VizieR Online Data Catalog: RefleX : X-ray-tracing code (Paltani+, 2017)

NASA Astrophysics Data System (ADS)

Paltani, S.; Ricci, C.

2017-11-01

We provide here the RefleX executable, for both Linux and MacOSX, together with the User Manual and example script file and output file Running (for instance): reflex_linux will produce the file reflex.out Note that the results may differ slightly depending on the OS, because of slight differences in some implementations numerical computations. The difference are scientifically meaningless. (5 data files).

Integrated Approach to User Account Management

NASA Technical Reports Server (NTRS)

Kesselman, Glenn; Smith, William

2007-01-01

IT environments consist of both Windows and other platforms. Providing user account management for this model has become increasingly diffi cult. If Microsoft#s Active Directory could be enhanced to extend a W indows identity for authentication services for Unix, Linux, Java and Macintosh systems, then an integrated approach to user account manag ement could be realized.

Understanding Unintended Consequences and Health Information Technology:. Contribution from the IMIA Organizational and Social Issues Working Group.

PubMed

Kuziemsky, C E; Randell, R; Borycki, E M

2016-11-10

No framework exists to identify and study unintended consequences (UICs) with a focus on organizational and social issues (OSIs). To address this shortcoming, we conducted a literature review to develop a framework for considering UICs and health information technology (HIT) from the perspective of OSIs. A literature review was conducted for the period 2000- 2015 using the search terms "unintended consequences" and "health information technology". 67 papers were screened, of which 18 met inclusion criteria. Data extraction was focused on the types of technologies studied, types of UICs identified, and methods of data collection and analysis used. A thematic analysis was used to identify themes related to UICs. We identified two overarching themes. One was the definition and terminology of how people classify and discuss UICs. Second was OSIs and UICs. For the OSI theme, we also identified four sub-themes: process change and evolution, individual-collaborative interchange, context of use, and approaches to model, study, and understand UICs. While there is a wide body of research on UICs, there is a lack of overall consensus on how they should be classified and reported, limiting our ability to understand the implications of UICs and how to manage them. More mixed-methods research and better proactive identification of UICs remain priorities. Our findings and framework of OSI considerations for studying UICs and HIT extend existing work on HIT and UICs by focusing on organizational and social issues.

Understanding Unintended Consequences and Health Information Technology:

PubMed Central

Randell, R.; Borycki, E. M.

2016-01-01

Summary Objective No framework exists to identify and study unintended consequences (UICs) with a focus on organizational and social issues (OSIs). To address this shortcoming, we conducted a literature review to develop a framework for considering UICs and health information technology (HIT) from the perspective of OSIs. Methods A literature review was conducted for the period 2000-2015 using the search terms “unintended consequences” and “health information technology”. 67 papers were screened, of which 18 met inclusion criteria. Data extraction was focused on the types of technologies studied, types of UICs identified, and methods of data collection and analysis used. A thematic analysis was used to identify themes related to UICs. Results We identified two overarching themes. One was the definition and terminology of how people classify and discuss UICs. Second was OSIs and UICs. For the OSI theme, we also identified four sub-themes: process change and evolution, individual-collaborative interchange, context of use, and approaches to model, study, and understand UICs. Conclusions While there is a wide body of research on UICs, there is a lack of overall consensus on how they should be classified and reported, limiting our ability to understand the implications of UICs and how to manage them. More mixed-methods research and better proactive identification of UICs remain priorities. Our findings and framework of OSI considerations for studying UICs and HIT extend existing work on HIT and UICs by focusing on organizational and social issues. PMID:27830231

A web-server of cell type discrimination system.

PubMed

Wang, Anyou; Zhong, Yan; Wang, Yanhua; He, Qianchuan

2014-01-01

Discriminating cell types is a daily request for stem cell biologists. However, there is not a user-friendly system available to date for public users to discriminate the common cell types, embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), and somatic cells (SCs). Here, we develop WCTDS, a web-server of cell type discrimination system, to discriminate the three cell types and their subtypes like fetal versus adult SCs. WCTDS is developed as a top layer application of our recent publication regarding cell type discriminations, which employs DNA-methylation as biomarkers and machine learning models to discriminate cell types. Implemented by Django, Python, R, and Linux shell programming, run under Linux-Apache web server, and communicated through MySQL, WCTDS provides a friendly framework to efficiently receive the user input and to run mathematical models for analyzing data and then to present results to users. This framework is flexible and easy to be expended for other applications. Therefore, WCTDS works as a user-friendly framework to discriminate cell types and subtypes and it can also be expended to detect other cell types like cancer cells.

A Web-Server of Cell Type Discrimination System

PubMed Central

Zhong, Yan

2014-01-01

Discriminating cell types is a daily request for stem cell biologists. However, there is not a user-friendly system available to date for public users to discriminate the common cell types, embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), and somatic cells (SCs). Here, we develop WCTDS, a web-server of cell type discrimination system, to discriminate the three cell types and their subtypes like fetal versus adult SCs. WCTDS is developed as a top layer application of our recent publication regarding cell type discriminations, which employs DNA-methylation as biomarkers and machine learning models to discriminate cell types. Implemented by Django, Python, R, and Linux shell programming, run under Linux-Apache web server, and communicated through MySQL, WCTDS provides a friendly framework to efficiently receive the user input and to run mathematical models for analyzing data and then to present results to users. This framework is flexible and easy to be expended for other applications. Therefore, WCTDS works as a user-friendly framework to discriminate cell types and subtypes and it can also be expended to detect other cell types like cancer cells. PMID:24578634

Toward Millions of File System IOPS on Low-Cost, Commodity Hardware

PubMed Central

Zheng, Da; Burns, Randal; Szalay, Alexander S.

2013-01-01

We describe a storage system that removes I/O bottlenecks to achieve more than one million IOPS based on a user-space file abstraction for arrays of commodity SSDs. The file abstraction refactors I/O scheduling and placement for extreme parallelism and non-uniform memory and I/O. The system includes a set-associative, parallel page cache in the user space. We redesign page caching to eliminate CPU overhead and lock-contention in non-uniform memory architecture machines. We evaluate our design on a 32 core NUMA machine with four, eight-core processors. Experiments show that our design delivers 1.23 million 512-byte read IOPS. The page cache realizes the scalable IOPS of Linux asynchronous I/O (AIO) and increases user-perceived I/O performance linearly with cache hit rates. The parallel, set-associative cache matches the cache hit rates of the global Linux page cache under real workloads. PMID:24402052

Toward Millions of File System IOPS on Low-Cost, Commodity Hardware.

PubMed

Zheng, Da; Burns, Randal; Szalay, Alexander S

2013-01-01

We describe a storage system that removes I/O bottlenecks to achieve more than one million IOPS based on a user-space file abstraction for arrays of commodity SSDs. The file abstraction refactors I/O scheduling and placement for extreme parallelism and non-uniform memory and I/O. The system includes a set-associative, parallel page cache in the user space. We redesign page caching to eliminate CPU overhead and lock-contention in non-uniform memory architecture machines. We evaluate our design on a 32 core NUMA machine with four, eight-core processors. Experiments show that our design delivers 1.23 million 512-byte read IOPS. The page cache realizes the scalable IOPS of Linux asynchronous I/O (AIO) and increases user-perceived I/O performance linearly with cache hit rates. The parallel, set-associative cache matches the cache hit rates of the global Linux page cache under real workloads.

Design notes for the next generation persistent object manager for CAP

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

Isely, M.; Fischler, M.; Galli, M.

1995-05-01

The CAP query system software at Fermilab has several major components, including SQS (for managing the query), the retrieval system (for fetching auxiliary data), and the query software itself. The central query software in particular is essentially a modified version of the `ptool` product created at UIC (University of Illinois at Chicago) as part of the PASS project under Bob Grossman. The original UIC version was designed for use in a single-user non-distributed Unix environment. The Fermi modifications were an attempt to permit multi-user access to a data set distributed over a set of storage nodes. (The hardware is anmore » IBM SP-x system - a cluster of AIX POWER2 nodes with an IBM-proprietary high speed switch interconnect). Since the implementation work of the Fermi-ized ptool, the CAP members have learned quite a bit about the nature of queries and where the current performance bottlenecks exist. This has lead them to design a persistent object manager that will overcome these problems. For backwards compatibility with ptool, the ptool persistent object API will largely be retained, but the implementation will be entirely different.« less

Historical Evaluation of Groundwater Responses to Underground Injection Controls in an Urban Watershed

NASA Astrophysics Data System (ADS)

Harrison, M.; Haggerty, R.; Santelmann, M. V.

2017-12-01

Underground injection controls (UICs) are drywells designed to recharge stormwater to alleviate flooding events. The development of UICs affect the dynamics of the urban hydrologic setting in which more than half of precipitation can be recharged directly into UICs systems. This study seeks to better understand how the development of UICs affect groundwater levels and streamflows. The Portland, OR metropolitan area consist of well over 10,000 of UICs to mitigate flooding during storm events. This study evaluates historical precipitation, streamflow, and groundwater levels from over 20 monitoring wells within a watershed in the city Portland, OR along with well log data of UICs. UICs within the study area are approximately 30 feet in depth and have noted to contribute to about 12% of recharge. This study evaluates the dynamics of groundwater levels in relation towards the development of UICs. The results of obtained from this analysis is applied to model seasonal groundwater, precipitation, and streamflow relationships within a neighborhood subcatchment.

X-LUNA: Extending Free/Open Source Real Time Executive for On-Board Space Applications

NASA Astrophysics Data System (ADS)

Braga, P.; Henriques, L.; Zulianello, M.

2008-08-01

In this paper we present xLuna, a system based on the RTEMS [1] Real-Time Operating System that is able to run on demand a GNU/Linux Operating System [2] as RTEMS' lowest priority task. Linux runs in user-mode and in a different memory partition. This allows running Hard Real-Time tasks and Linux applications on the same system sharing the Hardware resources while keeping a safe isolation and the Real-Time characteristics of RTEMS. Communication between both Systems is possible through a loose coupled mechanism based on message queues. Currently only SPARC LEON2 processor with Memory Management Unit (MMU) is supported. The advantage in having two isolated systems is that non critical components are quickly developed or simply ported reducing time-to-market and budget.

40 CFR 124.19 - Appeal of RCRA, UIC, NPDES, and PSD Permits.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 23 2012-07-01 2012-07-01 false Appeal of RCRA, UIC, NPDES, and PSD..., and PSD Permits. (a) Within 30 days after a RCRA, UIC, NPDES, or PSD final permit decision (or a... may also decide on its own initiative to review any condition of any RCRA, UIC, NPDES, or PSD permit...

40 CFR 124.19 - Appeal of RCRA, UIC, NPDES, and PSD Permits.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 21 2010-07-01 2010-07-01 false Appeal of RCRA, UIC, NPDES, and PSD..., and PSD Permits. (a) Within 30 days after a RCRA, UIC, NPDES, or PSD final permit decision (or a... may also decide on its own initiative to review any condition of any RCRA, UIC, NPDES, or PSD permit...

40 CFR 124.19 - Appeal of RCRA, UIC, NPDES, and PSD Permits.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 22 2011-07-01 2011-07-01 false Appeal of RCRA, UIC, NPDES, and PSD..., and PSD Permits. (a) Within 30 days after a RCRA, UIC, NPDES, or PSD final permit decision (or a... may also decide on its own initiative to review any condition of any RCRA, UIC, NPDES, or PSD permit...

Development of a Methodology for Customizing Insider Threat Auditing on a Linux Operating System

DTIC Science & Technology

2010-03-01

information /etc/group, passwd ,gshadow,shadow,/security/opasswd 16 User A attempts to access User B directory 17 User A attempts to access User B file w/o...configuration Handled by audit rules for root actions Audit user write attempts to system files -w /etc/group –p wxa -w /etc/ passwd –p wxa -w /etc/gshadow –p...information (/etc/group, /etc/ passwd , /etc/gshadow, /etc/shadow, /etc/sudoers, /etc/security/opasswd) Procedure: 1. User2 logs into the system

MAPA: Implementation of the Standard Interchange Format and use for analyzing lattices

NASA Astrophysics Data System (ADS)

Shasharina, Svetlana G.; Cary, John R.

1997-05-01

MAPA (Modular Accelerator Physics Analysis) is an object oriented application for accelerator design and analysis with a Motif based graphical user interface. MAPA has been ported to AIX, Linux, HPUX, Solaris, and IRIX. MAPA provides an intuitive environment for accelerator study and design. The user can bring up windows for fully nonlinear analysis of accelerator lattices in any number of dimensions. The current graphical analysis methods of Lifetime plots and Surfaces of Section have been used to analyze the improved lattice designs of Wan, Cary, and Shasharina (this conference). MAPA can now read and write Standard Interchange Format (MAD) accelerator description files and it has a general graphical user interface for adding, changing, and deleting elements. MAPA's consistency checks prevent deletion of used elements and prevent creation of recursive beam lines. Plans include development of a richer set of modeling tools and the ability to invoke existing modeling codes through the MAPA interface. MAPA will be demonstrated on a Pentium 150 laptop running Linux.

Financial Responsibilities for Underground Injection Well Owners or Operators

EPA Pesticide Factsheets

This page provides information on UIC financial responsibility requirements, qualifying financial instrumentsRoles and responsibilities for operators and UIC Directors UIC Director’s and review procedures for financial responsibility instruments.

HEP Computing

Science.gov Websites

Service Request Password Help New Users Back to HEP Computing Mail-Migration Procedure on Linux Mail -Migration Procedure on Windows How to Migrate a Folder to GMail using Pine U.S. Department of Energy The

Development of a portable Linux-based ECG measurement and monitoring system.

PubMed

Tan, Tan-Hsu; Chang, Ching-Su; Huang, Yung-Fa; Chen, Yung-Fu; Lee, Cheng

2011-08-01

This work presents a portable Linux-based electrocardiogram (ECG) signals measurement and monitoring system. The proposed system consists of an ECG front end and an embedded Linux platform (ELP). The ECG front end digitizes 12-lead ECG signals acquired from electrodes and then delivers them to the ELP via a universal serial bus (USB) interface for storage, signal processing, and graphic display. The proposed system can be installed anywhere (e.g., offices, homes, healthcare centers and ambulances) to allow people to self-monitor their health conditions at any time. The proposed system also enables remote diagnosis via Internet. Additionally, the system has a 7-in. interactive TFT-LCD touch screen that enables users to execute various functions, such as scaling a single-lead or multiple-lead ECG waveforms. The effectiveness of the proposed system was verified by using a commercial 12-lead ECG signal simulator and in vivo experiments. In addition to its portability, the proposed system is license-free as Linux, an open-source code, is utilized during software development. The cost-effectiveness of the system significantly enhances its practical application for personal healthcare.

An algorithm of a real time image tracking system using a camera with pan/tilt motors on an embedded system

NASA Astrophysics Data System (ADS)

Kim, Hie-Sik; Nam, Chul; Ha, Kwan-Yong; Ayurzana, Odgeral; Kwon, Jong-Won

2005-12-01

The embedded systems have been applied to many fields, including households and industrial sites. The user interface technology with simple display on the screen was implemented more and more. The user demands are increasing and the system has more various applicable fields due to a high penetration rate of the Internet. Therefore, the demand for embedded system is tend to rise. An embedded system for image tracking was implemented. This system is used a fixed IP for the reliable server operation on TCP/IP networks. Using an USB camera on the embedded Linux system developed a real time broadcasting of video image on the Internet. The digital camera is connected at the USB host port of the embedded board. All input images from the video camera are continuously stored as a compressed JPEG file in a directory at the Linux web-server. And each frame image data from web camera is compared for measurement of displacement Vector. That used Block matching algorithm and edge detection algorithm for past speed. And the displacement vector is used at pan/tilt motor control through RS232 serial cable. The embedded board utilized the S3C2410 MPU, which used the ARM 920T core form Samsung. The operating system was ported to embedded Linux kernel and mounted of root file system. And the stored images are sent to the client PC through the web browser. It used the network function of Linux and it developed a program with protocol of the TCP/IP.

Linux VPN Set Up | High-Performance Computing | NREL

Science.gov Websites

methods to connect to NREL's HPC systems via the HPC VPN: one using a simple command line, and a second UserID in place of the one in the example image. Connection name: hpcvpn Gateway: hpcvpn.nrel.gov User hpcvpn option as seen in the following screen shot. Screenshot image NetworkManager will present you with

A Prototype Implementation of a Time Interval File Protection System in Linux

DTIC Science & Technology

2006-09-01

when a user logs in, the /etc/ passwd file is read by the system to get the user’s home directory. The user’s login shell then changes the directory...and don. • Users can be added with the command: # useradd – m <username> • Set the password by: # passwd <username> • Make a copy of the

Iodine status of postpartum women and their infants in Australia after the introduction of mandatory iodine fortification.

PubMed

Huynh, Dao; Condo, Dominique; Gibson, Robert; Muhlhausler, Beverly; Ryan, Philip; Skeaff, Sheila; Makrides, Maria; Zhou, Shao J

2017-06-01

Mandatory I fortification in bread was introduced in Australia in 2009 in response to the re-emergence of biochemical I deficiency based on median urinary I concentration (UIC)<100 µg/l. Data on the I status of lactating mothers and their infants in Australia are scarce. The primary aim of this study was to assess the I status, determined by UIC and breast milk I concentration (BMIC), of breast-feeding mothers in South Australia and UIC of their infants. The secondary aim was to assess the relationship between the I status of mothers and their infants. The median UIC of the mothers (n 686) was 125 (interquartile range (IQR) 76-200) µg/l and median BMIC (n 538) was 127 (IQR 84-184) µg/l. In all, 38 and 36 % of the mothers had a UIC and BMIC below 100 µg/l, respectively. The median UIC of infants (n 628) was 198 (IQR 121-296) µg/l, and 17 % had UIC<100 µg/l. Infant UIC was positively associated with maternal UIC (β 0·26; 95 % CI 0·14, 0·37, P<0·001) and BMIC (β 0·85; 95 % CI 0·66, 1·04, P<0·001) at 3 months postpartum after adjustment for gestational age, parity, maternal secondary and further education, BMI category and infant feeding mode. The adjusted OR for infant UIC<100 µg/l was 6·49 (95 % CI 3·80, 11·08, P<0·001) in mothers with BMIC<100 µg/l compared with those with BMIC≥100 µg/l. The I status of mothers and breast-fed infants in South Australia, following mandatory I fortification, is indicative of I sufficiency. BMIC<100 µg/l increased the risk of biochemical I deficiency in breast-fed infants.

DOVIS: an implementation for high-throughput virtual screening using AutoDock.

PubMed

Zhang, Shuxing; Kumar, Kamal; Jiang, Xiaohui; Wallqvist, Anders; Reifman, Jaques

2008-02-27

Molecular-docking-based virtual screening is an important tool in drug discovery that is used to significantly reduce the number of possible chemical compounds to be investigated. In addition to the selection of a sound docking strategy with appropriate scoring functions, another technical challenge is to in silico screen millions of compounds in a reasonable time. To meet this challenge, it is necessary to use high performance computing (HPC) platforms and techniques. However, the development of an integrated HPC system that makes efficient use of its elements is not trivial. We have developed an application termed DOVIS that uses AutoDock (version 3) as the docking engine and runs in parallel on a Linux cluster. DOVIS can efficiently dock large numbers (millions) of small molecules (ligands) to a receptor, screening 500 to 1,000 compounds per processor per day. Furthermore, in DOVIS, the docking session is fully integrated and automated in that the inputs are specified via a graphical user interface, the calculations are fully integrated with a Linux cluster queuing system for parallel processing, and the results can be visualized and queried. DOVIS removes most of the complexities and organizational problems associated with large-scale high-throughput virtual screening, and provides a convenient and efficient solution for AutoDock users to use this software in a Linux cluster platform.

Dugong: a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses.

PubMed

Menegidio, Fabiano B; Jabes, Daniela L; Costa de Oliveira, Regina; Nunes, Luiz R

2018-02-01

This manuscript introduces and describes Dugong, a Docker image based on Ubuntu 16.04, which automates installation of more than 3500 bioinformatics tools (along with their respective libraries and dependencies), in alternative computational environments. The software operates through a user-friendly XFCE4 graphic interface that allows software management and installation by users not fully familiarized with the Linux command line and provides the Jupyter Notebook to assist in the delivery and exchange of consistent and reproducible protocols and results across laboratories, assisting in the development of open science projects. Source code and instructions for local installation are available at https://github.com/DugongBioinformatics, under the MIT open source license. Luiz.nunes@ufabc.edu.br. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Examination of iodine status in the German population: an example for methodological pitfalls of the current approach of iodine status assessment.

PubMed

Johner, S A; Thamm, M; Schmitz, R; Remer, T

2016-04-01

Preliminary iodine concentration (UIC) measurements in spot urines of the representative German adult study DEGS indicated a severe worsening of iodine status compared to previous results in German children (KiGGS study). Therefore, we aimed to evaluate adult iodine status in detail and to investigate the impact of hydration status on UIC. UIC and creatinine concentrations were measured in 6978 spot urines from the German nationwide DEGS study (2008-2011). Twenty-four-hour iodine excretions (24-h UIE) were estimated by relating iodine/creatinine ratios to age- and sex-specific 24-h creatinine reference values. Urine osmolality was measured in two subsamples of spot urines (n = 100 each) to determine the impact of hydration status on UIC. In DEGS, median UIC was 69 µg/L in men and 54 µg/L in women, lying clearly below the WHO cutoff for iodine sufficiency (100 µg/L). Estimated median 24-h UIE was 113 µg/day, accompanied by 32 % of DEGS adults, lying below the estimated average requirement (EAR) for iodine. Comparative analysis with the KiGGS data (>14,000 spot urines of children; median UIC 117 µg/L) revealed a comparable percentage

Excelsior Mining Arizona, Inc. Gunnison Copper Project Class III UIC Area Permit and Aquifer Exemption

EPA Pesticide Factsheets

UIC Area Permit R9UIC-AZ3-FY16-1 and supporting documents for Class III In-Situ Production of Copper: Gunnison Copper Project, Cochise County, AZ, issued to Excelsior Mining Arizona Inc., Concord Place, Suite 300, 2999 North 44th Street, Phoenix, AZ 85018.

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

Esser, Lothar; Shukla, Suneet; Zhou, Fei

P-glycoprotein (P-gp) is a polyspecific ATP-dependent transporter linked to multidrug resistance in cancers that plays important roles in the pharmacokinetics of a large number of drugs. The drug-resistance phenotype of P-gp can be modulated by the monoclonal antibody UIC2, which specifically recognizes human P-gp in a conformation-dependent manner. Here, the purification, sequence determination and high-resolution structure of the Fab fragment of UIC2 (UIC2/Fab) are reported. Purified UIC2/Fab binds human P-gp with a 1:1 stoichiometry. Crystals of UIC2/Fab are triclinic (space groupP1), with unit-cell parametersa= 40.67,b= 44.91,c= 58.09 Å, α = 97.62, β = 99.10, γ = 94.09°, and diffracted X-rays tomore » 1.6 Å resolution. The structure was determined by molecular replacement and refined to 1.65 Å resolution. The asymmetric unit contains one molecule of UIC2/Fab, which exhibits a positively charged antigen-binding surface, suggesting that it might recognize an oppositely charged extracellular epitope of P-gp.« less

Optimal and safe upper limits of iodine intake for early pregnancy in iodine-sufficient regions: a cross-sectional study of 7190 pregnant women in China.

PubMed

Shi, Xiaoguang; Han, Cheng; Li, Chenyan; Mao, Jinyuan; Wang, Weiwei; Xie, Xiaochen; Li, Chenyang; Xu, Bin; Meng, Tao; Du, Jianling; Zhang, Shaowei; Gao, Zhengnan; Zhang, Xiaomei; Fan, Chenling; Shan, Zhongyan; Teng, Weiping

2015-04-01

The WHO Technical Consultation recommends urinary iodine concentrations (UIC) from 250 to 499 μg/L as more-than-adequate iodine intake and UIC ≥ 500 μg/L as excessive iodine for pregnant and lactating women, but scientific evidence for this is weak. We investigated optimal and safe ranges of iodine intake during early pregnancy in an iodine-sufficient region of China. Seven thousand one hundred ninety pregnant women at 4-8 weeks gestation were investigated and their UIC, serum thyroid stimulating hormone (TSH), free thyroxine (FT4), thyroid-peroxidase antibody (TPOAb), thyroglobulin antibody (TgAb), and thyroglobulin (Tg) were measured. The prevalence of overt hypothyroidism was lowest in the group with UIC 150-249 μg/L, which corresponded to the lowest serum Tg concentration (10.18 μg/L). Prevalences of subclinical hypothyroidism (2.4%) and isolated hypothyroxinemia (1.7%) were lower in the group with UIC 150-249 μg/L. Multivariate logistic regression indicated that more-than-adequate iodine intake (UIC 250-499 μg/L) and excessive iodine intake (UIC ≥ 500 μg/L) were associated with a 1.72-fold and a 2.17-fold increased risk of subclinical hypothyroidism, respectively. Meanwhile, excessive iodine intake was associated with a 2.85-fold increased risk of isolated hypothyroxinemia. Moreover, the prevalence of TPOAb positivity and TgAb positivity presented a U-shaped curve, ranging from mild iodine deficiency to iodine excess. The upper limit of iodine intake during early pregnancy in an iodine-sufficient region should not exceed UIC 250 μg/L, because this is associated with a significantly high risk of subclinical hypothyroidism, and a UIC of 500 μg/L should not be exceeded, as it is associated with a significantly high risk of isolated hypothyroxinemia.

Supplementation during pregnancy with small-quantity lipid-based nutrient supplements or multiple micronutrients, compared with iron and folic acid, increases women's urinary iodine concentration in semiurban Ghana: A randomized controlled trial.

PubMed

Adu-Afarwuah, Seth; Young, Rebecca T; Lartey, Anna; Okronipa, Harriet; Ashorn, Per; Ashorn, Ulla; Zeilani, Mamane; Dewey, Kathryn G

2018-04-01

There is little information on whether prenatal multiple micronutrient (MMN) supplements containing iodine affect women's iodine status. In the International Lipid-based Nutrient Supplements DYAD-Ghana trial, we aimed to assess women's urinary iodine concentration (UIC, μg/L) during pregnancy, as one of the planned secondary outcomes. Women (n = 1,320) <20 weeks of gestation were randomized to consume 60 mg iron and 400 μg folic acid per day (iron and folic acid [IFA]); 18 vitamins and minerals including 250 μg iodine per day (MMN); or 20 g/day of small-quantity lipid-based nutrient supplements (LNS) with the same and additional 4 vitamins and minerals as the MMN (LNS). In a subsample (n = 295), we tested differences in groups' geometric mean UICs at 36 weeks of gestation controlling for baseline UIC and compared the geometric means (approximately median UICs) with the World Health Organization (WHO) cut-offs: median UIC <150, 150-249, and ≥500 reflecting low, adequate, and excessive iodine intakes, respectively. At baseline, overall median UIC was 137. At 36 weeks of gestation, controlling for baseline UIC, geometric mean (95% confidence interval) UICs of the MMN (161 [133, 184]) and LNS (158 [132, 185]) groups did not differ; both values were significantly greater (overall p = .004) than that of the IFA group (116 [101, 135]). The median UICs of the MMN and LNS groups were within the WHO "adequate" range, whereas that of the IFA group was below the WHO adequate range. In this setting, supplementation during pregnancy with small-quantity LNS or MMN providing iodine at the WHO-recommended dose, compared with IFA, increases the likelihood of adequate iodine status. © 2017 The Authors. Maternal & Child Nutrition published by John Wiley & Sons, Ltd.

Construction of a Linux based chemical and biological information system.

PubMed

Molnár, László; Vágó, István; Fehér, András

2003-01-01

A chemical and biological information system with a Web-based easy-to-use interface and corresponding databases has been developed. The constructed system incorporates all chemical, numerical and textual data related to the chemical compounds, including numerical biological screen results. Users can search the database by traditional textual/numerical and/or substructure or similarity queries through the web interface. To build our chemical database management system, we utilized existing IT components such as ORACLE or Tripos SYBYL for database management and Zope application server for the web interface. We chose Linux as the main platform, however, almost every component can be used under various operating systems.

Image Capture and Display Based on Embedded Linux

NASA Astrophysics Data System (ADS)

Weigong, Zhang; Suran, Di; Yongxiang, Zhang; Liming, Li

For the requirement of building a highly reliable communication system, SpaceWire was selected in the integrated electronic system. There was a need to test the performance of SpaceWire. As part of the testing work, the goal of this paper is to transmit image data from CMOS camera through SpaceWire and display real-time images on the graphical user interface with Qt in the embedded development platform of Linux & ARM. A point-to-point mode of transmission was chosen; the running result showed the two communication ends basically reach a consensus picture in succession. It suggests that the SpaceWire can transmit the data reliably.

Cyber Fundamental Exercises

DTIC Science & Technology

2013-03-01

the /bin, /sbin, /etc, /var/log, /home, /proc, /root, /dev, /tmp, and /lib directories • Describe the purpose of the /etc/shadow and /etc/ passwd ...UNLIMITED 19 2.6.2 /etc/ passwd and /etc/shadow The /etc/shadow file didn’t exist on early Linux distributions. Originally only root could access the...etc/ passwd file, which stored user names, user configuration information, and passwords. However, when common programs such as ls running under

Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis

PubMed Central

2011-01-01

Background A variety of neuroimaging software packages have been released from various laboratories worldwide, and many researchers use these packages in combination. Though most of these software packages are freely available, some people find them difficult to install and configure because they are mostly based on UNIX-like operating systems. We developed a live USB-bootable Linux package named "Lin4Neuro." This system includes popular neuroimaging analysis tools. The user interface is customized so that even Windows users can use it intuitively. Results The boot time of this system was only around 40 seconds. We performed a benchmark test of inhomogeneity correction on 10 subjects of three-dimensional T1-weighted MRI scans. The processing speed of USB-booted Lin4Neuro was as fast as that of the package installed on the hard disk drive. We also installed Lin4Neuro on a virtualization software package that emulates the Linux environment on a Windows-based operation system. Although the processing speed was slower than that under other conditions, it remained comparable. Conclusions With Lin4Neuro in one's hand, one can access neuroimaging software packages easily, and immediately focus on analyzing data. Lin4Neuro can be a good primer for beginners of neuroimaging analysis or students who are interested in neuroimaging analysis. It also provides a practical means of sharing analysis environments across sites. PMID:21266047

Lin4Neuro: a customized Linux distribution ready for neuroimaging analysis.

PubMed

Nemoto, Kiyotaka; Dan, Ippeita; Rorden, Christopher; Ohnishi, Takashi; Tsuzuki, Daisuke; Okamoto, Masako; Yamashita, Fumio; Asada, Takashi

2011-01-25

A variety of neuroimaging software packages have been released from various laboratories worldwide, and many researchers use these packages in combination. Though most of these software packages are freely available, some people find them difficult to install and configure because they are mostly based on UNIX-like operating systems. We developed a live USB-bootable Linux package named "Lin4Neuro." This system includes popular neuroimaging analysis tools. The user interface is customized so that even Windows users can use it intuitively. The boot time of this system was only around 40 seconds. We performed a benchmark test of inhomogeneity correction on 10 subjects of three-dimensional T1-weighted MRI scans. The processing speed of USB-booted Lin4Neuro was as fast as that of the package installed on the hard disk drive. We also installed Lin4Neuro on a virtualization software package that emulates the Linux environment on a Windows-based operation system. Although the processing speed was slower than that under other conditions, it remained comparable. With Lin4Neuro in one's hand, one can access neuroimaging software packages easily, and immediately focus on analyzing data. Lin4Neuro can be a good primer for beginners of neuroimaging analysis or students who are interested in neuroimaging analysis. It also provides a practical means of sharing analysis environments across sites.

40 CFR 124.3 - Application for a permit.

Code of Federal Regulations, 2014 CFR

2014-07-01

... requires a permit under the RCRA, UIC, NPDES, or PSD programs shall complete, sign, and submit to the Director an application for each permit required under §§ 270.1 (RCRA), 144.1 (UIC), 40 CFR 52.21 (PSD... (UIC), 40 CFR 52.21 (PSD), and 122.21 (NPDES). (3) Permit applications (except for PSD permits) must...

NSTX-U Control System Upgrades

DOE PAGES

Erickson, K. G.; Gates, D. A.; Gerhardt, S. P.; ...

2014-06-01

The National Spherical Tokamak Experiment (NSTX) is undergoing a wealth of upgrades (NSTX-U). These upgrades, especially including an elongated pulse length, require broad changes to the control system that has served NSTX well. A new fiber serial Front Panel Data Port input and output (I/O) stream will supersede the aging copper parallel version. Driver support for the new I/O and cyber security concerns require updating the operating system from Redhat Enterprise Linux (RHEL) v4 to RedHawk (based on RHEL) v6. While the basic control system continues to use the General Atomics Plasma Control System (GA PCS), the effort to forwardmore » port the entire software package to run under 64-bit Linux instead of 32-bit Linux included PCS modifications subsequently shared with GA and other PCS users. Software updates focused on three key areas: (1) code modernization through coding standards (C99/C11), (2) code portability and maintainability through use of the GA PCS code generator, and (3) support of 64-bit platforms. Central to the control system upgrade is the use of a complete real time (RT) Linux platform provided by Concurrent Computer Corporation, consisting of a computer (iHawk), an operating system and drivers (RedHawk), and RT tools (NightStar). Strong vendor support coupled with an extensive RT toolset influenced this decision. The new real-time Linux platform, I/O, and software engineering will foster enhanced capability and performance for NSTX-U plasma control.« less

A dynamic kernel modifier for linux

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

Minnich, R. G.

2002-09-03

Dynamic Kernel Modifier, or DKM, is a kernel module for Linux that allows user-mode programs to modify the execution of functions in the kernel without recompiling or modifying the kernel source in any way. Functions may be traced, either function entry only or function entry and exit; nullified; or replaced with some other function. For the tracing case, function execution results in the activation of a watchpoint. When the watchpoint is activated, the address of the function is logged in a FIFO buffer that is readable by external applications. The watchpoints are time-stamped with the resolution of the processor highmore » resolution timers, which on most modem processors are accurate to a single processor tick. DKM is very similar to earlier systems such as the SunOS trace device or Linux TT. Unlike these two systems, and other similar systems, DKM requires no kernel modifications. DKM allows users to do initial probing of the kernel to look for performance problems, or even to resolve potential problems by turning functions off or replacing them. DKM watchpoints are not without cost: it takes about 200 nanoseconds to make a log entry on an 800 Mhz Pentium-Ill. The overhead numbers are actually competitive with other hardware-based trace systems, although it has less 'Los Alamos National Laboratory is operated by the University of California for the National Nuclear Security Administration of the United States Department of Energy under contract W-7405-ENG-36. accuracy than an In-Circuit Emulator such as the American Arium. Once the user has zeroed in on a problem, other mechanisms with a higher degree of accuracy can be used.« less

40 CFR 124.19 - Appeal of RCRA, UIC, NPDES and PSD Permits.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 23 2013-07-01 2013-07-01 false Appeal of RCRA, UIC, NPDES and PSD... PSD Permits. (a) Petitioning for review of a permit decision. (1) Initiating an appeal. Appeal from a RCRA, UIC, NPDES, or PSD final permit decision issued under § 124.15 of this part, or a decision to...

40 CFR 124.19 - Appeal of RCRA, UIC, NPDES and PSD Permits.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 22 2014-07-01 2013-07-01 true Appeal of RCRA, UIC, NPDES and PSD... PSD Permits. (a) Petitioning for review of a permit decision. (1) Initiating an appeal. Appeal from a RCRA, UIC, NPDES, or PSD final permit decision issued under § 124.15 of this part, or a decision to...

New Statistical Approach to Apportion Dietary Sources of Iodine Intake: Findings from Kenya, Senegal and India

PubMed Central

Knowles, Jacky; Bukania, Zipporah; Camara, Boubacar; Pandav, Chandrakant S.; Mwai, John Maina; Toure, Ndeye Khady; Yadav, Kapil

2018-01-01

Progress of national Universal Salt Iodization (USI) strategies is typically assessed by household coverage of adequately iodized salt and median urinary iodine concentration (UIC) in spot urine collections. However, household coverage does not inform on the iodized salt used in preparation of processed foods outside homes, nor does the total UIC reflect the portion of population iodine intake attributable to the USI strategy. This study used data from three population-representative surveys of women of reproductive age (WRA) in Kenya, Senegal and India to develop and illustrate a new approach to apportion the population UIC levels by the principal dietary sources of iodine intake, namely native iodine, iodine in processed food salt and iodine in household salt. The technique requires measurement of urinary sodium concentrations (UNaC) in the same spot urine samples collected for iodine status assessment. Taking into account the different complex survey designs of each survey, generalized linear regression (GLR) analyses were performed in which the UIC data of WRA was set as the outcome variable that depends on their UNaC and household salt iodine (SI) data as explanatory variables. Estimates of the UIC portions that correspond to iodine intake sources were calculated with use of the intercept and regression coefficients for the UNaC and SI variables in each country’s regression equation. GLR coefficients for UNaC and SI were significant in all country-specific models. Rural location did not show a significant association in any country when controlled for other explanatory variables. The estimated UIC portion from native dietary iodine intake in each country fell below the minimum threshold for iodine sufficiency. The UIC portion arising from processed food salt in Kenya was substantially higher than in Senegal and India, while the UIC portions from household salt use varied in accordance with the mean level of household SI content in the country surveys. The UIC portions and all-salt-derived iodine intakes found in this study were illustrative of existing differences in national USI legislative frameworks and national salt supply situations between countries. The approach of apportioning the population UIC from spot urine collections may be useful for future monitoring of change in iodine nutrition from reduced salt use in processed foods and in households. PMID:29596369

Network Penetration Testing and Research

NASA Technical Reports Server (NTRS)

Murphy, Brandon F.

2013-01-01

This paper will focus the on research and testing done on penetrating a network for security purposes. This research will provide the IT security office new methods of attacks across and against a company's network as well as introduce them to new platforms and software that can be used to better assist with protecting against such attacks. Throughout this paper testing and research has been done on two different Linux based operating systems, for attacking and compromising a Windows based host computer. Backtrack 5 and BlackBuntu (Linux based penetration testing operating systems) are two different "attacker'' computers that will attempt to plant viruses and or NASA USRP - Internship Final Report exploits on a host Windows 7 operating system, as well as try to retrieve information from the host. On each Linux OS (Backtrack 5 and BlackBuntu) there is penetration testing software which provides the necessary tools to create exploits that can compromise a windows system as well as other operating systems. This paper will focus on two main methods of deploying exploits 1 onto a host computer in order to retrieve information from a compromised system. One method of deployment for an exploit that was tested is known as a "social engineering" exploit. This type of method requires interaction from unsuspecting user. With this user interaction, a deployed exploit may allow a malicious user to gain access to the unsuspecting user's computer as well as the network that such computer is connected to. Due to more advance security setting and antivirus protection and detection, this method is easily identified and defended against. The second method of exploit deployment is the method mainly focused upon within this paper. This method required extensive research on the best way to compromise a security enabled protected network. Once a network has been compromised, then any and all devices connected to such network has the potential to be compromised as well. With a compromised network, computers and devices can be penetrated through deployed exploits. This paper will illustrate the research done to test ability to penetrate a network without user interaction, in order to retrieve personal information from a targeted host.

Gaining Cyber Dominance

DTIC Science & Technology

2015-01-01

Robust team exercise and simulation • Air-gapped; isolation from production networks • “Train as you fight” scenarios • Advanced user and Internet...Security Onion • SIFT (Linux/Windows) • Kali • Rucksack • Docker • VTS 18 GCD Overview January 2015 © 2014 Carnegie Mellon University TEXN Architecture

BSD Portals for LINUX 2.0

NASA Technical Reports Server (NTRS)

McNab, A. David; woo, Alex (Technical Monitor)

1999-01-01

Portals, an experimental feature of 4.4BSD, extend the file system name space by exporting certain open () requests to a user-space daemon. A portal daemon is mounted into the file name space as if it were a standard file system. When the kernel resolves a pathname and encounters a portal mount point, the remainder of the path is passed to the portal daemon. Depending on the portal "pathname" and the daemon's configuration, some type of open (2) is performed. The resulting file descriptor is passed back to the kernel which eventually returns it to the user, to whom it appears that a "normal" open has occurred. A proxy portalfs file system is responsible for kernel interaction with the daemon. The overall effect is that the portal daemon performs an open (2) on behalf of the kernel, possibly hiding substantial complexity from the calling process. One particularly useful application is implementing a connection service that allows simple scripts to open network sockets. This paper describes the implementation of portals for LINUX 2.0.

CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing.

PubMed

Tristão Ramos, Ravi José; de Azevedo Martins, Allan Cézar; da Silva Delgado, Gabrielle; Ionescu, Crina-Maria; Ürményi, Turán Peter; Silva, Rosane; Koca, Jaroslav

2017-11-15

CrocoBLAST is a tool for dramatically speeding up BLAST+ execution on any computer. Alignments that would take days or weeks with NCBI BLAST+ can be run overnight with CrocoBLAST. Additionally, CrocoBLAST provides features critical for NGS data analysis, including: results identical to those of BLAST+; compatibility with any BLAST+ version; real-time information regarding calculation progress and remaining run time; access to partial alignment results; queueing, pausing, and resuming BLAST+ calculations without information loss. CrocoBLAST is freely available online, with ample documentation (webchem.ncbr.muni.cz/Platform/App/CrocoBLAST). No installation or user registration is required. CrocoBLAST is implemented in C, while the graphical user interface is implemented in Java. CrocoBLAST is supported under Linux and Windows, and can be run under Mac OS X in a Linux virtual machine. jkoca@ceitec.cz. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Effective electron-density map improvement and structure validation on a Linux multi-CPU web cluster: The TB Structural Genomics Consortium Bias Removal Web Service.

PubMed

Reddy, Vinod; Swanson, Stanley M; Segelke, Brent; Kantardjieff, Katherine A; Sacchettini, James C; Rupp, Bernhard

2003-12-01

Anticipating a continuing increase in the number of structures solved by molecular replacement in high-throughput crystallography and drug-discovery programs, a user-friendly web service for automated molecular replacement, map improvement, bias removal and real-space correlation structure validation has been implemented. The service is based on an efficient bias-removal protocol, Shake&wARP, and implemented using EPMR and the CCP4 suite of programs, combined with various shell scripts and Fortran90 routines. The service returns improved maps, converted data files and real-space correlation and B-factor plots. User data are uploaded through a web interface and the CPU-intensive iteration cycles are executed on a low-cost Linux multi-CPU cluster using the Condor job-queuing package. Examples of map improvement at various resolutions are provided and include model completion and reconstruction of absent parts, sequence correction, and ligand validation in drug-target structures.

NanoPack: visualizing and processing long read sequencing data.

PubMed

De Coster, Wouter; D'Hert, Svenn; Schultz, Darrin T; Cruts, Marc; Van Broeckhoven, Christine

2018-03-14

Here we describe NanoPack, a set of tools developed for visualization and processing of long read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available as a graphical user interface, a web service at http://nanoplot.bioinf.be and command line tools. wouter.decoster@molgen.vib-ua.be. Supplementary tables and figures are available at Bioinformatics online.

Real-time head movement system and embedded Linux implementation for the control of power wheelchairs.

PubMed

Nguyen, H T; King, L M; Knight, G

2004-01-01

Mobility has become very important for our quality of life. A loss of mobility due to an injury is usually accompanied by a loss of self-confidence. For many individuals, independent mobility is an important aspect of self-esteem. Head movement is a natural form of pointing and can be used to directly replace the joystick whilst still allowing for similar control. Through the use of embedded LINUX and artificial intelligence, a hands-free head movement wheelchair controller has been designed and implemented successfully. This system provides for severely disabled users an effective power wheelchair control method with improved posture, ease of use and attractiveness.

Real-time Experiment Interface for Biological Control Applications

PubMed Central

Lin, Risa J.; Bettencourt, Jonathan; White, John A.; Christini, David J.; Butera, Robert J.

2013-01-01

The Real-time Experiment Interface (RTXI) is a fast and versatile real-time biological experimentation system based on Real-Time Linux. RTXI is open source and free, can be used with an extensive range of experimentation hardware, and can be run on Linux or Windows computers (when using the Live CD). RTXI is currently used extensively for two experiment types: dynamic patch clamp and closed-loop stimulation pattern control in neural and cardiac single cell electrophysiology. RTXI includes standard plug-ins for implementing commonly used electrophysiology protocols with synchronized stimulation, event detection, and online analysis. These and other user-contributed plug-ins can be found on the website (http://www.rtxi.org). PMID:21096883

Bridges to the Doctorate: mentored transition to successful completion of doctoral study for underrepresented minorities in nursing science.

PubMed

Kim, Mi Ja; Holm, Karyn; Gerard, Peggy; McElmurry, Beverly; Foreman, Mark; Poslusny, Susan; Dallas, Constance

2009-01-01

Nursing has a shortage of doctorally-prepared underrepresented minority (URM) scientists/faculty. We describe a five-year University of Illinois at Chicago (UIC) Bridges program for URM master's students' transition to doctoral study and factors in retention/graduation from the PhD program. Four master' students from two partner schools were recruited/appointed per year and assigned UIC faculty advisors. They completed 10 UIC credits during master's study and were mentored by Bridges faculty. Administrative and financial support was provided during transition and doctoral study. Partner schools' faculty formed research dyads with UIC faculty. Seventeen Bridges students were appointed to the Bridges program: 12 were admitted to the UIC PhD program since 2004 and one graduated in 2007. Eight Bridges faculty research dyads published 5 articles and submitted 1 NIH R03 application. Mentored transition from master's through doctoral program completion and administrative/financial support for students were key factors in program success. Faculty research dyads enhanced the research climate in partner schools.

A simple micro-photometric method for urinary iodine determination.

PubMed

Grimm, Gabriele; Lindorfer, Heidelinde; Kieweg, Heidi; Marculescu, Rodrig; Hoffmann, Martha; Gessl, Alois; Sager, Manfred; Bieglmayer, Christian

2011-10-01

Urinary iodide concentration (UIC) is useful to evaluate nutritional iodine status. In clinical settings UIC helps to exclude blocking of the thyroid gland by excessive endogenous iodine, if diagnostic or therapeutic administration of radio-iodine is indicated. Therefore, this study established a simple test for the measurement of UIC. UIC was analyzed in urine samples of 200 patients. Samples were pre-treated at 95°C for 45 min with ammonium persulfate in a thermal cycler, followed by a photometric Sandell-Kolthoff reaction (SK) carried out in microtiter plates. For method comparison, UIC was analyzed in 30 samples by inductivity coupled plasma mass spectro-metry (ICP-MS) as a reference method. Incubation conditions were optimized concerning recovery. The photometric test correlated well to the reference method (SK=0.91*ICP-MS+1, r=0.962) and presented with a functional sensitivity of 20 μg/L. UIC of patient samples ranged from <20 to 750 μg/L (median 110 μg/L); 90% of the urine samples had iodide concentrations below 210 μg/L. The modified SK-test takes approximately 90 min for analyses of 20 urine samples compared with 27 h for ICP-MS. The photometric test provides satisfactory results and can be performed with the basic equipment of a clinical laboratory.

Iodine status in pregnancy: role of dietary habits and geographical origin.

PubMed

Mian, Caterina; Vitaliano, Pantaleo; Pozza, Dina; Barollo, Susi; Pitton, Mariangela; Callegari, Giovanna; Di Gianantonio, Elena; Casaro, Anna; Nacamulli, Davide; Busnardo, Benedetto; Mantero, Franco; Girelli, Maria Elisa

2009-05-01

A study was conducted on iodine status during pregnancy and its dependence on dietary habits, racial and geographical origin, and time since arrival in Italy. We enrolled 322 consecutive pregnant women: 217 Italians, 62 Eastern Europeans and 43 from Northern and Central Africa. All women completed a food frequency questionnaire on their dietary habits. The urinary iodide concentration (UIC) was determined in spot morning urine samples. In the group as a whole, the median UIC was 83 microg/l; the UIC was < 50 in 33% and of 150 microg/l or more in 27%; it was significantly lower in Africans and Eastern Europeans than in Italians (medians 45 and 46 vs. 100 microg/l, respectively, P = 0.005). For the foreign women, there was a significant correlation between UIC and time since arrival in Italy (r = 0.22, P = 0.02). A significant link emerged between UIC and cow's milk intake (P = 0.0001). Iodine supplements were used by 40% of the women, and UIC were higher in those who did so than in those who did not (median 103 vs. 75 microg/l, P = 0.03), particularly if the latter did not drink milk (median 98 vs. 42 microg/l, P = 0.01). Multivariate analysis showed that milk was the only variable influencing UIC (OR 1.29, P = 0.0005). (i) Iodine levels are too low among pregnant women in our region, and particularly in foreign women. (ii) Cow's milk intake is their main source of iodine. (iii) Iodine supplementation is mandatory during pregnancy, particularly for women do not drink milk.

Real Time Linux - The RTOS for Astronomy?

NASA Astrophysics Data System (ADS)

Daly, P. N.

The BoF was attended by about 30 participants and a free CD of real time Linux-based upon RedHat 5.2-was available. There was a detailed presentation on the nature of real time Linux and the variants for hard real time: New Mexico Tech's RTL and DIAPM's RTAI. Comparison tables between standard Linux and real time Linux responses to time interval generation and interrupt response latency were presented (see elsewhere in these proceedings). The present recommendations are to use RTL for UP machines running the 2.0.x kernels and RTAI for SMP machines running the 2.2.x kernel. Support, both academically and commercially, is available. Some known limitations were presented and the solutions reported e.g., debugging and hardware support. The features of RTAI (scheduler, fifos, shared memory, semaphores, message queues and RPCs) were described. Typical performance statistics were presented: Pentium-based oneshot tasks running > 30kHz, 486-based oneshot tasks running at ~ 10 kHz, periodic timer tasks running in excess of 90 kHz with average zero jitter peaking to ~ 13 mus (UP) and ~ 30 mus (SMP). Some detail on kernel module programming, including coding examples, were presented showing a typical data acquisition system generating simulated (random) data writing to a shared memory buffer and a fifo buffer to communicate between real time Linux and user space. All coding examples were complete and tested under RTAI v0.6 and the 2.2.12 kernel. Finally, arguments were raised in support of real time Linux: it's open source, free under GPL, enables rapid prototyping, has good support and the ability to have a fully functioning workstation capable of co-existing hard real time performance. The counter weight-the negatives-of lack of platforms (x86 and PowerPC only at present), lack of board support, promiscuous root access and the danger of ignorance of real time programming issues were also discussed. See ftp://orion.tuc.noao.edu/pub/pnd/rtlbof.tgz for the StarOffice overheads for this presentation.

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches.

PubMed

Vaudel, Marc; Barsnes, Harald; Berven, Frode S; Sickmann, Albert; Martens, Lennart

2011-03-01

The identification of proteins by mass spectrometry is a standard technique in the field of proteomics, relying on search engines to perform the identifications of the acquired spectra. Here, we present a user-friendly, lightweight and open-source graphical user interface called SearchGUI (http://searchgui.googlecode.com), for configuring and running the freely available OMSSA (open mass spectrometry search algorithm) and X!Tandem search engines simultaneously. Freely available under the permissible Apache2 license, SearchGUI is supported on Windows, Linux and OSX. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Iodine Nutrition and the Prevalence of Thyroid Disease after Salt Iodization: A Cross-Sectional Survey in Shanghai, a Coastal Area in China

PubMed Central

Zou, Shurong; Wu, Fan; Guo, Changyi; Song, Jun; Huang, Cuihua; Zhu, Zhenni; Yu, Huiting; Guo, Yanfei; Lu, Xi; Ruan, Ye

2012-01-01

Background Both insufficient and excess iodine may produce thyroid disease. After salt iodization in China, the median urine iodine concentration (UIC) of children aged 8–10 years appeared adequate. However, it is unknown whether dietary changes due to rapid economic development in Shanghai have affected whole population iodine nutrition. Objective To assess dietary iodine intake, UIC and the prevalence of thyroid disease in the general population of Shanghai. Design A cross-sectional survey was conducted with general participants aged 5–69 years (n = 7,904) plus pregnant and lactating women (n = 380 each) selected by stratified multistage sampling. The iodine concentrations in their salt, drinking water and urine were measured. Daily iodine intake was estimated using the total diet study approach. Serum thyroid hormone concentrations and thyroid-related antibodies were measured and thyroid ultrasonography was performed. Results The median iodine concentration in salt was 29.5 mg/kg, and 12.8 µg/L in drinking water. Iodized salt, used by 95.3% of participants, contributed 63.5% of total dietary iodine. Estimated daily iodine intake was 225.96 µg. The median UIC of general participants was 146.7 µg/L; UIC <100 µg/L (iodine insufficiency) was seen in 28.6%; UIC >300 µg/L (iodine excess) in 10.1%. Pregnant women had a median UIC of 135.9 µg/L, with UIC <150 µg/L in 55.4%. Thyroid nodules and subclinical hypothyroidism were found in 27.44% and 9.17%, respectively. Conclusions According to published criteria, the current dietary iodine intake in Shanghai was generally sufficient and safe, but insufficient in pregnant women. Thyroid nodules and subclinical hypothyroidism were the commonest thyroid diseases identified. PMID:22911705

The Iodine Status of Queensland Preschool Children After the Introduction of Mandatory Iodine Fortification in Bread: An Exploratory Study Using a Convenience Sample.

PubMed

Samidurai, A J; Ware, R S; Davies, P S W

2017-01-01

Introduction Appropriate dietary iodine is essential for thyroid hormone synthesis, especially in young children. Following an iodine fortification in bread initiative, approximately 6 % of Australian preschool children were expected to have an excessive iodine status. The aim of this study was to document the current iodine status of preschool children using urinary iodine concentration (UIC) as a biomarker of iodine intake. Methods A convenience sample of fifty-one preschool children, aged 2-3 years, were recruited from south east Queensland. UIC was ascertained from spot morning and afternoon urine samples collected on two consecutive days and food frequency questionnaires were completed for each participant. Dietary iodine intake was extrapolated from UIC assuming 90 % of dietary iodine is excreted in urine and a urine volume of 0.5 L/day. Results A median UIC of 223.3 μg/L was found. The calculated median dietary iodine intake was 124.8 μg/day (SD 47.0) with 9.8 % of samples above the upper level of 200 μg for dietary iodine for children within this age group. No foods were associated with UIC. Discussion Limited by sample size and recruitment strategies, no association was found between usual food intake and UIC. Extrapolated dietary iodine intake indicated that children within this cohort consumed adequate amounts of dietary iodine, although the number of children consuming above the upper limit of 300 μg/day was almost double of expected. The development of a UIC criteria to assess appropriate parameters for varying degrees of iodine status is required for the monitoring of iodine nutrition in this vulnerable age group.

An Increase in Consuming Adequately Iodized Salt May Not Be Enough to Rectify Iodine Deficiency in Pregnancy in an Iodine-Sufficient Area of China

PubMed Central

Wang, Zhifang; Zhu, Wenming; Mo, Zhe; Wang, Yuanyang; Mao, Guangming; Wang, Xiaofeng; Lou, Xiaoming

2017-01-01

Universal salt iodization (USI) has been implemented for two decades in China. It is crucial to periodically monitor iodine status in the most vulnerable population, such as pregnant women. A cross-sectional study was carried out in an evidence-proved iodine-sufficient province to evaluate iodine intake in pregnancy. According to the WHO/UNICEF/ICCIDD recommendation criteria of adequate iodine intake in pregnancy (150–249 µg/L), the median urinary iodine concentration (UIC) of the total 8159 recruited pregnant women was 147.5 µg/L, which indicated pregnant women had iodine deficiency at the province level. Overall, 51.0% of the total study participants had iodine deficiency with a UIC < 150 µg/L and only 32.9% of them had adequate iodine. Participants living in coastal areas had iodine deficiency with a median UIC of 130.1 µg/L, while those in inland areas had marginally adequate iodine intake with a median UIC of 158.1 µg/L (p < 0.001). Among the total study participants, 450 pregnant women consuming non-iodized salt had mild-moderate iodine deficiency with a median UIC of 99.6 µg/L; 7363 pregnant women consuming adequately iodized salt had a lightly statistically higher median UIC of 151.9 µg/L, compared with the recommended adequate level by the WHO/UNICEF/ICCIDD (p < 0.001). Consuming adequately iodized salt seemed to lightly increase the median UIC level, but it may not be enough to correct iodine nutrition status to an optimum level as recommended by the WHO/UNICEF/ICCIDD. We therefore suggest that, besides strengthening USI policy, additional interventive measure may be needed to improve iodine intake in pregnancy. PMID:28230748

An Increase in Consuming Adequately Iodized Salt May Not Be Enough to Rectify Iodine Deficiency in Pregnancy in an Iodine-Sufficient Area of China.

PubMed

Wang, Zhifang; Zhu, Wenming; Mo, Zhe; Wang, Yuanyang; Mao, Guangming; Wang, Xiaofeng; Lou, Xiaoming

2017-02-20

Universal salt iodization (USI) has been implemented for two decades in China. It is crucial to periodically monitor iodine status in the most vulnerable population, such as pregnant women. A cross-sectional study was carried out in an evidence-proved iodine-sufficient province to evaluate iodine intake in pregnancy. According to the WHO/UNICEF/ICCIDD recommendation criteria of adequate iodine intake in pregnancy (150-249 µg/L), the median urinary iodine concentration (UIC) of the total 8159 recruited pregnant women was 147.5 µg/L, which indicated pregnant women had iodine deficiency at the province level. Overall, 51.0% of the total study participants had iodine deficiency with a UIC < 150 µg/L and only 32.9% of them had adequate iodine. Participants living in coastal areas had iodine deficiency with a median UIC of 130.1 µg/L, while those in inland areas had marginally adequate iodine intake with a median UIC of 158.1 µg/L ( p < 0.001). Among the total study participants, 450 pregnant women consuming non-iodized salt had mild-moderate iodine deficiency with a median UIC of 99.6 µg/L; 7363 pregnant women consuming adequately iodized salt had a lightly statistically higher median UIC of 151.9 µg/L, compared with the recommended adequate level by the WHO/UNICEF/ICCIDD ( p < 0.001). Consuming adequately iodized salt seemed to lightly increase the median UIC level, but it may not be enough to correct iodine nutrition status to an optimum level as recommended by the WHO/UNICEF/ICCIDD. We therefore suggest that, besides strengthening USI policy, additional interventive measure may be needed to improve iodine intake in pregnancy.

TmoleX--a graphical user interface for TURBOMOLE.

PubMed

Steffen, Claudia; Thomas, Klaus; Huniar, Uwe; Hellweg, Arnim; Rubner, Oliver; Schroer, Alexander

2010-12-01

We herein present the graphical user interface (GUI) TmoleX for the quantum chemical program package TURBOMOLE. TmoleX allows users to execute the complete workflow of a quantum chemical investigation from the initial building of a structure to the visualization of the results in a user friendly graphical front end. The purpose of TmoleX is to make TURBOMOLE easy to use and to provide a high degree of flexibility. Hence, it should be a valuable tool for most users from beginners to experts. The program is developed in Java and runs on Linux, Windows, and Mac platforms. It can be used to run calculations on local desktops as well as on remote computers. © 2010 Wiley Periodicals, Inc.

OpenMx: An Open Source Extended Structural Equation Modeling Framework

ERIC Educational Resources Information Center

Boker, Steven; Neale, Michael; Maes, Hermine; Wilde, Michael; Spiegel, Michael; Brick, Timothy; Spies, Jeffrey; Estabrook, Ryne; Kenny, Sarah; Bates, Timothy; Mehta, Paras; Fox, John

2011-01-01

OpenMx is free, full-featured, open source, structural equation modeling (SEM) software. OpenMx runs within the "R" statistical programming environment on Windows, Mac OS-X, and Linux computers. The rationale for developing OpenMx is discussed along with the philosophy behind the user interface. The OpenMx data structures are…

Manipulation of volumetric patient data in a distributed virtual reality environment.

PubMed

Dech, F; Ai, Z; Silverstein, J C

2001-01-01

Due to increases in network speed and bandwidth, distributed exploration of medical data in immersive Virtual Reality (VR) environments is becoming increasingly feasible. The volumetric display of radiological data in such environments presents a unique set of challenges. The shear size and complexity of the datasets involved not only make them difficult to transmit to remote sites, but these datasets also require extensive user interaction in order to make them understandable to the investigator and manageable to the rendering hardware. A sophisticated VR user interface is required in order for the clinician to focus on the aspects of the data that will provide educational and/or diagnostic insight. We will describe a software system of data acquisition, data display, Tele-Immersion, and data manipulation that supports interactive, collaborative investigation of large radiological datasets. The hardware required in this strategy is still at the high-end of the graphics workstation market. Future software ports to Linux and NT, along with the rapid development of PC graphics cards, open the possibility for later work with Linux or NT PCs and PC clusters.

Iodine nutrition in elementary state schools of Queretaro, Mexico: correlations between urinary iodine concentration with global nutrition status and social gap index.

PubMed

García-Solís, Pablo; Solís-S, Juan Carlos; García-Gaytán, Ana Cristina; Reyes-Mendoza, Vanessa A; Robles-Osorio, Ludivina; Villarreal-Ríos, Enrique; Leal-García, Luisa; Hernández-Montiel, Hebert Luis

2013-08-01

To estimate median urinary iodine concentration (UIC), and to correlate it with global nutrition indicators and social gap index (SGI) in 50 elementary state schools from 10 municipalities in the State of Queretaro, Mexico. 1,544 students were enrolled and an above of requirements of iodine intake was found (median UIC of 297 µg/L). Iodine status was found as deficient, adequate, more than adequate and excessive in 2, 4, 19 and 25 schools, respectively. Seventy seven percent of table salt samples showed adequate iodine content (20-40 ppm), while 9.6% of the samples had low iodine content (< 15 ppm). Medians of UIC per school were positively correlated with medians of body mass index (BMI) by using the standard deviation score (SDS) (r = 0.47; p < 0.005), height SDS (r = 0.41; p < 0.05), and overweight and obesity prevalence (r = 0.41; p < 0.05). Medians of UIC per school were negatively correlated with stunting prevalence (r = -0.39; p = 005) and social gap index (r = -0.36; p < 0.05). Best multiple regression models showed that BMI SDS and height were significantly related with UIC (p < 0.05). There is coexistence between the two extremes of iodine intake (insufficient and excessive). To our knowledge, the observed positive correlation between UIC and overweight and obesity has not been described before, and could be explained by the availability and consumption of snack food rich in energy and iodized salt.

RTSPM: real-time Linux control software for scanning probe microscopy.

PubMed

Chandrasekhar, V; Mehta, M M

2013-01-01

Real time computer control is an essential feature of scanning probe microscopes, which have become important tools for the characterization and investigation of nanometer scale samples. Most commercial (and some open-source) scanning probe data acquisition software uses digital signal processors to handle the real time data processing and control, which adds to the expense and complexity of the control software. We describe here scan control software that uses a single computer and a data acquisition card to acquire scan data. The computer runs an open-source real time Linux kernel, which permits fast acquisition and control while maintaining a responsive graphical user interface. Images from a simulated tuning-fork based microscope as well as a standard topographical sample are also presented, showing some of the capabilities of the software.

Breast-Milk Iodine Concentrations, Iodine Status, and Thyroid Function of Breastfed Infants Aged 2-4 Months and Their Mothers Residing in a South African Township.

PubMed

Osei, Jennifer; Andersson, Maria; Reijden, Olivia van der; Dold, Susanne; Smuts, Cornelius M; Baumgartner, Jeannine

2016-12-01

Lactating women and their infants are susceptible to iodine deficiency and iodine excess. In South Africa, no data exist on the iodine status and thyroid function of these vulnerable groups. In a cross-sectional study, urinary iodine concentrations (UIC), thyroid function, and breast-milk iodine concentrations (BMIC) were assessed in 100 lactating women from a South African township and their 2-4-month-old breastfed infants. Potential predictors of UIC, thyroid function, and BMIC, including household salt iodine concentrations (SIC) and maternal sodium excretion, were also investigated. The median (25th-75th percentile) UIC was 373 (202-627) μg/L in infants and 118 (67-179) μg/L in mothers. Median household SIC was 44 (27-63) ppm. Household SIC and maternal urinary sodium excretion predicted UIC of lactating mothers. Median BMIC was 179 (126-269) μg/L. Age of infants, SIC, and maternal UIC predicted BMIC. In turn, infant age and BMIC predicted UIC of infants. Forty-two percent of SIC values were within the South African recommended salt iodine fortification level at production of 35-65 ppm, whilst 21% of SIC were >65 ppm. Thyroid-stimulating hormone, total thyroxine, and thyroglobulin concentrations in the dried whole blood spot specimens from the infants were 1.3 (0.8-1.9) mU/L, 128±33 mmol/L, and 77.1 (56.3-105.7) μg/L, respectively, and did not correlate with infant UIC or BMIC. Our results suggest that the salt fortification program in South Africa provides adequate iodine to lactating women and indirectly to their infants via breast milk. However, monitoring of salt iodine content of the mandatory salt iodization program in South Africa is important to avoid over-iodization of salt.

Iodine deficiency during pregnancy: a national cross-sectional survey in Latvia.

PubMed

Konrade, Ilze; Kalere, Ieva; Strele, Ieva; Makrecka-Kuka, Marina; Jekabsone, Anna; Tetere, Elina; Veisa, Vija; Gavars, Didzis; Rezeberga, Dace; Pīrāgs, Valdis; Lejnieks, Aivars; Dambrova, Maija

2015-11-01

Low iodine intake during pregnancy may cause thyroid dysfunction, which results in inadequate fetal brain development. In the absence of a universal salt iodization programme, we conducted a nationwide survey of iodine deficiency in pregnant women in Latvia. A countrywide twenty-cluster survey, with at least twenty women per cluster. Participants completed a questionnaire on dietary habits concerning iodine intake (n 739). Thyroid function (thyroid-stimulating hormone, free thyroxine and thyroperoxidase antibodies) was measured (n 550). Urinary iodine was measured using the ammonium persulfate method (n 696). The survey was performed in all regions of Latvia during the spring and autumn seasons in 2013. Pregnant women (n 829). The median creatinine (Cr)-standardized urinary iodine concentration (UIC) was 80·8 (interquartile range (IQR) 46·1-130·6) µg/g Cr or 69·4 (IQR 53·9-92·6) µg/l during pregnancy, and 81% of pregnant women had UIC levels below the WHO recommended range of 150-250 µg/g Cr. The UIC was lowest during the first trimester of pregnancy, 56·0 (IQR 36·4-100·6) µg/g Cr, reaching higher concentrations of 87·5 (IQR 46·4-141·7) µg/g Cr and 86·9 (IQR 53·8-140·6) µg/g Cr in the second and third trimesters, respectively. Women taking supplements containing ≥150 µg iodine (6·8% of respondents) had non-significantly higher UIC than did women without supplementation (96·2 v. 80·3 µg/g Cr, respectively, P=NS). Thyroperoxidase antibody concentration did not correlate significantly with UIC: Spearman's ρ=-0·012, P=0·78. The median UIC indicates iodine deficiency in pregnant women in Latvia. Iodine supplementation (150 µg daily) and regular UIC monitoring should be suggested to overcome iodine deficiency and to reach the recommended levels without inducing autoimmune processes.

Peregrine System User Basics | High-Performance Computing | NREL

Science.gov Websites

peregrine.hpc.nrel.gov or to one of the login nodes. Example commands to access Peregrine from a Linux or Mac OS X system Code Example Create a file called hello.F90 containing the following code: program hello write(6 information by enclosing it in brackets < >. For example: $ ssh -Y

Towards Efficient Scientific Data Management Using Cloud Storage

NASA Technical Reports Server (NTRS)

He, Qiming

2013-01-01

A software prototype allows users to backup and restore data to/from both public and private cloud storage such as Amazon's S3 and NASA's Nebula. Unlike other off-the-shelf tools, this software ensures user data security in the cloud (through encryption), and minimizes users operating costs by using space- and bandwidth-efficient compression and incremental backup. Parallel data processing utilities have also been developed by using massively scalable cloud computing in conjunction with cloud storage. One of the innovations in this software is using modified open source components to work with a private cloud like NASA Nebula. Another innovation is porting the complex backup to- cloud software to embedded Linux, running on the home networking devices, in order to benefit more users.

Excessive Iodine Intake and Subclinical Hypothyroidism in Children and Adolescents Aged 6-19 Years: Results of the Sixth Korean National Health and Nutrition Examination Survey, 2013-2015.

PubMed

Kang, Min Jae; Hwang, Il Tae; Chung, Hye Rim

2018-06-01

Iodine is an important element for the synthesis of thyroid hormone, and its deficiency or excessive intake is associated with various thyroid diseases. Little is known about the association between iodine status and thyroid function among children and adolescents living in iodine-rich areas. Therefore, this study analyzed this association using data from a nationwide survey. From the Korea National Health and Nutrition Examination Surveys VI (2013-2015) data, 1288 subjects (711 male) aged 6-19 years who underwent a urinary iodine concentration (UIC) test and 1000 subjects (564 male) aged 10-19 years who underwent a thyroid function test were included in this study. Serum levels of thyrotropin (TSH), free thyroxine (fT4), and thyroperoxidase antibodies (TPOAb) were analyzed. Subclinical hypothyroidism (SCH) was defined as TSH >5.5 μIU/mL with a normal fT4 level. Median daily iodine intake was calculated from the UIC. Daily sodium intake was derived from the nutritional survey data of 1181 subjects. The median UIC was 449 μg/L (range 15-21,905 μg/L), and the prevalence rates of UIC ≥300 μg/L and ≥1000 μg/L were 64.9% and 25.0%, respectively. The prevalence rates of a sodium intake >2000 mg/day and iodine intake >2400 μg/day were 75.0% (885/1181) and 12.7% (164/1288), respectively. The prevalence rates of SCH and TPOAb >34 IU/mL were 7.2% (72/1000) and 2.3% (23/1000), respectively. The prevalence of SCH was significantly higher in the iodine deficient and iodine excess groups compared to those in the UIC 100-299.9 μg/L group (p = 0.038). Therefore, there was a U-shaped and inverted U-shaped correlation between serum levels of TSH and fT4 with UIC, respectively. These correlations were especially prominent when UIC was >1000 μg/L. There was no definite correlation between TPOAb and UIC. Excess iodine was prevalent in Korean children and adolescents, and it may be associated with SCH. Therefore, monitoring the iodine status and education on adequate intake are needed in iodine-rich areas.

Iodine nutrition status in lactating mothers residing in countries with mandatory and voluntary iodine fortification programs: an updated systematic review.

PubMed

Nazeri, Pantea; Mirmiran, Parvin; Shiva, Niloofar; Mehrabi, Yadollah; Mojarrad, Mehdi; Azizi, Fereidoun

2015-06-01

The aim of this review is to assess data available on iodine nutrition status in lactating mothers residing in countries with mandatory and voluntary iodine fortification programs and/or iodine supplementation. A systematic review was conducted by searching articles published between 1964 and 2013 in Pub Med, ISI Web, and Cochrane Library using iodine nutrition, lactation, iodine supplementation, and iodine fortification as keywords for titles and/or abstracts. Relevant articles were included if they reported urinary iodine concentration (UIC) in lactating mothers and, if determined, the type of iodine fortification program and/or iodine supplementation. Forty-two studies met the inclusion criteria. Among these, 21 studies assessed lactating mothers in countries with a mandatory iodine fortification program, 17 studies were from countries with voluntary and/or without iodine fortification programs, and four studies assessed iodine nutrition status in lactating mothers undergoing iodine supplementation. Among countries with mandatory iodine fortification programs, the range of salt iodization level in lactating mothers with a UIC <100 μg/L was between 8 and 40 ppm, whereas among lactating mothers with UIC >100 μg/L, it was between 15 and 60 ppm. Levels of UIC <100 μg/L were observed among lactating women in India, Denmark, Mali, New Zealand, Australia, Slovakia, Sudan, and Turkey, whereas in countries such as Chile, Iran, Mongolia, New Guinea, and Nigeria, the median or mean of UIC was >100 μg/L. There was a median or mean UIC <100 μg/L in nearly all lactating mothers residing in countries where implementation of universal salt iodization program was voluntary, including Switzerland, Australia, New Zealand, Ireland, and Germany. However, in some countries with voluntary iodine fortification programs, such as the United States, Spain, and Japan, a mean or median UIC of >100 μg/L has been reported. Although universal salt iodization is still the most feasible and cost-effective approach for iodine deficiency control in pregnant and lactating mothers, UIC in lactating mothers of most countries with voluntary programs and in areas with mandatory iodine fortification is still within the iodine deficiency range, indicating that iodine supplementation in daily prenatal vitamin/mineral supplements in lactating mothers is warranted. However, further investigations are still recommended in this regard.

PsyToolkit: a software package for programming psychological experiments using Linux.

PubMed

Stoet, Gijsbert

2010-11-01

PsyToolkit is a set of software tools for programming psychological experiments on Linux computers. Given that PsyToolkit is freely available under the Gnu Public License, open source, and designed such that it can easily be modified and extended for individual needs, it is suitable not only for technically oriented Linux users, but also for students, researchers on small budgets, and universities in developing countries. The software includes a high-level scripting language, a library for the programming language C, and a questionnaire presenter. The software easily integrates with other open source tools, such as the statistical software package R. PsyToolkit is designed to work with external hardware (including IoLab and Cedrus response keyboards and two common digital input/output boards) and to support millisecond timing precision. Four in-depth examples explain the basic functionality of PsyToolkit. Example 1 demonstrates a stimulus-response compatibility experiment. Example 2 demonstrates a novel mouse-controlled visual search experiment. Example 3 shows how to control light emitting diodes using PsyToolkit, and Example 4 shows how to build a light-detection sensor. The last two examples explain the electronic hardware setup such that they can even be used with other software packages.

KNBD: A Remote Kernel Block Server for Linux

NASA Technical Reports Server (NTRS)

Becker, Jeff

1999-01-01

I am developing a prototype of a Linux remote disk block server whose purpose is to serve as a lower level component of a parallel file system. Parallel file systems are an important component of high performance supercomputers and clusters. Although supercomputer vendors such as SGI and IBM have their own custom solutions, there has been a void and hence a demand for such a system on Beowulf-type PC Clusters. Recently, the Parallel Virtual File System (PVFS) project at Clemson University has begun to address this need (1). Although their system provides much of the functionality of (and indeed was inspired by) the equivalent file systems in the commercial supercomputer market, their system is all in user-space. Migrating their 10 services to the kernel could provide a performance boost, by obviating the need for expensive system calls. Thanks to Pavel Machek, the Linux kernel has provided the network block device (2) with kernels 2.1.101 and later. You can configure this block device to redirect reads and writes to a remote machine's disk. This can be used as a building block for constructing a striped file system across several nodes.

Transitioning to Intel-based Linux Servers in the Payload Operations Integration Center

NASA Technical Reports Server (NTRS)

Guillebeau, P. L.

2004-01-01

The MSFC Payload Operations Integration Center (POIC) is the focal point for International Space Station (ISS) payload operations. The POIC contains the facilities, hardware, software and communication interface necessary to support payload operations. ISS ground system support for processing and display of real-time spacecraft and telemetry and command data has been operational for several years. The hardware components were reaching end of life and vendor costs were increasing while ISS budgets were becoming severely constrained. Therefore it has been necessary to migrate the Unix portions of our ground systems to commodity priced Intel-based Linux servers. hardware architecture including networks, data storage, and highly available resources. This paper will concentrate on the Linux migration implementation for the software portion of our ground system. The migration began with 3.5 million lines of code running on Unix platforms with separate servers for telemetry, command, Payload information management systems, web, system control, remote server interface and databases. The Intel-based system is scheduled to be available for initial operational use by August 2004 The overall migration to Intel-based Linux servers in the control center involves changes to the This paper will address the Linux migration study approach including the proof of concept, criticality of customer buy-in and importance of beginning with POSlX compliant code. It will focus on the development approach explaining the software lifecycle. Other aspects of development will be covered including phased implementation, interim milestones and metrics measurements and reporting mechanisms. This paper will also address the testing approach covering all levels of testing including development, development integration, IV&V, user beta testing and acceptance testing. Test results including performance numbers compared with Unix servers will be included. need for a smooth transition while maintaining real-time support. An important aspect of the paper will involve challenges and lessons learned. product compatibility, implications of phasing decisions and tracking of dependencies, particularly non- software dependencies. The paper will also discuss scheduling challenges providing real-time flight support during the migration and the requirement to incorporate in the migration changes being made simultaneously for flight support. This paper will also address the deployment approach including user involvement in testing and the , This includes COTS product compatibility, implications of phasing decisions and tracking of dependencies, particularly non- software dependencies. The paper will also discuss scheduling challenges providing real-time flight support during the migration and the requirement to incorporate in the migration changes being made simultaneously for flight support.

Merocyclophanes C and D from the Cultured Freshwater Cyanobacterium Nostoc sp. (UIC 10110).

PubMed

May, Daniel S; Chen, Wei-Lun; Lantvit, Daniel D; Zhang, Xiaoli; Krunic, Aleksej; Burdette, Joanna E; Eustaquio, Alessandra; Orjala, Jimmy

2017-04-28

Merocyclophanes C and D (1 and 2) were isolated from the cell extract of the cultured cyanobacterium UIC 10110. The structures were determined by one-dimensional nuclear magnetic resonance (NMR) and high-resolution electrospray ionization mass spectrometry and confirmed by 2D NMR techniques. The absolute configurations were determined using electronic circular dichroism spectroscopy. Merocyclophanes C and D represent the first known analogues of the merocyclophane core structure, a recently discovered scaffold of [7,7] paracyclophanes characterized by an α-branched methyl at C-1/C-14; 1 and 2 showed antiproliferative activity against the MDA-MB-435 cell line with IC 50 values of 1.6 and 0.9 μM, respectively. Partial 16S analysis determined UIC 10110 to be a Nostoc sp., and it was found to clade with UIC 10062 Nostoc sp., the only other strain known to produce merocyclophanes. The genome of UIC 10110 was sequenced, and a biosynthetic gene cluster was identified that is proposed to encode type I and type III polyketide synthases that are potentially responsible for production of the merocyclophanes; however, further experiments will be required to verify the true function of the gene cluster. The gene cluster provides a genetic basis for the observed structural differences of the [7,7] paracyclophane core structures.

CXA La Paloma, LLC: UIC Class I Permit No.CA10710001

EPA Pesticide Factsheets

Documents related to La Paloma Generating Company, LLC's (LPGC) application for a UIC permit renewal (of permit #CA199000001) to operate a Class I injection well facility to dispose of non-hazardous wastewater from the La Paloma Generating Plant.

County of Hawai’i: Administrative Order on Consent; Docket No. SDWA-UIC-AOC-2017-0002

EPA Pesticide Factsheets

Documents related to the Administrative Order on Consent (“Consent Order”) between the U.S. Environmental Protection Agency Region 9 (“EPA”) and the County of Hawai‘i. Docket No. SDWA-UIC-AOC-2017-0002.

MCR Container Tools

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

Haas, Nicholas Q; Gillen, Robert E; Karnowski, Thomas P

MathWorks' MATLAB is widely used in academia and industry for prototyping, data analysis, data processing, etc. Many users compile their programs using the MATLAB Compiler to run on workstations/computing clusters via the free MATLAB Compiler Runtime (MCR). The MCR facilitates the execution of code calling Application Programming Interfaces (API) functions from both base MATLAB and MATLAB toolboxes. In a Linux environment, a sizable number of third-party runtime dependencies (i.e. shared libraries) are necessary. Unfortunately, to the MTLAB community's knowledge, these dependencies are not documented, leaving system administrators and/or end-users to find/install the necessary libraries either as runtime errors resulting frommore » them missing or by inspecting the header information of Executable and Linkable Format (ELF) libraries of the MCR to determine which ones are missing from the system. To address various shortcomings, Docker Images based on Community Enterprise Operating System (CentOS) 7, a derivative of Redhat Enterprise Linux (RHEL) 7, containing recent (2015-2017) MCR releases and their dependencies were created. These images, along with a provided sample Docker Compose YAML Script, can be used to create a simulated computing cluster where MATLAB Compiler created binaries can be executed using a sample Slurm Workload Manager script.« less

Inadequate status of iodine nutrition among pregnant women residing in three districts of Niamey, the Niger Republic's capital.

PubMed

Sadou, Hassimi; Seyfoulaye, Amina; Malam Alma, Mousbahou; Daouda, Hamani

2014-10-01

Universal dietary salt iodisation (UDSI) programme was implemented in Niger in 1996. However, since 2000, there has been a slowdown in progress against iodine deficiency. The aim of our study was to assess the iodine status among pregnant women in a context where national controls are not effective at ensuring universal availability of adequately iodised salt. This is mainly to assess the impact of the slowdown in the fight against iodine deficiency in this vulnerable group. The study was centred on 240 healthy pregnant women volunteers recruited in three districts primary health centres. A control group of 60 non-pregnant, non-lactating healthy women was also studied and compared. Median urinary iodine concentration (UIC) of all pregnant women was 119 μg L(-1) , and 61.67% had UIC below 150 μg L(-1) . Median UIC for the first, second and third trimester were 144, 108 and 92 μg L(-1) , respectively. The percentage of pregnant women with UIC below 150 μg L(-1) increased from 52% in the first trimester to 66% in the third trimester. The median UIC of the control group was 166 μg L(-1) , and 28.33% had UIC below 100 μg L(-1) . No significant relationship was found between nutritional iodine status and provenance, age and parity. However, significant relationship was found between iodine status and stage of pregnancy, gestational age and educational level (P < 0.05). Iodine nutrition status thus observed was inadequate in 61.67% of all the pregnant women. It is therefore urgent to revitalise implementation of the UDSI programme, and in the short term to consider iodine supplementation for pregnant women. © 2013 John Wiley & Sons Ltd.

Iodine status in a Sherpa community in a village of the Khumbu region of Nepal.

PubMed

Heydon, Emma E; Thomson, Christine D; Mann, Jim; Williams, Sheila M; Skeaff, Sheila A; Sherpa, Kami T; Heydon, John L

2009-09-01

To assess the iodine status of Sherpa residents living in Kunde village, Khumbu region, Nepal. Prevalence of goitre was determined by palpation. Urinary iodine concentrations (UIC) were determined in casual morning samples, and thyroid-stimulating hormone (TSH) in finger-prick blood samples on filter paper. Dietary and demographic data were obtained via questionnaire, and selected foods analysed for iodine. Khumbu region is an area of low soil iodine in Nepal, where the prevalence of goitre was greater than 90% in the 1960s prior to iodine intervention. Two hundred and fifteen of 219 permanent residents of Kunde were studied. Overall prevalence of goitre was 31% (Grade 1 goitre, 27.0%; Grade 2, 4.2%). When adjusted to a world population, goitre prevalence was 27% (95% CI 23, 32%); Grade 2 goitre prevalence was 2.8% (95% CI 1.0, 4.6%). Median UIC was 97 microg/l, but only 75 microg/l in women of childbearing age. Thirty per cent had UIC < 50 microg/l and 52% had UIC < 100 microg/l, while 31% of children aged <14 years had UIC > 300 microg/l. Ten per cent of participants had TSH concentrations >5 microU/ml. The prevalence of severe iodine deficiency has decreased since the 1960s, but mild iodine deficiency persists, particularly in women of childbearing age. The consumption of high-iodine uncooked instant noodles and flavour sachets by school-aged children contributed to their low prevalence of goitre and excessive UIC values. This finding may obscure a more severe iodine deficiency in the population, while increasing the risk of iodine-induced hyperthyroidism in children. Ongoing monitoring is essential.

Pre-analytical Factors Influence Accuracy of Urine Spot Iodine Assessment in Epidemiological Surveys.

PubMed

Doggui, Radhouene; El Ati-Hellal, Myriam; Traissac, Pierre; El Ati, Jalila

2018-03-26

Urinary iodine concentration (UIC) is commonly used to assess iodine status of subjects in epidemiological surveys. As pre-analytical factors are an important source of measurement error and studies about this phase are scarce, our objective was to assess the influence of urine sampling conditions on UIC, i.e., whether the child ate breakfast or not, urine void rank of the day, and time span between last meal and urine collection. A nationwide, two-stage, stratified, cross-sectional study including 1560 children (6-12 years) was performed in 2012. UIC was determined by the Sandell-Kolthoff method. Pre-analytical factors were assessed from children's mothers by using a questionnaire. Association between iodine status and pre-analytical factors were adjusted for one another and socio-economic characteristics by multivariate linear and multinomial regression models (RPR: relative prevalence ratios). Skipping breakfast prior to morning urine sampling decreased UIC by 40 to 50 μg/L and the proportion of UIC < 100 μg/L was higher among children having those skipped breakfast (RPR = 3.2[1.0-10.4]). In unadjusted analyses, UIC was less among children sampled more than 5 h from their last meal. UIC decreased with rank of urine void (e.g., first vs. second, P < 0.001); also, the proportion of UIC < 100 μg/L was greater among 4th rank samples (vs. second RPR = 2.1[1.1-4.0]). Subjects' breakfast status and urine void rank should be accounted for when assessing iodine status. Providing recommendations to standardize pre-analytical factors is a key step toward improving accuracy and comparability of survey results for assessing iodine status from spot urine samples. These recommendations have to be evaluated by future research.

Regression Analysis to Identify Factors Associated with Urinary Iodine Concentration at the Sub-National Level in India, Ghana, and Senegal

PubMed Central

Knowles, Jacky; Kupka, Roland; Dumble, Sam; Garrett, Greg S.; Pandav, Chandrakant S.; Yadav, Kapil; Touré, Ndeye Khady; Foriwa Amoaful, Esi; Gorstein, Jonathan

2018-01-01

Single and multiple variable regression analyses were conducted using data from stratified, cluster sample design, iodine surveys in India, Ghana, and Senegal to identify factors associated with urinary iodine concentration (UIC) among women of reproductive age (WRA) at the national and sub-national level. Subjects were survey household respondents, typically WRA. For all three countries, UIC was significantly different (p < 0.05) by household salt iodine category. Other significant differences were by strata and by household vulnerability to poverty in India and Ghana. In multiple variable regression analysis, UIC was significantly associated with strata and household salt iodine category in India and Ghana (p < 0.001). Estimated UIC was 1.6 (95% confidence intervals (CI) 1.3, 2.0) times higher (India) and 1.4 (95% CI 1.2, 1.6) times higher (Ghana) among WRA from households using adequately iodised salt than among WRA from households using non-iodised salt. Other significant associations with UIC were found in India, with having heard of iodine deficiency (1.2 times higher; CI 1.1, 1.3; p < 0.001) and having improved dietary diversity (1.1 times higher, CI 1.0, 1.2; p = 0.015); and in Ghana, with the level of tomato paste consumption the previous week (p = 0.029) (UIC for highest consumption level was 1.2 times lowest level; CI 1.1, 1.4). No significant associations were found in Senegal. Sub-national data on iodine status are required to assess equity of access to optimal iodine intake and to develop strategic responses as needed. PMID:29690505

Adequacy Assessment of a Universal Salt Iodization Program Two Decades after Its Implementation: A National Cross-Sectional Study of Iodine Status among School-Age Children in Tunisia

PubMed Central

Doggui, Radhouene; El Ati-Hellal, Myriam; Traissac, Pierre; Lahmar, Lilia; El Ati, Jalila

2016-01-01

In the framework of a worldwide policy to eliminate iodine deficiency (ID) disorders, universal salt iodization was adopted in Tunisia two decades ago. The present study aims to evaluate this strategy, using both performance and impact indicators. A total of 1560 children, aged 6–12 years, were randomly sampled using a national, two-stage, stratified, cross-sectional cluster survey in 2012. Urinary iodine concentration (UIC) of the subjects, and household salt iodine content, were analyzed. The national median UIC was 220 µg/L (95% confidence interval (CI): 199–241), indicating an acceptable iodine status at the population level. Only 11.4% (95% CI: 8.6–14.9) of the children had UIC <100 µg/L, but with large regional disparities (4.3% to 25.5%, p < 0.01); however, more than a quarter of the subjects were at risk of adverse health consequences due to iodine excess. Children from households of low socio-economic levels were more prone to inadequate UIC. The national median iodine concentration of household salt was 22 mg/kg (95% CI: 21–23). Only half of the households used adequately iodized salt (15–25 ppm), with large regional disparities. National ID rates are now well below the target criteria of WHO (World Health Organization) certification (<20% of children with UIC <50 µg/L and <50% with UIC <100 µg/L). The coverage of adequately iodized salt fell short in meeting the goals of USI (Universal Salt Iodization), i.e., >90% of households. Regular monitoring of iodized salt production lines must be strengthened with involvement by producers. PMID:28029137

Adequacy Assessment of a Universal Salt Iodization Program Two Decades after Its Implementation: A National Cross-Sectional Study of Iodine Status among School-Age Children in Tunisia.

PubMed

Doggui, Radhouene; El Ati-Hellal, Myriam; Traissac, Pierre; Lahmar, Lilia; El Ati, Jalila

2016-12-25

In the framework of a worldwide policy to eliminate iodine deficiency (ID) disorders, universal salt iodization was adopted in Tunisia two decades ago. The present study aims to evaluate this strategy, using both performance and impact indicators. A total of 1560 children, aged 6-12 years, were randomly sampled using a national, two-stage, stratified, cross-sectional cluster survey in 2012. Urinary iodine concentration (UIC) of the subjects, and household salt iodine content, were analyzed. The national median UIC was 220 µg/L (95% confidence interval (CI): 199-241), indicating an acceptable iodine status at the population level. Only 11.4% (95% CI: 8.6-14.9) of the children had UIC <100 µg/L, but with large regional disparities (4.3% to 25.5%, p < 0.01); however, more than a quarter of the subjects were at risk of adverse health consequences due to iodine excess. Children from households of low socio-economic levels were more prone to inadequate UIC. The national median iodine concentration of household salt was 22 mg/kg (95% CI: 21-23). Only half of the households used adequately iodized salt (15-25 ppm), with large regional disparities. National ID rates are now well below the target criteria of WHO (World Health Organization) certification (<20% of children with UIC <50 µg/L and <50% with UIC <100 µg/L). The coverage of adequately iodized salt fell short in meeting the goals of USI (Universal Salt Iodization), i.e., >90% of households. Regular monitoring of iodized salt production lines must be strengthened with involvement by producers.

Charliecloud: Unprivileged containers for user-defined software stacks in HPC

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

Priedhorsky, Reid; Randles, Timothy C.

Supercomputing centers are seeing increasing demand for user-defined software stacks (UDSS), instead of or in addition to the stack provided by the center. These UDSS support user needs such as complex dependencies or build requirements, externally required configurations, portability, and consistency. The challenge for centers is to provide these services in a usable manner while minimizing the risks: security, support burden, missing functionality, and performance. We present Charliecloud, which uses the Linux user and mount namespaces to run industry-standard Docker containers with no privileged operations or daemons on center resources. Our simple approach avoids most security risks while maintaining accessmore » to the performance and functionality already on offer, doing so in less than 500 lines of code. Charliecloud promises to bring an industry-standard UDSS user workflow to existing, minimally altered HPC resources.« less

A Business Case Study of Open Source Software

DTIC Science & Technology

2001-07-01

LinuxPPC LinuxPPC www.linuxppc.com MandrakeSoft Linux -Mandrake www.linux-mandrake.com/ en / CLE Project CLE cle.linux.org.tw/CLE/e_index.shtml Red Hat... en Coyote Linux www2.vortech.net/coyte/coyte.htm MNIS www.mnis.fr Data-Portal www.data-portal.com Mr O’s Linux Emporium www.ouin.com DLX Linux www.wu...1998 1999 Year S h ip m en ts ( in m ill io n s) Source: IDC, 2000. Figure 11. Worldwide New Linux Shipments (Client and Server) 3.2.2 Market

Assessment of Nutritional Status of Iodine Through Urinary Iodine Screening Among Local Children and Adolescents After the Fukushima Daiichi Nuclear Power Plant Accident.

PubMed

Tsubokura, Masaharu; Nomura, Shuhei; Watanobe, Hajime; Nishikawa, Yoshitaka; Suzuki, Chiaki; Ochi, Sae; Leppold, Claire; Kinoshita, Hirokatsu; Kato, Shigeaki; Saito, Yasutoshi

2016-12-01

Iodine deficiency is an important modifier of the risk of thyroid cancer following irradiation. However, little information is available on the prevalence of iodine deficiency in Fukushima and its surroundings after the Fukushima Daiichi nuclear power plant accident that occurred in March 2011. In order to assess urinary iodine concentrations (UIC) and the prevalence of iodine deficiency and to elucidate any associations between demographic characteristics and UIC levels among children and adolescents aged ≤18 years at the time of the accident in Fukushima Prefecture and its surroundings, the data on voluntary UIC testing conducted by Hirata Central Hospital, Fukushima, were evaluated. A total of 4410 children and adolescents with a median age of 10 years at examination underwent UIC testing between October 2012 and October 2015. Calculated for all the participants, the median UIC level was 204 μg/L (range 25-21,100 μg/L). There were 133 (3.0%), 732 (16.6%), and 1472 (33.4%) participants with UIC levels of <50, <100, or ≥300 μg/L, respectively. Based on the World Health Organization criteria for nutritional iodine status, no participants were severely iodine deficient (<20 μg/L), but 16.6% of the population were mildly (50-100 μg/L) or moderately (20-50 μg/L) iodine deficient. While no significant difference in UIC was noted between those who did and did not increase dietary iodine intake after the accident (p = 0.93), there were significant differences by year (p < 0.01), school level (p < 0.001), and residential area at the time of the accident (p < 0.001). This study demonstrates that the children and adolescents examined had a sufficient amount of iodine during the period 1.5-4.5 years after the nuclear accident. In addition to the differences in the scale and the countermeasures undertaken between the Fukushima and Chernobyl accidents, differences in dietary iodine intake might have played an additional role in resulting in the reportedly different radiation doses to the thyroid between the two nuclear accidents.

Maternal urinary iodine concentration up to 1.0 mg/L is positively associated with birth weight, length, and head circumference of male offspring.

PubMed

Rydbeck, Filip; Rahman, Anisur; Grandér, Margaretha; Ekström, Eva-Charlotte; Vahter, Marie; Kippler, Maria

2014-09-01

Adequate iodine status in early life is crucial for neurodevelopment. However, little is known about the effects of maternal iodine status during pregnancy on fetal growth. The present study investigated the potential impact of maternal iodine status during pregnancy on offspring birth size. This large prospective cohort study was nested in a Bangladeshi population-based randomized supplementation trial in pregnant women [MINIMat (Maternal and Infant Nutrition Interventions in Matlab)]. Urine samples obtained at 8 wk of gestation from 1617 women were analyzed for iodine and other elements, such as arsenic and cadmium, using inductively coupled plasma mass spectrometry. Anthropometric measurements at birth included weight, length, and head and chest circumference. Maternal urinary iodine concentrations (UICs) ranged from 0.020 to 10 mg/L, with a median of 0.30 mg/L. Below ∼1.0 mg/L, UIC was significantly positively associated with birth weight and length. Birth weight and length increased by 9.3 g (95% CI: 2.9, 16) and 0.042 cm (95% CI: 0.0066, 0.076), respectively, for each 0.1-mg/L increase in maternal UIC. No associations were observed between UIC and head or chest circumference. When we stratified the analyses by newborn sex, the positive associations between maternal UIC (<1 mg/L) and measurements of size at birth were restricted to boys, with no evidence in girls. Among boys, the mean weight, length, and head circumference increased by 70 g (P = 0.019), 0.41 cm (P = 0.013), and 0.28 cm (P = 0.031) for every 0.5-mg/L increase in maternal UIC. Maternal iodine status was positively associated with weight, length, and head circumference in boys up to ∼1 mg/L, which is well above the recommended maximum concentration of 0.5 mg/L. The associations leveled off at UIC ≥ 1 mg/L. Our findings support previous conclusions that the advantages of correcting potential iodine deficiency outweigh the risks of excess exposure. © 2014 American Society for Nutrition.

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community.

PubMed

Krampis, Konstantinos; Booth, Tim; Chapman, Brad; Tiwari, Bela; Bicak, Mesude; Field, Dawn; Nelson, Karen E

2012-03-19

A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottleneck for smaller laboratories and institutes that do not have access to substantial computational resources. Sequencing instruments are typically bundled with only the minimal processing and storage capacity required for data capture during sequencing runs. Given the scale of sequence datasets, scientific value cannot be obtained from acquiring a sequencer unless it is accompanied by an equal investment in informatics infrastructure. Cloud BioLinux is a publicly accessible Virtual Machine (VM) that enables scientists to quickly provision on-demand infrastructures for high-performance bioinformatics computing using cloud platforms. Users have instant access to a range of pre-configured command line and graphical software applications, including a full-featured desktop interface, documentation and over 135 bioinformatics packages for applications including sequence alignment, clustering, assembly, display, editing, and phylogeny. Each tool's functionality is fully described in the documentation directly accessible from the graphical interface of the VM. Besides the Amazon EC2 cloud, we have started instances of Cloud BioLinux on a private Eucalyptus cloud installed at the J. Craig Venter Institute, and demonstrated access to the bioinformatic tools interface through a remote connection to EC2 instances from a local desktop computer. Documentation for using Cloud BioLinux on EC2 is available from our project website, while a Eucalyptus cloud image and VirtualBox Appliance is also publicly available for download and use by researchers with access to private clouds. Cloud BioLinux provides a platform for developing bioinformatics infrastructures on the cloud. An automated and configurable process builds Virtual Machines, allowing the development of highly customized versions from a shared code base. This shared community toolkit enables application specific analysis platforms on the cloud by minimizing the effort required to prepare and maintain them.

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community

PubMed Central

2012-01-01

Background A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottleneck for smaller laboratories and institutes that do not have access to substantial computational resources. Sequencing instruments are typically bundled with only the minimal processing and storage capacity required for data capture during sequencing runs. Given the scale of sequence datasets, scientific value cannot be obtained from acquiring a sequencer unless it is accompanied by an equal investment in informatics infrastructure. Results Cloud BioLinux is a publicly accessible Virtual Machine (VM) that enables scientists to quickly provision on-demand infrastructures for high-performance bioinformatics computing using cloud platforms. Users have instant access to a range of pre-configured command line and graphical software applications, including a full-featured desktop interface, documentation and over 135 bioinformatics packages for applications including sequence alignment, clustering, assembly, display, editing, and phylogeny. Each tool's functionality is fully described in the documentation directly accessible from the graphical interface of the VM. Besides the Amazon EC2 cloud, we have started instances of Cloud BioLinux on a private Eucalyptus cloud installed at the J. Craig Venter Institute, and demonstrated access to the bioinformatic tools interface through a remote connection to EC2 instances from a local desktop computer. Documentation for using Cloud BioLinux on EC2 is available from our project website, while a Eucalyptus cloud image and VirtualBox Appliance is also publicly available for download and use by researchers with access to private clouds. Conclusions Cloud BioLinux provides a platform for developing bioinformatics infrastructures on the cloud. An automated and configurable process builds Virtual Machines, allowing the development of highly customized versions from a shared code base. This shared community toolkit enables application specific analysis platforms on the cloud by minimizing the effort required to prepare and maintain them. PMID:22429538

Comparison of population iodine estimates from 24-hour urine and timed-spot urine samples.

PubMed

Perrine, Cria G; Cogswell, Mary E; Swanson, Christine A; Sullivan, Kevin M; Chen, Te-Ching; Carriquiry, Alicia L; Dodd, Kevin W; Caldwell, Kathleen L; Wang, Chia-Yih

2014-04-01

Median urine iodine concentration (UIC; μg/L) in spot urine samples is recommended for monitoring population iodine status. Other common measures are iodine:creatinine ratio (I/Cr; μg/g) and estimated 24-hour urine iodine excretion (UIE; I/Cr × predicted 24-hour Cr; μg/day). Despite different units, these measures are often used interchangeably, and it is unclear how they compare with the reference standard 24-hour UIE. Volunteers aged 18-39 years collected all their urine samples for 24 hours (n=400). Voids from morning, afternoon, evening, overnight, and a composite 24-hour sample were analyzed for iodine. We calculated median observed 24-hour UIE and 24-hour UIC, and spot UIC, I/Cr, and two measures of estimated UIE calculated using predicted 24-hour Cr from published estimates by Kesteloot and Joosens (varies by age and sex) and published equations by Mage et al. (varies by age, sex, race, and anthropometric measures). We examined mean differences and relative difference across iodine excretion levels using Bland-Altman plots. Median 24-hour UIE was 173.6 μg/day and 24-hour UIC was 144.8 μg/L. From timed-spot urine samples, estimates were: UIC 147.3-156.2 μg/L; I/Cr 103.6-114.3 μg/g, estimated 24-hour UIE (Kesteloot and Joosens) 145.7-163.3 μg/day; and estimated 24-hour UIE (Mage) 176.5-187.7 μg/day. Iodine measures did not vary consistently by timing of spot urine collection. Compared with observed 24-hour UIE, on average, estimated (Mage) 24-hour UIE was not significantly different, while estimated 24-hour UIE (Kesteloot and Joosens) was significantly different for some ethnicity/sex groups. Compared with 24-hour UIC, on average, spot UIC did not differ. Estimates of UIC, I/Cr, and estimated 24-hour UIE (I/Cr × predicted 24-hour Cr) from spot urine samples should not be used interchangeably. Estimated 24-hour UIE, where predicted 24-hour Cr varies by age, sex, ethnicity, and anthropometric measures and was calculated with prediction equations using data from the sample, was more comparable to observed 24-hour UIE than when predicted 24-hour Cr was from published estimates from a different population. However, currently no cutoffs exist to interpret population estimated 24-hour UIE values.

40 CFR 147.1651 - EPA-administered program.

Code of Federal Regulations, 2010 CFR

2010-07-01

... (CONTINUED) STATE, TRIBAL, AND EPA-ADMINISTERED UNDERGROUND INJECTION CONTROL PROGRAMS New York § 147.1651 EPA-administered program. (a) Contents. The UIC program for the State of New York, including all... effective date of the UIC program for New York for all injection activities except those on lands of the...

78 FR 14951 - State of Washington; Underground Injection Control (UIC) Program Revision

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-08

... of Ecology to the Energy Facility Site Evaluation Council to issue UIC permits at energy facilities... telephone number for the Library is (206) 553-1289. (2) Washington Department of Ecology, Water Quality... the Environmental Protection Agency, and MOUs between the Department of Ecology and the Department of...

Wiretapping the Internet

NASA Astrophysics Data System (ADS)

Antonelli, Charles J.; Honeyman, Peter

2001-02-01

This paper describes the Advanced Packet Vault, a technology for creating such a record by collecting and securely storing all packets observed on a network, with a scalable architecture intended to support network speeds in excess of 100 Mbps. Encryption is used to preserve users' security and privacy, permitting selected traffic to be made available without revealing other traffic. The Vault implementation, based on Linux and OpenBSD, is open-source.

Improved Distance Learning Environment For Marine Forces Reserve

DTIC Science & Technology

2016-09-01

keyboard, to 20 form a desktop computer . Laptop computers share similar components but add mobility to the user. If additional desktop computers ...for stationary computing devices such as desktop PCs and laptops include the Microsoft Windows, Mac OS, and Linux families of OSs 44 (Hopkins...opportunities to all Marines. For active duty Marines, government-provided desktops and laptops (GPDLs) typically support DL T&E or learning resource

Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files.

PubMed

Finney, Richard P; Chen, Qing-Rong; Nguyen, Cu V; Hsu, Chih Hao; Yan, Chunhua; Hu, Ying; Abawi, Massih; Bian, Xiaopeng; Meerzaman, Daoud M

2015-01-01

The name Alview is a contraction of the term Alignment Viewer. Alview is a compiled to native architecture software tool for visualizing the alignment of sequencing data. Inputs are files of short-read sequences aligned to a reference genome in the SAM/BAM format and files containing reference genome data. Outputs are visualizations of these aligned short reads. Alview is written in portable C with optional graphical user interface (GUI) code written in C, C++, and Objective-C. The application can run in three different ways: as a web server, as a command line tool, or as a native, GUI program. Alview is compatible with Microsoft Windows, Linux, and Apple OS X. It is available as a web demo at https://cgwb.nci.nih.gov/cgi-bin/alview. The source code and Windows/Mac/Linux executables are available via https://github.com/NCIP/alview.

University-Industry Cooperation and the Transition to Innovation Ecosystems in Japan

ERIC Educational Resources Information Center

Ranga, Marina; Mroczkowski, Tomasz; Araiso, Tsunehisa

2017-01-01

This article looks at the evolution of university-industry collaboration (UIC) policies in Japan since the mid-1990s to the present and analyses their role in shaping the country's innovation ecosystem. UIC policies are examined within a multidimensional innovation policy framework that encompasses five Science and Technology Basic Plans and a…

40 CFR 147.1252 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false EPA-administered program-Indian lands... § 147.1252 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Mississippi is administered by EPA. This program consists of the UIC...

40 CFR 147.1252 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 24 2013-07-01 2013-07-01 false EPA-administered program-Indian lands... § 147.1252 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Mississippi is administered by EPA. This program consists of the UIC...

40 CFR 147.60 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false EPA-administered program-Indian lands... § 147.60 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in Alabama is administered by EPA. This program consists of the UIC program...

40 CFR 147.60 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 24 2013-07-01 2013-07-01 false EPA-administered program-Indian lands... § 147.60 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in Alabama is administered by EPA. This program consists of the UIC program...

40 CFR 147.651 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false EPA-administered program-Indian lands....651 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Idaho is administered by EPA. This program consists of the UIC program...

40 CFR 147.60 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false EPA-administered program-Indian lands... § 147.60 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in Alabama is administered by EPA. This program consists of the UIC program...

40 CFR 147.353 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false EPA-administered program-Indian lands... § 147.353 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in Connecticut is administered by EPA. This program consists of the UIC program...

40 CFR 147.1001 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false EPA-administered program-Indian lands....1001 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Maine is administered by EPA. This program consists of the UIC program...

40 CFR 147.553 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 24 2013-07-01 2013-07-01 false EPA-administered program-Indian lands... § 147.553 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Georgia is administered by EPA. This program consists of the UIC...

40 CFR 147.2303 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 24 2013-07-01 2013-07-01 false EPA-administered program-Indian lands... § 147.2303 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Vermont is administered by EPA. This program consists of the UIC...

40 CFR 147.553 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 24 2012-07-01 2012-07-01 false EPA-administered program-Indian lands... § 147.553 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Georgia is administered by EPA. This program consists of the UIC...

40 CFR 147.2553 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false EPA-administered program-Indian lands... § 147.2553 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Wyoming is administered by EPA. This program consists of the UIC...

40 CFR 147.1551 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false EPA-administered program-Indian lands... § 147.1551 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of New Jersey is administered by EPA. This program consists of the UIC...

40 CFR 147.1403 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false EPA-administered program-Indian lands... § 147.1403 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Nebraska is administered by EPA. This program consists of the UIC...

40 CFR 147.353 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false EPA-administered program-Indian lands... § 147.353 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in Connecticut is administered by EPA. This program consists of the UIC program...

40 CFR 147.1551 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 24 2013-07-01 2013-07-01 false EPA-administered program-Indian lands... § 147.1551 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of New Jersey is administered by EPA. This program consists of the UIC...

40 CFR 147.1451 - EPA administered program-Indian lands.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false EPA administered program-Indian lands... § 147.1451 EPA administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Nevada is administered by EPA. This program consists of the UIC...

40 CFR 147.2553 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 24 2013-07-01 2013-07-01 false EPA-administered program-Indian lands... § 147.2553 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Wyoming is administered by EPA. This program consists of the UIC...

40 CFR 147.951 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 24 2013-07-01 2013-07-01 false EPA-administered program-Indian lands... § 147.951 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Louisiana is administered by EPA. This program consists of the UIC...

40 CFR 147.1901 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 24 2013-07-01 2013-07-01 false EPA-administered program-Indian lands... § 147.1901 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Oregon is administered by EPA. This program consists of the UIC...

40 CFR 147.1901 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false EPA-administered program-Indian lands... § 147.1901 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Oregon is administered by EPA. This program consists of the UIC...

40 CFR 147.2601 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 24 2013-07-01 2013-07-01 false EPA-administered program-Indian lands....2601 EPA-administered program—Indian lands. (a) Contents. The UIC program for Indian lands in the... effective date for the UIC program on Indian lands in the territory of Guam is November 25, 1988. [53 FR...

40 CFR 147.205 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 24 2013-07-01 2013-07-01 false EPA-administered program-Indian lands... § 147.205 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in Arkansas is administered by EPA. This program consists of the UIC program...

40 CFR 147.1252 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 24 2012-07-01 2012-07-01 false EPA-administered program-Indian lands... § 147.1252 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Mississippi is administered by EPA. This program consists of the UIC...

40 CFR 147.205 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false EPA-administered program-Indian lands... § 147.205 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in Arkansas is administered by EPA. This program consists of the UIC program...

40 CFR 147.1403 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false EPA-administered program-Indian lands... § 147.1403 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Nebraska is administered by EPA. This program consists of the UIC...

40 CFR 147.2205 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false EPA-administered program-Indian lands....2205 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Texas is administered by EPA. This program consists of the UIC program...

40 CFR 147.951 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false EPA-administered program-Indian lands... § 147.951 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Louisiana is administered by EPA. This program consists of the UIC...

40 CFR 147.1403 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false EPA-administered program-Indian lands... § 147.1403 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Nebraska is administered by EPA. This program consists of the UIC...

40 CFR 147.1901 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false EPA-administered program-Indian lands... § 147.1901 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Oregon is administered by EPA. This program consists of the UIC...

40 CFR 147.403 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false EPA-administered program-Indian lands... § 147.403 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in Delaware is administered by EPA. This program consists of the UIC program...

40 CFR 147.353 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false EPA-administered program-Indian lands... § 147.353 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in Connecticut is administered by EPA. This program consists of the UIC program...

40 CFR 147.703 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 24 2012-07-01 2012-07-01 false EPA-administered program-Indian lands... § 147.703 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Illinois is administered by EPA. This program consists of the UIC...

40 CFR 147.703 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false EPA-administered program-Indian lands... § 147.703 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Illinois is administered by EPA. This program consists of the UIC...

40 CFR 147.1805 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 24 2012-07-01 2012-07-01 false EPA-administered program-Indian lands....1805 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Ohio is administered by EPA. This program consists of the UIC program...

40 CFR 147.1403 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 24 2012-07-01 2012-07-01 false EPA-administered program-Indian lands... § 147.1403 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Nebraska is administered by EPA. This program consists of the UIC...

40 CFR 147.1303 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false EPA-administered program-Indian lands... § 147.1303 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Missouri is administered by EPA. This program consists of the UIC...

40 CFR 147.353 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 24 2013-07-01 2013-07-01 false EPA-administered program-Indian lands... § 147.353 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in Connecticut is administered by EPA. This program consists of the UIC program...

40 CFR 147.1001 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 24 2012-07-01 2012-07-01 false EPA-administered program-Indian lands....1001 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Maine is administered by EPA. This program consists of the UIC program...

40 CFR 147.353 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 24 2012-07-01 2012-07-01 false EPA-administered program-Indian lands... § 147.353 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in Connecticut is administered by EPA. This program consists of the UIC program...

40 CFR 147.2205 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 24 2013-07-01 2013-07-01 false EPA-administered program-Indian lands....2205 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Texas is administered by EPA. This program consists of the UIC program...

40 CFR 147.1451 - EPA administered program-Indian lands.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 24 2012-07-01 2012-07-01 false EPA administered program-Indian lands... § 147.1451 EPA administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Nevada is administered by EPA. This program consists of the UIC...

40 CFR 147.2205 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 24 2012-07-01 2012-07-01 false EPA-administered program-Indian lands....2205 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Texas is administered by EPA. This program consists of the UIC program...

40 CFR 147.2303 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 24 2012-07-01 2012-07-01 false EPA-administered program-Indian lands... § 147.2303 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Vermont is administered by EPA. This program consists of the UIC...

40 CFR 147.1001 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 24 2013-07-01 2013-07-01 false EPA-administered program-Indian lands....1001 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Maine is administered by EPA. This program consists of the UIC program...

40 CFR 147.1252 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false EPA-administered program-Indian lands... § 147.1252 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Mississippi is administered by EPA. This program consists of the UIC...

40 CFR 147.2205 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false EPA-administered program-Indian lands....2205 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Texas is administered by EPA. This program consists of the UIC program...

40 CFR 147.403 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 24 2013-07-01 2013-07-01 false EPA-administered program-Indian lands... § 147.403 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in Delaware is administered by EPA. This program consists of the UIC program...

40 CFR 147.205 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false EPA-administered program-Indian lands... § 147.205 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in Arkansas is administered by EPA. This program consists of the UIC program...

40 CFR 147.2553 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false EPA-administered program-Indian lands... § 147.2553 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Wyoming is administered by EPA. This program consists of the UIC...

40 CFR 147.1805 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 24 2013-07-01 2013-07-01 false EPA-administered program-Indian lands....1805 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Ohio is administered by EPA. This program consists of the UIC program...

40 CFR 147.2553 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 24 2012-07-01 2012-07-01 false EPA-administered program-Indian lands... § 147.2553 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Wyoming is administered by EPA. This program consists of the UIC...

40 CFR 147.403 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false EPA-administered program-Indian lands... § 147.403 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in Delaware is administered by EPA. This program consists of the UIC program...

40 CFR 147.1303 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false EPA-administered program-Indian lands... § 147.1303 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Missouri is administered by EPA. This program consists of the UIC...

40 CFR 147.860 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false EPA-administered program-Indian lands... § 147.860 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Kansas is administered by EPA. This program consists of the UIC...

40 CFR 147.205 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 24 2012-07-01 2012-07-01 false EPA-administered program-Indian lands... § 147.205 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in Arkansas is administered by EPA. This program consists of the UIC program...

40 CFR 147.2303 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false EPA-administered program-Indian lands... § 147.2303 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Vermont is administered by EPA. This program consists of the UIC...

40 CFR 147.553 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false EPA-administered program-Indian lands... § 147.553 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Georgia is administered by EPA. This program consists of the UIC...

40 CFR 147.651 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 24 2013-07-01 2013-07-01 false EPA-administered program-Indian lands....651 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Idaho is administered by EPA. This program consists of the UIC program...

40 CFR 147.1303 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 24 2013-07-01 2013-07-01 false EPA-administered program-Indian lands... § 147.1303 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Missouri is administered by EPA. This program consists of the UIC...

40 CFR 147.2303 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false EPA-administered program-Indian lands... § 147.2303 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Vermont is administered by EPA. This program consists of the UIC...

40 CFR 147.1053 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false EPA-administered program-Indian lands... § 147.1053 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Maryland is administered by EPA. This program consists of the UIC...

40 CFR 147.1451 - EPA administered program-Indian lands.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false EPA administered program-Indian lands... § 147.1451 EPA administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Nevada is administered by EPA. This program consists of the UIC...

40 CFR 147.2205 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false EPA-administered program-Indian lands....2205 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Texas is administered by EPA. This program consists of the UIC program...

40 CFR 147.1551 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false EPA-administered program-Indian lands... § 147.1551 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of New Jersey is administered by EPA. This program consists of the UIC...

40 CFR 147.951 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 24 2012-07-01 2012-07-01 false EPA-administered program-Indian lands... § 147.951 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Louisiana is administered by EPA. This program consists of the UIC...

40 CFR 147.1805 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false EPA-administered program-Indian lands....1805 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Ohio is administered by EPA. This program consists of the UIC program...

40 CFR 147.1252 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false EPA-administered program-Indian lands... § 147.1252 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Mississippi is administered by EPA. This program consists of the UIC...

40 CFR 147.403 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 24 2012-07-01 2012-07-01 false EPA-administered program-Indian lands... § 147.403 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in Delaware is administered by EPA. This program consists of the UIC program...

40 CFR 147.1901 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false EPA-administered program-Indian lands... § 147.1901 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Oregon is administered by EPA. This program consists of the UIC...

40 CFR 147.1303 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 24 2012-07-01 2012-07-01 false EPA-administered program-Indian lands... § 147.1303 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Missouri is administered by EPA. This program consists of the UIC...

40 CFR 147.651 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false EPA-administered program-Indian lands....651 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Idaho is administered by EPA. This program consists of the UIC program...

40 CFR 147.2601 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false EPA-administered program-Indian lands....2601 EPA-administered program—Indian lands. (a) Contents. The UIC program for Indian lands in the... effective date for the UIC program on Indian lands in the territory of Guam is November 25, 1988. [53 FR...

40 CFR 147.1805 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false EPA-administered program-Indian lands....1805 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Ohio is administered by EPA. This program consists of the UIC program...

40 CFR 147.1001 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false EPA-administered program-Indian lands....1001 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Maine is administered by EPA. This program consists of the UIC program...

40 CFR 147.1403 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 24 2013-07-01 2013-07-01 false EPA-administered program-Indian lands... § 147.1403 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Nebraska is administered by EPA. This program consists of the UIC...

40 CFR 147.1451 - EPA administered program-Indian lands.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false EPA administered program-Indian lands... § 147.1451 EPA administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Nevada is administered by EPA. This program consists of the UIC...

40 CFR 147.2601 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false EPA-administered program-Indian lands....2601 EPA-administered program—Indian lands. (a) Contents. The UIC program for Indian lands in the... effective date for the UIC program on Indian lands in the territory of Guam is November 25, 1988. [53 FR...

40 CFR 147.1053 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false EPA-administered program-Indian lands... § 147.1053 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Maryland is administered by EPA. This program consists of the UIC...

40 CFR 147.553 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false EPA-administered program-Indian lands... § 147.553 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Georgia is administered by EPA. This program consists of the UIC...

40 CFR 147.860 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 24 2013-07-01 2013-07-01 false EPA-administered program-Indian lands... § 147.860 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Kansas is administered by EPA. This program consists of the UIC...

40 CFR 147.651 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 24 2012-07-01 2012-07-01 false EPA-administered program-Indian lands....651 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Idaho is administered by EPA. This program consists of the UIC program...

40 CFR 147.403 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false EPA-administered program-Indian lands... § 147.403 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in Delaware is administered by EPA. This program consists of the UIC program...

40 CFR 147.1053 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 24 2012-07-01 2012-07-01 false EPA-administered program-Indian lands... § 147.1053 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Maryland is administered by EPA. This program consists of the UIC...

40 CFR 147.860 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false EPA-administered program-Indian lands... § 147.860 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Kansas is administered by EPA. This program consists of the UIC...

40 CFR 147.60 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false EPA-administered program-Indian lands... § 147.60 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in Alabama is administered by EPA. This program consists of the UIC program...

40 CFR 147.205 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false EPA-administered program-Indian lands... § 147.205 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in Arkansas is administered by EPA. This program consists of the UIC program...

40 CFR 147.703 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 24 2013-07-01 2013-07-01 false EPA-administered program-Indian lands... § 147.703 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Illinois is administered by EPA. This program consists of the UIC...

40 CFR 147.703 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false EPA-administered program-Indian lands... § 147.703 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Illinois is administered by EPA. This program consists of the UIC...

40 CFR 147.1053 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 24 2013-07-01 2013-07-01 false EPA-administered program-Indian lands... § 147.1053 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Maryland is administered by EPA. This program consists of the UIC...

40 CFR 147.2601 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false EPA-administered program-Indian lands....2601 EPA-administered program—Indian lands. (a) Contents. The UIC program for Indian lands in the... effective date for the UIC program on Indian lands in the territory of Guam is November 25, 1988. [53 FR...

40 CFR 147.1551 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 24 2012-07-01 2012-07-01 false EPA-administered program-Indian lands... § 147.1551 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of New Jersey is administered by EPA. This program consists of the UIC...

40 CFR 147.1901 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 24 2012-07-01 2012-07-01 false EPA-administered program-Indian lands... § 147.1901 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Oregon is administered by EPA. This program consists of the UIC...

40 CFR 147.2601 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 24 2012-07-01 2012-07-01 false EPA-administered program-Indian lands....2601 EPA-administered program—Indian lands. (a) Contents. The UIC program for Indian lands in the... effective date for the UIC program on Indian lands in the territory of Guam is November 25, 1988. [53 FR...

40 CFR 147.951 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false EPA-administered program-Indian lands... § 147.951 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Louisiana is administered by EPA. This program consists of the UIC...

40 CFR 147.2553 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false EPA-administered program-Indian lands... § 147.2553 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Wyoming is administered by EPA. This program consists of the UIC...

40 CFR 147.860 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false EPA-administered program-Indian lands... § 147.860 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Kansas is administered by EPA. This program consists of the UIC...

40 CFR 147.951 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false EPA-administered program-Indian lands... § 147.951 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Louisiana is administered by EPA. This program consists of the UIC...

40 CFR 147.1303 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false EPA-administered program-Indian lands... § 147.1303 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Missouri is administered by EPA. This program consists of the UIC...

40 CFR 147.553 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false EPA-administered program-Indian lands... § 147.553 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Georgia is administered by EPA. This program consists of the UIC...

40 CFR 147.1805 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false EPA-administered program-Indian lands....1805 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Ohio is administered by EPA. This program consists of the UIC program...

40 CFR 147.1053 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false EPA-administered program-Indian lands... § 147.1053 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Maryland is administered by EPA. This program consists of the UIC...

40 CFR 147.2303 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false EPA-administered program-Indian lands... § 147.2303 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Vermont is administered by EPA. This program consists of the UIC...

40 CFR 147.1551 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false EPA-administered program-Indian lands... § 147.1551 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of New Jersey is administered by EPA. This program consists of the UIC...

40 CFR 147.860 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 24 2012-07-01 2012-07-01 false EPA-administered program-Indian lands... § 147.860 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Kansas is administered by EPA. This program consists of the UIC...

40 CFR 147.651 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false EPA-administered program-Indian lands....651 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Idaho is administered by EPA. This program consists of the UIC program...

40 CFR 147.1451 - EPA administered program-Indian lands.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 24 2013-07-01 2013-07-01 false EPA administered program-Indian lands... § 147.1451 EPA administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Nevada is administered by EPA. This program consists of the UIC...

40 CFR 147.60 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 24 2012-07-01 2012-07-01 false EPA-administered program-Indian lands... § 147.60 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in Alabama is administered by EPA. This program consists of the UIC program...

40 CFR 147.703 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false EPA-administered program-Indian lands... § 147.703 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Illinois is administered by EPA. This program consists of the UIC...

40 CFR 147.1001 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false EPA-administered program-Indian lands....1001 EPA-administered program—Indian lands. (a) Contents. The UIC program for all classes of wells on Indian lands in the State of Maine is administered by EPA. This program consists of the UIC program...

40 CFR 124.3 - Application for a permit.

Code of Federal Regulations, 2011 CFR

2011-07-01

... person who requires a permit under the RCRA, UIC, NPDES, or PSD programs shall complete, sign, and submit....21 (PSD), and 122.1 (NPDES). Applications are not required for RCRA permits by rule (§ 270.60...), 144.31 (UIC), 40 CFR 52.21 (PSD), and 122.21 (NPDES). (3) Permit applications (except for PSD permits...

40 CFR 124.3 - Application for a permit.

Code of Federal Regulations, 2012 CFR

2012-07-01

... person who requires a permit under the RCRA, UIC, NPDES, or PSD programs shall complete, sign, and submit....21 (PSD), and 122.1 (NPDES). Applications are not required for RCRA permits by rule (§ 270.60...), 144.31 (UIC), 40 CFR 52.21 (PSD), and 122.21 (NPDES). (3) Permit applications (except for PSD permits...

40 CFR 124.3 - Application for a permit.

Code of Federal Regulations, 2013 CFR

2013-07-01

... person who requires a permit under the RCRA, UIC, NPDES, or PSD programs shall complete, sign, and submit....21 (PSD), and 122.1 (NPDES). Applications are not required for RCRA permits by rule (§ 270.60...), 144.31 (UIC), 40 CFR 52.21 (PSD), and 122.21 (NPDES). (3) Permit applications (except for PSD permits...

40 CFR 124.3 - Application for a permit.

Code of Federal Regulations, 2010 CFR

2010-07-01

... person who requires a permit under the RCRA, UIC, NPDES, or PSD programs shall complete, sign, and submit....21 (PSD), and 122.1 (NPDES). Applications are not required for RCRA permits by rule (§ 270.60...), 144.31 (UIC), 40 CFR 52.21 (PSD), and 122.21 (NPDES). (3) Permit applications (except for PSD permits...

77 FR 40354 - Permitting Guidance for Oil and Gas Hydraulic Fracturing Activities Using Diesel Fuels-Draft

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-09

... INFORMATION CONTACT: Sherri Comerford, Underground Injection Control (UIC) Program, Drinking Water Protection Division, Office of Ground Water and Drinking Water (MC-4606M), Environmental Protection Agency, 1200... Fracturing and the Safe Drinking Water Act Web site, http://water.epa.gov/type/groundwater/uic/class2...

40 CFR 147.101 - EPA-administered program.

Code of Federal Regulations, 2010 CFR

2010-07-01

... (CONTINUED) STATE, TRIBAL, AND EPA-ADMINISTERED UNDERGROUND INJECTION CONTROL PROGRAMS Alaska § 147.101 EPA-administered program. (a) Contents. The UIC program in the State of Alaska for Class I, III, IV, and V wells, and for all classes of wells on Indian lands, is administered by EPA. This program consists of the UIC...

The iodized salt programme in Bangalore, India provides adequate iodine intakes in pregnant women and more-than-adequate iodine intakes in their children.

PubMed

Jaiswal, Nidhi; Melse-Boonstra, Alida; Sharma, Surjeet Kaur; Srinivasan, Krishnamachari; Zimmermann, Michael B

2015-02-01

To compare the iodine status of pregnant women and their children who were sharing all meals in Bangalore, India. A cross-sectional study evaluating demographic characteristics, household salt iodine concentration and salt usage patterns, urinary iodine concentrations (UIC) in women and children, and maternal thyroid volume (ultrasound). Antenatal clinic of an urban tertiary-care hospital, which serves a low-income population. Healthy pregnant women in all trimesters, aged 18-35 years, who had healthy children aged 3-15 years. Median (range) iodine concentrations of household powdered and crystal salt were 55·9 (17·2-65·9) ppm and 18·9 (2·2-68·2) ppm, respectively. The contribution of iodine-containing supplements and multi-micronutrient powders to iodine intake in the families was negligible. Adequately iodized salt, together with small amounts of iodine in local foods, were providing adequate iodine during pregnancy: (i) the overall median (range) UIC in women was 172 (5-1024) µg/l; (ii) the median UIC was >150 µg/l in all trimesters; and (iii) thyroid size was not significantly different across trimesters. At the same time, the median (range) UIC in children was 220 (10-782) µg/l, indicating more-than-adequate iodine intake at this age. Median UIC was significantly higher in children than in their mothers (P=0·008). In this selected urban population of southern India, the iodized salt programme provides adequate iodine to women throughout pregnancy, at the expense of higher iodine intake in their children. Thus we suggest that the current cut-off for median UIC in children indicating more-than-adequate intake, recommended by the WHO/UNICEF/International Council for the Control of Iodine Deficiency Disorders may, need to be reconsidered.

Low Urinary Iodine Concentrations Associated with Dyslipidemia in US Adults.

PubMed

Lee, Kyung Won; Shin, Dayeon; Song, Won O

2016-03-17

Iodine is an essential component of the thyroid hormone which plays crucial roles in healthy thyroid function and lipid metabolism. However, the association between iodine status and dyslipidemia has not been well established at a population level. We aimed to test the hypothesis that the odds of dyslipidemia including elevated total cholesterol, triglycerides, low-density lipoprotein (LDL) cholesterol and apolipoprotein B, and lowered high-density lipoprotein (HDL) cholesterol and HDL/LDL ratio are associated with urinary iodine concentration (UIC) in a population perspective. Data of 2495 US adults (≥20 years) in the National Health and Nutrition Examination Survey 2007-2012 were used in this study. Two subgroups (i.e., UIC below vs. above the 10th percentile) were compared of dyslipidemia as defined based on NCEP ATP III guidelines. The differences between the groups were tested statistically by chi-square test, simple linear regressions, and multiple logistic regressions. Serum lipid concentrations differed significantly between two iodine status groups when sociodemographic and lifestyle covariates were controlled (all, p < 0.05). Those with the lowest decile of UIC were more likely to be at risk for elevated total cholesterol (>200 mg/dL) (adjusted odds ratio (AOR) = 1.51, 95% confidence interval (CI): 1.03-2.23) and elevated LDL cholesterol (>130 mg/dL) (AOR = 1.58, 95% CI: 1.11-2.23) and lowered HDL/LDL ratio (<0.4) (AOR = 1.66, 95% CI: 1.18-2.33), compared to those with UIC above the 10th percentile. In US adults, low UIC was associated with increased odds for dyslipidemia. Findings of the present cross-sectional study with spot urine samples highlight the significant association between UIC and serum lipids at population level, but do not substantiate a causal relationship. Further investigations are warranted to elucidate the causal relationship among iodine intakes, iodine status, and serum lipid profiles.

Iodine Status of Vulnerable Populations in Henan Province of China 2013-2014 After the Implementation of the New Iodized Salt Standard.

PubMed

Yang, Jin; Zhu, Lin; Li, Xiaofeng; Zheng, Heming; Wang, Zhe; Liu, Yang; Hao, Zongyu

2016-09-01

The standard of salt iodine content in China has been adjusted several times since implementation of the universal salt iodization (USI) in 1995. The new standard of iodized salt content was adjusted from 35 ± 15 to 30 ± 9 mg/kg in Henan province in 2012. We aimed to determine whether the vulnerable populations were iodine sufficient after the adjustment of salt iodine content and to provide a guideline for the adjustment of USI policy in China. Two cross-sectional surveys of iodine status in vulnerable populations, including reproductive-age, pregnant and lactating women, infants <2 years, and children aged 8-10 years, were conducted in Henan province in 2013 and 2014. In 2013, the median urinary iodine concentration (mUIC) of reproductive-age women was 200.1 μg/L and that of school children aged 8-10 years was 221.0 μg/L. These mUICs were considered as "more than adequate." The mUICs of reproductive-age women and school children in 2014 showed a significant decline compared to the mUICs in 2013 (P = 0.012 and P = 0.001, respectively). The mUICs of the pregnant women were 204.2 μg/L in 2013 and 202.5 μg/L in 2014, which both met the requirement level recommended by WHO. In 2013, the mUIC of lactating women was 169.1 μg/L and that of infants <2 years was 203.2 μg/L, which were significantly lower than that of 2014 (P < 0.001 and P < 0.001, respectively). The lactating women and infants in 2013 and 2014 were both regarded as "iodine adequate." Iodine status of the vulnerable populations is still adequate as a whole in Henan province after decreasing the salt iodine content. However, the mUIC of school children aged 8-10 years is slightly above the adequate level. To reduce the risk of iodine excess in the general population and prevent the possibility of iodine deficiency of the vulnerable population, it is necessary to explore the appropriate level of iodized salt content.

JESPP: Joint Experimentation on Scalable Parallel Processors Supercomputers

DTIC Science & Technology

2010-03-01

were for the relatively small market of scientific and engineering applications. Contrast this with GPUs that are designed to improve the end- user...experience in mass- market arenas such as gaming. In order to get meaningful speed-up using the GPU, it was determined that the data transfer and...Included) Conference Year Effectively using a Large GPGPU-Enhanced Linux Cluster HPCMP UGC 2009 FLOPS per Watt: Heterogeneous-Computing’s Approach

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

Perry, Marcia

The IRCD is an IRC server that was originally distributed by the IRCD Hybrid developer team for use as a server in IRC message over the public Internet. By supporting the IRC protocol defined in the IRC RFC, IRCD allows the users to create and join channels for group or one-to-one text-based instant messaging. It stores information about channels (e.g., whether it is public, secret, or invite-only, the topic set, membership) and users (who is online and what channels they are members of). It receives messages for a specific user or channel and forwards these messages to the targeted destination.more » Since server-to-server communication is also supported, these targeted destinations may be connected to different IRC servers. Messages are exchanged over TCP connections that remain open between the client and the server. The IRCD is being used within the Pervasive Computing Collaboration Environment (PCCE) as the 'chat server' for message exchange over public and private channels. After an LBNLSecureMessaging(PCCE chat) client has been authenticated, the client connects to IRCD with its assigned nickname or 'nick.' The client can then create or join channels for group discussions or one-to-one conversations. These channels can have an initial mode of public or invite-only and the mode may be changed after creation. If a channel is public, any one online can join the discussion; if a channel is invite-only, users can only join if existing members of the channel explicity invite them. Users can be invited to any type of channel and users may be members of multiple channels simultaneously. For use with the PCCE environment, the IRCD application (which was written in C) was ported to Linux and has been tested and installed under Linux Redhat 7.2. The source code was also modified with SSL so that all messages exchanged over the network are encrypted. This modified IRC server also verifies with an authentication server that the client is who he or she claims to be and that this user is authorized to ain access to the IRCD.« less

40 CFR 147.1852 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 24 2012-07-01 2012-07-01 false EPA-administered program-Indian lands... § 147.1852 EPA-administered program—Indian lands. (a) Contents. The UIC program for all wells on Indian... forth in subpart GGG of this part. The UIC program for all other wells on Indian lands consists of the...

40 CFR 147.1852 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false EPA-administered program-Indian lands... § 147.1852 EPA-administered program—Indian lands. (a) Contents. The UIC program for all wells on Indian... forth in subpart GGG of this part. The UIC program for all other wells on Indian lands consists of the...

40 CFR 147.1852 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false EPA-administered program-Indian lands... § 147.1852 EPA-administered program—Indian lands. (a) Contents. The UIC program for all wells on Indian... forth in subpart GGG of this part. The UIC program for all other wells on Indian lands consists of the...

40 CFR 147.1852 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 23 2011-07-01 2011-07-01 false EPA-administered program-Indian lands... § 147.1852 EPA-administered program—Indian lands. (a) Contents. The UIC program for all wells on Indian... forth in subpart GGG of this part. The UIC program for all other wells on Indian lands consists of the...

40 CFR 147.1852 - EPA-administered program-Indian lands.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 24 2013-07-01 2013-07-01 false EPA-administered program-Indian lands... § 147.1852 EPA-administered program—Indian lands. (a) Contents. The UIC program for all wells on Indian... forth in subpart GGG of this part. The UIC program for all other wells on Indian lands consists of the...

40 CFR 124.6 - Draft permits.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 270.32 (RCRA) (except for PSD permits))); (2) All compliance schedules under §§ 122.47 (NPDES), 144.53 (UIC), 233.10 (404), or 270.33 (RCRA) (except for PSD permits); (3) All monitoring requirements under §§ 122.48 (NPDES), 144.54 (UIC), 233.11 (404), or 270.31 (RCRA) (except for PSD permits); and (4) For: (i...

40 CFR 124.6 - Draft permits.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 270.32 (RCRA) (except for PSD permits))); (2) All compliance schedules under §§ 122.47 (NPDES), 144.53 (UIC), 233.10 (404), or 270.33 (RCRA) (except for PSD permits); (3) All monitoring requirements under §§ 122.48 (NPDES), 144.54 (UIC), 233.11 (404), or 270.31 (RCRA) (except for PSD permits); and (4) For: (i...

40 CFR 124.6 - Draft permits.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 270.32 (RCRA) (except for PSD permits))); (2) All compliance schedules under §§ 122.47 (NPDES), 144.53 (UIC), 233.10 (404), or 270.33 (RCRA) (except for PSD permits); (3) All monitoring requirements under §§ 122.48 (NPDES), 144.54 (UIC), 233.11 (404), or 270.31 (RCRA) (except for PSD permits); and (4) For: (i...

40 CFR 124.6 - Draft permits.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 270.32 (RCRA) (except for PSD permits))); (2) All compliance schedules under §§ 122.47 (NPDES), 144.53 (UIC), 233.10 (404), or 270.33 (RCRA) (except for PSD permits); (3) All monitoring requirements under §§ 122.48 (NPDES), 144.54 (UIC), 233.11 (404), or 270.31 (RCRA) (except for PSD permits); and (4) For: (i...

40 CFR 124.6 - Draft permits.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 270.32 (RCRA) (except for PSD permits))); (2) All compliance schedules under §§ 122.47 (NPDES), 144.53 (UIC), 233.10 (404), or 270.33 (RCRA) (except for PSD permits); (3) All monitoring requirements under §§ 122.48 (NPDES), 144.54 (UIC), 233.11 (404), or 270.31 (RCRA) (except for PSD permits); and (4) For: (i...

PyFDAP: automated analysis of fluorescence decay after photoconversion (FDAP) experiments.

PubMed

Bläßle, Alexander; Müller, Patrick

2015-03-15

We developed the graphical user interface PyFDAP for the fitting of linear and non-linear decay functions to data from fluorescence decay after photoconversion (FDAP) experiments. PyFDAP structures and analyses large FDAP datasets and features multiple fitting and plotting options. PyFDAP was written in Python and runs on Ubuntu Linux, Mac OS X and Microsoft Windows operating systems. The software, a user guide and a test FDAP dataset are freely available for download from http://people.tuebingen.mpg.de/mueller-lab. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

WAZA-ARI: computational dosimetry system for X-ray CT examinations II: development of web-based system.

PubMed

Ban, Nobuhiko; Takahashi, Fumiaki; Ono, Koji; Hasegawa, Takayuki; Yoshitake, Takayasu; Katsunuma, Yasushi; Sato, Kaoru; Endo, Akira; Kai, Michiaki

2011-07-01

A web-based dose computation system, WAZA-ARI, is being developed for patients undergoing X-ray CT examinations. The system is implemented in Java on a Linux server running Apache Tomcat. Users choose scanning options and input parameters via a web browser over the Internet. Dose coefficients, which were calculated in a Japanese adult male phantom (JM phantom) are called upon user request and are summed over the scan range specified by the user to estimate a normalised dose. Tissue doses are finally computed based on the radiographic exposure (mA s) and the pitch factor. While dose coefficients are currently available only for limited CT scanner models, the system has achieved a high degree of flexibility and scalability without the use of commercial software.

Expanding the Boundaries of Museum Studies: Popular Education through Engagement with Hidden Histories of Organising and Activism

ERIC Educational Resources Information Center

Toth, Emese R.; Guttman, Sandy; Kimura, Andie; Quinn, Therese

2016-01-01

This article shares a descriptive case study of a popular education project entitled Alternative Tours UIC (ALTourUIC) that took place during a graduate course in the Museum and Exhibition Studies Programme at University of Illinois at Chicago. The educational activities created by the students included a map locating historically rich areas of…

Discovery of Bioactive Compounds by the UIC-ICBG Drug Discovery Program in the 18 Years Since 1998.

PubMed

Zhang, Hong-Jie; Li, Wan-Fei; Fong, Harry H S; Soejarto, Djaja Doel

2016-10-31

The International Cooperative Biodiversity Groups (ICBG) Program based at the University of Illinois at Chicago (UIC) is a program aimed to address the interdependent issues of inventory and conservation of biodiversity, drug discovery and sustained economic growth in both developing and developed countries. It is an interdisciplinary program involving the extensive synergies and collaborative efforts of botanists, chemists and biologists in the countries of Vietnam, Laos and the USA. The UIC-ICBG drug discovery efforts over the past 18 years have resulted in the collection of a cumulative total of more than 5500 plant samples (representing more than 2000 species), that were evaluated for their potential biological effects against cancer, HIV, bird flu, tuberculosis and malaria. The bioassay-guided fractionation and separation of the bioactive plant leads resulted in the isolation of approximately 300 compounds of varying degrees of structural complexity and/or biological activity. The present paper summarizes the significant drug discovery achievements made by the UIC-ICBG team of multidisciplinary collaborators in the project over the period of 1998-2012 and the projects carried on in the subsequent years by involving the researchers in Hong Kong.

PixelLearn

NASA Technical Reports Server (NTRS)

Mazzoni, Dominic; Wagstaff, Kiri; Bornstein, Benjamin; Tang, Nghia; Roden, Joseph

2006-01-01

PixelLearn is an integrated user-interface computer program for classifying pixels in scientific images. Heretofore, training a machine-learning algorithm to classify pixels in images has been tedious and difficult. PixelLearn provides a graphical user interface that makes it faster and more intuitive, leading to more interactive exploration of image data sets. PixelLearn also provides image-enhancement controls to make it easier to see subtle details in images. PixelLearn opens images or sets of images in a variety of common scientific file formats and enables the user to interact with several supervised or unsupervised machine-learning pixel-classifying algorithms while the user continues to browse through the images. The machinelearning algorithms in PixelLearn use advanced clustering and classification methods that enable accuracy much higher than is achievable by most other software previously available for this purpose. PixelLearn is written in portable C++ and runs natively on computers running Linux, Windows, or Mac OS X.

Scalable Unix commands for parallel processors : a high-performance implementation.

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

Ong, E.; Lusk, E.; Gropp, W.

2001-06-22

We describe a family of MPI applications we call the Parallel Unix Commands. These commands are natural parallel versions of common Unix user commands such as ls, ps, and find, together with a few similar commands particular to the parallel environment. We describe the design and implementation of these programs and present some performance results on a 256-node Linux cluster. The Parallel Unix Commands are open source and freely available.

A package of Linux scripts for the parallelization of Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Badal, Andreu; Sempau, Josep

2006-09-01

Despite the fact that fast computers are nowadays available at low cost, there are many situations where obtaining a reasonably low statistical uncertainty in a Monte Carlo (MC) simulation involves a prohibitively large amount of time. This limitation can be overcome by having recourse to parallel computing. Most tools designed to facilitate this approach require modification of the source code and the installation of additional software, which may be inconvenient for some users. We present a set of tools, named clonEasy, that implement a parallelization scheme of a MC simulation that is free from these drawbacks. In clonEasy, which is designed to run under Linux, a set of "clone" CPUs is governed by a "master" computer by taking advantage of the capabilities of the Secure Shell (ssh) protocol. Any Linux computer on the Internet that can be ssh-accessed by the user can be used as a clone. A key ingredient for the parallel calculation to be reliable is the availability of an independent string of random numbers for each CPU. Many generators—such as RANLUX, RANECU or the Mersenne Twister—can readily produce these strings by initializing them appropriately and, hence, they are suitable to be used with clonEasy. This work was primarily motivated by the need to find a straightforward way to parallelize PENELOPE, a code for MC simulation of radiation transport that (in its current 2005 version) employs the generator RANECU, which uses a combination of two multiplicative linear congruential generators (MLCGs). Thus, this paper is focused on this class of generators and, in particular, we briefly present an extension of RANECU that increases its period up to ˜5×10 and we introduce seedsMLCG, a tool that provides the information necessary to initialize disjoint sequences of an MLCG to feed different CPUs. This program, in combination with clonEasy, allows to run PENELOPE in parallel easily, without requiring specific libraries or significant alterations of the sequential code. Program summary 1Title of program:clonEasy Catalogue identifier:ADYD_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYD_v1_0 Program obtainable from:CPC Program Library, Queen's University of Belfast, Northern Ireland Computer for which the program is designed and others in which it is operable:Any computer with a Unix style shell (bash), support for the Secure Shell protocol and a FORTRAN compiler Operating systems under which the program has been tested:Linux (RedHat 8.0, SuSe 8.1, Debian Woody 3.1) Compilers:GNU FORTRAN g77 (Linux); g95 (Linux); Intel Fortran Compiler 7.1 (Linux) Programming language used:Linux shell (bash) script, FORTRAN 77 No. of bits in a word:32 No. of lines in distributed program, including test data, etc.:1916 No. of bytes in distributed program, including test data, etc.:18 202 Distribution format:tar.gz Nature of the physical problem:There are many situations where a Monte Carlo simulation involves a huge amount of CPU time. The parallelization of such calculations is a simple way of obtaining a relatively low statistical uncertainty using a reasonable amount of time. Method of solution:The presented collection of Linux scripts and auxiliary FORTRAN programs implement Secure Shell-based communication between a "master" computer and a set of "clones". The aim of this communication is to execute a code that performs a Monte Carlo simulation on all the clones simultaneously. The code is unique, but each clone is fed with a different set of random seeds. Hence, clonEasy effectively permits the parallelization of the calculation. Restrictions on the complexity of the program:clonEasy can only be used with programs that produce statistically independent results using the same code, but with a different sequence of random numbers. Users must choose the initialization values for the random number generator on each computer and combine the output from the different executions. A FORTRAN program to combine the final results is also provided. Typical running time:The execution time of each script largely depends on the number of computers that are used, the actions that are to be performed and, to a lesser extent, on the network connexion bandwidth. Unusual features of the program:Any computer on the Internet with a Secure Shell client/server program installed can be used as a node of a virtual computer cluster for parallel calculations with the sequential source code. The simplicity of the parallelization scheme makes the use of this package a straightforward task, which does not require installing any additional libraries. Program summary 2Title of program:seedsMLCG Catalogue identifier:ADYE_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYE_v1_0 Program obtainable from:CPC Program Library, Queen's University of Belfast, Northern Ireland Computer for which the program is designed and others in which it is operable:Any computer with a FORTRAN compiler Operating systems under which the program has been tested:Linux (RedHat 8.0, SuSe 8.1, Debian Woody 3.1), MS Windows (2000, XP) Compilers:GNU FORTRAN g77 (Linux and Windows); g95 (Linux); Intel Fortran Compiler 7.1 (Linux); Compaq Visual Fortran 6.1 (Windows) Programming language used:FORTRAN 77 No. of bits in a word:32 Memory required to execute with typical data:500 kilobytes No. of lines in distributed program, including test data, etc.:492 No. of bytes in distributed program, including test data, etc.:5582 Distribution format:tar.gz Nature of the physical problem:Statistically independent results from different runs of a Monte Carlo code can be obtained using uncorrelated sequences of random numbers on each execution. Multiplicative linear congruential generators (MLCG), or other generators that are based on them such as RANECU, can be adapted to produce these sequences. Method of solution:For a given MLCG, the presented program calculates initialization values that produce disjoint, consecutive sequences of pseudo-random numbers. The calculated values initiate the generator in distant positions of the random number cycle and can be used, for instance, on a parallel simulation. The values are found using the formula S=(aS)MODm, which gives the random value that will be generated after J iterations of the MLCG. Restrictions on the complexity of the program:The 32-bit length restriction for the integer variables in standard FORTRAN 77 limits the produced seeds to be separated a distance smaller than 2 31, when the distance J is expressed as an integer value. The program allows the user to input the distance as a power of 10 for the purpose of efficiently splitting the sequence of generators with a very long period. Typical running time:The execution time depends on the parameters of the used MLCG and the distance between the generated seeds. The generation of 10 6 seeds separated 10 12 units in the sequential cycle, for one of the MLCGs found in the RANECU generator, takes 3 s on a 2.4 GHz Intel Pentium 4 using the g77 compiler.

High speed real-time wavefront processing system for a solid-state laser system

NASA Astrophysics Data System (ADS)

Liu, Yuan; Yang, Ping; Chen, Shanqiu; Ma, Lifang; Xu, Bing

2008-03-01

A high speed real-time wavefront processing system for a solid-state laser beam cleanup system has been built. This system consists of a core2 Industrial PC (IPC) using Linux and real-time Linux (RT-Linux) operation system (OS), a PCI image grabber, a D/A card. More often than not, the phase aberrations of the output beam from solid-state lasers vary fast with intracavity thermal effects and environmental influence. To compensate the phase aberrations of solid-state lasers successfully, a high speed real-time wavefront processing system is presented. Compared to former systems, this system can improve the speed efficiently. In the new system, the acquisition of image data, the output of control voltage data and the implementation of reconstructor control algorithm are treated as real-time tasks in kernel-space, the display of wavefront information and man-machine conversation are treated as non real-time tasks in user-space. The parallel processing of real-time tasks in Symmetric Multi Processors (SMP) mode is the main strategy of improving the speed. In this paper, the performance and efficiency of this wavefront processing system are analyzed. The opened-loop experimental results show that the sampling frequency of this system is up to 3300Hz, and this system can well deal with phase aberrations from solid-state lasers.

Urinary iodine in early pregnancy is associated with subclinical hypothyroidism in Tianjin, China: an observational study.

PubMed

Wang, Kunling; Zhang, Jie; Li, Fengao; Zhang, Wanqi; Wang, Hao; Ding, Li; Liu, Yaxin; Lin, Laixiang; Zhang, Shuang; Zhu, Mei

2017-02-17

Subclinical hypothyroidism (SH) is associated with adverse obstetric outcomes and neurodevelopment disorders. Both iodine deficiency and excess are associated with SH; however, few data regarding iodine nutrition status of pregnant women with SH are available. This study aimed to clarify whether iodine deficiency or excess is associated with SH, especially, when test results for anti-thyroid autoantibodies are negative. A total of 115 women with SH and 104 women with euthyroidism (EH) in early pregnancy in Tianjin, China were investigated, and their serum thyroid-stimulating hormone, free thyroxine, free triiodothyronine, anti-thyroid peroxidase antibody (TPOAb), anti-thyroid globulin antibody (TGAb), urinary iodine (UIC), and urinary creatinine (UCr) concentrations were measured. Thyroid ultrasonography was performed to determine thyroid echogenicity and volume. The UIC, UIC/UCr ratio, prevalence of TPOAb and TGAb positivity, and thyroid gland volume were compared between the EH and SH groups. UIC and ultrasonographic features were analysed in subjects in the SH group who were negative for TPOAb and TGAb. Median UIC of SH (154.0 μg/L) and EH (150.1 μg/L) met the World Health Organization criterion for iodine sufficiency in pregnant women. Neither UIC nor the UIC/UCr ratio differed significantly between groups. The prevalence of TPOAb and TGAb positivity in the SH group was significantly higher than that in the EH group (P < 0.01). The percentage of subjects with UIC ≥ 250 μg/L in the SH group was significantly higher than that in the EH group (p = 0.004). The percentage of subjects negative for autoantibodies and UIC ≥ 250 μg/L in the SH group tended to be higher than that in subjects in the EH group negative for autoantibodies, but the difference was not statistically significant (p = 0.025, adjusted test level α = 0.0167). Eight of 18 subjects in the SH group with negative results for TPOAb and TGAb were diagnosed with Hashimoto thyroiditis by means of thyroid ultrasonography. Women in early pregnancy with SH in Tianjin were iodine sufficient, but still at risk of iodine deficiency as pregnancy progressed. UIC ≥ 250 μg/L was associated with increased risk of SH. Serological negative autoimmune thyroiditis and UIC ≥ 250 μg/L may play a role in pathogenesis of SH cases with negative results for autoantibodies.

Automated confidence ranked classification of randomized controlled trial articles: an aid to evidence-based medicine

PubMed Central

Smalheiser, Neil R; McDonagh, Marian S; Yu, Clement; Adams, Clive E; Davis, John M; Yu, Philip S

2015-01-01

Objective: For many literature review tasks, including systematic review (SR) and other aspects of evidence-based medicine, it is important to know whether an article describes a randomized controlled trial (RCT). Current manual annotation is not complete or flexible enough for the SR process. In this work, highly accurate machine learning predictive models were built that include confidence predictions of whether an article is an RCT. Materials and Methods: The LibSVM classifier was used with forward selection of potential feature sets on a large human-related subset of MEDLINE to create a classification model requiring only the citation, abstract, and MeSH terms for each article. Results: The model achieved an area under the receiver operating characteristic curve of 0.973 and mean squared error of 0.013 on the held out year 2011 data. Accurate confidence estimates were confirmed on a manually reviewed set of test articles. A second model not requiring MeSH terms was also created, and performs almost as well. Discussion: Both models accurately rank and predict article RCT confidence. Using the model and the manually reviewed samples, it is estimated that about 8000 (3%) additional RCTs can be identified in MEDLINE, and that 5% of articles tagged as RCTs in Medline may not be identified. Conclusion: Retagging human-related studies with a continuously valued RCT confidence is potentially more useful for article ranking and review than a simple yes/no prediction. The automated RCT tagging tool should offer significant savings of time and effort during the process of writing SRs, and is a key component of a multistep text mining pipeline that we are building to streamline SR workflow. In addition, the model may be useful for identifying errors in MEDLINE publication types. The RCT confidence predictions described here have been made available to users as a web service with a user query form front end at: http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/RCT_Tagger.cgi. PMID:25656516

More than a decade of iodine prophylaxis is needed to eradicate goiter among school age children in a moderately iodine-deficient region.

PubMed

Erdoğan, Murat Faik; Demir, Ozgür; Emral, Rifat; Kamel, Ahmet Nuri; Erdoğan, Gürbüz

2009-03-01

There are many studies regarding the effect of iodine supplementation on goiter, but relatively few reports on the duration of iodine supplementation required to eradicate goiter in iodine-deficient regions. In the current study, we aimed to determine goiter prevalence as determined by sonographic methods, as it relates to changes in median urinary iodine concentrations (UIC) among school age children (SAC), ages 9-11. This study was performed in Ankara, Turkey, before and 5-10 years after mandatory iodination of table salt. Three hundred to 400 SAC from the same primary schools were studied every year by measurement of UIC as part of Turkish Iodine Surveys. Sonographically determined thyroid volume of the SAC had been measured before the mandatory iodination in 1997 and 5-10 years afterward, in 2002 and 2007. The prevalence of goiter in children was evaluated using World Health Organization/International Council for the Control of Iodine Deficiency Disorders recommendations for age and sex. Moderate iodine deficiency was present in 1997 (median UIC, 25.5 microg/L), and it improved to mild iodine deficiency in 2001 (median UIC, 87 microg/L). Sufficient iodine intake (median UIC, 117 microg/L) was achieved by the year 2004. Goiter prevalence was 25% in 1997, 12.3% in 2001, and decreased to 1.3% in 2004. The time required to normalize the prevalence of goiter in SAC living in a moderately iodine-deficient environment was at least a decade. To achieve a goiter rate of less than 5% among SAC, it may require that, as a population, they were born and grew up under conditions of iodine sufficiency.

A Paleolithic-type diet results in iodine deficiency: a 2-year randomized trial in postmenopausal obese women.

PubMed

Manousou, S; Stål, M; Larsson, C; Mellberg, C; Lindahl, B; Eggertsen, R; Hulthén, L; Olsson, T; Ryberg, M; Sandberg, S; Nyström, H F

2018-01-01

Different diets are used for weight loss. A Paleolithic-type diet (PD) has beneficial metabolic effects, but two of the largest iodine sources, table salt and dairy products, are excluded. The objectives of this study were to compare 24-h urinary iodine concentration (24-UIC) in subjects on PD with 24-UIC in subjects on a diet according to the Nordic Nutrition Recommendations (NNR) and to study if PD results in a higher risk of developing iodine deficiency (ID), than NNR diet. A 2-year prospective randomized trial in a tertiary referral center where healthy postmenopausal overweight or obese women were randomized to either PD (n=35) or NNR diet (n=35). Dietary iodine intake, 24-UIC, 24-h urinary iodine excretion (24-UIE), free thyroxin (FT4), free triiodothyronine (FT3) and thyrotropin (TSH) were measured at baseline, 6 and 24 months. Completeness of urine sampling was monitored by para-aminobenzoic acid and salt intake by urinary sodium. At baseline, median 24-UIC (71.0 μg/l) and 24-UIE (134.0 μg/d) were similar in the PD and NNR groups. After 6 months, 24-UIC had decreased to 36.0 μg/l (P=0.001) and 24-UIE to 77.0 μg/d (P=0.001) in the PD group; in the NNR group, levels were unaltered. FT4, TSH and FT3 were similar in both groups, except for FT3 at 6 months being lower in PD than in NNR group. A PD results in a higher risk of developing ID, than a diet according to the NNR. Therefore, we suggest iodine supplementation should be considered when on a PD.

Drinking water contributes to excessive iodine intake among children in Hebei, China.

PubMed

Lv, S; Wang, Y; Xu, D; Rutherford, S; Chong, Z; Du, Y; Jia, L; Zhao, J

2013-09-01

In Hebei province, China, over six million people are potentially exposed to excessive iodine through consumption of high iodine underground drinking water and consumption of iodized salt. The aim of this study is to evaluate the contributions of drinking water and iodized salt on children's iodine nutrition in one area of Hebei province in order to refine strategies to correct the excessive iodine intake in these areas. To investigate the relationships between iodine content in water, iodized salt and urinary iodine content (UIC) in children (8-10 years), we randomly sampled three towns with a known median water iodine (MWI) of 150-300 μg/l in Hengshui City, Hebei province and collected water, salt and urine samples. The median UIC was 518.1 μg/l, the overall MWI was 247.0 μg/l, and 83% of children sampled were found to have urinary iodine concentrations higher than the WHO criterion of 300 μg/l. There was a significant and positive correlation between the median UIC of the children and the MWI in the 12 villages where the children lived (Spearman R=0.79, P=0.002), but the UIC was not significantly correlated with the median salt intake (MSI) (Spearman R=-0.17, P=0.6). A multiple linear regression analysis indicated that 68.7% of the variability in median UIC is associated with variability in MWI in the 12 villages. Iodine in drinking water was identified to be the key contributor to this excessive iodine in children indicating that in these areas, intervention should focus on providing alternative drinking water supplies.

Repetitive behavior profiles: Consistency across autism spectrum disorder cohorts and divergence from Prader-Willi syndrome.

PubMed

Flores, Cindi G; Valcante, Gregory; Guter, Steve; Zaytoun, Annette; Wray, Emily; Bell, Lindsay; Jacob, Suma; Lewis, Mark H; Driscoll, Daniel J; Cook, Edwin H; Kim, Soo-Jeong

2011-12-01

Restricted and repetitive behavior (RRB) is a group of heterogeneous maladaptive behaviors. RRB is one of the key diagnostic features of autism spectrum disorders (ASDs) and also commonly observed in Prader-Willi syndrome (PWS). In this study, we assessed RRB using the Repetitive Behavior Scale-Revised (RBS-R) in two ASD samples (University of Illinois at Chicago [UIC] and University of Florida [UF]) and one PWS sample. We compared the RBS-R item endorsements across three ASD cohorts (UIC, UF and an ASD sample from Lam, The Repetitive Behavior Scale-Revised: independent validation and the effect of subject variables, PhD thesis, 2004), and a PWS sample. We also compared the mean RBS-R subscale/sum scores across the UIC, UF and PWS samples; across the combined ASD (UIC + UF), PWS-deletion and PWS-disomy groups; and across the combined ASD sample, PWS subgroup with a Social Communication Questionnaire (SCQ) score ≥15, and PWS subgroup with a SCQ score <15. Despite the highly heterogeneous nature, the three ASD samples (UIC, UF and Lam's) showed a similar pattern of the RBS-R endorsements, and the mean RBS-R scores were not different between the UIC and UF samples. However, higher RRB was noted in the ASD sample compared with the PWS sample, as well as in the PWS subgroup with a SCQ score ≥15 compared with the PWS subgroup with a SCQ score <15. Study limitations include a small sample size, a wide age range of our participants, and not controlling for potential covariates. A future replication study using a larger sample and further investigation into the genetic bases of overlapping ASD and RRB phenomenology are needed, given the higher RRB in the PWS subgroup with a SCQ score ≥15.

BioconductorBuntu: a Linux distribution that implements a web-based DNA microarray analysis server.

PubMed

Geeleher, Paul; Morris, Dermot; Hinde, John P; Golden, Aaron

2009-06-01

BioconductorBuntu is a custom distribution of Ubuntu Linux that automatically installs a server-side microarray processing environment, providing a user-friendly web-based GUI to many of the tools developed by the Bioconductor Project, accessible locally or across a network. System installation is via booting off a CD image or by using a Debian package provided to upgrade an existing Ubuntu installation. In its current version, several microarray analysis pipelines are supported including oligonucleotide, dual-or single-dye experiments, including post-processing with Gene Set Enrichment Analysis. BioconductorBuntu is designed to be extensible, by server-side integration of further relevant Bioconductor modules as required, facilitated by its straightforward underlying Python-based infrastructure. BioconductorBuntu offers an ideal environment for the development of processing procedures to facilitate the analysis of next-generation sequencing datasets. BioconductorBuntu is available for download under a creative commons license along with additional documentation and a tutorial from (http://bioinf.nuigalway.ie).

BioSMACK: a linux live CD for genome-wide association analyses.

PubMed

Hong, Chang Bum; Kim, Young Jin; Moon, Sanghoon; Shin, Young-Ah; Go, Min Jin; Kim, Dong-Joon; Lee, Jong-Young; Cho, Yoon Shin

2012-01-01

Recent advances in high-throughput genotyping technologies have enabled us to conduct a genome-wide association study (GWAS) on a large cohort. However, analyzing millions of single nucleotide polymorphisms (SNPs) is still a difficult task for researchers conducting a GWAS. Several difficulties such as compatibilities and dependencies are often encountered by researchers using analytical tools, during the installation of software. This is a huge obstacle to any research institute without computing facilities and specialists. Therefore, a proper research environment is an urgent need for researchers working on GWAS. We developed BioSMACK to provide a research environment for GWAS that requires no configuration and is easy to use. BioSMACK is based on the Ubuntu Live CD that offers a complete Linux-based operating system environment without installation. Moreover, we provide users with a GWAS manual consisting of a series of guidelines for GWAS and useful examples. BioSMACK is freely available at http://ksnp.cdc. go.kr/biosmack.

Efficient Comparison between Windows and Linux Platform Applicable in a Virtual Architectural Walkthrough Application

NASA Astrophysics Data System (ADS)

Thubaasini, P.; Rusnida, R.; Rohani, S. M.

This paper describes Linux, an open source platform used to develop and run a virtual architectural walkthrough application. It proposes some qualitative reflections and observations on the nature of Linux in the concept of Virtual Reality (VR) and on the most popular and important claims associated with the open source approach. The ultimate goal of this paper is to measure and evaluate the performance of Linux used to build the virtual architectural walkthrough and develop a proof of concept based on the result obtain through this project. Besides that, this study reveals the benefits of using Linux in the field of virtual reality and reflects a basic comparison and evaluation between Windows and Linux base operating system. Windows platform is use as a baseline to evaluate the performance of Linux. The performance of Linux is measured based on three main criteria which is frame rate, image quality and also mouse motion.

TankSIM: A Cryogenic Tank Performance Prediction Program

NASA Technical Reports Server (NTRS)

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

2015-01-01

Developed for predicting the behavior of cryogenic liquids inside propellant tanks under various environmental and operating conditions. Provides a multi-node analysis of pressurization, ullage venting and thermodynamic venting systems (TVS) pressure control using axial jet or spray bar TVS. Allows user to combine several different phases for predicting the liquid behavior for the entire flight mission timeline or part of it. Is a NASA in-house code, based on FORTRAN 90-95 and Intel Visual FORTRAN compiler, but can be used on any other platform (Unix-Linux, Compaq Visual FORTRAN, etc.). The last Version 7, released on December 2014, included detailed User's Manual. Includes the use of several RefPROP subroutines for calculating fluid properties.

Semi-Automated Identification of Rocks in Images

NASA Technical Reports Server (NTRS)

Bornstein, Benjamin; Castano, Andres; Anderson, Robert

2006-01-01

Rock Identification Toolkit Suite is a computer program that assists users in identifying and characterizing rocks shown in images returned by the Mars Explorer Rover mission. Included in the program are components for automated finding of rocks, interactive adjustments of outlines of rocks, active contouring of rocks, and automated analysis of shapes in two dimensions. The program assists users in evaluating the surface properties of rocks and soil and reports basic properties of rocks. The program requires either the Mac OS X operating system running on a G4 (or more capable) processor or a Linux operating system running on a Pentium (or more capable) processor, plus at least 128MB of random-access memory.

A Dedicated Computational Platform for Cellular Monte Carlo T-CAD Software Tools

DTIC Science & Technology

2015-07-14

computer that establishes an encrypted Virtual Private Network ( OpenVPN [44]) based on the Secure Socket Layer (SSL) paradigm. Each user is given a...security certificate for each device used to connect to the computing nodes. Stable OpenVPN clients are available for Linux, Microsoft Windows, Apple OSX...platform is granted by an encrypted connection base on the Secure Socket Layer (SSL) protocol, and implemented in the OpenVPN Virtual Personal Network

Comparative visualization of genetic and physical maps with Strudel.

PubMed

Bayer, Micha; Milne, Iain; Stephen, Gordon; Shaw, Paul; Cardle, Linda; Wright, Frank; Marshall, David

2011-05-01

Data visualization can play a key role in comparative genomics, for example, underpinning the investigation of conserved synteny patterns. Strudel is a desktop application that allows users to easily compare both genetic and physical maps interactively and efficiently. It can handle large datasets from several genomes simultaneously, and allows all-by-all comparisons between these. Installers for Strudel are available for Windows, Linux, Solaris and Mac OS X at http://bioinf.scri.ac.uk/strudel/.

Research and Design of Embedded Wireless Meal Ordering System Based on SQLite

NASA Astrophysics Data System (ADS)

Zhang, Jihong; Chen, Xiaoquan

The paper describes features and internal architecture and developing method of SQLite. And then it gives a design and program of meal ordering system. The system realizes the information interaction among the users and embedded devices with SQLite as database system. The embedded database SQLite manages the data and achieves wireless communication by using Bluetooth. A system program based on Qt/Embedded and Linux drivers realizes the local management of environmental data.

Development of Automatic Live Linux Rebuilding System with Flexibility in Science and Engineering Education and Applying to Information Processing Education

NASA Astrophysics Data System (ADS)

Sonoda, Jun; Yamaki, Kota

We develop an automatic Live Linux rebuilding system for science and engineering education, such as information processing education, numerical analysis and so on. Our system is enable to easily and automatically rebuild a customized Live Linux from a ISO image of Ubuntu, which is one of the Linux distribution. Also, it is easily possible to install/uninstall packages and to enable/disable init daemons. When we rebuild a Live Linux CD using our system, we show number of the operations is 8, and the rebuilding time is about 33 minutes on CD version and about 50 minutes on DVD version. Moreover, we have applied the rebuilded Live Linux CD in a class of information processing education in our college. As the results of a questionnaires survey from our 43 students who used the Live Linux CD, we obtain that the our Live Linux is useful for about 80 percents of students. From these results, we conclude that our system is able to easily and automatically rebuild a useful Live Linux in short time.

Setting Up the JBrowse Genome Browser

PubMed Central

Skinner, Mitchell E; Holmes, Ian H

2010-01-01

JBrowse is a web-based tool for visualizing genomic data. Unlike most other web-based genome browsers, JBrowse exploits the capabilities of the user's web browser to make scrolling and zooming fast and smooth. It supports the browsers used by almost all internet users, and is relatively simple to install. JBrowse can utilize multiple types of data in a variety of common genomic data formats, including genomic feature data in bioperl databases, GFF files, and BED files, and quantitative data in wiggle files. This unit describes how to obtain the JBrowse software, set it up on a Linux or Mac OS X computer running as a web server and incorporate genome annotation data from multiple sources into JBrowse. After completing the protocols described in this unit, the reader will have a web site that other users can visit to browse the genomic data. PMID:21154710

Implementation of a Forth-Order Aeroelastic Coupling into a Viscous-Inviscid Flow Solver with Experimental Validation (for One Degree of Freedom)

NASA Astrophysics Data System (ADS)

Bartholomay, Sirko; Ramos-García, Néstor; Mikkelsen, Robert Flemming; Technical University of Denmark (DTU)-WInd Energy Team

2014-11-01

The viscous-inviscid flow solver Q3UIC for 2D aerodynamics has recently been developed at the Technical University of Denmark. The Q3UIC solver takes viscous and unsteady effects into account by coupling an unsteady inviscid panel method with the integral boundary layer equations by means of a strong coupling between the viscous and inviscid parts, and in this respect differs from other classic panel codes e.g. Xfoil. In the current work a Runge-Kutta-Nyström scheme was employed to couple inertial, elastic and aerodynamical forces and moments calculated by Q3UIC for a two-dimensional blade section in the time-domain. Numerical simulations are validated by a three step experimental verification process carried out in the low-turbulence wind tunnel at DTU. First, a comparison against steady experiments for a NACA 64418 profile and a flexible trailing edge flap is presented for different fixed flap angles, and second, the measured aerodynamic characteristics considering prescribed motion of the airfoil with a moving flap are compared to the Q3UIC predictions. Finally, an aeroelastic experiment for one degree of freedom-airfoil pitching- is used to evaluate the accuracy of aeroelastic coupling.

Urinary Iodine Concentrations in Cancer Patients

PubMed Central

Kargar, Saeed; Shiryazdi, Seyed Mostafa; Atashi, Seyed Reza; Neamatzadeh, Hossein; Kamali, Mahdieh

2017-01-01

Background: It has been suggested that incidence of some cancers, especially examples in the breast and stomach may be influenced by the iodine intake. However, only few studies are available at present. Therefore, we have conducted the present assessment of iodine status in Iranian patients diagnosed with a malignancy. Materials and Methods: This cross-sectional study was conducted in 85 patients diagnosed with different types of cancer at Shahid Sadoughi Hospital, Yazd, Iran. The method used was based on the Sandell–Kolthoff reaction. Results: The median urinary iodine concentration (UIC) was 17.4 μg/L, with ≤20 μg/L indicative of severe iodine deficiency. According to the WHO/IC C IDD/UNIC EF classification, 88.1%, 7.1% and 2.4% of patients had a UIC <20 (severe), 20–49 (mild), and 50–99 μg/L (moderate), respectively. There was no statistically significant differences in UIC between men and women. Conclusion: The UIC values indicate that Iranian cancer patients were seriously iodine deficient according to WHO/UNIC EF/IC C IDD, and that this is a suitable index to assess iodine status in Iranians. Daily consumption of salt fortified with iodine or other approaches to increase intake might be effective strategies for prevention or reduction of malignancies. PMID:28441792

Innovative data tools: a suite for managing peer outreach to key affected populations in Viet Nam

PubMed Central

Jacka, David; Van Hai, Nguyen; Trinh, Nguyen Kieu; Boisen, Neil; Neukom, Josselyn

2012-01-01

Problem The paper tools used to monitor outreach work in all major cities in Viet Nam had substantial writing requirements for each contact with difficulty maintaining confidentiality. Action This paper describes the development of a Unique Identifier Code (UIC), a field data collection notebook (databook) and a computer data entry system in Viet Nam. The databook can document 40 individual clients and has space for commodity distribution, group contacts and needles/syringe collection for each month. Outcome Field implementation trials of the UIC and databook have been undertaken by more than 160 peer outreach workers to document their work with people who inject drugs (PWID) and sex workers (SW). Following an expanded trial in Hai Phong province, there have been requests for national circulation of the databook to be used by peer educators documenting outreach to PWID, SW and men who have sex with men. The standardized UIC and databook, in a variety of locally adapted formats, have now been introduced in more than 40 of the 63 provinces in Viet Nam. Discussion This development in Viet Nam is, to our knowledge, the first example of the combination of a confidential UIC and an innovative, simple pocket-sized paper instrument with associated customized data-entry software for documenting outreach. PMID:23908919

Innovative data tools: a suite for managing peer outreach to key affected populations in Viet Nam.

PubMed

Nga, Nguyen Thien; Jacka, David; Van Hai, Nguyen; Trinh, Nguyen Kieu; Boisen, Neil; Neukom, Josselyn

2012-07-01

The paper tools used to monitor outreach work in all major cities in Viet Nam had substantial writing requirements for each contact with difficulty maintaining confidentiality. This paper describes the development of a Unique Identifier Code (UIC), a field data collection notebook (databook) and a computer data entry system in Viet Nam. The databook can document 40 individual clients and has space for commodity distribution, group contacts and needles/syringe collection for each month. Field implementation trials of the UIC and databook have been undertaken by more than 160 peer outreach workers to document their work with people who inject drugs (PWID) and sex workers (SW). Following an expanded trial in Hai Phong province, there have been requests for national circulation of the databook to be used by peer educators documenting outreach to PWID, SW and men who have sex with men. The standardized UIC and databook, in a variety of locally adapted formats, have now been introduced in more than 40 of the 63 provinces in Viet Nam. This development in Viet Nam is, to our knowledge, the first example of the combination of a confidential UIC and an innovative, simple pocket-sized paper instrument with associated customized data-entry software for documenting outreach.

WOD - Weather On Demand forecasting system

NASA Astrophysics Data System (ADS)

Rognvaldsson, Olafur; Ragnarsson, Logi; Stanislawska, Karolina

2017-04-01

The backbone of the Belgingur forecasting system (called WOD - Weather On Demand) is the WRF-Chem atmospheric model, with a number of in-house customisations. Initial and boundary data are taken from the Global Forecasting System, operated by the National Oceanic and Atmospheric Administration (NOAA). Operational forecasts use cycling of a number of parameters, mainly deep soil and surface fields. This is done to minimise spin-up effects and to ensure proper book-keeping of hydrological fields such as snow accumulation and runoff, as well as the constituents of various chemical parameters. The WOD system can be used to create conventional short- to medium-range weather forecasts for any location on the globe. The WOD system can also be used for air quality purposes (e.g. dispersion forecasts from volcanic eruptions) and as a tool to provide input to other modelling systems, such as hydrological models. A wide variety of post-processing options are also available, making WOD an ideal tool for creating highly customised output that can be tailored to the specific needs of individual end-users. The most recent addition to the WOD system is an integrated verification system where forecasts can be compared to surface observations from chosen locations. Forecast visualisation, such as weather charts, meteograms, weather icons and tables, is done via number of web components that can be configured to serve the varying needs of different end-users. The WOD system itself can be installed in an automatic way on hardware running a range of Linux based OS. System upgrades can also be done in semi-automatic fashion, i.e. upgrades and/or bug-fixes can be pushed to the end-user hardware without system downtime. Importantly, the WOD system requires only rudimentary knowledge of the WRF modelling, and the Linux operating systems on behalf of the end-user, making it an ideal NWP tool in locations with limited IT infrastructure.

Preparing a scientific manuscript in Linux: Today's possibilities and limitations.

PubMed

Tchantchaleishvili, Vakhtang; Schmitto, Jan D

2011-10-22

Increasing number of scientists are enthusiastic about using free, open source software for their research purposes. Authors' specific goal was to examine whether a Linux-based operating system with open source software packages would allow to prepare a submission-ready scientific manuscript without the need to use the proprietary software. Preparation and editing of scientific manuscripts is possible using Linux and open source software. This letter to the editor describes key steps for preparation of a publication-ready scientific manuscript in a Linux-based operating system, as well as discusses the necessary software components. This manuscript was created using Linux and open source programs for Linux.

Potential performance bottleneck in Linux TCP

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

Wu, Wenji; Crawford, Matt; /Fermilab

2006-12-01

TCP is the most widely used transport protocol on the Internet today. Over the years, especially recently, due to requirements of high bandwidth transmission, various approaches have been proposed to improve TCP performance. The Linux 2.6 kernel is now preemptible. It can be interrupted mid-task, making the system more responsive and interactive. However, we have noticed that Linux kernel preemption can interact badly with the performance of the networking subsystem. In this paper we investigate the performance bottleneck in Linux TCP. We systematically describe the trip of a TCP packet from its ingress into a Linux network end system tomore » its final delivery to the application; we study the performance bottleneck in Linux TCP through mathematical modeling and practical experiments; finally we propose and test one possible solution to resolve this performance bottleneck in Linux TCP.« less

PyCorrFit-generic data evaluation for fluorescence correlation spectroscopy.

PubMed

Müller, Paul; Schwille, Petra; Weidemann, Thomas

2014-09-01

We present a graphical user interface (PyCorrFit) for the fitting of theoretical model functions to experimental data obtained by fluorescence correlation spectroscopy (FCS). The program supports many data file formats and features a set of tools specialized in FCS data evaluation. The Python source code is freely available for download from the PyCorrFit web page at http://pycorrfit.craban.de. We offer binaries for Ubuntu Linux, Mac OS X and Microsoft Windows. © The Author 2014. Published by Oxford University Press.

GRAMM-X public web server for protein–protein docking

PubMed Central

Tovchigrechko, Andrey; Vakser, Ilya A.

2006-01-01

Protein docking software GRAMM-X and its web interface () extend the original GRAMM Fast Fourier Transformation methodology by employing smoothed potentials, refinement stage, and knowledge-based scoring. The web server frees users from complex installation of database-dependent parallel software and maintaining large hardware resources needed for protein docking simulations. Docking problems submitted to GRAMM-X server are processed by a 320 processor Linux cluster. The server was extensively tested by benchmarking, several months of public use, and participation in the CAPRI server track. PMID:16845016

MYRaf: An Easy Aperture Photometry GUI for IRAF

NASA Astrophysics Data System (ADS)

Niaei, M. S.; KiliÇ, Y.; Özeren, F. F.

2015-07-01

We describe the design and development of MYRaf, a GUI (Graphical User Interface) that aims to be completely open-source under General Public License (GPL). MYRaf is an easy to use, reliable, and a fast IRAF aperture photometry GUI tool for those who are conversant with text-based software and command-line procedures in GNU/Linux OSs. MYRaf uses IRAF, PyRAF, matplotlib, ginga, alipy, and SExtractor with the general-purpose and high-level programming language Python, and uses the Qt framework.

CHROMA: consensus-based colouring of multiple alignments for publication.

PubMed

Goodstadt, L; Ponting, C P

2001-09-01

CHROMA annotates multiple protein sequence alignments by consensus to produce formatted and coloured text suitable for incorporation into other documents for publication. The package is designed to be flexible and reliable, and has a simple-to-use graphical user interface running under Microsoft Windows. Both the executables and source code for CHROMA running under Windows and Linux (portable command-line only) are freely available at http://www.lg.ndirect.co.uk/chroma. Software enquiries should be directed to CHROMA@lg.ndirect.co.uk.

Learnable Models for Information Diffusion and its Associated User Behavior in Micro-blogosphere

DTIC Science & Technology

2012-08-30

According to the work of Even-Dar and Shapira (2007), we recall the definition of the ba- sic voter model on network G. In the model, each node of G...reason as follows. We started with the K distinct initial nodes and all the other nodes were neutral in the beginning. Recall that we set the average time... memory , running under Linux. Learning to predict opinion share and detect anti-majority opinionists in social networks 29 7 Conclusion Unlike the popular

PKPass

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

Adamson, Ryan M.

Password management solutions exist, but few are designed for enterprise systems administrators sharing oncall rotations. Due to the Multi-Factor Level of Assurance 4 effort, DOE is now distributing PIV cards with cryptographically signed certificate and private key pairs to administrators and other security-significant users. We utilize this public key infrastructure (PKI) to encrypt passwords for other recipients in a secure way. This is cross platform (works on OSX and Linux systems), and has already been adopted internally by the NCCS systems administration staff to replace their old password book system.

Preparing a scientific manuscript in Linux: Today's possibilities and limitations

PubMed Central

2011-01-01

Background Increasing number of scientists are enthusiastic about using free, open source software for their research purposes. Authors' specific goal was to examine whether a Linux-based operating system with open source software packages would allow to prepare a submission-ready scientific manuscript without the need to use the proprietary software. Findings Preparation and editing of scientific manuscripts is possible using Linux and open source software. This letter to the editor describes key steps for preparation of a publication-ready scientific manuscript in a Linux-based operating system, as well as discusses the necessary software components. This manuscript was created using Linux and open source programs for Linux. PMID:22018246

LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis.

PubMed

Nagraj, V P; Magee, Neal E; Sheffield, Nathan C

2018-06-06

The past few years have seen an explosion of interest in understanding the role of regulatory DNA. This interest has driven large-scale production of functional genomics data and analytical methods. One popular analysis is to test for enrichment of overlaps between a query set of genomic regions and a database of region sets. In this way, new genomic data can be easily connected to annotations from external data sources. Here, we present an interactive interface for enrichment analysis of genomic locus overlaps using a web server called LOLAweb. LOLAweb accepts a set of genomic ranges from the user and tests it for enrichment against a database of region sets. LOLAweb renders results in an R Shiny application to provide interactive visualization features, enabling users to filter, sort, and explore enrichment results dynamically. LOLAweb is built and deployed in a Linux container, making it scalable to many concurrent users on our servers and also enabling users to download and run LOLAweb locally.

Embedded systems for supporting computer accessibility.

PubMed

Mulfari, Davide; Celesti, Antonio; Fazio, Maria; Villari, Massimo; Puliafito, Antonio

2015-01-01

Nowadays, customized AT software solutions allow their users to interact with various kinds of computer systems. Such tools are generally available on personal devices (e.g., smartphones, laptops and so on) commonly used by a person with a disability. In this paper, we investigate a way of using the aforementioned AT equipments in order to access many different devices without assistive preferences. The solution takes advantage of open source hardware and its core component consists of an affordable Linux embedded system: it grabs data coming from the assistive software, which runs on the user's personal device, then, after processing, it generates native keyboard and mouse HID commands for the target computing device controlled by the end user. This process supports any operating system available on the target machine and it requires no specialized software installation; therefore the user with a disability can rely on a single assistive tool to control a wide range of computing platforms, including conventional computers and many kinds of mobile devices, which receive input commands through the USB HID protocol.

Iodine Intakes of Victorian Schoolchildren Measured Using 24-h Urinary Iodine Excretion

PubMed Central

Beckford, Kelsey; Margerison, Claire; Skeaff, Sheila A.

2017-01-01

Mandatory fortification of bread with iodized salt was introduced in Australia in 2009, and studies using spot urine collections conducted post fortification indicate that Australian schoolchildren are now replete. However an accurate estimate of daily iodine intake utilizing 24-h urinary iodine excretion (UIE μg/day) has not been reported and compared to the estimated average requirement (EAR). This study aimed to assess daily total iodine intake and status of a sample of primary schoolchildren using 24-h urine samples. Victorian primary school children provided 24-h urine samples between 2011 and 2013, from which urinary iodine concentration (UIC, μg/L) and total iodine excretion (UIE, μg/day) as an estimate of intake was determined. Valid 24-h urine samples were provided by 650 children, mean (SD) age 9.3 (1.8) years (n = 359 boys). The mean UIE of 4–8 and 9–13 year olds was 94 (48) and 111 (57) μg/24-h, respectively, with 29% and 26% having a UIE below the age-specific EAR. The median (IQR) UIC was 124 (83,172) μg/L, with 36% of participants having a UIC < 100 μg/L. This convenience sample of Victorian schoolchildren were found to be iodine replete, based on UIC and estimated iodine intakes derived from 24-h urine collections, confirming the findings of the Australian Health Survey. PMID:28867787

Evaluation of Thyroid Hormone Levels and Urinary Iodine Concentrations in Koreans Based on the Data from Korea National Health and Nutrition Examination Survey VI (2013 to 2015).

PubMed

Chung, Jae Hoon

2018-06-01

No nationwide data have been published about thyroid hormone levels and urinary iodine concentrations (UICs) in Korea. The Korea Centers for Disease Control and Prevention and the Korean Thyroid Association established a project to evaluate the nationwide thyroid hormone profile and UICs in healthy Koreans as part of the Korea National Health and Nutrition Examination Survey (KNHANES) VI (2013 to 2015), a nationwide, cross-sectional survey of the Korean population that enrolled 7,061 individuals who were weighted to represent the entire Korean population. Based on the KNHANES VI, the geometric mean value of serum thyroid stimulating hormone was 2.16 mIU/L, and its reference interval was 0.59 to 7.03 mIU/L. The mean value of serum free thyroxine was 1.25 ng/dL, and its reference interval was 0.92 to 1.60 ng/dL. The median UIC in the Korean population was reported to be 294 μg/L, corresponding to 'above requirements' iodine intake according to the World Health Organization recommendations. A U-shaped relationship of UIC with age was found. The prevalence of overt hyperthyroidism and overt hypothyroidism in the Korean population based on the KNHANES VI was 0.54% and 0.73%, respectively. Copyright © 2018 Korean Endocrine Society.

Urinary iodine concentration identifies pregnant women as iodine deficient yet school-aged children as iodine sufficient in rural Niger.

PubMed

Hess, Sonja Y; Ouédraogo, Césaire T; Young, Rebecca R; Bamba, Ibrahim F; Stinca, Sara; Zimmermann, Michael B; Wessells, K Ryan

2017-05-01

To assess iodine status among pregnant women in rural Zinder, Niger and to compare their status with the iodine status of school-aged children from the same households. Seventy-three villages in the catchment area of sixteen health centres were randomly selected to participate in the cross-sectional survey. Salt iodization is mandatory in Niger, requiring 20-60 ppm iodine at the retail level. A spot urine sample was collected from randomly selected pregnant women (n 662) and one school-aged child from the same household (n 373). Urinary iodine concentration (UIC) was assessed as an indicator of iodine status in both groups. Dried blood spots (DBS) were collected from venous blood samples of pregnant women and thyroglobulin (Tg), thyroid-stimulating hormone and total thyroxine were measured. Iodine content of household salt samples (n 108) was assessed by titration. Median iodine content of salt samples was 5·5 ppm (range 0-41 ppm), 98 % had an iodine content 40 µg/l. In this region of Niger, most salt is inadequately iodized. UIC in pregnant women indicated iodine deficiency, whereas UIC of school-aged children indicated marginally adequate iodine status. Thus, estimating population iodine status based solely on monitoring of UIC among school-aged children may underestimate the risk of iodine deficiency in pregnant women.

Inadequate Iodine Intake in Population Groups Defined by Age, Life Stage and Vegetarian Dietary Practice in a Norwegian Convenience Sample.

PubMed

Brantsæter, Anne Lise; Knutsen, Helle Katrine; Johansen, Nina Cathrine; Nyheim, Kristine Aastad; Erlund, Iris; Meltzer, Helle Margrete; Henjum, Sigrun

2018-02-17

Inadequate iodine intake has been identified in populations considered iodine replete for decades. The objective of the current study is to evaluate urinary iodine concentration (UIC) and the probability of adequate iodine intake in subgroups of the Norwegian population defined by age, life stage and vegetarian dietary practice. In a cross-sectional survey, we assessed the probability of adequate iodine intake by two 24-h food diaries and UIC from two fasting morning spot urine samples in 276 participants. The participants included children ( n = 47), adolescents ( n = 46), adults ( n = 71), the elderly ( n = 23), pregnant women ( n = 45), ovo-lacto vegetarians ( n = 25), and vegans ( n = 19). In all participants combined, the median (95% CI) UIC was 101 (90, 110) µg/L, median (25th, 75th percentile) calculated iodine intake was 112 (77, 175) µg/day and median (25th, 75th percentile) estimated usual iodine intake was 101 (75, 150) µg/day. According to WHOs criteria for evaluation of median UIC, iodine intake was inadequate in the elderly, pregnant women, vegans and non-pregnant women of childbearing age. Children had the highest (82%) and vegans the lowest (14%) probability of adequate iodine intake according to reported food and supplement intakes. This study confirms the need for monitoring iodine intake and status in nationally representative study samples in Norway.

Inadequate Iodine Intake in Population Groups Defined by Age, Life Stage and Vegetarian Dietary Practice in a Norwegian Convenience Sample

PubMed Central

Knutsen, Helle Katrine; Johansen, Nina Cathrine; Nyheim, Kristine Aastad; Erlund, Iris; Meltzer, Helle Margrete

2018-01-01

Inadequate iodine intake has been identified in populations considered iodine replete for decades. The objective of the current study is to evaluate urinary iodine concentration (UIC) and the probability of adequate iodine intake in subgroups of the Norwegian population defined by age, life stage and vegetarian dietary practice. In a cross-sectional survey, we assessed the probability of adequate iodine intake by two 24-h food diaries and UIC from two fasting morning spot urine samples in 276 participants. The participants included children (n = 47), adolescents (n = 46), adults (n = 71), the elderly (n = 23), pregnant women (n = 45), ovo-lacto vegetarians (n = 25), and vegans (n = 19). In all participants combined, the median (95% CI) UIC was 101 (90, 110) µg/L, median (25th, 75th percentile) calculated iodine intake was 112 (77, 175) µg/day and median (25th, 75th percentile) estimated usual iodine intake was 101 (75, 150) µg/day. According to WHOs criteria for evaluation of median UIC, iodine intake was inadequate in the elderly, pregnant women, vegans and non-pregnant women of childbearing age. Children had the highest (82%) and vegans the lowest (14%) probability of adequate iodine intake according to reported food and supplement intakes. This study confirms the need for monitoring iodine intake and status in nationally representative study samples in Norway. PMID:29462974

The Linux operating system: An introduction

NASA Technical Reports Server (NTRS)

Bokhari, Shahid H.

1995-01-01

Linux is a Unix-like operating system for Intel 386/486/Pentium based IBM-PCs and compatibles. The kernel of this operating system was written from scratch by Linus Torvalds and, although copyrighted by the author, may be freely distributed. A world-wide group has collaborated in developing Linux on the Internet. Linux can run the powerful set of compilers and programming tools of the Free Software Foundation, and XFree86, a port of the X Window System from MIT. Most capabilities associated with high performance workstations, such as networking, shared file systems, electronic mail, TeX, LaTeX, etc. are freely available for Linux. It can thus transform cheap IBM-PC compatible machines into Unix workstations with considerable capabilities. The author explains how Linux may be obtained, installed and networked. He also describes some interesting applications for Linux that are freely available. The enormous consumer market for IBM-PC compatible machines continually drives down prices of CPU chips, memory, hard disks, CDROMs, etc. Linux can convert such machines into powerful workstations that can be used for teaching, research and software development. For professionals who use Unix based workstations at work, Linux permits virtually identical working environments on their personal home machines. For cost conscious educational institutions Linux can create world-class computing environments from cheap, easily maintained, PC clones. Finally, for university students, it provides an essentially cost-free path away from DOS into the world of Unix and X Windows.

The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation.

PubMed

Kocher, Jean-Pierre A; Quest, Daniel J; Duffy, Patrick; Meiners, Michael A; Moore, Raymond M; Rider, David; Hossain, Asif; Hart, Steven N; Dinu, Valentin

2014-07-01

The Biological Reference Repository (BioR) is a toolkit for annotating variants. BioR stores public and user-specific annotation sources in indexed JSON-encoded flat files (catalogs). The BioR toolkit provides the functionality to combine and retrieve annotation from these catalogs via the command-line interface. Several catalogs from commonly used annotation sources and instructions for creating user-specific catalogs are provided. Commands from the toolkit can be combined with other UNIX commands for advanced annotation processing. We also provide instructions for the development of custom annotation pipelines. The package is implemented in Java and makes use of external tools written in Java and Perl. The toolkit can be executed on Mac OS X 10.5 and above or any Linux distribution. The BioR application, quickstart, and user guide documents and many biological examples are available at http://bioinformaticstools.mayo.edu. © The Author 2014. Published by Oxford University Press.

Freeing Worldview's development process: Open source everything!

NASA Astrophysics Data System (ADS)

Gunnoe, T.

2016-12-01

Freeing your code and your project are important steps for creating an inviting environment for collaboration, with the added side effect of keeping a good relationship with your users. NASA Worldview's codebase was released with the open source NOSA (NASA Open Source Agreement) license in 2014, but this is only the first step. We also have to free our ideas, empower our users by involving them in the development process, and open channels that lead to the creation of a community project. There are many highly successful examples of Free and Open Source Software (FOSS) projects of which we can take note: the Linux kernel, Debian, GNOME, etc. These projects owe much of their success to having a passionate mix of developers/users with a great community and a common goal in mind. This presentation will describe the scope of this openness and how Worldview plans to move forward with a more community-inclusive approach.

T-LECS: The Control Software System for MOIRCS

NASA Astrophysics Data System (ADS)

Yoshikawa, T.; Omata, K.; Konishi, M.; Ichikawa, T.; Suzuki, R.; Tokoku, C.; Katsuno, Y.; Nishimura, T.

2006-07-01

MOIRCS (Multi-Object Infrared Camera and Spectrograph) is a new instrument for the Subaru Telescope. We present the system design of the control software system for MOIRCS, named T-LECS (Tohoku University - Layered Electronic Control System). T-LECS is a PC-Linux based network distributed system. Two PCs equipped with the focal plane array system operate two HAWAII2 detectors, respectively, and another PC is used for user interfaces and a database server. Moreover, these PCs control various devices for observations distributed on a TCP/IP network. T-LECS has three interfaces; interfaces to the devices and two user interfaces. One of the user interfaces is to the integrated observation control system (Subaru Observation Software System) for observers, and another one provides the system developers the direct access to the devices of MOIRCS. In order to help the communication between these interfaces, we employ an SQL database system.

Make Movies out of Your Dynamical Simulations with OGRE!

NASA Astrophysics Data System (ADS)

Tamayo, Daniel; Douglas, R. W.; Ge, H. W.; Burns, J. A.

2013-10-01

We have developed OGRE, the Orbital GRaphics Environment, an open-source project comprising a graphical user interface that allows the user to view the output from several dynamical integrators (e.g., SWIFT) that are commonly used for academic work. One can interactively vary the display speed, rotate the view and zoom the camera. This makes OGRE a great tool for students or the general public to explore accurate orbital histories that may display interesting dynamical features, e.g. the destabilization of Solar System orbits under the Nice model, or interacting pairs of exoplanets. Furthermore, OGRE allows the user to choreograph sequences of transformations as the simulation is played to generate movies for use in public talks or professional presentations. The graphical user interface is coded using Qt to ensure portability across different operating systems. OGRE will run on Linux and Mac OS X. The program is available as a self-contained executable, or as source code that the user can compile. We are continually updating the code, and hope that people who find it useful will contribute to the development of new features.

Make Movies out of Your Dynamical Simulations with OGRE!

NASA Astrophysics Data System (ADS)

Tamayo, Daniel; Douglas, R. W.; Ge, H. W.; Burns, J. A.

2014-01-01

We have developed OGRE, the Orbital GRaphics Environment, an open-source project comprising a graphical user interface that allows the user to view the output from several dynamical integrators (e.g., SWIFT) that are commonly used for academic work. One can interactively vary the display speed, rotate the view and zoom the camera. This makes OGRE a great tool for students or the general public to explore accurate orbital histories that may display interesting dynamical features, e.g. the destabilization of Solar System orbits under the Nice model, or interacting pairs of exoplanets. Furthermore, OGRE allows the user to choreograph sequences of transformations as the simulation is played to generate movies for use in public talks or professional presentations. The graphical user interface is coded using Qt to ensure portability across different operating systems. OGRE will run on Linux and Mac OS X. The program is available as a self-contained executable, or as source code that the user can compile. We are continually updating the code, and hope that people who find it useful will contribute to the development of new features.

Intra-individual variation in urinary iodine concentration: effect of statistical correction on population distribution using seasonal three-consecutive-day spot urine in children

PubMed Central

Ji, Xiaohong; Liu, Peng; Sun, Zhenqi; Su, Xiaohui; Wang, Wei; Gao, Yanhui; Sun, Dianjun

2016-01-01

Objective To determine the effect of statistical correction for intra-individual variation on estimated urinary iodine concentration (UIC) by sampling on 3 consecutive days in four seasons in children. Setting School-aged children from urban and rural primary schools in Harbin, Heilongjiang, China. Participants 748 and 640 children aged 8–11 years were recruited from urban and rural schools, respectively, in Harbin. Primary and secondary outcome measures The spot urine samples were collected once a day for 3 consecutive days in each season over 1 year. The UIC of the first day was corrected by two statistical correction methods: the average correction method (average of days 1, 2; average of days 1, 2 and 3) and the variance correction method (UIC of day 1 corrected by two replicates and by three replicates). The variance correction method determined the SD between subjects (Sb) and within subjects (Sw), and calculated the correction coefficient (Fi), Fi=Sb/(Sb+Sw/di), where di was the number of observations. The UIC of day 1 was then corrected using the following equation: Results The variance correction methods showed the overall Fi was 0.742 for 2 days’ correction and 0.829 for 3 days’ correction; the values for the seasons spring, summer, autumn and winter were 0.730, 0.684, 0.706 and 0.703 for 2 days’ correction and 0.809, 0.742, 0.796 and 0.804 for 3 days’ correction, respectively. After removal of the individual effect, the correlation coefficient between consecutive days was 0.224, and between non-consecutive days 0.050. Conclusions The variance correction method is effective for correcting intra-individual variation in estimated UIC following sampling on 3 consecutive days in four seasons in children. The method varies little between ages, sexes and urban or rural setting, but does vary between seasons. PMID:26920442

Sustainability of a well-monitored salt iodization program in Iran: marked reduction in goiter prevalence and eventual normalization of urinary iodine concentrations without alteration in iodine content of salt.

PubMed

Azizi, F; Mehran, L; Sheikholeslam, R; Ordookhani, A; Naghavi, M; Hedayati, M; Padyab, M; Mirmiran, P

2008-05-01

Two yr after legislation of salt iodization of 40 parts per million (ppm) in 1994, goiter was still endemic and urinary iodine concentration (UIC) remained elevated in many provinces of Iran. Goiter prevalence and UIC were compared 2 and 7 yr after sustained consumption of uniformly iodized salt by Iranian households. Schoolchildren (7-10 yr) of all provinces were randomly selected by cluster sampling from December 2000 to June 2001. Goiter rate, UIC, and household salt iodine values were compared to those in 1996. Factory salt iodine was also compared in 2001 vs 1996. Ultrasonographically determined thyroid volumes of 7-10 yr old children were compared in 2001 vs 1999. In 2001 (no.=33600) vs 1996 (no.=36178), total, grade 1, and grade 2 goiter rates were 13.9 vs 53.8%, 11.0 vs 44.8%, and 2.9 vs 9.0%, respectively (p<0.0001). Weighted total goiter rate was 9.8% in 2001. Median (range) UIC in 2001 (no.=3329) was 165 (18-499) microg/l and in 1996 (no.=2917) was 205 (10-2300) microg/l (p<0.0001). In 2001 vs 1996, mean+/-SD for iodine salt content was 32.7+/-10.1 vs 33.0+/-10.2 ppm (p=0.68) in households and was 33.2+/-13.4 and 33.8+/-13.2 ppm (p=0.57) in factories, respectively. Among 7-10 yr old children in 2001 (no.=400) vs 1999 (no.=396), only 7-yr-old children in 2001 (the only group with probably no history of iodine deficiency) showed significant smaller thyroid volumes by ultrasonography compared to those in 1999. After 7 yr of optimized iodized-salt supplementation in Iran, adequate UIC values and marked reduction in goiter rate have been achieved.

High prevalence of iodine deficiency in pregnant women living in adequate iodine area

PubMed Central

Mioto, Verônica Carneiro Borges; Monteiro, Ana Carolina de Castro Nassif Gomes; de Camargo, Rosalinda Yossie Asato; Borel, Andréia Rodrigues; Catarino, Regina Maria; Kobayashi, Sergio; Chammas, Maria Cristina; Marui, Suemi

2018-01-01

Objectives Iodine deficiency during pregnancy is associated with obstetric and neonatal adverse outcomes. Serum thyroglobulin (sTg) and thyroid volume (TV) are optional tools to urinary iodine concentration (UIC) for defining iodine status. This cross-sectional study aims to evaluate the iodine status of pregnant women living in iodine-adequate area by spot UIC and correlation with sTg, TV and thyroid function. Methods Two hundred and seventy-three pregnant women were evaluated at three trimesters. All had no previous thyroid disease, no iodine supplementation and negative thyroperoxidase and thyroglobulin antibodies. Thyroid function and sTg were measured using electrochemiluminescence immunoassays. TV was determined by ultrasonography; UIC was determined using a modified Sandell–Kolthoff method. Results Median UIC was 146 µg/L, being 52% iodine deficient and only 4% excessive. TSH values were 1.50 ± 0.92, 1.50 ± 0.92 and 1.91 ± 0.96 mIU/L, respectively, in each trimester (P = 0.001). sTg did not change significantly during trimesters with median 11.2 ng/mL and only 3.3% had above 40 ng/mL. Mean TV was 9.3 ± 3.4 mL, which positively correlated with body mass index, but not with sTg. Only 4.5% presented with goitre. When pregnant women were categorized as iodine deficient (UIC < 150 µg/L), adequate (≥150 and <250 µg/L) and excessive (≥250 µg/L), sTg, thyroid hormones and TV at each trimester showed no statistical differences. Conclusions Iodine deficiency was detected frequently in pregnant women living in iodine-adequate area. sTg concentration and TV did not correlate to UIC. Our observation also demonstrated that the Brazilian salt-iodization programme prevents deficiency, but does not maintain iodine status within adequate and recommended ranges for pregnant women. PMID:29700098

High prevalence of iodine deficiency in pregnant women living in adequate iodine area.

PubMed

Mioto, Verônica Carneiro Borges; Monteiro, Ana Carolina de Castro Nassif Gomes; de Camargo, Rosalinda Yossie Asato; Borel, Andréia Rodrigues; Catarino, Regina Maria; Kobayashi, Sergio; Chammas, Maria Cristina; Marui, Suemi

2018-05-01

Iodine deficiency during pregnancy is associated with obstetric and neonatal adverse outcomes. Serum thyroglobulin (sTg) and thyroid volume (TV) are optional tools to urinary iodine concentration (UIC) for defining iodine status. This cross-sectional study aims to evaluate the iodine status of pregnant women living in iodine-adequate area by spot UIC and correlation with sTg, TV and thyroid function. Two hundred and seventy-three pregnant women were evaluated at three trimesters. All had no previous thyroid disease, no iodine supplementation and negative thyroperoxidase and thyroglobulin antibodies. Thyroid function and sTg were measured using electrochemiluminescence immunoassays. TV was determined by ultrasonography; UIC was determined using a modified Sandell-Kolthoff method. Median UIC was 146 µg/L, being 52% iodine deficient and only 4% excessive. TSH values were 1.50 ± 0.92, 1.50 ± 0.92 and 1.91 ± 0.96 mIU/L, respectively, in each trimester ( P  = 0.001). sTg did not change significantly during trimesters with median 11.2 ng/mL and only 3.3% had above 40 ng/mL. Mean TV was 9.3 ± 3.4 mL, which positively correlated with body mass index, but not with sTg. Only 4.5% presented with goitre.When pregnant women were categorized as iodine deficient (UIC < 150 µg/L), adequate (≥150 and <250 µg/L) and excessive (≥250 µg/L), sTg, thyroid hormones and TV at each trimester showed no statistical differences. Iodine deficiency was detected frequently in pregnant women living in iodine-adequate area. sTg concentration and TV did not correlate to UIC. Our observation also demonstrated that the Brazilian salt-iodization programme prevents deficiency, but does not maintain iodine status within adequate and recommended ranges for pregnant women. © 2018 The authors.

Development of a platform-independent receiver control system for SISIFOS

NASA Astrophysics Data System (ADS)

Lemke, Roland; Olberg, Michael

1998-05-01

Up to now receiver control software was a time consuming development usually written by receiver engineers who had mainly the hardware in mind. We are presenting a low-cost and very flexible system which uses a minimal interface to the real hardware, and which makes it easy to adapt to new receivers. Our system uses Tcl/Tk as a graphical user interface (GUI), SpecTcl as a GUI builder, Pgplot as plotting software, a simple query language (SQL) database for information storage and retrieval, Ethernet socket to socket communication and SCPI as a command control language. The complete system is in principal platform independent but for cost saving reasons we are using it actually on a PC486 running Linux 2.0.30, which is a copylefted Unix. The only hardware dependent part are the digital input/output boards, analog to digital and digital to analog convertors. In the case of the Linux PC we are using a device driver development kit to integrate the boards fully into the kernel of the operating system, which indeed makes them look like an ordinary device. The advantage of this system is firstly the low price and secondly the clear separation between the different software components which are available for many operating systems. If it is not possible, due to CPU performance limitations, to run all the software in a single machine,the SQL-database or the graphical user interface could be installed on separate computers.

A New Generation of Real-Time Systems in the JET Tokamak

NASA Astrophysics Data System (ADS)

Alves, Diogo; Neto, Andre C.; Valcarcel, Daniel F.; Felton, Robert; Lopez, Juan M.; Barbalace, Antonio; Boncagni, Luca; Card, Peter; De Tommasi, Gianmaria; Goodyear, Alex; Jachmich, Stefan; Lomas, Peter J.; Maviglia, Francesco; McCullen, Paul; Murari, Andrea; Rainford, Mark; Reux, Cedric; Rimini, Fernanda; Sartori, Filippo; Stephen, Adam V.; Vega, Jesus; Vitelli, Riccardo; Zabeo, Luca; Zastrow, Klaus-Dieter

2014-04-01

Recently, a new recipe for developing and deploying real-time systems has become increasingly adopted in the JET tokamak. Powered by the advent of x86 multi-core technology and the reliability of JET's well established Real-Time Data Network (RTDN) to handle all real-time I/O, an official Linux vanilla kernel has been demonstrated to be able to provide real-time performance to user-space applications that are required to meet stringent timing constraints. In particular, a careful rearrangement of the Interrupt ReQuests' (IRQs) affinities together with the kernel's CPU isolation mechanism allows one to obtain either soft or hard real-time behavior depending on the synchronization mechanism adopted. Finally, the Multithreaded Application Real-Time executor (MARTe) framework is used for building applications particularly optimised for exploring multi-core architectures. In the past year, four new systems based on this philosophy have been installed and are now part of JET's routine operation. The focus of the present work is on the configuration aspects that enable these new systems' real-time capability. Details are given about the common real-time configuration of these systems, followed by a brief description of each system together with results regarding their real-time performance. A cycle time jitter analysis of a user-space MARTe based application synchronizing over a network is also presented. The goal is to compare its deterministic performance while running on a vanilla and on a Messaging Real time Grid (MRG) Linux kernel.

MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters.

PubMed

Abreu, Rui Mv; Froufe, Hugo Jc; Queiroz, Maria João Rp; Ferreira, Isabel Cfr

2010-10-28

Virtual screening of small molecules using molecular docking has become an important tool in drug discovery. However, large scale virtual screening is time demanding and usually requires dedicated computer clusters. There are a number of software tools that perform virtual screening using AutoDock4 but they require access to dedicated Linux computer clusters. Also no software is available for performing virtual screening with Vina using computer clusters. In this paper we present MOLA, an easy-to-use graphical user interface tool that automates parallel virtual screening using AutoDock4 and/or Vina in bootable non-dedicated computer clusters. MOLA automates several tasks including: ligand preparation, parallel AutoDock4/Vina jobs distribution and result analysis. When the virtual screening project finishes, an open-office spreadsheet file opens with the ligands ranked by binding energy and distance to the active site. All results files can automatically be recorded on an USB-flash drive or on the hard-disk drive using VirtualBox. MOLA works inside a customized Live CD GNU/Linux operating system, developed by us, that bypass the original operating system installed on the computers used in the cluster. This operating system boots from a CD on the master node and then clusters other computers as slave nodes via ethernet connections. MOLA is an ideal virtual screening tool for non-experienced users, with a limited number of multi-platform heterogeneous computers available and no access to dedicated Linux computer clusters. When a virtual screening project finishes, the computers can just be restarted to their original operating system. The originality of MOLA lies on the fact that, any platform-independent computer available can he added to the cluster, without ever using the computer hard-disk drive and without interfering with the installed operating system. With a cluster of 10 processors, and a potential maximum speed-up of 10x, the parallel algorithm of MOLA performed with a speed-up of 8,64× using AutoDock4 and 8,60× using Vina.

A Guidance Document for Kentucky's Oil and Gas Operators

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

Bender, Rick

The accompanying report, manual and assimilated data represent the initial preparation for submission of an Application for Primacy under the Class II Underground Injection Control (UIC) program on behalf of the Commonwealth of Kentucky. The purpose of this study was to identify deficiencies in Kentucky law and regulation that would prevent the Kentucky Division of Oil and Gas from receiving approval of primacy of the UIC program, currently under control of the United States Environmental Protection Agency (EPA) in Atlanta, Georgia.

A Design and Development of Multi-Purpose CCD Camera System with Thermoelectric Cooling: Software

NASA Astrophysics Data System (ADS)

Oh, S. H.; Kang, Y. W.; Byun, Y. I.

2007-12-01

We present a software which we developed for the multi-purpose CCD camera. This software can be used on the all 3 types of CCD - KAF-0401E (768×512), KAF-1602E (15367times;1024), KAF-3200E (2184×1472) made in KODAK Co.. For the efficient CCD camera control, the software is operated with two independent processes of the CCD control program and the temperature/shutter operation program. This software is designed to fully automatic operation as well as manually operation under LINUX system, and is controled by LINUX user signal procedure. We plan to use this software for all sky survey system and also night sky monitoring and sky observation. As our results, the read-out time of each CCD are about 15sec, 64sec, 134sec for KAF-0401E, KAF-1602E, KAF-3200E., because these time are limited by the data transmission speed of parallel port. For larger format CCD, the data transmission is required more high speed. we are considering this control software to one using USB port for high speed data transmission.

I/O performance evaluation of a Linux-based network-attached storage device

NASA Astrophysics Data System (ADS)

Sun, Zhaoyan; Dong, Yonggui; Wu, Jinglian; Jia, Huibo; Feng, Guanping

2002-09-01

In a Local Area Network (LAN), clients are permitted to access the files on high-density optical disks via a network server. But the quality of read service offered by the conventional server is not satisfied because of the multiple functions on the server and the overmuch caller. This paper develops a Linux-based Network-Attached Storage (NAS) server. The Operation System (OS), composed of an optimized kernel and a miniaturized file system, is stored in a flash memory. After initialization, the NAS device is connected into the LAN. The administrator and users could configure the access the server through the web page respectively. In order to enhance the quality of access, the management of buffer cache in file system is optimized. Some benchmark programs are peformed to evaluate the I/O performance of the NAS device. Since data recorded in optical disks are usually for reading accesses, our attention is focused on the reading throughput of the device. The experimental results indicate that the I/O performance of our NAS device is excellent.

Open Technologies at Athabasca University's Geospace Observatories

NASA Astrophysics Data System (ADS)

Connors, M. G.; Schofield, I. S.

2012-12-01

Athabasca University Geophysical Observatories feature two auroral observation sites situated in the subauroral zone of western Canada, separated by approximately 25 km. These sites are both on high-speed internet and ideal for observing phenomena detectable from this latitude, which include noctilucent clouds, meteors, and magnetic and optical aspects of the aurora. General aspects of use of Linux in observatory management are described, with emphasis on recent imaging projects involving control of high resolution digital SLR cameras at low cadence, and inexpensive white light analog video cameras at 30 Hz. Linux shell scripts are extensively used, with image capture controlled by gphoto2, the ivtv-utils package, x264 video coding library, and ffmpeg. Imagemagick allows processing of images in an automated fashion. Image archives and movies are created and can be correlated with magnetic data. Much of the magnetic data stream also uses GMT (Generic Mapping Tools) within shell scripts for display. Additionally, SPASE metadata are generated for most of the magnetic data, thus allowing users of our AUTUMN magnetic data repository to perform SPASE queries on the dataset. Visualization products from our twin observatories will be presented.

Development of a User Interface for a Regression Analysis Software Tool

NASA Technical Reports Server (NTRS)

Ulbrich, Norbert Manfred; Volden, Thomas R.

2010-01-01

An easy-to -use user interface was implemented in a highly automated regression analysis tool. The user interface was developed from the start to run on computers that use the Windows, Macintosh, Linux, or UNIX operating system. Many user interface features were specifically designed such that a novice or inexperienced user can apply the regression analysis tool with confidence. Therefore, the user interface s design minimizes interactive input from the user. In addition, reasonable default combinations are assigned to those analysis settings that influence the outcome of the regression analysis. These default combinations will lead to a successful regression analysis result for most experimental data sets. The user interface comes in two versions. The text user interface version is used for the ongoing development of the regression analysis tool. The official release of the regression analysis tool, on the other hand, has a graphical user interface that is more efficient to use. This graphical user interface displays all input file names, output file names, and analysis settings for a specific software application mode on a single screen which makes it easier to generate reliable analysis results and to perform input parameter studies. An object-oriented approach was used for the development of the graphical user interface. This choice keeps future software maintenance costs to a reasonable limit. Examples of both the text user interface and graphical user interface are discussed in order to illustrate the user interface s overall design approach.

Excessive iodine intake does not increase the recurrence rate of graves' disease after withdrawal of the antithyroid drug in an iodine-replete area.

PubMed

Park, Sun Mi; Cho, Yoon Young; Joung, Ji Young; Sohn, Seo Young; Kim, Sun Wook; Chung, Jae Hoon

2015-03-01

The relationship between iodine intake and effects of antithyroid drugs (ATD) for Graves' disease, especially in iodine-deficient areas, has been demonstrated in many studies. However, it was not clear how chronic high iodine intake influenced the effectiveness of ATD in an iodine-replete area. This study aimed to clarify the effect of iodine intake on clinical outcomes of Graves' disease after discontinuation of ATD in Korea, an iodine-replete area. A total of 142 patients with Graves' disease who visited the outpatient clinic regularly and stopped their ATD between October 2011 and April 2013 were enrolled in our study. Urinary iodine concentration (UIC) was measured just before and after the discontinuation of ATD. Median UIC was not significantly different between the remission and relapse groups, as well as among the four treatment groups (group 1, remission after initial treatment; group 2, remission after repeated treatment; group 3, early relapse within a year; group 4, late relapse after a year). Remission rates did not show a significant difference between the excessive iodine intake (UIC ≥300 μg/l) and average iodine intake groups (UIC <300 μg/l). The present study suggests that excessive iodine intake does not have an effect on the clinical outcomes of Graves' disease in an iodine-replete area, and therefore diet control with iodine restriction might not be necessary in the management of Graves' disease.

Excessive Iodine Intake Does Not Increase the Recurrence Rate of Graves' Disease after Withdrawal of the Antithyroid Drug in an Iodine-Replete Area

PubMed Central

Park, Sun Mi; Cho, Yoon Young; Joung, Ji Young; Sohn, Seo Young; Kim, Sun Wook; Chung, Jae Hoon

2015-01-01

Background and Objectives The relationship between iodine intake and effects of antithyroid drugs (ATD) for Graves' disease, especially in iodine-deficient areas, has been demonstrated in many studies. However, it was not clear how chronic high iodine intake influenced the effectiveness of ATD in an iodine-replete area. This study aimed to clarify the effect of iodine intake on clinical outcomes of Graves' disease after discontinuation of ATD in Korea, an iodine-replete area. Methods A total of 142 patients with Graves' disease who visited the outpatient clinic regularly and stopped their ATD between October 2011 and April 2013 were enrolled in our study. Urinary iodine concentration (UIC) was measured just before and after the discontinuation of ATD. Results Median UIC was not significantly different between the remission and relapse groups, as well as among the four treatment groups (group 1, remission after initial treatment; group 2, remission after repeated treatment; group 3, early relapse within a year; group 4, late relapse after a year). Remission rates did not show a significant difference between the excessive iodine intake (UIC ≥300 μg/l) and average iodine intake groups (UIC <300 μg/l). Conclusions The present study suggests that excessive iodine intake does not have an effect on the clinical outcomes of Graves' disease in an iodine-replete area, and therefore diet control with iodine restriction might not be necessary in the management of Graves' disease. PMID:25960960

Reduced Educational Outcomes Persist into Adolescence Following Mild Iodine Deficiency in Utero, Despite Adequacy in Childhood: 15-Year Follow-Up of the Gestational Iodine Cohort Investigating Auditory Processing Speed and Working Memory.

PubMed

Hynes, Kristen L; Otahal, Petr; Burgess, John R; Oddy, Wendy H; Hay, Ian

2017-12-13

There is increasing evidence that even mild gestational iodine deficiency (GID) results in adverse neurocognitive impacts on offspring. It's unclear, however, if these persist long-term and whether they can be ameliorated by iodine sufficiency in childhood. We followed a unique cohort (Gestational Iodine Cohort, n = 266) where gestation occurred during a period of mild population iodine deficiency, with children subsequently growing-up in an iodine replete environment. We investigated whether associations between mild GID and reductions in literacy outcomes, observed at age 9-years, persisted into adolescence. Comparisons were made between offspring of mothers with gestational urinary iodine concentrations (UICs) ≥ 150 μg/L and < 150 μg/L. Educational outcomes were measured using Australian National Assessment Program-Literacy and Numeracy (NAPLAN) tests. Children whose mothers had UICs < 150 μg/L exhibited persistent reductions in spelling from Year 3 (10%, -41.4 points (95% Confidence Interval -65.1 to -17.6, p = 0.001)) to Year 9 (5.6%, -31.6 (-57.0 to -6.2, p = 0.015)) compared to children whose mothers had UICs ≥ 150 μg/L. Associations remained after adjustment for biological factors, socioeconomic status and adolescent UIC. Results support the hypothesis that mild GID may impact working memory and auditory processing speed. The findings have important public health implications for management of iodine nutrition in pregnancy.

Building CHAOS: An Operating System for Livermore Linux Clusters

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

Garlick, J E; Dunlap, C M

2003-02-21

The Livermore Computing (LC) Linux Integration and Development Project (the Linux Project) produces and supports the Clustered High Availability Operating System (CHAOS), a cluster operating environment based on Red Hat Linux. Each CHAOS release begins with a set of requirements and ends with a formally tested, packaged, and documented release suitable for use on LC's production Linux clusters. One characteristic of CHAOS is that component software packages come from different sources under varying degrees of project control. Some are developed by the Linux Project, some are developed by other LC projects, some are external open source projects, and some aremore » commercial software packages. A challenge to the Linux Project is to adhere to release schedules and testing disciplines in a diverse, highly decentralized development environment. Communication channels are maintained for externally developed packages in order to obtain support, influence development decisions, and coordinate/understand release schedules. The Linux Project embraces open source by releasing locally developed packages under open source license, by collaborating with open source projects where mutually beneficial, and by preferring open source over proprietary software. Project members generally use open source development tools. The Linux Project requires system administrators and developers to work together to resolve problems that arise in production. This tight coupling of production and development is a key strategy for making a product that directly addresses LC's production requirements. It is another challenge to balance support and development activities in such a way that one does not overwhelm the other.« less

Development of an Autonomous Navigation Technology Test Vehicle

DTIC Science & Technology

2004-08-01

as an independent thread on processors using the Linux operating system. The computer hardware selected for the nodes that host the MRS threads...communications system design. Linux was chosen as the operating system for all of the single board computers used on the Mule. Linux was specifically...used for system analysis and development. The simple realization of multi-thread processing and inter-process communications in Linux made it a

SUFFICIENT IODINE INTAKE IN SCHOOLCHILDREN FROM THE ZAGREB AREA: ASSESSMENT WITH DRIED BLOD SPOT THYROGLOBULIN AS A NEW FUNCTIONAL BIOMARKER FOR IODINE DEFICIENCY.

PubMed

Jukić, Tomislav; Zimmermann, Michael Bruce; Granić, Roko; Prpić, Marin; Krilić, Drazena; Juresa, Vesna; Katalenić, Marijan; Kusić, Zvonko

2015-12-01

Current methods for assessment of iodine intake in a population comprise measurements of urinary iodine concentration (UIC), thyroid volume by ultrasound (US-Tvol), and newborn TSH. Serum or dried blood spot thyroglobulin (DBS-Tg) is a new promising functional iodine status biomarker in children. In 1996, a new act on universal salt iodination was introduced in Croatia with 25 mg of potassium iodideper kg of salt. In 2002, Croatia finally reached iodine sufficiency. However, in 2009, median UIC in 101 schoolchildren from Zagreb, the capital of Croatia, was 288 µg/L, posing to be excessive. The aim of the study was to assess iodine intake in schoolchildren from the Zagreb area and to evaluate the value of DBS-Tg in schoolchildren as a new functional biomarker of iodine deficiency (and iodine excess). The study was part of a large international study in 6- to 12-year-old children supported by UNICEF, the Swiss Federal Institute of Technology (ETH Zurich) and the International Council for the Control of Iodine Deficiency Disorders (ICCIDD). According to international study results, the median cut-off Tg < 13 µg/L and/or < 3% Tg values > 40 µg/L indicate iodine sufficiency. The study included 159 schoolchildren (median age 9.1 ± 1.4 years) from Zagreb and a nearby small town of Jastrebarsko with measurements of UIC, US-Tvol, DBS-Tg, T4, TSH and iodine content in salt from households of schoolchildren (KI/kg of salt). Overall median UIC was 205 µg/L (range 1-505 µg/L). Thyroid volumes in schoolchildren measured by US were within the normal range according to reference values. Median DBS-Tg in schoolchildren was 12.1 µg/L with 3% of Tg values > 40 µg/L. High Tg values were in the UIC range < 50 µg/L and > 300 µg/L (U-shaped curve of Tg plotted against UIC). All children were euthyroid with geometric mean TSH 0.7 ± 0.3 mU/L and arithmetic mean T4 62 ± 12.5 nmol/L. The mean KI content per kg of salt was 24.9 ± 3.1 mg/kg (range 19-36 mg/kg). Study results indicated iodine sufficiency in schoolchildren from the Zagreb area. Thyroglobulin proved to be a sensitive indicator of both iodine deficiency and iodine excess in children. Iodine content in salt from households of schoolchildren was in good compliance with the Croatian act (20-30 mg KI/kg of salt).

Evaluation of efficacy of iodine prophylaxis in Poland based on the examination of schoolchildren living in Opoczno Town (Lodz Voivodship).

PubMed

Zygmunt, Arkadiusz; Adamczewski, Zbigniew; Wojciechowska-Durczyńska, Katarzyna; Cyniak-Magierska, Anna; Krawczyk-Rusiecka, Kinga; Zygmunt, Agnieszka; Karbownik-Lewińska, Małgorzata; Lewiński, Andrzej

2012-12-22

In 1997 a currently obligatory model of iodine prophylaxis, based on mandatory iodization of household salt with 30 mg KI/kg, was introduced. The aim of our study was to assess the iodine intake among school-age children living in Opoczno in 3 subsequent time points - in 1994, before establishment of currently operating model of iodine prophylaxis, in 1999 - 2 years after implementation of iodine prophylaxis and in 2010, - 14 years after its implementation. We assessed goitre incidence and urine iodine concentration (UIC) in 104 children in 1994, 207 children in 1999 and 174 children in 2012. Age of examined children ranged from 6 to 15 years. The thyroid volumes evaluated by ultrasound were compared to reference values for thyroid volume proposed by Zimmermann at al. Moreover, we have introduced a new index - V/BSA ratio (comparison of thyroid volume to the body surface area), which to our belief allows for more accurate assessment of thyroid volume. The median of UICs was 45.5 μg/L (1994), 101.1 μg/L (1999) and 100.6 μg/L (2010). The distribution of obtained results has changed as well - iodine concentrations below 50 μg/L were present in 59.1% children in 1994, in 12.6% children - in 1999 and in 7.1% children - in 2010.Although a significant decrease in goitre incidence with regard to age - 92.6% (1994) vs 18.5% (1999) and 15.8% (2010), as well as with regard to BSA - 95.4% (1994) vs 15.2% (1999) and 11.6% (2010) was observed, it still points to the iodine deficiency, which is in contradiction with UICs as they are within normal limits. V/BSA ratio avoids such discrepancy. The values of ratio V/BSA were higher in 1994 (7.079 ± 2.775) than in 1999 (2.935 ± 1.112) (p<0.05) and in 2010 (2.846 ± 1.029) (p<0.05). Hitherto model of iodine prophylaxis has proved to be effective in eliminating the iodine deficiency. The iodine intake is now more even, homogenous, which translates into smaller scatter of UICs and less percentage of children, in whom UIC is less than 50 μg/L. However, the iodine intake only slightly exceeds the recommended values, so median of UICs oscillates around the lower limit of references values.

Evaluation of efficacy of iodine prophylaxis in Poland based on the examination of schoolchildren living in Opoczno Town (Lodz Voivodship)

PubMed Central

2012-01-01

Background In 1997 a currently obligatory model of iodine prophylaxis, based on mandatory iodization of household salt with 30 mg KI/kg, was introduced. The aim of our study was to assess the iodine intake among school-age children living in Opoczno in 3 subsequent time points – in 1994, before establishment of currently operating model of iodine prophylaxis, in 1999 – 2 years after implementation of iodine prophylaxis and in 2010, – 14 years after its implementation. Methods We assessed goitre incidence and urine iodine concentration (UIC) in 104 children in 1994, 207 children in 1999 and 174 children in 2012. Age of examined children ranged from 6 to 15 years. The thyroid volumes evaluated by ultrasound were compared to reference values for thyroid volume proposed by Zimmermann at al. Moreover, we have introduced a new index – V/BSA ratio (comparison of thyroid volume to the body surface area), which to our belief allows for more accurate assessment of thyroid volume. Results The median of UICs was 45.5 μg/L (1994), 101.1 μg/L (1999) and 100.6 μg/L (2010). The distribution of obtained results has changed as well – iodine concentrations below 50 μg/L were present in 59.1% children in 1994, in 12.6% children – in 1999 and in 7.1% children – in 2010. Although a significant decrease in goitre incidence with regard to age – 92.6% (1994) vs 18.5% (1999) and 15.8% (2010), as well as with regard to BSA – 95.4% (1994) vs 15.2% (1999) and 11.6% (2010) was observed, it still points to the iodine deficiency, which is in contradiction with UICs as they are within normal limits. V/BSA ratio avoids such discrepancy. The values of ratio V/BSA were higher in 1994 (7.079 ± 2.775) than in 1999 (2.935 ± 1.112) (p<0.05) and in 2010 (2.846 ± 1.029) (p<0.05). Conclusions Hitherto model of iodine prophylaxis has proved to be effective in eliminating the iodine deficiency. The iodine intake is now more even, homogenous, which translates into smaller scatter of UICs and less percentage of children, in whom UIC is less than 50 μg/L. However, the iodine intake only slightly exceeds the recommended values, so median of UICs oscillates around the lower limit of references values. PMID:23259538

Urinary iodine excretion (UIE) estimated by iodine/creatinine ratio from spot urine in Chinese school-age children.

PubMed

Chen, Wen; Li, Xiang; Guo, Xiaohui; Shen, Jun; Tan, Long; Lin, Laixiang; Wu, Yalan; Wang, Wei; Wang, Wenqiang; Bian, Jianchao; Zhang, Wanqi

2017-04-01

To assess the validity of urinary iodine excretion (UIE) estimated by urinary iodine/creatinine ratio (UI/Cr) from spot urines in Chinese school-age children. A cross-sectional survey was performed in which twice-repeated collections of 24-h urine, and spot urine samples were obtained within 1 month. Urinary iodine concentration (UIC), urinary creatinine concentration (UCr), urine volume (Uvol) of spot and 24-h urine samples were measured. Measured 24-h UIE was calculated from 24-h UIC multiplied by 24-h Uvol, while the estimated 24-h UIE was calculated from spot UI/Cr multiplied by 24-h urinary creatinine excretion (24-h UCrE). No significant difference was observed in 24-h Uvol between two repeated collections (P = 0·70), while spot UIC, 24-h UIC, spot UI/Cr and measured 24-h UIE were significantly different (P < 0·05). The estimated 24-h UIE was 247 (136-431) μg/day in the first collection, lower than the measured 24-h UIE of 329 (183-536) μg/day (P < 0·001), while no significant difference was observed (P = 0·30) in the second sampling as the estimated 24-h UIE was 355 (168-624) μg/day and the measured 24-h UIE 350 (181-615) μg/day. The spot UIC (r = 0·57, P < 0·001), spot UI/Cr (r = 0·63, P < 0·001) and the estimated 24-h UIE (r = 0·83, P < 0·001) were strongly correlated with the measured 24-h UIE in the first collection. Likewise, in the second sampling, spot UIC (r = 0·60, P < 0·001), spot UI/Cr (r = 0·72, P < 0·001) and the estimated 24-h UIE (r = 0·89, P < 0·001) were also correlated with measured 24-h UIE. The Bland-Altman results indicated 95% of subjects were expected to locate within the limits of agreement (LOA), but showed an underestimation of the urinary iodine excretion by the estimated 24-h UIE. In addition, moderate-to-good agreement was found for the estimated and measured 24-h UIE, with kappa values of 0·55 and 0·66. Estimated 24-h UIE by UI/Cr ratio from spot urine could represent a valid and reliable alternative for measured 24-h UIE in estimating iodine excretion in children. © 2016 John Wiley & Sons Ltd.

Space Communications Emulation Facility

NASA Technical Reports Server (NTRS)

Hill, Chante A.

2004-01-01

Establishing space communication between ground facilities and other satellites is a painstaking task that requires many precise calculations dealing with relay time, atmospheric conditions, and satellite positions, to name a few. The Space Communications Emulation Facility (SCEF) team here at NASA is developing a facility that will approximately emulate the conditions in space that impact space communication. The emulation facility is comprised of a 32 node distributed cluster of computers; each node representing a satellite or ground station. The objective of the satellites is to observe the topography of the Earth (water, vegetation, land, and ice) and relay this information back to the ground stations. Software originally designed by the University of Kansas, labeled the Emulation Manager, controls the interaction of the satellites and ground stations, as well as handling the recording of data. The Emulation Manager is installed on a Linux Operating System, employing both Java and C++ programming codes. The emulation scenarios are written in extensible Markup Language, XML. XML documents are designed to store, carry, and exchange data. With XML documents data can be exchanged between incompatible systems, which makes it ideal for this project because Linux, MAC and Windows Operating Systems are all used. Unfortunately, XML documents cannot display data like HTML documents. Therefore, the SCEF team uses XML Schema Definition (XSD) or just schema to describe the structure of an XML document. Schemas are very important because they have the capability to validate the correctness of data, define restrictions on data, define data formats, and convert data between different data types, among other things. At this time, in order for the Emulation Manager to open and run an XML emulation scenario file, the user must first establish a link between the schema file and the directory under which the XML scenario files are saved. This procedure takes place on the command line on the Linux Operating System. Once this link has been established the Emulation manager validates all the XML files in that directory against the schema file, before the actual scenario is run. Using some very sophisticated commercial software called the Satellite Tool Kit (STK) installed on the Linux box, the Emulation Manager is able to display the data and graphics generated by the execution of a XML emulation scenario file. The Emulation Manager software is written in JAVA programming code. Since the SCEF project is in the developmental stage, the source code for this type of software is being modified to better fit the requirements of the SCEF project. Some parameters for the emulation are hard coded, set at fixed values. Members of the SCEF team are altering the code to allow the user to choose the values of these hard coded parameters by inserting a toolbar onto the preexisting GUI.

Simple Linux Utility for Resource Management

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

Jette, M.

2009-09-09

SLURM is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for large and small computer clusters. As a cluster resource manager, SLURM has three key functions. First, it allocates exclusive and/or non exclusive access to resources (compute nodes) to users for some duration of time so they can perform work. Second, it provides a framework for starting, executing, and monitoring work (normally a parallel job) on the set of allciated nodes. Finally, it arbitrates conflicting requests for resouces by managing a queue of pending work.

AdvoCATE - User Guide

NASA Technical Reports Server (NTRS)

Denney, Ewen W.

2015-01-01

The basic vision of AdvoCATE is to automate the creation, manipulation, and management of large-scale assurance cases based on a formal theory of argument structures. Its main purposes are for creating and manipulating argument structures for safety assurance cases using the Goal Structuring Notation (GSN), and as a test bed and proof-of-concept for the formal theory of argument structures. AdvoCATE is available for Windows 7, Macintosh OSX, and Linux. Eventually, AdvoCATE will serve as a dashboard for safety related information and provide an infrastructure for safety decisions and management.

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

PubMed

Kumar, Sudhir; Stecher, Glen; Li, Michael; Knyaz, Christina; Tamura, Koichiro

2018-06-01

The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

Comparative visualization of genetic and physical maps with Strudel

PubMed Central

Bayer, Micha; Milne, Iain; Stephen, Gordon; Shaw, Paul; Cardle, Linda; Wright, Frank; Marshall, David

2011-01-01

Summary: Data visualization can play a key role in comparative genomics, for example, underpinning the investigation of conserved synteny patterns. Strudel is a desktop application that allows users to easily compare both genetic and physical maps interactively and efficiently. It can handle large datasets from several genomes simultaneously, and allows all-by-all comparisons between these. Availability and implementation: Installers for Strudel are available for Windows, Linux, Solaris and Mac OS X at http://bioinf.scri.ac.uk/strudel/. Contact: strudel@scri.ac.uk; micha.bayer@scri.ac.uk PMID:21372085

Turning a remotely controllable observatory into a fully autonomous system

NASA Astrophysics Data System (ADS)

Swindell, Scott; Johnson, Chris; Gabor, Paul; Zareba, Grzegorz; Kubánek, Petr; Prouza, Michael

2014-08-01

We describe a complex process needed to turn an existing, old, operational observatory - The Steward Observatory's 61" Kuiper Telescope - into a fully autonomous system, which observers without an observer. For this purpose, we employed RTS2,1 an open sourced, Linux based observatory control system, together with other open sourced programs and tools (GNU compilers, Python language for scripting, JQuery UI for Web user interface). This presentation provides a guide with time estimates needed for a newcomers to the field to handle such challenging tasks, as fully autonomous observatory operations.

The EPICS-based remote control system for muon beam line devices at J-PARC MUSE

NASA Astrophysics Data System (ADS)

Ito, T. U.; Nakahara, K.; Kawase, M.; Fujimori, H.; Kobayashi, Y.; Higemoto, W.; Miyake, Y.

2010-04-01

The remote control system for muon beam line devices of J-PARC MUSE has been developed with the Experimental Physics and Industrial Control System (EPICS). The EPICS input/output controller was installed in standard Linux PCs for slow control of the devices. Power supplies for 21 magnetic elements and four slit controllers for the decay-surface muon beam line in the Materials and Life Science Experimental Facility are now accessible via Ethernet from a graphical user interface which has been composed using the Motif Editor and Display Manger.

Estimating aquifer transmissivity from specific capacity using MATLAB.

PubMed

McLin, Stephen G

2005-01-01

Historically, specific capacity information has been used to calculate aquifer transmissivity when pumping test data are unavailable. This paper presents a simple computer program written in the MATLAB programming language that estimates transmissivity from specific capacity data while correcting for aquifer partial penetration and well efficiency. The program graphically plots transmissivity as a function of these factors so that the user can visually estimate their relative importance in a particular application. The program is compatible with any computer operating system running MATLAB, including Windows, Macintosh OS, Linux, and Unix. Two simple examples illustrate program usage.

Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows.

PubMed

Specht, Michael; Kuhlgert, Sebastian; Fufezan, Christian; Hippler, Michael

2011-04-15

We present Proteomatic, an operating system independent and user-friendly platform that enables the construction and execution of MS/MS data evaluation pipelines using free and commercial software. Required external programs such as for peptide identification are downloaded automatically in the case of free software. Due to a strict separation of functionality and presentation, and support for multiple scripting languages, new processing steps can be added easily. Proteomatic is implemented in C++/Qt, scripts are implemented in Ruby, Python and PHP. All source code is released under the LGPL. Source code and installers for Windows, Mac OS X, and Linux are freely available at http://www.proteomatic.org. michael.specht@uni-muenster.de Supplementary data are available at Bioinformatics online.

Integrating a Trusted Computing Base Extension Server and Secure Session Server into the LINUX Operating System

DTIC Science & Technology

2001-09-01

Readily Available Linux has been copyrighted under the terms of the GNU General Public 5 License (GPL)1. This is a license written by the Free...GNOME and KDE . d. Portability Linux is highly compatible with many common operating systems. For...using suitable libraries, Linux is able to run programs written for other operating systems. [Ref. 8] 1 The GNU Project is coordinated by the

Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking.

PubMed

McMurdie, Paul J; Holmes, Susan

2015-01-15

We have created a Shiny-based Web application, called Shiny-phyloseq, for dynamic interaction with microbiome data that runs on any modern Web browser and requires no programming, increasing the accessibility and decreasing the entrance requirement to using phyloseq and related R tools. Along with a data- and context-aware dynamic interface for exploring the effects of parameter and method choices, Shiny-phyloseq also records the complete user input and subsequent graphical results of a user's session, allowing the user to archive, share and reproduce the sequence of steps that created their result-without writing any new code themselves. Shiny-phyloseq is implemented entirely in the R language. It can be hosted/launched by any system with R installed, including Windows, Mac OS and most Linux distributions. Information technology administrators can also host Shiny--phyloseq from a remote server, in which case users need only have a Web browser installed. Shiny-phyloseq is provided free of charge under a GPL-3 open-source license through GitHub at http://joey711.github.io/shiny-phyloseq/. © The Author 2014. Published by Oxford University Press.

Multichannel Networked Phasemeter Readout and Analysis

NASA Technical Reports Server (NTRS)

Edmonds, Karina

2008-01-01

Netmeter software reads a data stream from up to 250 networked phasemeters, synchronizes the data, saves the reduced data to disk (after applying a low-pass filter), and provides a Web server interface for remote control. Unlike older phasemeter software that requires a special, real-time operating system, this program can run on any general-purpose computer. It needs about five percent of the CPU (central processing unit) to process 20 channels because it adds built-in data logging and network-based GUIs (graphical user interfaces) that are implemented in Scalable Vector Graphics (SVG). Netmeter runs on Linux and Windows. It displays the instantaneous displacements measured by several phasemeters at a user-selectable rate, up to 1 kHz. The program monitors the measure and reference channel frequencies. For ease of use, levels of status in Netmeter are color coded: green for normal operation, yellow for network errors, and red for optical misalignment problems. Netmeter includes user-selectable filters up to 4 k samples, and user-selectable averaging windows (after filtering). Before filtering, the program saves raw data to disk using a burst-write technique.

Current iodine nutrition status and progress toward elimination of iodine deficiency disorders in Jazan, Saudi Arabia

PubMed Central

2012-01-01

Background The term iodine deficiency disorders (IDD) refers to all the effects of iodine deficiency on growth and development in human and animal populations that can be prevented by correction of the iodine deficiency. The objective of this paper was to determine the iodine nutrition status among schoolchildren in the Jazan Region of the Kingdom of Saudi Arabia (KSA), by measuring urinary iodine concentrations and by clinical assessments of goiter rate. Methods A school-based cross-sectional survey was conducted in the Jazan region of southwestern KSA from May to November 2010. A total of 311 children, aged 6–13 years, drawn from 12 schools, were selected by a three-stage cluster random sampling method. Data on sociodemographic characteristics were collected using a structured questionnaire. Urine samples were collected and physical examinations were conducted to determine the presence or absence of goiter. Data were analyzed using SPSS version 17.0. Chi square and independent t-tests were used for proportions and mean comparisons between groups. Results Out of 360 selected children, 311 were examined. There were 131 males (42%) and 180 females (58%). The median urinary iodine concentration (UIC) of the study group was 421 μg/L. The study population proportion with UIC > 300 μg/L was 74% with a higher proportion among males and urban populations. The proportion of children with UIC of 100–300 μg/L was only 21% and was significantly higher among females compared with males (p < 0.001). Only about 3% of the children had a median UIC less than 50 μg/L. The prevalence of total goiter rate (TGR) among the sample of schoolchildren in Jazan was 11%, with significant variations between rural and urban populations and by gender. Conclusions The present study demonstrates a remarkable achievement in Universal Salt Iodization (USI) and IDD elimination goals in the Jazan area. However, UIC levels reflect excessive iodine intake and may put the population at risk of adverse health consequences like iodine-induced hyperthyroidism and autoimmune thyroid diseases. PMID:23167286

Thyroglobulin as a Biomarker of Iodine Deficiency: A Review

PubMed Central

Ma, Zheng Feei

2014-01-01

Background: Thyroglobulin, produced exclusively by the thyroid gland, has been proposed to be a more sensitive biomarker of iodine status than thyrotropin or the thyroid hormones triiodothyronine and thyroxine. However, evidence on the usefulness of thyroglobulin (Tg) to assess iodine status has not been extensively reviewed, particularly in pregnant women and adults. Summary: An electronic literature search was conducted using the Cochrane CENTRAL, Web of Science, PubMed, and Medline to locate relevant studies on Tg as a biomarker of iodine status. Since urinary iodine concentration (UIC) is the recommended method to assess iodine status in populations, only studies that clearly reported both Tg and UIC were included. For the purpose of this review, a median Tg <13 μg/L and a median UIC ≥100 μg/L (UIC ≥150 μg/L for pregnant women) were used to indicate adequate iodine status. We excluded studies conducted in subjects with either known thyroid disease or those with thyroglobulin antibodies. The search strategy and selection criteria yielded 34 articles of which nine were intervention studies. The majority of studies (six of eight) reported that iodine-deficient pregnant women had a median Tg ≥13 μg/L. However, large observational studies of pregnant women, including women with adequate and inadequate iodine status, as well as well-designed intervention trials that include both Tg and UIC, are needed. In adults, the results were equivocal because iodine-deficient adults were reported to have median Tg values of either <13 or ≥13 μg/L. Only studies in school-aged children showed that iodine-sufficient children typically had a median Tg <13 μg/L. Some of the inconsistent results may be partially explained by the use of different methodological assays and failure to assess assay accuracy using a certified reference material. Conclusions: These data suggest that Tg does hold promise as a biomarker of iodine deficiency. However, it is associated with limitations. A median Tg cutoff of 13 μg/L warrants further investigation, particularly in adults or pregnant women, as there is a lack of both observational and intervention studies in these groups. PMID:24762031

Fortification of bread with iodized salt corrected iodine deficiency in school-aged children, but not in their mothers: a national cross-sectional survey in Belgium.

PubMed

Vandevijvere, Stefanie; Mourri, Ahmed Bensouda; Amsalkhir, Sihame; Avni, Freddy; Van Oyen, Herman; Moreno-Reyes, Rodrigo

2012-10-01

In the years 1985-1998, it was noted that mild iodine deficiency (MID) was a public health problem in Belgium. Therefore, an agreement was signed in 2009 between the bakery sector and the Ministry of Health, to fortify bread with iodized salt. We tested the hypothesis that the iodine status of Belgian children improved after the introduction of bread fortified with iodized salt. Since the dietary habits of children and adults may differ, we also investigated whether the median urinary iodine concentration (UIC) among the children in this study reflected the iodine status of their mothers. The study was cross-sectional. In a van, equipped with an ultrasound device, the thyroid volumes (Tvol) of children were measured and household salt samples and urine samples were collected from the children and their mothers. From across Belgium, 60 schools were selected and 1541 children participated in the study. The median UIC in children was 113.1 and 84.4 μg/L among their mothers. The median UIC among children was substantially greater compared to more than 10 years ago (80 μg/L; p<0.001). The median UIC in school-aged children was lower in Wallonia than in Flanders (p<0.001) and was higher in boys than in girls (p<0.001). The percentage of children with goiter was 7.2%. Of the 904 salt samples received, 63.2% did not contain iodine. Fortification of bread with iodized salt corrected iodine deficiency in Belgian children, but not in their mothers. To provide these women with an adequate iodine intake, the use of both iodized salt in bread and iodized instead of noniodized household salt needs to increase. Our findings suggest that the median UIC in children may not be an adequate surrogate of adults' iodine status. Therefore, monitoring iodine status should not be limited to children, but should be extended to women of child-bearing age.

Tuning Linux to meet real time requirements

NASA Astrophysics Data System (ADS)

Herbel, Richard S.; Le, Dang N.

2007-04-01

There is a desire to use Linux in military systems. Customers are requesting contractors to use open source to the maximal possible extent in contracts. Linux is probably the best operating system of choice to meet this need. It is widely used. It is free. It is royalty free, and, best of all, it is completely open source. However, there is a problem. Linux was not originally built to be a real time operating system. There are many places where interrupts can and will be blocked for an indeterminate amount of time. There have been several attempts to bridge this gap. One of them is from RTLinux, which attempts to build a microkernel underneath Linux. The microkernel will handle all interrupts and then pass it up to the Linux operating system. This does insure good interrupt latency; however, it is not free [1]. Another is RTAI, which provides a similar typed interface; however, the PowerPC platform, which is used widely in real time embedded community, was stated as "recovering" [2]. Thus this is not suited for military usage. This paper provides a method for tuning a standard Linux kernel so it can meet the real time requirement of an embedded system.

Food Group Intakes as Determinants of Iodine Status among US Adult Population.

PubMed

Lee, Kyung Won; Shin, Dayeon; Cho, Mi Sook; Song, Won O

2016-05-26

Adequate intake of iodine is essential for proper thyroid function. Although dietary reference intakes for iodine have been established, iodine intake cannot be estimated due to the lack of data on iodine contents in foods. We aimed to determine if food group intakes can predict iodine status assessed by urinary iodine concentration (UIC) from spot urine samples of 5967 US adults in the National Health and Nutrition Examination Survey (NHANES) 2007-2012. From an in-person 24-h dietary recall, all foods consumed were aggregated into 12 main food groups using the individual food code of the US Department of Agriculture (USDA); dairy products, meat/poultry, fish/seaweed, eggs, legumes/nuts/seeds, breads, other grain products, fruits, vegetables, fats/oils, sugars/sweets, and beverages. Chi-square test, Spearman correlation, and multiple linear regression analyses were conducted to investigate the predictability of food group intakes in iodine status assessed by UIC. From the multiple linear regressions, the consumption of dairy products, eggs, and breads, and iodine-containing supplement use were positively associated with UIC, whereas beverage consumption was negatively associated with UIC. Among various food group intakes, dairy product intake was the most important determinant of iodine status in both US men and women. Subpopulation groups with a high risk of iodine deficiency may need nutritional education regarding the consumption of dairy products, eggs, and breads to maintain an adequate iodine status. Efforts toward a better understanding of iodine content in each food and a continued monitoring of iodine status within US adults are both warranted.

HARE: Final Report

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

Mckie, Jim

2012-01-09

This report documents the results of work done over a 6 year period under the FAST-OS programs. The first effort was called Right-Weight Kernels, (RWK) and was concerned with improving measurements of OS noise so it could be treated quantitatively; and evaluating the use of two operating systems, Linux and Plan 9, on HPC systems and determining how these operating systems needed to be extended or changed for HPC, while still retaining their general-purpose nature. The second program, HARE, explored the creation of alternative runtime models, building on RWK. All of the HARE work was done on Plan 9. Themore » HARE researchers were mindful of the very good Linux and LWK work being done at other labs and saw no need to recreate it. Even given this limited funding, the two efforts had outsized impact: _ Helped Cray decide to use Linux, instead of a custom kernel, and provided the tools needed to make Linux perform well _ Created a successor operating system to Plan 9, NIX, which has been taken in by Bell Labs for further development _ Created a standard system measurement tool, Fixed Time Quantum or FTQ, which is widely used for measuring operating systems impact on applications _ Spurred the use of the 9p protocol in several organizations, including IBM _ Built software in use at many companies, including IBM, Cray, and Google _ Spurred the creation of alternative runtimes for use on HPC systems _ Demonstrated that, with proper modifications, a general purpose operating systems can provide communications up to 3 times as effective as user-level libraries Open source was a key part of this work. The code developed for this project is in wide use and available at many places. The core Blue Gene code is available at https://bitbucket.org/ericvh/hare. We describe details of these impacts in the following sections. The rest of this report is organized as follows: First, we describe commercial impact; next, we describe the FTQ benchmark and its impact in more detail; operating systems and runtime research follows; we discuss infrastructure software; and close with a description of the new NIX operating system, future work, and conclusions.« less

General Mission Analysis Tool (GMAT) Architectural Specification. Draft

NASA Technical Reports Server (NTRS)

Hughes, Steven P.; Conway, Darrel, J.

2007-01-01

Early in 2002, Goddard Space Flight Center (GSFC) began to identify requirements for the flight dynamics software needed to fly upcoming missions that use formations of spacecraft to collect data. These requirements ranged from low level modeling features to large scale interoperability requirements. In 2003 we began work on a system designed to meet these requirement; this system is GMAT. The General Mission Analysis Tool (GMAT) is a general purpose flight dynamics modeling tool built on open source principles. The GMAT code is written in C++, and uses modern C++ constructs extensively. GMAT can be run through either a fully functional Graphical User Interface (GUI) or as a command line program with minimal user feedback. The system is built and runs on Microsoft Windows, Linux, and Macintosh OS X platforms. The GMAT GUI is written using wxWidgets, a cross platform library of components that streamlines the development and extension of the user interface Flight dynamics modeling is performed in GMAT by building components that represent the players in the analysis problem that is being modeled. These components interact through the sequential execution of instructions, embodied in the GMAT Mission Sequence. A typical Mission Sequence will model the trajectories of a set of spacecraft evolving over time, calculating relevant parameters during this propagation, and maneuvering individual spacecraft to maintain a set of mission constraints as established by the mission analyst. All of the elements used in GMAT for mission analysis can be viewed in the GMAT GUI or through a custom scripting language. Analysis problems modeled in GMAT are saved as script files, and these files can be read into GMAT. When a script is read into the GMAT GUI, the corresponding user interface elements are constructed in the GMAT GUI. The GMAT system was developed from the ground up to run in a platform agnostic environment. The source code compiles on numerous different platforms, and is regularly exercised running on Windows, Linux and Macintosh computers by the development and analysis teams working on the project. The system can be run using either a graphical user interface, written using the open source wxWidgets framework, or from a text console. The GMAT source code was written using open source tools. GSFC has released the code using the NASA open source license.

ALPHACAL: A new user-friendly tool for the calibration of alpha-particle sources.

PubMed

Timón, A Fernández; Vargas, M Jurado; Gallardo, P Álvarez; Sánchez-Oro, J; Peralta, L

2018-05-01

In this work, we present and describe the program ALPHACAL, specifically developed for the calibration of alpha-particle sources. It is therefore more user-friendly and less time-consuming than multipurpose codes developed for a wide range of applications. The program is based on the recently developed code AlfaMC, which simulates specifically the transport of alpha particles. Both cylindrical and point sources mounted on the surface of polished backings can be simulated, as is the convention in experimental measurements of alpha-particle sources. In addition to the efficiency calculation and determination of the backscattering coefficient, some additional tools are available to the user, like the visualization of energy spectrum, use of energy cut-off or low-energy tail corrections. ALPHACAL has been implemented in C++ language using QT library, so it is available for Windows, MacOs and Linux platforms. It is free and can be provided under request to the authors. Copyright © 2018 Elsevier Ltd. All rights reserved.

SFT: Scalable Fault Tolerance

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

Petrini, Fabrizio; Nieplocha, Jarek; Tipparaju, Vinod

2006-04-15

In this paper we will present a new technology that we are currently developing within the SFT: Scalable Fault Tolerance FastOS project which seeks to implement fault tolerance at the operating system level. Major design goals include dynamic reallocation of resources to allow continuing execution in the presence of hardware failures, very high scalability, high efficiency (low overhead), and transparency—requiring no changes to user applications. Our technology is based on a global coordination mechanism, that enforces transparent recovery lines in the system, and TICK, a lightweight, incremental checkpointing software architecture implemented as a Linux kernel module. TICK is completely user-transparentmore » and does not require any changes to user code or system libraries; it is highly responsive: an interrupt, such as a timer interrupt, can trigger a checkpoint in as little as 2.5μs; and it supports incremental and full checkpoints with minimal overhead—less than 6% with full checkpointing to disk performed as frequently as once per minute.« less

JAX Colony Management System (JCMS): an extensible colony and phenotype data management system.

PubMed

Donnelly, Chuck J; McFarland, Mike; Ames, Abigail; Sundberg, Beth; Springer, Dave; Blauth, Peter; Bult, Carol J

2010-04-01

The Jackson Laboratory Colony Management System (JCMS) is a software application for managing data and information related to research mouse colonies, associated biospecimens, and experimental protocols. JCMS runs directly on computers that run one of the PC Windows operating systems, but can be accessed via web browser interfaces from any computer running a Windows, Macintosh, or Linux operating system. JCMS can be configured for a single user or multiple users in small- to medium-size work groups. The target audience for JCMS includes laboratory technicians, animal colony managers, and principal investigators. The application provides operational support for colony management and experimental workflows, sample and data tracking through transaction-based data entry forms, and date-driven work reports. Flexible query forms allow researchers to retrieve database records based on user-defined criteria. Recent advances in handheld computers with integrated barcode readers, middleware technologies, web browsers, and wireless networks add to the utility of JCMS by allowing real-time access to the database from any networked computer.

Online plasma calculator

NASA Astrophysics Data System (ADS)

Wisniewski, H.; Gourdain, P.-A.

2017-10-01

APOLLO is an online, Linux based plasma calculator. Users can input variables that correspond to their specific plasma, such as ion and electron densities, temperatures, and external magnetic fields. The system is based on a webserver where a FastCGI protocol computes key plasma parameters including frequencies, lengths, velocities, and dimensionless numbers. FastCGI was chosen to overcome security problems caused by JAVA-based plugins. The FastCGI also speeds up calculations over PHP based systems. APOLLO is built upon the WT library, which turns any web browser into a versatile, fast graphic user interface. All values with units are expressed in SI units except temperature, which is in electron-volts. SI units were chosen over cgs units because of the gradual shift to using SI units within the plasma community. APOLLO is intended to be a fast calculator that also provides the user with the proper equations used to calculate the plasma parameters. This system is intended to be used by undergraduates taking plasma courses as well as graduate students and researchers who need a quick reference calculation.

AirShow 1.0 CFD Software Users' Guide

NASA Technical Reports Server (NTRS)

Mohler, Stanley R., Jr.

2005-01-01

AirShow is visualization post-processing software for Computational Fluid Dynamics (CFD). Upon reading binary PLOT3D grid and solution files into AirShow, the engineer can quickly see how hundreds of complex 3-D structured blocks are arranged and numbered. Additionally, chosen grid planes can be displayed and colored according to various aerodynamic flow quantities such as Mach number and pressure. The user may interactively rotate and translate the graphical objects using the mouse. The software source code was written in cross-platform Java, C++, and OpenGL, and runs on Unix, Linux, and Windows. The graphical user interface (GUI) was written using Java Swing. Java also provides multiple synchronized threads. The Java Native Interface (JNI) provides a bridge between the Java code and the C++ code where the PLOT3D files are read, the OpenGL graphics are rendered, and numerical calculations are performed. AirShow is easy to learn and simple to use. The source code is available for free from the NASA Technology Transfer and Partnership Office.

Linux thin-client conversion in a large cardiology practice: initial experience.

PubMed

Echt, Martin P; Rosen, Jordan

2004-01-01

Capital Cardiology Associates (CCA) is a single-specialty cardiology practice with offices in New York and Massachusetts. In 2003, CCA converted its IT system from a Microsoft-based network to a Linux network employing Linux thin-client technology with overall positive outcomes.

OSG-GEM: Gene Expression Matrix Construction Using the Open Science Grid.

PubMed

Poehlman, William L; Rynge, Mats; Branton, Chris; Balamurugan, D; Feltus, Frank A

2016-01-01

High-throughput DNA sequencing technology has revolutionized the study of gene expression while introducing significant computational challenges for biologists. These computational challenges include access to sufficient computer hardware and functional data processing workflows. Both these challenges are addressed with our scalable, open-source Pegasus workflow for processing high-throughput DNA sequence datasets into a gene expression matrix (GEM) using computational resources available to U.S.-based researchers on the Open Science Grid (OSG). We describe the usage of the workflow (OSG-GEM), discuss workflow design, inspect performance data, and assess accuracy in mapping paired-end sequencing reads to a reference genome. A target OSG-GEM user is proficient with the Linux command line and possesses basic bioinformatics experience. The user may run this workflow directly on the OSG or adapt it to novel computing environments.

OSG-GEM: Gene Expression Matrix Construction Using the Open Science Grid

PubMed Central

Poehlman, William L.; Rynge, Mats; Branton, Chris; Balamurugan, D.; Feltus, Frank A.

2016-01-01

High-throughput DNA sequencing technology has revolutionized the study of gene expression while introducing significant computational challenges for biologists. These computational challenges include access to sufficient computer hardware and functional data processing workflows. Both these challenges are addressed with our scalable, open-source Pegasus workflow for processing high-throughput DNA sequence datasets into a gene expression matrix (GEM) using computational resources available to U.S.-based researchers on the Open Science Grid (OSG). We describe the usage of the workflow (OSG-GEM), discuss workflow design, inspect performance data, and assess accuracy in mapping paired-end sequencing reads to a reference genome. A target OSG-GEM user is proficient with the Linux command line and possesses basic bioinformatics experience. The user may run this workflow directly on the OSG or adapt it to novel computing environments. PMID:27499617

CERNBox + EOS: end-user storage for science

NASA Astrophysics Data System (ADS)

Mascetti, L.; Gonzalez Labrador, H.; Lamanna, M.; Mościcki, JT; Peters, AJ

2015-12-01

CERNBox is a cloud synchronisation service for end-users: it allows syncing and sharing files on all major mobile and desktop platforms (Linux, Windows, MacOSX, Android, iOS) aiming to provide offline availability to any data stored in the CERN EOS infrastructure. The successful beta phase of the service confirmed the high demand in the community for an easily accessible cloud storage solution such as CERNBox. Integration of the CERNBox service with the EOS storage back-end is the next step towards providing “sync and share” capabilities for scientific and engineering use-cases. In this report we will present lessons learnt in offering the CERNBox service, key technical aspects of CERNBox/EOS integration and new, emerging usage possibilities. The latter includes the ongoing integration of “sync and share” capabilities with the LHC data analysis tools and transfer services.

Next Generation Security for the 10,240 Processor Columbia System

NASA Technical Reports Server (NTRS)

Hinke, Thomas; Kolano, Paul; Shaw, Derek; Keller, Chris; Tweton, Dave; Welch, Todd; Liu, Wen (Betty)

2005-01-01

This presentation includes a discussion of the Columbia 10,240-processor system located at the NASA Advanced Supercomputing (NAS) division at the NASA Ames Research Center which supports each of NASA's four missions: science, exploration systems, aeronautics, and space operations. It is comprised of 20 Silicon Graphics nodes, each consisting of 512 Itanium II processors. A 64 processor Columbia front-end system supports users as they prepare their jobs and then submits them to the PBS system. Columbia nodes and front-end systems use the Linux OS. Prior to SC04, the Columbia system was used to attain a processing speed of 51.87 TeraFlops, which made it number two on the Top 500 list of the world's supercomputers and the world's fastest "operational" supercomputer since it was fully engaged in supporting NASA users.

The General Mission Analysis Tool (GMAT): Current Features And Adding Custom Functionality

NASA Technical Reports Server (NTRS)

Conway, Darrel J.; Hughes, Steven P.

2010-01-01

The General Mission Analysis Tool (GMAT) is a software system for trajectory optimization, mission analysis, trajectory estimation, and prediction developed by NASA, the Air Force Research Lab, and private industry. GMAT's design and implementation are based on four basic principles: open source visibility for both the source code and design documentation; platform independence; modular design; and user extensibility. The system, released under the NASA Open Source Agreement, runs on Windows, Mac and Linux. User extensions, loaded at run time, have been built for optimization, trajectory visualization, force model extension, and estimation, by parties outside of GMAT's development group. The system has been used to optimize maneuvers for the Lunar Crater Observation and Sensing Satellite (LCROSS) and ARTEMIS missions and is being used for formation design and analysis for the Magnetospheric Multiscale Mission (MMS).

Development and Testing of a High-Speed Real-Time Kinematic Precise DGPS Positioning System Between Two Aircraft

DTIC Science & Technology

2006-09-01

work-horse for this thesis. He spent hours writing some of the more tedious code, and as much time helping me learn C++ and Linux . He was always there...compared with C++, and the need to use Linux as the operating system, the filter was coded using C++ and KDevelop [28] in SUSE LINUX Professional 9.2 [42...The driving factor for using Linux was the operating system’s ability to access the serial ports in a reliable fashion. Under the original MATLAB® and

Open discovery: An integrated live Linux platform of Bioinformatics tools.

PubMed

Vetrivel, Umashankar; Pilla, Kalabharath

2008-01-01

Historically, live linux distributions for Bioinformatics have paved way for portability of Bioinformatics workbench in a platform independent manner. Moreover, most of the existing live Linux distributions limit their usage to sequence analysis and basic molecular visualization programs and are devoid of data persistence. Hence, open discovery - a live linux distribution has been developed with the capability to perform complex tasks like molecular modeling, docking and molecular dynamics in a swift manner. Furthermore, it is also equipped with complete sequence analysis environment and is capable of running windows executable programs in Linux environment. Open discovery portrays the advanced customizable configuration of fedora, with data persistency accessible via USB drive or DVD. The Open Discovery is distributed free under Academic Free License (AFL) and can be downloaded from http://www.OpenDiscovery.org.in.

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

Wagner, Robert; Rivers, Wilmer

any single computer program for seismic data analysis will not have all the capabilities needed to study reference events, since hese detailed studies will be highly specialized. It may be necessary to develop and test new algorithms, and then these special ;odes must be integrated with existing software to use their conventional data-processing routines. We have investigated two neans of establishing communications between the legacy and new codes: CORBA and XML/SOAP Web services. We have nvestigated making new Java code communicate with a legacy C-language program, geotool, running under Linux. Both methods vere successful, but both were difficult to implement.more » C programs on UNIX/Linux are poorly supported for Web services, compared vith the Java and .NET languages and platforms. Easier-to-use middleware will be required for scientists to construct distributed applications as easily as stand-alone ones. Considerable difficulty was encountered in modifying geotool, and this problem shows he need to use component-based user interfaces instead of large C-language codes where changes to one part of the program nay introduce side effects into other parts. We have nevertheless made bug fixes and enhancements to that legacy program, but t remains difficult to expand it through communications with external software.« less

Optimizing ion channel models using a parallel genetic algorithm on graphical processors.

PubMed

Ben-Shalom, Roy; Aviv, Amit; Razon, Benjamin; Korngreen, Alon

2012-01-01

We have recently shown that we can semi-automatically constrain models of voltage-gated ion channels by combining a stochastic search algorithm with ionic currents measured using multiple voltage-clamp protocols. Although numerically successful, this approach is highly demanding computationally, with optimization on a high performance Linux cluster typically lasting several days. To solve this computational bottleneck we converted our optimization algorithm for work on a graphical processing unit (GPU) using NVIDIA's CUDA. Parallelizing the process on a Fermi graphic computing engine from NVIDIA increased the speed ∼180 times over an application running on an 80 node Linux cluster, considerably reducing simulation times. This application allows users to optimize models for ion channel kinetics on a single, inexpensive, desktop "super computer," greatly reducing the time and cost of building models relevant to neuronal physiology. We also demonstrate that the point of algorithm parallelization is crucial to its performance. We substantially reduced computing time by solving the ODEs (Ordinary Differential Equations) so as to massively reduce memory transfers to and from the GPU. This approach may be applied to speed up other data intensive applications requiring iterative solutions of ODEs. Copyright © 2012 Elsevier B.V. All rights reserved.

Data Collection with Linux in the Undergraduate Physics Lab

NASA Astrophysics Data System (ADS)

Ramey, R. Dwayne

2004-11-01

Electronic data devices such as photogates can greatly facilitate data collection in the undergraduate physics laboratory. Unfortunately, these devices have several practical drawbacks. While the photogates themselves are not particularly expensive, manufacturers of these devices have created intermediary hardware devices for data buffering and manipulation. These devices, while useful in some contexts, greatly increase the overall price of data collection and, through the use of proprietary software, limit the ability of the enduser to customize the software. As an alternative, I outline the procedure for establishing a computer-based data collection system that consists of opensource software and user constructed connections. The data collection system consists of the wiring needed to connect a data device to a computer and the software needed to collect and manipulate data. Data devices can be connected to a computer through either through the USB port or the gameport of a sound card. Software capable of collecting and manipulating the data from a photogate type device on a Linux system has been developed and will be discrussed. Results for typical undergraduate photogate based experiments will be shown, error limits and data collect rates will be discussed for both the gameport and USB connections.

MCBooster: a library for fast Monte Carlo generation of phase-space decays on massively parallel platforms.

NASA Astrophysics Data System (ADS)

Alves Júnior, A. A.; Sokoloff, M. D.

2017-10-01

MCBooster is a header-only, C++11-compliant library that provides routines to generate and perform calculations on large samples of phase space Monte Carlo events. To achieve superior performance, MCBooster is capable to perform most of its calculations in parallel using CUDA- and OpenMP-enabled devices. MCBooster is built on top of the Thrust library and runs on Linux systems. This contribution summarizes the main features of MCBooster. A basic description of the user interface and some examples of applications are provided, along with measurements of performance in a variety of environments

Efficient Parallel Engineering Computing on Linux Workstations

NASA Technical Reports Server (NTRS)

Lou, John Z.

2010-01-01

A C software module has been developed that creates lightweight processes (LWPs) dynamically to achieve parallel computing performance in a variety of engineering simulation and analysis applications to support NASA and DoD project tasks. The required interface between the module and the application it supports is simple, minimal and almost completely transparent to the user applications, and it can achieve nearly ideal computing speed-up on multi-CPU engineering workstations of all operating system platforms. The module can be integrated into an existing application (C, C++, Fortran and others) either as part of a compiled module or as a dynamically linked library (DLL).

SLURM: Simple Linux Utility for Resource Management

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

Jette, M; Grondona, M

2002-12-19

Simple Linux Utility for Resource Management (SLURM) is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for Linux clusters of thousands of nodes. Components include machine status, partition management, job management, scheduling and stream copy modules. This paper presents an overview of the SLURM architecture and functionality.

SLURM: Simplex Linux Utility for Resource Management

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

Jette, M; Grondona, M

2003-04-22

Simple Linux Utility for Resource Management (SLURM) is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for Linux clusters of thousands of nodes. Components include machine status, partition management, job management, scheduling, and stream copy modules. This paper presents an overview of the SLURM architecture and functionality.

77 FR 5864 - BluePoint Linux Software Corp., China Bottles Inc., Long-e International, Inc., and Nano...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-06

... SECURITIES AND EXCHANGE COMMISSION [File No. 500-1] BluePoint Linux Software Corp., China Bottles Inc., Long-e International, Inc., and Nano Superlattice Technology, Inc.; Order of Suspension of... current and accurate information concerning the securities of BluePoint Linux Software Corp. because it...

Excessive iodine intake during pregnancy in Somali refugees.

PubMed

Kassim, Ismail A R; Ruth, Laird J; Creeke, Paul I; Gnat, Danielle; Abdalla, Fathia; Seal, Andrew J

2012-01-01

Iodine deficiency and excess are both associated with adverse health consequences, with fetuses, children and pregnant women being most vulnerable to the devastating effects of severe deficiency. It is often assumed that the iodine status of a population if displaced or in a remote or emergency situation is low. However, there is little evidence available to support this assumption, especially among long-term food-aid-dependent pregnant women. An effectiveness trial of a prenatal multiple-micronutrient supplement that contained 150 µg day(-1) iodine was conducted in two refugee camps in the North Eastern Province of Kenya in 2002. Urinary iodine concentration (UIC) was measured in a subsample of pregnant women attending antenatal care in Dagahaley (control camp) (n = 74) and Ifo (intervention camp) (n = 63). There was no significant difference in median UIC between the two camps (P = 0.118). The combined median UIC was 730 µg L(-1) (interquartile range, 780) (5.77 µmol L(-1)) and exceeded the upper safe limit of 500 µg L(-1) (3.95 µmol L(-1)) for pregnant women (P < 0.001), indicating excessive iodine intake. About 20% of the study subjects had 'more than adequate' urinary iodine, while over 71% had excessive UIC. Salt iodine content varied between 5.1 and 80.1 ppm in the five market salt samples analysed. In conclusion, excessive iodine intake was evident in the Dadaab refugee camps. Further research needs to be conducted to investigate the source of excess iodine, to determine the measures needed to address excessive iodine intake and to reconsider the World Health Organization/World Food Programme/United Nations Children's Fund guidance on supplementation of vulnerable groups in emergencies.

Adequate Iodine Status in New Zealand School Children Post-Fortification of Bread with Iodised Salt

PubMed Central

Jones, Emma; McLean, Rachael; Davies, Briar; Hawkins, Rochelle; Meiklejohn, Eva; Ma, Zheng Feei; Skeaff, Sheila

2016-01-01

Iodine deficiency re-emerged in New Zealand in the 1990s, prompting the mandatory fortification of bread with iodised salt from 2009. This study aimed to determine the iodine status of New Zealand children when the fortification of bread was well established. A cross-sectional survey of children aged 8–10 years was conducted in the cities of Auckland and Christchurch, New Zealand, from March to May 2015. Children provided a spot urine sample for the determination of urinary iodine concentration (UIC), a fingerpick blood sample for Thyroglobulin (Tg) concentration, and completed a questionnaire ascertaining socio-demographic information that also included an iodine-specific food frequency questionnaire (FFQ). The FFQ was used to estimate iodine intake from all main food sources including bread and iodised salt. The median UIC for all children (n = 415) was 116 μg/L (females 106 μg/L, males 131 μg/L) indicative of adequate iodine status according to the World Health Organisation (WHO, i.e., median UIC of 100–199 μg/L). The median Tg concentration was 8.7 μg/L, which was <10 μg/L confirming adequate iodine status. There was a significant difference in UIC by sex (p = 0.001) and ethnicity (p = 0.006). The mean iodine intake from the food-only model was 65 μg/day. Bread contributed 51% of total iodine intake in the food-only model, providing a mean iodine intake of 35 μg/day. The mean iodine intake from the food-plus-iodised salt model was 101 μg/day. In conclusion, the results of this study confirm that the iodine status in New Zealand school children is now adequate. PMID:27196925

Iodine deficiency a persisting problem: assessment of iodine nutrition and evaluation of thyroid nodular pathology in Portugal.

PubMed

Santos, J E C; Freitas, M; Fonseca, C P; Castilho, P; Carreira, I M; Rombeau, J L; Branco, M C

2017-02-01

The goal of eliminating iodine deficiency (ID) by the year 2000 has still not been achieved in several countries. More than 2 billion people worldwide (over 260 million school age children) remain ID. In Europe, there are still countries, such as Portugal, without national general population data on iodine nutrition (IN). This study aims at evaluating combined complementary data of the IN of the general population through urinary iodine concentration (UIC) and the thyroid histology profile from the inland region of Beira Interior (BI), in Portugal. UIC from a population sample of 214 volunteers (131 females and 83 males), with ages ranging from 8 to 97 years (mean 51.5 years ± SD 20.74 years), from BI was determined; the thyroid histology pattern in BI (6-year period) was evaluated; and the iodine content of the largest surface water reservoir of BI, never previously reported, was measured. Median UIC of 62.6 μg/L was measured. Over 92 % of the population had UIC less than 100 μg/L. From 279 histology reports evaluated, the incidence of the different types of thyroid nodular pathology in BI was established. There were 60 histologic diagnoses of malignancy. The observed ratio of papillary to follicular carcinoma relatively close to 1 and the fairly high percentage of anaplastic carcinomas are characteristic of ID areas. The findings of this first general population study on IN from the inland region of BI, Portugal, document significant ID. This problem, with its serious public health implications, could be corrected by having affordable iodised salt widely and generally available and by promoting a proactive population attitude generated by ample public information and educational programs as to the negative consequences of ID.

Assessment of iodine status and associated factors in vulnerable populations in Henan Province, China, in 2012.

PubMed

Yang, Jin; Zheng, Heming; Li, Xiaofeng; Zhu, Lin; Hao, Zongyu; Chen, Gan; Liu, Yang; Wang, Yanli

2014-01-01

Iodine content in table salt was adjusted from 30-50 mg/kg to 21-39 mg/kg from March of 2012 in Henan Province, China. The vulnerable population may be at risk of iodine deficiency. To determine whether the iodine intake was sufficient in vulnerable populations and to investigate what factors may be associated with iodine status in these vulnerable populations in Henan Province, China. A cross-sectional survey was conducted in 17 cities in Henan Province, China, from April 2012 to December 2012 to assess the iodine status in vulnerable populations, including women of reproductive-age (n=2648), pregnant women (n=39684), lactating women (n=6859), infants <2 years of age (n=16481), and children aged 8-10 years (n=3198). Questionnaires (n=4865) related to demographic and dietary factors were collected from the investigated women to identify factors that were related to iodine intake and iodine status. The median urinary iodine concentrations (mUICs) were 205 μg/L, 198 μg/L, 167 μg/L, 205 μg/L and 200 μg/L, respectively, in reproductiveage, pregnant and lactating women, infants <2 years of age and children aged 8-10 years. Higher income, and consuming more poultry and fish in the diet had positive impact on UIC levels. Low salt intake, consuming more rice and vegetables in the diet were negative factors for UIC. Iodine status of the vulnerable populations was generally adequate in Henan Province, China, according to WHO criteria. But the mUICs were slightly above the adequate level in reproductive-age women and children aged 8-10 years. It's important to monitor the iodine status in vulnerable populations after the adjustment on iodine content in table salt.

Can an Educational Intervention Improve Iodine Nutrition Status in Pregnant Women? A Randomized Controlled Trial.

PubMed

Amiri, Parisa; Hamzavi Zarghani, Najmeh; Nazeri, Pantea; Ghofranipour, Fazlollah; Karimi, Mehrdad; Amouzegar, Atieh; Mirmiran, Parvin; Azizi, Fereidoun

2017-03-01

Because of their increased need for iodine, pregnant women are among the high-risk groups for iodine deficiency. The purpose of this study was to evaluate the effectiveness of an educational program on the iodine nutrition status of pregnant women. In this randomized controlled trial, 100 pregnant women were randomly selected from five healthcare centers in the southern region of Tehran, the capital of Iran. In the intervention group, pregnant women received a four-month educational program, which included two face-to-face educational sessions, using a researcher-designed educational pamphlet in the second and third trimesters, and two follow-up telephone calls. Knowledge, attitude, and practice (KAP) scores, urinary iodine concentration (UIC), and salt iodine content were assessed at baseline and four months after the intervention. At baseline, there were significant associations between knowledge and attitude (r = 0.38, p = 0.03) between practice and UIC (r = 0.28, p = 0.01) and between UIC and iodine content of salt (r = 0.24, p = 0.009). Although a significant difference was found in mean KAP scores between the two groups after the educational intervention, scores were significantly higher in the intervention group compared with controls (p < 0.01). There were no significant differences in UIC and iodine content of salt between the two groups at follow-up. Despite educational intervention increasing KAP among women regarding the importance of iodine and iodized salt consumption during pregnancy, their iodine status did not improve. Considering the main socio-environmental determinants of iodine deficiency, in particular, the monitoring of salt fortification, prescribing iodine containing supplements as well as improving health literacy in pregnant women seem essential strategies.

Urinary and Milk Iodine Status in Neonates and Their Mothers during Congenital Hypothyroidism Screening Program in Eastern Azerbaijan: A Pilot Study

PubMed Central

MOBASSERI, Majid; ROSHANRAVAN, Neda; MESRI ALAMDARI, Naimeh; OSTADRAHIMI, Alireza; ASGHARI JAFARABADI, Mohammad; ANARI, Farideh; HEDAYATI, Mehdi

2014-01-01

Abstract Background Iodine is essential element in thyroid hormones synthesis and normal growth and development of the brain. Milk and iodine concentrations can be appropriate indicator of body iodine status; in this study, we evaluated the concentrations of urine and milk iodine in newborns and their mothers. Methods In a cross-sectional study conducted in 2013, urine and milk iodine in 106 neonates and their mothers referred to healthcare center in Shabestar, Eastern Azerbaijan for congenital hypothyroidism screening program were determined. Median urinary iodine < 100 µg/L and milk iodine < 50 µg/L was considered as iodine deficiency. Results The median urine iodine concentrations (UIC) in mothers and infants were 142.31 µg/L (.0 - 1260) and 306.76 µg/L (23.56-1020) respectively. Urine iodine concentrations were < 100 µg/L in 33.9% of mothers and 14.2% of neonates. The median milk iodine concentration (MIC) was 58.23 µg/L (20.31- 425) and in 41.9% of mothers was <50 µg/L. A positive significant correlation was found between milk iodine and maternal urinary iodine concentration (r=0.533, P= 0.000). There was significant correlation between neonatal UIC and maternal UIC (r=0.462, P= 0.000), neonatal UIC and MIC (r=0.414, P= 0.000). Conclusions Urinary and milk iodine concentrations in mothers and infants were within acceptable range, which indicates adequate iodine intake. However, there were moderate and marginal iodine deficiencies in about half percentage of participants. Insufficient amount of milk iodine in about half of the mothers can result in iodine deficiency in breast-fed infants. PMID:26060700

Open discovery: An integrated live Linux platform of Bioinformatics tools

PubMed Central

Vetrivel, Umashankar; Pilla, Kalabharath

2008-01-01

Historically, live linux distributions for Bioinformatics have paved way for portability of Bioinformatics workbench in a platform independent manner. Moreover, most of the existing live Linux distributions limit their usage to sequence analysis and basic molecular visualization programs and are devoid of data persistence. Hence, open discovery ‐ a live linux distribution has been developed with the capability to perform complex tasks like molecular modeling, docking and molecular dynamics in a swift manner. Furthermore, it is also equipped with complete sequence analysis environment and is capable of running windows executable programs in Linux environment. Open discovery portrays the advanced customizable configuration of fedora, with data persistency accessible via USB drive or DVD. Availability The Open Discovery is distributed free under Academic Free License (AFL) and can be downloaded from http://www.OpenDiscovery.org.in PMID:19238235

The Research on Linux Memory Forensics

NASA Astrophysics Data System (ADS)

Zhang, Jun; Che, ShengBing

2018-03-01

Memory forensics is a branch of computer forensics. It does not depend on the operating system API, and analyzes operating system information from binary memory data. Based on the 64-bit Linux operating system, it analyzes system process and thread information from physical memory data. Using ELF file debugging information and propose a method for locating kernel structure member variable, it can be applied to different versions of the Linux operating system. The experimental results show that the method can successfully obtain the sytem process information from physical memory data, and can be compatible with multiple versions of the Linux kernel.

Iodine Nutritional Status of School Children in Nauru 2015

PubMed Central

Huang, Chun-Jui; Tseng, Chi-Lung; Chen, Harn-Shen; Garabwan, Chanda; Korovo, Samuela; Tang, Kam-Tsun; Won, Justin Ging-Shing; Hsieh, Chang-Hsun; Wang, Fan-Fen

2016-01-01

Little is known about iodine nutritional status in island countries in the Pacific Ocean. The primary objective of this study was to report for the first time the iodine nutritional status of people in Nauru. In addition, sources of iodine nutrition (i.e., water and salt) were investigated. A school-based cross-sectional survey of children aged 6–12 years was conducted in three primary schools of Nauru. Urinary iodine concentration (UIC) was determined by spot urine samples. Available water and salt samples in Nauru were collected for the measurement of iodine content. A food frequency questionnaire was conducted. The median UIC was 142 μg/L, and 25.2% and 7.4% of the population had median UIC below 100 μg/L and 50 μg/L, respectively. Natural iodine-containing foods such as seaweeds and agar were rare. Iodine was undetectable in Nauruan tank water, filtered tap water, and raindrops. Of the analyzed salt products, five kinds were non-iodized, and three were iodized (iodine content: 15 ppm, 65 ppm, and 68 ppm, respectively). The results indicate that the iodine status in Nauruan school children is adequate. Iodized salt may serve as an important source of iodine nutrition in Nauru. PMID:27563920

Low Urinary Iodine Concentration among Mothers and Children in Cambodia

PubMed Central

Laillou, Arnaud; Sophonneary, Prak; Kuong, Khov; Hong, Rathavuth; Un, Samoeurn; Chamnan, Chhoun; Poirot, Etienne; Berger, Jacques; Wieringa, Frank

2016-01-01

A 2014 national assessment of salt iodization coverage in Cambodia found that 62% of samples were non-iodized, suggesting a significant decline in daily iodine intakes. The Cambodian Micronutrient Survey conducted in 2014 (CMNS-2014) permitted obtaining national data on urinary iodine concentrations (UIC) to assess iodine status and whether iodized salt use had an impact. Urine samples were collected from mothers (n = 736) and children (n = 950). The median UIC was 63 µg/L and 72 µg/L in mothers and children respectively. More than 60% of mothers and their children had a UIC < 100 µg/L, thereby indicating a serious public health problem. Iodine status was significantly lower among mothers and children living in rural areas, belonging to the poorest socioeconomic category, or living in a household not using iodized salt. The limited enforcement of the legislation for iodized salt has resulted in a major decrease in the prevalence of iodized salt, which in turn has compromised iodine status in Cambodia. It is essential for the government to enhance enforcement of the iodized salt legislation, and implement short term strategies, such as iodine supplementation, to prevent an increase of severe complications due to iodine deficiency in the Cambodian population. PMID:27058551

Urinary Iodine Concentrations and Mortality Among U.S. Adults.

PubMed

Inoue, Kosuke; Leung, Angela M; Sugiyama, Takehiro; Tsujimoto, Tetsuro; Makita, Noriko; Nangaku, Masaomi; Ritz, Beate R

2018-06-08

Iodine deficiency has long been recognized as an important public health problem. Global approaches such as salt iodization that aim to overcome iodine deficiency have been successful. Meanwhile, they have led to excessive iodine consumption in some populations, thereby increasing the risks of iodine-induced thyroid dysfunction, as well as the comorbidities and mortality associated with hypothyroidism and hyperthyroidism. We aimed to elucidate whether iodine intake is associated with mortality among U.S. adults. This is an observational study to estimate mortality risks according to urinary iodine concentrations (UIC) utilizing a nationally representative sample of 12,264 adults ages 20 to 80 years enrolled in the National Health and Nutrition Examination Survey (NHANES) III. Crude and multivariable Cox proportional hazards regression models were employed to investigate the association between UIC (<50, 50-99, 100-299, 300-399, and >400 μg/L) and mortalities (all-cause, cardiovascular, and cancer). In sensitivity analyses, we adjusted for total sodium intake and fat/calorie ratio in addition to other potential confounders. We also conducted stratum-specific analyses to estimate the effects of UIC on mortality according to age, sex, race/ethnicity, and eGFR category. Over a median follow-up of 19.2 years, there were 3,159 deaths from all causes. Participants with excess iodine exposure (UIC >400 μg/L) were at higher risk for all-cause mortality compared to those with adequate iodine nutrition (HR, 1.19; 95% confidence interval [CI], 1.04-1.37). We also found elevated HRs of cardiovascular and cancer mortality, but the 95% CI of our effect estimates included the null value for both outcomes. Low UIC was not associated with increased mortality. Restricted cubic spline models showed similar results for all outcomes. The results did not change substantially after adjusting for total sodium intake and fat/calorie ratio. None of the potential interactions were statistically significant on a multiplicative scale. Higher all-cause mortality among those with excess iodine intake, compared with individuals with adequate iodine intake, highlights the importance of monitoring population iodine status. Further studies with longitudinal measures of iodine status are needed to validate our results and assess the potential risks excess iodine intake may have on long-term health outcomes.

Real-time data collection in Linux: a case study.

PubMed

Finney, S A

2001-05-01

Multiuser UNIX-like operating systems such as Linux are often considered unsuitable for real-time data collection because of the potential for indeterminate timing latencies resulting from preemptive scheduling. In this paper, Linux is shown to be fully adequate for precisely controlled programming with millisecond resolution or better. The Linux system calls that subserve such timing control are described and tested and then utilized in a MIDI-based program for tapping and music performance experiments. The timing of this program, including data input and output, is shown to be accurate at the millisecond level. This demonstrates that Linux, with proper programming, is suitable for real-time experiment software. In addition, the detailed description and test of both the operating system facilities and the application program itself may serve as a model for publicly documenting programming methods and software performance on other operating systems.

NASA's Climate in a Box: Desktop Supercomputing for Open Scientific Model Development

NASA Astrophysics Data System (ADS)

Wojcik, G. S.; Seablom, M. S.; Lee, T. J.; McConaughy, G. R.; Syed, R.; Oloso, A.; Kemp, E. M.; Greenseid, J.; Smith, R.

2009-12-01

NASA's High Performance Computing Portfolio in cooperation with its Modeling, Analysis, and Prediction program intends to make its climate and earth science models more accessible to a larger community. A key goal of this effort is to open the model development and validation process to the scientific community at large such that a natural selection process is enabled and results in a more efficient scientific process. One obstacle to others using NASA models is the complexity of the models and the difficulty in learning how to use them. This situation applies not only to scientists who regularly use these models but also non-typical users who may want to use the models such as scientists from different domains, policy makers, and teachers. Another obstacle to the use of these models is that access to high performance computing (HPC) accounts, from which the models are implemented, can be restrictive with long wait times in job queues and delays caused by an arduous process of obtaining an account, especially for foreign nationals. This project explores the utility of using desktop supercomputers in providing a complete ready-to-use toolkit of climate research products to investigators and on demand access to an HPC system. One objective of this work is to pre-package NASA and NOAA models so that new users will not have to spend significant time porting the models. In addition, the prepackaged toolkit will include tools, such as workflow, visualization, social networking web sites, and analysis tools, to assist users in running the models and analyzing the data. The system architecture to be developed will allow for automatic code updates for each user and an effective means with which to deal with data that are generated. We plan to investigate several desktop systems, but our work to date has focused on a Cray CX1. Currently, we are investigating the potential capabilities of several non-traditional development environments. While most NASA and NOAA models are designed for Linux operating systems (OS), the arrival of the WindowsHPC 2008 OS provides the opportunity to evaluate the use of a new platform on which to develop and port climate and earth science models. In particular, we are evaluating Microsoft's Visual Studio Integrated Developer Environment to determine its appropriateness for the climate modeling community. In the initial phases of this project, we have ported GEOS-5, WRF, GISS ModelE, and GFS to Linux on a CX1 and are in the process of porting WRF and ModelE to WindowsHPC 2008. Initial tests on the CX1 Linux OS indicate favorable comparisons in terms of performance and consistency of scientific results when compared with experiments executed on NASA high end systems. As in the past, NASA's large clusters will continue to be an important part of our objectives. We envision a seamless environment in which an investigator performs model development and testing on a desktop system and can seamlessly transfer execution to supercomputer clusters for production.

Virtual network computing: cross-platform remote display and collaboration software.

PubMed

Konerding, D E

1999-04-01

VNC (Virtual Network Computing) is a computer program written to address the problem of cross-platform remote desktop/application display. VNC uses a client/server model in which an image of the desktop of the server is transmitted to the client and displayed. The client collects mouse and keyboard input from the user and transmits them back to the server. The VNC client and server can run on Windows 95/98/NT, MacOS, and Unix (including Linux) operating systems. VNC is multi-user on Unix machines (any number of servers can be run are unrelated to the primary display of the computer), while it is effectively single-user on Macintosh and Windows machines (only one server can be run, displaying the contents of the primary display of the server). The VNC servers can be configured to allow more than one client to connect at one time, effectively allowing collaboration through the shared desktop. I describe the function of VNC, provide details of installation, describe how it achieves its goal, and evaluate the use of VNC for molecular modelling. VNC is an extremely useful tool for collaboration, instruction, software development, and debugging of graphical programs with remote users.

Consed: a graphical editor for next-generation sequencing.

PubMed

Gordon, David; Green, Phil

2013-11-15

The rapid growth of DNA sequencing throughput in recent years implies that graphical interfaces for viewing and correcting errors must now handle large numbers of reads, efficiently pinpoint regions of interest and automate as many tasks as possible. We have adapted consed to reflect this. To allow full-feature editing of large datasets while keeping memory requirements low, we developed a viewer, bamScape, that reads billion-read BAM files, identifies and displays problem areas for user review and launches the consed graphical editor on user-selected regions, allowing, in addition to longstanding consed capabilities such as assembly editing, a variety of new features including direct editing of the reference sequence, variant and error detection, display of annotation tracks and the ability to simultaneously process a group of reads. Many batch processing capabilities have been added. The consed package is free to academic, government and non-profit users, and licensed to others for a fee by the University of Washington. The current version (26.0) is available for linux, macosx and solaris systems or as C++ source code. It includes a user's manual (with exercises) and example datasets. http://www.phrap.org/consed/consed.html dgordon@uw.edu .

XOP: a multiplatform graphical user interface for synchrotron radiation spectral and optics calculations

NASA Astrophysics Data System (ADS)

Sanchez del Rio, Manuel; Dejus, Roger J.

1997-11-01

XOP (X-ray OPtics utilities) is a graphical user interface (GUI) created to execute several computer programs that calculate the basic information needed by a synchrotron beamline scientist (designer or experimentalist). Typical examples of such calculations are: insertion device (undulator or wiggler) spectral and angular distributions, mirror and multilayer reflectivities, and crystal diffraction profiles. All programs are provided to the user under a unified GUI, which greatly simplifies their execution. The XOP optics applications (especially mirror calculations) take their basic input (optical constants, compound and mixture tables) from a flexible file-oriented database, which allows the user to select data from a large number of choices and also to customize their own data sets. XOP includes many mathematical and visualization capabilities. It also permits the combination of reflectivities from several mirrors and filters, and their effect, onto a source spectrum. This feature is very useful when calculating thermal load on a series of optical elements. The XOP interface is written in the IDL (Interactive Data Language). An embedded version of XOP, which freely runs under most Unix platforms (HP, Sun, Dec, Linux, etc) and under Windows95 and NT, is available upon request.

Microprocessor-controlled, wide-range streak camera

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

Amy E. Lewis, Craig Hollabaugh

Bechtel Nevada/NSTec recently announced deployment of their fifth generation streak camera. This camera incorporates many advanced features beyond those currently available for streak cameras. The arc-resistant driver includes a trigger lockout mechanism, actively monitors input trigger levels, and incorporates a high-voltage fault interrupter for user safety and tube protection. The camera is completely modular and may deflect over a variable full-sweep time of 15 nanoseconds to 500 microseconds. The camera design is compatible with both large- and small-format commercial tubes from several vendors. The embedded microprocessor offers Ethernet connectivity, and XML [extensible markup language]-based configuration management with non-volatile parameter storagemore » using flash-based storage media. The camera’s user interface is platform-independent (Microsoft Windows, Unix, Linux, Macintosh OSX) and is accessible using an AJAX [asynchronous Javascript and XML]-equipped modem browser, such as Internet Explorer 6, Firefox, or Safari. User interface operation requires no installation of client software or browser plug-in technology. Automation software can also access the camera configuration and control using HTTP [hypertext transfer protocol]. The software architecture supports multiple-simultaneous clients, multiple cameras, and multiple module access with a standard browser. The entire user interface can be customized.« less

Microprocessor-controlled wide-range streak camera

NASA Astrophysics Data System (ADS)

Lewis, Amy E.; Hollabaugh, Craig

2006-08-01

Bechtel Nevada/NSTec recently announced deployment of their fifth generation streak camera. This camera incorporates many advanced features beyond those currently available for streak cameras. The arc-resistant driver includes a trigger lockout mechanism, actively monitors input trigger levels, and incorporates a high-voltage fault interrupter for user safety and tube protection. The camera is completely modular and may deflect over a variable full-sweep time of 15 nanoseconds to 500 microseconds. The camera design is compatible with both large- and small-format commercial tubes from several vendors. The embedded microprocessor offers Ethernet connectivity, and XML [extensible markup language]-based configuration management with non-volatile parameter storage using flash-based storage media. The camera's user interface is platform-independent (Microsoft Windows, Unix, Linux, Macintosh OSX) and is accessible using an AJAX [asynchronous Javascript and XML]-equipped modem browser, such as Internet Explorer 6, Firefox, or Safari. User interface operation requires no installation of client software or browser plug-in technology. Automation software can also access the camera configuration and control using HTTP [hypertext transfer protocol]. The software architecture supports multiple-simultaneous clients, multiple cameras, and multiple module access with a standard browser. The entire user interface can be customized.

Profex: a graphical user interface for the Rietveld refinement program BGMN.

PubMed

Doebelin, Nicola; Kleeberg, Reinhard

2015-10-01

Profex is a graphical user interface for the Rietveld refinement program BGMN . Its interface focuses on preserving BGMN 's powerful and flexible scripting features by giving direct access to BGMN input files. Very efficient workflows for single or batch refinements are achieved by managing refinement control files and structure files, by providing dialogues and shortcuts for many operations, by performing operations in the background, and by providing import filters for CIF and XML crystal structure files. Refinement results can be easily exported for further processing. State-of-the-art graphical export of diffraction patterns to pixel and vector graphics formats allows the creation of publication-quality graphs with minimum effort. Profex reads and converts a variety of proprietary raw data formats and is thus largely instrument independent. Profex and BGMN are available under an open-source license for Windows, Linux and OS X operating systems.

poRe: an R package for the visualization and analysis of nanopore sequencing data.

PubMed

Watson, Mick; Thomson, Marian; Risse, Judith; Talbot, Richard; Santoyo-Lopez, Javier; Gharbi, Karim; Blaxter, Mark

2015-01-01

The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the bioinformatics community will need to design and build a suite of tools specifically for MinION data. Here we present poRe, a package for R that enables users to manipulate, organize, summarize and visualize MinION nanopore sequencing data. As a package for R, poRe has been tested on Windows, Linux and MacOSX. Crucially, the Windows version allows users to analyse MinION data on the Windows laptop attached to the device. poRe is released as a package for R at http://sourceforge.net/projects/rpore/. A tutorial and further information are available at https://sourceforge.net/p/rpore/wiki/Home/. © The Author 2014. Published by Oxford University Press.

Profex: a graphical user interface for the Rietveld refinement program BGMN

PubMed Central

Doebelin, Nicola; Kleeberg, Reinhard

2015-01-01

Profex is a graphical user interface for the Rietveld refinement program BGMN. Its interface focuses on preserving BGMN’s powerful and flexible scripting features by giving direct access to BGMN input files. Very efficient workflows for single or batch refinements are achieved by managing refinement control files and structure files, by providing dialogues and shortcuts for many operations, by performing operations in the background, and by providing import filters for CIF and XML crystal structure files. Refinement results can be easily exported for further processing. State-of-the-art graphical export of diffraction patterns to pixel and vector graphics formats allows the creation of publication-quality graphs with minimum effort. Profex reads and converts a variety of proprietary raw data formats and is thus largely instrument independent. Profex and BGMN are available under an open-source license for Windows, Linux and OS X operating systems. PMID:26500466

FLASH Interface; a GUI for managing runtime parameters in FLASH simulations

NASA Astrophysics Data System (ADS)

Walker, Christopher; Tzeferacos, Petros; Weide, Klaus; Lamb, Donald; Flocke, Norbert; Feister, Scott

2017-10-01

We present FLASH Interface, a novel graphical user interface (GUI) for managing runtime parameters in simulations performed with the FLASH code. FLASH Interface supports full text search of available parameters; provides descriptions of each parameter's role and function; allows for the filtering of parameters based on categories; performs input validation; and maintains all comments and non-parameter information already present in existing parameter files. The GUI can be used to edit existing parameter files or generate new ones. FLASH Interface is open source and was implemented with the Electron framework, making it available on Mac OSX, Windows, and Linux operating systems. The new interface lowers the entry barrier for new FLASH users and provides an easy-to-use tool for experienced FLASH simulators. U.S. Department of Energy (DOE), NNSA ASC/Alliances Center for Astrophysical Thermonuclear Flashes, U.S. DOE NNSA ASC through the Argonne Institute for Computing in Science, U.S. National Science Foundation.

ShelXle: a Qt graphical user interface for SHELXL.

PubMed

Hübschle, Christian B; Sheldrick, George M; Dittrich, Birger

2011-12-01

ShelXle is a graphical user interface for SHELXL [Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122], currently the most widely used program for small-molecule structure refinement. It combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (F(o)) and difference density (F(o)-F(c)) maps. Special features of ShelXle include intuitive atom (re-)naming, a strongly coupled editor, structure visualization in various mono and stereo modes, and a novel way of displaying disorder extending over special positions. ShelXle is completely compatible with all features of SHELXL and is written entirely in C++ using the Qt4 and FFTW libraries. It is available at no cost for Windows, Linux and Mac-OS X and as source code.

Apollo: a community resource for genome annotation editing

PubMed Central

Ed, Lee; Nomi, Harris; Mark, Gibson; Raymond, Chetty; Suzanna, Lewis

2009-01-01

Summary: Apollo is a genome annotation-editing tool with an easy to use graphical interface. It is a component of the GMOD project, with ongoing development driven by the community. Recent additions to the software include support for the generic feature format version 3 (GFF3), continuous transcriptome data, a full Chado database interface, integration with remote services for on-the-fly BLAST and Primer BLAST analyses, graphical interfaces for configuring user preferences and full undo of all edit operations. Apollo's user community continues to grow, including its use as an educational tool for college and high-school students. Availability: Apollo is a Java application distributed under a free and open source license. Installers for Windows, Linux, Unix, Solaris and Mac OS X are available at http://apollo.berkeleybop.org, and the source code is available from the SourceForge CVS repository at http://gmod.cvs.sourceforge.net/gmod/apollo. Contact: elee@berkeleybop.org PMID:19439563

Apollo: a community resource for genome annotation editing.

PubMed

Lee, Ed; Harris, Nomi; Gibson, Mark; Chetty, Raymond; Lewis, Suzanna

2009-07-15

Apollo is a genome annotation-editing tool with an easy to use graphical interface. It is a component of the GMOD project, with ongoing development driven by the community. Recent additions to the software include support for the generic feature format version 3 (GFF3), continuous transcriptome data, a full Chado database interface, integration with remote services for on-the-fly BLAST and Primer BLAST analyses, graphical interfaces for configuring user preferences and full undo of all edit operations. Apollo's user community continues to grow, including its use as an educational tool for college and high-school students. Apollo is a Java application distributed under a free and open source license. Installers for Windows, Linux, Unix, Solaris and Mac OS X are available at http://apollo.berkeleybop.org, and the source code is available from the SourceForge CVS repository at http://gmod.cvs.sourceforge.net/gmod/apollo.

Simulation Platform: a cloud-based online simulation environment.

PubMed

Yamazaki, Tadashi; Ikeno, Hidetoshi; Okumura, Yoshihiro; Satoh, Shunji; Kamiyama, Yoshimi; Hirata, Yutaka; Inagaki, Keiichiro; Ishihara, Akito; Kannon, Takayuki; Usui, Shiro

2011-09-01

For multi-scale and multi-modal neural modeling, it is needed to handle multiple neural models described at different levels seamlessly. Database technology will become more important for these studies, specifically for downloading and handling the neural models seamlessly and effortlessly. To date, conventional neuroinformatics databases have solely been designed to archive model files, but the databases should provide a chance for users to validate the models before downloading them. In this paper, we report our on-going project to develop a cloud-based web service for online simulation called "Simulation Platform". Simulation Platform is a cloud of virtual machines running GNU/Linux. On a virtual machine, various software including developer tools such as compilers and libraries, popular neural simulators such as GENESIS, NEURON and NEST, and scientific software such as Gnuplot, R and Octave, are pre-installed. When a user posts a request, a virtual machine is assigned to the user, and the simulation starts on that machine. The user remotely accesses to the machine through a web browser and carries out the simulation, without the need to install any software but a web browser on the user's own computer. Therefore, Simulation Platform is expected to eliminate impediments to handle multiple neural models that require multiple software. Copyright © 2011 Elsevier Ltd. All rights reserved.

Reprint of: Simulation Platform: a cloud-based online simulation environment.

PubMed

Yamazaki, Tadashi; Ikeno, Hidetoshi; Okumura, Yoshihiro; Satoh, Shunji; Kamiyama, Yoshimi; Hirata, Yutaka; Inagaki, Keiichiro; Ishihara, Akito; Kannon, Takayuki; Usui, Shiro

2011-11-01

For multi-scale and multi-modal neural modeling, it is needed to handle multiple neural models described at different levels seamlessly. Database technology will become more important for these studies, specifically for downloading and handling the neural models seamlessly and effortlessly. To date, conventional neuroinformatics databases have solely been designed to archive model files, but the databases should provide a chance for users to validate the models before downloading them. In this paper, we report our on-going project to develop a cloud-based web service for online simulation called "Simulation Platform". Simulation Platform is a cloud of virtual machines running GNU/Linux. On a virtual machine, various software including developer tools such as compilers and libraries, popular neural simulators such as GENESIS, NEURON and NEST, and scientific software such as Gnuplot, R and Octave, are pre-installed. When a user posts a request, a virtual machine is assigned to the user, and the simulation starts on that machine. The user remotely accesses to the machine through a web browser and carries out the simulation, without the need to install any software but a web browser on the user's own computer. Therefore, Simulation Platform is expected to eliminate impediments to handle multiple neural models that require multiple software. Copyright © 2011 Elsevier Ltd. All rights reserved.

PASMet: a web-based platform for prediction, modelling and analyses of metabolic systems

PubMed Central

Sriyudthsak, Kansuporn; Mejia, Ramon Francisco; Arita, Masanori; Hirai, Masami Yokota

2016-01-01

PASMet (Prediction, Analysis and Simulation of Metabolic networks) is a web-based platform for proposing and verifying mathematical models to understand the dynamics of metabolism. The advantages of PASMet include user-friendliness and accessibility, which enable biologists and biochemists to easily perform mathematical modelling. PASMet offers a series of user-functions to handle the time-series data of metabolite concentrations. The functions are organised into four steps: (i) Prediction of a probable metabolic pathway and its regulation; (ii) Construction of mathematical models; (iii) Simulation of metabolic behaviours; and (iv) Analysis of metabolic system characteristics. Each function contains various statistical and mathematical methods that can be used independently. Users who may not have enough knowledge of computing or programming can easily and quickly analyse their local data without software downloads, updates or installations. Users only need to upload their files in comma-separated values (CSV) format or enter their model equations directly into the website. Once the time-series data or mathematical equations are uploaded, PASMet automatically performs computation on server-side. Then, users can interactively view their results and directly download them to their local computers. PASMet is freely available with no login requirement at http://pasmet.riken.jp/ from major web browsers on Windows, Mac and Linux operating systems. PMID:27174940

SLURM: Simple Linux Utility for Resource Management

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

Jette, M; Dunlap, C; Garlick, J

2002-07-08

Simple Linux Utility for Resource Management (SLURM) is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for Linux clusters of thousands of nodes. Components include machine status, partition management, job management, scheduling and stream copy modules. The design also includes a scalable, general-purpose communication infrastructure. This paper presents a overview of the SLURM architecture and functionality.

WILBER and PyWEED: Event-based Seismic Data Request Tools

NASA Astrophysics Data System (ADS)

Falco, N.; Clark, A.; Trabant, C. M.

2017-12-01

WILBER and PyWEED are two user-friendly tools for requesting event-oriented seismic data. Both tools provide interactive maps and other controls for browsing and filtering event and station catalogs, and downloading data for selected event/station combinations, where the data window for each event/station pair may be defined relative to the arrival time of seismic waves from the event to that particular station. Both tools allow data to be previewed visually, and can download data in standard miniSEED, SAC, and other formats, complete with relevant metadata for performing instrument correction. WILBER is a web application requiring only a modern web browser. Once the user has selected an event, WILBER identifies all data available for that time period, and allows the user to select stations based on criteria such as the station's distance and orientation relative to the event. When the user has finalized their request, the data is collected and packaged on the IRIS server, and when it is ready the user is sent a link to download. PyWEED is a downloadable, cross-platform (Macintosh / Windows / Linux) application written in Python. PyWEED allows a user to select multiple events and stations, and will download data for each event/station combination selected. PyWEED is built around the ObsPy seismic toolkit, and allows direct interaction and control of the application through a Python interactive console.

MMX-I: A data-processing software for multi-modal X-ray imaging and tomography

NASA Astrophysics Data System (ADS)

Bergamaschi, A.; Medjoubi, K.; Messaoudi, C.; Marco, S.; Somogyi, A.

2017-06-01

Scanning hard X-ray imaging allows simultaneous acquisition of multimodal information, including X-ray fluorescence, absorption, phase and dark-field contrasts, providing structural and chemical details of the samples. Combining these scanning techniques with the infrastructure developed for fast data acquisition at Synchrotron Soleil permits to perform multimodal imaging and tomography during routine user experiments at the Nanoscopium beamline. A main challenge of such imaging techniques is the online processing and analysis of the generated very large volume (several hundreds of Giga Bytes) multimodal data-sets. This is especially important for the wide user community foreseen at the user oriented Nanoscopium beamline (e.g. from the fields of Biology, Life Sciences, Geology, Geobiology), having no experience in such data-handling. MMX-I is a new multi-platform open-source freeware for the processing and reconstruction of scanning multi-technique X-ray imaging and tomographic datasets. The MMX-I project aims to offer, both expert users and beginners, the possibility of processing and analysing raw data, either on-site or off-site. Therefore we have developed a multi-platform (Mac, Windows and Linux 64bit) data processing tool, which is easy to install, comprehensive, intuitive, extendable and user-friendly. MMX-I is now routinely used by the Nanoscopium user community and has demonstrated its performance in treating big data.

FingerScanner: Embedding a Fingerprint Scanner in a Raspberry Pi.

PubMed

Sapes, Jordi; Solsona, Francesc

2016-02-06

Nowadays, researchers are paying increasing attention to embedding systems. Cost reduction has lead to an increase in the number of platforms supporting the operating system Linux, jointly with the Raspberry Pi motherboard. Thus, embedding devices on Raspberry-Linux systems is a goal in order to make competitive commercial products. This paper presents a low-cost fingerprint recognition system embedded into a Raspberry Pi with Linux.

deepTools2: a next generation web server for deep-sequencing data analysis.

PubMed

Ramírez, Fidel; Ryan, Devon P; Grüning, Björn; Bhardwaj, Vivek; Kilpert, Fabian; Richter, Andreas S; Heyne, Steffen; Dündar, Friederike; Manke, Thomas

2016-07-08

We present an update to our Galaxy-based web server for processing and visualizing deeply sequenced data. Its core tool set, deepTools, allows users to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. Since we first described our deepTools Galaxy server in 2014, we have implemented new solutions for many requests from the community and our users. Here, we introduce significant enhancements and new tools to further improve data visualization and interpretation. deepTools continue to be open to all users and freely available as a web service at deeptools.ie-freiburg.mpg.de The new deepTools2 suite can be easily deployed within any Galaxy framework via the toolshed repository, and we also provide source code for command line usage under Linux and Mac OS X. A public and documented API for access to deepTools functionality is also available. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

Wahanani, Nursinta Adi, E-mail: sintaadi@batan.go.id; Natsir, Khairina, E-mail: sintaadi@batan.go.id; Hartini, Entin, E-mail: sintaadi@batan.go.id

Data processing software packages such as VSOP and MCNPX are softwares that has been scientifically proven and complete. The result of VSOP and MCNPX are huge and complex text files. In the analyze process, user need additional processing like Microsoft Excel to show informative result. This research develop an user interface software for output of VSOP and MCNPX. VSOP program output is used to support neutronic analysis and MCNPX program output is used to support burn-up analysis. Software development using iterative development methods which allow for revision and addition of features according to user needs. Processing time with this softwaremore » 500 times faster than with conventional methods using Microsoft Excel. PYTHON is used as a programming language, because Python is available for all major operating systems: Windows, Linux/Unix, OS/2, Mac, Amiga, among others. Values that support neutronic analysis are k-eff, burn-up and mass Pu{sup 239} and Pu{sup 241}. Burn-up analysis used the mass inventory values of actinide (Thorium, Plutonium, Neptunium and Uranium). Values are visualized in graphical shape to support analysis.« less

PuffinPlot: A versatile, user-friendly program for paleomagnetic analysis

NASA Astrophysics Data System (ADS)

Lurcock, P. C.; Wilson, G. S.

2012-06-01

PuffinPlot is a user-friendly desktop application for analysis of paleomagnetic data, offering a unique combination of features. It runs on several operating systems, including Windows, Mac OS X, and Linux; supports both discrete and long core data; and facilitates analysis of very weakly magnetic samples. As well as interactive graphical operation, PuffinPlot offers batch analysis for large volumes of data, and a Python scripting interface for programmatic control of its features. Available data displays include demagnetization/intensity, Zijderveld, equal-area (for sample, site, and suite level demagnetization data, and for magnetic susceptibility anisotropy data), a demagnetization data table, and a natural remanent magnetization intensity histogram. Analysis types include principal component analysis, Fisherian statistics, and great-circle path intersections. The results of calculations can be exported as CSV (comma-separated value) files; graphs can be printed, and can also be saved as publication-quality vector files in SVG or PDF format. PuffinPlot is free, and the program, user manual, and fully documented source code may be downloaded from http://code.google.com/p/puffinplot/.

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

Hart, William Eugene

These slides describe different strategies for installing Python software. Although I am a big fan of Python software development, robust strategies for software installation remains a challenge. This talk describes several different installation scenarios. The Good: the user has administrative privileges - Installing on Windows with an installer executable, Installing with Linux application utility, Installing a Python package from the PyPI repository, and Installing a Python package from source. The Bad: the user does not have administrative privileges - Using a virtual environment to isolate package installations, and Using an installer executable on Windows with a virtual environment. The Ugly:more » the user needs to install an extension package from source - Installing a Python extension package from source, and PyCoinInstall - Managing builds for Python extension packages. The last item referring to PyCoinInstall describes a utility being developed for the COIN-OR software, which is used within the operations research community. COIN-OR includes a variety of Python and C++ software packages, and this script uses a simple plug-in system to support the management of package builds and installation.« less

BioVEC: a program for biomolecule visualization with ellipsoidal coarse-graining.

PubMed

Abrahamsson, Erik; Plotkin, Steven S

2009-09-01

Biomolecule Visualization with Ellipsoidal Coarse-graining (BioVEC) is a tool for visualizing molecular dynamics simulation data while allowing coarse-grained residues to be rendered as ellipsoids. BioVEC reads in configuration files, which may be output from molecular dynamics simulations that include orientation output in either quaternion or ANISOU format, and can render frames of the trajectory in several common image formats for subsequent concatenation into a movie file. The BioVEC program is written in C++, uses the OpenGL API for rendering, and is open source. It is lightweight, allows for user-defined settings for and texture, and runs on either Windows or Linux platforms.

LK Scripting Language

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

The LK scripting language is a simple and fast computer programming language designed for easy integration with existing software to enable automation of tasks. The LK language is used by NREL’s System Advisor Model (SAM), the SAM Software Development Kit (SDK), and SolTrace products. LK is easy extensible and adaptable to new software due to its small footprint and is designed to be statically linked into other software. It is written in standard C++, is cross-platform (Windows, Linux, and OSX), and includes optional portions that enable direct integration with graphical user interfaces written in the open source C++ wxWidgets Versionmore » 3.0+ toolkit.« less

ImagePy: an open-source, Python-based and platform-independent software package for boimage analysis.

PubMed

Wang, Anliang; Yan, Xiaolong; Wei, Zhijun

2018-04-27

This note presents the design of a scalable software package named ImagePy for analysing biological images. Our contribution is concentrated on facilitating extensibility and interoperability of the software through decoupling the data model from the user interface. Especially with assistance from the Python ecosystem, this software framework makes modern computer algorithms easier to be applied in bioimage analysis. ImagePy is free and open source software, with documentation and code available at https://github.com/Image-Py/imagepy under the BSD license. It has been tested on the Windows, Mac and Linux operating systems. wzjdlut@dlut.edu.cn or yxdragon@imagepy.org.

Molmil: a molecular viewer for the PDB and beyond.

PubMed

Bekker, Gert-Jan; Nakamura, Haruki; Kinjo, Akira R

2016-01-01

We have developed a new platform-independent web-based molecular viewer using JavaScript and WebGL. The molecular viewer, Molmil, has been integrated into several services offered by Protein Data Bank Japan and can be easily extended with new functionality by third party developers. Furthermore, the viewer can be used to load files in various formats from the user's local hard drive without uploading the data to a server. Molmil is available for all platforms supporting WebGL (e.g. Windows, Linux, iOS, Android) from http://gjbekker.github.io/molmil/. The source code is available at http://github.com/gjbekker/molmil under the LGPLv3 licence.

Introduction to an Open Source Internet-Based Testing Program for Medical Student Examinations

PubMed Central

2009-01-01

The author developed a freely available open source internet-based testing program for medical examination. PHP and Java script were used as the programming language and postgreSQL as the database management system on an Apache web server and Linux operating system. The system approach was that a super user inputs the items, each school administrator inputs the examinees' information, and examinees access the system. The examinee's score is displayed immediately after examination with item analysis. The set-up of the system beginning with installation is described. This may help medical professors to easily adopt an internet-based testing system for medical education. PMID:20046457

Digital Image Correlation Engine

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

Turner, Dan; Crozier, Paul; Reu, Phil

DICe is an open source digital image correlation (DIC) tool intended for use as a module in an external application or as a standalone analysis code. It's primary capability is computing full-field displacements and strains from sequences of digital These images are typically of a material sample undergoing a materials characterization experiment, but DICe is also useful for other applications (for example, trajectory tracking). DICe is machine portable (Windows, Linux and Mac) and can be effectively deployed on a high performance computing platform. Capabilities from DICe can be invoked through a library interface, via source code integration of DICe classesmore » or through a graphical user interface.« less

Using Stellarium to cyber-observe the Great American Eclipse

NASA Astrophysics Data System (ADS)

Prim, Ellie R.; Sitar, David J.

2017-09-01

The Great American Eclipse is over. Somewhat sad, is it not? Individuals who were unable to experience the event on August 21, 2017, can now cyber-observe the eclipse with Stellarium (http://www.stellarium.org). In the authors' opinion, it is fun and has many great applications in the classroom. In addition it is open source and available for Android, iOS, and Linux users. We here at Appalachian use it in our introductory astronomy labs for specific activities such as investigating coordinate systems, discovering differences between solar and sidereal days, as well as determining why your "astrological sign" is most often not your "astronomical sign."

NREL's OpenStudio Helps Design More Efficient Buildings (Fact Sheet)

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

Not Available

2014-07-01

The National Renewable Energy Laboratory (NREL) has created the OpenStudio software platform that makes it easier for architects and engineers to evaluate building energy efficiency measures throughout the design process. OpenStudio makes energy modeling more accessible and affordable, helping professionals to design structures with lower utility bills and less carbon emissions, resulting in a healthier environment. OpenStudio includes a user-friendly application suite that makes the U.S. Department of Energy's EnergyPlus and Radiance simulation engines easier to use for whole building energy and daylighting performance analysis. OpenStudio is freely available and runs on Windows, Mac, and Linux operating systems.

Secure Video Surveillance System Acquisition Software

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

2009-12-04

The SVSS Acquisition Software collects and displays video images from two cameras through a VPN, and store the images onto a collection controller. The software is configured to allow a user to enter a time window to display up to 2 1/2, hours of video review. The software collects images from the cameras at a rate of 1 image per second and automatically deletes images older than 3 hours. The software code operates in a linux environment and can be run in a virtual machine on Windows XP. The Sandia software integrates the different COTS software together to build themore » video review system.« less

Introduction to an open source internet-based testing program for medical student examinations.

PubMed

Lee, Yoon-Hwan

2009-12-20

The author developed a freely available open source internet-based testing program for medical examination. PHP and Java script were used as the programming language and postgreSQL as the database management system on an Apache web server and Linux operating system. The system approach was that a super user inputs the items, each school administrator inputs the examinees' information, and examinees access the system. The examinee's score is displayed immediately after examination with item analysis. The set-up of the system beginning with installation is described. This may help medical professors to easily adopt an internet-based testing system for medical education.

Open Source Live Distributions for Computer Forensics

NASA Astrophysics Data System (ADS)

Giustini, Giancarlo; Andreolini, Mauro; Colajanni, Michele

Current distributions of open source forensic software provide digital investigators with a large set of heterogeneous tools. Their use is not always focused on the target and requires high technical expertise. We present a new GNU/Linux live distribution, named CAINE (Computer Aided INvestigative Environment) that contains a collection of tools wrapped up into a user friendly environment. The CAINE forensic framework introduces novel important features, aimed at filling the interoperability gap across different forensic tools. Moreover, it provides a homogeneous graphical interface that drives digital investigators during the acquisition and analysis of electronic evidence, and it offers a semi-automatic mechanism for the creation of the final report.

Alcator C-Mod Digital Plasma Control System

NASA Astrophysics Data System (ADS)

Wolfe, S. M.

2005-10-01

A new digital plasma control system (DPCS) has been implemented for Alcator C-Mod. The new system was put into service at the start of the 2005 run campaign and has been in routine operation since. The system consists of two 64-input, 16-output cPCI digitizers attached to a rack-mounted single-CPU Linux server, which performs both the I/O and the computation. During initial operation, the system was set up to directly emulate the original C-Mod ``Hybrid'' MIMO linear control system. Compatibility with the previous control system allows the existing user interface software and data structures to be used with the new hardware. The control program is written in IDL and runs under standard Linux. Interrupts are disabled during the plasma pulses to achieve real-time operation. A synchronous loop is executed with a nominal cycle rate of 10 kHz. Emulation of the original linear control algorithms requires 50 μsec per iteration, with the time evenly split between I/O and computation, so rates of about 20 KHz are achievable. Reliable vertical position control has been demonstrated with cycle rates as low as 5 KHz. Additional computations, including non-linear algorithms and adaptive response, are implemented as optional procedure calls within the main real-time loop.

Climate tools in mainstream Linux distributions

NASA Astrophysics Data System (ADS)

McKinstry, Alastair

2015-04-01

Debian/meterology is a project to integrate climate tools and analysis software into the mainstream Debian/Ubuntu Linux distributions. This work describes lessons learnt, and recommends practices for scientific software to be adopted and maintained in OS distributions. In addition to standard analysis tools (cdo,, grads, ferret, metview, ncl, etc.), software used by the Earth System Grid Federation was chosen for integraion, to enable ESGF portals to be built on this base; however exposing scientific codes via web APIs enables security weaknesses, normally ignorable, to be exposed. How tools are hardened, and what changes are required to handle security upgrades, are described. Secondly, to enable libraries and components (e.g. Python modules) to be integrated requires planning by writers: it is not sufficient to assume users can upgrade their code when you make incompatible changes. Here, practices are recommended to enable upgrades and co-installability of C, C++, Fortran and Python codes. Finally, software packages such as NetCDF and HDF5 can be built in multiple configurations. Tools may then expect incompatible versions of these libraries (e.g. serial and parallel) to be simultaneously available; how this was solved in Debian using "pkg-config" and shared library interfaces is described, and best practices for software writers to enable this are summarised.

Source Code Analysis Laboratory (SCALe)

DTIC Science & Technology

2012-04-01

Versus Flagged Nonconformities (FNC) Software System TP/FNC Ratio Mozilla Firefox version 2.0 6/12 50% Linux kernel version 2.6.15 10/126 8...is inappropriately tuned for analysis of the Linux kernel, which has anomalous results. Customizing SCALe to work with software for a particular...servers support a collection of virtual machines (VMs) that can be configured to support analysis in various environments, such as Windows XP and Linux . A

FingerScanner: Embedding a Fingerprint Scanner in a Raspberry Pi

PubMed Central

Sapes, Jordi; Solsona, Francesc

2016-01-01

Nowadays, researchers are paying increasing attention to embedding systems. Cost reduction has lead to an increase in the number of platforms supporting the operating system Linux, jointly with the Raspberry Pi motherboard. Thus, embedding devices on Raspberry-Linux systems is a goal in order to make competitive commercial products. This paper presents a low-cost fingerprint recognition system embedded into a Raspberry Pi with Linux. PMID:26861340

Improving Block-level Efficiency with scsi-mq

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

Caldwell, Blake A

2015-01-01

Current generation solid-state storage devices are exposing a new bottlenecks in the SCSI and block layers of the Linux kernel, where IO throughput is limited by lock contention, inefficient interrupt handling, and poor memory locality. To address these limitations, the Linux kernel block layer underwent a major rewrite with the blk-mq project to move from a single request queue to a multi-queue model. The Linux SCSI subsystem rework to make use of this new model, known as scsi-mq, has been merged into the Linux kernel and work is underway for dm-multipath support in the upcoming Linux 4.0 kernel. These piecesmore » were necessary to make use of the multi-queue block layer in a Lustre parallel filesystem with high availability requirements. We undertook adding support of the 3.18 kernel to Lustre with scsi-mq and dm-multipath patches to evaluate the potential of these efficiency improvements. In this paper we evaluate the block-level performance of scsi-mq with backing storage hardware representative of a HPC-targerted Lustre filesystem. Our findings show that SCSI write request latency is reduced by as much as 13.6%. Additionally, when profiling the CPU usage of our prototype Lustre filesystem, we found that CPU idle time increased by a factor of 7 with Linux 3.18 and blk-mq as compared to a standard 2.6.32 Linux kernel. Our findings demonstrate increased efficiency of the multi-queue block layer even with disk-based caching storage arrays used in existing parallel filesystems.« less

Underground Injection Control (UIC)

EPA Pesticide Factsheets

Provide information on: individual injection well classes; regulations specific to each well class; technical guidance; compliance assistance; federal, state, and tribal/territory roles and responsibilities.

Research highlights from the UIC/NIH Center for Botanical Dietary Supplements Research for Women’s Health: Black cohosh from the field to the clinic

PubMed Central

Farnsworth, Norman R; Mahady, Gail B.

2009-01-01

In 1999, the Department of Medicinal Chemistry and Pharmacognosy at the College of Pharmacy, University of Illinois (UIC) at Chicago was funded to establish a Botanical Dietary Supplements Research Center from the National Institutes of Health (NIH). The emphasis of the UIC/NIH Center for Botanical Dietary Supplements Research (CBDSR) is botanical dietary supplements (BDS) for women's health. Center’s research has focused on BDS that may improve women's health and quality of life, specifically in the areas of menopause, premenstrual syndrome, and persistent urinary tract infections. Center investigators have overcome many challenges associated with botanical dietary supplements research, including acquiring and identifying plant species for investigation, isolating and identifying active constituents, elucidating the mechanisms of action of these botanicals, and conducting phase I and phase II clinical studies. Black cohosh [Actaea racemosa L. (Ranunculaceae)] has been used as a model to illustrate the steps involved in taking a botanical dietary supplement from the field, all the way to clinical trials. Bioassays are described that were necessary to elucidate the pertinent biological studies of plant extracts and their mechanisms of action. The Center has used an innovative multidisciplinary approach to this type of research, and thus has been very successful in fulfilling its specific aims. PMID:20161501

Iodine Status and Iodised Salt Consumption in Portuguese School-Aged Children: The Iogeneration Study

PubMed Central

Costa Leite, João; Keating, Elisa; Pestana, Diogo; Cruz Fernandes, Virgínia; Maia, Maria Luz; Norberto, Sónia; Pinto, Edgar; Moreira-Rosário, André; Sintra, Diana; Moreira, Bárbara; Costa, Ana; Silva, Sofia; Costa, Vera; Martins, Inês; Castro Mendes, Francisca; Queirós, Pedro; Peixoto, Bruno; Carlos Caldas, José; Guerra, António; Fontoura, Manuel; Leal, Sandra; Moreira, Roxana; Palmares Carvalho, Irene; Matias Lima, Rui; Martins, Catia; Delerue-Matos, Cristina; Almeida, Agostinho; Azevedo, Luís; Calhau, Conceição

2017-01-01

The World Health Organization promotes salt iodisation to control iodine deficiency. In Portugal, the use of iodised salt in school canteens has been mandatory since 2013. The present study aimed to evaluate iodine status in school-aged children (6–12 years) and to monitor the use of iodised salt in school canteens. A total of 2018 participants were randomly selected to participate in a cross-sectional survey in northern Portugal. Children’s urine and salt samples from households and school canteens were collected. A lifestyle questionnaire was completed by parents to assess children’s eating frequency of iodine food sources. Urinary iodine concentration (UIC) was measured by inductively coupled plasma-mass spectrometry. The median UIC was 129 µg/L which indicates the adequacy of iodine status and 32% of the children had UIC < 100 µg/L. No school canteen implemented the iodised salt policy and only 2% of the households were using iodised salt. Lower consumption of milk, but not fish, was associated with a higher risk of iodine deficiency. Estimation of sodium intake from spot urine samples could be an opportunity for adequate monitoring of population means. Implementation of iodine deficiency control policies should include a monitoring program aligned with the commitment of reducing the population salt intake. PMID:28475154

Iodine Status and Iodised Salt Consumption in Portuguese School-Aged Children: The Iogeneration Study.

PubMed

Costa Leite, João; Keating, Elisa; Pestana, Diogo; Cruz Fernandes, Virgínia; Maia, Maria Luz; Norberto, Sónia; Pinto, Edgar; Moreira-Rosário, André; Sintra, Diana; Moreira, Bárbara; Costa, Ana; Silva, Sofia; Costa, Vera; Martins, Inês; Castro Mendes, Francisca; Queirós, Pedro; Peixoto, Bruno; Carlos Caldas, José; Guerra, António; Fontoura, Manuel; Leal, Sandra; Moreira, Roxana; Palmares Carvalho, Irene; Matias Lima, Rui; Martins, Catia; Delerue-Matos, Cristina; Almeida, Agostinho; Azevedo, Luís; Calhau, Conceição

2017-05-05

The World Health Organization promotes salt iodisation to control iodine deficiency. In Portugal, the use of iodised salt in school canteens has been mandatory since 2013. The present study aimed to evaluate iodine status in school-aged children (6-12 years) and to monitor the use of iodised salt in school canteens. A total of 2018 participants were randomly selected to participate in a cross-sectional survey in northern Portugal. Children's urine and salt samples from households and school canteens were collected. A lifestyle questionnaire was completed by parents to assess children's eating frequency of iodine food sources. Urinary iodine concentration (UIC) was measured by inductively coupled plasma-mass spectrometry. The median UIC was 129 µg/L which indicates the adequacy of iodine status and 32% of the children had UIC < 100 µg/L. No school canteen implemented the iodised salt policy and only 2% of the households were using iodised salt. Lower consumption of milk, but not fish, was associated with a higher risk of iodine deficiency. Estimation of sodium intake from spot urine samples could be an opportunity for adequate monitoring of population means. Implementation of iodine deficiency control policies should include a monitoring program aligned with the commitment of reducing the population salt intake.

Thyroid Function among Breastfed Children with Chronically Excessive Iodine Intakes

PubMed Central

Aakre, Inger; Strand, Tor A.; Bjøro, Trine; Norheim, Ingrid; Barikmo, Ingrid; Ares, Susana; Alcorta, Marta Duque; Henjum, Sigrun

2016-01-01

Iodine excess may impair thyroid function and trigger adverse health consequences for children. This study aims to describe iodine status among breastfed infants with high iodine exposure in the Saharawi refugee camps Algeria, and further assess thyroid function and iodine status among the children three years later. In 2010, a cross-sectional study among 111 breastfed children aged 0–6 months was performed (baseline study). In 2013, a second cross-sectional study (follow-up study) was conducted among 289 children; 213 newly selected and 76 children retrieved from baseline. Urinary iodine concentration (UIC) and breast milk iodine concentration (BMIC) were measured at baseline. UIC, thyroid hormones and serum thyroglobulin (Tg) were measured at follow-up. At baseline and follow-up, 88% and 72% had excessive iodine intakes (UIC ≥ 300 µg/L), respectively. At follow-up, 24% had a thyroid hormone disturbance and/or elevated serum Tg, including 9% with subclinical hypothyroidism (SCH), 4% with elevated fT3 and 14% with elevated Tg. Children with SCH had poorer linear growth and were more likely to be underweight than the children without SCH. Excessive iodine intakes and thyroid disturbances were common among children below four years of age in our study. Further, SCH seemed to be associated with poor growth and weight. PMID:27367720

CANEapp: a user-friendly application for automated next generation transcriptomic data analysis.

PubMed

Velmeshev, Dmitry; Lally, Patrick; Magistri, Marco; Faghihi, Mohammad Ali

2016-01-13

Next generation sequencing (NGS) technologies are indispensable for molecular biology research, but data analysis represents the bottleneck in their application. Users need to be familiar with computer terminal commands, the Linux environment, and various software tools and scripts. Analysis workflows have to be optimized and experimentally validated to extract biologically meaningful data. Moreover, as larger datasets are being generated, their analysis requires use of high-performance servers. To address these needs, we developed CANEapp (application for Comprehensive automated Analysis of Next-generation sequencing Experiments), a unique suite that combines a Graphical User Interface (GUI) and an automated server-side analysis pipeline that is platform-independent, making it suitable for any server architecture. The GUI runs on a PC or Mac and seamlessly connects to the server to provide full GUI control of RNA-sequencing (RNA-seq) project analysis. The server-side analysis pipeline contains a framework that is implemented on a Linux server through completely automated installation of software components and reference files. Analysis with CANEapp is also fully automated and performs differential gene expression analysis and novel noncoding RNA discovery through alternative workflows (Cuffdiff and R packages edgeR and DESeq2). We compared CANEapp to other similar tools, and it significantly improves on previous developments. We experimentally validated CANEapp's performance by applying it to data derived from different experimental paradigms and confirming the results with quantitative real-time PCR (qRT-PCR). CANEapp adapts to any server architecture by effectively using available resources and thus handles large amounts of data efficiently. CANEapp performance has been experimentally validated on various biological datasets. CANEapp is available free of charge at http://psychiatry.med.miami.edu/research/laboratory-of-translational-rna-genomics/CANE-app . We believe that CANEapp will serve both biologists with no computational experience and bioinformaticians as a simple, timesaving but accurate and powerful tool to analyze large RNA-seq datasets and will provide foundations for future development of integrated and automated high-throughput genomics data analysis tools. Due to its inherently standardized pipeline and combination of automated analysis and platform-independence, CANEapp is an ideal for large-scale collaborative RNA-seq projects between different institutions and research groups.

Linux Kernel Co-Scheduling and Bulk Synchronous Parallelism

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

Jones, Terry R

2012-01-01

This paper describes a kernel scheduling algorithm that is based on coscheduling principles and that is intended for parallel applications running on 1000 cores or more. Experimental results for a Linux implementation on a Cray XT5 machine are presented. The results indicate that Linux is a suitable operating system for this new scheduling scheme, and that this design provides a dramatic improvement in scaling performance for synchronizing collective operations at scale.

Iodine nutritional status of women in their first trimester of pregnancy in Catalonia.

PubMed

Torres, Maria Teresa; Francés, Lidia; Vila, Lluis; Manresa, Josep María; Falguera, Gemma; Prieto, Gemma; Casamitjana, Roser; Toran, Pere

2017-07-26

Sufficient iodine intake is needed during pregnancy to ensure proper fetal development. The iodine levels of women in their first trimester of pregnancy in Catalonia are currently unknown. This data would help to determine whether our public health services should establish recommendations or interventions in this line. The aim of this study was to investigate the iodine nutritional status, prevalence of urinary iodine <150 μg/L, and tobacco use in the first trimester of pregnancy in our setting. Cross-sectional study. Data were collected during 2008-2009 from women in their first trimester at the primary care centers of the province of Barcelona (Spain). Pregnant women included in the study completed a questionnaire on eating habits and underwent urinary iodine concentration (UIC) assessment. Nine hundred forty five women completed the dietary questionnaire and urinary iodine testing. Median UIC was 172 μg/L, with 407 participants (43.1%) showing levels <150 μg/L. On multivariate logistic regression analysis, intake of 1-2 glasses of milk per day, OR = 0.636 95% CI (0.45-0.90) or >2 glasses, OR = 0.593 95% CI (0.37-0.95); iodized salt consumption, OR = 0.678 95% CI (0.51-0. 90); and use of iodine supplementation, OR = 0.410 95% CI (0.31-0.54), protected against the risk of UIC <150 μg/L. Simultaneous consumption of iodized salt and milk (≥1 glass/day) showed a larger protective effect: OR = 0.427, 95% CI (0.31-0.54). The median UIC of the pregnant women surveyed indicated an acceptable iodine nutritional status according to the criteria established by the WHO and ICCIDD. The risk of urinary iodine <150 μg/L decreased with simultaneous consumption of milk and iodized salt, similar to the decrease seen with iodine supplementation.

Collaboration rules.

PubMed

Evans, Philip; Wolf, Bob

2005-01-01

Corporate leaders seeking to boost growth, learning, and innovation may find the answer in a surprising place: the Linux open-source software community. Linux is developed by an essentially volunteer, self-organizing community of thousands of programmers. Most leaders would sell their grandmothers for workforces that collaborate as efficiently, frictionlessly, and creatively as the self-styled Linux hackers. But Linux is software, and software is hardly a model for mainstream business. The authors have, nonetheless, found surprising parallels between the anarchistic, caffeinated, hirsute world of Linux hackers and the disciplined, tea-sipping, clean-cut world of Toyota engineering. Specifically, Toyota and Linux operate by rules that blend the self-organizing advantages of markets with the low transaction costs of hierarchies. In place of markets' cash and contracts and hierarchies' authority are rules about how individuals and groups work together (with rigorous discipline); how they communicate (widely and with granularity); and how leaders guide them toward a common goal (through example). Those rules, augmented by simple communication technologies and a lack of legal barriers to sharing information, create rich common knowledge, the ability to organize teams modularly, extraordinary motivation, and high levels of trust, which radically lowers transaction costs. Low transaction costs, in turn, make it profitable for organizations to perform more and smaller transactions--and so increase the pace and flexibility typical of high-performance organizations. Once the system achieves critical mass, it feeds on itself. The larger the system, the more broadly shared the knowledge, language, and work style. The greater individuals' reputational capital, the louder the applause and the stronger the motivation. The success of Linux is evidence of the power of that virtuous circle. Toyota's success is evidence that it is also powerful in conventional companies.

FLY MPI-2: a parallel tree code for LSS

NASA Astrophysics Data System (ADS)

Becciani, U.; Comparato, M.; Antonuccio-Delogu, V.

2006-04-01

New version program summaryProgram title: FLY 3.1 Catalogue identifier: ADSC_v2_0 Licensing provisions: yes Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADSC_v2_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland No. of lines in distributed program, including test data, etc.: 158 172 No. of bytes in distributed program, including test data, etc.: 4 719 953 Distribution format: tar.gz Programming language: Fortran 90, C Computer: Beowulf cluster, PC, MPP systems Operating system: Linux, Aix RAM: 100M words Catalogue identifier of previous version: ADSC_v1_0 Journal reference of previous version: Comput. Phys. Comm. 155 (2003) 159 Does the new version supersede the previous version?: yes Nature of problem: FLY is a parallel collisionless N-body code for the calculation of the gravitational force Solution method: FLY is based on the hierarchical oct-tree domain decomposition introduced by Barnes and Hut (1986) Reasons for the new version: The new version of FLY is implemented by using the MPI-2 standard: the distributed version 3.1 was developed by using the MPICH2 library on a PC Linux cluster. Today the FLY performance allows us to consider the FLY code among the most powerful parallel codes for tree N-body simulations. Another important new feature regards the availability of an interface with hydrodynamical Paramesh based codes. Simulations must follow a box large enough to accurately represent the power spectrum of fluctuations on very large scales so that we may hope to compare them meaningfully with real data. The number of particles then sets the mass resolution of the simulation, which we would like to make as fine as possible. The idea to build an interface between two codes, that have different and complementary cosmological tasks, allows us to execute complex cosmological simulations with FLY, specialized for DM evolution, and a code specialized for hydrodynamical components that uses a Paramesh block structure. Summary of revisions: The parallel communication schema was totally changed. The new version adopts the MPICH2 library. Now FLY can be executed on all Unix systems having an MPI-2 standard library. The main data structure, is declared in a module procedure of FLY (fly_h.F90 routine). FLY creates the MPI Window object for one-sided communication for all the shared arrays, with a call like the following: CALL MPI_WIN_CREATE(POS, SIZE, REAL8, MPI_INFO_NULL, MPI_COMM_WORLD, WIN_POS, IERR) the following main window objects are created: win_pos, win_vel, win_acc: particles positions velocities and accelerations, win_pos_cell, win_mass_cell, win_quad, win_subp, win_grouping: cells positions, masses, quadrupole momenta, tree structure and grouping cells. Other windows are created for dynamic load balance and global counters. Restrictions: The program uses the leapfrog integrator schema, but could be changed by the user. Unusual features: FLY uses the MPI-2 standard: the MPICH2 library on Linux systems was adopted. To run this version of FLY the working directory must be shared among all the processors that execute FLY. Additional comments: Full documentation for the program is included in the distribution in the form of a README file, a User Guide and a Reference manuscript. Running time: IBM Linux Cluster 1350, 512 nodes with 2 processors for each node and 2 GB RAM for each processor, at Cineca, was adopted to make performance tests. Processor type: Intel Xeon Pentium IV 3.0 GHz and 512 KB cache (128 nodes have Nocona processors). Internal Network: Myricom LAN Card "C" Version and "D" Version. Operating System: Linux SuSE SLES 8. The code was compiled using the mpif90 compiler version 8.1 and with basic optimization options in order to have performances that could be useful compared with other generic clusters Processors

Memory Analysis of the KBeast Linux Rootkit: Investigating Publicly Available Linux Rootkit Using the Volatility Memory Analysis Framework

DTIC Science & Technology

2015-06-01

examine how a computer forensic investigator/incident handler, without specialised computer memory or software reverse engineering skills , can successfully...memory images and malware, this new series of reports will be directed at those who must analyse Linux malware-infected memory images. The skills ...disable 1287 1000 1000 /usr/lib/policykit-1-gnome/polkit-gnome-authentication- agent-1 1310 1000 1000 /usr/lib/pulseaudio/pulse/gconf- helper 1350

Reproducible Large-Scale Neuroimaging Studies with the OpenMOLE Workflow Management System.

PubMed

Passerat-Palmbach, Jonathan; Reuillon, Romain; Leclaire, Mathieu; Makropoulos, Antonios; Robinson, Emma C; Parisot, Sarah; Rueckert, Daniel

2017-01-01

OpenMOLE is a scientific workflow engine with a strong emphasis on workload distribution. Workflows are designed using a high level Domain Specific Language (DSL) built on top of Scala. It exposes natural parallelism constructs to easily delegate the workload resulting from a workflow to a wide range of distributed computing environments. OpenMOLE hides the complexity of designing complex experiments thanks to its DSL. Users can embed their own applications and scale their pipelines from a small prototype running on their desktop computer to a large-scale study harnessing distributed computing infrastructures, simply by changing a single line in the pipeline definition. The construction of the pipeline itself is decoupled from the execution context. The high-level DSL abstracts the underlying execution environment, contrary to classic shell-script based pipelines. These two aspects allow pipelines to be shared and studies to be replicated across different computing environments. Workflows can be run as traditional batch pipelines or coupled with OpenMOLE's advanced exploration methods in order to study the behavior of an application, or perform automatic parameter tuning. In this work, we briefly present the strong assets of OpenMOLE and detail recent improvements targeting re-executability of workflows across various Linux platforms. We have tightly coupled OpenMOLE with CARE, a standalone containerization solution that allows re-executing on a Linux host any application that has been packaged on another Linux host previously. The solution is evaluated against a Python-based pipeline involving packages such as scikit-learn as well as binary dependencies. All were packaged and re-executed successfully on various HPC environments, with identical numerical results (here prediction scores) obtained on each environment. Our results show that the pair formed by OpenMOLE and CARE is a reliable solution to generate reproducible results and re-executable pipelines. A demonstration of the flexibility of our solution showcases three neuroimaging pipelines harnessing distributed computing environments as heterogeneous as local clusters or the European Grid Infrastructure (EGI).

Reproducible Large-Scale Neuroimaging Studies with the OpenMOLE Workflow Management System

PubMed Central

Passerat-Palmbach, Jonathan; Reuillon, Romain; Leclaire, Mathieu; Makropoulos, Antonios; Robinson, Emma C.; Parisot, Sarah; Rueckert, Daniel

2017-01-01

OpenMOLE is a scientific workflow engine with a strong emphasis on workload distribution. Workflows are designed using a high level Domain Specific Language (DSL) built on top of Scala. It exposes natural parallelism constructs to easily delegate the workload resulting from a workflow to a wide range of distributed computing environments. OpenMOLE hides the complexity of designing complex experiments thanks to its DSL. Users can embed their own applications and scale their pipelines from a small prototype running on their desktop computer to a large-scale study harnessing distributed computing infrastructures, simply by changing a single line in the pipeline definition. The construction of the pipeline itself is decoupled from the execution context. The high-level DSL abstracts the underlying execution environment, contrary to classic shell-script based pipelines. These two aspects allow pipelines to be shared and studies to be replicated across different computing environments. Workflows can be run as traditional batch pipelines or coupled with OpenMOLE's advanced exploration methods in order to study the behavior of an application, or perform automatic parameter tuning. In this work, we briefly present the strong assets of OpenMOLE and detail recent improvements targeting re-executability of workflows across various Linux platforms. We have tightly coupled OpenMOLE with CARE, a standalone containerization solution that allows re-executing on a Linux host any application that has been packaged on another Linux host previously. The solution is evaluated against a Python-based pipeline involving packages such as scikit-learn as well as binary dependencies. All were packaged and re-executed successfully on various HPC environments, with identical numerical results (here prediction scores) obtained on each environment. Our results show that the pair formed by OpenMOLE and CARE is a reliable solution to generate reproducible results and re-executable pipelines. A demonstration of the flexibility of our solution showcases three neuroimaging pipelines harnessing distributed computing environments as heterogeneous as local clusters or the European Grid Infrastructure (EGI). PMID:28381997

Java application for the superposition T-matrix code to study the optical properties of cosmic dust aggregates

NASA Astrophysics Data System (ADS)

Halder, P.; Chakraborty, A.; Deb Roy, P.; Das, H. S.

2014-09-01

In this paper, we report the development of a java application for the Superposition T-matrix code, JaSTA (Java Superposition T-matrix App), to study the light scattering properties of aggregate structures. It has been developed using Netbeans 7.1.2, which is a java integrated development environment (IDE). The JaSTA uses double precession superposition codes for multi-sphere clusters in random orientation developed by Mackowski and Mischenko (1996). It consists of a graphical user interface (GUI) in the front hand and a database of related data in the back hand. Both the interactive GUI and database package directly enable a user to model by self-monitoring respective input parameters (namely, wavelength, complex refractive indices, grain size, etc.) to study the related optical properties of cosmic dust (namely, extinction, polarization, etc.) instantly, i.e., with zero computational time. This increases the efficiency of the user. The database of JaSTA is now created for a few sets of input parameters with a plan to create a large database in future. This application also has an option where users can compile and run the scattering code directly for aggregates in GUI environment. The JaSTA aims to provide convenient and quicker data analysis of the optical properties which can be used in different fields like planetary science, atmospheric science, nano science, etc. The current version of this software is developed for the Linux and Windows platform to study the light scattering properties of small aggregates which will be extended for larger aggregates using parallel codes in future. Catalogue identifier: AETB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AETB_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.: 571570 No. of bytes in distributed program, including test data, etc.: 120226886 Distribution format: tar.gz Programming language: Java, Fortran95. Computer: Any Windows or Linux systems capable of hosting a java runtime environment, java3D and fortran95 compiler; Developed on 2.40 GHz Intel Core i3. Operating system: Any Windows or Linux systems capable of hosting a java runtime environment, java3D and fortran95 compiler. RAM: Ranging from a few Mbytes to several Gbytes, depending on the input parameters. Classification: 1.3. External routines: jfreechart-1.0.14 [1] (free plotting library for java), j3d-jre-1.5.2 [2] (3D visualization). Nature of problem: Optical properties of cosmic dust aggregates. Solution method: Java application based on Mackowski and Mischenko's Superposition T-Matrix code. Restrictions: The program is designed for single processor systems. Additional comments: The distribution file for this program is over 120 Mbytes and therefore is not delivered directly when Download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. Running time: Ranging from few minutes to several hours, depending on the input parameters. References: [1] http://www.jfree.org/index.html [2] https://java3d.java.net/

Linux Kernel Co-Scheduling For Bulk Synchronous Parallel Applications

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

Jones, Terry R

2011-01-01

This paper describes a kernel scheduling algorithm that is based on co-scheduling principles and that is intended for parallel applications running on 1000 cores or more where inter-node scalability is key. Experimental results for a Linux implementation on a Cray XT5 machine are presented.1 The results indicate that Linux is a suitable operating system for this new scheduling scheme, and that this design provides a dramatic improvement in scaling performance for synchronizing collective operations at scale.

Develop, Build, and Test a Virtual Lab to Support a Vulnerability Training System

DTIC Science & Technology

2004-09-01

docs.us.dell.com/support/edocs/systems/pe1650/ en /it/index.htm> (20 August 2004) “HOWTO: Installing Web Services with Linux /Tomcat/Apache/Struts...configured as host machines with VMware and VNC running on a Linux RedHat 9 Kernel. An Apache-Tomcat web server was configured as the external interface to...1650, dual processor, blade servers were configured as host machines with VMware and VNC running on a Linux RedHat 9 Kernel. An Apache-Tomcat web

myChEMBL: a virtual machine implementation of open data and cheminformatics tools.

PubMed

Ochoa, Rodrigo; Davies, Mark; Papadatos, George; Atkinson, Francis; Overington, John P

2014-01-15

myChEMBL is a completely open platform, which combines public domain bioactivity data with open source database and cheminformatics technologies. myChEMBL consists of a Linux (Ubuntu) Virtual Machine featuring a PostgreSQL schema with the latest version of the ChEMBL database, as well as the latest RDKit cheminformatics libraries. In addition, a self-contained web interface is available, which can be modified and improved according to user specifications. The VM is available at: ftp://ftp.ebi.ac.uk/pub/databases/chembl/VM/myChEMBL/current. The web interface and web services code is available at: https://github.com/rochoa85/myChEMBL.

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.

PubMed

Wehe, André; Bansal, Mukul S; Burleigh, J Gordon; Eulenstein, Oliver

2008-07-01

DupTree is a new software program for inferring rooted species trees from collections of gene trees using the gene tree parsimony approach. The program implements a novel algorithm that significantly improves upon the run time of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phylogenetic analyses. In addition, DupTree allows users to examine alternate rootings and to weight the reconciliation costs for gene trees. DupTree is an open source project written in C++. DupTree for Mac OS X, Windows, and Linux along with a sample dataset and an on-line manual are available at http://genome.cs.iastate.edu/CBL/DupTree

DAMBE7: New and Improved Tools for Data Analysis in Molecular Biology and Evolution.

PubMed

Xia, Xuhua

2018-06-01

DAMBE is a comprehensive software package for genomic and phylogenetic data analysis on Windows, Linux, and Macintosh computers. New functions include imputing missing distances and phylogeny simultaneously (paving the way to build large phage and transposon trees), new bootstrapping/jackknifing methods for PhyPA (phylogenetics from pairwise alignments), and an improved function for fast and accurate estimation of the shape parameter of the gamma distribution for fitting rate heterogeneity over sites. Previous method corrects multiple hits for each site independently. DAMBE's new method uses all sites simultaneously for correction. DAMBE, featuring a user-friendly graphic interface, is freely available from http://dambe.bio.uottawa.ca (last accessed, April 17, 2018).

KITTEN Lightweight Kernel 0.1 Beta

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

Pedretti, Kevin; Levenhagen, Michael; Kelly, Suzanne

2007-12-12

The Kitten Lightweight Kernel is a simplified OS (operating system) kernel that is intended to manage a compute node's hardware resources. It provides a set of mechanisms to user-level applications for utilizing hardware resources (e.g., allocating memory, creating processes, accessing the network). Kitten is much simpler than general-purpose OS kernels, such as Linux or Windows, but includes all of the esssential functionality needed to support HPC (high-performance computing) MPI, PGAS and OpenMP applications. Kitten provides unique capabilities such as physically contiguous application memory, transparent large page support, and noise-free tick-less operation, which enable HPC applications to obtain greater efficiency andmore » scalability than with general purpose OS kernels.« less

Free and open source software for the manipulation of digital images.

PubMed

Solomon, Robert W

2009-06-01

Free and open source software is a type of software that is nearly as powerful as commercial software but is freely downloadable. This software can do almost everything that the expensive programs can. GIMP (gnu image manipulation program) is the free program that is comparable to Photoshop, and versions are available for Windows, Macintosh, and Linux platforms. This article briefly describes how GIMP can be installed and used to manipulate radiology images. It is no longer necessary to budget large amounts of money for high-quality software to achieve the goals of image processing and document creation because free and open source software is available for the user to download at will.

Low Cost Night Vision System for Intruder Detection

NASA Astrophysics Data System (ADS)

Ng, Liang S.; Yusoff, Wan Azhar Wan; R, Dhinesh; Sak, J. S.

2016-02-01

The growth in production of Android devices has resulted in greater functionalities as well as lower costs. This has made previously more expensive systems such as night vision affordable for more businesses and end users. We designed and implemented robust and low cost night vision systems based on red-green-blue (RGB) colour histogram for a static camera as well as a camera on an unmanned aerial vehicle (UAV), using OpenCV library on Intel compatible notebook computers, running Ubuntu Linux operating system, with less than 8GB of RAM. They were tested against human intruders under low light conditions (indoor, outdoor, night time) and were shown to have successfully detected the intruders.

GRIL: genome rearrangement and inversion locator.

PubMed

Darling, Aaron E; Mau, Bob; Blattner, Frederick R; Perna, Nicole T

2004-01-01

GRIL is a tool to automatically identify collinear regions in a set of bacterial-size genome sequences. GRIL uses three basic steps. First, regions of high sequence identity are located. Second, some of these regions are filtered based on user-specified criteria. Finally, the remaining regions of sequence identity are used to define significant collinear regions among the sequences. By locating collinear regions of sequence, GRIL provides a basis for multiple genome alignment using current alignment systems. GRIL also provides a basis for using current inversion distance tools to infer phylogeny. GRIL is implemented in C++ and runs on any x86-based Linux or Windows platform. It is available from http://asap.ahabs.wisc.edu/gril

MAX: Multiplatform Applications for XAFS

NASA Astrophysics Data System (ADS)

Alain, Michalowicz; Jacques, Moscovici; Diane, Muller-Bouvet; Karine, Provost

2009-11-01

MAX is a new EXAFS and XANES analysis package, replacing our old "EXAFS pour le Mac" software suite. The major improvement is the ability to work with strictly the same code, compiled at once for Microsoft Windows, Apple MacOSX and LINUX systems, justifying the title "Multiplatform Applications for XAFS". It is organized as four modules: ABSORBIX (X-ray absorbance and fluorescence self-absorption calculations), CHEROKEE (EXAFS and XANES data treatment), ROUNDMIDNIGHT (EXAFS modeling and fit) and CRYSTALFFREV (from crystal structures and molecular modeling to FEFF EXAFS and XANES theoretical calculations). Most features developed in "EXAFS pour le Mac" are still available, but with much improvements in the user's interface, data treatment algorithms and new functionalities.

Raven-II: an open platform for surgical robotics research.

PubMed

Hannaford, Blake; Rosen, Jacob; Friedman, Diana W; King, Hawkeye; Roan, Phillip; Cheng, Lei; Glozman, Daniel; Ma, Ji; Kosari, Sina Nia; White, Lee

2013-04-01

The Raven-II is a platform for collaborative research on advances in surgical robotics. Seven universities have begun research using this platform. The Raven-II system has two 3-DOF spherical positioning mechanisms capable of attaching interchangeable four DOF instruments. The Raven-II software is based on open standards such as Linux and ROS to maximally facilitate software development. The mechanism is robust enough for repeated experiments and animal surgery experiments, but is not engineered to sufficient safety standards for human use. Mechanisms in place for interaction among the user community and dissemination of results include an electronic forum, an online software SVN repository, and meetings and workshops at major robotics conferences.

Environmental Info for South Dakota

EPA Pesticide Factsheets

This page contains information about air and water in South Dakota, including state implementation programs (SIPs), air permitting, underground injection control (UIC) and National Pollution Discharge Elimination System (NPDES).

HEP Computing

Science.gov Websites

Computing Visitors who do not need a HEP linux account Visitors with laptops can use wireless network HEP linux account Step 1: Click Here for New Account Application After submitting the application, you

Scalability of a Low-Cost Multi-Teraflop Linux Cluster for High-End Classical Atomistic and Quantum Mechanical Simulations

NASA Technical Reports Server (NTRS)

Kikuchi, Hideaki; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Shimojo, Fuyuki; Saini, Subhash

2003-01-01

Scalability of a low-cost, Intel Xeon-based, multi-Teraflop Linux cluster is tested for two high-end scientific applications: Classical atomistic simulation based on the molecular dynamics method and quantum mechanical calculation based on the density functional theory. These scalable parallel applications use space-time multiresolution algorithms and feature computational-space decomposition, wavelet-based adaptive load balancing, and spacefilling-curve-based data compression for scalable I/O. Comparative performance tests are performed on a 1,024-processor Linux cluster and a conventional higher-end parallel supercomputer, 1,184-processor IBM SP4. The results show that the performance of the Linux cluster is comparable to that of the SP4. We also study various effects, such as the sharing of memory and L2 cache among processors, on the performance.

PathwayAccess: CellDesigner plugins for pathway databases.

PubMed

Van Hemert, John L; Dickerson, Julie A

2010-09-15

CellDesigner provides a user-friendly interface for graphical biochemical pathway description. Many pathway databases are not directly exportable to CellDesigner models. PathwayAccess is an extensible suite of CellDesigner plugins, which connect CellDesigner directly to pathway databases using respective Java application programming interfaces. The process is streamlined for creating new PathwayAccess plugins for specific pathway databases. Three PathwayAccess plugins, MetNetAccess, BioCycAccess and ReactomeAccess, directly connect CellDesigner to the pathway databases MetNetDB, BioCyc and Reactome. PathwayAccess plugins enable CellDesigner users to expose pathway data to analytical CellDesigner functions, curate their pathway databases and visually integrate pathway data from different databases using standard Systems Biology Markup Language and Systems Biology Graphical Notation. Implemented in Java, PathwayAccess plugins run with CellDesigner version 4.0.1 and were tested on Ubuntu Linux, Windows XP and 7, and MacOSX. Source code, binaries, documentation and video walkthroughs are freely available at http://vrac.iastate.edu/~jlv.

The GNAT: A new tool for processing NMR data.

PubMed

Castañar, Laura; Poggetto, Guilherme Dal; Colbourne, Adam A; Morris, Gareth A; Nilsson, Mathias

2018-06-01

The GNAT (General NMR Analysis Toolbox) is a free and open-source software package for processing, visualising, and analysing NMR data. It supersedes the popular DOSY Toolbox, which has a narrower focus on diffusion NMR. Data import of most common formats from the major NMR platforms is supported, as well as a GNAT generic format. Key basic processing of NMR data (e.g., Fourier transformation, baseline correction, and phasing) is catered for within the program, as well as more advanced techniques (e.g., reference deconvolution and pure shift FID reconstruction). Analysis tools include DOSY and SCORE for diffusion data, ROSY T 1 /T 2 estimation for relaxation data, and PARAFAC for multilinear analysis. The GNAT is written for the MATLAB® language and comes with a user-friendly graphical user interface. The standard version is intended to run with a MATLAB installation, but completely free-standing compiled versions for Windows, Mac, and Linux are also freely available. © 2018 The Authors Magnetic Resonance in Chemistry Published by John Wiley & Sons Ltd.

Radio Astronomy Software Defined Receiver Project

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

Vacaliuc, Bogdan; Leech, Marcus; Oxley, Paul

The paper describes a Radio Astronomy Software Defined Receiver (RASDR) that is currently under development. RASDR is targeted for use by amateurs and small institutions where cost is a primary consideration. The receiver will operate from HF thru 2.8 GHz. Front-end components such as preamps, block down-converters and pre-select bandpass filters are outside the scope of this development and will be provided by the user. The receiver includes RF amplifiers and attenuators, synthesized LOs, quadrature down converters, dual 8 bit ADCs and a Signal Processor that provides firmware processing of the digital bit stream. RASDR will interface to a usermore » s PC via a USB or higher speed Ethernet LAN connection. The PC will run software that provides processing of the bit stream, a graphical user interface, as well as data analysis and storage. Software should support MAC OS, Windows and Linux platforms and will focus on such radio astronomy applications as total power measurements, pulsar detection, and spectral line studies.« less

A Secure Web Application Providing Public Access to High-Performance Data Intensive Scientific Resources - ScalaBLAST Web Application

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

Curtis, Darren S.; Peterson, Elena S.; Oehmen, Chris S.

2008-05-04

This work presents the ScalaBLAST Web Application (SWA), a web based application implemented using the PHP script language, MySQL DBMS, and Apache web server under a GNU/Linux platform. SWA is an application built as part of the Data Intensive Computer for Complex Biological Systems (DICCBS) project at the Pacific Northwest National Laboratory (PNNL). SWA delivers accelerated throughput of bioinformatics analysis via high-performance computing through a convenient, easy-to-use web interface. This approach greatly enhances emerging fields of study in biology such as ontology-based homology, and multiple whole genome comparisons which, in the absence of a tool like SWA, require a heroicmore » effort to overcome the computational bottleneck associated with genome analysis. The current version of SWA includes a user account management system, a web based user interface, and a backend process that generates the files necessary for the Internet scientific community to submit a ScalaBLAST parallel processing job on a dedicated cluster.« less

Gener: a minimal programming module for chemical controllers based on DNA strand displacement

PubMed Central

Kahramanoğulları, Ozan; Cardelli, Luca

2015-01-01

Summary: Gener is a development module for programming chemical controllers based on DNA strand displacement. Gener is developed with the aim of providing a simple interface that minimizes the opportunities for programming errors: Gener allows the user to test the computations of the DNA programs based on a simple two-domain strand displacement algebra, the minimal available so far. The tool allows the user to perform stepwise computations with respect to the rules of the algebra as well as exhaustive search of the computation space with different options for exploration and visualization. Gener can be used in combination with existing tools, and in particular, its programs can be exported to Microsoft Research’s DSD tool as well as to LaTeX. Availability and implementation: Gener is available for download at the Cosbi website at http://www.cosbi.eu/research/prototypes/gener as a windows executable that can be run on Mac OS X and Linux by using Mono. Contact: ozan@cosbi.eu PMID:25957353

Healthwatch-2 System Overview

NASA Technical Reports Server (NTRS)

Barszcz, Eric; Mosher, Marianne; Huff, Edward M.

2004-01-01

Healthwatch-2 (HW-2) is a research tool designed to facilitate the development and testing of in-flight health monitoring algorithms. HW-2 software is written in C/C++ and executes on an x86-based computer running the Linux operating system. The executive module has interfaces for collecting various signal data, such as vibration, torque, tachometer, and GPS. It is designed to perform in-flight time or frequency averaging based on specifications defined in a user-supplied configuration file. Averaged data are then passed to a user-supplied algorithm written as a Matlab function. This allows researchers a convenient method for testing in-flight algorithms. In addition to its in-flight capabilities, HW-2 software is also capable of reading archived flight data and processing it as if collected in-flight. This allows algorithms to be developed and tested in the laboratory before being flown. Currently HW-2 has passed its checkout phase and is collecting data on a Bell OH-58C helicopter operated by the U.S. Army at NASA Ames Research Center.

ACS sampling system: design, implementation, and performance evaluation

NASA Astrophysics Data System (ADS)

Di Marcantonio, Paolo; Cirami, Roberto; Chiozzi, Gianluca

2004-09-01

By means of ACS (ALMA Common Software) framework we designed and implemented a sampling system which allows sampling of every Characteristic Component Property with a specific, user-defined, sustained frequency limited only by the hardware. Collected data are sent to various clients (one or more Java plotting widgets, a dedicated GUI or a COTS application) using the ACS/CORBA Notification Channel. The data transport is optimized: samples are cached locally and sent in packets with a lower and user-defined frequency to keep network load under control. Simultaneous sampling of the Properties of different Components is also possible. Together with the design and implementation issues we present the performance of the sampling system evaluated on two different platforms: on a VME based system using VxWorks RTOS (currently adopted by ALMA) and on a PC/104+ embedded platform using Red Hat 9 Linux operating system. The PC/104+ solution offers, as an alternative, a low cost PC compatible hardware environment with free and open operating system.

Gener: a minimal programming module for chemical controllers based on DNA strand displacement.

PubMed

Kahramanoğulları, Ozan; Cardelli, Luca

2015-09-01

: Gener is a development module for programming chemical controllers based on DNA strand displacement. Gener is developed with the aim of providing a simple interface that minimizes the opportunities for programming errors: Gener allows the user to test the computations of the DNA programs based on a simple two-domain strand displacement algebra, the minimal available so far. The tool allows the user to perform stepwise computations with respect to the rules of the algebra as well as exhaustive search of the computation space with different options for exploration and visualization. Gener can be used in combination with existing tools, and in particular, its programs can be exported to Microsoft Research's DSD tool as well as to LaTeX. Gener is available for download at the Cosbi website at http://www.cosbi.eu/research/prototypes/gener as a windows executable that can be run on Mac OS X and Linux by using Mono. ozan@cosbi.eu. © The Author 2015. Published by Oxford University Press.

Iodine nutrition status and knowledge, attitude, and behavior in Tehranian women following 2 decades without public education.

PubMed

Mirmiran, Parvin; Nazeri, Pantea; Amiri, Parisa; Mehran, Ladan; Shakeri, Nezhat; Azizi, Fereidoun

2013-01-01

To evaluate the association of iodine nutrition status and knowledge, attitude, and behavior in Tehranian women after 2 decades without updating public education. Cross-sectional study. Eight health care centers from 4 district areas of Tehran. A total of 383 women aged ≥ 19 years, randomly selected. Iodine concentration of 24-hour urine samples, iodine content of household salts, and knowledge, attitude, and practice scores regarding iodine nutrition and iodized salt. Multiple logistic regression was used to identify the association of knowledge, attitude, and practice scores with urinary iodine concentration (UIC) < 100 μg/L. The percentages of Tehranian women with high knowledge, attitude, and practice scores were 26%, 26%, and 14%, respectively. Practice score was significantly different between females with UIC < 100 and > 100 μg/L (P = .001). Risk of UIC < 100 μg/L in women of childbearing age (19-45 years) after adjustment of education level, region of residence, and iodine content of salt was significantly associated with intermediate practice score (odds ratio = 2.6; 95% confidence interval, 1.3-13.2). Marginally suboptimal iodine status in women of childbearing age can be attributed to inappropriate practices, but not to knowledge and attitude. Copyright © 2013 Society for Nutrition Education and Behavior. Published by Elsevier Inc. All rights reserved.

Iodine Status of Women of Reproductive Age in Sierra Leone and Its Association with Household Coverage with Adequately Iodized Salt

PubMed Central

Rohner, Fabian; Wirth, James P.; Woodruff, Bradley A.; Chiwile, Faraja; Yankson, Hannah; Sesay, Fatmata; Koroma, Aminata S.; Petry, Nicolai; Pyne-Bailey, Solade; Dominguez, Elisa; Kupka, Roland; Hodges, Mary H.; de Onis, Mercedes

2016-01-01

Salt iodization programs are a public health success in tackling iodine deficiency. Yet, a large proportion of the world’s population remains at risk for iodine deficiency. In a nationally representative cross-sectional survey in Sierra Leone, household salt samples and women’s urine samples were quantitatively analyzed for iodine content. Salt was collected from 1123 households, and urine samples from 817 non-pregnant and 154 pregnant women. Household coverage with adequately iodized salt (≥15 mg/kg iodine) was 80.7%. The median urinary iodine concentration (UIC) of pregnant women was 175.8 µg/L and of non-pregnant women 190.8 µg/L. Women living in households with adequately iodized salt had higher median UIC (for pregnant women: 180.6 µg/L vs. 100.8 µg/L, respectively, p < 0.05; and for non-pregnant women: 211.3 µg/L vs. 97.8 µg/L, p < 0.001). Differences in UIC by residence, region, household wealth, and women’s education were much smaller in women living in households with adequately iodized salt than in households without. Despite the high household coverage of iodized salt in Sierra Leone, it is important to reach the 20% of households not consuming adequately iodized salt. Salt iodization has the potential for increasing equity in iodine status even with the persistence of other risk factors for deficiency. PMID:26848685

Experimental verification of numerical calculations of railway passenger seats

NASA Astrophysics Data System (ADS)

Ligaj, B.; Wirwicki, M.; Karolewska, K.; Jasińska, A.

2018-04-01

The construction of railway seats is based on industry regulations and the requirements of end users, i.e. passengers. The two main documents in this context are the UIC 566 (3rd Edition, dated 7 January 1994) and the EN 12663-1: 2010+A1:2014. The study was to carry out static load tests of passenger seat frames. The paper presents the construction of the test bench and the results of experimental and numerical studies of passenger seat rail frames. The test bench consists of a frame, a transverse beam, two electric cylinders with a force value of 6 kN, and a strain gauge amplifier. It has a modular structure that allows for its expansion depending on the structure of the seats. Comparing experimental results with numerical results for points A and B allowed to determine the existing differences. It follows from it that higher stress values are obtained by numerical calculations in the range of 0.2 MPa to 35.9 MPa.

GOCE User Toolbox and Tutorial

NASA Astrophysics Data System (ADS)

Knudsen, P.; Benveniste, J.

2011-07-01

The GOCE User Toolbox GUT is a compilation of tools for the utilisation and analysis of GOCE Level 2 products. GUT support applications in Geodesy, Oceanography and Solid Earth Physics. The GUT Tutorial provides information and guidance in how to use the toolbox for a variety of applications. GUT consists of a series of advanced computer routines that carry out the required computations. It may be used on Windows PCs, UNIX/Linux Workstations, and Mac. The toolbox is supported by The GUT Algorithm Description and User Guide and The GUT Install Guide. A set of a-priori data and models are made available as well. GUT has been developed in a collaboration within the GUT Core Group. The GUT Core Group: S. Dinardo, D. Serpe, B.M. Lucas, R. Floberghagen, A. Horvath (ESA), O. Andersen, M. Herceg (DTU), M.-H. Rio, S. Mulet, G. Larnicol (CLS), J. Johannessen, L.Bertino (NERSC), H. Snaith, P. Challenor (NOC), K. Haines, D. Bretherton (NCEO), C. Hughes (POL), R.J. Bingham (NU), G. Balmino, S. Niemeijer, I. Price, L. Cornejo (S&T), M. Diament, I Panet (IPGP), C.C. Tscherning (KU), D. Stammer, F. Siegismund (UH), T. Gruber (TUM),

World Wide Web Metaphors for Search Mission Data

NASA Technical Reports Server (NTRS)

Norris, Jeffrey S.; Wallick, Michael N.; Joswig, Joseph C.; Powell, Mark W.; Torres, Recaredo J.; Mittman, David S.; Abramyan, Lucy; Crockett, Thomas M.; Shams, Khawaja S.; Fox, Jason M.;

Iris: Constructing and Analyzing Spectral Energy Distributions with the Virtual Observatory

NASA Astrophysics Data System (ADS)

Laurino, O.; Budynkiewicz, J.; Busko, I.; Cresitello-Dittmar, M.; D'Abrusco, R.; Doe, S.; Evans, J.; Pevunova, O.

2014-05-01

We present Iris 2.0, the latest release of the Virtual Astronomical Observatory application for building and analyzing Spectral Energy Distributions (SEDs). With Iris, users may read in and display SEDs inspect and edit any selection of SED data, fit models to SEDs in arbitrary spectral ranges, and calculate confidence limits on best-fit parameters. SED data may be loaded into the application from VOTable and FITS files compliant with the International Virtual Observatoy Alliance interoperable data models, or retrieved directly from NED or the Italian Space Agency Science Data Center; data in non-standard formats may also be converted within the application. Users may seamlessy exchange data between Iris and other Virtual Observatoy tools using the Simple Application Messaging Protocol. Iris 2.0 also provides a tool for redshifting, interpolating, and measuring integratd fluxes, and allows simple aperture corrections for individual points and SED segments. Custom Python functions, template models and template libraries may be imported into Iris for fitting SEDs. Iris may be extended through Java plugins; users can install third-party packages, or develop their own plugin using Iris' Software Development Kit. Iris 2.0 is available for Linux and Mac OS X systems.

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

PubMed Central

Kearse, Matthew; Moir, Richard; Wilson, Amy; Stones-Havas, Steven; Cheung, Matthew; Sturrock, Shane; Buxton, Simon; Cooper, Alex; Markowitz, Sidney; Duran, Chris; Thierer, Tobias; Ashton, Bruce; Meintjes, Peter; Drummond, Alexei

2012-01-01

Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com PMID:22543367

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.

PubMed

Kearse, Matthew; Moir, Richard; Wilson, Amy; Stones-Havas, Steven; Cheung, Matthew; Sturrock, Shane; Buxton, Simon; Cooper, Alex; Markowitz, Sidney; Duran, Chris; Thierer, Tobias; Ashton, Bruce; Meintjes, Peter; Drummond, Alexei

2012-06-15

The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.

The instrument control software package for the Habitable-Zone Planet Finder spectrometer

NASA Astrophysics Data System (ADS)

Bender, Chad F.; Robertson, Paul; Stefansson, Gudmundur Kari; Monson, Andrew; Anderson, Tyler; Halverson, Samuel; Hearty, Frederick; Levi, Eric; Mahadevan, Suvrath; Nelson, Matthew; Ramsey, Larry; Roy, Arpita; Schwab, Christian; Shetrone, Matthew; Terrien, Ryan

2016-08-01

We describe the Instrument Control Software (ICS) package that we have built for The Habitable-Zone Planet Finder (HPF) spectrometer. The ICS controls and monitors instrument subsystems, facilitates communication with the Hobby-Eberly Telescope facility, and provides user interfaces for observers and telescope operators. The backend is built around the asynchronous network software stack provided by the Python Twisted engine, and is linked to a suite of custom hardware communication protocols. This backend is accessed through Python-based command-line and PyQt graphical frontends. In this paper we describe several of the customized subsystem communication protocols that provide access to and help maintain the hardware systems that comprise HPF, and show how asynchronous communication benefits the numerous hardware components. We also discuss our Detector Control Subsystem, built as a set of custom Python wrappers around a C-library that provides native Linux access to the SIDECAR ASIC and Hawaii-2RG detector system used by HPF. HPF will be one of the first astronomical instruments on sky to utilize this native Linux capability through the SIDECAR Acquisition Module (SAM) electronics. The ICS we have created is very flexible, and we are adapting it for NEID, NASA's Extreme Precision Doppler Spectrometer for the WIYN telescope; we will describe this adaptation, and describe the potential for use in other astronomical instruments.

40 CFR 147.2921 - Schedule of compliance.

Code of Federal Regulations, 2010 CFR

2010-07-01

... (CONTINUED) STATE, TRIBAL, AND EPA-ADMINISTERED UNDERGROUND INJECTION CONTROL PROGRAMS Osage Mineral Reserve... of compliance leading to compliance with the Safe Drinking Water Act and the Osage UIC regulations...

RELAP5-3D developmental assessment: Comparison of version 4.2.1i on Linux and Windows

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

Bayless, Paul D.

2014-06-01

Figures have been generated comparing the parameters used in the developmental assessment of the RELAP5-3D code, version 4.2i, compiled on Linux and Windows platforms. The figures, which are the same as those used in Volume III of the RELAP5-3D code manual, compare calculations using the semi-implicit solution scheme with available experiment data. These figures provide a quick, visual indication of how the code predictions differ between the Linux and Windows versions.

RELAP5-3D Developmental Assessment. Comparison of Version 4.3.4i on Linux and Windows

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

Bayless, Paul David

2015-10-01

Figures have been generated comparing the parameters used in the developmental assessment of the RELAP5-3D code, version 4.3i, compiled on Linux and Windows platforms. The figures, which are the same as those used in Volume III of the RELAP5-3D code manual, compare calculations using the semi-implicit solution scheme with available experiment data. These figures provide a quick, visual indication of how the code predictions differ between the Linux and Windows versions.

Container-Based Clinical Solutions for Portable and Reproducible Image Analysis.

PubMed

Matelsky, Jordan; Kiar, Gregory; Johnson, Erik; Rivera, Corban; Toma, Michael; Gray-Roncal, William

2018-05-08

Medical imaging analysis depends on the reproducibility of complex computation. Linux containers enable the abstraction, installation, and configuration of environments so that software can be both distributed in self-contained images and used repeatably by tool consumers. While several initiatives in neuroimaging have adopted approaches for creating and sharing more reliable scientific methods and findings, Linux containers are not yet mainstream in clinical settings. We explore related technologies and their efficacy in this setting, highlight important shortcomings, demonstrate a simple use-case, and endorse the use of Linux containers for medical image analysis.

Assessment of the subsurface hydrology of the UIC-NARL main camp, near Barrow, Alaska, 1993-94

USGS Publications Warehouse

McCarthy, K.A.; Solin, G.L.

1995-01-01

Imikpuk Lake serves as the drinking-water source for the Ukpeagvik Inupiat Corporation-National Arctic Research Laboratory (UIC-NARL, formerly known as the Naval Arctic Research Laboratory) near Barrow, Alaska. Previously acceptable hazardous-waste disposal practices and accidental releases of various fuels and solvents during the past several decades have resulted in contamination of soil and ground water in the vicinity of the lake. As part of an assessment of the risk that subsurface contamination poses to the quality of water in the lake, the subsurface hydrology of the UIC-NARL main camp was examined. The study area is located approximately 530 kilometers north of the Arctic Circle, on the northern coast of Alaska, and the short annual thaw season and the presence of shallow, areally continuous permafrost restrict hydrologic processes. A transient ground-water system is present within the active layer-the shallow subsurface layer that thaws each summer and refreezes each winter. Water-level and thaw-depth data collected during the summers of 1993 and 1994 show that the configurations of both the water table and the subsurface frost govern the ground- water flow system in the UIC-NARL main camp and indicate that recharge to and discharge from the system are small. Spatial irregularities in the vertical extent of the active layer result from variations in land-surface elevation, variations in soil type, and the presence of buildings and other structures that either act as a heat source or block heat transfer to and from the subsurface. Distinct features in the active-layer hydrologic system in the UIC-NARL main camp include a permafrost ridge, which generally acts as a flow-system divide between the Arctic Ocean and inland water bodies; a mound in the water table, which indicates increased impedance to ground- water flow toward Imikpuk Lake and acts as a flow-system divide between the lake and Middle Salt Lagoon; and a depression in the water table, which suggests a local breach in the permafrost ridge that allows some ground water to flow directly from the main camp to the Arctic Ocean. Similar thaw depths and water-table elevations were measured during the summers of 1993 and 1994, and little change occurred in the thickness of the ground-water zone between mid- and late-thaw- season measurements. These data suggest that the system is in a state of quasi-equilibrium and that ground-water discharge is small. The observed drop in the water table as the active layer develops over the summer is probably largely the result of evapotranspiration losses rather than system outflow.

Performance and scalability evaluation of "Big Memory" on Blue Gene Linux.

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

Yoshii, K.; Iskra, K.; Naik, H.

2011-05-01

We address memory performance issues observed in Blue Gene Linux and discuss the design and implementation of 'Big Memory' - an alternative, transparent memory space introduced to eliminate the memory performance issues. We evaluate the performance of Big Memory using custom memory benchmarks, NAS Parallel Benchmarks, and the Parallel Ocean Program, at a scale of up to 4,096 nodes. We find that Big Memory successfully resolves the performance issues normally encountered in Blue Gene Linux. For the ocean simulation program, we even find that Linux with Big Memory provides better scalability than does the lightweight compute node kernel designed solelymore » for high-performance applications. Originally intended exclusively for compute node tasks, our new memory subsystem dramatically improves the performance of certain I/O node applications as well. We demonstrate this performance using the central processor of the LOw Frequency ARray radio telescope as an example.« less

A General Purpose High Performance Linux Installation Infrastructure

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

Wachsmann, Alf

2002-06-17

With more and more and larger and larger Linux clusters, the question arises how to install them. This paper addresses this question by proposing a solution using only standard software components. This installation infrastructure scales well for a large number of nodes. It is also usable for installing desktop machines or diskless Linux clients, thus, is not designed for cluster installations in particular but is, nevertheless, highly performant. The infrastructure proposed uses PXE as the network boot component on the nodes. It uses DHCP and TFTP servers to get IP addresses and a bootloader to all nodes. It then usesmore » kickstart to install Red Hat Linux over NFS. We have implemented this installation infrastructure at SLAC with our given server hardware and installed a 256 node cluster in 30 minutes. This paper presents the measurements from this installation and discusses the bottlenecks in our installation.« less

40 CFR 144.3 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... facility” Improved sinkhole means a naturally occurring karst depression or other natural crevice found in... the Administrator under the “appropriate Act and regulations.” Major facility means any UIC “facility...

homepage of A Ismail

Science.gov Websites

@anl.gov Ahmed Ismail Research Associate at the ANL High Energy Physics Theory Group and UIC ELEMENTARY PARTICLE PHYSICS THEORY High Energy Phenomenology Updated October 2013 aismail@anl.gov

Glenn Heat Transfer Simulation and Solver Graphical User Interface: Development and Testing

NASA Technical Reports Server (NTRS)

Kardamis, Joseph R.

2004-01-01

In the Tui ine Branch of the Turbomachinery and Propulsion Systems Division, researching and developing efficient turbine aerothermodynamics technologies is the main objective. Creating effective turbines for jet engines is a process which, if based purely on physical experimental testing, would be extremely expensive. It is for this reason, and also for the reasons of speed and ease, that the Turbine Branch spends a large amount of effort working with simulations of turbines. Specifically, they focus their work on two main fields: Computational Field Dynamics (CFD), and Experimental data analysis. The experimental field involves comparing experimental results to simulated results, whereas the CFD field involves running these simulations. The simulations are applied to aerodynamics and heat transfer cases, for both steady and unsteady flow conditions. By and large this work is applied to the domain of flow and heat transfer in axial turbines. The main application used to run these heat flow simulations is GlennHT. This program, recently rewritten in FORTRAN 90, allows the user to input a job file which specifies all the necessary parameters needed to simulate flow through a user-defined grid. There are several other executables used as well, ranging in application from converting grid files to and from particular formats, to merging blocks in a connectivity file, to converting connectivity files to a GlennHT compatible format. All of these executables are run from the command line in a terminal; some of them have interactive prompts where the user must specify the files to be manipulated after the program starts, while others take all of their parameters from the command line. With this amount of variation comes a good deal of commands and formats to memorize, which can cause slower and less efficient work, as users may forget how to execute a certain program, or not remember the pathnames of the files they wish to use. Two years ago, steps were made to expedite this process with a graphical user interface (GUI) that combines the functionality of all the executables along with adding some new functionality, such as residuals graphing and boundary conditions creation. Upon my beginning here at Glenn, many parts of the GUI, which was developed in Java, were nonfunctional. There were also issues with cross-platforming, as systems in the branch were transitioning from Silicon Graphics (SGI) machines to Linux machines. My goals this summer are to finish the parts of the GUI that are not yet completed, fix parts that did not work correctly, expand the functionality to include other useful features, such as grid surface highlighting, and make the system compatible with both Linux and SGI. I will also be heavily testing the system and providing sufficient documentation on how to use the GUI, as no such documentation existed previously.

[Study for lung sound acquisition module based on ARM and Linux].

PubMed

Lu, Qiang; Li, Wenfeng; Zhang, Xixue; Li, Junmin; Liu, Longqing

2011-07-01

A acquisition module with ARM and Linux as a core was developed. This paper presents the hardware configuration and the software design. It is shown that the module can extract human lung sound reliably and effectively.

Tanzania national survey on iodine deficiency: impact after twelve years of salt iodation.

PubMed

Assey, Vincent D; Peterson, Stefan; Kimboka, Sabas; Ngemera, Daniel; Mgoba, Celestin; Ruhiye, Deusdedit M; Ndossi, Godwin D; Greiner, Ted; Tylleskär, Thorkild

2009-09-03

In many low-income countries, children are at high risk of iodine deficiency disorders, including brain damage. In the early 1990s, Tanzania, a country that previously suffered from moderate to severe iodine deficiency, adopted universal salt iodation (USI) as an intervention strategy, but its impact remained unknown. We report on the first national survey in mainland Tanzania, conducted in 2004 to assess the extent to which iodated salt was used and its apparent impact on the total goitre prevalence (TGP) and urinary iodine concentrations (UIC) among the schoolchildren after USI was initiated. In 2004, a cross-sectional goitre survey was conducted; covering 140,758 schoolchildren aged 6 - 18 years were graded for goitre according to new WHO goitre classification system. Comparisons were made with district surveys conducted throughout most of the country during the 1980s and 90s. 131,941 salt samples from households were tested for iodine using rapid field test kits. UIC was determined spectrophotometrically using the ammonium persulfate digestion method in 4523 sub-sampled children. 83.6% (95% CI: 83.4 - 83.8) of salt samples tested positive for iodine. Whereas the TGP was about 25% on average in the earlier surveys, it was 6.9% (95%CI: 6.8-7.0) in 2004. The TGP for the younger children, 6-9 years old, was 4.2% (95%CI: 4.0-4.4), n = 41,965. In the 27 goitre-endemic districts, TGP decreased from 61% (1980s) to 12.3% (2004). The median UIC was 204 (95% CF: 192-215) microg/L. Only 25% of children had UIC <100 microg/L and 35% were > or = 300 microg/L, indicating low and excess iodine intake, respectively. Our study demonstrates a marked improvement in iodine nutrition in Tanzania, twelve years after the initiation of salt iodation programme. The challenge in sustaining IDD elimination in Tanzania is now two-fold: to better reach the areas with low coverage of iodated salt, and to reduce iodine intake in areas where it is excessive. Particular attention is needed in improving quality control at production level and perhaps the national salt iodation regulations may need to be reviewed.

Associations of maternal iodine status and thyroid function with adverse pregnancy outcomes in Henan Province of China.

PubMed

Yang, Jin; Liu, Yang; Liu, Hongjie; Zheng, Heming; Li, Xiaofeng; Zhu, Lin; Wang, Zhe

2018-05-01

The study aimed to explore the effects of maternal iodine status and thyroid diseases on adverse pregnancy outcomes. A prospective study was conducted on 2347 pregnant women, who provided 2347 urinary samples tested for iodine, 1082 serum samples tested for thyroid function, and 2347 questionnaires about demographic information. Their pregnancy outcomes were recorded and compared between different urinary iodine concentration (UIC) and thyroid function groups. Pregnant women with UIC between 150 and 249 μg/L had lower incidences of preeclampsia (adjusted odds ratio (OR) 0.12, 95% CI: 0.01-0.87), placenta previa (adjusted OR 0.06, 95% CI: 0.01-0.69) and fetal distress (adjusted OR 0.10, 95% CI: 0.02-0.64) than the reference group (UIC < 50 μg/L). Women with UIC between 100 and 149 μg/L had lower risks of abnormal amniotic fluid (adjusted OR 0.32, 95% CI: 0.12-0.87) and fetal distress (adjusted OR 0.08, 95% CI: 0.01-0.82). Women with UIC above 249 μg/L had a significant higher rate of abnormal amniotic fluid (adjusted OR 0.38, 95% CI: 0.16-0.89). Clinical and subclinical hypothyroidism during pregnancy increased the risk of preterm delivery by 4.4 times (P = 0.009) and 3.0 times (P =  0.014), respectively. Isolated hypothyroxinemia had increased odds of having macrosomia (adjusted OR 2.22, 95% CI: 1.13-4.85). Clinical hyperthyroidism was significantly associated with miscarriage (adjusted OR 2.12, 95% CI: 1.92-96.67) and fetal distress (adjusted OR 9.53, 95% CI: 1.05--81.81). Subclinical hyperthyroidism had a significant association with umbilical cord entanglement (adjusted OR 3.82, 95% CI: 1.38-10.58). Isolated hyperthyroxinemia was associated with preterm delivery (adjusted OR 4.73, 95% CI: 1.49-15.05). Maternal iodine status and thyroid diseases during pregnancy were associated with adverse pregnancy outcomes. Copyright © 2018 Elsevier GmbH. All rights reserved.

Centralized Authorization Using a Direct Service, Part II

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

Wachsmann, A

Authorization is the process of deciding if entity X is allowed to have access to resource Y. Determining the identity of X is the job of the authentication process. One task of authorization in computer networks is to define and determine which user has access to which computers in the network. On Linux, the tendency exists to create a local account for each single user who should be allowed to logon to a computer. This is typically the case because a user not only needs login privileges to a computer but also additional resources like a home directory to actuallymore » do some work. Creating a local account on every computer takes care of all this. The problem with this approach is that these local accounts can be inconsistent with each other. The same user name could have a different user ID and/or group ID on different computers. Even more problematic is when two different accounts share the same user ID and group ID on different computers: User joe on computer1 could have user ID 1234 and group ID 56 and user jane on computer2 could have the same user ID 1234 and group ID 56. This is a big security risk in case shared resources like NFS are used. These two different accounts are the same for an NFS server so that these users can wipe out each other's files. The solution to this inconsistency problem is to have only one central, authoritative data source for this kind of information and a means of providing all your computers with access to this central source. This is what a ''Directory Service'' is. The two directory services most widely used for centralizing authorization data are the Network Information Service (NIS, formerly known as Yellow Pages or YP) and Lightweight Directory Access Protocol (LDAP).« less

Social Tagging of Mission Data

NASA Technical Reports Server (NTRS)

Norris, Jeffrey S.; Wallick, Michael N.; Joswig, Joseph C.; Powell, Mark W.; Torres, Recaredo J.; Mittman, David S.; Abramyan, Lucy; Crockett, Thomas M.; Shams, Khawaja S.; Fox, Jason M.;

40 CFR 124.2 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 271.2 (RCRA), the definitions below apply to this part, except for PSD permits which are governed by... Administrator delegates authority to the Environmental Appeals Board to issue final decisions in RCRA, PSD, UIC...

40 CFR 124.2 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 271.2 (RCRA), the definitions below apply to this part, except for PSD permits which are governed by... Administrator delegates authority to the Environmental Appeals Board to issue final decisions in RCRA, PSD, UIC...

40 CFR 124.2 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 271.2 (RCRA), the definitions below apply to this part, except for PSD permits which are governed by... Administrator delegates authority to the Environmental Appeals Board to issue final decisions in RCRA, PSD, UIC...

40 CFR 124.2 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 271.2 (RCRA), the definitions below apply to this part, except for PSD permits which are governed by... Administrator delegates authority to the Environmental Appeals Board to issue final decisions in RCRA, PSD, UIC...

40 CFR 124.2 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 271.2 (RCRA), the definitions below apply to this part, except for PSD permits which are governed by... Administrator delegates authority to the Environmental Appeals Board to issue final decisions in RCRA, PSD, UIC...

PhyLIS: a simple GNU/Linux distribution for phylogenetics and phyloinformatics.

PubMed

Thomson, Robert C

2009-07-30

PhyLIS is a free GNU/Linux distribution that is designed to provide a simple, standardized platform for phylogenetic and phyloinformatic analysis. The operating system incorporates most commonly used phylogenetic software, which has been pre-compiled and pre-configured, allowing for straightforward application of phylogenetic methods and development of phyloinformatic pipelines in a stable Linux environment. The software is distributed as a live CD and can be installed directly or run from the CD without making changes to the computer. PhyLIS is available for free at http://www.eve.ucdavis.edu/rcthomson/phylis/.

PhyLIS: A Simple GNU/Linux Distribution for Phylogenetics and Phyloinformatics

PubMed Central

Thomson, Robert C.

2009-01-01

PhyLIS is a free GNU/Linux distribution that is designed to provide a simple, standardized platform for phylogenetic and phyloinformatic analysis. The operating system incorporates most commonly used phylogenetic software, which has been pre-compiled and pre-configured, allowing for straightforward application of phylogenetic methods and development of phyloinformatic pipelines in a stable Linux environment. The software is distributed as a live CD and can be installed directly or run from the CD without making changes to the computer. PhyLIS is available for free at http://www.eve.ucdavis.edu/rcthomson/phylis/. PMID:19812729

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research

PubMed Central

Yeung, Ka Yee

2016-01-01

Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface. PMID:27045593

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research.

PubMed

Hung, Ling-Hong; Kristiyanto, Daniel; Lee, Sung Bong; Yeung, Ka Yee

2016-01-01

Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface.

Trajectory Optimization: OTIS 4

NASA Technical Reports Server (NTRS)

Riehl, John P.; Sjauw, Waldy K.; Falck, Robert D.; Paris, Stephen W.

2010-01-01

The latest release of the Optimal Trajectories by Implicit Simulation (OTIS4) allows users to simulate and optimize aerospace vehicle trajectories. With OTIS4, one can seamlessly generate optimal trajectories and parametric vehicle designs simultaneously. New features also allow OTIS4 to solve non-aerospace continuous time optimal control problems. The inputs and outputs of OTIS4 have been updated extensively from previous versions. Inputs now make use of objectoriented constructs, including one called a metastring. Metastrings use a greatly improved calculator and common nomenclature to reduce the user s workload. They allow for more flexibility in specifying vehicle physical models, boundary conditions, and path constraints. The OTIS4 calculator supports common mathematical functions, Boolean operations, and conditional statements. This allows users to define their own variables for use as outputs, constraints, or objective functions. The user-defined outputs can directly interface with other programs, such as spreadsheets, plotting packages, and visualization programs. Internally, OTIS4 has more explicit and implicit integration procedures, including high-order collocation methods, the pseudo-spectral method, and several variations of multiple shooting. Users may switch easily between the various methods. Several unique numerical techniques such as automated variable scaling and implicit integration grid refinement, support the integration methods. OTIS4 is also significantly more user friendly than previous versions. The installation process is nearly identical on various platforms, including Microsoft Windows, Apple OS X, and Linux operating systems. Cross-platform scripts also help make the execution of OTIS and post-processing of data easier. OTIS4 is supplied free by NASA and is subject to ITAR (International Traffic in Arms Regulations) restrictions. Users must have a Fortran compiler, and a Python interpreter is highly recommended.

Creating interactive physics simulations using the power of GeoGebra

NASA Astrophysics Data System (ADS)

Walsh, Tom

2017-05-01

I have long incorporated physics simulations in my physics teaching, and truly appreciate those who have made their simulations available to the public. I often would think of an idea for a simulation I would love to be able to use, but with no real programming background I did not know how I could make my own. That was the case until I discovered GeoGebra, which is an open source software offering "Dynamic Mathematics for Teaching and Learning." GeoGebra is freely available for non-commercial users. It is powerful, easy to learn, and versatile. There are versions for Windows, Mac, and Linux, as well as tablet and phone versions. It can also be run directly from a Chrome browser.

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels.

PubMed

Jossinet, Fabrice; Ludwig, Thomas E; Westhof, Eric

2010-08-15

Assemble is an intuitive graphical interface to analyze, manipulate and build complex 3D RNA architectures. It provides several advanced and unique features within the framework of a semi-automated modeling process that can be performed by homology and ab initio with or without electron density maps. Those include the interactive editing of a secondary structure and a searchable, embedded library of annotated tertiary structures. Assemble helps users with performing recurrent and otherwise tedious tasks in structural RNA research. Assemble is released under an open-source license (MIT license) and is freely available at http://bioinformatics.org/assemble. It is implemented in the Java language and runs on MacOSX, Linux and Windows operating systems.

Public Notice: KYV0070

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency, Region 4 intends to issue one Class 5 UIC permit to the Warrior Coal, LLC. This permit would cover six (6) mine-backfill injection wells located in Hopkins County, Kentucky.

Simon of Bolivar, Inc

EPA Pesticide Factsheets

Simon of Bolivar, Inc. (“Simon”) has applied to the U.S. Environmental Protection Agency (“EPA”) under the provisions of the Safe Drinking Water Act for a major modification of its Underground Injection Control (UIC) permit.

Evaluation of iodine nutritional status in Tehran, Iran: iodine deficiency within iodine sufficiency.

PubMed

Nazeri, Pantea; Mirmiran, Parvin; Mehrabi, Yadollah; Hedayati, Mehdi; Delshad, Hossein; Azizi, Fereidoun

2010-12-01

Production of iodized salt in Iran for household consumption began in 1990. Previous studies have reported sustainable elimination of iodine deficiency disorders in Iran. The aim of this study was to evaluate the iodine nutritional status in Tehran in 2009. In this cross-sectional study, 383 Tehranian households were enrolled through randomized cluster sampling and a total of 639 adult subjects (242 men and 397 women), aged 19 and over, participated. A 24-hour urine sample was collected for measurement of urinary iodine, sodium, and creatinine concentrations using the digestion method, flame photometry, and autoanalyzer assay, respectively. Salt intake was estimated and iodine content of household salt was measured by titration. Median (interquartile range) iodine content of household salt and urinary iodine concentration (UIC) in Tehran were 21.2 (3.2-31.7) parts per million and 70.0 (34.0-131.2) μg/L, respectively. There was no statistically significant difference in 24-hour UICs between men and women. Median (interquartile range) daily salt intake was 7.6 (5.5-9.8) g, which was not different in the two genders. According to the WHO/ICCIDD/UNICEF classification, 11.2%, 25.9%, 26.7%, 25.1%, 8.0%, and 3.2% of participants had UIC <20, 20-49, 50-99, 100-199, 200-299, and >300 μg/L, respectively. Mild iodine deficiency has recurred in Tehranians. The results emphasize the need for continuous monitoring in all regions, even in a country with iodine sufficiency.

Haemoglobinuria is associated with chronic kidney disease and its progression in patients with sickle cell anaemia

PubMed Central

Saraf, Santosh L.; Zhang, Xu; Kanias, Tamir; Lash, James P.; Molokie, Robert E.; Oza, Bharvi; Lai, Catherine; Rowe, Julie H.; Gowhari, Michel; Hassan, Johara; DeSimone, Joseph; Machado, Roberto F.; Gladwin, Mark T.; Little, Jane A.; Gordeuk, Victor R.

2014-01-01

Summary To evaluate the association between haemoglobinuria and chronic kidney disease (CKD) in sickle cell anaemia (SCA), we analysed 356 adult haemoglobin SS or Sβ° thalassaemia patients from the University of Illinois at Chicago (UIC) and 439 from the multi-centre Walk-Treatment of Pulmonary Hypertension and Sickle Cell Disease with Sildenafil Therapy (PHaSST) cohort. CKD was classified according to National Kidney Foundation Kidney Disease Outcomes Quality Initiatives guidelines. Haemoglobinuria, defined as positive haem on urine dipstick with absent red blood cells on microscopy, was confirmed by enzyme-linked immunosorbent assay in a subset of patients. The prevalence of CKD was 58% in the UIC cohort and 54% in the Walk-PHaSST cohort, and haemoglobinuria was observed in 36% and 20% of the patients, respectively. Pathway analysis in both cohorts indicated an independent association of lactate dehydrogenase with haemoglobinuria and, in turn, independent associations of haemoglobinuria and age with CKD (P<0.0001). After a median of 32 months of follow-up in the UIC cohort, haemoglobinuria was associated with progression of CKD (halving of estimated glomerular filtration rate or requirement for dialysis; Hazard ratio [HR] 13.9, 95% confidence interval [CI] 1.7-113.2, P=0.0012) and increasing albuminuria (HR 3.1, 95% CI: 1.3-7.7; logrank P=0.0035). In conclusion haemoglobinuria is common in SCA and is associated with CKD, consistent with a role for intravascular haemolysis in the pathogenesis of renal dysfunction in SCA. PMID:24329963

Status of Iodine Nutrition among Pregnant Women Attending Antenatal Clinic of a Secondary Care Hospital: A Cross-sectional Study from Northern India.

PubMed

Kant, Shashi; Haldar, Partha; Lohiya, Ayush; Yadav, Kapil; Pandav, Chandrakant S

2017-01-01

Daily requirement of iodine increases during pregnancy making pregnant women a high-risk group for iodine deficiency disorders. The limited available literature shows that even in iodine sufficient population, pregnant women are iodine deficient. The objective of this study is to assess the current iodine nutrition status among pregnant women in Ballabgarh, district Faridabad, Haryana. Pregnant women were recruited from antenatal clinic (ANC) of subdistrict hospital (SDH), Ballabgarh, Haryana. Consecutive sampling strategy was followed to recruit pregnant women, and women of all trimesters were included in the study. Urinary iodine estimation was done using simple microplate method, and salt iodine was estimated using iodometric titration. The study was approved by Institute Ethics Committee, All India Institute of Medical Sciences (AIIMS), New Delhi. Out of the total 1031 pregnant women, 90.9% were using adequately iodized salt. Median (interquartile range [IQR]) salt consumption by the pregnant women was 8.3 (6.7, 11.1) g/day. Median (IQR) urinary iodine concentration (UIC) for the pregnant women was 260 (199, 323) μg/L. Only 13.5% of pregnant women had insufficient iodine intake (UIC <150 μg/L). There was no significant difference in median UIC values by household salt iodine content and across three trimesters of pregnancy. Iodine nutrition status of the pregnant women attending ANC clinic of SDH Ballabgarh was adequate with attainment of universal salt iodization goal of >90% adequately iodized salt coverage in the study population.

Switching the JLab Accelerator Operations Environment from an HP-UX Unix-based to a PC/Linux-based environment

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

Mcguckin, Theodore

2008-10-01

The Jefferson Lab Accelerator Controls Environment (ACE) was predominantly based on the HP-UX Unix platform from 1987 through the summer of 2004. During this period the Accelerator Machine Control Center (MCC) underwent a major renovation which included introducing Redhat Enterprise Linux machines, first as specialized process servers and then gradually as general login servers. As computer programs and scripts required to run the accelerator were modified, and inherent problems with the HP-UX platform compounded, more development tools became available for use with Linux and the MCC began to be converted over. In May 2008 the last HP-UX Unix login machinemore » was removed from the MCC, leaving only a few Unix-based remote-login servers still available. This presentation will explore the process of converting an operational Control Room environment from the HP-UX to Linux platform as well as the many hurdles that had to be overcome throughout the transition period (including a discussion of« less

Metra operations management development program : 2010 - 2015.

DOT National Transportation Integrated Search

2016-11-04

On behalf of the Urban Transportation Center, the University of Illinois (UIC) Great Cities Institute (GCI) provided curriculum development and training services to Metra for a workforce education program targeted to new and experienced managers. Met...

Rcount: simple and flexible RNA-Seq read counting.

PubMed

Schmid, Marc W; Grossniklaus, Ueli

2015-02-01

Analysis of differential gene expression by RNA sequencing (RNA-Seq) is frequently done using feature counts, i.e. the number of reads mapping to a gene. However, commonly used count algorithms (e.g. HTSeq) do not address the problem of reads aligning with multiple locations in the genome (multireads) or reads aligning with positions where two or more genes overlap (ambiguous reads). Rcount specifically addresses these issues. Furthermore, Rcount allows the user to assign priorities to certain feature types (e.g. higher priority for protein-coding genes compared to rRNA-coding genes) or to add flanking regions. Rcount provides a fast and easy-to-use graphical user interface requiring no command line or programming skills. It is implemented in C++ using the SeqAn (www.seqan.de) and the Qt libraries (qt-project.org). Source code and 64 bit binaries for (Ubuntu) Linux, Windows (7) and MacOSX are released under the GPLv3 license and are freely available on github.com/MWSchmid/Rcount. marcschmid@gmx.ch Test data, genome annotation files, useful Python and R scripts and a step-by-step user guide (including run-time and memory usage tests) are available on github.com/MWSchmid/Rcount. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Poster — Thur Eve — 52: A Web-based Platform for Collaborative Document Management in Radiotherapy

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

Kildea, J.; Joseph, A.

We describe DepDocs, a web-based platform that we have developed to manage the committee meetings, policies, procedures and other documents within our otherwise paperless radiotherapy clinic. DepDocs is essentially a document management system based on the popular Drupal content management software. For security and confidentiality, it is hosted on a linux server internal to our hospital network such that documents are never sent to the cloud or outside of the hospital firewall. We used Drupal's in-built role-based user rights management system to assign a role, and associated document editing rights, to each user. Documents are accessed for viewing using eithermore » a simple Google-like search or by generating a list of related documents from a taxonomy of categorization terms. Our system provides document revision tracking and an document review and approval mechanism for all official policies and procedures. Committee meeting schedules, agendas and minutes are maintained by committee chairs and are restricted to committee members. DepDocs has been operational within our department for over six months and has already 45 unique users and an archive of over 1000 documents, mostly policies and procedures. Documents are easily retrievable from the system using any web browser within our hospital's network.« less

Recent improvements to Binding MOAD: a resource for protein–ligand binding affinities and structures

PubMed Central

Ahmed, Aqeel; Smith, Richard D.; Clark, Jordan J.; Dunbar, James B.; Carlson, Heather A.

2015-01-01

For over 10 years, Binding MOAD (Mother of All Databases; http://www.BindingMOAD.org) has been one of the largest resources for high-quality protein–ligand complexes and associated binding affinity data. Binding MOAD has grown at the rate of 1994 complexes per year, on average. Currently, it contains 23 269 complexes and 8156 binding affinities. Our annual updates curate the data using a semi-automated literature search of the references cited within the PDB file, and we have recently upgraded our website and added new features and functionalities to better serve Binding MOAD users. In order to eliminate the legacy application server of the old platform and to accommodate new changes, the website has been completely rewritten in the LAMP (Linux, Apache, MySQL and PHP) environment. The improved user interface incorporates current third-party plugins for better visualization of protein and ligand molecules, and it provides features like sorting, filtering and filtered downloads. In addition to the field-based searching, Binding MOAD now can be searched by structural queries based on the ligand. In order to remove redundancy, Binding MOAD records are clustered in different families based on 90% sequence identity. The new Binding MOAD, with the upgraded platform, features and functionalities, is now equipped to better serve its users. PMID:25378330

Broadband network on-line data acquisition system with web based interface for control and basic analysis

NASA Astrophysics Data System (ADS)

Polkowski, Marcin; Grad, Marek

2016-04-01

Passive seismic experiment "13BB Star" is operated since mid 2013 in northern Poland and consists of 13 broadband seismic stations. One of the elements of this experiment is dedicated on-line data acquisition system comprised of both client (station) side and server side modules with web based interface that allows monitoring of network status and provides tools for preliminary data analysis. Station side is controlled by ARM Linux board that is programmed to maintain 3G/EDGE internet connection, receive data from digitizer, send data do central server among with additional auxiliary parameters like temperatures, voltages and electric current measurements. Station side is controlled by set of easy to install PHP scripts. Data is transmitted securely over SSH protocol to central server. Central server is a dedicated Linux based machine. Its duty is receiving and processing all data from all stations including auxiliary parameters. Server side software is written in PHP and Python. Additionally, it allows remote station configuration and provides web based interface for user friendly interaction. All collected data can be displayed for each day and station. It also allows manual creation of event oriented plots with different filtering abilities and provides numerous status and statistic information. Our solution is very flexible and easy to modify. In this presentation we would like to share our solution and experience. National Science Centre Poland provided financial support for this work via NCN grant DEC-2011/02/A/ST10/00284.

Linux Incident Response Volatile Data Analysis Framework

ERIC Educational Resources Information Center

McFadden, Matthew

2013-01-01

Cyber incident response is an emphasized subject area in cybersecurity in information technology with increased need for the protection of data. Due to ongoing threats, cybersecurity imposes many challenges and requires new investigative response techniques. In this study a Linux Incident Response Framework is designed for collecting volatile data…

Onboard Flow Sensing For Downwash Detection and Avoidance On Small Quadrotor Helicopters

DTIC Science & Technology

2015-01-01

onboard computers, one for flight stabilization and a Linux computer for sensor integration and control calculations . The Linux computer runs Robot...Hirokawa, D. Kubo , S. Suzuki, J. Meguro, and T. Suzuki. Small uav for immediate hazard map generation. In AIAA Infotech@Aerospace Conf, May 2007. 8F

Cross platform development using Delphi and Kylix

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

McDonald, J.L.; Nishimura, H.; Timossi, C.

2002-10-08

A cross platform component for EPICS Simple Channel Access (SCA) has been developed for the use with Delphi on Windows and Kylix on Linux. An EPICS controls GUI application developed on Windows runs on Linux by simply rebuilding it, and vice versa. This paper describes the technical details of the component.

Public Notice 2017-13: Simon of Bolivar

EPA Pesticide Factsheets

Simon of Bolivar, Inc. (“Simon”) has applied to the U.S. Environmental Protection Agency (“EPA”) under the provisions of the Safe Drinking Water Act for a major modification of its Underground Injection Control (UIC) permit.

County of Hawaii Department of Public Works: Consent Agreement and Final Order (2005)

EPA Pesticide Factsheets

Consent Agreement and Final Order for The County of Hawaii Department of Public Works, Hilo, Hawaii, including proposed order of compliance, closure of large capacity cesspools. Docket no. UIC-AO-2005-0013

75 FR 70918 - Meeting of the National Drinking Water Advisory Council-Notice of Public Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-19

... evaluating the report and determining what recommendations the Council will transmit to the Administrator..., the Underground Injection Control (UIC) Program, and revisions to the 1989 Total Coliform Rule (RTCR...

d-Tagatose production by permeabilized and immobilized Lactobacillus plantarum using whey permeate.

PubMed

Jayamuthunagai, J; Srisowmeya, G; Chakravarthy, M; Gautam, P

2017-07-01

The aim of the work is to produce d-Tagatose by direct addition of alginate immobilized Lactobacillus plantarum cells to lactose hydrolysed whey permeate. The cells were untreated and immobilized (UIC), permeabilized and immobilized (PIC) and the relative activities were compared with purified l-arabinose isomerase (l-AI) for d-galactose isomerization. Successive lactose hydrolysis by β-galactosidase from Escherichia coli and d-galactose isomerization using l-AI from Lactobacillus plantarum was performed to investigate the in vivo production of d-tagatose in whey permeate. In whey permeate, maximum conversion of 38% and 33% (w/w) d-galactose isomerization by PIC and UIC has been obtained. 162mg/g and 141mg/g of d-tagatose production was recorded in a 48h reaction time at 50°C, pH 7.0 with 5mM Mn 2+ ion concentration in the initial substrate mixture. Copyright © 2017 Elsevier Ltd. All rights reserved.