrated over arbitrary bandpasses for comparison to data. BART's statistical package, Multi-core Markov-chain Monte Carlo (MC3), is a general-purpose MCMC module. MC3 implements the Differental-evolution Markov-chain Monte Carlo algorithm (ter Braak 2006, 2009). MC3 converges 20-400 times faster than the usual Metropolis-Hastings MCMC algorithm, and in addition uses the Message Passing Interface (MPI) to parallelize the MCMC chains. We apply the BART retrieval code to the HD 209458b data set to estimate the planet's temperature profile and molecular abundances. This work was supported by NASA Planetary Atmospheres grant NNX12AI69G and NASA Astrophysics Data Analysis Program grant NNX13AF38G. JB holds a NASA Earth and Space Science Fellowship.

Modular assembly of chimeric phi29 packaging RNAs that support DNA packaging.

PubMed

Fang, Yun; Shu, Dan; Xiao, Feng; Guo, Peixuan; Qin, Peter Z

2008-08-08

The bacteriophage phi29 DNA packaging motor is a protein/RNA complex that can produce strong force to condense the linear-double-stranded DNA genome into a pre-formed protein capsid. The RNA component, called the packaging RNA (pRNA), utilizes magnesium-dependent inter-molecular base-pairing interactions to form ring-shaped complexes. The pRNA is a class of non-coding RNA, interacting with phi29 motor proteins to enable DNA packaging. Here, we report a two-piece chimeric pRNA construct that is fully competent in interacting with partner pRNA to form ring-shaped complexes, in packaging DNA via the motor, and in assembling infectious phi29 virions in vitro. This is the first example of a fully functional pRNA assembled using two non-covalently interacting fragments. The results support the notion of modular pRNA architecture in the phi29 packaging motor.

Modular assembly of chimeric phi29 packaging RNAs that support DNA packaging

PubMed Central

Fang, Yun; Shu, Dan; Xiao, Feng; Guo, Peixuan; Qin, Peter Z.

2008-01-01

The bacteriophage phi29 DNA packaging motor is a protein/RNA complex that can produce strong force to condense the linear-double stranded DNA genome into a pre-formed protein capsid. The RNA component, called the packaging RNA (pRNA), utilizes magnesium-dependent intermolecular base-pairing interactions to form ring-shaped complexes. The pRNA is a class of non-coding RNA, interacting with phi29 motor proteins to enable DNA packaging. Here, we report a 2-piece chimeric pRNA construct that is fully competent in interacting with partner pRNA to form ring-shaped complexes, in packaging DNA via the motor, and in assembling infectious phi29 virions in vitro. This is the first example of a fully functional pRNA assembled using two non-covalently interacting fragments. The results support the notion of modular pRNA architecture in the phi29 packaging motor. PMID:18514064

49 CFR 178.517 - Standards for plastic boxes.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Standards for plastic boxes. 178.517 Section 178... PACKAGINGS Non-bulk Performance-Oriented Packaging Standards § 178.517 Standards for plastic boxes. (a) The following are identification codes for plastic boxes: (1) 4H1 for an expanded plastic box; and (2) 4H2 for a...

Entity- Version 1.0

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

Hart, Brian; Oppel, Fred; Rigdon, Brian

2012-09-13

This package contains classes that capture high-level aspects of characters and vehicles. Vehicles manage seats and riders. Vehicles and characters now can be configured to compose different behaviors and have certain capabilities, by adding them through xml data. These behaviors and capabilities are not included in this package, but instead are part of other packages such as mobility behavior, path planning, sight, sound. Entity is not dependent on these other packages. This package also contains the icons used for Umbra applications Dante Scenario Editor, Dante Tabletop and OpShed. This assertion includes a managed C++ wrapper code (EntityWrapper) to enable C#more » applications, such as Dante Scenario Editor, Dante Tabletop, and OpShed, to incorporate this library.« less

Interactive Finite Elements for General Engine Dynamics Analysis

NASA Technical Reports Server (NTRS)

Adams, M. L.; Padovan, J.; Fertis, D. G.

1984-01-01

General nonlinear finite element codes were adapted for the purpose of analyzing the dynamics of gas turbine engines. In particular, this adaptation required the development of a squeeze-film damper element software package and its implantation into a representative current generation code. The ADINA code was selected because of prior use of it and familiarity with its internal structure and logic. This objective was met and the results indicate that such use of general purpose codes is viable alternative to specialized codes for general dynamics analysis of engines.

49 CFR 171.25 - Additional requirements for the use of the IMDG Code.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 176 of this subchapter. (3) Packages containing primary lithium batteries and cells that are transported in accordance with Special Provision 188 of the IMDG Code must be marked “PRIMARY LITHIUM BATTERIES—FORBIDDEN FOR TRANSPORT ABOARD PASSENGER AIRCRAFT” or “LITHIUM METAL BATTERIES—FORBIDDEN FOR...

49 CFR 171.25 - Additional requirements for the use of the IMDG Code.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 176 of this subchapter. (3) Packages containing primary lithium batteries and cells that are transported in accordance with Special Provision 188 of the IMDG Code must be marked “PRIMARY LITHIUM BATTERIES—FORBIDDEN FOR TRANSPORT ABOARD PASSENGER AIRCRAFT” or “LITHIUM METAL BATTERIES—FORBIDDEN FOR...

49 CFR 171.25 - Additional requirements for the use of the IMDG Code.

Code of Federal Regulations, 2010 CFR

2010-10-01

...) Packages containing primary lithium batteries and cells that are transported in accordance with Special Provision 188 of the IMDG Code must be marked “PRIMARY LITHIUM BATTERIES—FORBIDDEN FOR TRANSPORT ABOARD PASSENGER AIRCRAFT” or “LITHIUM METAL BATTERIES—FORBIDDEN FOR TRANSPORT ABOARD PASSENGER AIRCRAFT.” This...

49 CFR 171.25 - Additional requirements for the use of the IMDG Code.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 176 of this subchapter. (3) Packages containing primary lithium batteries and cells that are transported in accordance with Special Provision 188 of the IMDG Code must be marked “PRIMARY LITHIUM BATTERIES—FORBIDDEN FOR TRANSPORT ABOARD PASSENGER AIRCRAFT” or “LITHIUM METAL BATTERIES—FORBIDDEN FOR...

The fastclime Package for Linear Programming and Large-Scale Precision Matrix Estimation in R.

PubMed

Pang, Haotian; Liu, Han; Vanderbei, Robert

2014-02-01

We develop an R package fastclime for solving a family of regularized linear programming (LP) problems. Our package efficiently implements the parametric simplex algorithm, which provides a scalable and sophisticated tool for solving large-scale linear programs. As an illustrative example, one use of our LP solver is to implement an important sparse precision matrix estimation method called CLIME (Constrained L 1 Minimization Estimator). Compared with existing packages for this problem such as clime and flare, our package has three advantages: (1) it efficiently calculates the full piecewise-linear regularization path; (2) it provides an accurate dual certificate as stopping criterion; (3) it is completely coded in C and is highly portable. This package is designed to be useful to statisticians and machine learning researchers for solving a wide range of problems.

Introducing Python tools for magnetotellurics: MTpy

NASA Astrophysics Data System (ADS)

Krieger, L.; Peacock, J.; Inverarity, K.; Thiel, S.; Robertson, K.

2013-12-01

Within the framework of geophysical exploration techniques, the magnetotelluric method (MT) is relatively immature: It is still not as widely spread as other geophysical methods like seismology, and its processing schemes and data formats are not thoroughly standardized. As a result, the file handling and processing software within the academic community is mainly based on a loose collection of codes, which are sometimes highly adapted to the respective local specifications. Although tools for the estimation of the frequency dependent MT transfer function, as well as inversion and modelling codes, are available, the standards and software for handling MT data are generally not unified throughout the community. To overcome problems that arise from missing standards, and to simplify the general handling of MT data, we have developed the software package "MTpy", which allows the handling, processing, and imaging of magnetotelluric data sets. It is written in Python and the code is open-source. The setup of this package follows the modular approach of successful software packages like GMT or Obspy. It contains sub-packages and modules for various tasks within the standard MT data processing and handling scheme. Besides pure Python classes and functions, MTpy provides wrappers and convenience scripts to call external software, e.g. modelling and inversion codes. Even though still under development, MTpy already contains ca. 250 functions that work on raw and preprocessed data. However, as our aim is not to produce a static collection of software, we rather introduce MTpy as a flexible framework, which will be dynamically extended in the future. It then has the potential to help standardise processing procedures and at same time be a versatile supplement for existing algorithms. We introduce the concept and structure of MTpy, and we illustrate the workflow of MT data processing utilising MTpy on an example data set collected over a geothermal exploration site in South Australia. Workflow of MT data processing. Within the structural diagram, the MTpy sub-packages are shown in red (time series data processing), green (handling of EDI files and impedance tensor data), yellow (connection to modelling/inversion algorithms), black (impedance tensor interpretation, e.g. by Phase Tensor calculations), and blue (generation of visual representations, e.g pseudo sections or resistivity models).

An Analysis of Information Assurance Relating to the Department of Defense Radio Frequency Identification (RFID) Passive Network

DTIC Science & Technology

2005-03-01

codes speed up consumer shopping, package shipping, and inventory tracking. RFID offers many advantages over bar codes, as the table below shows...sunlight” (Accenture, 2001, p. 4). Finally, one of the most significant advantages of RFID is the advent of anti-collision. Anti-collision allows an...RFID reader to read and/or write to multiple tags at one time, which is not possible for bar codes. Despite the many advantages RFID over bar codes

39 CFR Appendix A to Part 121 - Tables Depicting Service Standard Day Ranges

Code of Federal Regulations, 2012 CFR

2012-07-01

... & USVI Periodicals 1 1-3 1 1-3 1-4 (AK) 11 (JNU) 11 (KTN) 1 (HI) 2 (GU) 1-4 10-11 10 8-10 Standard Mail 2 3 3-4 3-4 14 13 12 Package Services 1 2 2-3 2-3 12 11 11 AK = Alaska 3-digit ZIP Codes 995-997; JNU = Juneau AK 3-digit ZIP Code 998; KTN = Ketchikan AK 3-digit ZIP Code 999; HI = Hawaii 3-digit ZIP Codes...

39 CFR Appendix A to Part 121 - Tables Depicting Service Standard Day Ranges

Code of Federal Regulations, 2013 CFR

2013-07-01

... & USVI Periodicals 1 1-3 1 1-3 1-4 (AK) 11 (JNU) 11 (KTN) 1 (HI) 2 (GU) 1-4 10-11 10 8-10 Standard Mail 2 3 3-4 3-4 14 13 12 Package Services 1 2 2-3 2-3 12 11 11 AK = Alaska 3-digit ZIP Codes 995-997; JNU = Juneau AK 3-digit ZIP Code 998; KTN = Ketchikan AK 3-digit ZIP Code 999; HI = Hawaii 3-digit ZIP Codes...

Development of Fuel Shuffling Module for PHISICS

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

Allan Mabe; Andrea Alfonsi; Cristian Rabiti

2013-06-01

PHISICS (Parallel and Highly Innovative Simulation for the INL Code System) [4] code toolkit has been in development at the Idaho National Laboratory. This package is intended to provide a modern analysis tool for reactor physics investigation. It is designed with the mindset to maximize accuracy for a given availability of computational resources and to give state of the art tools to the modern nuclear engineer. This is obtained by implementing several different algorithms and meshing approaches among which the user will be able to choose, in order to optimize his computational resources and accuracy needs. The software is completelymore » modular in order to simplify the independent development of modules by different teams and future maintenance. The package is coupled with the thermo-hydraulic code RELAP5-3D [3]. In the following the structure of the different PHISICS modules is briefly recalled, focusing on the new shuffling module (SHUFFLE), object of this paper.« less

The EGS4 Code System: Solution of Gamma-ray and Electron Transport Problems

DOE R&D Accomplishments Database

Nelson, W. R.; Namito, Yoshihito

1990-03-01

In this paper we present an overview of the EGS4 Code System -- a general purpose package for the Monte Carlo simulation of the transport of electrons and photons. During the last 10-15 years EGS has been widely used to design accelerators and detectors for high-energy physics. More recently the code has been found to be of tremendous use in medical radiation physics and dosimetry. The problem-solving capabilities of EGS4 will be demonstrated by means of a variety of practical examples. To facilitate this review, we will take advantage of a new add-on package, called SHOWGRAF, to display particle trajectories in complicated geometries. These are shown as 2-D laser pictures in the written paper and as photographic slides of a 3-D high-resolution color monitor during the oral presentation. 11 refs., 15 figs.

Lattice stabilities, mechanical and thermodynamic properties of Al3Tm and Al3Lu intermetallics under high pressure from first-principles calculations

NASA Astrophysics Data System (ADS)

Xu-Dong, Zhang; Wei, Jiang

2016-02-01

The effects of high pressure on lattice stability, mechanical and thermodynamic properties of L12 structure Al3Tm and Al3Lu are studied by first-principles calculations within the VASP code. The phonon dispersion curves and density of phonon states are calculated by using the PHONONPY code. Our results agree well with the available experimental and theoretical values. The vibrational properties indicate that Al3Tm and Al3Lu keep their dynamical stabilities in L12 structure up to 100 GPa. The elastic properties and Debye temperatures for Al3Tm and Al3Lu increase with the increase of pressure. The mechanical anisotropic properties are discussed by using anisotropic indices AG, AU, AZ, and the three-dimensional (3D) curved surface of Young’s modulus. The calculated results show that Al3Tm and Al3Lu are both isotropic at 0 GPa and anisotropic under high pressure. In the present work, the sound velocities in different directions for Al3Tm and Al3Lu are also predicted under high pressure. We also calculate the thermodynamic properties and provide the relationships between thermal parameters and temperature/pressure. These results can provide theoretical support for further experimental work and industrial applications. Project supported by the Scientific Technology Plan of the Educational Department of Liaoning Province and Liaoning Innovative Research Team in University, China (Grant No. LT2014004) and the Program for the Young Teacher Cultivation Fund of Shenyang University of Technology, China (Grant No. 005612).

A Roadmap to Continuous Integration for ATLAS Software Development

NASA Astrophysics Data System (ADS)

Elmsheuser, J.; Krasznahorkay, A.; Obreshkov, E.; Undrus, A.; ATLAS Collaboration

2017-10-01

The ATLAS software infrastructure facilitates efforts of more than 1000 developers working on the code base of 2200 packages with 4 million lines of C++ and 1.4 million lines of python code. The ATLAS offline code management system is the powerful, flexible framework for processing new package versions requests, probing code changes in the Nightly Build System, migration to new platforms and compilers, deployment of production releases for worldwide access and supporting physicists with tools and interfaces for efficient software use. It maintains multi-stream, parallel development environment with about 70 multi-platform branches of nightly releases and provides vast opportunities for testing new packages, for verifying patches to existing software and for migrating to new platforms and compilers. The system evolution is currently aimed on the adoption of modern continuous integration (CI) practices focused on building nightly releases early and often, with rigorous unit and integration testing. This paper describes the CI incorporation program for the ATLAS software infrastructure. It brings modern open source tools such as Jenkins and GitLab into the ATLAS Nightly System, rationalizes hardware resource allocation and administrative operations, provides improved feedback and means to fix broken builds promptly for developers. Once adopted, ATLAS CI practices will improve and accelerate innovation cycles and result in increased confidence in new software deployments. The paper reports the status of Jenkins integration with the ATLAS Nightly System as well as short and long term plans for the incorporation of CI practices.

Report of AAPM Task Group 162: Software for planar image quality metrology.

PubMed

Samei, Ehsan; Ikejimba, Lynda C; Harrawood, Brian P; Rong, John; Cunningham, Ian A; Flynn, Michael J

2018-02-01

The AAPM Task Group 162 aimed to provide a standardized approach for the assessment of image quality in planar imaging systems. This report offers a description of the approach as well as the details of the resultant software bundle to measure detective quantum efficiency (DQE) as well as its basis components and derivatives. The methodology and the associated software include the characterization of the noise power spectrum (NPS) from planar images acquired under specific acquisition conditions, modulation transfer function (MTF) using an edge test object, the DQE, and effective DQE (eDQE). First, a methodological framework is provided to highlight the theoretical basis of the work. Then, a step-by-step guide is included to assist in proper execution of each component of the code. Lastly, an evaluation of the method is included to validate its accuracy against model-based and experimental data. The code was built using a Macintosh OSX operating system. The software package contains all the source codes to permit an experienced user to build the suite on a Linux or other *nix type system. The package further includes manuals and sample images and scripts to demonstrate use of the software for new users. The results of the code are in close alignment with theoretical expectations and published results of experimental data. The methodology and the software package offered in AAPM TG162 can be used as baseline for characterization of inherent image quality attributes of planar imaging systems. © 2017 American Association of Physicists in Medicine.

49 CFR 178.502 - Identification codes for packagings.

Code of Federal Regulations, 2013 CFR

2013-10-01

...” means a jerrican. (iv) “4” means a box. (v) “5” means a bag. (vi) “6” means a composite packaging. (vii... natural wood. (iv) “D” means plywood. (v) “F” means reconstituted wood. (vi) “G” means fiberboard. (vii... (other than steel or aluminum). (xi) “P” means glass, porcelain or stoneware. (3) A numeral indicating...

49 CFR 178.502 - Identification codes for packagings.

Code of Federal Regulations, 2014 CFR

2014-10-01

...” means a jerrican. (iv) “4” means a box. (v) “5” means a bag. (vi) “6” means a composite packaging. (vii... natural wood. (iv) “D” means plywood. (v) “F” means reconstituted wood. (vi) “G” means fiberboard. (vii... (other than steel or aluminum). (xi) “P” means glass, porcelain or stoneware. (3) A numeral indicating...

49 CFR 178.502 - Identification codes for packagings.

Code of Federal Regulations, 2011 CFR

2011-10-01

...” means a jerrican. (iv) “4” means a box. (v) “5” means a bag. (vi) “6” means a composite packaging. (vii... natural wood. (iv) “D” means plywood. (v) “F” means reconstituted wood. (vi) “G” means fiberboard. (vii... (other than steel or aluminum). (xi) “P” means glass, porcelain or stoneware. (3) A numeral indicating...

49 CFR 178.502 - Identification codes for packagings.

Code of Federal Regulations, 2012 CFR

2012-10-01

...” means a jerrican. (iv) “4” means a box. (v) “5” means a bag. (vi) “6” means a composite packaging. (vii... natural wood. (iv) “D” means plywood. (v) “F” means reconstituted wood. (vi) “G” means fiberboard. (vii... (other than steel or aluminum). (xi) “P” means glass, porcelain or stoneware. (3) A numeral indicating...

49 CFR 173.240 - Bulk packaging for certain low hazard solid materials.

Code of Federal Regulations, 2014 CFR

2014-10-01

... this subchapter and the special provisions specified in column 7 of the § 172.101 table. (a) Rail cars... the IBC packaging code specified for the specific hazardous material in Column (7) of the § 172.101... subchapter at the Packing Group performance level as specified in Column (5) of the § 172.101 Table of this...

49 CFR 173.240 - Bulk packaging for certain low hazard solid materials.

Code of Federal Regulations, 2012 CFR

2012-10-01

... this subchapter and the special provisions specified in column 7 of the § 172.101 table. (a) Rail cars... the IBC packaging code specified for the specific hazardous material in Column (7) of the § 172.101... subchapter at the Packing Group performance level as specified in Column (5) of the § 172.101 Table of this...

49 CFR 173.240 - Bulk packaging for certain low hazard solid materials.

Code of Federal Regulations, 2011 CFR

2011-10-01

... this subchapter and the special provisions specified in column 7 of the § 172.101 table. (a) Rail cars... the IBC packaging code specified for the specific hazardous material in Column (7) of the § 172.101... subchapter at the Packing Group performance level as specified in Column (5) of the § 172.101 Table of this...

49 CFR 173.240 - Bulk packaging for certain low hazard solid materials.

Code of Federal Regulations, 2013 CFR

2013-10-01

... this subchapter and the special provisions specified in column 7 of the § 172.101 table. (a) Rail cars... the IBC packaging code specified for the specific hazardous material in Column (7) of the § 172.101... subchapter at the Packing Group performance level as specified in Column (5) of the § 172.101 Table of this...

49 CFR 173.240 - Bulk packaging for certain low hazard solid materials.

Code of Federal Regulations, 2010 CFR

2010-10-01

... this subchapter and the special provisions specified in column 7 of the § 172.101 table. (a) Rail cars... the IBC packaging code specified for the specific hazardous material in Column (7) of the § 172.101... subchapter at the Packing Group performance level as specified in Column (5) of the § 172.101 Table of this...

CoFFEE: Corrections For Formation Energy and Eigenvalues for charged defect simulations

NASA Astrophysics Data System (ADS)

Naik, Mit H.; Jain, Manish

2018-05-01

Charged point defects in materials are widely studied using Density Functional Theory (DFT) packages with periodic boundary conditions. The formation energy and defect level computed from these simulations need to be corrected to remove the contributions from the spurious long-range interaction between the defect and its periodic images. To this effect, the CoFFEE code implements the Freysoldt-Neugebauer-Van de Walle (FNV) correction scheme. The corrections can be applied to charged defects in a complete range of material shapes and size: bulk, slab (or two-dimensional), wires and nanoribbons. The code is written in Python and features MPI parallelization and optimizations using the Cython package for slow steps.

Validation of the new code package APOLLO2.8 for accurate PWR neutronics calculations

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

Santamarina, A.; Bernard, D.; Blaise, P.

2013-07-01

This paper summarizes the Qualification work performed to demonstrate the accuracy of the new APOLLO2.S/SHEM-MOC package based on JEFF3.1.1 nuclear data file for the prediction of PWR neutronics parameters. This experimental validation is based on PWR mock-up critical experiments performed in the EOLE/MINERVE zero-power reactors and on P.I. Es on spent fuel assemblies from the French PWRs. The Calculation-Experiment comparison for the main design parameters is presented: reactivity of UOX and MOX lattices, depletion calculation and fuel inventory, reactivity loss with burnup, pin-by-pin power maps, Doppler coefficient, Moderator Temperature Coefficient, Void coefficient, UO{sub 2}-Gd{sub 2}O{sub 3} poisoning worth, Efficiency ofmore » Ag-In-Cd and B4C control rods, Reflector Saving for both standard 2-cm baffle and GEN3 advanced thick SS reflector. From this qualification process, calculation biases and associated uncertainties are derived. This code package APOLLO2.8 is already implemented in the ARCADIA new AREVA calculation chain for core physics and is currently under implementation in the future neutronics package of the French utility Electricite de France. (authors)« less

The U. S. Department of Energy SARP review training program

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

Mauck, C.J.

1988-01-01

In support of its radioactive material packaging certification program, the U.S. Department of Energy (DOE) has established a special training workshop. The purpose of the two-week workshop is to develop skills in reviewing Safety Analysis Reports for Packagings (SARPs) and performing confirmatory analyses. The workshop, conducted by the Lawrence Livermore National Laboratory (LLNL) for DOE, is divided into two parts: methods of review and methods of analysis. The sessions covering methods of review are based on the DOE document, ''Packaging Review Guide for Reviewing Safety Analysis Reports for Packagings'' (PRG). The sessions cover relevant DOE Orders and all areas ofmore » review in the applicable Nuclear Regulatory Commission (NRC) Regulatory Guides. The technical areas addressed include structural and thermal behavior, materials, shielding, criticality, and containment. The course sessions on methods of analysis provide hands-on experience in the use of calculational methods and codes for reviewing SARPs. Analytical techniques and computer codes are discussed and sample problems are worked. Homework is assigned each night and over the included weekend; at the conclusion, a comprehensive take-home examination is given requiring six to ten hours to complete.« less

Basic mathematical function libraries for scientific computation

NASA Technical Reports Server (NTRS)

Galant, David C.

1989-01-01

Ada packages implementing selected mathematical functions for the support of scientific and engineering applications were written. The packages provide the Ada programmer with the mathematical function support found in the languages Pascal and FORTRAN as well as an extended precision arithmetic and a complete complex arithmetic. The algorithms used are fully described and analyzed. Implementation assumes that the Ada type FLOAT objects fully conform to the IEEE 754-1985 standard for single binary floating-point arithmetic, and that INTEGER objects are 32-bit entities. Codes for the Ada packages are included as appendixes.

PSRPOPPy: an open-source package for pulsar population simulations

NASA Astrophysics Data System (ADS)

Bates, S. D.; Lorimer, D. R.; Rane, A.; Swiggum, J.

2014-04-01

We have produced a new software package for the simulation of pulsar populations, PSRPOPPY, based on the PSRPOP package. The codebase has been re-written in Python (save for some external libraries, which remain in their native Fortran), utilizing the object-oriented features of the language, and improving the modularity of the code. Pre-written scripts are provided for running the simulations in `standard' modes of operation, but the code is flexible enough to support the writing of personalised scripts. The modular structure also makes the addition of experimental features (such as new models for period or luminosity distributions) more straightforward than with the previous code. We also discuss potential additions to the modelling capabilities of the software. Finally, we demonstrate some potential applications of the code; first, using results of surveys at different observing frequencies, we find pulsar spectral indices are best fitted by a normal distribution with mean -1.4 and standard deviation 1.0. Secondly, we model pulsar spin evolution to calculate the best fit for a relationship between a pulsar's luminosity and spin parameters. We used the code to replicate the analysis of Faucher-Giguère & Kaspi, and have subsequently optimized their power-law dependence of radio luminosity, L, with period, P, and period derivative, Ṗ. We find that the underlying population is best described by L ∝ P-1.39±0.09 Ṗ0.48±0.04 and is very similar to that found for γ-ray pulsars by Perera et al. Using this relationship, we generate a model population and examine the age-luminosity relation for the entire pulsar population, which may be measurable after future large-scale surveys with the Square Kilometre Array.

PelePhysics

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

2017-05-17

PelePhysics is a suite of physics packages that provides functionality of use to reacting hydrodynamics CFD codes. The initial release includes an interface to reaction rate mechanism evaluation, transport coefficient evaluation, and a generalized equation of state (EOS) facility. Both generic evaluators and interfaces to code from externally available tools (Fuego for chemical rates, EGLib for transport coefficients) are provided.

SolTrace | Concentrating Solar Power | NREL

Science.gov Websites

NREL packaged distribution or from source code at the SolTrace open source project website. NREL Publications Support FAQs SolTrace open source project The code uses Monte-Carlo ray-tracing methodology. The -tracing capabilities. With the release of the SolTrace open source project, the software has adopted

PlasmaPy: initial development of a Python package for plasma physics

NASA Astrophysics Data System (ADS)

Murphy, Nicholas; Leonard, Andrew J.; Stańczak, Dominik; Haggerty, Colby C.; Parashar, Tulasi N.; Huang, Yu-Min; PlasmaPy Community

2017-10-01

We report on initial development of PlasmaPy: an open source community-driven Python package for plasma physics. PlasmaPy seeks to provide core functionality that is needed for the formation of a fully open source Python ecosystem for plasma physics. PlasmaPy prioritizes code readability, consistency, and maintainability while using best practices for scientific computing such as version control, continuous integration testing, embedding documentation in code, and code review. We discuss our current and planned capabilities, including features presently under development. The development roadmap includes features such as fluid and particle simulation capabilities, a Grad-Shafranov solver, a dispersion relation solver, atomic data retrieval methods, and tools to analyze simulations and experiments. We describe several ways to contribute to PlasmaPy. PlasmaPy has a code of conduct and is being developed under a BSD license, with a version 0.1 release planned for 2018. The success of PlasmaPy depends on active community involvement, so anyone interested in contributing to this project should contact the authors. This work was partially supported by the U.S. Department of Energy.

qtcm 0.1.2: A Python Implementation of the Neelin-Zeng Quasi-Equilibrium Tropical Circulation model

NASA Astrophysics Data System (ADS)

Lin, J. W.-B.

2008-10-01

Historically, climate models have been developed incrementally and in compiled languages like Fortran. While the use of legacy compiled languages results in fast, time-tested code, the resulting model is limited in its modularity and cannot take advantage of functionality available with modern computer languages. Here we describe an effort at using the open-source, object-oriented language Python to create more flexible climate models: the package qtcm, a Python implementation of the intermediate-level Neelin-Zeng Quasi-Equilibrium Tropical Circulation model (QTCM1) of the atmosphere. The qtcm package retains the core numerics of QTCM1, written in Fortran to optimize model performance, but uses Python structures and utilities to wrap the QTCM1 Fortran routines and manage model execution. The resulting "mixed language" modeling package allows order and choice of subroutine execution to be altered at run time, and model analysis and visualization to be integrated in interactively with model execution at run time. This flexibility facilitates more complex scientific analysis using less complex code than would be possible using traditional languages alone, and provides tools to transform the traditional "formulate hypothesis → write and test code → run model → analyze results" sequence into a feedback loop that can be executed automatically by the computer.

qtcm 0.1.2: a Python implementation of the Neelin-Zeng Quasi-Equilibrium Tropical Circulation Model

NASA Astrophysics Data System (ADS)

Lin, J. W.-B.

2009-02-01

Historically, climate models have been developed incrementally and in compiled languages like Fortran. While the use of legacy compiled languages results in fast, time-tested code, the resulting model is limited in its modularity and cannot take advantage of functionality available with modern computer languages. Here we describe an effort at using the open-source, object-oriented language Python to create more flexible climate models: the package qtcm, a Python implementation of the intermediate-level Neelin-Zeng Quasi-Equilibrium Tropical Circulation model (QTCM1) of the atmosphere. The qtcm package retains the core numerics of QTCM1, written in Fortran to optimize model performance, but uses Python structures and utilities to wrap the QTCM1 Fortran routines and manage model execution. The resulting "mixed language" modeling package allows order and choice of subroutine execution to be altered at run time, and model analysis and visualization to be integrated in interactively with model execution at run time. This flexibility facilitates more complex scientific analysis using less complex code than would be possible using traditional languages alone, and provides tools to transform the traditional "formulate hypothesis → write and test code → run model → analyze results" sequence into a feedback loop that can be executed automatically by the computer.

A Python Implementation of an Intermediate-Level Tropical Circulation Model and Implications for How Modeling Science is Done

NASA Astrophysics Data System (ADS)

Lin, J. W. B.

2015-12-01

Historically, climate models have been developed incrementally and in compiled languages like Fortran. While the use of legacy compiledlanguages results in fast, time-tested code, the resulting model is limited in its modularity and cannot take advantage of functionalityavailable with modern computer languages. Here we describe an effort at using the open-source, object-oriented language Pythonto create more flexible climate models: the package qtcm, a Python implementation of the intermediate-level Neelin-Zeng Quasi-Equilibrium Tropical Circulation model (QTCM1) of the atmosphere. The qtcm package retains the core numerics of QTCM1, written in Fortran, to optimize model performance but uses Python structures and utilities to wrap the QTCM1 Fortran routines and manage model execution. The resulting "mixed language" modeling package allows order and choice of subroutine execution to be altered at run time, and model analysis and visualization to be integrated in interactively with model execution at run time. This flexibility facilitates more complex scientific analysis using less complex code than would be possible using traditional languages alone and provides tools to transform the traditional "formulate hypothesis → write and test code → run model → analyze results" sequence into a feedback loop that can be executed automatically by the computer.

Validation of a Laser-Ray Package in an Eulerian Code

NASA Astrophysics Data System (ADS)

Bradley, Paul; Hall, Mike; McKenty, Patrick; Collins, Tim; Keller, David

2014-10-01

A laser-ray absorption package was recently installed in the RAGE code by the Laboratory for Laser Energetics (LLE). In this presentation, we describe our use of this package to implode Omega 60 beam symmetric direct drive capsules. The capsules have outer diameters of about 860 microns, CH plastic shell thicknesses between 8 and 32 microns, DD or DT gas fills between 5 and 20 atmospheres, and a 1 ns square pulse of 23 to 27 kJ. These capsule implosions were previously modeled with a calibrated energy source in the outer layer of the capsule, where we matched bang time and burn ion temperature well, but the simulated yields were two to three times higher than the data. We will run simulations with laser ray energy deposition to the experiments and the results to the yield and spectroscopic data. Work performed by Los Alamos National Laboratory under Contract DE-AC52-06NA25396 for the National Nuclear Security Administration of the U.S. Department of Energy.

Development of an object-oriented ORIGEN for advanced nuclear fuel modeling applications

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

Skutnik, S.; Havloej, F.; Lago, D.

2013-07-01

The ORIGEN package serves as the core depletion and decay calculation module within the SCALE code system. A recent major re-factor to the ORIGEN code architecture as part of an overall modernization of the SCALE code system has both greatly enhanced its maintainability as well as afforded several new capabilities useful for incorporating depletion analysis into other code frameworks. This paper will present an overview of the improved ORIGEN code architecture (including the methods and data structures introduced) as well as current and potential future applications utilizing the new ORIGEN framework. (authors)

High rates of prasugrel and ticagrelor non-responder in patients treated with therapeutic hypothermia after cardiac arrest.

PubMed

Ibrahim, K; Christoph, M; Schmeinck, S; Schmieder, K; Steiding, K; Schoener, L; Pfluecke, C; Quick, S; Mues, C; Jellinghaus, S; Wunderlich, C; Strasser, R H; Kolschmann, S

2014-05-01

After cardiac arrest due to acute coronary syndromes (ACS) therapeutic hypothermia (HT) is the standard care to reduce neurologic damage. Additionally, the concomitant medical treatment with aspirin and a P2Y12 receptor inhibitor like clopidogrel (Cl), prasugrel (Pr) or ticagrelor (Ti) is mandatory. The platelet inhibitory effect of these drugs under hypothermia remains unclear. 164 patients with ACS were prospectively enrolled in this study. 84 patients were treated with HT, 80 patients were under normothermia (NT). All patients were treated with aspirin and one of the P2Y12 receptor inhibitors Cl, Pr or Ti. 24h after the initial loading dose the platelet reactivity index (PRI/VASP-index) was determined to achieve the platelet inhibitory effect. In the HT-group the PRI/VASP-index was significantly higher compared to the NT-group (54.86%±25.1 vs. 28.98%±22.8; p<0.001). In patients under HT receiving Cl, the platelet inhibition was most markedly reduced (HT vs. NT: 66.39%±19.1 vs. 33.36%±22.1; p<0.001) compared to Pr (HT vs. NT: 37.6%±25.0 vs. 27.04%±25.5; p=0.143) and Ti (HT vs. NT: 41.5%±21.0 vs. 17.83%±14.5; p=0.009). The rate of non-responder defined as PRI/VASP-index>50% was increased in HT compared to NT (60.7% vs. 22.5%; p<0.001) with the highest rates in the group receiving Cl (CL: 82% vs. 26%, p<0.001; Pr: 32% vs. 23%; n.s.; Ti: 30% vs. 8%, n.s.). The platelet inhibitory effect in patients treated with HT after cardiac arrest is significantly reduced. This effect was most marked with the use of Cl. The new P2Y12-inhibitors Pr and Ti improved platelet inhibition in HT, but could not completely prevent non-responsiveness. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Impact of P2Y12 inhibition by clopidogrel on cardiovascular mortality in unselected patients treated by percutaneous coronary angioplasty: a prospective registry.

PubMed

El Ghannudi, Soraya; Ohlmann, Patrick; Meyer, Nicolas; Wiesel, Marie-Louise; Radulescu, Bogdan; Chauvin, Michel; Bareiss, Pierre; Gachet, Christian; Morel, Olivier

2010-06-01

The aim of this study was to determine whether low platelet response to the P2Y(12) receptor antagonist clopidogrel as assessed by Vasodilator-stimulated phosphoprotein flow cytometry test (VASP- FCT) predicts cardiovascular events in a high-risk population undergoing percutaneous coronary intervention (PCI). Impaired platelet responsiveness to clopidogrel is thought to be a determinant of cardiovascular events after PCI. The platelet VASP-FCT is a new assay specific to the P2Y(12) adenosine diphosphate receptor-pathway. In this test, platelet activation is expressed as platelet reactivity index (PRI). Four-hundred sixty-one unselected patients undergoing urgent (n = 346) or planned (n = 115) PCI were prospectively enrolled. Patients were classified as low-response (LR) and response (R) to clopidogrel, depending on their PRI. Optimal PRI cutoff was determined by receiver-operator characteristic curve analysis to 61% (LR: PRI > or =61% and R: PRI <61%). Follow-up was obtained at a mean of 9 +/- 2 months in 453 patients (98.3%). At follow-up, total cardiac mortality rates and possible and total stent thrombosis were higher in LR patients. Multivariate analysis identified creatinine clearance (hazard ratio [HR]: 0.95; 95% confidence interval [CI]: 0.93 to 0.98, p < 0.001), drug-eluting stent (HR: 5.73; 95% CI: 1.40 to 23.43, p = 0.015), C-reactive protein (HR: 1.01; 95% CI: 1.001 to 1.019, p = 0.024), and LR to clopidogrel (HR: 4.00; 95% CI: 1.08 to 14.80, p = 0.037) as independent predictors of cardiac death. The deleterious impact of LR to clopidogrel on cardiovascular death was significantly higher in patients implanted with drug-eluting stent. In patients undergoing PCI, LR to clopidogrel assessed by VASP-FCT is an independent predictor of cardiovascular death at the PRI cutoff value of > or =61%. The LR clinical impact seems to be dependent on the type of stent implanted. Copyright 2010 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

Large-scale 3D simulations of ICF and HEDP targets

NASA Astrophysics Data System (ADS)

Marinak, Michael M.

2000-10-01

The radiation hydrodynamics code HYDRA continues to be developed and applied to 3D simulations of a variety of targets for both inertial confinement fusion (ICF) and high energy density physics. Several packages have been added enabling this code to perform ICF target simulations with similar accuracy as two-dimensional codes of long-time historical use. These include a laser ray trace and deposition package, a heavy ion deposition package, implicit Monte Carlo photonics, and non-LTE opacities, derived from XSN or the linearized response matrix approach.(R. More, T. Kato, Phys. Rev. Lett. 81, 814 (1998), S. Libby, F. Graziani, R. More, T. Kato, Proceedings of the 13th International Conference on Laser Interactions and Related Plasma Phenomena, (AIP, New York, 1997).) LTE opacities can also be calculated for arbitrary mixtures online by combining tabular values generated by different opacity codes. Thermonuclear burn, charged particle transport, neutron energy deposition, electron-ion coupling and conduction, and multigroup radiation diffusion packages are also installed. HYDRA can employ ALE hydrodynamics; a number of grid motion algorithms are available. Multi-material flows are resolved using material interface reconstruction. Results from large-scale simulations run on up to 1680 processors, using a combination of massively parallel processing and symmetric multiprocessing, will be described. A large solid angle simulation of Rayleigh-Taylor instability growth in a NIF ignition capsule has resolved simultaneously the full spectrum of the most dangerous modes that grow from surface roughness. Simulations of a NIF hohlraum illuminated with the initial 96 beam configuration have also been performed. The effect of the hohlraum’s 3D intrinsic drive asymmetry on the capsule implosion will be considered. We will also discuss results from a Nova experiment in which a copper sphere is crushed by a planar shock. Several interacting hydrodynamic instabilities, including the Widnall instability, cause breakup of the resulting vortex ring.

Flight experiment of thermal energy storage

NASA Technical Reports Server (NTRS)

Namkoong, David

1989-01-01

Thermal energy storage (TES) enables a solar dynamic system to deliver constant electric power through periods of sun and shade. Brayton and Stirling power systems under current considerations for missions in the near future require working fluid temperatures in the 1100 to 1300+ K range. TES materials that meet these requirements fall into the fluoride family of salts. These salts store energy as a heat of fusion, thereby transferring heat to the fluid at constant temperature during shade. The principal feature of fluorides that must be taken into account is the change in volume that occurs with melting and freezing. Salts shrink as they solidify, a change reaching 30 percent for some salts. The location of voids that form as result of the shrinkage is critical when the solar dynamic system reemerges into the sun. Hot spots can develop in the TES container or the container can become distorted if the melting salt cannot expand elsewhere. Analysis of the transient, two-phase phenomenon is being incorporated into a three-dimensional computer code. The code is capable of analysis under microgravity as well as 1 g. The objective of the flight program is to verify the predictions of the code, particularly of the void location and its effect on containment temperature. The four experimental packages comprising the program will be the first tests of melting and freezing conducted under microgravity. Each test package will be installed in a Getaway Special container to be carried by the shuttle. The package will be self-contained and independent of shuttle operations other than the initial opening of the container lid and the final closing of the lid. Upon the return of the test package from flight, the TES container will be radiographed and finally partitioned to examine the exact location and shape of the void. Visual inspection of the void and the temperature data during flight will constitute the bases for code verification.

Training and support to improve ICD coding quality: A controlled before-and-after impact evaluation.

PubMed

Dyers, Robin; Ward, Grant; Du Plooy, Shane; Fourie, Stephanus; Evans, Juliet; Mahomed, Hassan

2017-05-24

The proposed National Health Insurance policy for South Africa (SA) requires hospitals to maintain high-quality International Statistical Classification of Diseases (ICD) codes for patient records. While considerable strides had been made to improve ICD coding coverage by digitising the discharge process in the Western Cape Province, further intervention was required to improve data quality. The aim of this controlled before-and-after study was to evaluate the impact of a clinician training and support initiative to improve ICD coding quality. To compare ICD coding quality between two central hospitals in the Western Cape before and after the implementation of a training and support initiative for clinicians at one of the sites. The difference in differences in data quality between the intervention site and the control site was calculated. Multiple logistic regression was also used to determine the odds of data quality improvement after the intervention and to adjust for potential differences between the groups. The intervention had a positive impact of 38.0% on ICD coding completeness over and above changes that occurred at the control site. Relative to the baseline, patient records at the intervention site had a 6.6 (95% confidence interval 3.5 - 16.2) adjusted odds ratio of having a complete set of ICD codes for an admission episode after the introduction of the training and support package. The findings on impact on ICD coding accuracy were not significant. There is sufficient pragmatic evidence that a training and support package will have a considerable positive impact on ICD coding completeness in the SA setting.

Suitability of point kernel dose calculation techniques in brachytherapy treatment planning

PubMed Central

Lakshminarayanan, Thilagam; Subbaiah, K. V.; Thayalan, K.; Kannan, S. E.

2010-01-01

Brachytherapy treatment planning system (TPS) is necessary to estimate the dose to target volume and organ at risk (OAR). TPS is always recommended to account for the effect of tissue, applicator and shielding material heterogeneities exist in applicators. However, most brachytherapy TPS software packages estimate the absorbed dose at a point, taking care of only the contributions of individual sources and the source distribution, neglecting the dose perturbations arising from the applicator design and construction. There are some degrees of uncertainties in dose rate estimations under realistic clinical conditions. In this regard, an attempt is made to explore the suitability of point kernels for brachytherapy dose rate calculations and develop new interactive brachytherapy package, named as BrachyTPS, to suit the clinical conditions. BrachyTPS is an interactive point kernel code package developed to perform independent dose rate calculations by taking into account the effect of these heterogeneities, using two regions build up factors, proposed by Kalos. The primary aim of this study is to validate the developed point kernel code package integrated with treatment planning computational systems against the Monte Carlo (MC) results. In the present work, three brachytherapy applicators commonly used in the treatment of uterine cervical carcinoma, namely (i) Board of Radiation Isotope and Technology (BRIT) low dose rate (LDR) applicator and (ii) Fletcher Green type LDR applicator (iii) Fletcher Williamson high dose rate (HDR) applicator, are studied to test the accuracy of the software. Dose rates computed using the developed code are compared with the relevant results of the MC simulations. Further, attempts are also made to study the dose rate distribution around the commercially available shielded vaginal applicator set (Nucletron). The percentage deviations of BrachyTPS computed dose rate values from the MC results are observed to be within plus/minus 5.5% for BRIT LDR applicator, found to vary from 2.6 to 5.1% for Fletcher green type LDR applicator and are up to −4.7% for Fletcher-Williamson HDR applicator. The isodose distribution plots also show good agreements with the results of previous literatures. The isodose distributions around the shielded vaginal cylinder computed using BrachyTPS code show better agreement (less than two per cent deviation) with MC results in the unshielded region compared to shielded region, where the deviations are observed up to five per cent. The present study implies that the accurate and fast validation of complicated treatment planning calculations is possible with the point kernel code package. PMID:20589118

Technical Review Report for the Model 9978-96 Package Safety Analysis Report for Packaging (S-SARP-G-00002, Revision 1, March 2009)

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

West, M

2009-03-06

This Technical Review Report (TRR) documents the review, performed by Lawrence Livermore National Laboratory (LLNL) Staff, at the request of the Department of Energy (DOE), on the 'Safety Analysis Report for Packaging (SARP), Model 9978 B(M)F-96', Revision 1, March 2009 (S-SARP-G-00002). The Model 9978 Package complies with 10 CFR 71, and with 'Regulations for the Safe Transport of Radioactive Material-1996 Edition (As Amended, 2000)-Safety Requirements', International Atomic Energy Agency (IAEA) Safety Standards Series No. TS-R-1. The Model 9978 Packaging is designed, analyzed, fabricated, and tested in accordance with Section III of the American Society of Mechanical Engineers Boiler and Pressuremore » Vessel Code (ASME B&PVC). The review presented in this TRR was performed using the methods outlined in Revision 3 of the DOE's 'Packaging Review Guide (PRG) for Reviewing Safety Analysis Reports for Packages'. The format of the SARP follows that specified in Revision 2 of the Nuclear Regulatory Commission's Regulatory Guide 7.9, i.e., 'Standard Format and Content of Part 71 Applications for Approval of Packages for Radioactive Material'. Although the two documents are similar in their content, they are not identical. Formatting differences have been noted in this TRR, where appropriate. The Model 9978 Packaging is a single containment package, using a 5-inch containment vessel (5CV). It uses a nominal 35-gallon drum package design. In comparison, the Model 9977 Packaging uses a 6-inch containment vessel (6CV). The Model 9977 and Model 9978 Packagings were developed concurrently, and they were referred to as the General Purpose Fissile Material Package, Version 1 (GPFP). Both packagings use General Plastics FR-3716 polyurethane foam as insulation and as impact limiters. The 5CV is used as the Primary Containment Vessel (PCV) in the Model 9975-96 Packaging. The Model 9975-96 Packaging also has the 6CV as its Secondary Containment Vessel (SCV). In comparison, the Model 9975 Packagings use Celotex{trademark} for insulation and as impact limiters. To provide a historical perspective, it is noted that the Model 9975-96 Packaging is a 35-gallon drum package design that has evolved from a family of packages designed by DOE contractors at the Savannah River Site. Earlier package designs, i.e., the Model 9965, the Model 9966, the Model 9967, and the Model 9968 Packagings, were originally designed and certified in the early 1980s. In the 1990s, updated package designs that incorporated design features consistent with the then-newer safety requirements were proposed. The updated package designs at the time were the Model 9972, the Model 9973, the Model 9974, and the Model 9975 Packagings, respectively. The Model 9975 Package was certified by the Packaging Certification Program, under the Office of Safety Management and Operations. The Model 9978 Package has six Content Envelopes: C.1 ({sup 238}Pu Heat Sources), C.2 ( Pu/U Metals), C.3 (Pu/U Oxides, Reserved), C.4 (U Metal or Alloy), C.5 (U Compounds), and C.6 (Samples and Sources). Per 10 CFR 71.59 (Code of Federal Regulations), the value of N is 50 for the Model 9978 Package leading to a Criticality Safety Index (CSI) of 1.0. The Transport Index (TI), based on dose rate, is calculated to be a maximum of 4.1.« less

Incorporation of coupled nonequilibrium chemistry into a two-dimensional nozzle code (SEAGULL)

NASA Technical Reports Server (NTRS)

Ratliff, A. W.

1979-01-01

A two-dimensional multiple shock nozzle code (SEAGULL) was extended to include the effects of finite rate chemistry. The basic code that treats multiple shocks and contact surfaces was fully coupled with a generalized finite rate chemistry and vibrational energy exchange package. The modified code retains all of the original SEAGULL features plus the capability to treat chemical and vibrational nonequilibrium reactions. Any chemical and/or vibrational energy exchange mechanism can be handled as long as thermodynamic data and rate constants are available for all participating species.

An Examination of the Reliability of the Organizational Assessment Package (OAP).

DTIC Science & Technology

1981-07-01

reactiv- ity or pretest sensitization (Bracht and Glass, 1968) may occur. In this case, the change from pretest to posttest can be caused just by the...content items. The blocks for supervisor’s code were left blank, work group code was coded as all ones , and each person’s seminar number was coded in...63 5 19 .91 .74 5 (Work Group Effective- ness) 822 19 .83 .42 7 17 .90 .57 7 (Job Related Sati sfacti on ) 823 16 .91 .84 2 18 .93 .87 2 (Job Related

ab initio MD simulations of geomaterials with ~1000 atoms

NASA Astrophysics Data System (ADS)

Martin, G. B.; Kirtman, B.; Spera, F. J.

2009-12-01

In the last two decades, ab initio studies of materials using Density Functional Theory (DFT) have increased exponentially in popularity. DFT codes are now used routinely to simulate properties of geomaterials--mainly silicates and geochemically important metals such as Fe. These materials are ubiquitous in the Earth’s mantle and core and in terrestrial exoplanets. Because of computational limitations, most First Principles Molecular Dynamics (FPMD) calculations are done on systems of only ~100 atoms for a few picoseconds. While this approach can be useful for calculating physical quantities related to crystal structure, vibrational frequency, and other lattice-scale properties (especially in crystals), it is statistically marginal for duplicating physical properties of the liquid state like transport and structure. In MD simulations in the NEV ensemble, temperature (T), and pressure (P) fluctuations scale as N-1/2; small particle number (N) systems are therefore characterized by greater statistical state point location uncertainty than large N systems. Previous studies have used codes such as VASP where CPU time increases with N2, making calculations with N much greater than 100 impractical. SIESTA (Soler, et al. 2002) is a DFT code that enables electronic structure and MD computations on larger systems (N~103) by making some approximations, such as localized numerical orbitals, that would be useful in modeling some properties of geomaterials. Here we test the applicability of SIESTA to simulate geosilicates, both hydrous and anhydrous, in the solid and liquid state. We have used SIESTA for lattice calculations of brucite, Mg(OH)2, that compare very well to experiment and calculations using CRYSTAL, another DFT code. Good agreement between more classical DFT calculations and SIESTA is needed to justify study of geosilicates using SIESTA across a range of pressures and temperatures relevant to the Earth’s interior. Thus, it is useful to adjust parameters in SIESTA in accordance with calculations from CRYSTAL as a check on feasibility. Results are reported here that suggest SIESTA may indeed be useful to model silicate liquids at very high T and P.

Child-resistant and tamper-resistant packaging: A systematic review to inform tobacco packaging regulation.

PubMed

Jo, Catherine L; Ambs, Anita; Dresler, Carolyn M; Backinger, Cathy L

2017-02-01

We aimed to investigate the effects of special packaging (child-resistant, adult-friendly) and tamper-resistant packaging on health and behavioral outcomes in order to identify research gaps and implications for packaging standards for tobacco products. We searched seven databases for keywords related to special and tamper-resistant packaging, consulted experts, and reviewed citations of potentially relevant studies. 733 unique papers were identified. Two coders independently screened each title and abstract for eligibility. They then reviewed the full text of the remaining papers for a second round of eligibility screening. Included studies investigated a causal relationship between type of packaging or packaging regulation and behavioral or health outcomes and had a study population composed of consumers. Studies were excluded on the basis of publication type, if they were not peer-reviewed, and if they had low external validity. Two reviewers independently coded each paper for study and methodological characteristics and limitations. Discrepancies were discussed and resolved. The review included eight studies: four assessing people's ability to access the contents of different packaging types and four evaluating the impact of packaging requirements on health-related outcomes. Child-resistant packaging was generally more difficult to open than non-child-resistant packaging. Child-resistant packaging requirements have been associated with reductions in child mortality. Child-resistant packaging holds the expectation to reduce tobacco product poisonings among children under six. Published by Elsevier Inc.

Child-resistant and tamper-resistant packaging: A systematic review to inform tobacco packaging regulation

PubMed Central

Jo, Catherine L.; Ambs, Anita; Dresler, Carolyn M.; Backinger, Cathy L.

2017-01-01

Objective We aimed to investigate the effects of special packaging (child-resistant, adult-friendly) and tamper-resistant packaging on health and behavioral outcomes in order to identify research gaps and implications for packaging standards for tobacco products. Methods We searched seven databases for keywords related to special and tamper-resistant packaging, consulted experts, and reviewed citations of potentially relevant studies. 733 unique papers were identified. Two coders independently screened each title and abstract for eligibility. They then reviewed the full text of the remaining papers for a second round of eligibility screening. Included studies investigated a causal relationship between type of packaging or packaging regulation and behavioral or health outcomes and had a study population composed of consumers. Studies were excluded on the basis of publication type, if they were not peer-reviewed, and if they had low external validity. Two reviewers independently coded each paper for study and methodological characteristics and limitations. Discrepancies were discussed and resolved. Results The review included eight studies: four assessing people’s ability to access the contents of different packaging types and four evaluating the impact of packaging requirements on health-related outcomes. Child-resistant packaging was generally more difficult to open than non-child-resistant packaging. Child-resistant packaging requirements have been associated with reductions in child mortality. Conclusions Child-resistant packaging holds the expectation to reduce tobacco product poisonings among children under six. PMID:27939602

Impact of external influences on food packaging.

PubMed

Brody, A L

1977-09-01

Since the food supply is dependent upon an effective packaging system, threats to packaging represent implied threats to food processing and distribution. Enacted and potential legislation and regulation are retarding technological and commercial progress in food packaging and have already restricted some food packaging/processins systems. The results of these external influences is not simply the sum of the individual acts, but is a cascading self-imposed arresting of food packaging/processing advancement. The technological bases for the enacted and proposed legislation and regulation are presented in the enumeration of the external influences on food packaging. Economic and sociological arguments and facts surrounding the issues are also presented. Among the external influences on food packaging detailed are indirect additives, nutritional labeling, benefit:risk, solid waste and litter, environmental pollution, universal product code, and food industry productivity. The magnitude of the total impact of these external influences upon the food supply is so large that assertive action must be taken to channel these influences into more productive awareness. An objective and comprehensive public communications program supported by the technological community appears mandatory.

Real-Time Pattern Recognition - An Industrial Example

NASA Astrophysics Data System (ADS)

Fitton, Gary M.

1981-11-01

Rapid advancements in cost effective sensors and micro computers are now making practical the on-line implementation of pattern recognition based systems for a variety of industrial applications requiring high processing speeds. One major application area for real time pattern recognition is in the sorting of packaged/cartoned goods at high speed for automated warehousing and return goods cataloging. While there are many OCR and bar code readers available to perform these functions, it is often impractical to use such codes (package too small, adverse esthetics, poor print quality) and an approach which recognizes an item by its graphic content alone is desirable. This paper describes a specific application within the tobacco industry, that of sorting returned cigarette goods by brand and size.

Dakota Uncertainty Quantification Methods Applied to the CFD code Nek5000

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

Delchini, Marc-Olivier; Popov, Emilian L.; Pointer, William David

This report presents the state of advancement of a Nuclear Energy Advanced Modeling and Simulation (NEAMS) project to characterize the uncertainty of the computational fluid dynamics (CFD) code Nek5000 using the Dakota package for flows encountered in the nuclear engineering industry. Nek5000 is a high-order spectral element CFD code developed at Argonne National Laboratory for high-resolution spectral-filtered large eddy simulations (LESs) and unsteady Reynolds-averaged Navier-Stokes (URANS) simulations.

An initial investigation into methods of computing transonic aerodynamic sensitivity coefficients

NASA Technical Reports Server (NTRS)

Carlson, Leland A.

1991-01-01

The three dimensional quasi-analytical sensitivity analysis and the ancillary driver programs are developed needed to carry out the studies and perform comparisons. The code is essentially contained in one unified package which includes the following: (1) a three dimensional transonic wing analysis program (ZEBRA); (2) a quasi-analytical portion which determines the matrix elements in the quasi-analytical equations; (3) a method for computing the sensitivity coefficients from the resulting quasi-analytical equations; (4) a package to determine for comparison purposes sensitivity coefficients via the finite difference approach; and (5) a graphics package.

SHIPMENT OF TWO DOE-STD-3013 CONTAINERS IN A 9977 TYPE B PACKAGE

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

Abramczyk, G.; Bellamy, S.; Loftin, B.

2011-06-06

The 9977 is a certified Type B Packaging authorized to ship uranium and plutonium in metal and oxide forms. Historically, the standard container for these materials has been the DOE-STD-3013 which was specifically designed for the long term storage of plutonium bearing materials. The Department of Energy has used the 9975 Packaging containing a single 3013 container for the transportation and storage of these materials. In order to reduce container, shipping, and storage costs, the 9977 Packaging is being certified for transportation and storage of two 3013 containers. The challenges and risks of this content and the 9977s ability tomore » meet the Code of Federal Regulations for the transport of these materials are presented.« less

A domain specific language for performance portable molecular dynamics algorithms

NASA Astrophysics Data System (ADS)

Saunders, William Robert; Grant, James; Müller, Eike Hermann

2018-03-01

Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be experts both in their own domain (physics/chemistry/biology) and specialists in the low level parallelisation and optimisation of their codes. To address this challenge, we describe a "Separation of Concerns" approach for the development of parallel and optimised MD codes: the science specialist writes code at a high abstraction level in a domain specific language (DSL), which is then translated into efficient computer code by a scientific programmer. In a related context, an abstraction for the solution of partial differential equations with grid based methods has recently been implemented in the (Py)OP2 library. Inspired by this approach, we develop a Python code generation system for molecular dynamics simulations on different parallel architectures, including massively parallel distributed memory systems and GPUs. We demonstrate the efficiency of the auto-generated code by studying its performance and scalability on different hardware and compare it to other state-of-the-art simulation packages. With growing data volumes the extraction of physically meaningful information from the simulation becomes increasingly challenging and requires equally efficient implementations. A particular advantage of our approach is the easy expression of such analysis algorithms. We consider two popular methods for deducing the crystalline structure of a material from the local environment of each atom, show how they can be expressed in our abstraction and implement them in the code generation framework.

MODEL 9977 B(M)F-96 SAFETY ANALYSIS REPORT FOR PACKAGING

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

Abramczyk, G; Paul Blanton, P; Kurt Eberl, K

2006-05-18

This Safety Analysis Report for Packaging (SARP) documents the analysis and testing performed on and for the 9977 Shipping Package, referred to as the General Purpose Fissile Package (GPFP). The performance evaluation presented in this SARP documents the compliance of the 9977 package with the regulatory safety requirements for Type B packages. Per 10 CFR 71.59, for the 9977 packages evaluated in this SARP, the value of ''N'' is 50, and the Transport Index based on nuclear criticality control is 1.0. The 9977 package is designed with a high degree of single containment. The 9977 complies with 10 CFR 71more » (2002), Department of Energy (DOE) Order 460.1B, DOE Order 460.2, and 10 CFR 20 (2003) for As Low As Reasonably Achievable (ALARA) principles. The 9977 also satisfies the requirements of the Regulations for the Safe Transport of Radioactive Material--1996 Edition (Revised)--Requirements. IAEA Safety Standards, Safety Series No. TS-R-1 (ST-1, Rev.), International Atomic Energy Agency, Vienna, Austria (2000). The 9977 package is designed, analyzed and fabricated in accordance with Section III of the American Society of Mechanical Engineers (ASME) Boiler and Pressure Vessel (B&PV) Code, 1992 edition.« less

AELAS: Automatic ELAStic property derivations via high-throughput first-principles computation

NASA Astrophysics Data System (ADS)

Zhang, S. H.; Zhang, R. F.

2017-11-01

The elastic properties are fundamental and important for crystalline materials as they relate to other mechanical properties, various thermodynamic qualities as well as some critical physical properties. However, a complete set of experimentally determined elastic properties is only available for a small subset of known materials, and an automatic scheme for the derivations of elastic properties that is adapted to high-throughput computation is much demanding. In this paper, we present the AELAS code, an automated program for calculating second-order elastic constants of both two-dimensional and three-dimensional single crystal materials with any symmetry, which is designed mainly for high-throughput first-principles computation. Other derivations of general elastic properties such as Young's, bulk and shear moduli as well as Poisson's ratio of polycrystal materials, Pugh ratio, Cauchy pressure, elastic anisotropy and elastic stability criterion, are also implemented in this code. The implementation of the code has been critically validated by a lot of evaluations and tests on a broad class of materials including two-dimensional and three-dimensional materials, providing its efficiency and capability for high-throughput screening of specific materials with targeted mechanical properties. Program Files doi:http://dx.doi.org/10.17632/f8fwg4j9tw.1 Licensing provisions: BSD 3-Clause Programming language: Fortran Nature of problem: To automate the calculations of second-order elastic constants and the derivations of other elastic properties for two-dimensional and three-dimensional materials with any symmetry via high-throughput first-principles computation. Solution method: The space-group number is firstly determined by the SPGLIB code [1] and the structure is then redefined to unit cell with IEEE-format [2]. Secondly, based on the determined space group number, a set of distortion modes is automatically specified and the distorted structure files are generated. Afterwards, the total energy for each distorted structure is calculated by the first-principles codes, e.g. VASP [3]. Finally, the second-order elastic constants are determined from the quadratic coefficients of the polynomial fitting of the energies vs strain relationships and other elastic properties are accordingly derived. References [1] http://atztogo.github.io/spglib/. [2] A. Meitzler, H.F. Tiersten, A.W. Warner, D. Berlincourt, G.A. Couqin, F.S. Welsh III, IEEE standard on piezoelectricity, Society, 1988. [3] G. Kresse, J. Furthmüller, Phys. Rev. B 54 (1996) 11169.

Performance oriented packaging testing of nine Mk 3 Mod 0 signal containers in PPP-B-621 wood box for packing group II solid hazardous materials. Final report

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

Libbert, K.J.

1992-10-01

A PPP-B-621 wood box containing nine Mk 3 Mod 0 Signal containers was tested for conformance to Performance Oriented Packaging criteria established by Code of Federal Regulations Title 49 CFR. The container was tested with a gross weight of 123.3 pounds (56 kilograms) and met all requirements.

Smurf2 Regulates DNA Repair and Packaging to Prevent Tumors | Center for Cancer Research

Cancer.gov

The blueprint for all of a cell’s functions is written in the genetic code of DNA sequences as well as in the landscape of DNA and histone modifications. DNA is wrapped around histones to package it into chromatin, which is stored in the nucleus. It is important to maintain the integrity of the chromatin structure to ensure that the cell continues to behave appropriately.

CPMC-Lab: A MATLAB package for Constrained Path Monte Carlo calculations

NASA Astrophysics Data System (ADS)

Nguyen, Huy; Shi, Hao; Xu, Jie; Zhang, Shiwei

2014-12-01

We describe CPMC-Lab, a MATLAB program for the constrained-path and phaseless auxiliary-field Monte Carlo methods. These methods have allowed applications ranging from the study of strongly correlated models, such as the Hubbard model, to ab initio calculations in molecules and solids. The present package implements the full ground-state constrained-path Monte Carlo (CPMC) method in MATLAB with a graphical interface, using the Hubbard model as an example. The package can perform calculations in finite supercells in any dimensions, under periodic or twist boundary conditions. Importance sampling and all other algorithmic details of a total energy calculation are included and illustrated. This open-source tool allows users to experiment with various model and run parameters and visualize the results. It provides a direct and interactive environment to learn the method and study the code with minimal overhead for setup. Furthermore, the package can be easily generalized for auxiliary-field quantum Monte Carlo (AFQMC) calculations in many other models for correlated electron systems, and can serve as a template for developing a production code for AFQMC total energy calculations in real materials. Several illustrative studies are carried out in one- and two-dimensional lattices on total energy, kinetic energy, potential energy, and charge- and spin-gaps.

Status report on the 'Merging' of the Electron-Cloud Code POSINST with the 3-D Accelerator PIC CODE WARP

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

Vay, J.-L.; Furman, M.A.; Azevedo, A.W.

2004-04-19

We have integrated the electron-cloud code POSINST [1] with WARP [2]--a 3-D parallel Particle-In-Cell accelerator code developed for Heavy Ion Inertial Fusion--so that the two can interoperate. Both codes are run in the same process, communicate through a Python interpreter (already used in WARP), and share certain key arrays (so far, particle positions and velocities). Currently, POSINST provides primary and secondary sources of electrons, beam bunch kicks, a particle mover, and diagnostics. WARP provides the field solvers and diagnostics. Secondary emission routines are provided by the Tech-X package CMEE.

Advanced simulation of mixed-material erosion/evolution and application to low and high-Z containing plasma facing components

NASA Astrophysics Data System (ADS)

Brooks, J. N.; Hassanein, A.; Sizyuk, T.

2013-07-01

Plasma interactions with mixed-material surfaces are being analyzed using advanced modeling of time-dependent surface evolution/erosion. Simulations use the REDEP/WBC erosion/redeposition code package coupled to the HEIGHTS package ITMC-DYN mixed-material formation/response code, with plasma parameter input from codes and data. We report here on analysis for a DIII-D Mo/C containing tokamak divertor. A DIII-D/DiMES probe experiment simulation predicts that sputtered molybdenum from a 1 cm diameter central spot quickly saturates (˜4 s) in the 5 cm diameter surrounding carbon probe surface, with subsequent re-sputtering and transport to off-probe divertor regions, and with high (˜50%) redeposition on the Mo spot. Predicted Mo content in the carbon agrees well with post-exposure probe data. We discuss implications and mixed-material analysis issues for Be/W mixing at the ITER outer divertor, and Li, C, Mo mixing at an NSTX divertor.

Modelling of an Orthovoltage X-ray Therapy Unit with the EGSnrc Monte Carlo Package

NASA Astrophysics Data System (ADS)

Knöös, Tommy; Rosenschöld, Per Munck Af; Wieslander, Elinore

2007-06-01

Simulations with the EGSnrc code package of an orthovoltage x-ray machine have been performed. The BEAMnrc code was used to transport electrons, produce x-ray photons in the target and transport of these through the treatment machine down to the exit level of the applicator. Further transport in water or CT based phantoms was facilitated by the DOSXYZnrc code. Phase space files were scored with BEAMnrc and analysed regarding the energy spectra at the end of the applicator. Tuning of simulation parameters was based on the half-value layer quantity for the beams in either Al or Cu. Calculated depth dose and profile curves have been compared against measurements and show good agreement except at shallow depths. The MC model tested in this study can be used for various dosimetric studies as well as generating a library of typical treatment cases that can serve as both educational material and guidance in the clinical practice

CFD analyses for advanced pump design

NASA Technical Reports Server (NTRS)

Dejong, F. J.; Choi, S.-K.; Govindan, T. R.

1994-01-01

As one of the activities of the NASA/MSFC Pump Stage Technology Team, the present effort was focused on using CFD in the design and analysis of high performance rocket engine pumps. Under this effort, a three-dimensional Navier-Stokes code was used for various inducer and impeller flow field calculations. An existing algebraic grid generation procedure was-extended to allow for nonzero blade thickness, splitter blades, and hub/shroud cavities upstream or downstream of the (main) blades. This resulted in a fast, robust inducer/impeller geometry/grid generation package. Problems associated with running a compressible flow code to simulate an incompressible flow were resolved; related aspects of the numerical algorithm (viz., the matrix preconditioning, the artificial dissipation, and the treatment of low Mach number flows) were addressed. As shown by the calculations performed under the present effort, the resulting code, in conjunction with the grid generation package, is an effective tool for the rapid solution of three-dimensional viscous inducer and impeller flows.

LARC: computer codes for Lagrangian analysis of stress-gauge data to obtain decomposition rates through correlation to thermodynamic variables

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

Anderson, A.B.; Wackerle, J.

1983-07-01

This report describes a package of five computer codes for analyzing stress-gauge data from shock-wave experiments on reactive materials. The aim of the analysis is to obtain rate laws from experiment. A Lagrangian analysis of the stress records, performed by program LANAL, provides flow histories of particle velocity, density, and energy. Three postprocessing programs, LOOKIT, LOOK1, and LOOK2, are included in the package of codes for producing graphical output of the results of LANAL. Program RATE uses the flow histories in conjunction with an equation of state to calculate reaction-rate histories. RATE can be programmed to examine correlations between themore » rate histories and thermodynamic variables. Observed correlations can be incorporated into an appropriately parameterized rate law. Program RATE determines the values of these parameters that best reproduce the observed rate histories. The procedure is illustrated with a sample problem.« less

Analytical Design Package (ADP2): A computer aided engineering tool for aircraft transparency design

NASA Technical Reports Server (NTRS)

Wuerer, J. E.; Gran, M.; Held, T. W.

1994-01-01

The Analytical Design Package (ADP2) is being developed as a part of the Air Force Frameless Transparency Program (FTP). ADP2 is an integrated design tool consisting of existing analysis codes and Computer Aided Engineering (CAE) software. The objective of the ADP2 is to develop and confirm an integrated design methodology for frameless transparencies, related aircraft interfaces, and their corresponding tooling. The application of this methodology will generate high confidence for achieving a qualified part prior to mold fabrication. ADP2 is a customized integration of analysis codes, CAE software, and material databases. The primary CAE integration tool for the ADP2 is P3/PATRAN, a commercial-off-the-shelf (COTS) software tool. The open architecture of P3/PATRAN allows customized installations with different applications modules for specific site requirements. Integration of material databases allows the engineer to select a material, and those material properties are automatically called into the relevant analysis code. The ADP2 materials database will be composed of four independent schemas: CAE Design, Processing, Testing, and Logistics Support. The design of ADP2 places major emphasis on the seamless integration of CAE and analysis modules with a single intuitive graphical interface. This tool is being designed to serve and be used by an entire project team, i.e., analysts, designers, materials experts, and managers. The final version of the software will be delivered to the Air Force in Jan. 1994. The Analytical Design Package (ADP2) will then be ready for transfer to industry. The package will be capable of a wide range of design and manufacturing applications.

Nearly metastable rhombohedral phases of bcc metals

NASA Astrophysics Data System (ADS)

Mehl, Michael J.; Finkenstadt, Daniel

2008-02-01

The energy E(c/a) for a bcc element stretched along its [001] axis (the Bain path) has a minimum at c/a=1 , a maximum at c/a=2 , and an elastically unstable local minimum at c/a>2 . An alternative path connecting the bcc and fcc structures is the rhombohedral lattice. The primitive lattice has R3¯m symmetry, with the angle α changing from 109.4° (bcc), to 90° (simple cubic), to 60 ° (fcc). We study this path for the non-magnetic bcc transition metals (V, Nb, Mo, Ta, and W) using both all-electron linearized augmented plane wave and projector augmented wave VASP codes. Except for Ta, the energy E(α) has a local maximum at α=60° , with local minima near 55° and 70° , the latter having lower energy, suggesting the possibility of a metastable rhombohedral state for these materials. We first examine the elastic stability of the 70° minimum structure, and determine that only W is elastically stable in this structure, with the smallest eigenvalue of the elastic tensor at 4GPa . We then consider the possibility that tungsten is actually metastable in this structure by looking at its vibrational and third-order elastic stability.

Muon simulation codes MUSIC and MUSUN for underground physics

NASA Astrophysics Data System (ADS)

Kudryavtsev, V. A.

2009-03-01

The paper describes two Monte Carlo codes dedicated to muon simulations: MUSIC (MUon SImulation Code) and MUSUN (MUon Simulations UNderground). MUSIC is a package for muon transport through matter. It is particularly useful for propagating muons through large thickness of rock or water, for instance from the surface down to underground/underwater laboratory. MUSUN is designed to use the results of muon transport through rock/water to generate muons in or around underground laboratory taking into account their energy spectrum and angular distribution.

Burner liner thermal-structural load modeling

NASA Technical Reports Server (NTRS)

Maffeo, R.

1986-01-01

The software package Transfer Analysis Code to Interface Thermal/Structural Problems (TRANCITS) was developed. The TRANCITS code is used to interface temperature data between thermal and structural analytical models. The use of this transfer module allows the heat transfer analyst to select the thermal mesh density and thermal analysis code best suited to solve the thermal problem and gives the same freedoms to the stress analyst, without the efficiency penalties associated with common meshes and the accuracy penalties associated with the manual transfer of thermal data.

BCM-2.0 - The new version of computer code ;Basic Channeling with Mathematica©;

NASA Astrophysics Data System (ADS)

Abdrashitov, S. V.; Bogdanov, O. V.; Korotchenko, K. B.; Pivovarov, Yu. L.; Rozhkova, E. I.; Tukhfatullin, T. A.; Eikhorn, Yu. L.

2017-07-01

The new symbolic-numerical code devoted to investigation of the channeling phenomena in periodic potential of a crystal has been developed. The code has been written in Wolfram Language taking advantage of analytical programming method. Newly developed different packages were successfully applied to simulate scattering, radiation, electron-positron pair production and other effects connected with channeling of relativistic particles in aligned crystal. The result of the simulation has been validated against data from channeling experiments carried out at SAGA LS.

SEGY to ASCII: Conversion and Plotting Program

USGS Publications Warehouse

Goldman, Mark R.

1999-01-01

This report documents a computer program to convert standard 4 byte, IBM floating point SEGY files to ASCII xyz format. The program then optionally plots the seismic data using the GMT plotting package. The material for this publication is contained in a standard tar file (of99-126.tar) that is uncompressed and 726 K in size. It can be downloaded by any Unix machine. Move the tar file to the directory you wish to use it in, then type 'tar xvf of99-126.tar' The archive files (and diskette) contain a NOTE file, a README file, a version-history file, source code, a makefile for easy compilation, and an ASCII version of the documentation. The archive files (and diskette) also contain example test files, including a typical SEGY file along with the resulting ASCII xyz and postscript files. Requirements for compiling the source code into an executable are a C++ compiler. The program has been successfully compiled using Gnu's g++ version 2.8.1, and use of other compilers may require modifications to the existing source code. The g++ compiler is a free, high quality C++ compiler and may be downloaded from the ftp site: ftp://ftp.gnu.org/gnu Requirements for plotting the seismic data is the existence of the GMT plotting package. The GMT plotting package may be downloaded from the web site: http://www.soest.hawaii.edu/gmt/

PynPoint code for exoplanet imaging

NASA Astrophysics Data System (ADS)

Amara, A.; Quanz, S. P.; Akeret, J.

2015-04-01

We announce the public release of PynPoint, a Python package that we have developed for analysing exoplanet data taken with the angular differential imaging observing technique. In particular, PynPoint is designed to model the point spread function of the central star and to subtract its flux contribution to reveal nearby faint companion planets. The current version of the package does this correction by using a principal component analysis method to build a basis set for modelling the point spread function of the observations. We demonstrate the performance of the package by reanalysing publicly available data on the exoplanet β Pictoris b, which consists of close to 24,000 individual image frames. We show that PynPoint is able to analyse this typical data in roughly 1.5 min on a Mac Pro, when the number of images is reduced by co-adding in sets of 5. The main computational work, the calculation of the Singular-Value-Decomposition, parallelises well as a result of a reliance on the SciPy and NumPy packages. For this calculation the peak memory load is 6 GB, which can be run comfortably on most workstations. A simpler calculation, by co-adding over 50, takes 3 s with a peak memory usage of 600 MB. This can be performed easily on a laptop. In developing the package we have modularised the code so that we will be able to extend functionality in future releases, through the inclusion of more modules, without it affecting the users application programming interface. We distribute the PynPoint package under GPLv3 licence through the central PyPI server, and the documentation is available online (http://pynpoint.ethz.ch).

Potential Flow Theory and Operation Guide for the Panel Code PMARC. Version 14

NASA Technical Reports Server (NTRS)

Ashby, Dale L.

1999-01-01

The theoretical basis for PMARC, a low-order panel code for modeling complex three-dimensional bodies, in potential flow, is outlined. PMARC can be run on a wide variety of computer platforms, including desktop machines, workstations, and supercomputers. Execution times for PMARC vary tremendously depending on the computer resources used, but typically range from several minutes for simple or moderately complex cases to several hours for very large complex cases. Several of the advanced features currently included in the code, such as internal flow modeling, boundary layer analysis, and time-dependent flow analysis, including problems involving relative motion, are discussed in some detail. The code is written in Fortran77, using adjustable-size arrays so that it can be easily redimensioned to match problem requirements and computer hardware constraints. An overview of the program input is presented. A detailed description of the input parameters is provided in the appendices. PMARC results for several test cases are presented along with analytic or experimental data, where available. The input files for these test cases are given in the appendices. PMARC currently supports plotfile output formats for several commercially available graphics packages. The supported graphics packages are Plot3D, Tecplot, and PmarcViewer.

Modeling of displacement damage in silicon carbide detectors resulting from neutron irradiation

NASA Astrophysics Data System (ADS)

Khorsandi, Behrooz

There is considerable interest in developing a power monitor system for Generation IV reactors (for instance GT-MHR). A new type of semiconductor radiation detector is under development based on silicon carbide (SiC) technology for these reactors. SiC has been selected as the semiconductor material due to its superior thermal-electrical-neutronic properties. Compared to Si, SiC is a radiation hard material; however, like Si, the properties of SiC are changed by irradiation by a large fluence of energetic neutrons, as a consequence of displacement damage, and that irradiation decreases the life-time of detectors. Predictions of displacement damage and the concomitant radiation effects are important for deciding where the SiC detectors should be placed. The purpose of this dissertation is to develop computer simulation methods to estimate the number of various defects created in SiC detectors, because of neutron irradiation, and predict at what positions of a reactor, SiC detectors could monitor the neutron flux with high reliability. The simulation modeling includes several well-known---and commercial---codes (MCNP5, TRIM, MARLOWE and VASP), and two kinetic Monte Carlo codes written by the author (MCASIC and DCRSIC). My dissertation will highlight the displacement damage that may happen in SiC detectors located in available positions in the OSURR, GT-MHR and IRIS. As extra modeling output data, the count rates of SiC for the specified locations are calculated. A conclusion of this thesis is SiC detectors that are placed in the thermal neutron region of a graphite moderator-reflector reactor have a chance to survive at least one reactor refueling cycle, while their count rates are acceptably high.

Models for Amorphous Calcium Carbonate

NASA Astrophysics Data System (ADS)

Sinha, Sourabh

Many species e.g. sea urchin form amorphous calcium carbonate (ACC) precursor phases that subsequently transform into crystalline CaCO3. It is certainly possible that the biogenic ACC might have more than 10 wt% Mg and ˜3 wt% of water. The structure of ACC and the mechanisms by which it transforms to crystalline phase are still poorly understood. In this dissertation our goal is to determine an atomic structure model that is consistent with diffraction and IR measurements of ACC. For this purpose a calcite supercell with 24 formula units, containing 120 atoms, was constructed. Various configurations with substitution of Ca by 6 Mg ions (6 wt.%) and insertion of 3-5 H 2O molecules (2.25-3.75 wt.%) in the interstitial positions of the supercell, were relaxed using a robust density function code VASP. The most noticeable effects were the tilts of CO3 groups and the distortion of Ca sub-lattice, especially in the hydrated case. The distributions of Ca-Ca nearest neighbor distance and CO3 tilts were extracted from various configurations. The same methods were also applied to aragonite. Sampling from the calculated distortion distributions, we built models for amorphous calcite/aragonite of size ˜ 1700 nm3 based on a multi-scale modeling scheme. We used these models to generate diffraction patterns and profiles with our diffraction code. We found that the induced distortions were not enough to generate a diffraction profile typical of an amorphous material. We then studied the diffraction profiles from several nano-crystallites as recent studies suggest that ACC might be a random array of nano-cryatallites. It was found that the generated diffraction profile from a nano-crystallite of size ˜ 2 nm3 is similar to that from the ACC.

Mocking the weak lensing universe: The LensTools Python computing package

NASA Astrophysics Data System (ADS)

Petri, A.

2016-10-01

We present a newly developed software package which implements a wide range of routines frequently used in Weak Gravitational Lensing (WL). With the continuously increasing size of the WL scientific community we feel that easy to use Application Program Interfaces (APIs) for common calculations are a necessity to ensure efficiency and coordination across different working groups. Coupled with existing open source codes, such as CAMB (Lewis et al., 2000) and Gadget2 (Springel, 2005), LensTools brings together a cosmic shear simulation pipeline which, complemented with a variety of WL feature measurement tools and parameter sampling routines, provides easy access to the numerics for theoretical studies of WL as well as for experiment forecasts. Being implemented in PYTHON (Rossum, 1995), LensTools takes full advantage of a range of state-of-the art techniques developed by the large and growing open-source software community (Jones et al., 2001; McKinney, 2010; Astrophy Collaboration, 2013; Pedregosa et al., 2011; Foreman-Mackey et al., 2013). We made the LensTools code available on the Python Package Index and published its documentation on http://lenstools.readthedocs.io.

WinTRAX: A raytracing software package for the design of multipole focusing systems

NASA Astrophysics Data System (ADS)

Grime, G. W.

2013-07-01

The software package TRAX was a simulation tool for modelling the path of charged particles through linear cylindrical multipole fields described by analytical expressions and was a development of the earlier OXRAY program (Grime and Watt, 1983; Grime et al., 1982) [1,2]. In a 2005 comparison of raytracing software packages (Incerti et al., 2005) [3], TRAX/OXRAY was compared with Geant4 and Zgoubi and was found to give close agreement with the more modern codes. TRAX was a text-based program which was only available for operation in a now rare VMS workstation environment, so a new program, WinTRAX, has been developed for the Windows operating system. This implements the same basic computing strategy as TRAX, and key sections of the code are direct translations from FORTRAN to C++, but the Windows environment is exploited to make an intuitive graphical user interface which simplifies and enhances many operations including system definition and storage, optimisation, beam simulation (including with misaligned elements) and aberration coefficient determination. This paper describes the program and presents comparisons with other software and real installations.

Amesos2 and Belos: Direct and Iterative Solvers for Large Sparse Linear Systems

DOE PAGES

Bavier, Eric; Hoemmen, Mark; Rajamanickam, Sivasankaran; ...

2012-01-01

Solvers for large sparse linear systems come in two categories: direct and iterative. Amesos2, a package in the Trilinos software project, provides direct methods, and Belos, another Trilinos package, provides iterative methods. Amesos2 offers a common interface to many different sparse matrix factorization codes, and can handle any implementation of sparse matrices and vectors, via an easy-to-extend C++ traits interface. It can also factor matrices whose entries have arbitrary “Scalar” type, enabling extended-precision and mixed-precision algorithms. Belos includes many different iterative methods for solving large sparse linear systems and least-squares problems. Unlike competing iterative solver libraries, Belos completely decouples themore » algorithms from the implementations of the underlying linear algebra objects. This lets Belos exploit the latest hardware without changes to the code. Belos favors algorithms that solve higher-level problems, such as multiple simultaneous linear systems and sequences of related linear systems, faster than standard algorithms. The package also supports extended-precision and mixed-precision algorithms. Together, Amesos2 and Belos form a complete suite of sparse linear solvers.« less

40 CFR 98.9 - Addresses.

Code of Federal Regulations, 2014 CFR

2014-07-01

.... Director, Climate Change Division, 1200 Pennsylvania Ave., NW., Mail Code: 6207J, Washington, DC 20460. (b) For package deliveries. Director, Climate Change Division, 1310 L St, NW., Washington, DC 20005. [74...

40 CFR 98.9 - Addresses.

Code of Federal Regulations, 2012 CFR

2012-07-01

.... Director, Climate Change Division, 1200 Pennsylvania Ave., NW., Mail Code: 6207J, Washington, DC 20460. (b) For package deliveries. Director, Climate Change Division, 1310 L St, NW., Washington, DC 20005. [74...

40 CFR 98.9 - Addresses.

Code of Federal Regulations, 2013 CFR

2013-07-01

.... Director, Climate Change Division, 1200 Pennsylvania Ave., NW., Mail Code: 6207J, Washington, DC 20460. (b) For package deliveries. Director, Climate Change Division, 1310 L St, NW., Washington, DC 20005. [74...

49 CFR 176.2 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-10-01

..., spillage, or other accident. INF cargo means packaged irradiated nuclear fuel, plutonium or high-level... Irradiated Nuclear Fuel, Plutonium and High-Level Radioactive Wastes on Board Ships” (INF Code) contained in...

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

Lanier, Nicholas Edward

We have completed implementation of a laser package in LANL's principal AGEX design code, Cassio. Although we have greatly improved our target characterization and uncertainty quantification, we remain unable to satisfactorily simulate the NIF Pleiades data.

Turbofan noise generation. Volume 2: Computer programs

NASA Technical Reports Server (NTRS)

Ventres, C. S.; Theobald, M. A.; Mark, W. D.

1982-01-01

The use of a package of computer programs developed to calculate the in duct acoustic mods excited by a fan/stator stage operating at subsonic tip speed is described. The following three noise source mechanisms are included: (1) sound generated by the rotor blades interacting with turbulence ingested into, or generated within, the inlet duct; (2) sound generated by the stator vanes interacting with the turbulent wakes of the rotor blades; and (3) sound generated by the stator vanes interacting with the velocity deficits in the mean wakes of the rotor blades. The computations for three different noise mechanisms are coded as three separate computer program packages. The computer codes are described by means of block diagrams, tables of data and variables, and example program executions; FORTRAN listings are included.

Seismology software: state of the practice

NASA Astrophysics Data System (ADS)

Smith, W. Spencer; Zeng, Zheng; Carette, Jacques

2018-05-01

We analyzed the state of practice for software development in the seismology domain by comparing 30 software packages on four aspects: product, implementation, design, and process. We found room for improvement in most seismology software packages. The principal areas of concern include a lack of adequate requirements and design specification documents, a lack of test data to assess reliability, a lack of examples to get new users started, and a lack of technological tools to assist with managing the development process. To assist going forward, we provide recommendations for a document-driven development process that includes a problem statement, development plan, requirement specification, verification and validation (V&V) plan, design specification, code, V&V report, and a user manual. We also provide advice on tool use, including issue tracking, version control, code documentation, and testing tools.

Numerical Simulation of Doped Targets for ICF

NASA Astrophysics Data System (ADS)

Phillips, Lee; Gardner, John H.; Bodner, Stephen E.; Colombant, Denis; Klapisch, Marcel; Bar-Shalom, Avraham

1997-11-01

The ablative Rayleigh-Taylor (RT) instability can be reduced by preheating the ablator, thereby reducing the peak density and increasing the mass ablation velocity. The ablator can be preheated with radiation from higher Z dopants.(Gardner, J.H., Bodner, S.E., Dahlburg, J.P., Phys. Fluids 3), 1070 (1991) Dopants also reduce the density gradient at the ablator, which provides a second mechanism to reduce the RT growth rate. We have recently developed a more sophisticated and detailed radiation package that uses opacities generated by an STA code, with non-LTE radiation transport based on the Busquet method. This radiation package has been incorporated into NRL's FAST2D radiation hydrodynamics code, which has been used to evaluate and optimize the use of various dopants that can provide interesting levels of preheat for an ICF target.

Turbofan noise generation. Volume 2: Computer programs

NASA Astrophysics Data System (ADS)

Ventres, C. S.; Theobald, M. A.; Mark, W. D.

1982-07-01

The use of a package of computer programs developed to calculate the in duct acoustic mods excited by a fan/stator stage operating at subsonic tip speed is described. The following three noise source mechanisms are included: (1) sound generated by the rotor blades interacting with turbulence ingested into, or generated within, the inlet duct; (2) sound generated by the stator vanes interacting with the turbulent wakes of the rotor blades; and (3) sound generated by the stator vanes interacting with the velocity deficits in the mean wakes of the rotor blades. The computations for three different noise mechanisms are coded as three separate computer program packages. The computer codes are described by means of block diagrams, tables of data and variables, and example program executions; FORTRAN listings are included.

Seismology software: state of the practice

NASA Astrophysics Data System (ADS)

Smith, W. Spencer; Zeng, Zheng; Carette, Jacques

2018-02-01

We analyzed the state of practice for software development in the seismology domain by comparing 30 software packages on four aspects: product, implementation, design, and process. We found room for improvement in most seismology software packages. The principal areas of concern include a lack of adequate requirements and design specification documents, a lack of test data to assess reliability, a lack of examples to get new users started, and a lack of technological tools to assist with managing the development process. To assist going forward, we provide recommendations for a document-driven development process that includes a problem statement, development plan, requirement specification, verification and validation (V&V) plan, design specification, code, V&V report, and a user manual. We also provide advice on tool use, including issue tracking, version control, code documentation, and testing tools.

AstroBlend: Visualization package for use with Blender

NASA Astrophysics Data System (ADS)

Naiman, J. P.

2015-12-01

AstroBlend is a visualization package for use in the three dimensional animation and modeling software, Blender. It reads data in via a text file or can use pre-fab isosurface files stored as OBJ or Wavefront files. AstroBlend supports a variety of codes such as FLASH (ascl:1010.082), Enzo (ascl:1010.072), and Athena (ascl:1010.014), and combines artistic 3D models with computational astrophysics datasets to create models and animations.

Total Ionizing Dose Test Report BFR92A NPN 5 GHz Wide Band Transistor from NXP

NASA Technical Reports Server (NTRS)

Phan, Anthony M.; Oldham, Timothy R.

2011-01-01

The purpose of this test was to characterize the Philips/NXP BFR92A NPN 5 gigahertz wide band silicon transistor for total dose response. This test shall serves as the radiation lot acceptance test (RLAT) for the lot date code (LDC) 1027. The BFR92A is packaged in a 3-pin plastic SOT23 package. Low dose rate (LDR/ELDRS) irradiations was performed.

EUPDF: An Eulerian-Based Monte Carlo Probability Density Function (PDF) Solver. User's Manual

NASA Technical Reports Server (NTRS)

Raju, M. S.

1998-01-01

EUPDF is an Eulerian-based Monte Carlo PDF solver developed for application with sprays, combustion, parallel computing and unstructured grids. It is designed to be massively parallel and could easily be coupled with any existing gas-phase flow and spray solvers. The solver accommodates the use of an unstructured mesh with mixed elements of either triangular, quadrilateral, and/or tetrahedral type. The manual provides the user with the coding required to couple the PDF code to any given flow code and a basic understanding of the EUPDF code structure as well as the models involved in the PDF formulation. The source code of EUPDF will be available with the release of the National Combustion Code (NCC) as a complete package.

Test report dot 7A type a liquid packaging

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

Ketusky, E. T.; Brandjes, C.; Benoit, T. J.

This test report documents the performance of Savannah River National Laboratory’s (SRNL’s) U.S. Department of Transportation (DOT) Specification 7A; General Packaging, Type A shielded liquid shipping packaging and compliance with the regulatory requirements of Title 49 of the Code of Federal Regulations (CFR). The primary use of this packaging design is for the transport of radioactive liquids of up to 1.3 liters in an unshielded configuration and up to 113 mL of radioactive liquids in a shielded configuration, with no more than an A2 quantity in either configuration, over public highways and/or commercial aircraft. The contents are liquid radioactive materialsmore » sufficiently shielded and within the activity limits specified in173.435 or 173.433 for A2 (normal form) materials, as well as within the analyzed thermal heat limits. Any contents must be compatibly packaged and must be compatible with the packaging. The basic packaging design is based on the U.S. Department of Energy’s (DOE’s) Model 9979 Type A fissile shipping packaging designed and tested by SRNL. The shielded liquid configuration consists of the outer and inner drums of the 9979 package with additional low density polyethylene (LDPE) dunnage nesting a tungsten shielded cask assembly (WSCA) within the 30-gallon inner drum. The packaging model for the DOT Specification 7A, Type A liquids packaging is HVYTAL.« less

Powerlaw: a Python package for analysis of heavy-tailed distributions.

PubMed

Alstott, Jeff; Bullmore, Ed; Plenz, Dietmar

2014-01-01

Power laws are theoretically interesting probability distributions that are also frequently used to describe empirical data. In recent years, effective statistical methods for fitting power laws have been developed, but appropriate use of these techniques requires significant programming and statistical insight. In order to greatly decrease the barriers to using good statistical methods for fitting power law distributions, we developed the powerlaw Python package. This software package provides easy commands for basic fitting and statistical analysis of distributions. Notably, it also seeks to support a variety of user needs by being exhaustive in the options available to the user. The source code is publicly available and easily extensible.

Modeling unsaturated zone flow and runoff processes by integrating MODFLOW-LGR and VSF, and creating the new CFL package

USGS Publications Warehouse

Borsia, I.; Rossetto, R.; Schifani, C.; Hill, Mary C.

2013-01-01

In this paper two modifications to the MODFLOW code are presented. One concerns an extension of Local Grid Refinement (LGR) to Variable Saturated Flow process (VSF) capability. This modification allows the user to solve the 3D Richards’ equation only in selected parts of the model domain. The second modification introduces a new package, named CFL (Cascading Flow), which improves the computation of overland flow when ground surface saturation is simulated using either VSF or the Unsaturated Zone Flow (UZF) package. The modeling concepts are presented and demonstrated. Programmer documentation is included in appendices.

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

Lee, Edwin S.

Under the CRADA, NREL will provide assistance to NRGsim to debug and convert the EnergyPlus Hysteresis Phase Change Material ('PCM') model to C++ for adoption into the main code package of the EnergyPlus simulation engine.

Automatic generation of user material subroutines for biomechanical growth analysis.

PubMed

Young, Jonathan M; Yao, Jiang; Ramasubramanian, Ashok; Taber, Larry A; Perucchio, Renato

2010-10-01

The analysis of the biomechanics of growth and remodeling in soft tissues requires the formulation of specialized pseudoelastic constitutive relations. The nonlinear finite element analysis package ABAQUS allows the user to implement such specialized material responses through the coding of a user material subroutine called UMAT. However, hand coding UMAT subroutines is a challenge even for simple pseudoelastic materials and requires substantial time to debug and test the code. To resolve this issue, we develop an automatic UMAT code generation procedure for pseudoelastic materials using the symbolic mathematics package MATHEMATICA and extend the UMAT generator to include continuum growth. The performance of the automatically coded UMAT is tested by simulating the stress-stretch response of a material defined by a Fung-orthotropic strain energy function, subject to uniaxial stretching, equibiaxial stretching, and simple shear in ABAQUS. The MATHEMATICA UMAT generator is then extended to include continuum growth by adding a growth subroutine to the automatically generated UMAT. The MATHEMATICA UMAT generator correctly derives the variables required in the UMAT code, quickly providing a ready-to-use UMAT. In turn, the UMAT accurately simulates the pseudoelastic response. In order to test the growth UMAT, we simulate the growth-based bending of a bilayered bar with differing fiber directions in a nongrowing passive layer. The anisotropic passive layer, being topologically tied to the growing isotropic layer, causes the bending bar to twist laterally. The results of simulations demonstrate the validity of the automatically coded UMAT, used in both standardized tests of hyperelastic materials and for a biomechanical growth analysis.

TU-AB-BRC-12: Optimized Parallel MonteCarlo Dose Calculations for Secondary MU Checks

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

French, S; Nazareth, D; Bellor, M

Purpose: Secondary MU checks are an important tool used during a physics review of a treatment plan. Commercial software packages offer varying degrees of theoretical dose calculation accuracy, depending on the modality involved. Dose calculations of VMAT plans are especially prone to error due to the large approximations involved. Monte Carlo (MC) methods are not commonly used due to their long run times. We investigated two methods to increase the computational efficiency of MC dose simulations with the BEAMnrc code. Distributed computing resources, along with optimized code compilation, will allow for accurate and efficient VMAT dose calculations. Methods: The BEAMnrcmore » package was installed on a high performance computing cluster accessible to our clinic. MATLAB and PYTHON scripts were developed to convert a clinical VMAT DICOM plan into BEAMnrc input files. The BEAMnrc installation was optimized by running the VMAT simulations through profiling tools which indicated the behavior of the constituent routines in the code, e.g. the bremsstrahlung splitting routine, and the specified random number generator. This information aided in determining the most efficient compiling parallel configuration for the specific CPU’s available on our cluster, resulting in the fastest VMAT simulation times. Our method was evaluated with calculations involving 10{sup 8} – 10{sup 9} particle histories which are sufficient to verify patient dose using VMAT. Results: Parallelization allowed the calculation of patient dose on the order of 10 – 15 hours with 100 parallel jobs. Due to the compiler optimization process, further speed increases of 23% were achieved when compared with the open-source compiler BEAMnrc packages. Conclusion: Analysis of the BEAMnrc code allowed us to optimize the compiler configuration for VMAT dose calculations. In future work, the optimized MC code, in conjunction with the parallel processing capabilities of BEAMnrc, will be applied to provide accurate and efficient secondary MU checks.« less

A new software for deformation source optimization, the Bayesian Earthquake Analysis Tool (BEAT)

NASA Astrophysics Data System (ADS)

Vasyura-Bathke, H.; Dutta, R.; Jonsson, S.; Mai, P. M.

2017-12-01

Modern studies of crustal deformation and the related source estimation, including magmatic and tectonic sources, increasingly use non-linear optimization strategies to estimate geometric and/or kinematic source parameters and often consider both jointly, geodetic and seismic data. Bayesian inference is increasingly being used for estimating posterior distributions of deformation source model parameters, given measured/estimated/assumed data and model uncertainties. For instance, some studies consider uncertainties of a layered medium and propagate these into source parameter uncertainties, while others use informative priors to reduce the model parameter space. In addition, innovative sampling algorithms have been developed to efficiently explore the high-dimensional parameter spaces. Compared to earlier studies, these improvements have resulted in overall more robust source model parameter estimates that include uncertainties. However, the computational burden of these methods is high and estimation codes are rarely made available along with the published results. Even if the codes are accessible, it is usually challenging to assemble them into a single optimization framework as they are typically coded in different programing languages. Therefore, further progress and future applications of these methods/codes are hampered, while reproducibility and validation of results has become essentially impossible. In the spirit of providing open-access and modular codes to facilitate progress and reproducible research in deformation source estimations, we undertook the effort of developing BEAT, a python package that comprises all the above-mentioned features in one single programing environment. The package builds on the pyrocko seismological toolbox (www.pyrocko.org), and uses the pymc3 module for Bayesian statistical model fitting. BEAT is an open-source package (https://github.com/hvasbath/beat), and we encourage and solicit contributions to the project. Here, we present our strategy for developing BEAT and show application examples; especially the effect of including the model prediction uncertainty of the velocity model in following source optimizations: full moment tensor, Mogi source, moderate strike-slip earth-quake.

CIF2Cell: Generating geometries for electronic structure programs

NASA Astrophysics Data System (ADS)

Björkman, Torbjörn

2011-05-01

The CIF2Cell program generates the geometrical setup for a number of electronic structure programs based on the crystallographic information in a Crystallographic Information Framework (CIF) file. The program will retrieve the space group number, Wyckoff positions and crystallographic parameters, make a sensible choice for Bravais lattice vectors (primitive or principal cell) and generate all atomic positions. Supercells can be generated and alloys are handled gracefully. The code currently has output interfaces to the electronic structure programs ABINIT, CASTEP, CPMD, Crystal, Elk, Exciting, EMTO, Fleur, RSPt, Siesta and VASP. Program summaryProgram title: CIF2Cell Catalogue identifier: AEIM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU GPL version 3 No. of lines in distributed program, including test data, etc.: 12 691 No. of bytes in distributed program, including test data, etc.: 74 933 Distribution format: tar.gz Programming language: Python (versions 2.4-2.7) Computer: Any computer that can run Python (versions 2.4-2.7) Operating system: Any operating system that can run Python (versions 2.4-2.7) Classification: 7.3, 7.8, 8 External routines: PyCIFRW [1] Nature of problem: Generate the geometrical setup of a crystallographic cell for a variety of electronic structure programs from data contained in a CIF file. Solution method: The CIF file is parsed using routines contained in the library PyCIFRW [1], and crystallographic as well as bibliographic information is extracted. The program then generates the principal cell from symmetry information, crystal parameters, space group number and Wyckoff sites. Reduction to a primitive cell is then performed, and the resulting cell is output to suitably named files along with documentation of the information source generated from any bibliographic information contained in the CIF file. If the space group symmetries is not present in the CIF file the program will fall back on internal tables, so only the minimal input of space group, crystal parameters and Wyckoff positions are required. Additional key features are handling of alloys and supercell generation. Additional comments: Currently implements support for the following general purpose electronic structure programs: ABINIT [2,3], CASTEP [4], CPMD [5], Crystal [6], Elk [7], exciting [8], EMTO [9], Fleur [10], RSPt [11], Siesta [12] and VASP [13-16]. Running time: The examples provided in the distribution take only seconds to run.

Color-coded automated signal intensity curves for detection and characterization of breast lesions: preliminary evaluation of a new software package for integrated magnetic resonance-based breast imaging.

PubMed

Pediconi, Federica; Catalano, Carlo; Venditti, Fiammetta; Ercolani, Mauro; Carotenuto, Luigi; Padula, Simona; Moriconi, Enrica; Roselli, Antonella; Giacomelli, Laura; Kirchin, Miles A; Passariello, Roberto

2005-07-01

The objective of this study was to evaluate the value of a color-coded automated signal intensity curve software package for contrast-enhanced magnetic resonance mammography (CE-MRM) in patients with suspected breast cancer. Thirty-six women with suspected breast cancer based on mammographic and sonographic examinations were preoperatively evaluated on CE-MRM. CE-MRM was performed on a 1.5-T magnet using a 2D Flash dynamic T1-weighted sequence. A dosage of 0.1 mmol/kg of Gd-BOPTA was administered at a flow rate of 2 mL/s followed by 10 mL of saline. Images were analyzed with the new software package and separately with a standard display method. Statistical comparison was performed of the confidence for lesion detection and characterization with the 2 methods and of the diagnostic accuracy for characterization compared with histopathologic findings. At pathology, 54 malignant lesions and 14 benign lesions were evaluated. All 68 (100%) lesions were detected with both methods and good correlation with histopathologic specimens was obtained. Confidence for both detection and characterization was significantly (P < or = 0.025) better with the color-coded method, although no difference (P > 0.05) between the methods was noted in terms of the sensitivity, specificity, and overall accuracy for lesion characterization. Excellent agreement between the 2 methods was noted for both the determination of lesion size (kappa = 0.77) and determination of SI/T curves (kappa = 0.85). The novel color-coded signal intensity curve software allows lesions to be visualized as false color maps that correspond to conventional signal intensity time curves. Detection and characterization of breast lesions with this method is quick and easily interpretable.

Sedimentary rhythms in coastal dunes as a record of intra-annual changes in wind climate (Łeba, Poland)

NASA Astrophysics Data System (ADS)

Ludwig, J.; Lindhorst, S.; Betzler, C.; Bierstedt, S. E.; Borówka, R. K.

2017-08-01

It is shown that coastal dunes bear a so far unread archive of annual wind intensity. Active dunes at the Polish coast near Łeba consist of two genetic units: primary dunes with up to 18 m high eastward-dipping foresets, temporarily superimposed by smaller secondary dunes. Ground-penetrating radar (GPR) data reveal that the foresets of the primary dunes are bundled into alternating packages imaged as either low- or high-amplitude reflections. High-amplitude packages are composed of quartz sand with intercalated heavy-minerals layers. Low-amplitude packages lack these heavy-mineral concentrations. Dune net-progradation is towards the east, reflecting the prevalence of westerly winds. Winds blowing parallel to the dune crest winnow the lee slope, leaving layers enriched in heavy minerals. Sediment transport to the slip face of the dunes is enhanced during the winter months, whereas winnowing predominantly takes place during the spring to autumn months, when the wind field is bi-directional. As a consequence of this seasonal shift, the sedimentary record of one year comprises one low- and one high-amplitude GPR reflection interval. This sedimentary pattern is a persistent feature of the Łeba dunes and recognized to resemble a sedimentary "bar code". To overcome hiatuses in the bar code of individual dunes and dune-to-dune variations in bar-code quality, dendrochronological methods were adopted to compile a composite bar code from several dunes. The resulting data series shows annual variations in west-wind intensity at the southern Baltic coast for the time period 1987 to 2012. Proxy-based wind data are validated against instrumental based weather observations.

Creating Synthetic Coronal Observational Data From MHD Models: The Forward Technique

NASA Technical Reports Server (NTRS)

Rachmeler, Laurel A.; Gibson, Sarah E.; Dove, James; Kucera, Therese Ann

2010-01-01

We present a generalized forward code for creating simulated corona) observables off the limb from numerical and analytical MHD models. This generalized forward model is capable of creating emission maps in various wavelengths for instruments such as SXT, EIT, EIS, and coronagraphs, as well as spectropolari metric images and line profiles. The inputs to our code can be analytic models (of which four come with the code) or 2.5D and 3D numerical datacubes. We present some examples of the observable data created with our code as well as its functional capabilities. This code is currently available for beta-testing (contact authors), with the ultimate goal of release as a SolarSoft package

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

Prasad, M.K.; Kershaw, D.S.; Shaw, M.J.

The authors present detailed features of the ICF3D hydrodynamics code used for inertial fusion simulations. This code is intended to be a state-of-the-art upgrade of the well-known fluid code, LASNEX. ICF3D employs discontinuous finite elements on a discrete unstructured mesh consisting of a variety of 3D polyhedra including tetrahedra, prisms, and hexahedra. The authors discussed details of how the ROE-averaged second-order convection was applied on the discrete elements, and how the C++ coding interface has helped to simplify implementing the many physics and numerics modules within the code package. The author emphasized the virtues of object-oriented design in large scalemore » projects such as ICF3D.« less

Data Parallel Line Relaxation (DPLR) Code User Manual: Acadia - Version 4.01.1

NASA Technical Reports Server (NTRS)

Wright, Michael J.; White, Todd; Mangini, Nancy

2009-01-01

Data-Parallel Line Relaxation (DPLR) code is a computational fluid dynamic (CFD) solver that was developed at NASA Ames Research Center to help mission support teams generate high-value predictive solutions for hypersonic flow field problems. The DPLR Code Package is an MPI-based, parallel, full three-dimensional Navier-Stokes CFD solver with generalized models for finite-rate reaction kinetics, thermal and chemical non-equilibrium, accurate high-temperature transport coefficients, and ionized flow physics incorporated into the code. DPLR also includes a large selection of generalized realistic surface boundary conditions and links to enable loose coupling with external thermal protection system (TPS) material response and shock layer radiation codes.

Packaging Software Assets for Reuse

NASA Astrophysics Data System (ADS)

Mattmann, C. A.; Marshall, J. J.; Downs, R. R.

2010-12-01

The reuse of existing software assets such as code, architecture, libraries, and modules in current software and systems development projects can provide many benefits, including reduced costs, in time and effort, and increased reliability. Many reusable assets are currently available in various online catalogs and repositories, usually broken down by disciplines such as programming language (Ibiblio for Maven/Java developers, PyPI for Python developers, CPAN for Perl developers, etc.). The way these assets are packaged for distribution can play a role in their reuse - an asset that is packaged simply and logically is typically easier to understand, install, and use, thereby increasing its reusability. A well-packaged asset has advantages in being more reusable and thus more likely to provide benefits through its reuse. This presentation will discuss various aspects of software asset packaging and how they can affect the reusability of the assets. The characteristics of well-packaged software will be described. A software packaging domain model will be introduced, and some existing packaging approaches examined. An example case study of a Reuse Enablement System (RES), currently being created by near-term Earth science decadal survey missions, will provide information about the use of the domain model. Awareness of these factors will help software developers package their reusable assets so that they can provide the most benefits for software reuse.

The NJOY Nuclear Data Processing System, Version 2016

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

Macfarlane, Robert; Muir, Douglas W.; Boicourt, R. M.

The NJOY Nuclear Data Processing System, version 2016, is a comprehensive computer code package for producing pointwise and multigroup cross sections and related quantities from evaluated nuclear data in the ENDF-4 through ENDF-6 legacy card-image formats. NJOY works with evaluated files for incident neutrons, photons, and charged particles, producing libraries for a wide variety of particle transport and reactor analysis codes.

SQA of finite element method (FEM) codes used for analyses of pit storage/transport packages

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

Russel, E.

1997-11-01

This report contains viewgraphs on the software quality assurance of finite element method codes used for analyses of pit storage and transport projects. This methodology utilizes the ISO 9000-3: Guideline for application of 9001 to the development, supply, and maintenance of software, for establishing well-defined software engineering processes to consistently maintain high quality management approaches.

Common Ada Missile Packages. Phase 2. (CAMP-2). Volume 2. 11th Missile Demonstration

DTIC Science & Technology

1988-11-01

report describes the work performed, Ihe results obtained, and the conclusions reached during the Common Ada Missile Packages Phase-2 (CAMP-2) contract ... contract was performed between Sep- tember 1985. and March 1988. The MDAC-STL CAMP program manager was: Dr. Daniel G. McNicholl Technology Branch...j DEC Code Management System X X Software Development Files x x Development Status Database x ! X i Smart Cade Counter X j

YAMM - Yet Another Menu Manager

NASA Technical Reports Server (NTRS)

Mazer, Alan S.; Weidner, Richard J.

1991-01-01

Yet Another Menu Manager (YAMM) computer program an application-independent menuing package of software designed to remove much difficulty and save much time inherent in implementation of front ends of large packages of software. Provides complete menuing front end for wide variety of applications, with provisions for independence from specific types of terminals, configurations that meet specific needs of users, and dynamic creation of menu trees. Consists of two parts: description of menu configuration and body of application code. Written in C.

Hypercholesterolemia-induced erectile dysfunction: endothelial nitric oxide synthase (eNOS) uncoupling in the mouse penis by NAD(P)H oxidase

PubMed Central

Musicki, Biljana; Liu, Tongyun; Lagoda, Gwen A.; Strong, Travis D.; Sezen, Sena F.; Johnson, Justin M.; Burnett, Arthur L.

2010-01-01

INTRODUCTION Hypercholesterolemia induces erectile dysfunction (ED) mostly by increasing oxidative stress and impairing endothelial function in the penis, but the mechanisms regulating reactive oxygen species (ROS) production in the penis are not understood. AIMS We evaluated whether hypercholesterolemia activates nicotinamide adenine dinucleotide phosphate (NAD[P]H) oxidase in the penis, providing an initial source of ROS to induce endothelial nitric oxide synthase (eNOS) uncoupling and endothelial dysfunction resulting in ED. METHODS Low-density-lipoprotein receptor (LDLR)–null mice were fed Western diet for 4 weeks to induce early-stage hyperlipidemia. Wild type (WT) mice fed regular chow served as controls. Mice received NAD(P)H oxidase inhibitor apocynin (10 mM in drinking water) or vehicle. Erectile function was assessed in response to cavernous nerve electrical stimulation. Markers of endothelial function (phospho [P]-vasodilator-stimulated-protein [VASP]-Ser-239), oxidative stress (4-hydroxy-2-nonenal [HNE]), sources of ROS (eNOS uncoupling and NAD[P]H oxidase subunits p67phox, p47phox, and gp91phox), P-eNOS-Ser-1177, and eNOS were measured by Western blot in penes. MAIN OUTCOME MEASURES Molecular mechanisms of ROS generation and endothelial dysfunction in hypercholesterolemia-induced ED. RESULTS Erectile response was significantly (P<0.05) reduced in hypercholesterolemic LDLR-null mice compared to WT mice. Relative to WT mice, hypercholesterolemia increased (P<0.05) protein expressions of NAD(P)H oxidase subunits p67phox, p47phox and gp91phox, eNOS uncoupling, and 4-HNE-modified proteins, and reduced (P<0.05) P-VASP-Ser-239 expression in the penis. Apocynin treatment of LDLR-null mice preserved (P<0.05) maximal intracavernosal pressure, and reversed (P < 0.05) the abnormalities in protein expressions of gp67phox and gp47phox, 4-HNE, P-VASP-Ser-239, and eNOS uncoupling in the penis. Apocynin treatment of WT mice did not affect any of these parameters. Protein expressions of P-eNOS-Ser-1177 and total eNOS were unaffected by hypercholesterolemia. CONCLUSION Activated NAD(P)H oxidase in the penis is an initial source of oxidative stress resulting in eNOS uncoupling, thus providing a mechanism of eNOS uncoupling and endothelial dysfunction in hypercholesterolemia-induced ED. PMID:20626609

STEMsalabim: A high-performance computing cluster friendly code for scanning transmission electron microscopy image simulations of thin specimens.

PubMed

Oelerich, Jan Oliver; Duschek, Lennart; Belz, Jürgen; Beyer, Andreas; Baranovskii, Sergei D; Volz, Kerstin

2017-06-01

We present a new multislice code for the computer simulation of scanning transmission electron microscope (STEM) images based on the frozen lattice approximation. Unlike existing software packages, the code is optimized to perform well on highly parallelized computing clusters, combining distributed and shared memory architectures. This enables efficient calculation of large lateral scanning areas of the specimen within the frozen lattice approximation and fine-grained sweeps of parameter space. Copyright © 2017 Elsevier B.V. All rights reserved.

3D-PDR: Three-dimensional photodissociation region code

NASA Astrophysics Data System (ADS)

Bisbas, T. G.; Bell, T. A.; Viti, S.; Yates, J.; Barlow, M. J.

2018-03-01

3D-PDR is a three-dimensional photodissociation region code written in Fortran. It uses the Sundials package (written in C) to solve the set of ordinary differential equations and it is the successor of the one-dimensional PDR code UCL_PDR (ascl:1303.004). Using the HEALpix ray-tracing scheme (ascl:1107.018), 3D-PDR solves a three-dimensional escape probability routine and evaluates the attenuation of the far-ultraviolet radiation in the PDR and the propagation of FIR/submm emission lines out of the PDR. The code is parallelized (OpenMP) and can be applied to 1D and 3D problems.

Custodial Management in the Information Age.

ERIC Educational Resources Information Center

Harris, Jim, Sr.

1999-01-01

Explains how computerizing the custodial department can be achieved through bar coding, hand-held readers, and the appropriate software packages. Software programs that aid cleaning management, track assets, and manage stock are discussed. (GR)

21 CFR 129.80 - Processes and controls.

Code of Federal Regulations, 2010 CFR

2010-04-01

... determine whether any of the coliform organisms are E. coli. (2) For chemical, physical, and radiological... bactericidal action to that required in paragraph (d)(3) of this section. (e) Unit package production code...

21 CFR 129.80 - Processes and controls.

Code of Federal Regulations, 2011 CFR

2011-04-01

... determine whether any of the coliform organisms are E. coli. (2) For chemical, physical, and radiological... bactericidal action to that required in paragraph (d)(3) of this section. (e) Unit package production code...

PyMC: Bayesian Stochastic Modelling in Python

PubMed Central

Patil, Anand; Huard, David; Fonnesbeck, Christopher J.

2010-01-01

This user guide describes a Python package, PyMC, that allows users to efficiently code a probabilistic model and draw samples from its posterior distribution using Markov chain Monte Carlo techniques. PMID:21603108

Lessons learned from an Ada conversion project

NASA Technical Reports Server (NTRS)

Porter, Tim

1988-01-01

Background; SAVVAS architecture; software portability; history of Ada; isolation of non-portable code; simple terminal interface package; constraints of language features; and virtual interfaces are outlined. This presentation is represented by viewgraphs only.

DFTBaby: A software package for non-adiabatic molecular dynamics simulations based on long-range corrected tight-binding TD-DFT(B)

NASA Astrophysics Data System (ADS)

Humeniuk, Alexander; Mitrić, Roland

2017-12-01

A software package, called DFTBaby, is published, which provides the electronic structure needed for running non-adiabatic molecular dynamics simulations at the level of tight-binding DFT. A long-range correction is incorporated to avoid spurious charge transfer states. Excited state energies, their analytic gradients and scalar non-adiabatic couplings are computed using tight-binding TD-DFT. These quantities are fed into a molecular dynamics code, which integrates Newton's equations of motion for the nuclei together with the electronic Schrödinger equation. Non-adiabatic effects are included by surface hopping. As an example, the program is applied to the optimization of excited states and non-adiabatic dynamics of polyfluorene. The python and Fortran source code is available at http://www.dftbaby.chemie.uni-wuerzburg.de.

PAREMD: A parallel program for the evaluation of momentum space properties of atoms and molecules

NASA Astrophysics Data System (ADS)

Meena, Deep Raj; Gadre, Shridhar R.; Balanarayan, P.

2018-03-01

The present work describes a code for evaluating the electron momentum density (EMD), its moments and the associated Shannon information entropy for a multi-electron molecular system. The code works specifically for electronic wave functions obtained from traditional electronic structure packages such as GAMESS and GAUSSIAN. For the momentum space orbitals, the general expression for Gaussian basis sets in position space is analytically Fourier transformed to momentum space Gaussian basis functions. The molecular orbital coefficients of the wave function are taken as an input from the output file of the electronic structure calculation. The analytic expressions of EMD are evaluated over a fine grid and the accuracy of the code is verified by a normalization check and a numerical kinetic energy evaluation which is compared with the analytic kinetic energy given by the electronic structure package. Apart from electron momentum density, electron density in position space has also been integrated into this package. The program is written in C++ and is executed through a Shell script. It is also tuned for multicore machines with shared memory through OpenMP. The program has been tested for a variety of molecules and correlated methods such as CISD, Møller-Plesset second order (MP2) theory and density functional methods. For correlated methods, the PAREMD program uses natural spin orbitals as an input. The program has been benchmarked for a variety of Gaussian basis sets for different molecules showing a linear speedup on a parallel architecture.

RNAi knockdown of the focal adhesion protein TES reveals its role in actin stress fibre organisation.

PubMed

Griffith, Elen; Coutts, Amanda S; Black, Donald M

2005-03-01

TES was originally identified as a candidate tumour suppressor gene and has subsequently been found to encode a novel focal adhesion protein. As well as localising to cell-matrix adhesions, TES localises to cell-cell contacts and to actin stress fibres. TES interacts with a variety of cytoskeletal proteins including zyxin, mena, VASP, talin and actin. There is evidence that TES may function in actin-dependent processes as overexpression of TES results in increased cell spreading and decreased cell motility. Together with TES's interacting partners, these data suggest that TES might be involved in regulation of the actin cytoskeleton. Here, for the first time, we have used RNAi to successfully knockdown TES in HeLa cells and we demonstrate that loss of TES from focal adhesions results in loss of actin stress fibres. Similarly, and as previously reported, RNAi-mediated knockdown of zyxin results in loss of actin stress fibres. TES siRNA treated cells show reduced RhoA activity, suggesting that the Rho GTPase pathway may be involved in the TES RNAi-induced loss of stress fibres. We have also used RNAi to examine the requirement of TES and zyxin for each other's localisation at focal adhesions, and we propose a hierarchy of recruitment, with zyxin being first, followed by VASP and then TES. Cell Motil. Copyright 2005 Wiley-Liss, Inc.

Extracellular superoxide dismutase is necessary to maintain renal blood flow during sepsis development.

PubMed

Constantino, Larissa; Galant, Letícia Selinger; Vuolo, Francieli; Guarido, Karla Lorena; Kist, Luiza Wilges; de Oliveira, Giovanna Medeiros Tavares; Pasquali, Matheus Augusto de Bittencourt; de Souza, Cláudio Teodoro; da Silva-Santos, José Eduardo; Bogo, Maurício Reis; Moreira, José Cláudio Fonseca; Ritter, Cristiane; Dal-Pizzol, Felipe

2017-12-01

Extracellular superoxide dismutase (ECSOD) protects nitric oxide (NO) bioavailability by decreasing superoxide levels and preventing peroxynitrite generation, which is important in maintaining renal blood flow and in preventing acute kidney injury. However, the profile of ECSOD expression after sepsis is not fully understood. Therefore, we intended to evaluate the content and gene expression of superoxide dismutase (SOD) isoforms in the renal artery and their relation to renal blood flow. Sepsis was induced in Wistar rats by caecal ligation and perforation. Several times after sepsis induction, renal blood flow (12, 24 and 48 h); the renal arterial content of SOD isoforms, nitrotyrosine, endothelial and inducible nitric oxide synthase (e-NOS and i-NOS), and phosphorylated vasodilator-stimulated phosphoprotein (pVASP); and SOD activity (3, 6 and 12 h) were measured. The influence of a SOD inhibitor was also evaluated. An increase in ECSOD content was associated with decreased 3-nitrotyrosine levels. These events were associated with an increase in pVASP content and maintenance of renal blood flow. Moreover, previous treatment with a SOD inhibitor increased nitrotyrosine content and reduced renal blood flow. ECSOD appears to have a major role in decreasing peroxynitrite formation in the renal artery during the early stages of sepsis development, and its application can be important in renal blood flow control and maintenance during septic insult.

Solid state perovskite solar modules by vacuum-vapor assisted sequential deposition on Nd:YVO₄ laser patterned rutile TiO₂ nanorods.

PubMed

Fakharuddin, Azhar; Palma, Alessandro L; Di Giacomo, Francesco; Casaluci, Simone; Matteocci, Fabio; Wali, Qamar; Rauf, Muhammad; Di Carlo, Aldo; Brown, Thomas M; Jose, Rajan

2015-12-11

The past few years have witnessed remarkable progress in solution-processed methylammonium lead halide (CH3NH3PbX3, X = halide) perovskite solar cells (PSCs) with reported photoconversion efficiency (η) exceeding 20% in laboratory-scale devices and reaching up to 13% in their large area perovskite solar modules (PSMs). These devices mostly employ mesoporous TiO2 nanoparticles (NPs) as an electron transport layer (ETL) which provides a scaffold on which the perovskite semiconductor can grow. However, limitations exist which are due to trap-limited electron transport and non-complete pore filling. Herein, we have employed TiO2 nanorods (NRs), a material offering a two-fold higher electronic mobility and higher pore-filing compared to their particle analogues, as an ETL. A crucial issue in NRs' patterning over substrates is resolved by using precise Nd:YVO4 laser ablation, and a champion device with η ∼ 8.1% is reported via a simple and low cost vacuum-vapor assisted sequential processing (V-VASP) of a CH3NH3PbI3 film. Our experiments showed a successful demonstration of NRs-based PSMs via the V-VASP technique which can be applied to fabricate large area modules with a pin-hole free, smooth and dense perovskite layer which is required to build high efficiency devices.

Mass decomposition of galaxies using DECA software package

NASA Astrophysics Data System (ADS)

Mosenkov, A. V.

2014-01-01

The new DECA software package, which is designed to perform photometric analysis of the images of disk and elliptical galaxies having a regular structure, is presented. DECA is written in Python interpreted language and combines the capabilities of several widely used packages for astronomical data processing such as IRAF, SExtractor, and the GALFIT code used to perform two-dimensional decomposition of galaxy images into several photometric components (bulge+disk). DECA has the advantage that it can be applied to large samples of galaxies with different orientations with respect to the line of sight (including edge-on galaxies) and requires minimum human intervention. Examples of using the package to study a sample of simulated galaxy images and a sample of real objects are shown to demonstrate that DECA can be a reliable tool for the study of the structure of galaxies.

Schroedinger’s code: Source code availability and transparency in astrophysics

NASA Astrophysics Data System (ADS)

Ryan, PW; Allen, Alice; Teuben, Peter

2018-01-01

Astronomers use software for their research, but how many of the codes they use are available as source code? We examined a sample of 166 papers from 2015 for clearly identified software use, then searched for source code for the software packages mentioned in these research papers. We categorized the software to indicate whether source code is available for download and whether there are restrictions to accessing it, and if source code was not available, whether some other form of the software, such as a binary, was. Over 40% of the source code for the software used in our sample was not available for download.As URLs have often been used as proxy citations for software, we also extracted URLs from one journal’s 2015 research articles, removed those from certain long-term, reliable domains, and tested the remainder to determine what percentage of these URLs were still accessible in September and October, 2017.

Study of SOL in DIII-D tokamak with SOLPS suite of codes.

NASA Astrophysics Data System (ADS)

Pankin, Alexei; Bateman, Glenn; Brennan, Dylan; Coster, David; Hogan, John; Kritz, Arnold; Kukushkin, Andrey; Schnack, Dalton; Snyder, Phil

2005-10-01

The scrape-of-layer (SOL) region in DIII-D tokamak is studied with the SOLPS integrated suite of codes. The SOLPS package includes the 3D multi-species Monte-Carlo neutral code EIRINE and 2D multi-fluid code B2. The EIRINE and B2 codes are cross-coupled through B2-EIRINE interface. The results of SOLPS simulations are used in the integrated modeling of the plasma edge in DIII-D tokamak with the ASTRA transport code. Parameterized dependences for neutral particle fluxes that are computed with the SOLPS code are implemented in a model for the H-mode pedestal and ELMs [1] in the ASTRA code. The effects of neutrals on the H-mode pedestal and ELMs are studied in this report. [1] A. Y. Pankin, I. Voitsekhovitch, G. Bateman, et al., Plasma Phys. Control. Fusion 47, 483 (2005).

Scoria: a Python module for manipulating 3D molecular data.

PubMed

Ropp, Patrick; Friedman, Aaron; Durrant, Jacob D

2017-09-18

Third-party packages have transformed the Python programming language into a powerful computational-biology tool. Package installation is easy for experienced users, but novices sometimes struggle with dependencies and compilers. This presents a barrier that can hinder the otherwise broad adoption of new tools. We present Scoria, a Python package for manipulating three-dimensional molecular data. Unlike similar packages, Scoria requires no dependencies, compilation, or system-wide installation. One can incorporate the Scoria source code directly into their own programs. But Scoria is not designed to compete with other similar packages. Rather, it complements them. Our package leverages others (e.g. NumPy, SciPy), if present, to speed and extend its own functionality. To show its utility, we use Scoria to analyze a molecular dynamics trajectory. Our FootPrint script colors the atoms of one chain by the frequency of their contacts with a second chain. We are hopeful that Scoria will be a useful tool for the computational-biology community. A copy is available for download free of charge (Apache License 2.0) at http://durrantlab.com/scoria/ . Graphical abstract .

Simulation of nonlinear propagation of biomedical ultrasound using pzflex and the Khokhlov-Zabolotskaya-Kuznetsov Texas code

PubMed Central

Qiao, Shan; Jackson, Edward; Coussios, Constantin C.; Cleveland, Robin O.

2016-01-01

Nonlinear acoustics plays an important role in both diagnostic and therapeutic applications of biomedical ultrasound and a number of research and commercial software packages are available. In this manuscript, predictions of two solvers available in a commercial software package, pzflex, one using the finite-element-method (FEM) and the other a pseudo-spectral method, spectralflex, are compared with measurements and the Khokhlov-Zabolotskaya-Kuznetsov (KZK) Texas code (a finite-difference time-domain algorithm). The pzflex methods solve the continuity equation, momentum equation and equation of state where they account for nonlinearity to second order whereas the KZK code solves a nonlinear wave equation with a paraxial approximation for diffraction. Measurements of the field from a single element 3.3 MHz focused transducer were compared with the simulations and there was good agreement for the fundamental frequency and the harmonics; however the FEM pzflex solver incurred a high computational cost to achieve equivalent accuracy. In addition, pzflex results exhibited non-physical oscillations in the spatial distribution of harmonics when the amplitudes were relatively low. It was found that spectralflex was able to accurately capture the nonlinear fields at reasonable computational cost. These results emphasize the need to benchmark nonlinear simulations before using codes as predictive tools. PMID:27914432

Simulation of nonlinear propagation of biomedical ultrasound using pzflex and the Khokhlov-Zabolotskaya-Kuznetsov Texas code.

PubMed

Qiao, Shan; Jackson, Edward; Coussios, Constantin C; Cleveland, Robin O

2016-09-01

Nonlinear acoustics plays an important role in both diagnostic and therapeutic applications of biomedical ultrasound and a number of research and commercial software packages are available. In this manuscript, predictions of two solvers available in a commercial software package, pzflex, one using the finite-element-method (FEM) and the other a pseudo-spectral method, spectralflex, are compared with measurements and the Khokhlov-Zabolotskaya-Kuznetsov (KZK) Texas code (a finite-difference time-domain algorithm). The pzflex methods solve the continuity equation, momentum equation and equation of state where they account for nonlinearity to second order whereas the KZK code solves a nonlinear wave equation with a paraxial approximation for diffraction. Measurements of the field from a single element 3.3 MHz focused transducer were compared with the simulations and there was good agreement for the fundamental frequency and the harmonics; however the FEM pzflex solver incurred a high computational cost to achieve equivalent accuracy. In addition, pzflex results exhibited non-physical oscillations in the spatial distribution of harmonics when the amplitudes were relatively low. It was found that spectralflex was able to accurately capture the nonlinear fields at reasonable computational cost. These results emphasize the need to benchmark nonlinear simulations before using codes as predictive tools.

WannierTools: An open-source software package for novel topological materials

NASA Astrophysics Data System (ADS)

Wu, QuanSheng; Zhang, ShengNan; Song, Hai-Feng; Troyer, Matthias; Soluyanov, Alexey A.

2018-03-01

We present an open-source software package WannierTools, a tool for investigation of novel topological materials. This code works in the tight-binding framework, which can be generated by another software package Wannier90 (Mostofi et al., 2008). It can help to classify the topological phase of a given material by calculating the Wilson loop, and can get the surface state spectrum, which is detected by angle resolved photoemission (ARPES) and in scanning tunneling microscopy (STM) experiments. It also identifies positions of Weyl/Dirac points and nodal line structures, calculates the Berry phase around a closed momentum loop and Berry curvature in a part of the Brillouin zone (BZ).

Morse Monte Carlo Radiation Transport Code System

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

Emmett, M.B.

1975-02-01

The report contains sections containing descriptions of the MORSE and PICTURE codes, input descriptions, sample problems, deviations of the physical equations and explanations of the various error messages. The MORSE code is a multipurpose neutron and gamma-ray transport Monte Carlo code. Time dependence for both shielding and criticality problems is provided. General three-dimensional geometry may be used with an albedo option available at any material surface. The PICTURE code provide aid in preparing correct input data for the combinatorial geometry package CG. It provides a printed view of arbitrary two-dimensional slices through the geometry. By inspecting these pictures one maymore » determine if the geometry specified by the input cards is indeed the desired geometry. 23 refs. (WRF)« less

Coded Modulation in C and MATLAB

NASA Technical Reports Server (NTRS)

Hamkins, Jon; Andrews, Kenneth S.

2011-01-01

This software, written separately in C and MATLAB as stand-alone packages with equivalent functionality, implements encoders and decoders for a set of nine error-correcting codes and modulators and demodulators for five modulation types. The software can be used as a single program to simulate the performance of such coded modulation. The error-correcting codes implemented are the nine accumulate repeat-4 jagged accumulate (AR4JA) low-density parity-check (LDPC) codes, which have been approved for international standardization by the Consultative Committee for Space Data Systems, and which are scheduled to fly on a series of NASA missions in the Constellation Program. The software implements the encoder and decoder functions, and contains compressed versions of generator and parity-check matrices used in these operations.

Program Package for 3d PIC Model of Plasma Fiber

NASA Astrophysics Data System (ADS)

Kulhánek, Petr; Břeň, David

2007-08-01

A fully three dimensional Particle in Cell model of the plasma fiber had been developed. The code is written in FORTRAN 95, implementation CVF (Compaq Visual Fortran) under Microsoft Visual Studio user interface. Five particle solvers and two field solvers are included in the model. The solvers have relativistic and non-relativistic variants. The model can deal both with periodical and non-periodical boundary conditions. The mechanism of the surface turbulences generation in the plasma fiber was successfully simulated with the PIC program package.

A Tutorial on RxODE: Simulating Differential Equation Pharmacometric Models in R.

PubMed

Wang, W; Hallow, K M; James, D A

2016-01-01

This tutorial presents the application of an R package, RxODE, that facilitates quick, efficient simulations of ordinary differential equation models completely within R. Its application is illustrated through simulation of design decision effects on an adaptive dosing regimen. The package provides an efficient, versatile way to specify dosing scenarios and to perform simulation with variability with minimal custom coding. Models can be directly translated to Rshiny applications to facilitate interactive, real-time evaluation/iteration on simulation scenarios.

Influence of Interpretation Aids on Attentional Capture, Visual Processing, and Understanding of Front-of-Package Nutrition Labels.

PubMed

Antúnez, Lucía; Giménez, Ana; Maiche, Alejandro; Ares, Gastón

2015-01-01

To study the influence of 2 interpretational aids of front-of-package (FOP) nutrition labels (color code and text descriptors) on attentional capture and consumers' understanding of nutritional information. A full factorial design was used to assess the influence of color code and text descriptors using visual search and eye tracking. Ten trained assessors participated in the visual search study and 54 consumers completed the eye-tracking study. In the visual search study, assessors were asked to indicate whether there was a label high in fat within sets of mayonnaise labels with different FOP labels. In the eye-tracking study, assessors answered a set of questions about the nutritional content of labels. The researchers used logistic regression to evaluate the influence of interpretational aids of FOP nutrition labels on the percentage of correct answers. Analyses of variance were used to evaluate the influence of the studied variables on attentional measures and participants' response times. Response times were significantly higher for monochromatic FOP labels compared with color-coded ones (3,225 vs 964 ms; P < .001), which suggests that color codes increase attentional capture. The highest number and duration of fixations and visits were recorded on labels that did not include color codes or text descriptors (P < .05). The lowest percentage of incorrect answers was observed when the nutrient level was indicated using color code and text descriptors (P < .05). The combination of color codes and text descriptors seems to be the most effective alternative to increase attentional capture and understanding of nutritional information. Copyright © 2015 Society for Nutrition Education and Behavior. Published by Elsevier Inc. All rights reserved.

spMC: an R-package for 3D lithological reconstructions based on spatial Markov chains

NASA Astrophysics Data System (ADS)

Sartore, Luca; Fabbri, Paolo; Gaetan, Carlo

2016-09-01

The paper presents the spatial Markov Chains (spMC) R-package and a case study of subsoil simulation/prediction located in a plain site of Northeastern Italy. spMC is a quite complete collection of advanced methods for data inspection, besides spMC implements Markov Chain models to estimate experimental transition probabilities of categorical lithological data. Furthermore, simulation methods based on most known prediction methods (as indicator Kriging and CoKriging) were implemented in spMC package. Moreover, other more advanced methods are available for simulations, e.g. path methods and Bayesian procedures, that exploit the maximum entropy. Since the spMC package was developed for intensive geostatistical computations, part of the code is implemented for parallel computations via the OpenMP constructs. A final analysis of this computational efficiency compares the simulation/prediction algorithms by using different numbers of CPU cores, and considering the example data set of the case study included in the package.

PAT-1 safety analysis report addendum.

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

Weiner, Ruth F.; Schmale, David T.; Kalan, Robert J.

2010-09-01

The Plutonium Air Transportable Package, Model PAT-1, is certified under Title 10, Code of Federal Regulations Part 71 by the U.S. Nuclear Regulatory Commission (NRC) per Certificate of Compliance (CoC) USA/0361B(U)F-96 (currently Revision 9). The purpose of this SAR Addendum is to incorporate plutonium (Pu) metal as a new payload for the PAT-1 package. The Pu metal is packed in an inner container (designated the T-Ampoule) that replaces the PC-1 inner container. The documentation and results from analysis contained in this addendum demonstrate that the replacement of the PC-1 and associated packaging material with the T-Ampoule and associated packaging withmore » the addition of the plutonium metal content are not significant with respect to the design, operating characteristics, or safe performance of the containment system and prevention of criticality when the package is subjected to the tests specified in 10 CFR 71.71, 71.73 and 71.74.« less

Evolution of a modular software network

PubMed Central

Fortuna, Miguel A.; Bonachela, Juan A.; Levin, Simon A.

2011-01-01

“Evolution behaves like a tinkerer” (François Jacob, Science, 1977). Software systems provide a singular opportunity to understand biological processes using concepts from network theory. The Debian GNU/Linux operating system allows us to explore the evolution of a complex network in a unique way. The modular design detected during its growth is based on the reuse of existing code in order to minimize costs during programming. The increase of modularity experienced by the system over time has not counterbalanced the increase in incompatibilities between software packages within modules. This negative effect is far from being a failure of design. A random process of package installation shows that the higher the modularity, the larger the fraction of packages working properly in a local computer. The decrease in the relative number of conflicts between packages from different modules avoids a failure in the functionality of one package spreading throughout the entire system. Some potential analogies with the evolutionary and ecological processes determining the structure of ecological networks of interacting species are discussed. PMID:22106260

49 CFR 178.910 - Marking of Large Packagings.

Code of Federal Regulations, 2014 CFR

2014-10-01

... stamped or embossed, the capital letters “UN” may be applied instead of the symbol; (ii) The code number...) The country authorizing the allocation of the mark. The letters “USA” indicate that the Large...

49 CFR 178.910 - Marking of Large Packagings.

Code of Federal Regulations, 2013 CFR

2013-10-01

... stamped or embossed, the capital letters “UN” may be applied instead of the symbol; (ii) The code number...) The country authorizing the allocation of the mark. The letters “USA” indicate that the Large...

lpNet: a linear programming approach to reconstruct signal transduction networks.

PubMed

Matos, Marta R A; Knapp, Bettina; Kaderali, Lars

2015-10-01

With the widespread availability of high-throughput experimental technologies it has become possible to study hundreds to thousands of cellular factors simultaneously, such as coding- or non-coding mRNA or protein concentrations. Still, extracting information about the underlying regulatory or signaling interactions from these data remains a difficult challenge. We present a flexible approach towards network inference based on linear programming. Our method reconstructs the interactions of factors from a combination of perturbation/non-perturbation and steady-state/time-series data. We show both on simulated and real data that our methods are able to reconstruct the underlying networks fast and efficiently, thus shedding new light on biological processes and, in particular, into disease's mechanisms of action. We have implemented the approach as an R package available through bioconductor. This R package is freely available under the Gnu Public License (GPL-3) from bioconductor.org (http://bioconductor.org/packages/release/bioc/html/lpNet.html) and is compatible with most operating systems (Windows, Linux, Mac OS) and hardware architectures. bettina.knapp@helmholtz-muenchen.de 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.

Bar code, good for industry and trade--how does it benefit the dentist?

PubMed

Oehlmann, H

2001-10-01

Every dentist who attentively follows the change in product labelling can easily see that the HIBC bar code is on the increase. In fact, according to information from FIDE/VDDI and ADE/BVD, the dental industry and trade are firmly resolved to apply the HIBC bar code to all products used internationally in dental practices. Why? Indeed, at first it looks like extra expense to additionally print a bar code on the packages. Good reasons can only lie in advantages which manufacturers and the trade expect from the HIBC bar code, Indications in dental technician circles are that the HIBC bar code is coming. If there are advantages, what are these, and can the dentist also profit from them? What does HIBC bar code mean and what items of interest does it include? What does bar code cost and does only one code exist? This is explained briefly, concentrating on the benefits bar code can bring for different users.

An insight into the dopant selection for CeO2-based resistive-switching memory system: a DFT and experimental study

NASA Astrophysics Data System (ADS)

Hussain, Fayyaz; Imran, Muhammad; Rana, Anwar Manzoor; Khalil, R. M. Arif; Khera, Ejaz Ahmad; Kiran, Saira; Javid, M. Arshad; Sattar, M. Atif; Ismail, Muhammad

2018-03-01

The aim of this study is to figure out better metal dopants for CeO2 for designing highly efficient non-volatile memory (NVM) devices. The present DFT work involves four different metals doped interstitially and substitutionally in CeO2 thin films. First principle calculations involve electron density of states (DOS) and partial density of states (PDOS), and isosurface charge densities are carried out within the plane-wave density functional theory using GGA and GGA + U approach by employing the Vienna ab initio simulation package VASP. Isosurface charge density plots confirmed that interstitial doping of Zr and Ti metals truly assists in generating conduction filaments (CFs), while substitutional doping of these metals cannot do so. Substitutional doping of W may contribute in generating CFs in CeO2 directly, but its interstitial doping improves conductivity of CeO2. However, Ni-dopant is capable of directly generating CFs both as substitutional and interstitial dopants in ceria. Such a capability of Ni appears acting as top electrode in Ni/CeO2/Pt memory devices, but its RS behavior is not so good. On inserting Zr layer to make Ni/Zr:CeO2/Pt memory stacks, Ni does not contribute in RS characteristics, but Zr plays a vital role in forming CFs by creating oxygen vacancies and forming ZrO2 interfacial layer. Therefore, Zr-doped devices exhibit high-resistance ratio of 104 and good endurance as compared to undoped devices suitable for RRAM applications.

First-principles study on silicon atom doped monolayer graphene

NASA Astrophysics Data System (ADS)

Rafique, Muhammad; Shuai, Yong; Hussain, Nayyar

2018-01-01

This paper illustrates the structural, electronic and optical properties of individual silicon (Si) atom-doped single layer graphene using density functional theory method. Si atom forms tight bonding with graphene layer. The effect of doping has been investigated by varying the concentration of Si atoms from 3.125% to 9.37% (i.e. From one to three Si atoms in 4 × 4 pure graphene supercell containing 32 carbon atoms), respectively. Electronic structure, partial density of states (PDOS) and optical properties of pure and Si atom-doped graphene sheet were calculated using VASP (Vienna ab-initio Simulation Package). The calculated results for pure graphene sheet were then compared with Si atom doped graphene. It is revealed that upon Si doping in graphene, a finite band gap appears at the high symmetric K-point, thereby making graphene a direct band gap semiconductor. Moreover, the band gap value is directly proportional to the concentration of impurity Si atoms present in graphene lattice. Upon analyzing the optical properties of Si atom-doped graphene structures, it is found that, there is significant change in the refractive index of the graphene after Si atom substitution in graphene. In addition, the overall absorption spectrum of graphene is decreased after Si atom doping. Although a significant red shift in absorption is found to occur towards visible range of radiation when Si atom is substituted in its lattice. The reflectivity of graphene improves in low energy region after Si atom substitution in graphene. These results can be useful for tuning the electronic structure and to manipulate the optical properties of graphene layer in the visible region.

HydroApps: An R package for statistical simulation to use in regional analysis

NASA Astrophysics Data System (ADS)

Ganora, D.

2013-12-01

The HydroApps package is a newborn R extension initially developed to support the use of a recent model for flood frequency estimation developed for applications in Northwestern Italy; it also contains some general tools for regional analyses and can be easily extended to include other statistical models. The package is currently at an experimental level of development. The HydroApps is a corollary of the SSEM project for regional flood frequency analysis, although it was developed independently to support various instances of regional analyses. Its aim is to provide a basis for interplay between statistical simulation and practical operational use. In particular, the main module of the package deals with the building of the confidence bands of flood frequency curves expressed by means of their L-moments. Other functions include pre-processing and visualization of hydrologic time series, analysis of the optimal design-flood under uncertainty, but also tools useful in water resources management for the estimation of flow duration curves and their sensitivity to water withdrawals. Particular attention is devoted to the code granularity, i.e. the level of detail and aggregation of the code: a greater detail means more low-level functions, which entails more flexibility but reduces the ease of use for practical use. A balance between detail and simplicity is necessary and can be resolved with appropriate wrapping functions and specific help pages for each working block. From a more general viewpoint, the package has not really and user-friendly interface, but runs on multiple operating systems and it's easy to update, as many other open-source projects., The HydroApps functions and their features are reported in order to share ideas and materials to improve the ';technological' and information transfer between scientist communities and final users like policy makers.

QuantWorm: a comprehensive software package for Caenorhabditis elegans phenotypic assays.

PubMed

Jung, Sang-Kyu; Aleman-Meza, Boanerges; Riepe, Celeste; Zhong, Weiwei

2014-01-01

Phenotypic assays are crucial in genetics; however, traditional methods that rely on human observation are unsuitable for quantitative, large-scale experiments. Furthermore, there is an increasing need for comprehensive analyses of multiple phenotypes to provide multidimensional information. Here we developed an automated, high-throughput computer imaging system for quantifying multiple Caenorhabditis elegans phenotypes. Our imaging system is composed of a microscope equipped with a digital camera and a motorized stage connected to a computer running the QuantWorm software package. Currently, the software package contains one data acquisition module and four image analysis programs: WormLifespan, WormLocomotion, WormLength, and WormEgg. The data acquisition module collects images and videos. The WormLifespan software counts the number of moving worms by using two time-lapse images; the WormLocomotion software computes the velocity of moving worms; the WormLength software measures worm body size; and the WormEgg software counts the number of eggs. To evaluate the performance of our software, we compared the results of our software with manual measurements. We then demonstrated the application of the QuantWorm software in a drug assay and a genetic assay. Overall, the QuantWorm software provided accurate measurements at a high speed. Software source code, executable programs, and sample images are available at www.quantworm.org. Our software package has several advantages over current imaging systems for C. elegans. It is an all-in-one package for quantifying multiple phenotypes. The QuantWorm software is written in Java and its source code is freely available, so it does not require use of commercial software or libraries. It can be run on multiple platforms and easily customized to cope with new methods and requirements.

Infrastructure for Multiphysics Software Integration in High Performance Computing-Aided Science and Engineering

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

Campbell, Michael T.; Safdari, Masoud; Kress, Jessica E.

The project described in this report constructed and exercised an innovative multiphysics coupling toolkit called the Illinois Rocstar MultiPhysics Application Coupling Toolkit (IMPACT). IMPACT is an open source, flexible, natively parallel infrastructure for coupling multiple uniphysics simulation codes into multiphysics computational systems. IMPACT works with codes written in several high-performance-computing (HPC) programming languages, and is designed from the beginning for HPC multiphysics code development. It is designed to be minimally invasive to the individual physics codes being integrated, and has few requirements on those physics codes for integration. The goal of IMPACT is to provide the support needed to enablemore » coupling existing tools together in unique and innovative ways to produce powerful new multiphysics technologies without extensive modification and rewrite of the physics packages being integrated. There are three major outcomes from this project: 1) construction, testing, application, and open-source release of the IMPACT infrastructure, 2) production of example open-source multiphysics tools using IMPACT, and 3) identification and engagement of interested organizations in the tools and applications resulting from the project. This last outcome represents the incipient development of a user community and application echosystem being built using IMPACT. Multiphysics coupling standardization can only come from organizations working together to define needs and processes that span the space of necessary multiphysics outcomes, which Illinois Rocstar plans to continue driving toward. The IMPACT system, including source code, documentation, and test problems are all now available through the public gitHUB.org system to anyone interested in multiphysics code coupling. Many of the basic documents explaining use and architecture of IMPACT are also attached as appendices to this document. Online HTML documentation is available through the gitHUB site. There are over 100 unit tests provided that run through the Illinois Rocstar Application Development (IRAD) lightweight testing infrastructure that is also supplied along with IMPACT. The package as a whole provides an excellent base for developing high-quality multiphysics applications using modern software development practices. To facilitate understanding how to utilize IMPACT effectively, two multiphysics systems have been developed and are available open-source through gitHUB. The simpler of the two systems, named ElmerFoamFSI in the repository, is a multiphysics, fluid-structure-interaction (FSI) coupling of the solid mechanics package Elmer with a fluid dynamics module from OpenFOAM. This coupling illustrates how to combine software packages that are unrelated by either author or architecture and combine them into a robust, parallel multiphysics system. A more complex multiphysics tool is the Illinois Rocstar Rocstar Multiphysics code that was rebuilt during the project around IMPACT. Rocstar Multiphysics was already an HPC multiphysics tool, but now that it has been rearchitected around IMPACT, it can be readily expanded to capture new and different physics in the future. In fact, during this project, the Elmer and OpenFOAM tools were also coupled into Rocstar Multiphysics and demonstrated. The full Rocstar Multiphysics codebase is also available on gitHUB, and licensed for any organization to use as they wish. Finally, the new IMPACT product is already being used in several multiphysics code coupling projects for the Air Force, NASA and the Missile Defense Agency, and initial work on expansion of the IMPACT-enabled Rocstar Multiphysics has begun in support of a commercial company. These initiatives promise to expand the interest and reach of IMPACT and Rocstar Multiphysics, ultimately leading to the envisioned standardization and consortium of users that was one of the goals of this project.« less

Graphene symmetry-breaking with molecular adsorbates: modeling and experiment

NASA Astrophysics Data System (ADS)

Groce, M. A.; Hawkins, M. K.; Wang, Y. L.; Cullen, W. G.; Einstein, T. L.

2012-02-01

Graphene's structure and electronic properties provide a framework for understanding molecule-substrate interactions and developing techniques for band gap engineering. Controlled deposition of molecular adsorbates can create superlattices which break the degeneracy of graphene's two-atom unit cell, opening a band gap. We simulate scanning tunneling microscopy and spectroscopy measurements for a variety of organic molecule/graphene systems, including pyridine, trimesic acid, and isonicotinic acid, based on density functional theory calculations using VASP. We also compare our simulations to ultra-high vacuum STM and STS results.

Magnetic Tape Recording for the Eighties

NASA Technical Reports Server (NTRS)

Kalil, Ford (Editor)

1982-01-01

The practical and theoretical aspects of state-of-the-art magnetic tape recording technology are reviewed. Topics covered include the following: (1) analog and digital magnetic tape recording, (2) tape and head wear, (3) wear testing, (4) magnetic tape certification, (5) care, handling, and management of magnetic tape, (6) cleaning, packing, and winding of magnetic tape, (7) tape reels, bands, and packaging, (8) coding techniques for high-density digital recording, and (9) tradeoffs of coding techniques.

40 CFR 98.9 - Addresses.

Code of Federal Regulations, 2011 CFR

2011-07-01

... submitted to the following address: (a) For U.S. mail. Director, Climate Change Division, 1200 Pennsylvania Ave., NW., Mail Code: 6207J, Washington, DC 20460. (b) For package deliveries. Director, Climate Change Division, 1310 L St, NW., Washington, DC 20005. ...

Multifunction audio digitizer for communications systems

NASA Technical Reports Server (NTRS)

Monford, L. G., Jr.

1971-01-01

Digitizer accomplishes both N bit pulse code modulation /PCM/ and delta modulation, and provides modulation indicating variable signal gain and variable sidetone. Other features include - low package count, variable clock rate to optimize bandwidth, and easily expanded PCM output.

40 CFR 98.9 - Addresses.

Code of Federal Regulations, 2010 CFR

2010-07-01

... submitted to the following address: (a) For U.S. mail. Director, Climate Change Division, 1200 Pennsylvania Ave., NW., Mail Code: 6207J, Washington, DC 20460. (b) For package deliveries. Director, Climate Change Division, 1310 L St, NW., Washington, DC 20005. ...

Full 3D visualization tool-kit for Monte Carlo and deterministic transport codes

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

Frambati, S.; Frignani, M.

2012-07-01

We propose a package of tools capable of translating the geometric inputs and outputs of many Monte Carlo and deterministic radiation transport codes into open source file formats. These tools are aimed at bridging the gap between trusted, widely-used radiation analysis codes and very powerful, more recent and commonly used visualization software, thus supporting the design process and helping with shielding optimization. Three main lines of development were followed: mesh-based analysis of Monte Carlo codes, mesh-based analysis of deterministic codes and Monte Carlo surface meshing. The developed kit is considered a powerful and cost-effective tool in the computer-aided design formore » radiation transport code users of the nuclear world, and in particular in the fields of core design and radiation analysis. (authors)« less

Integrated Composite Analyzer (ICAN): Users and programmers manual

NASA Technical Reports Server (NTRS)

Murthy, P. L. N.; Chamis, C. C.

1986-01-01

The use of and relevant equations programmed in a computer code designed to carry out a comprehensive linear analysis of multilayered fiber composites is described. The analysis contains the essential features required to effectively design structural components made from fiber composites. The inputs to the code are constituent material properties, factors reflecting the fabrication process, and composite geometry. The code performs micromechanics, macromechanics, and laminate analysis, including the hygrothermal response of fiber composites. The code outputs are the various ply and composite properties, composite structural response, and composite stress analysis results with details on failure. The code is in Fortran IV and can be used efficiently as a package in complex structural analysis programs. The input-output format is described extensively through the use of a sample problem. The program listing is also included. The code manual consists of two parts.

Packaging printed circuit boards: A production application of interactive graphics

NASA Technical Reports Server (NTRS)

Perrill, W. A.

1975-01-01

The structure and use of an Interactive Graphics Packaging Program (IGPP), conceived to apply computer graphics to the design of packaging electronic circuits onto printed circuit boards (PCB), were described. The intent was to combine the data storage and manipulative power of the computer with the imaginative, intuitive power of a human designer. The hardware includes a CDC 6400 computer and two CDC 777 terminals with CRT screens, light pens, and keyboards. The program is written in FORTRAN 4 extended with the exception of a few functions coded in COMPASS (assembly language). The IGPP performs four major functions for the designer: (1) data input and display, (2) component placement (automatic or manual), (3) conductor path routing (automatic or manual), and (4) data output. The most complex PCB packaged to date measured 16.5 cm by 19 cm and contained 380 components, two layers of ground planes and four layers of conductors mixed with ground planes.

Structural testing of the Los Alamos National Laboratory Heat Source/Radioisotopic Thermoelectric Generator shipping container

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

Bronowski, D.R.; Madsen, M.M.

The Heat Source/Radioisotopic Thermoelectric Generator shipping container is a Type B packaging design currently under development by Los Alamos National Laboratory. Type B packaging for transporting radioactive material is required to maintain containment and shielding after being exposed to the normal and hypothetical accident environments defined in Title 10 Code of Federal Regulations Part 71. A combination of testing and analysis is used to verify the adequacy of this package design. This report documents the test program portion of the design verification, using several prototype packages. Four types of testing were performed: 30-foot hypothetical accident condition drop tests in threemore » orientations, 40-inch hypothetical accident condition puncture tests in five orientations, a 21 psi external overpressure test, and a normal conditions of transport test consisting of a water spray and a 4 foot drop test. 18 refs., 104 figs., 13 tabs.« less

Spin wave Feynman diagram vertex computation package

NASA Astrophysics Data System (ADS)

Price, Alexander; Javernick, Philip; Datta, Trinanjan

Spin wave theory is a well-established theoretical technique that can correctly predict the physical behavior of ordered magnetic states. However, computing the effects of an interacting spin wave theory incorporating magnons involve a laborious by hand derivation of Feynman diagram vertices. The process is tedious and time consuming. Hence, to improve productivity and have another means to check the analytical calculations, we have devised a Feynman Diagram Vertex Computation package. In this talk, we will describe our research group's effort to implement a Mathematica based symbolic Feynman diagram vertex computation package that computes spin wave vertices. Utilizing the non-commutative algebra package NCAlgebra as an add-on to Mathematica, symbolic expressions for the Feynman diagram vertices of a Heisenberg quantum antiferromagnet are obtained. Our existing code reproduces the well-known expressions of a nearest neighbor square lattice Heisenberg model. We also discuss the case of a triangular lattice Heisenberg model where non collinear terms contribute to the vertex interactions.

chimeraviz: a tool for visualizing chimeric RNA.

PubMed

Lågstad, Stian; Zhao, Sen; Hoff, Andreas M; Johannessen, Bjarne; Lingjærde, Ole Christian; Skotheim, Rolf I

2017-09-15

Advances in high-throughput RNA sequencing have enabled more efficient detection of fusion transcripts, but the technology and associated software used for fusion detection from sequencing data often yield a high false discovery rate. Good prioritization of the results is important, and this can be helped by a visualization framework that automatically integrates RNA data with known genomic features. Here we present chimeraviz , a Bioconductor package that automates the creation of chimeric RNA visualizations. The package supports input from nine different fusion-finder tools: deFuse, EricScript, InFusion, JAFFA, FusionCatcher, FusionMap, PRADA, SOAPfuse and STAR-FUSION. chimeraviz is an R package available via Bioconductor ( https://bioconductor.org/packages/release/bioc/html/chimeraviz.html ) under Artistic-2.0. Source code and support is available at GitHub ( https://github.com/stianlagstad/chimeraviz ). rolf.i.skotheim@rr-research.no. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Software design for analysis of multichannel intracardial and body surface electrocardiograms.

PubMed

Potse, Mark; Linnenbank, André C; Grimbergen, Cornelis A

2002-11-01

Analysis of multichannel ECG recordings (body surface maps (BSMs) and intracardial maps) requires special software. We created a software package and a user interface on top of a commercial data analysis package (MATLAB) by a combination of high-level and low-level programming. Our software was created to satisfy the needs of a diverse group of researchers. It can handle a large variety of recording configurations. It allows for interactive usage through a fast and robust user interface, and batch processing for the analysis of large amounts of data. The package is user-extensible, includes routines for both common and experimental data processing tasks, and works on several computer platforms. The source code is made intelligible using software for structured documentation and is available to the users. The package is currently used by more than ten research groups analysing ECG data worldwide.

regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests.

PubMed

Gel, Bernat; Díez-Villanueva, Anna; Serra, Eduard; Buschbeck, Marcus; Peinado, Miguel A; Malinverni, Roberto

2016-01-15

Statistically assessing the relation between a set of genomic regions and other genomic features is a common challenging task in genomic and epigenomic analyses. Randomization based approaches implicitly take into account the complexity of the genome without the need of assuming an underlying statistical model. regioneR is an R package that implements a permutation test framework specifically designed to work with genomic regions. In addition to the predefined randomization and evaluation strategies, regioneR is fully customizable allowing the use of custom strategies to adapt it to specific questions. Finally, it also implements a novel function to evaluate the local specificity of the detected association. regioneR is an R package released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor (http://www.bioconductor.org/packages/regioneR). rmalinverni@carrerasresearch.org. © The Author 2015. Published by Oxford University Press.

Semi-automated Anatomical Labeling and Inter-subject Warping of High-Density Intracranial Recording Electrodes in Electrocorticography.

PubMed

Hamilton, Liberty S; Chang, David L; Lee, Morgan B; Chang, Edward F

2017-01-01

In this article, we introduce img_pipe, our open source python package for preprocessing of imaging data for use in intracranial electrocorticography (ECoG) and intracranial stereo-EEG analyses. The process of electrode localization, labeling, and warping for use in ECoG currently varies widely across laboratories, and it is usually performed with custom, lab-specific code. This python package aims to provide a standardized interface for these procedures, as well as code to plot and display results on 3D cortical surface meshes. It gives the user an easy interface to create anatomically labeled electrodes that can also be warped to an atlas brain, starting with only a preoperative T1 MRI scan and a postoperative CT scan. We describe the full capabilities of our imaging pipeline and present a step-by-step protocol for users.

Programming with BIG data in R: Scaling analytics from one to thousands of nodes

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

Schmidt, Drew; Chen, Wei -Chen; Matheson, Michael A.

Here, we present a tutorial overview showing how one can achieve scalable performance with R. We do so by utilizing several package extensions, including those from the pbdR project. These packages consist of high performance, high-level interfaces to and extensions of MPI, PBLAS, ScaLAPACK, I/O libraries, profiling libraries, and more. While these libraries shine brightest on large distributed platforms, they also work rather well on small clusters and often, surprisingly, even on a laptop with only two cores. Our tutorial begins with recommendations on how to get more performance out of your R code before considering parallel implementations. Because Rmore » is a high-level language, a function can have a deep hierarchy of operations. For big data, this can easily lead to inefficiency. Profiling is an important tool to understand the performance of an R code for both serial and parallel improvements.« less

A Shifted Block Lanczos Algorithm 1: The Block Recurrence

NASA Technical Reports Server (NTRS)

Grimes, Roger G.; Lewis, John G.; Simon, Horst D.

1990-01-01

In this paper we describe a block Lanczos algorithm that is used as the key building block of a software package for the extraction of eigenvalues and eigenvectors of large sparse symmetric generalized eigenproblems. The software package comprises: a version of the block Lanczos algorithm specialized for spectrally transformed eigenproblems; an adaptive strategy for choosing shifts, and efficient codes for factoring large sparse symmetric indefinite matrices. This paper describes the algorithmic details of our block Lanczos recurrence. This uses a novel combination of block generalizations of several features that have only been investigated independently in the past. In particular new forms of partial reorthogonalization, selective reorthogonalization and local reorthogonalization are used, as is a new algorithm for obtaining the M-orthogonal factorization of a matrix. The heuristic shifting strategy, the integration with sparse linear equation solvers and numerical experience with the code are described in a companion paper.

Coronal Magnetism and Forward Solarsoft Idl Package

NASA Astrophysics Data System (ADS)

Gibson, S. E.

2014-12-01

The FORWARD suite of Solar Soft IDL codes is a community resource for model-data comparison, with a particular emphasis on analyzing coronal magnetic fields. FORWARD may be used both to synthesize a broad range of coronal observables, and to access and compare to existing data. FORWARD works with numerical model datacubes, interfaces with the web-served Predictive Science Inc MAS simulation datacubes and the Solar Soft IDL Potential Field Source Surface (PFSS) package, and also includes several analytic models (more can be added). It connects to the Virtual Solar Observatory and other web-served observations to download data in a format directly comparable to model predictions. It utilizes the CHIANTI database in modeling UV/EUV lines, and links to the CLE polarimetry synthesis code for forbidden coronal lines. FORWARD enables "forward-fitting" of specific observations, and helps to build intuition into how the physical properties of coronal magnetic structures translate to observable properties.

Semi-automated Anatomical Labeling and Inter-subject Warping of High-Density Intracranial Recording Electrodes in Electrocorticography

PubMed Central

Hamilton, Liberty S.; Chang, David L.; Lee, Morgan B.; Chang, Edward F.

2017-01-01

In this article, we introduce img_pipe, our open source python package for preprocessing of imaging data for use in intracranial electrocorticography (ECoG) and intracranial stereo-EEG analyses. The process of electrode localization, labeling, and warping for use in ECoG currently varies widely across laboratories, and it is usually performed with custom, lab-specific code. This python package aims to provide a standardized interface for these procedures, as well as code to plot and display results on 3D cortical surface meshes. It gives the user an easy interface to create anatomically labeled electrodes that can also be warped to an atlas brain, starting with only a preoperative T1 MRI scan and a postoperative CT scan. We describe the full capabilities of our imaging pipeline and present a step-by-step protocol for users. PMID:29163118

Programming with BIG data in R: Scaling analytics from one to thousands of nodes

DOE PAGES

Schmidt, Drew; Chen, Wei -Chen; Matheson, Michael A.; ...

2016-11-09

Here, we present a tutorial overview showing how one can achieve scalable performance with R. We do so by utilizing several package extensions, including those from the pbdR project. These packages consist of high performance, high-level interfaces to and extensions of MPI, PBLAS, ScaLAPACK, I/O libraries, profiling libraries, and more. While these libraries shine brightest on large distributed platforms, they also work rather well on small clusters and often, surprisingly, even on a laptop with only two cores. Our tutorial begins with recommendations on how to get more performance out of your R code before considering parallel implementations. Because Rmore » is a high-level language, a function can have a deep hierarchy of operations. For big data, this can easily lead to inefficiency. Profiling is an important tool to understand the performance of an R code for both serial and parallel improvements.« less

Qualification of Simulation Software for Safety Assessment of Sodium Cooled Fast Reactors. Requirements and Recommendations

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

Brown, Nicholas R.; Pointer, William David; Sieger, Matt

2016-04-01

The goal of this review is to enable application of codes or software packages for safety assessment of advanced sodium-cooled fast reactor (SFR) designs. To address near-term programmatic needs, the authors have focused on two objectives. First, the authors have focused on identification of requirements for software QA that must be satisfied to enable the application of software to future safety analyses. Second, the authors have collected best practices applied by other code development teams to minimize cost and time of initial code qualification activities and to recommend a path to the stated goal.

Kranc: a Mathematica package to generate numerical codes for tensorial evolution equations

NASA Astrophysics Data System (ADS)

Husa, Sascha; Hinder, Ian; Lechner, Christiane

2006-06-01

We present a suite of Mathematica-based computer-algebra packages, termed "Kranc", which comprise a toolbox to convert certain (tensorial) systems of partial differential evolution equations to parallelized C or Fortran code for solving initial boundary value problems. Kranc can be used as a "rapid prototyping" system for physicists or mathematicians handling very complicated systems of partial differential equations, but through integration into the Cactus computational toolkit we can also produce efficient parallelized production codes. Our work is motivated by the field of numerical relativity, where Kranc is used as a research tool by the authors. In this paper we describe the design and implementation of both the Mathematica packages and the resulting code, we discuss some example applications, and provide results on the performance of an example numerical code for the Einstein equations. Program summaryTitle of program: Kranc Catalogue identifier: ADXS_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXS_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Distribution format: tar.gz Computer for which the program is designed and others on which it has been tested: General computers which run Mathematica (for code generation) and Cactus (for numerical simulations), tested under Linux Programming language used: Mathematica, C, Fortran 90 Memory required to execute with typical data: This depends on the number of variables and gridsize, the included ADM example requires 4308 KB Has the code been vectorized or parallelized: The code is parallelized based on the Cactus framework. Number of bytes in distributed program, including test data, etc.: 1 578 142 Number of lines in distributed program, including test data, etc.: 11 711 Nature of physical problem: Solution of partial differential equations in three space dimensions, which are formulated as an initial value problem. In particular, the program is geared towards handling very complex tensorial equations as they appear, e.g., in numerical relativity. The worked out examples comprise the Klein-Gordon equations, the Maxwell equations, and the ADM formulation of the Einstein equations. Method of solution: The method of numerical solution is finite differencing and method of lines time integration, the numerical code is generated through a high level Mathematica interface. Restrictions on the complexity of the program: Typical numerical relativity applications will contain up to several dozen evolution variables and thousands of source terms, Cactus applications have shown scaling up to several thousand processors and grid sizes exceeding 500 3. Typical running time: This depends on the number of variables and the grid size: the included ADM example takes approximately 100 seconds on a 1600 MHz Intel Pentium M processor. Unusual features of the program: based on Mathematica and Cactus

PCP METHODOLOGY FOR DETERMINING DOSE RATES FOR SMALL GRAM QUANTITIES IN SHIPPING PACKAGINGS

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

Nathan, S.

The Small Gram Quantity (SGQ) concept is based on the understanding that small amounts of hazardous materials, in this case radioactive materials, are significantly less hazardous than large amounts of the same materials. This study describes a methodology designed to estimate an SGQ for several neutron and gamma emitting isotopes that can be shipped in a package compliant with 10 CFR Part 71 external radiation level limits regulations. These regulations require packaging for the shipment of radioactive materials perform, under both normal and accident conditions, the essential functions of material containment, subcriticality, and maintain external radiation levels within regulatory limits.more » 10 CFR 71.33(b)(1)(2)&(3) state radioactive and fissile materials must be identified and their maximum quantity, chemical and physical forms be included in an application. Furthermore, the U.S. Federal Regulations require application contain an evaluation demonstrating the package (i.e., the packaging and its contents) satisfies the external radiation standards for all packages (10 CFR 71.31(2), 71.35(a), & 71.47). By placing the contents in a He leak-tight containment vessel, and limiting the mass to ensure subcriticality, the first two essential functions are readily met. Some isotopes emit sufficiently strong photon radiation that small amounts of material can yield a large external dose rate. Quantifying of the dose rate for a proposed content is a challenging issue for the SGQ approach. It is essential to quantify external radiation levels from several common gamma and neutron sources that can be safely placed in a specific packaging, to ensure compliance with federal regulations. The Packaging Certification Program (PCP) Methodology for Determining Dose Rate for Small Gram Quantities in Shipping Packagings described in this report provides bounding mass limits for a set of proposed SGQ isotopes. Methodology calculations were performed to estimate external radiation levels for the 9977 shipping package using the MCNP radiation transport code to develop a set of response multipliers (Green's functions) for 'dose per particle' for each neutron and photon spectral group. The source spectrum for each isotope generated using the ORIGEN-S and RASTA computer codes was folded with the response multipliers to generate the dose rate per gram of each isotope in the 9977 shipping package and its associated shielded containers. The maximum amount of a single isotope that could be shipped within the regulatory limits contained in 10 CFR 71.47 for dose rate at the surface of the package is determined. If a package contains a mixture of isotopes, the acceptability for shipment can be determined by a sum of fractions approach. Furthermore, the results of this analysis can be easily extended to additional radioisotopes by simply evaluating the neutron and/or photon spectra of those isotopes and folding the spectral data with the Green's functions provided.« less

MsSpec-1.0: A multiple scattering package for electron spectroscopies in material science

NASA Astrophysics Data System (ADS)

Sébilleau, Didier; Natoli, Calogero; Gavaza, George M.; Zhao, Haifeng; Da Pieve, Fabiana; Hatada, Keisuke

2011-12-01

We present a multiple scattering package to calculate the cross-section of various spectroscopies namely photoelectron diffraction (PED), Auger electron diffraction (AED), X-ray absorption (XAS), low-energy electron diffraction (LEED) and Auger photoelectron coincidence spectroscopy (APECS). This package is composed of three main codes, computing respectively the cluster, the potential and the cross-section. In the latter case, in order to cover a range of energies as wide as possible, three different algorithms are provided to perform the multiple scattering calculation: full matrix inversion, series expansion or correlation expansion of the multiple scattering matrix. Numerous other small Fortran codes or bash/csh shell scripts are also provided to perform specific tasks. The cross-section code is built by the user from a library of subroutines using a makefile. Program summaryProgram title: MsSpec-1.0 Catalogue identifier: AEJT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJT_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 504 438 No. of bytes in distributed program, including test data, etc.: 14 448 180 Distribution format: tar.gz Programming language: Fortran 77 Computer: Any Operating system: Linux, MacOs RAM: Bytes Classification: 7.2 External routines: Lapack ( http://www.netlib.org/lapack/) Nature of problem: Calculation of the cross-section of various spectroscopies. Solution method: Multiple scattering. Running time: The test runs provided only take a few seconds to run.

Pyteomics--a Python framework for exploratory data analysis and rapid software prototyping in proteomics.

PubMed

Goloborodko, Anton A; Levitsky, Lev I; Ivanov, Mark V; Gorshkov, Mikhail V

2013-02-01

Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics. It provides modules for reading LC-MS/MS data, search engine output, protein sequence databases, theoretical prediction of retention times, electrochemical properties of polypeptides, mass and m/z calculations, and sequence parsing. Pyteomics is available under Apache license; release versions are available at the Python Package Index http://pypi.python.org/pyteomics, the source code repository at http://hg.theorchromo.ru/pyteomics, documentation at http://packages.python.org/pyteomics. Pyteomics.biolccc documentation is available at http://packages.python.org/pyteomics.biolccc/. Questions on installation and usage can be addressed to pyteomics mailing list: pyteomics@googlegroups.com.

Study of the TRAC Airfoil Table Computational System

NASA Technical Reports Server (NTRS)

Hu, Hong

1999-01-01

The report documents the study of the application of the TRAC airfoil table computational package (TRACFOIL) to the prediction of 2D airfoil force and moment data over a wide range of angle of attack and Mach number. The TRACFOIL generates the standard C-81 airfoil table for input into rotorcraft comprehensive codes such as CAM- RAD. The existing TRACFOIL computer package is successfully modified to run on Digital alpha workstations and on Cray-C90 supercomputers. A step-by-step instruction for using the package on both computer platforms is provided. Application of the newer version of TRACFOIL is made for two airfoil sections. The C-81 data obtained using the TRACFOIL method are compared with those of wind-tunnel data and results are presented.

Explosive Model Tarantula V1/JWL++ Calibration of LX-17: #2

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

Souers, P C; Vitello, P

2009-05-01

Tarantula V1 is a kinetic package for reactive flow codes that seeks to describe initiation, failure, dead zones and detonation simultaneously. The most important parameter is P1, the pressure between the initiation and failure regions. Both dead zone formation and failure can be largely controlled with this knob. However, V1 does failure with low settings and dead zones with higher settings, so that it cannot fulfill its purpose in the current format. To this end, V2 is under test. The derivation of the initiation threshold P0 is discussed. The derivation of the initiation pressure-tau curve as an output of Tarantulamore » shows that the initiation package is sound. A desensitization package is also considered.« less

A new Bayesian Earthquake Analysis Tool (BEAT)

NASA Astrophysics Data System (ADS)

Vasyura-Bathke, Hannes; Dutta, Rishabh; Jónsson, Sigurjón; Mai, Martin

2017-04-01

Modern earthquake source estimation studies increasingly use non-linear optimization strategies to estimate kinematic rupture parameters, often considering geodetic and seismic data jointly. However, the optimization process is complex and consists of several steps that need to be followed in the earthquake parameter estimation procedure. These include pre-describing or modeling the fault geometry, calculating the Green's Functions (often assuming a layered elastic half-space), and estimating the distributed final slip and possibly other kinematic source parameters. Recently, Bayesian inference has become popular for estimating posterior distributions of earthquake source model parameters given measured/estimated/assumed data and model uncertainties. For instance, some research groups consider uncertainties of the layered medium and propagate these to the source parameter uncertainties. Other groups make use of informative priors to reduce the model parameter space. In addition, innovative sampling algorithms have been developed that efficiently explore the often high-dimensional parameter spaces. Compared to earlier studies, these improvements have resulted in overall more robust source model parameter estimates that include uncertainties. However, the computational demands of these methods are high and estimation codes are rarely distributed along with the published results. Even if codes are made available, it is often difficult to assemble them into a single optimization framework as they are typically coded in different programing languages. Therefore, further progress and future applications of these methods/codes are hampered, while reproducibility and validation of results has become essentially impossible. In the spirit of providing open-access and modular codes to facilitate progress and reproducible research in earthquake source estimations, we undertook the effort of producing BEAT, a python package that comprises all the above-mentioned features in one single programing environment. The package is build on top of the pyrocko seismological toolbox (www.pyrocko.org) and makes use of the pymc3 module for Bayesian statistical model fitting. BEAT is an open-source package (https://github.com/hvasbath/beat) and we encourage and solicit contributions to the project. In this contribution, we present our strategy for developing BEAT, show application examples, and discuss future developments.

49 CFR 178.502 - Identification codes for packagings.

Code of Federal Regulations, 2010 CFR

2010-10-01

... construction, as follows: (i) “A” means steel (all types and surface treatments). (ii) “B” means aluminum. (iii) “C” means natural wood. (iv) “D” means plywood. (v) “F” means reconstituted wood. (vi) “G” means...

CH-TRU Waste Content Codes (CH-TRUCON)

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

Washington TRU Solutions LLC

2007-08-15

The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled Shipments" (10-day shipping period).« less

CH-TRU Waste Content Codes (CH-TRUCON)

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

Washington TRU Solutions LLC

2007-06-15

The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled Shipments" (10-day shipping period).« less

CH-TRU Waste Content Codes (CH-TRUCON)

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

Washington TRU Solutions LLC

2007-09-20

The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled Shipments" (10-day shipping period).« less

CH-TRU Waste Content Codes (CH-TRUCON)

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

Washington TRU Solutions LLC

2006-06-20

The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled Shipments" (10-day shipping period).« less

CH-TRU Waste Content Codes (CH-TRUCON)

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

Washington TRU Solutions LLC

2006-01-18

The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled Shipments" (10-day shipping period).« less

CH-TRU Waste Content Codes (CH-TRUCON)

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

Washington TRU Solutions LLC

2006-08-15

The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled Shipments" (10-day shipping period).« less

CH-TRU Waste Content Codes (CH-TRUCON)

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

Washington TRU Solutions LLC

2006-12-20

The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled Shipments" (10-day shipping period).« less

CH-TRU Waste Content Codes (CH-TRUCON)

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

Washington TRU Solutions LLC

2007-02-15

The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled Shipments" (10-day shipping period).« less

CH-TRU Waste Content Codes (CH-TRUCON)

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

Washington TRU Solutions LLC

2006-09-15

The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled Shipments" (10-day shipping period).« less

CH-TRU Waste Content Codes

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

Washington TRU Solutions LLC

2008-01-16

The CH-TRU Waste Content Codes (CH-TRUCON) document describes the inventory of the U.S. Department of Energy (DOE) CH-TRU waste within the transportation parameters specified by the Contact-Handled Transuranic Waste Authorized Methods for Payload Control (CH-TRAMPAC). The CH-TRAMPAC defines the allowable payload for the Transuranic Package Transporter-II (TRUPACT-II) and HalfPACT packagings. This document is a catalog of TRUPACT-II and HalfPACT authorized contents and a description of the methods utilized to demonstrate compliance with the CH-TRAMPAC. A summary of currently approved content codes by site is presented in Table 1. The CH-TRAMPAC describes "shipping categories" that are assigned to each payload container.more » Multiple shipping categories may be assigned to a single content code. A summary of approved content codes and corresponding shipping categories is provided in Table 2, which consists of Tables 2A, 2B, and 2C. Table 2A provides a summary of approved content codes and corresponding shipping categories for the "General Case," which reflects the assumption of a 60-day shipping period as described in the CH-TRAMPAC and Appendix 3.4 of the CH-TRU Payload Appendices. For shipments to be completed within an approximately 1,000-mile radius, a shorter shipping period of 20 days is applicable as described in the CH-TRAMPAC and Appendix 3.5 of the CH-TRU Payload Appendices. For shipments to WIPP from Los Alamos National Laboratory (LANL), Nevada Test Site, and Rocky Flats Environmental Technology Site, a 20-day shipping period is applicable. Table 2B provides a summary of approved content codes and corresponding shipping categories for "Close-Proximity Shipments" (20-day shipping period). For shipments implementing the controls specified in the CH-TRAMPAC and Appendix 3.6 of the CH-TRU Payload Appendices, a 10-day shipping period is applicable. Table 2C provides a summary of approved content codes and corresponding shipping categories for "Controlled Shipments" (10-day shipping period).« less

iGC-an integrated analysis package of gene expression and copy number alteration.

PubMed

Lai, Yi-Pin; Wang, Liang-Bo; Wang, Wei-An; Lai, Liang-Chuan; Tsai, Mong-Hsun; Lu, Tzu-Pin; Chuang, Eric Y

2017-01-14

With the advancement in high-throughput technologies, researchers can simultaneously investigate gene expression and copy number alteration (CNA) data from individual patients at a lower cost. Traditional analysis methods analyze each type of data individually and integrate their results using Venn diagrams. Challenges arise, however, when the results are irreproducible and inconsistent across multiple platforms. To address these issues, one possible approach is to concurrently analyze both gene expression profiling and CNAs in the same individual. We have developed an open-source R/Bioconductor package (iGC). Multiple input formats are supported and users can define their own criteria for identifying differentially expressed genes driven by CNAs. The analysis of two real microarray datasets demonstrated that the CNA-driven genes identified by the iGC package showed significantly higher Pearson correlation coefficients with their gene expression levels and copy numbers than those genes located in a genomic region with CNA. Compared with the Venn diagram approach, the iGC package showed better performance. The iGC package is effective and useful for identifying CNA-driven genes. By simultaneously considering both comparative genomic and transcriptomic data, it can provide better understanding of biological and medical questions. The iGC package's source code and manual are freely available at https://www.bioconductor.org/packages/release/bioc/html/iGC.html .

Development of high performance scientific components for interoperability of computing packages

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

Gulabani, Teena Pratap

2008-01-01

Three major high performance quantum chemistry computational packages, NWChem, GAMESS and MPQC have been developed by different research efforts following different design patterns. The goal is to achieve interoperability among these packages by overcoming the challenges caused by the different communication patterns and software design of each of these packages. A chemistry algorithm is hard to develop as well as being a time consuming process; integration of large quantum chemistry packages will allow resource sharing and thus avoid reinvention of the wheel. Creating connections between these incompatible packages is the major motivation of the proposed work. This interoperability is achievedmore » by bringing the benefits of Component Based Software Engineering through a plug-and-play component framework called Common Component Architecture (CCA). In this thesis, I present a strategy and process used for interfacing two widely used and important computational chemistry methodologies: Quantum Mechanics and Molecular Mechanics. To show the feasibility of the proposed approach the Tuning and Analysis Utility (TAU) has been coupled with NWChem code and its CCA components. Results show that the overhead is negligible when compared to the ease and potential of organizing and coping with large-scale software applications.« less

PharmacoGx: an R package for analysis of large pharmacogenomic datasets.

PubMed

Smirnov, Petr; Safikhani, Zhaleh; El-Hachem, Nehme; Wang, Dong; She, Adrian; Olsen, Catharina; Freeman, Mark; Selby, Heather; Gendoo, Deena M A; Grossmann, Patrick; Beck, Andrew H; Aerts, Hugo J W L; Lupien, Mathieu; Goldenberg, Anna; Haibe-Kains, Benjamin

2016-04-15

Pharmacogenomics holds great promise for the development of biomarkers of drug response and the design of new therapeutic options, which are key challenges in precision medicine. However, such data are scattered and lack standards for efficient access and analysis, consequently preventing the realization of the full potential of pharmacogenomics. To address these issues, we implemented PharmacoGx, an easy-to-use, open source package for integrative analysis of multiple pharmacogenomic datasets. We demonstrate the utility of our package in comparing large drug sensitivity datasets, such as the Genomics of Drug Sensitivity in Cancer and the Cancer Cell Line Encyclopedia. Moreover, we show how to use our package to easily perform Connectivity Map analysis. With increasing availability of drug-related data, our package will open new avenues of research for meta-analysis of pharmacogenomic data. PharmacoGx is implemented in R and can be easily installed on any system. The package is available from CRAN and its source code is available from GitHub. bhaibeka@uhnresearch.ca or benjamin.haibe.kains@utoronto.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.

tran-SAS v1.0: a numerical model to compute catchment-scale hydrologic transport using StorAge Selection functions

NASA Astrophysics Data System (ADS)

Benettin, Paolo; Bertuzzo, Enrico

2018-04-01

This paper presents the tran-SAS package, which includes a set of codes to model solute transport and water residence times through a hydrological system. The model is based on a catchment-scale approach that aims at reproducing the integrated response of the system at one of its outlets. The codes are implemented in MATLAB and are meant to be easy to edit, so that users with minimal programming knowledge can adapt them to the desired application. The problem of large-scale solute transport has both theoretical and practical implications. On the one side, the ability to represent the ensemble of water flow trajectories through a heterogeneous system helps unraveling streamflow generation processes and allows us to make inferences on plant-water interactions. On the other side, transport models are a practical tool that can be used to estimate the persistence of solutes in the environment. The core of the package is based on the implementation of an age master equation (ME), which is solved using general StorAge Selection (SAS) functions. The age ME is first converted into a set of ordinary differential equations, each addressing the transport of an individual precipitation input through the catchment, and then it is discretized using an explicit numerical scheme. Results show that the implementation is efficient and allows the model to run in short times. The numerical accuracy is critically evaluated and it is shown to be satisfactory in most cases of hydrologic interest. Additionally, a higher-order implementation is provided within the package to evaluate and, if necessary, to improve the numerical accuracy of the results. The codes can be used to model streamflow age and solute concentration, but a number of additional outputs can be obtained by editing the codes to further advance the ability to understand and model catchment transport processes.

Design Considerations of a Virtual Laboratory for Advanced X-ray Sources

NASA Astrophysics Data System (ADS)

Luginsland, J. W.; Frese, M. H.; Frese, S. D.; Watrous, J. J.; Heileman, G. L.

2004-11-01

The field of scientific computation has greatly advanced in the last few years, resulting in the ability to perform complex computer simulations that can predict the performance of real-world experiments in a number of fields of study. Among the forces driving this new computational capability is the advent of parallel algorithms, allowing calculations in three-dimensional space with realistic time scales. Electromagnetic radiation sources driven by high-voltage, high-current electron beams offer an area to further push the state-of-the-art in high fidelity, first-principles simulation tools. The physics of these x-ray sources combine kinetic plasma physics (electron beams) with dense fluid-like plasma physics (anode plasmas) and x-ray generation (bremsstrahlung). There are a number of mature techniques and software packages for dealing with the individual aspects of these sources, such as Particle-In-Cell (PIC), Magneto-Hydrodynamics (MHD), and radiation transport codes. The current effort is focused on developing an object-oriented software environment using the Rational© Unified Process and the Unified Modeling Language (UML) to provide a framework where multiple 3D parallel physics packages, such as a PIC code (ICEPIC), a MHD code (MACH), and a x-ray transport code (ITS) can co-exist in a system-of-systems approach to modeling advanced x-ray sources. Initial software design and assessments of the various physics algorithms' fidelity will be presented.

Microscale synthesis and characterization of polystyrene: NSF-POLYED scholars project

NASA Technical Reports Server (NTRS)

Quaal, Karen S.; Wu, Chang-Ning

1994-01-01

Polystyrene is a familiar polymer with many commercial uses. Its applications range from the clear, high index of refraction, brittle plastic used to form audio cassette and CD cases to the foamed material used in insulated drink cups and packaging material. Polystyrene constitutes 11 percent of the plastics used in packaging with only High Density Polyethylene (HDPE) and Low Density Polyethylene (LDPE) contributing a larger share: so much polystyrene is used today, it is one of six common plastics that manufacturers have assigned an identification code. The code helps recycling efforts. Polystyrene's code is (PS code 6). During the summer and fall of 1992 several new polymeric experiments were developed by the NSF POLYED Scholars for introduction into the chemistry core curriculum. In this presentation, one such project will be discussed. This laboratory project is recommended for a first or second year laboratory course allowing the introduction of polymeric science to undergraduates at the earliest opportunity. The reliability of the experiments which make up this project and the recognition factor of polystyrene, a material we come in contact with everyday, makes the synthesis and characterization of polystyrene a good choice for the introduction of polymerization to undergraduates. This laboratory project appeals to the varied interests of students enrolled in the typical first year chemistry course and becomes an ideal way to introduce polymers to a wide variety of science and engineering students.

Python-Assisted MODFLOW Application and Code Development

NASA Astrophysics Data System (ADS)

Langevin, C.

2013-12-01

The U.S. Geological Survey (USGS) has a long history of developing and maintaining free, open-source software for hydrological investigations. The MODFLOW program is one of the most popular hydrologic simulation programs released by the USGS, and it is considered to be the most widely used groundwater flow simulation code. MODFLOW was written using a modular design and a procedural FORTRAN style, which resulted in code that could be understood, modified, and enhanced by many hydrologists. The code is fast, and because it uses standard FORTRAN it can be run on most operating systems. Most MODFLOW users rely on proprietary graphical user interfaces for constructing models and viewing model results. Some recent efforts, however, have focused on construction of MODFLOW models using open-source Python scripts. Customizable Python packages, such as FloPy (https://code.google.com/p/flopy), can be used to generate input files, read simulation results, and visualize results in two and three dimensions. Automating this sequence of steps leads to models that can be reproduced directly from original data and rediscretized in space and time. Python is also being used in the development and testing of new MODFLOW functionality. New packages and numerical formulations can be quickly prototyped and tested first with Python programs before implementation in MODFLOW. This is made possible by the flexible object-oriented design capabilities available in Python, the ability to call FORTRAN code from Python, and the ease with which linear systems of equations can be solved using SciPy, for example. Once new features are added to MODFLOW, Python can then be used to automate comprehensive regression testing and ensure reliability and accuracy of new versions prior to release.

EFTofPNG: a package for high precision computation with the effective field theory of post-Newtonian gravity

NASA Astrophysics Data System (ADS)

Levi, Michele; Steinhoff, Jan

2017-12-01

We present a novel public package ‘EFTofPNG’ for high precision computation in the effective field theory of post-Newtonian (PN) gravity, including spins. We created this package in view of the timely need to publicly share automated computation tools, which integrate the various types of physics manifested in the expected increasing influx of gravitational wave (GW) data. Hence, we created a free and open source package, which is self-contained, modular, all-inclusive, and accessible to the classical gravity community. The ‘EFTofPNG’ Mathematica package also uses the power of the ‘xTensor’ package, suited for complicated tensor computation, where our coding also strategically approaches the generic generation of Feynman contractions, which is universal to all perturbation theories in physics, by efficiently treating n-point functions as tensors of rank n. The package currently contains four independent units, which serve as subsidiaries to the main one. Its final unit serves as a pipeline chain for the obtainment of the final GW templates, and provides the full computation of derivatives and physical observables of interest. The upcoming ‘EFTofPNG’ package version 1.0 should cover the point mass sector, and all the spin sectors, up to the fourth PN order, and the two-loop level. We expect and strongly encourage public development of the package to improve its efficiency, and to extend it to further PN sectors, and observables useful for the waveform modelling.

Draco,Version 6.x.x

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

Thompson, Kelly; Budge, Kent; Lowrie, Rob

2016-03-03

Draco is an object-oriented component library geared towards numerically intensive, radiation (particle) transport applications built for parallel computing hardware. It consists of semi-independent packages and a robust build system. The packages in Draco provide a set of components that can be used by multiple clients to build transport codes. The build system can also be extracted for use in clients. Software includes smart pointers, Design-by-Contract assertions, unit test framework, wrapped MPI functions, a file parser, unstructured mesh data structures, a random number generator, root finders and an angular quadrature component.

FREQ: A computational package for multivariable system loop-shaping procedures

NASA Technical Reports Server (NTRS)

Giesy, Daniel P.; Armstrong, Ernest S.

1989-01-01

Many approaches in the field of linear, multivariable time-invariant systems analysis and controller synthesis employ loop-sharing procedures wherein design parameters are chosen to shape frequency-response singular value plots of selected transfer matrices. A software package, FREQ, is documented for computing within on unified framework many of the most used multivariable transfer matrices for both continuous and discrete systems. The matrices are evaluated at user-selected frequency-response values, and singular values against frequency. Example computations are presented to demonstrate the use of the FREQ code.

Prospective study of outcomes after percutaneous biliary drainage for malignant biliary obstruction

PubMed Central

Robson, P. C.; Heffernan, N.; Gonen, M.; Thornton, R.; Brody, L. A.; Holmes, R.; Brown, K. T.; Covey, A. M.; Fleischer, D.; Getrajdman, G. I.; Jarnagin, W.; Sofocleous, C.; Blumgart, L.; D’Angelica, M.

2015-01-01

Purpose Percutaneous biliary drainage (PBD) is used to relieve malignant bile duct obstruction (MBO) when endoscopic drainage is not feasible. Little is known about the effects of PBD on the quality of life (QoL) in patients with MBO. The aim of this study was to evaluate changes in QoL and pruritus after PBD and to explore the variables that impact these changes. Patients and Methods Eligible patients reported their QoL and pruritus before and after PBD using the Functional Assessment of Cancer Therapy – Hepatobiliary instrument (FACT-HS) and the Visual Analog Scale for Pruritus (VASP). Instruments were completed pre-procedure and at one and four weeks following PBD. Results One hundred and nine (60 male/49 female) patients enrolled, 102 (94%) had unresectable disease. PBD was technically successful (hepatic ducts cannulated at the conclusion of procedure) in all patients. There were two procedure-related deaths. All-cause mortality was 10% (N=11) at 4 weeks and 28% (N=31) at 8 weeks post PBD with a median survival of 4.74 months. The mean FACT-HS scores declined significantly (P<.01) over time (101.3, 94.8, 94.7 at baseline, 1 week, 4 weeks, respectively). The VASP scores showed significant improvement at 1 week with continued improvement at 4 weeks (P<.01). Conclusion PBD improves pruritus but not QoL in patients with MBO and advanced malignancy. There is high early mortality in this population. PMID:20358300

A randomised controlled trial of exercise and hot water bottle in the management of dysmenorrhoea in school girls of Chandigarh, India.

PubMed

Chaudhuri, Aditi; Singh, Amarjeet; Dhaliwal, Lakhbir

2013-01-01

To estimate the prevalence of primary dysmenorrhoea among school girls and to compare the impact of exercise and hot water bottle on the occurrence and severity of primary dysmenorrhoea among the study population. A cross sectional study was done to estimate the prevalence of dysmenorrhoea in two schools of Chandigarh, India. For the Randomised Controlled Trial, group randomisation of the two schools was done into 2 intervention groups (exercise & hot water bottle groups). 53 girls in school 1 and 75 girls in school 2 participated in the intervention. Comparison of baseline Menstrual Distress Questionnaire (MDQ) scores & Visual Analogue Scale for Pain (VASP) scores were done with 1st, 2nd & 3rd month post intervention scores using mean, standard deviation, t-test. Prevalence of dysmenorrhoea was 60.7%. Median age of the school girls was 14 years. The mean VASP score decreased from 5.75 to 2.96 (P < 0.0001) and from 5.16 to 2.06 (P < 0.0001) at 3 months, in the exercise and hot water bottle group respectively. The mean MDQ score decreased from 14.53 to 7.85 (P < 0.0001) and from 14.92 to 8.16 (P < 0.0001) at 3 months, in the exercise and hot water bottle group respectively. Both exercise & hot water bottle can be used in dysmenorrhoeic girls in home setting to provide relief from pain and menstrual distress.

Waste Generator Instructions: Key to Successful Implementation of the US DOE's 435.1 for Transuranic Waste Packaging Instructions (LA-UR-12-24155) - 13218

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

French, David M.; Hayes, Timothy A.; Pope, Howard L.

In times of continuing fiscal constraints, a management and operation tool that is straightforward to implement, works as advertised, and virtually ensures compliant waste packaging should be carefully considered and employed wherever practicable. In the near future, the Department of Energy (DOE) will issue the first major update to DOE Order 435.1, Radioactive Waste Management. This update will contain a requirement for sites that do not have a Waste Isolation Pilot Plant (WIPP) waste certification program to use two newly developed technical standards: Contact-Handled Defense Transuranic Waste Packaging Instructions and Remote-Handled Defense Transuranic Waste Packaging Instructions. The technical standards aremore » being developed from the DOE O 435.1 Notice, Contact-Handled and Remote-Handled Transuranic Waste Packaging, approved August 2011. The packaging instructions will provide detailed information and instruction for packaging almost every conceivable type of transuranic (TRU) waste for disposal at WIPP. While providing specificity, the packaging instructions leave to each site's own discretion the actual mechanics of how those Instructions will be functionally implemented at the floor level. While the Technical Standards are designed to provide precise information for compliant packaging, the density of the information in the packaging instructions necessitates a type of Rosetta Stone that translates the requirements into concise, clear, easy to use and operationally practical recipes that are waste stream and facility specific for use by both first line management and hands-on operations personnel. The Waste Generator Instructions provide the operator with step-by-step instructions that will integrate the sites' various operational requirements (e.g., health and safety limits, radiological limits or dose limits) and result in a WIPP certifiable waste and package that can be transported to and emplaced at WIPP. These little known but widely productive Waste Generator Instructions (WGIs) have been used occasionally in the past at large sites for treatment and packaging of TRU waste. The WGIs have resulted in highly efficient waste treatment, packaging and certification for disposal of TRU waste at WIPP. For example, a single WGI at LANL, combined with an increase in gram loading, resulted in a mind boggling 6,400% increase in waste loading for {sup 238}Pu heat source waste. In fact, the WGI combined with a new Contact Handled (CH) TRU Waste Content (TRUCON) Code provided a massive increase in shippable wattage per Transuranic Package Transporter-II (TRUPACT-II) over the previously used and more restrictive TRUCON Code that have been used previously for the heat source waste. In fact, the use of the WGI process at LANL's TA-55 facility reduced non-compliant drums for WIPP certification and disposal from a 13% failure rate down to a 0.5% failure rate and is expected to further reduce the failure rate to zero drums per year. The inherent value of the WGI is that it can be implemented in a site's current procedure issuance process and it provides documented proof of what actions were taken for each waste stream packaged. The WGI protocol provides a key floor-level operational component to achieve goal alignment between actual site operations, the WIPP TRU waste packaging instructions, and DOE O 435.1. (authors)« less

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA, and mRNA data in GDC.

PubMed

Li, Ruidong; Qu, Han; Wang, Shibo; Wei, Julong; Zhang, Le; Ma, Renyuan; Lu, Jianming; Zhu, Jianguo; Zhong, Wei-De; Jia, Zhenyu

2018-03-02

The large-scale multidimensional omics data in the Genomic Data Commons (GDC) provides opportunities to investigate the crosstalk among different RNA species and their regulatory mechanisms in cancers. Easy-to-use bioinformatics pipelines are needed to facilitate such studies. We have developed a user-friendly R/Bioconductor package, named GDCRNATools, for downloading, organizing, and analyzing RNA data in GDC with an emphasis on deciphering the lncRNA-mRNA related competing endogenous RNAs (ceRNAs) regulatory network in cancers. Many widely used bioinformatics tools and databases are utilized in our package. Users can easily pack preferred downstream analysis pipelines or integrate their own pipelines into the workflow. Interactive shiny web apps built in GDCRNATools greatly improve visualization of results from the analysis. GDCRNATools is an R/Bioconductor package that is freely available at Bioconductor (http://bioconductor.org/packages/devel/bioc/html/GDCRNATools.html). Detailed instructions, manual and example code are also available in Github (https://github.com/Jialab-UCR/GDCRNATools). arthur.jia@ucr.edu or zhongwd2009@live.cn or doctorzhujianguo@163.com.

Monte Carlo Particle Lists: MCPL

NASA Astrophysics Data System (ADS)

Kittelmann, T.; Klinkby, E.; Knudsen, E. B.; Willendrup, P.; Cai, X. X.; Kanaki, K.

2017-09-01

A binary format with lists of particle state information, for interchanging particles between various Monte Carlo simulation applications, is presented. Portable C code for file manipulation is made available to the scientific community, along with converters and plugins for several popular simulation packages.

Effect of girder spacing on bridge deck response.

DOT National Transportation Integrated Search

2000-12-01

The purpose of this investigation was to evaluate the use of the commercial finite element code ABAQUS for analysis of reinforced concrete bridge decks and to employ this analysis package to determine the effect of girder spacing on deck response. A ...

Automotive Gas Turbine Power System-Performance Analysis Code

NASA Technical Reports Server (NTRS)

Juhasz, Albert J.

1997-01-01

An open cycle gas turbine numerical modelling code suitable for thermodynamic performance analysis (i.e. thermal efficiency, specific fuel consumption, cycle state points, working fluid flowrates etc.) of automotive and aircraft powerplant applications has been generated at the NASA Lewis Research Center's Power Technology Division. The use this code can be made available to automotive gas turbine preliminary design efforts, either in its present version, or, assuming that resources can be obtained to incorporate empirical models for component weight and packaging volume, in later version that includes the weight-volume estimator feature. The paper contains a brief discussion of the capabilities of the presently operational version of the code, including a listing of input and output parameters and actual sample output listings.

Comparative Long-Term Effect of Three Anti-P2Y12 Drugs after Percutaneous Angioplasty: An Observational Study Based on Electronic Drug Adherence Monitoring

PubMed Central

Forni Ogna, Valentina; Bassi, Isabelle; Menetrey, Isabelle; Muller, Olivier; Tousset, Eric; Fontana, Pierre; Eeckhout, Eric; Eap, Chin B.; Vrijens, Bernard; Burnier, Michel; Wuerzner, Grégoire

2017-01-01

Aims: Dual platelet inhibition using anti-P2Y12 drugs and aspirin is the standard of care in patients after percutaneous coronary interventions (PCI). Prasugrel and ticagrelor have been shown to be more potent than clopidogrel with less high on-treatment platelet reactivity. Whether differences in long-term adherence to these drugs can partly explain different antiplatelet efficacy has not been studied so far. The objective was to compare the long-term P2Y12 receptor inhibition and drug adherence to different anti-P2Y12 drugs, and to assess the impact of adherence on the pharmacodynamic effect. Methods: Monocentric, prospective, observational study. Stable outpatients treated with clopidogrel 75 mg once daily, prasugrel 10 mg once daily or ticagrelor 90 mg twice daily after PCI with stent implantation were included. Drug adherence was recorded during 6 months using electronic monitoring. Platelet responsiveness was assessed with the vasodilator-stimulated phosphoprotein platelet reactivity index (VASP-PRI) at inclusion, 3 and 6 months. Results: 120 patients had VASP-PRI and adherence data available. At 6-months, mean VASP-PRI (±SD) was 17.7 ± 11.0% with ticagrelor, 29.2 ± 15.5% with prasugrel and 47.2 ± 17.6% with clopidogrel (ANOVA, P < 0.0001). Median [IQR] taking adherence was 96 [82–100]% with ticagrelor, 100 [97–101]% with prasugrel and 100 [99–101]% with clopidogrel (p = 0.0001). Median [IQR] correct dosing was 88 [73–95]% with ticagrelor, 97 [92.5–98]% with prasugrel and 98 [96–99]% with clopidogrel (p = 0.0001). Anti-P2Y12 drug (p ≤ 0.001) and diabetes (p = 0.014) emerged as predictors of poor antiplatelet response after adjusting for age, BMI, sex, and CYP2C19∗2 carriers status. Conclusion: Drug adherence to anti-P2Y12 drugs assessed with electronic monitoring was very high. However, anti-P2Y12 drugs showed significant differences in antiplatelet activity, with newer anti-P2Y12 drugs ticagrelor and prasugrel exerting a stronger P2Y12 receptor inhibition. These data suggest that pharmacokinetic-pharmacodynamic differences between oral anti-P2Y12 drugs are more important than adherence in determining antiplatelet efficacy when adherence to prescription is high. The study was registered (Current Controlled Trials ISRCTN85949729). PMID:29118712

Modeling the Galaxy-Halo Connection: An open-source approach with Halotools

NASA Astrophysics Data System (ADS)

Hearin, Andrew

2016-03-01

Although the modern form of galaxy-halo modeling has been in place for over ten years, there exists no common code base for carrying out large-scale structure calculations. Considering, for example, the advances in CMB science made possible by Boltzmann-solvers such as CMBFast, CAMB and CLASS, there are clear precedents for how theorists working in a well-defined subfield can mutually benefit from such a code base. Motivated by these and other examples, I present Halotools: an open-source, object-oriented python package for building and testing models of the galaxy-halo connection. Halotools is community-driven, and already includes contributions from over a dozen scientists spread across numerous universities. Designed with high-speed performance in mind, the package generates mock observations of synthetic galaxy populations with sufficient speed to conduct expansive MCMC likelihood analyses over a diverse and highly customizable set of models. The package includes an automated test suite and extensive web-hosted documentation and tutorials (halotools.readthedocs.org). I conclude the talk by describing how Halotools can be used to analyze existing datasets to obtain robust and novel constraints on galaxy evolution models, and by outlining the Halotools program to prepare the field of cosmology for the arrival of Stage IV dark energy experiments.

JADAMILU: a software code for computing selected eigenvalues of large sparse symmetric matrices

NASA Astrophysics Data System (ADS)

Bollhöfer, Matthias; Notay, Yvan

2007-12-01

A new software code for computing selected eigenvalues and associated eigenvectors of a real symmetric matrix is described. The eigenvalues are either the smallest or those closest to some specified target, which may be in the interior of the spectrum. The underlying algorithm combines the Jacobi-Davidson method with efficient multilevel incomplete LU (ILU) preconditioning. Key features are modest memory requirements and robust convergence to accurate solutions. Parameters needed for incomplete LU preconditioning are automatically computed and may be updated at run time depending on the convergence pattern. The software is easy to use by non-experts and its top level routines are written in FORTRAN 77. Its potentialities are demonstrated on a few applications taken from computational physics. Program summaryProgram title: JADAMILU Catalogue identifier: ADZT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZT_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 101 359 No. of bytes in distributed program, including test data, etc.: 7 493 144 Distribution format: tar.gz Programming language: Fortran 77 Computer: Intel or AMD with g77 and pgf; Intel EM64T or Itanium with ifort; AMD Opteron with g77, pgf and ifort; Power (IBM) with xlf90. Operating system: Linux, AIX RAM: problem dependent Word size: real:8; integer: 4 or 8, according to user's choice Classification: 4.8 Nature of problem: Any physical problem requiring the computation of a few eigenvalues of a symmetric matrix. Solution method: Jacobi-Davidson combined with multilevel ILU preconditioning. Additional comments: We supply binaries rather than source code because JADAMILU uses the following external packages: MC64. This software is copyrighted software and not freely available. COPYRIGHT (c) 1999 Council for the Central Laboratory of the Research Councils. AMD. Copyright (c) 2004-2006 by Timothy A. Davis, Patrick R. Amestoy, and Iain S. Duff. Source code is distributed by the authors under the GNU LGPL licence. BLAS. The reference BLAS is a freely-available software package. It is available from netlib via anonymous ftp and the World Wide Web. LAPACK. The complete LAPACK package or individual routines from LAPACK are freely available on netlib and can be obtained via the World Wide Web or anonymous ftp. For maximal benefit to the community, we added the sources we are proprietary of to the tar.gz file submitted for inclusion in the CPC library. However, as explained in the README file, users willing to compile the code instead of using binaries should first obtain the sources for the external packages mentioned above (email and/or web addresses are provided). Running time: Problem dependent; the test examples provided with the code only take a few seconds to run; timing results for large scale problems are given in Section 5.

Fourteen Years of R/qtl: Just Barely Sustainable

PubMed Central

Broman, Karl W.

2014-01-01

R/qtl is an R package for mapping quantitative trait loci (genetic loci that contribute to variation in quantitative traits) in experimental crosses. Its development began in 2000. There have been 38 software releases since 2001. The latest release contains 35k lines of R code and 24k lines of C code, plus 15k lines of code for the documentation. Challenges in the development and maintenance of the software are discussed. A key to the success of R/qtl is that it remains a central tool for the chief developer's own research work, and so its maintenance is of selfish importance. PMID:25364504

The Cloud Feedback Model Intercomparison Project Observational Simulator Package: Version 2

NASA Astrophysics Data System (ADS)

Swales, Dustin J.; Pincus, Robert; Bodas-Salcedo, Alejandro

2018-01-01

The Cloud Feedback Model Intercomparison Project Observational Simulator Package (COSP) gathers together a collection of observation proxies or satellite simulators that translate model-simulated cloud properties to synthetic observations as would be obtained by a range of satellite observing systems. This paper introduces COSP2, an evolution focusing on more explicit and consistent separation between host model, coupling infrastructure, and individual observing proxies. Revisions also enhance flexibility by allowing for model-specific representation of sub-grid-scale cloudiness, provide greater clarity by clearly separating tasks, support greater use of shared code and data including shared inputs across simulators, and follow more uniform software standards to simplify implementation across a wide range of platforms. The complete package including a testing suite is freely available.

A Zeus++ Code Tool, a Method for Implementing Same, and Storage Medium Storing Computer Readable Instructions for Instantiating the Zeus++ Code Tool

DTIC Science & Technology

1999-12-01

applications, it should be understood that the invention is not limited thereto. Those having - 9 - Navy Case No. 79694 ordinary skill in the art and access...processing. It should also be mentioned that Tecplot is a commercial plotting software package produced by Amtec Engineering, Inc. The following...conditions) 7. Ch (base on edge conditions) -43- 10 Navy Case No. 79694 8. Ch (base on reference conditions) 9 . Momentum thickness 10. Displacement

Software for Computing, Archiving, and Querying Semisimple Braided Monoidal Category Data

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

This software package collects various open source and freely available codes and algorithms to compute and archive the categorical data for certain semisimple braided monoidal categories. In particular, it computes the data for of group theoretical categories for academic research.

GENERAL PURPOSE ADA PACKAGES

NASA Technical Reports Server (NTRS)

Klumpp, A. R.

1994-01-01

Ten families of subprograms are bundled together for the General-Purpose Ada Packages. The families bring to Ada many features from HAL/S, PL/I, FORTRAN, and other languages. These families are: string subprograms (INDEX, TRIM, LOAD, etc.); scalar subprograms (MAX, MIN, REM, etc.); array subprograms (MAX, MIN, PROD, SUM, GET, and PUT); numerical subprograms (EXP, CUBIC, etc.); service subprograms (DATE_TIME function, etc.); Linear Algebra II; Runge-Kutta integrators; and three text I/O families of packages. In two cases, a family consists of a single non-generic package. In all other cases, a family comprises a generic package and its instances for a selected group of scalar types. All generic packages are designed to be easily instantiated for the types declared in the user facility. The linear algebra package is LINRAG2. This package includes subprograms supplementing those in NPO-17985, An Ada Linear Algebra Package Modeled After HAL/S (LINRAG). Please note that LINRAG2 cannot be compiled without LINRAG. Most packages have widespread applicability, although some are oriented for avionics applications. All are designed to facilitate writing new software in Ada. Several of the packages use conventions introduced by other programming languages. A package of string subprograms is based on HAL/S (a language designed for the avionics software in the Space Shuttle) and PL/I. Packages of scalar and array subprograms are taken from HAL/S or generalized current Ada subprograms. A package of Runge-Kutta integrators is patterned after a built-in MAC (MIT Algebraic Compiler) integrator. Those packages modeled after HAL/S make it easy to translate existing HAL/S software to Ada. The General-Purpose Ada Packages program source code is available on two 360K 5.25" MS-DOS format diskettes. The software was developed using VAX Ada v1.5 under DEC VMS v4.5. It should be portable to any validated Ada compiler and it should execute either interactively or in batch. The largest package requires 205K of main memory on a DEC VAX running VMS. The software was developed in 1989, and is a copyrighted work with all copyright vested in NASA.

Light element opacities of astrophysical interest from ATOMIC

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

Colgan, J.; Kilcrease, D. P.; Magee, N. H. Jr.

We present new calculations of local-thermodynamic-equilibrium (LTE) light element opacities from the Los Alamos ATOMIC code for systems of astrophysical interest. ATOMIC is a multi-purpose code that can generate LTE or non-LTE quantities of interest at various levels of approximation. Our calculations, which include fine-structure detail, represent a systematic improvement over previous Los Alamos opacity calculations using the LEDCOP legacy code. The ATOMIC code uses ab-initio atomic structure data computed from the CATS code, which is based on Cowan's atomic structure codes, and photoionization cross section data computed from the Los Alamos ionization code GIPPER. ATOMIC also incorporates a newmore » equation-of-state (EOS) model based on the chemical picture. ATOMIC incorporates some physics packages from LEDCOP and also includes additional physical processes, such as improved free-free cross sections and additional scattering mechanisms. Our new calculations are made for elements of astrophysical interest and for a wide range of temperatures and densities.« less

WDEC: A Code for Modeling White Dwarf Structure and Pulsations

NASA Astrophysics Data System (ADS)

Bischoff-Kim, Agnès; Montgomery, Michael H.

2018-05-01

The White Dwarf Evolution Code (WDEC), written in Fortran, makes models of white dwarf stars. It is fast, versatile, and includes the latest physics. The code evolves hot (∼100,000 K) input models down to a chosen effective temperature by relaxing the models to be solutions of the equations of stellar structure. The code can also be used to obtain g-mode oscillation modes for the models. WDEC has a long history going back to the late 1960s. Over the years, it has been updated and re-packaged for modern computer architectures and has specifically been used in computationally intensive asteroseismic fitting. Generations of white dwarf astronomers and dozens of publications have made use of the WDEC, although the last true instrument paper is the original one, published in 1975. This paper discusses the history of the code, necessary to understand why it works the way it does, details the physics and features in the code today, and points the reader to where to find the code and a user guide.

Various Approaches to Forward and Inverse Wide-Angle Seismic Modelling Tested on Data from DOBRE-4 Experiment

NASA Astrophysics Data System (ADS)

Janik, Tomasz; Środa, Piotr; Czuba, Wojciech; Lysynchuk, Dmytro

2016-12-01

The interpretation of seismic refraction and wide angle reflection data usually involves the creation of a velocity model based on an inverse or forward modelling of the travel times of crustal and mantle phases using the ray theory approach. The modelling codes differ in terms of model parameterization, data used for modelling, regularization of the result, etc. It is helpful to know the capabilities, advantages and limitations of the code used compared to others. This work compares some popular 2D seismic modelling codes using the dataset collected along the seismic wide-angle profile DOBRE-4, where quite peculiar/uncommon reflected phases were observed in the wavefield. The 505 km long profile was realized in southern Ukraine in 2009, using 13 shot points and 230 recording stations. Double PMP phases with a different reduced time (7.5-11 s) and a different apparent velocity, intersecting each other, are observed in the seismic wavefield. This is the most striking feature of the data. They are interpreted as reflections from strongly dipping Moho segments with an opposite dip. Two steps were used for the modelling. In the previous work by Starostenko et al. (2013), the trial-and-error forward model based on refracted and reflected phases (SEIS83 code) was published. The interesting feature is the high-amplitude (8-17 km) variability of the Moho depth in the form of downward and upward bends. This model is compared with results from other seismic inversion methods: the first arrivals tomography package FAST based on first arrivals; the JIVE3D code, which can also use later refracted arrivals and reflections; and the forward and inversion code RAYINVR using both refracted and reflected phases. Modelling with all the codes tested showed substantial variability of the Moho depth along the DOBRE-4 profile. However, SEIS83 and RAYINVR packages seem to give the most coincident results.

Parallelization of Rocket Engine System Software (Press)

NASA Technical Reports Server (NTRS)

Cezzar, Ruknet

1996-01-01

The main goal is to assess parallelization requirements for the Rocket Engine Numeric Simulator (RENS) project which, aside from gathering information on liquid-propelled rocket engines and setting forth requirements, involve a large FORTRAN based package at NASA Lewis Research Center and TDK software developed by SUBR/UWF. The ultimate aim is to develop, test, integrate, and suitably deploy a family of software packages on various aspects and facets of rocket engines using liquid-propellants. At present, all project efforts by the funding agency, NASA Lewis Research Center, and the HBCU participants are disseminated over the internet using world wide web home pages. Considering obviously expensive methods of actual field trails, the benefits of software simulators are potentially enormous. When realized, these benefits will be analogous to those provided by numerous CAD/CAM packages and flight-training simulators. According to the overall task assignments, Hampton University's role is to collect all available software, place them in a common format, assess and evaluate, define interfaces, and provide integration. Most importantly, the HU's mission is to see to it that the real-time performance is assured. This involves source code translations, porting, and distribution. The porting will be done in two phases: First, place all software on Cray XMP platform using FORTRAN. After testing and evaluation on the Cray X-MP, the code will be translated to C + + and ported to the parallel nCUBE platform. At present, we are evaluating another option of distributed processing over local area networks using Sun NFS, Ethernet, TCP/IP. Considering the heterogeneous nature of the present software (e.g., first started as an expert system using LISP machines) which now involve FORTRAN code, the effort is expected to be quite challenging.

DarkBit: a GAMBIT module for computing dark matter observables and likelihoods

NASA Astrophysics Data System (ADS)

Bringmann, Torsten; Conrad, Jan; Cornell, Jonathan M.; Dal, Lars A.; Edsjö, Joakim; Farmer, Ben; Kahlhoefer, Felix; Kvellestad, Anders; Putze, Antje; Savage, Christopher; Scott, Pat; Weniger, Christoph; White, Martin; Wild, Sebastian

2017-12-01

We introduce DarkBit, an advanced software code for computing dark matter constraints on various extensions to the Standard Model of particle physics, comprising both new native code and interfaces to external packages. This release includes a dedicated signal yield calculator for gamma-ray observations, which significantly extends current tools by implementing a cascade-decay Monte Carlo, as well as a dedicated likelihood calculator for current and future experiments ( gamLike). This provides a general solution for studying complex particle physics models that predict dark matter annihilation to a multitude of final states. We also supply a direct detection package that models a large range of direct detection experiments ( DDCalc), and that provides the corresponding likelihoods for arbitrary combinations of spin-independent and spin-dependent scattering processes. Finally, we provide custom relic density routines along with interfaces to DarkSUSY, micrOMEGAs, and the neutrino telescope likelihood package nulike. DarkBit is written in the framework of the Global And Modular Beyond the Standard Model Inference Tool ( GAMBIT), providing seamless integration into a comprehensive statistical fitting framework that allows users to explore new models with both particle and astrophysics constraints, and a consistent treatment of systematic uncertainties. In this paper we describe its main functionality, provide a guide to getting started quickly, and show illustrative examples for results obtained with DarkBit (both as a stand-alone tool and as a GAMBIT module). This includes a quantitative comparison between two of the main dark matter codes ( DarkSUSY and micrOMEGAs), and application of DarkBit 's advanced direct and indirect detection routines to a simple effective dark matter model.

GOplot: an R package for visually combining expression data with functional analysis.

PubMed

Walter, Wencke; Sánchez-Cabo, Fátima; Ricote, Mercedes

2015-09-01

Despite the plethora of methods available for the functional analysis of omics data, obtaining comprehensive-yet detailed understanding of the results remains challenging. This is mainly due to the lack of publicly available tools for the visualization of this type of information. Here we present an R package called GOplot, based on ggplot2, for enhanced graphical representation. Our package takes the output of any general enrichment analysis and generates plots at different levels of detail: from a general overview to identify the most enriched categories (bar plot, bubble plot) to a more detailed view displaying different types of information for molecules in a given set of categories (circle plot, chord plot, cluster plot). The package provides a deeper insight into omics data and allows scientists to generate insightful plots with only a few lines of code to easily communicate the findings. The R package GOplot is available via CRAN-The Comprehensive R Archive Network: http://cran.r-project.org/web/packages/GOplot. The shiny web application of the Venn diagram can be found at: https://wwalter.shinyapps.io/Venn/. A detailed manual of the package with sample figures can be found at https://wencke.github.io/ fscabo@cnic.es or mricote@cnic.es. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

SIMA: Python software for analysis of dynamic fluorescence imaging data.

PubMed

Kaifosh, Patrick; Zaremba, Jeffrey D; Danielson, Nathan B; Losonczy, Attila

2014-01-01

Fluorescence imaging is a powerful method for monitoring dynamic signals in the nervous system. However, analysis of dynamic fluorescence imaging data remains burdensome, in part due to the shortage of available software tools. To address this need, we have developed SIMA, an open source Python package that facilitates common analysis tasks related to fluorescence imaging. Functionality of this package includes correction of motion artifacts occurring during in vivo imaging with laser-scanning microscopy, segmentation of imaged fields into regions of interest (ROIs), and extraction of signals from the segmented ROIs. We have also developed a graphical user interface (GUI) for manual editing of the automatically segmented ROIs and automated registration of ROIs across multiple imaging datasets. This software has been designed with flexibility in mind to allow for future extension with different analysis methods and potential integration with other packages. Software, documentation, and source code for the SIMA package and ROI Buddy GUI are freely available at http://www.losonczylab.org/sima/.

graphkernels: R and Python packages for graph comparison

PubMed Central

Ghisu, M Elisabetta; Llinares-López, Felipe; Borgwardt, Karsten

2018-01-01

Abstract Summary Measuring the similarity of graphs is a fundamental step in the analysis of graph-structured data, which is omnipresent in computational biology. Graph kernels have been proposed as a powerful and efficient approach to this problem of graph comparison. Here we provide graphkernels, the first R and Python graph kernel libraries including baseline kernels such as label histogram based kernels, classic graph kernels such as random walk based kernels, and the state-of-the-art Weisfeiler-Lehman graph kernel. The core of all graph kernels is implemented in C ++ for efficiency. Using the kernel matrices computed by the package, we can easily perform tasks such as classification, regression and clustering on graph-structured samples. Availability and implementation The R and Python packages including source code are available at https://CRAN.R-project.org/package=graphkernels and https://pypi.python.org/pypi/graphkernels. Contact mahito@nii.ac.jp or elisabetta.ghisu@bsse.ethz.ch Supplementary information Supplementary data are available online at Bioinformatics. PMID:29028902

Cluster-lensing: A Python Package for Galaxy Clusters and Miscentering

NASA Astrophysics Data System (ADS)

Ford, Jes; VanderPlas, Jake

2016-12-01

We describe a new open source package for calculating properties of galaxy clusters, including Navarro, Frenk, and White halo profiles with and without the effects of cluster miscentering. This pure-Python package, cluster-lensing, provides well-documented and easy-to-use classes and functions for calculating cluster scaling relations, including mass-richness and mass-concentration relations from the literature, as well as the surface mass density {{Σ }}(R) and differential surface mass density {{Δ }}{{Σ }}(R) profiles, probed by weak lensing magnification and shear. Galaxy cluster miscentering is especially a concern for stacked weak lensing shear studies of galaxy clusters, where offsets between the assumed and the true underlying matter distribution can lead to a significant bias in the mass estimates if not accounted for. This software has been developed and released in a public GitHub repository, and is licensed under the permissive MIT license. The cluster-lensing package is archived on Zenodo. Full documentation, source code, and installation instructions are available at http://jesford.github.io/cluster-lensing/.

graphkernels: R and Python packages for graph comparison.

PubMed

Sugiyama, Mahito; Ghisu, M Elisabetta; Llinares-López, Felipe; Borgwardt, Karsten

2018-02-01

Measuring the similarity of graphs is a fundamental step in the analysis of graph-structured data, which is omnipresent in computational biology. Graph kernels have been proposed as a powerful and efficient approach to this problem of graph comparison. Here we provide graphkernels, the first R and Python graph kernel libraries including baseline kernels such as label histogram based kernels, classic graph kernels such as random walk based kernels, and the state-of-the-art Weisfeiler-Lehman graph kernel. The core of all graph kernels is implemented in C ++ for efficiency. Using the kernel matrices computed by the package, we can easily perform tasks such as classification, regression and clustering on graph-structured samples. The R and Python packages including source code are available at https://CRAN.R-project.org/package=graphkernels and https://pypi.python.org/pypi/graphkernels. mahito@nii.ac.jp or elisabetta.ghisu@bsse.ethz.ch. Supplementary data are available online at Bioinformatics. © The Author(s) 2017. Published by Oxford University Press.

Consumer preferences for beef color and packaging did not affect eating satisfaction.

PubMed

Carpenter, C E; Cornforth, D P; Whittier, D

2001-04-01

We investigated whether consumer preferences for beef colors (red, purple, and brown) or for beef packaging systems (modified atmosphere, MAP; vacuum skin pack, VSP; or overwrap with polyvinyl chloride, PVC) influenced taste scores of beef steaks and patties. To test beef color effects, boneless beef top loin steaks (choice) and ground beef patties (20% fat) were packaged in different atmospheres to promote development of red, purple, and brown color. To test effects of package type, steaks and patties were pre-treated with carbon monoxide in MAP to promote development of red color, and some meat was repackaged using VSP or PVC overwrap. The differently colored and packaged meats were separately displayed for members of four consumer panels who evaluated appearance and indicated their likelihood to purchase similar meat. Next, the panelists tasted meat samples from what they had been told were the packaging treatments just observed. However, the meat samples actually served were from a single untreated steak or patty. Thus, any difference in taste scores should reflect expectations established during the visual evaluation. The same ballot and sample coding were used for both the visual and taste evaluations. Color and packaging influenced (P<0.001) appearance scores and likelihood to purchase. Appearance scores were rated red>purple >brown and PVC >VSP>MAP. Appearance scores and likelihood to purchase were correlated (r=0.9). However, color or packaging did not affect (P>0.5) taste scores. Thus, consumer preferences for beef color and packaging influenced likelihood to purchase, but did not bias eating satisfaction.

Aquarius - A Modelling Package for Groundwater Flow and Coupled Heat Transport in the Range 0.1 to 100 MPa and 0.1 to 1000 C

NASA Astrophysics Data System (ADS)

Cook, S. J.

2009-05-01

Aquarius is a Windows application that models fluid flow and heat transport under conditions in which fluid buoyancy can significantly impact patterns and magnitudes of fluid flow. The package is designed as a visualization tool through which users can examine flow systems in environments, both low temperature aquifers and regions with elevated PT regimes such as deep sedimentary basins, hydrothermal systems, and contact thermal aureoles. The package includes 4 components: (1) A finite-element mesh generator/assembler capable of representing complex geologic structures. Left-hand, right-hand and alternating linear triangles can be mixed within the mesh. Planer horizontal, planer vertical and cylindrical vertical coordinate sections are supported. (2) A menu-selectable system for setting properties and boundary/initial conditions. The design retains mathematical terminology for all input parameters such as scalars (e.g., porosity), tensors (e.g., permeability), and boundary/initial conditions (e.g., fixed potential). This makes the package an effective instructional aide by linking model requirements with the underlying mathematical concepts of partial differential equations and the solution logic of boundary/initial value problems. (3) Solution algorithms for steady-state and time-transient fluid flow/heat transport problems. For all models, the nonlinear global matrix equations are solved sequentially using over-relaxation techniques. Matrix storage design allows for large (e.g., 20000) element models to run efficiently on a typical PC. (4) A plotting system that supports contouring nodal data (e.g., head), vector plots for flux data (e.g., specific discharge), and colour gradient plots for elemental data (e.g., porosity), water properties (e.g., density), and performance measures (e.g., Peclet numbers). Display graphics can be printed or saved in standard graphic formats (e.g., jpeg). This package was developed from procedural codes in C written originally to model the hydrothermal flow system responsible for contact metamorphism of Utah's Alta Stock (Cook et al., AJS 1997). These codes were reprogrammed in Microsoft C# to take advantage of object oriented design and the capabilities of Microsoft's .NET framework. The package is available at no cost by e-mail request from the author.

PMIX_Ring patch for SLURM

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

Moody, A. T.

2014-04-20

This code adds an implementation of PMIX_Ring to the existing PM12 Library in the SLURM open source software package (Simple Linux Utility for Resource Management). PMIX_Ring executes a particular communication pattern that is used to bootstrap connections between MPI processes in a parallel job.

Efficient Calculation of Exact Exchange Within the Quantum Espresso Software Package

NASA Astrophysics Data System (ADS)

Barnes, Taylor; Kurth, Thorsten; Carrier, Pierre; Wichmann, Nathan; Prendergast, David; Kent, Paul; Deslippe, Jack

Accurate simulation of condensed matter at the nanoscale requires careful treatment of the exchange interaction between electrons. In the context of plane-wave DFT, these interactions are typically represented through the use of approximate functionals. Greater accuracy can often be obtained through the use of functionals that incorporate some fraction of exact exchange; however, evaluation of the exact exchange potential is often prohibitively expensive. We present an improved algorithm for the parallel computation of exact exchange in Quantum Espresso, an open-source software package for plane-wave DFT simulation. Through the use of aggressive load balancing and on-the-fly transformation of internal data structures, our code exhibits speedups of approximately an order of magnitude for practical calculations. Additional optimizations are presented targeting the many-core Intel Xeon-Phi ``Knights Landing'' architecture, which largely powers NERSC's new Cori system. We demonstrate the successful application of the code to difficult problems, including simulation of water at a platinum interface and computation of the X-ray absorption spectra of transition metal oxides.

AIRSLUG: A fortran program for the computation of type curves to estimate transmissivity and storativity from prematurely terminated air-pressurized slug tests

USGS Publications Warehouse

Greene, E.A.; Shapiro, A.M.

1998-01-01

The Fortran code AIRSLUG can be used to generate the type curves needed to analyze the recovery data from prematurely terminated air-pressurized slug tests. These type curves, when used with a graphical software package, enable the engineer or scientist to analyze field tests to estimate transmissivity and storativity. Prematurely terminating the slug test can significantly reduce the overall time needed to conduct the test, especially at low-permeability sites, thus saving time and money.The Fortran code AIRSLUG can be used to generate the type curves needed to analyze the recovery data from prematurely terminated air-pressurized slug tests. These type curves, when used with a graphical software package, enable the engineer or scientist to analyze field tests to estimate transmissivity and storativity. Prematurely terminating the slug test can significantly reduce the overall time needed to conduct the test, especially at low-permeability sites, thus saving time and money.

PyVCI: A flexible open-source code for calculating accurate molecular infrared spectra

NASA Astrophysics Data System (ADS)

Sibaev, Marat; Crittenden, Deborah L.

2016-06-01

The PyVCI program package is a general purpose open-source code for simulating accurate molecular spectra, based upon force field expansions of the potential energy surface in normal mode coordinates. It includes harmonic normal coordinate analysis and vibrational configuration interaction (VCI) algorithms, implemented primarily in Python for accessibility but with time-consuming routines written in C. Coriolis coupling terms may be optionally included in the vibrational Hamiltonian. Non-negligible VCI matrix elements are stored in sparse matrix format to alleviate the diagonalization problem. CPU and memory requirements may be further controlled by algorithmic choices and/or numerical screening procedures, and recommended values are established by benchmarking using a test set of 44 molecules for which accurate analytical potential energy surfaces are available. Force fields in normal mode coordinates are obtained from the PyPES library of high quality analytical potential energy surfaces (to 6th order) or by numerical differentiation of analytic second derivatives generated using the GAMESS quantum chemical program package (to 4th order).

Advanced complex trait analysis.

PubMed

Gray, A; Stewart, I; Tenesa, A

2012-12-01

The Genome-wide Complex Trait Analysis (GCTA) software package can quantify the contribution of genetic variation to phenotypic variation for complex traits. However, as those datasets of interest continue to increase in size, GCTA becomes increasingly computationally prohibitive. We present an adapted version, Advanced Complex Trait Analysis (ACTA), demonstrating dramatically improved performance. We restructure the genetic relationship matrix (GRM) estimation phase of the code and introduce the highly optimized parallel Basic Linear Algebra Subprograms (BLAS) library combined with manual parallelization and optimization. We introduce the Linear Algebra PACKage (LAPACK) library into the restricted maximum likelihood (REML) analysis stage. For a test case with 8999 individuals and 279,435 single nucleotide polymorphisms (SNPs), we reduce the total runtime, using a compute node with two multi-core Intel Nehalem CPUs, from ∼17 h to ∼11 min. The source code is fully available under the GNU Public License, along with Linux binaries. For more information see http://www.epcc.ed.ac.uk/software-products/acta. a.gray@ed.ac.uk Supplementary data are available at Bioinformatics online.

Practical Thermal Evaluation Methods For HAC Fire Analysis In Type B Radiaoactive Material (RAM) Packages

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

Abramczyk, Glenn; Hensel, Stephen J; Gupta, Narendra K.

Title 10 of the United States Code of Federal Regulations Part 71 for the Nuclear Regulatory Commission (10 CFR Part 71.73) requires that Type B radioactive material (RAM) packages satisfy certain Hypothetical Accident Conditions (HAC) thermal design requirements to ensure package safety during accidental fire conditions. Compliance with thermal design requirements can be met by prototype tests, analyses only or a combination of tests and analyses. Normally, it is impractical to meet all the HAC using tests only and the analytical methods are too complex due to the multi-physics non-linear nature of the fire event. Therefore, a combination of testsmore » and thermal analyses methods using commercial heat transfer software are used to meet the necessary design requirements. The authors, along with his other colleagues at Savannah River National Laboratory in Aiken, SC, USA, have successfully used this 'tests and analyses' approach in the design and certification of several United States' DOE/NNSA certified packages, e.g. 9975, 9977, 9978, 9979, H1700, and Bulk Tritium Shipping Package (BTSP). This paper will describe these methods and it is hoped that the RAM Type B package designers and analysts can use them for their applications.« less

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

Kelly, D L

The US Department of Energy (DOE) has been conducting, through several of its operating contractors, an evaluation and testing program to qualify Type A radioactive material packagings per US Department of Transportation (DOT) Specification 7A (DOT-7A) of the Code of Federal Regulations (CFR), Title 49, Part 178 (49 CFR 178). This document summarizes the evaluation and testing performed for all of the packagings successfully qualified in this program. This document supersedes DOE Evaluation Document for DOT-7A Type A Packaging (Edling 1987), originally issued in 1987 by Monsanto Research Corporation Mound Laboratory (MLM), Miamisburg, Ohio, for the Department of Energy, Securitymore » Evaluation Program (I)P-4. Mound Laboratory issued four revisions to the document between November 1988 and December 1989. In September 1989, the program was transferred to Westinghouse Hanford Company (Westinghouse Hanford) in Richland, Washington. One additional revision was issued in March 1990 by Westinghouse Hanford. This revision reflects the earlier material and incorporates a number of changes. Evaluation and testing activities on 1208 three DOT-7A Program Dockets resulted in the qualification of three new packaging configurations, which are incorporated herein and summarized. This document presents approximately 300 different packagings that have been determined to meet the requirements for a DOT-7A, type A packaging per 49 CFR 178.350.« less

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

Anderson, James; Goins, Monty; Paul, Pran

This safety analysis report for packaging (SARP) presents the results of the safety analysis prepared in support of the Consolidated Nuclear Security, LLC (CNS) request for licensing of the Model ES-3100 package with bulk highly enriched uranium (HEU) contents and issuance of a Type B(U) Fissile Material Certificate of Compliance. This SARP, published in the format specified in the Nuclear Regulatory Commission (NRC) Regulatory Guide 7.9 and using information provided in UCID-21218 and NRC Regulatory Guide 7.10, demonstrates that the Y-12 National Security Complex (Y-12) ES-3100 package with bulk HEU contents meets the established NRC regulations for packaging, preparation formore » shipment, and transportation of radioactive materials given in Title 10, Part 71, of the Code of Federal Regulations (CFR) [10 CFR 71] as well as U.S. Department of Transportation (DOT) regulations for packaging and shipment of hazardous materials given in Title 49 CFR. To protect the health and safety of the public, shipments of adioactive materials are made in packaging that is designed, fabricated, assembled, tested, procured, used, maintained, and repaired in accordance with the provisions cited above. Safety requirements addressed by the regulations that must be met when transporting radioactive materials are containment of radioactive materials, radiation shielding, and assurance of nuclear subcriticality.« less

The complex metal-rich boride Ti1+xRh2-x+yIr3-yB3 (x=0.68, y=1.06) with a new structure type containing B4 zigzag fragments: Synthesis, crystal chemistry and theoretical calculations

NASA Astrophysics Data System (ADS)

Goerens, Christian; Fokwa, Boniface P. T.

2012-08-01

Polycrystalline samples and single crystals of the new complex boride Ti1+xRh2-x+yIr3-yB3 (x=0.68; y=1.06) were synthesized by arc-melting the elements in a water-cooled copper crucible under an argon atmosphere and characterized by X-Ray diffraction as well as EDX measurements. The crystal structure was refined on the basis of single crystal data. The new phase, which represents a new structure type containing trans zigzag B4 fragments as well as isolated boron atoms crystallizes in the orthorhombic space group Pbam (Nr. 55) with the lattice parameters a=8.620(1) Å, b=14.995(2) Å and c=3.234(1) Å. First-principles density functional theory calculations using the Vienna ab-initio simulation package (VASP) were performed on an appropriate structural model (using a supercell approach) and the experimental crystallographic data could be reproduced accurately. Based on this model, the density of states and crystal orbital Hamilton population (for bonding analysis) were calculated, using the linear muffin-tin orbital atomic sphere approximation (LMTO-ASA) method. According to these calculations, this metal-rich compound should be metallic, as expected. Furthermore, very strong boron-boron interactions are observed in the trans zigzag B4 fragment, which induce a clear differentiation of two types of metal-boron contacts with different strength. The observed three-dimensional metal-metal interaction is in good agreement with the predicted metallic behavior.

Periodic density functional theory calculations of bulk and the (010) surface of goethite

PubMed Central

Kubicki, James D; Paul, Kristian W; Sparks, Donald L

2008-01-01

Background Goethite is a common and reactive mineral in the environment. The transport of contaminants and anaerobic respiration of microbes are significantly affected by adsorption and reduction reactions involving goethite. An understanding of the mineral-water interface of goethite is critical for determining the molecular-scale mechanisms of adsorption and reduction reactions. In this study, periodic density functional theory (DFT) calculations were performed on the mineral goethite and its (010) surface, using the Vienna Ab Initio Simulation Package (VASP). Results Calculations of the bulk mineral structure accurately reproduced the observed crystal structure and vibrational frequencies, suggesting that this computational methodology was suitable for modeling the goethite-water interface. Energy-minimized structures of bare, hydrated (one H2O layer) and solvated (three H2O layers) (010) surfaces were calculated for 1 × 1 and 3 × 3 unit cell slabs. A good correlation between the calculated and observed vibrational frequencies was found for the 1 × 1 solvated surface. However, differences between the 1 × 1 and 3 × 3 slab calculations indicated that larger models may be necessary to simulate the relaxation of water at the interface. Comparison of two hydrated surfaces with molecularly and dissociatively adsorbed H2O showed a significantly lower potential energy for the former. Conclusion Surface Fe-O and (Fe)O-H bond lengths are reported that may be useful in surface complexation models (SCM) of the goethite (010) surface. These bond lengths were found to change significantly as a function of solvation (i.e., addition of two extra H2O layers above the surface), indicating that this parameter should be carefully considered in future SCM studies of metal oxide-water interfaces. PMID:18477389

An ab initio study on the structural, electronic and mechanical properties of quaternary full-Heusler alloys FeMnCrSn and FeMnCrSb

NASA Astrophysics Data System (ADS)

Erkişi, Aytaç

2018-06-01

The quaternary full Heusler alloys FeMnCrSn and FeMnCrSb, which have face-centred cubic (FCC) crystal structure and conform to ? space group with 216 space number, have been investigated using Generalised Gradient Approximation (GGA) in the Density Functional Theory (DFT) as implemented in VASP (Vienna Ab initio Simulation Package) software. These alloys are considered in ferromagnetic (FM) order. After the investigation of structural stability of these alloys, their mechanical and thermal properties and also electronic band structures have been examined. The calculated spin-polarised electronic band structures and total electronic density of states (DOS) within GGA approximation show that these alloys can exhibit both metallic and half-metallic characters in different structural phases. The calculated formation enthalpies and the plotted energy-volume graphs show that Type-III phase is most stable structural phase for these materials. Also, FeMnCrSb alloy in Type-I/Type-III phases and FeMnCrSn alloy in Type-III phase show half-metallic behaviour with integer total magnetic moments almost 2 and 1 μB per formula unit, respectively, since there are band gaps observed in spin-down states, whereas they have metallic behaviour in majority bands. Other structural phases of both systems are also metallic. Moreover, the calculated elastic constants and the estimated anisotropy shear factors indicate that these materials are stable mechanically in all of three phases except FeMnCrSn in Type-I phase that does not satisfy Born stability criteria in this phase and have high anisotropic behaviour.

Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms.

PubMed

Cerveau, Nicolas; Jackson, Daniel J

2016-12-09

Next-generation sequencing (NGS) technologies are arguably the most revolutionary technical development to join the list of tools available to molecular biologists since PCR. For researchers working with nonconventional model organisms one major problem with the currently dominant NGS platform (Illumina) stems from the obligatory fragmentation of nucleic acid material that occurs prior to sequencing during library preparation. This step creates a significant bioinformatic challenge for accurate de novo assembly of novel transcriptome data. This challenge becomes apparent when a variety of modern assembly tools (of which there is no shortage) are applied to the same raw NGS dataset. With the same assembly parameters these tools can generate markedly different assembly outputs. In this study we present an approach that generates an optimized consensus de novo assembly of eukaryotic coding transcriptomes. This approach does not represent a new assembler, rather it combines the outputs of a variety of established assembly packages, and removes redundancy via a series of clustering steps. We test and validate our approach using Illumina datasets from six phylogenetically diverse eukaryotes (three metazoans, two plants and a yeast) and two simulated datasets derived from metazoan reference genome annotations. All of these datasets were assembled using three currently popular assembly packages (CLC, Trinity and IDBA-tran). In addition, we experimentally demonstrate that transcripts unique to one particular assembly package are likely to be bioinformatic artefacts. For all eight datasets our pipeline generates more concise transcriptomes that in fact possess more unique annotatable protein domains than any of the three individual assemblers we employed. Another measure of assembly completeness (using the purpose built BUSCO databases) also confirmed that our approach yields more information. Our approach yields coding transcriptome assemblies that are more likely to be closer to biological reality than any of the three individual assembly packages we investigated. This approach (freely available as a simple perl script) will be of use to researchers working with species for which there is little or no reference data against which the assembly of a transcriptome can be performed.

PyPanda: a Python package for gene regulatory network reconstruction

PubMed Central

van IJzendoorn, David G.P.; Glass, Kimberly; Quackenbush, John; Kuijjer, Marieke L.

2016-01-01

Summary: PANDA (Passing Attributes between Networks for Data Assimilation) is a gene regulatory network inference method that uses message-passing to integrate multiple sources of ‘omics data. PANDA was originally coded in C ++. In this application note we describe PyPanda, the Python version of PANDA. PyPanda runs considerably faster than the C ++ version and includes additional features for network analysis. Availability and implementation: The open source PyPanda Python package is freely available at http://github.com/davidvi/pypanda. Contact: mkuijjer@jimmy.harvard.edu or d.g.p.van_ijzendoorn@lumc.nl PMID:27402905

PyPanda: a Python package for gene regulatory network reconstruction.

PubMed

van IJzendoorn, David G P; Glass, Kimberly; Quackenbush, John; Kuijjer, Marieke L

2016-11-01

PANDA (Passing Attributes between Networks for Data Assimilation) is a gene regulatory network inference method that uses message-passing to integrate multiple sources of 'omics data. PANDA was originally coded in C ++. In this application note we describe PyPanda, the Python version of PANDA. PyPanda runs considerably faster than the C ++ version and includes additional features for network analysis. The open source PyPanda Python package is freely available at http://github.com/davidvi/pypanda CONTACT: mkuijjer@jimmy.harvard.edu or d.g.p.van_ijzendoorn@lumc.nl. © The Author 2016. Published by Oxford University Press.

Finite element for rotor/stator interactive forces in general engine dynamic simulation. Part 1: Development of bearing damper element

NASA Technical Reports Server (NTRS)

Adams, M. L.; Padovan, J.; Fertis, D. G.

1980-01-01

A general purpose squeeze-film damper interactive force element was developed, coded into a software package (module) and debugged. This software package was applied to nonliner dynamic analyses of some simple rotor systems. Results for pressure distributions show that the long bearing (end sealed) is a stronger bearing as compared to the short bearing as expected. Results of the nonlinear dynamic analysis, using a four degree of freedom simulation model, showed that the orbit of the rotating shaft increases nonlinearity to fill the bearing clearance as the unbalanced weight increases.

Coding considerations for standalone molecular dynamics simulations of atomistic structures

NASA Astrophysics Data System (ADS)

Ocaya, R. O.; Terblans, J. J.

2017-10-01

The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

A Character Segmentation Proposal for High-Speed Visual Monitoring of Expiration Codes on Beverage Cans.

PubMed

Rodríguez-Rodríguez, José C; Quesada-Arencibia, Alexis; Moreno-Díaz, Roberto; García, Carmelo R

2016-04-13

Expiration date labels are ubiquitous in the food industry. With the passage of time, almost any food becomes unhealthy, even when well preserved. The expiration date is estimated based on the type and manufacture/packaging time of that particular food unit. This date is then printed on the container so it is available to the end user at the time of consumption. MONICOD (MONItoring of CODes); an industrial validator of expiration codes; allows the expiration code printed on a drink can to be read. This verification occurs immediately after printing. MONICOD faces difficulties due to the high printing rate (35 cans per second) and problematic lighting caused by the metallic surface on which the code is printed. This article describes a solution that allows MONICOD to extract shapes and presents quantitative results for the speed and quality.

Deciphering the role of the Gag-Pol ribosomal frameshift signal in HIV-1 RNA genome packaging.

PubMed

Nikolaitchik, Olga A; Hu, Wei-Shau

2014-04-01

A key step of retroviral replication is packaging of the viral RNA genome during virus assembly. Specific packaging is mediated by interactions between the viral protein Gag and elements in the viral RNA genome. In HIV-1, similar to most retroviruses, the packaging signal is located within the 5' untranslated region and extends into the gag-coding region. A recent study reported that a region including the Gag-Pol ribosomal frameshift signal plays an important role in HIV-1 RNA packaging; deletions or mutations that affect the RNA structure of this signal lead to drastic decreases (10- to 50-fold) in viral RNA packaging and virus titer. We examined here the role of the ribosomal frameshift signal in HIV-1 RNA packaging by studying the RNA packaging and virus titer in the context of proviruses. Three mutants with altered ribosomal frameshift signal, either through direct deletion of the signal, mutation of the 6U slippery sequence, or alterations of the secondary structure were examined. We found that RNAs from all three mutants were packaged efficiently, and they generate titers similar to that of a virus containing the wild-type ribosomal frameshift signal. We conclude that although the ribosomal frameshift signal plays an important role in regulating the replication cycle, this RNA element is not directly involved in regulating RNA encapsidation. To generate infectious viruses, HIV-1 must package viral RNA genome during virus assembly. The specific HIV-1 genome packaging is mediated by interactions between the structural protein Gag and elements near the 5' end of the viral RNA known as packaging signal. In this study, we examined whether the Gag-Pol ribosomal frameshift signal is important for HIV-1 RNA packaging as recently reported. Our results demonstrated that when Gag/Gag-Pol is supplied in trans, none of the tested ribosomal frameshift signal mutants has defects in RNA packaging or virus titer. These studies provide important information on how HIV-1 regulates its genome packaging and generate infectious viruses necessary for transmission to new hosts.

Deciphering the Role of the Gag-Pol Ribosomal Frameshift Signal in HIV-1 RNA Genome Packaging

PubMed Central

Nikolaitchik, Olga A.

2014-01-01

ABSTRACT A key step of retroviral replication is packaging of the viral RNA genome during virus assembly. Specific packaging is mediated by interactions between the viral protein Gag and elements in the viral RNA genome. In HIV-1, similar to most retroviruses, the packaging signal is located within the 5′ untranslated region and extends into the gag-coding region. A recent study reported that a region including the Gag-Pol ribosomal frameshift signal plays an important role in HIV-1 RNA packaging; deletions or mutations that affect the RNA structure of this signal lead to drastic decreases (10- to 50-fold) in viral RNA packaging and virus titer. We examined here the role of the ribosomal frameshift signal in HIV-1 RNA packaging by studying the RNA packaging and virus titer in the context of proviruses. Three mutants with altered ribosomal frameshift signal, either through direct deletion of the signal, mutation of the 6U slippery sequence, or alterations of the secondary structure were examined. We found that RNAs from all three mutants were packaged efficiently, and they generate titers similar to that of a virus containing the wild-type ribosomal frameshift signal. We conclude that although the ribosomal frameshift signal plays an important role in regulating the replication cycle, this RNA element is not directly involved in regulating RNA encapsidation. IMPORTANCE To generate infectious viruses, HIV-1 must package viral RNA genome during virus assembly. The specific HIV-1 genome packaging is mediated by interactions between the structural protein Gag and elements near the 5′ end of the viral RNA known as packaging signal. In this study, we examined whether the Gag-Pol ribosomal frameshift signal is important for HIV-1 RNA packaging as recently reported. Our results demonstrated that when Gag/Gag-Pol is supplied in trans, none of the tested ribosomal frameshift signal mutants has defects in RNA packaging or virus titer. These studies provide important information on how HIV-1 regulates its genome packaging and generate infectious viruses necessary for transmission to new hosts. PMID:24453371

Moving code - Sharing geoprocessing logic on the Web

NASA Astrophysics Data System (ADS)

Müller, Matthias; Bernard, Lars; Kadner, Daniel

2013-09-01

Efficient data processing is a long-standing challenge in remote sensing. Effective and efficient algorithms are required for product generation in ground processing systems, event-based or on-demand analysis, environmental monitoring, and data mining. Furthermore, the increasing number of survey missions and the exponentially growing data volume in recent years have created demand for better software reuse as well as an efficient use of scalable processing infrastructures. Solutions that address both demands simultaneously have begun to slowly appear, but they seldom consider the possibility to coordinate development and maintenance efforts across different institutions, community projects, and software vendors. This paper presents a new approach to share, reuse, and possibly standardise geoprocessing logic in the field of remote sensing. Drawing from the principles of service-oriented design and distributed processing, this paper introduces moving-code packages as self-describing software components that contain algorithmic code and machine-readable descriptions of the provided functionality, platform, and infrastructure, as well as basic information about exploitation rights. Furthermore, the paper presents a lean publishing mechanism by which to distribute these packages on the Web and to integrate them in different processing environments ranging from monolithic workstations to elastic computational environments or "clouds". The paper concludes with an outlook toward community repositories for reusable geoprocessing logic and their possible impact on data-driven science in general.

NIFTY - Numerical Information Field Theory. A versatile PYTHON library for signal inference

NASA Astrophysics Data System (ADS)

Selig, M.; Bell, M. R.; Junklewitz, H.; Oppermann, N.; Reinecke, M.; Greiner, M.; Pachajoa, C.; Enßlin, T. A.

2013-06-01

NIFTy (Numerical Information Field Theory) is a software package designed to enable the development of signal inference algorithms that operate regardless of the underlying spatial grid and its resolution. Its object-oriented framework is written in Python, although it accesses libraries written in Cython, C++, and C for efficiency. NIFTy offers a toolkit that abstracts discretized representations of continuous spaces, fields in these spaces, and operators acting on fields into classes. Thereby, the correct normalization of operations on fields is taken care of automatically without concerning the user. This allows for an abstract formulation and programming of inference algorithms, including those derived within information field theory. Thus, NIFTy permits its user to rapidly prototype algorithms in 1D, and then apply the developed code in higher-dimensional settings of real world problems. The set of spaces on which NIFTy operates comprises point sets, n-dimensional regular grids, spherical spaces, their harmonic counterparts, and product spaces constructed as combinations of those. The functionality and diversity of the package is demonstrated by a Wiener filter code example that successfully runs without modification regardless of the space on which the inference problem is defined. NIFTy homepage http://www.mpa-garching.mpg.de/ift/nifty/; Excerpts of this paper are part of the NIFTy source code and documentation.

3D Laser Imprint Using a Smoother Ray-Traced Power Deposition Method

NASA Astrophysics Data System (ADS)

Schmitt, Andrew J.

2017-10-01

Imprinting of laser nonuniformities in directly-driven icf targets is a challenging problem to accurately simulate with large radiation-hydro codes. One of the most challenging aspects is the proper construction of the complex and rapidly changing laser interference structure driving the imprint using the reduced laser propagation models (usually ray-tracing) found in these codes. We have upgraded the modelling capability in our massively-parallel fastrad3d code by adding a more realistic EM-wave interference structure. This interference model adds an axial laser speckle to the previous transverse-only laser structure, and can be impressed on our improved smoothed 3D raytrace package. This latter package, which connects rays to form bundles and performs power deposition calculations on the bundles, is intended to decrease ray-trace noise (which can mask or add to imprint) while using fewer rays. We apply this improved model to 3D simulations of recent imprint experiments performed on the Omega-EP laser and the Nike laser that examined the reduction of imprinting due to very thin high-Z target coatings. We report on the conditions in which this new model makes a significant impact on the development of laser imprint. Supported by US DoE/NNSA.

Safety Criticality Standards Using the French CRISTAL Code Package: Application to the AREVA NP UO{sub 2} Fuel Fabrication Plant

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

Doucet, M.; Durant Terrasson, L.; Mouton, J.

2006-07-01

Criticality safety evaluations implement requirements to proof of sufficient sub critical margins outside of the reactor environment for example in fuel fabrication plants. Basic criticality data (i.e., criticality standards) are used in the determination of sub critical margins for all processes involving plutonium or enriched uranium. There are several criticality international standards, e.g., ARH-600, which is one the US nuclear industry relies on. The French Nuclear Safety Authority (DGSNR and its advising body IRSN) has requested AREVA NP to review the criticality standards used for the evaluation of its Low Enriched Uranium fuel fabrication plants with CRISTAL V0, the recentlymore » updated French criticality evaluation package. Criticality safety is a concern for every phase of the fabrication process including UF{sub 6} cylinder storage, UF{sub 6}-UO{sub 2} conversion, powder storage, pelletizing, rod loading, assembly fabrication, and assembly transportation. Until 2003, the accepted criticality standards were based on the French CEA work performed in the late seventies with the APOLLO1 cell/assembly computer code. APOLLO1 is a spectral code, used for evaluating the basic characteristics of fuel assemblies for reactor physics applications, which has been enhanced to perform criticality safety calculations. Throughout the years, CRISTAL, starting with APOLLO1 and MORET 3 (a 3D Monte Carlo code), has been improved to account for the growth of its qualification database and for increasing user requirements. Today, CRISTAL V0 is an up-to-date computational tool incorporating a modern basic microscopic cross section set based on JEF2.2 and the comprehensive APOLLO2 and MORET 4 codes. APOLLO2 is well suited for criticality standards calculations as it includes a sophisticated self shielding approach, a P{sub ij} flux determination, and a 1D transport (S{sub n}) process. CRISTAL V0 is the result of more than five years of development work focusing on theoretical approaches and the implementation of user-friendly graphical interfaces. Due to its comprehensive physical simulation and thanks to its broad qualification database with more than a thousand benchmark/calculation comparisons, CRISTAL V0 provides outstanding and reliable accuracy for criticality evaluations for configurations covering the entire fuel cycle (i.e. from enrichment, pellet/assembly fabrication, transportation, to fuel reprocessing). After a brief description of the calculation scheme and the physics algorithms used in this code package, results for the various fissile media encountered in a UO{sub 2} fuel fabrication plant will be detailed and discussed. (authors)« less

MetaboAnalystR: an R package for flexible and reproducible analysis of metabolomics data.

PubMed

Chong, Jasmine; Xia, Jianguo

2018-06-28

The MetaboAnalyst web application has been widely used for metabolomics data analysis and interpretation. Despite its user-friendliness, the web interface has presented its inherent limitations (especially for advanced users) with regard to flexibility in creating customized workflow, support for reproducible analysis, and capacity in dealing with large data. To address these limitations, we have developed a companion R package (MetaboAnalystR) based on the R code base of the web server. The package has been thoroughly tested to ensure that the same R commands will produce identical results from both interfaces. MetaboAnalystR complements the MetaboAnalyst web server to facilitate transparent, flexible and reproducible analysis of metabolomics data. MetaboAnalystR is freely available from https://github.com/xia-lab/MetaboAnalystR. Supplementary data are available at Bioinformatics online.

seawaveQ: an R package providing a model and utilities for analyzing trends in chemical concentrations in streams with a seasonal wave (seawave) and adjustment for streamflow (Q) and other ancillary variables

USGS Publications Warehouse

Ryberg, Karen R.; Vecchia, Aldo V.

2013-01-01

The seawaveQ R package fits a parametric regression model (seawaveQ) to pesticide concentration data from streamwater samples to assess variability and trends. The model incorporates the strong seasonality and high degree of censoring common in pesticide data and users can incorporate numerous ancillary variables, such as streamflow anomalies. The model is fitted to pesticide data using maximum likelihood methods for censored data and is robust in terms of pesticide, stream location, and degree of censoring of the concentration data. This R package standardizes this methodology for trend analysis, documents the code, and provides help and tutorial information, as well as providing additional utility functions for plotting pesticide and other chemical concentration data.

Improvements and new features in the PDF module

NASA Technical Reports Server (NTRS)

Norris, Andrew T.

1995-01-01

This viewgraph presentation discusses what models are used in this package and what their advantages and disadvantages are, how the probability density function (PDF) model is implemented and the features of the program, and what can be expected in the future from the NASA Lewis PDF code.