76 FR 5390 - National Human Genome Research Institute; Notice of Closed Meeting

Science.gov (United States)

2011-01-31

... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Place: National Human Genome Research Institute Special Emphasis... Officer, Scientific Review Branch, National Human Genome Research Institute, 5635 Fishers Lane, Suite 4076...

76 FR 3917 - National Human Genome Research Institute; Notice of Closed Meeting

Science.gov (United States)

2011-01-21

... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Special... Branch, National Human Genome Research Institute, 5635 Fishers Lane, Suite 4076, MSC 9306, Rockville, MD...

77 FR 74676 - National Human Genome Research Institute; Notice of Closed Meeting

Science.gov (United States)

2012-12-17

... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Suite 4075, Bethesda.... 93.172, Human Genome Research, National Institutes of Health, HHS) Dated: December 11, 2012. David...

76 FR 10909 - National Human Genome Research Institute; Notice of Closed Meeting

Science.gov (United States)

2011-02-28

... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome..., National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Suite 4076, MSC..., Human Genome Research, National Institutes of Health, HHS). Dated: February 18, 2011. Jennifer S. Spaeth...

77 FR 35991 - National Human Genome Research Institute; Notice of Closed Meeting

Science.gov (United States)

2012-06-15

... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Suite 4075, Bethesda.... 93.172, Human Genome Research, National Institutes of Health, HHS) Dated: June 8, 2012. Jennifer S...

75 FR 8977 - National Human Genome Research Institute; Notice of Closed Meeting

Science.gov (United States)

2010-02-26

... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome..., National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Suite 4076, MSC..., Human Genome Research, National Institutes of Health, HHS) Dated: February 18, 2010. Jennifer Spaeth...

78 FR 66752 - National Human Genome Research Institute; Amended Notice of Meeting

Science.gov (United States)

2013-11-06

... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... National Human Genome Research Institute Special Emphasis Panel, October 15, 2013, 01:00 p.m. to October 15, 2013, 02:30 p.m., National Human Genome Research Institute, 5635 Fishers Lane, Suite 3055, Rockville...

Validation suite for MCNP

International Nuclear Information System (INIS)

Mosteller, Russell D.

2002-01-01

Two validation suites, one for criticality and another for radiation shielding, have been defined and tested for the MCNP Monte Carlo code. All of the cases in the validation suites are based on experiments so that calculated and measured results can be compared in a meaningful way. The cases in the validation suites are described, and results from those cases are discussed. For several years, the distribution package for the MCNP Monte Carlo code1 has included an installation test suite to verify that MCNP has been installed correctly. However, the cases in that suite have been constructed primarily to test options within the code and to execute quickly. Consequently, they do not produce well-converged answers, and many of them are physically unrealistic. To remedy these deficiencies, sets of validation suites are being defined and tested for specific types of applications. All of the cases in the validation suites are based on benchmark experiments. Consequently, the results from the measurements are reliable and quantifiable, and calculated results can be compared with them in a meaningful way. Currently, validation suites exist for criticality and radiation-shielding applications.

The Calyptogena magnifica chemoautotrophic symbiont genome

Energy Technology Data Exchange (ETDEWEB)

Newton, I.L.; Woyke, T.; Auchtung, T.A.; Dilly, G.F.; Dutton,R.J.; Fisher, M.C.; Fontanez, K.M.; Lau, E.; Stewart, F.J.; Richardson,P.M.; Barry, K.W.; Saunders, E.; Detter, J.C.; Wu, D.; Eisen, J.A.; Cavanaugh, C.M.

2007-03-01

Chemoautotrophic endosymbionts are the metabolic cornerstone of hydrothermal vent communities, providing invertebrate hosts with nearly all of their nutrition. The Calyptogena magnifica (Bivalvia: Vesicomyidae) symbiont, Candidatus Ruthia magnifica, is the first intracellular sulfur-oxidizing endosymbiont to have its genome sequenced, revealing a suite of metabolic capabilities. The genome encodes major chemoautotrophic pathways as well as pathways for biosynthesis of vitamins, cofactors, and all 20 amino acids required by the clam.

A comprehensive software suite for protein family construction and functional site prediction.

Directory of Open Access Journals (Sweden)

David Renfrew Haft

Full Text Available In functionally diverse protein families, conservation in short signature regions may outperform full-length sequence comparisons for identifying proteins that belong to a subgroup within which one specific aspect of their function is conserved. The SIMBAL workflow (Sites Inferred by Metabolic Background Assertion Labeling is a data-mining procedure for finding such signature regions. It begins by using clues from genomic context, such as co-occurrence or conserved gene neighborhoods, to build a useful training set from a large number of uncharacterized but mutually homologous proteins. When training set construction is successful, the YES partition is enriched in proteins that share function with the user's query sequence, while the NO partition is depleted. A selected query sequence is then mined for short signature regions whose closest matches overwhelmingly favor proteins from the YES partition. High-scoring signature regions typically contain key residues critical to functional specificity, so proteins with the highest sequence similarity across these regions tend to share the same function. The SIMBAL algorithm was described previously, but significant manual effort, expertise, and a supporting software infrastructure were required to prepare the requisite training sets. Here, we describe a new, distributable software suite that speeds up and simplifies the process for using SIMBAL, most notably by providing tools that automate training set construction. These tools have broad utility for comparative genomics, allowing for flexible collection of proteins or protein domains based on genomic context as well as homology, a capability that can greatly assist in protein family construction. Armed with this new software suite, SIMBAL can serve as a fast and powerful in silico alternative to direct experimentation for characterizing proteins and their functional interactions.

Instant Spring Tool Suite

CERN Document Server

Chiang, Geoff

2013-01-01

Filled with practical, step-by-step instructions and clear explanations for the most important and useful tasks. A tutorial guide that walks you through how to use the features of Spring Tool Suite using well defined sections for the different parts of Spring.Instant Spring Tool Suite is for novice to intermediate Java developers looking to get a head-start in enterprise application development using Spring Tool Suite and the Spring framework. If you are looking for a guide for effective application development using Spring Tool Suite, then this book is for you.

Space suit bioenergetics: framework and analysis of unsuited and suited activity.

Science.gov (United States)

Carr, Christopher E; Newman, Dava J

2007-11-01

Metabolic costs limit the duration and intensity of extravehicular activity (EVA), an essential component of future human missions to the Moon and Mars. Energetics Framework: We present a framework for comparison of energetics data across and between studies. This framework, applied to locomotion, differentiates between muscle efficiency and energy recovery, two concepts often confused in the literature. The human run-walk transition in Earth gravity occurs at the point for which energy recovery is approximately the same for walking and running, suggesting a possible role for recovery in gait transitions. Muscular Energetics: Muscle physiology limits the overall efficiency by which chemical energy is converted through metabolism to useful work. Unsuited Locomotion: Walking and running use different methods of energy storage and release. These differences contribute to the relative changes in the metabolic cost of walking and running as gravity is varied, with the metabolic cost of locomoting at a given velocity changing in proportion to gravity for running and less than in proportion for walking. Space Suits: Major factors affecting the energetic cost of suited movement include suit pressurization, gravity, velocity, surface slope, and space suit configuration. Apollo lunar surface EVA traverse metabolic rates, while unexpectedly low, were higher than other activity categories. The Lunar Roving Vehicle facilitated even lower metabolic rates, thus longer duration EVAs. Muscles and tendons act like springs during running; similarly, longitudinal pressure forces in gas pressure space suits allow spring-like storage and release of energy when suits are self-supporting.

The genome sequence of the commercially cultivated mushroom Agrocybe aegerita reveals a conserved repertoire of fruiting-related genes and a versatile suite of biopolymer-degrading enzymes.

Science.gov (United States)

Gupta, Deepak K; Rühl, Martin; Mishra, Bagdevi; Kleofas, Vanessa; Hofrichter, Martin; Herzog, Robert; Pecyna, Marek J; Sharma, Rahul; Kellner, Harald; Hennicke, Florian; Thines, Marco

2018-01-15

Agrocybe aegerita is an agaricomycete fungus with typical mushroom features, which is commercially cultivated for its culinary use. In nature, it is a saprotrophic or facultative pathogenic fungus causing a white-rot of hardwood in forests of warm and mild climate. The ease of cultivation and fructification on solidified media as well as its archetypal mushroom fruit body morphology render A. aegerita a well-suited model for investigating mushroom developmental biology. Here, the genome of the species is reported and analysed with respect to carbohydrate active genes and genes known to play a role during fruit body formation. In terms of fruit body development, our analyses revealed a conserved repertoire of fruiting-related genes, which corresponds well to the archetypal fruit body morphology of this mushroom. For some genes involved in fruit body formation, paralogisation was observed, but not all fruit body maturation-associated genes known from other agaricomycetes seem to be conserved in the genome sequence of A. aegerita. In terms of lytic enzymes, our analyses suggest a versatile arsenal of biopolymer-degrading enzymes that likely account for the flexible life style of this species. Regarding the amount of genes encoding CAZymes relevant for lignin degradation, A. aegerita shows more similarity to white-rot fungi than to litter decomposers, including 18 genes coding for unspecific peroxygenases and three dye-decolourising peroxidase genes expanding its lignocellulolytic machinery. The genome resource will be useful for developing strategies towards genetic manipulation of A. aegerita, which will subsequently allow functional genetics approaches to elucidate fundamentals of fruiting and vegetative growth including lignocellulolysis.

RAJA Performance Suite

Energy Technology Data Exchange (ETDEWEB)

2017-09-01

The RAJA Performance Suite is designed to evaluate performance of the RAJA performance portability library on a wide variety of important high performance computing (HPC) algorithmic lulmels. These kernels assess compiler optimizations and various parallel programming model backends accessible through RAJA, such as OpenMP, CUDA, etc. The Initial version of the suite contains 25 computational kernels, each of which appears in 6 variants: Baseline SequcntiaJ, RAJA SequentiaJ, Baseline OpenMP, RAJA OpenMP, Baseline CUDA, RAJA CUDA. All variants of each kernel perform essentially the same mathematical operations and the loop body code for each kernel is identical across all variants. There are a few kernels, such as those that contain reduction operations, that require CUDA-specific coding for their CUDA variants. ActuaJ computer instructions executed and how they run in parallel differs depending on the parallel programming model backend used and which optimizations are perfonned by the compiler used to build the Perfonnance Suite executable. The Suite will be used primarily by RAJA developers to perform regular assessments of RAJA performance across a range of hardware platforms and compilers as RAJA features are being developed. It will also be used by LLNL hardware and software vendor panners for new defining requirements for future computing platform procurements and acceptance testing. In particular, the RAJA Performance Suite will be used for compiler acceptance testing of the upcoming CORAUSierra machine {initial LLNL delivery expected in late-2017/early 2018) and the CORAL-2 procurement. The Suite will aJso be used to generate concise source code reproducers of compiler and runtime issues we uncover so that we may provide them to relevant vendors to be fixed.

Apparatus for storing protective suits

International Nuclear Information System (INIS)

Englemann, H.J.; Koller, J.; Schrader, H.R.; Schade, G.; Pedrerol, J.

1975-01-01

Arrangements are described for storing one or more protective suits when contaminated on the outside. In order to permit a person wearing a contaminated suit to leave a contaminated area safely, and without contaminating the environment, it has hitherto been the practice for the suit to be passed through a 'lock' and cleansed under decontaminating showers whilst still being worn. This procedure is time wasting and not always completely effective, and it may be necessary to provide a second suit for use whilst the first suit is being decontaminated. Repeated decontamination may also result in undue wear and tear. The arrangements described provide a 'lock' chamber in which a contaminated suit may be stowed away without its interior becoming contaminated, thus allowing repeated use by persons donning and shedding it. (U.K.)

Pharmacy settles suit.

Science.gov (United States)

1998-10-02

A suit was filed by an HIV-positive man against a pharmacy that inadvertently disclosed his HIV status to his ex-wife and children. His ex-wife tried to use the information in a custody battle for their two children. The suit against the pharmacy was settled, but the terms of the settlement remain confidential.

Metaproteomics: Harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities

Science.gov (United States)

Hettich, Robert L.; Pan, Chongle; Chourey, Karuna; Giannone, Richard J.

2013-01-01

Summary The availability of extensive genome information for many different microbes, including unculturable species in mixed communities from environmental samples, has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, and proteomic information. To this end, metaproteomics exploits the power of high performance mass spectrometry for extensive characterization of the complete suite of proteins expressed by a microbial community in an environmental sample. PMID:23469896

Durable Suit Bladder with Improved Water Permeability for Pressure and Environment Suits

Science.gov (United States)

Bue, Grant C.; Kuznetz, Larry; Orndoff, Evelyne; Tang, Henry; Aitchison, Lindsay; Ross, Amy

2009-01-01

Water vapor permeability is shown to be useful in rejecting heat and managing moisture accumulation in launch-and-entry pressure suits. Currently this is accomplished through a porous Gortex layer in the Advanced Crew and Escape Suit (ACES) and in the baseline design of the Constellation Suit System Element (CSSE) Suit 1. Non-porous dense monolithic membranes (DMM) that are available offer potential improvements for water vapor permeability with reduced gas leak. Accordingly, three different pressure bladder materials were investigated for water vapor permeability and oxygen leak: ElasthaneTM 80A (thermoplastic polyether urethane) provided from stock polymer material and two custom thermoplastic polyether urethanes. Water vapor, carbon dioxide and oxygen permeability of the DMM's was measured in a 0.13 mm thick stand-alone layer, a 0.08 mm and 0.05 mm thick layer each bonded to two different nylon and polyester woven reinforcing materials. Additional water vapor permeability and mechanical compression measurements were made with the reinforced 0.05 mm thick layers, further bonded with a polyester wicking and overlaid with moistened polyester fleece thermal underwear .This simulated the pressure from a supine crew person. The 0.05 mm thick nylon reinforced sample with polyester wicking layer was further mechanically tested for wear and abrasion. Concepts for incorporating these materials in launch/entry and Extravehicular Activity pressure suits are presented.

GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface.

Science.gov (United States)

Lajugie, Julien; Fourel, Nicolas; Bouhassira, Eric E

2015-01-01

Parallel visualization of multiple individual human genomes is a complex endeavor that is rapidly gaining importance with the increasing number of personal, phased and cancer genomes that are being generated. It requires the display of variants such as SNPs, indels and structural variants that are unique to specific genomes and the introduction of multiple overlapping gaps in the reference sequence. Here, we describe GenPlay Multi-Genome, an application specifically written to visualize and analyze multiple human genomes in parallel. GenPlay Multi-Genome is ideally suited for the comparison of allele-specific expression and functional genomic data obtained from multiple phased genomes in a graphical interface with access to multiple-track operation. It also allows the analysis of data that have been aligned to custom genomes rather than to a standard reference and can be used as a variant calling format file browser and as a tool to compare different genome assembly, such as hg19 and hg38. GenPlay is available under the GNU public license (GPL-3) from http://genplay.einstein.yu.edu. The source code is available at https://github.com/JulienLajugie/GenPlay. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context.

Science.gov (United States)

Faith, Jeremiah J; Olson, Andrew J; Gardner, Timothy S; Sachidanandam, Ravi

2007-09-18

Lightweight genome viewer (lwgv) is a web-based tool for visualization of sequence annotations in their chromosomal context. It performs most of the functions of larger genome browsers, while relying on standard flat-file formats and bypassing the database needs of most visualization tools. Visualization as an aide to discovery requires display of novel data in conjunction with static annotations in their chromosomal context. With database-based systems, displaying dynamic results requires temporary tables that need to be tracked for removal. lwgv simplifies the visualization of user-generated results on a local computer. The dynamic results of these analyses are written to transient files, which can import static content from a more permanent file. lwgv is currently used in many different applications, from whole genome browsers to single-gene RNAi design visualization, demonstrating its applicability in a large variety of contexts and scales. lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses in their chromosomal context. It is particularly suited for applications ranging from short sequences to medium-sized genomes when the creation and maintenance of a large software and database infrastructure is not necessary or desired.

Development of Power Assisting Suit

Science.gov (United States)

Yamamoto, Keijiro; Ishii, Mineo; Hyodo, Kazuhito; Yoshimitsu, Toshihiro; Matsuo, Takashi

In order to realize a wearable power assisting suit for assisting a nurse to carry a patient in her arms, the power supply and control systems of the suit have to be miniaturized, and it has to be wireless and pipeline-less. The new wearable suit consists of shoulders, arms, back, waist and legs units to be fitted on the nurse's body. The arms, waist and legs have new pneumatic rotary actuators driven directly by micro air pumps supplied by portable Ni-Cd batteries. The muscle forces are sensed by a new muscle hardness sensor utilizing a sensing tip mounted on a force sensing film device. An embedded microcomputer is used for the calculations of control signals. The new wearable suit was applied practically to a human body and a series of movement experiments that weights in the arms were held and taken up and down was performed. Each unit of the suit could transmit assisting torque directly to each joint verifying its practicability.

Space Suit Joint Torque Testing

Science.gov (United States)

Valish, Dana J.

2011-01-01

In 2009 and early 2010, a test was performed to quantify the torque required to manipulate joints in several existing operational and prototype space suits in an effort to develop joint torque requirements appropriate for a new Constellation Program space suit system. The same test method was levied on the Constellation space suit contractors to verify that their suit design meets the requirements. However, because the original test was set up and conducted by a single test operator there was some question as to whether this method was repeatable enough to be considered a standard verification method for Constellation or other future space suits. In order to validate the method itself, a representative subset of the previous test was repeated, using the same information that would be available to space suit contractors, but set up and conducted by someone not familiar with the previous test. The resultant data was compared using graphical and statistical analysis and a variance in torque values for some of the tested joints was apparent. Potential variables that could have affected the data were identified and re-testing was conducted in an attempt to eliminate these variables. The results of the retest will be used to determine if further testing and modification is necessary before the method can be validated.

Evaluating Suit Fit Using Performance Degradation

Science.gov (United States)

Margerum, Sarah E.; Cowley, Matthew; Harvill, Lauren; Benson, Elizabeth; Rajulu, Sudhakar

2011-01-01

The Mark III suit has multiple sizes of suit components (arm, leg, and gloves) as well as sizing inserts to tailor the fit of the suit to an individual. This study sought to determine a way to identify the point an ideal suit fit transforms into a bad fit and how to quantify this breakdown using mobility-based physical performance data. This study examined the changes in human physical performance via degradation of the elbow and wrist range of motion of the planetary suit prototype (Mark III) with respect to changes in sizing and as well as how to apply that knowledge to suit sizing options and improvements in suit fit. The methods implemented in this study focused on changes in elbow and wrist mobility due to incremental suit sizing modifications. This incremental sizing was within a range that included both optimum and poor fit. Suited range of motion data was collected using a motion analysis system for nine isolated and functional tasks encompassing the elbow and wrist joints. A total of four subjects were tested with motions involving both arms simultaneously as well as the right arm only. The results were then compared across sizing configurations. The results of this study indicate that range of motion may be used as a viable parameter to quantify at what stage suit sizing causes a detriment in performance; however the human performance decrement appeared to be based on the interaction of multiple joints along a limb, not a single joint angle. The study was able to identify a preliminary method to quantify the impact of size on performance and to develop a means to gauge tolerances around optimal size. More work is needed to improve the assessment of optimal fit and to compensate for multiple joint interactions.

Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context

Directory of Open Access Journals (Sweden)

Gardner Timothy S

2007-09-01

Full Text Available Abstract Background Lightweight genome viewer (lwgv is a web-based tool for visualization of sequence annotations in their chromosomal context. It performs most of the functions of larger genome browsers, while relying on standard flat-file formats and bypassing the database needs of most visualization tools. Visualization as an aide to discovery requires display of novel data in conjunction with static annotations in their chromosomal context. With database-based systems, displaying dynamic results requires temporary tables that need to be tracked for removal. Results lwgv simplifies the visualization of user-generated results on a local computer. The dynamic results of these analyses are written to transient files, which can import static content from a more permanent file. lwgv is currently used in many different applications, from whole genome browsers to single-gene RNAi design visualization, demonstrating its applicability in a large variety of contexts and scales. Conclusion lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses in their chromosomal context. It is particularly suited for applications ranging from short sequences to medium-sized genomes when the creation and maintenance of a large software and database infrastructure is not necessary or desired.

Adobe Creative Suite 4 Bible

CERN Document Server

Padova, Ted

2009-01-01

As one of the few books to cover integration and workflow issues between Photoshop, Illustrator, InDesign, GoLive, Acrobat, and Version Cue, this comprehensive reference is the one book that Creative Suite users need; Two well-known and respected authors cover topics such as developing consistent color-managed workflows, moving files among the Creative Suite applications, preparing files for print or the Web, repurposing documents, and using the Creative Suite with Microsoft Office documents; More than 1,200 pages are packed with valuable advice and techniques for tackling common everyday issu

Improved airline-type supplied-air plastic suit

International Nuclear Information System (INIS)

Jolley, L. Jr.; Zippler, D.B.; Cofer, C.H.; Harper, J.A.

1978-06-01

Two piece supplied-air plastic suits are used extensively at the Savannah River Plant for personnel protection against inhalation of airborne plutonium and tritium. Worker comfort and noise level problems gave impetus to development of an improved suit and aid distribution system. The resulting plastic suit and development work are discussed. The plastic suit unit cost is less than $20, the hearing zone noise level is less than 75 dBA, protection factors exceed 10,000, and user comfort is approved. This suit is expected to meet performance requirements for unrestricted use

Z-1 Prototype Space Suit Testing Summary

Science.gov (United States)

Ross, Amy

2013-01-01

The Advanced Space Suit team of the NASA-Johnson Space Center performed a series of test with the Z-1 prototype space suit in 2012. This paper discusses, at a summary level, the tests performed and results from those tests. The purpose of the tests were two-fold: 1) characterize the suit performance so that the data could be used in the downselection of components for the Z-2 Space Suit and 2) develop interfaces with the suitport and exploration vehicles through pressurized suit evaluations. Tests performed included isolated and functional range of motion data capture, Z-1 waist and hip testing, joint torque testing, CO2 washout testing, fit checks and subject familiarizations, an exploration vehicle aft deck and suitport controls interface evaluation, delta pressure suitport tests including pressurized suit don and doff, and gross mobility and suitport ingress and egress demonstrations in reduced gravity. Lessons learned specific to the Z-1 prototype and to suit testing techniques will be presented.

Hybrid Enhanced Epidermal SpaceSuit Design Approaches

Science.gov (United States)

Jessup, Joseph M.

A Space suit that does not rely on gas pressurization is a multi-faceted problem that requires major stability controls to be incorporated during design and construction. The concept of Hybrid Epidermal Enhancement space suit integrates evolved human anthropomorphic and physiological adaptations into its functionality, using commercially available bio-medical technologies to address shortcomings of conventional gas pressure suits, and the impracticalities of MCP suits. The prototype HEE Space Suit explored integumentary homeostasis, thermal control and mobility using advanced bio-medical materials technology and construction concepts. The goal was a space suit that functions as an enhanced, multi-functional bio-mimic of the human epidermal layer that works in attunement with the wearer rather than as a separate system. In addressing human physiological requirements for design and construction of the HEE suit, testing regimes were devised and integrated into the prototype which was then subject to a series of detailed tests using both anatomical reproduction methods and human subject.

Empowering Mayo Clinic Individualized Medicine with Genomic Data Warehousing

Directory of Open Access Journals (Sweden)

Iain Horton

2017-08-01

Full Text Available Individualized medicine enables better diagnoses and treatment decisions for patients and promotes research in understanding the molecular underpinnings of disease. Linking individual patient’s genomic and molecular information with their clinical phenotypes is crucial to these efforts. To address this need, the Center for Individualized Medicine at Mayo Clinic has implemented a genomic data warehouse and a workflow management system to bring data from institutional electronic health records and genomic sequencing data from both clinical and research bioinformatics sources into the warehouse. The system is the foundation for Mayo Clinic to build a suite of tools and interfaces to support various clinical and research use cases. The genomic data warehouse is positioned to play a key role in enhancing the research capabilities and advancing individualized patient care at Mayo Clinic.

Empowering Mayo Clinic Individualized Medicine with Genomic Data Warehousing.

Science.gov (United States)

Horton, Iain; Lin, Yaxiong; Reed, Gay; Wiepert, Mathieu; Hart, Steven

2017-08-22

Individualized medicine enables better diagnoses and treatment decisions for patients and promotes research in understanding the molecular underpinnings of disease. Linking individual patient's genomic and molecular information with their clinical phenotypes is crucial to these efforts. To address this need, the Center for Individualized Medicine at Mayo Clinic has implemented a genomic data warehouse and a workflow management system to bring data from institutional electronic health records and genomic sequencing data from both clinical and research bioinformatics sources into the warehouse. The system is the foundation for Mayo Clinic to build a suite of tools and interfaces to support various clinical and research use cases. The genomic data warehouse is positioned to play a key role in enhancing the research capabilities and advancing individualized patient care at Mayo Clinic.

The BRITNeY Suite Animation Tool

DEFF Research Database (Denmark)

Westergaard, Michael; Lassen, Kristian Bisgaard

2006-01-01

This paper describes the BRITNeY suite, a tool which enables users to create visualizations of formal models. BRITNeY suite is integrated with CPN Tools, and we give an example of how to extend a simple stop-and-wait protocol with a visualization in the form of message sequence charts. We also sh...... examples of animations created during industrial projects to give an impression of what is possible with the BRITNeY suite....

Translating the cancer genome: Going beyond p values

Energy Technology Data Exchange (ETDEWEB)

Chin, Lynda; Chin, Lynda; Gray, Joe W.

2008-04-03

Cancer cells are endowed with diverse biological capabilities driven by myriad inherited and somatic genetic and epigenetic aberrations that commandeer key cancer-relevant pathways. Efforts to elucidate these aberrations began with Boveri's hypothesis of aberrant mitoses causing cancer and continue today with a suite of powerful high-resolution technologies that enable detailed catalogues of genomic aberrations and epigenomic modifications. Tomorrow will likely bring the complete atlas of reversible and irreversible alteration in individual cancers. The challenge now is to discern causal molecular abnormalities from genomic and epigenomic 'noise', to understand how the ensemble of these aberrations collaborate to drive cancer pathophysiology. Here, we highlight lessons learned from now classical examples of successful translation of genomic discoveries into clinical practice, lessons that may be used to guide and accelerate translation of emerging genomic insights into practical clinical endpoints that can impact on practice of cancer medicine.

Genome size evolution in Ontario ferns (Polypodiidae): evolutionary correlations with cell size, spore size, and habitat type and an absence of genome downsizing.

Science.gov (United States)

Henry, Thomas A; Bainard, Jillian D; Newmaster, Steven G

2014-10-01

Genome size is known to correlate with a number of traits in angiosperms, but less is known about the phenotypic correlates of genome size in ferns. We explored genome size variation in relation to a suite of morphological and ecological traits in ferns. Thirty-six fern taxa were collected from wild populations in Ontario, Canada. 2C DNA content was measured using flow cytometry. We tested for genome downsizing following polyploidy using a phylogenetic comparative analysis to explore the correlation between 1Cx DNA content and ploidy. There was no compelling evidence for the occurrence of widespread genome downsizing during the evolution of Ontario ferns. The relationship between genome size and 11 morphological and ecological traits was explored using a phylogenetic principal component regression analysis. Genome size was found to be significantly associated with cell size, spore size, spore type, and habitat type. These results are timely as past and recent studies have found conflicting support for the association between ploidy/genome size and spore size in fern polyploid complexes; this study represents the first comparative analysis of the trend across a broad taxonomic group of ferns.

Enabling interoperability in Geoscience with GI-suite

Science.gov (United States)

Boldrini, Enrico; Papeschi, Fabrizio; Santoro, Mattia; Nativi, Stefano

2015-04-01

GI-suite is a brokering framework targeting interoperability of heterogeneous systems in the Geoscience domain. The framework is composed by different brokers each one focusing on a specific functionality: discovery, access and semantics (i.e. GI-cat, GI-axe, GI-sem). The brokering takes place between a set of heterogeneous publishing services and a set of heterogeneous consumer applications: the brokering target is represented by resources (e.g. coverages, features, or metadata information) required to seamlessly flow from the providers to the consumers. Different international and community standards are now supported by GI-suite, making possible the successful deployment of GI-suite in many international projects and initiatives (such as GEOSS, NSF BCube and several EU funded projects). As for the publisher side more than 40 standards and implementations are supported (e.g. Dublin Core, OAI-PMH, OGC W*S, Geonetwork, THREDDS Data Server, Hyrax Server, etc.). The support for each individual standard is provided by means of specific GI-suite components, called accessors. As for the consumer applications side more than 15 standards and implementations are supported (e.g. ESRI ArcGIS, Openlayers, OGC W*S, OAI-PMH clients, etc.). The support for each individual standard is provided by means of specific profiler components. The GI-suite can be used in different scenarios by different actors: - A data provider having a pre-existent data repository can deploy and configure GI-suite to broker it and making thus available its data resources through different protocols to many different users (e.g. for data discovery and/or data access) - A data consumer can use GI-suite to discover and/or access resources from a variety of publishing services that are already publishing data according to well-known standards. - A community can deploy and configure GI-suite to build a community (or project-specific) broker: GI-suite can broker a set of community related repositories and

A Perfect Match Genomic Landscape Provides a Unified Framework for the Precise Detection of Variation in Natural and Synthetic Haploid Genomes.

Science.gov (United States)

Palacios-Flores, Kim; García-Sotelo, Jair; Castillo, Alejandra; Uribe, Carina; Aguilar, Luis; Morales, Lucía; Gómez-Romero, Laura; Reyes, José; Garciarubio, Alejandro; Boege, Margareta; Dávila, Guillermo

2018-04-01

We present a conceptually simple, sensitive, precise, and essentially nonstatistical solution for the analysis of genome variation in haploid organisms. The generation of a Perfect Match Genomic Landscape (PMGL), which computes intergenome identity with single nucleotide resolution, reveals signatures of variation wherever a query genome differs from a reference genome. Such signatures encode the precise location of different types of variants, including single nucleotide variants, deletions, insertions, and amplifications, effectively introducing the concept of a general signature of variation. The precise nature of variants is then resolved through the generation of targeted alignments between specific sets of sequence reads and known regions of the reference genome. Thus, the perfect match logic decouples the identification of the location of variants from the characterization of their nature, providing a unified framework for the detection of genome variation. We assessed the performance of the PMGL strategy via simulation experiments. We determined the variation profiles of natural genomes and of a synthetic chromosome, both in the context of haploid yeast strains. Our approach uncovered variants that have previously escaped detection. Moreover, our strategy is ideally suited for further refining high-quality reference genomes. The source codes for the automated PMGL pipeline have been deposited in a public repository. Copyright © 2018 by the Genetics Society of America.

Genome-wide DNA polymorphism analyses using VariScan

Directory of Open Access Journals (Sweden)

Vilella Albert J

2006-09-01

Full Text Available Abstract Background DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis. Results We have developed methods for the analysis of DNA sequence polymorphisms at the genome-wide scale. These methods, which have been tested on a coalescent-simulated and actual data files from mouse and human, have been implemented in the VariScan software package version 2.0. Additionally, we have also incorporated a graphical-user interface. The main features of this software are: i exhaustive population-genetic analyses including those based on the coalescent theory; ii analysis adapted to the shallow data generated by the high-throughput genome projects; iii use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v visualization of the results integrated with current genome annotations in commonly available genome browsers. Conclusion VariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms. The current version implements new algorithms, methods, and capabilities, providing an important tool for an exhaustive exploratory analysis of genome-wide DNA polymorphism data.

ASDA - Advanced Suit Design Analyzer computer program

Science.gov (United States)

Bue, Grant C.; Conger, Bruce C.; Iovine, John V.; Chang, Chi-Min

1992-01-01

An ASDA model developed to evaluate the heat and mass transfer characteristics of advanced pressurized suit design concepts for low pressure or vacuum planetary applications is presented. The model is based on a generalized 3-layer suit that uses the Systems Integrated Numerical Differencing Analyzer '85 in conjunction with a 41-node FORTRAN routine. The latter simulates the transient heat transfer and respiratory processes of a human body in a suited environment. The user options for the suit encompass a liquid cooled garment, a removable jacket, a CO2/H2O permeable layer, and a phase change layer.

Complete genomes of Hairstreak butterflies, their speciation, and nucleo-mitochondrial incongruence.

Science.gov (United States)

Cong, Qian; Shen, Jinhui; Borek, Dominika; Robbins, Robert K; Otwinowski, Zbyszek; Grishin, Nick V

2016-04-28

Comparison of complete genomes of closely related species enables research on speciation and how phenotype is determined by genotype. Lepidoptera, an insect order of 150,000 species with diverse phenotypes, is well-suited for such comparative genomics studies if new genomes, which cover additional Lepidoptera families are acquired. We report a 729 Mbp genome assembly of the Calycopis cecrops, the first genome from the family Lycaenidae and the largest available Lepidoptera genome. As detritivore, Calycopis shows expansion in detoxification and digestion enzymes. We further obtained complete genomes of 8 Calycopis specimens: 3 C. cecrops and 5 C. isobeon, including a dry specimen stored in the museum for 30 years. The two species differ subtly in phenotype and cannot be differentiated by mitochondrial DNA. However, nuclear genomes revealed a deep split between them. Genes that can clearly separate the two species (speciation hotspots) mostly pertain to circadian clock, mating behavior, transcription regulation, development and cytoskeleton. The speciation hotspots and their function significantly overlap with those we previously found in Pterourus, suggesting common speciation mechanisms in these butterflies.

Simultaneous gene finding in multiple genomes.

Science.gov (United States)

König, Stefanie; Romoth, Lars W; Gerischer, Lizzy; Stanke, Mario

2016-11-15

As the tree of life is populated with sequenced genomes ever more densely, the new challenge is the accurate and consistent annotation of entire clades of genomes. We address this problem with a new approach to comparative gene finding that takes a multiple genome alignment of closely related species and simultaneously predicts the location and structure of protein-coding genes in all input genomes, thereby exploiting negative selection and sequence conservation. The model prefers potential gene structures in the different genomes that are in agreement with each other, or-if not-where the exon gains and losses are plausible given the species tree. We formulate the multi-species gene finding problem as a binary labeling problem on a graph. The resulting optimization problem is NP hard, but can be efficiently approximated using a subgradient-based dual decomposition approach. The proposed method was tested on whole-genome alignments of 12 vertebrate and 12 Drosophila species. The accuracy was evaluated for human, mouse and Drosophila melanogaster and compared to competing methods. Results suggest that our method is well-suited for annotation of (a large number of) genomes of closely related species within a clade, in particular, when RNA-Seq data are available for many of the genomes. The transfer of existing annotations from one genome to another via the genome alignment is more accurate than previous approaches that are based on protein-spliced alignments, when the genomes are at close to medium distances. The method is implemented in C ++ as part of Augustus and available open source at http://bioinf.uni-greifswald.de/augustus/ CONTACT: stefaniekoenig@ymail.com or mario.stanke@uni-greifswald.deSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Use MACES IVA Suit for EVA Mobility Evaluations

Science.gov (United States)

Watson, Richard D.

2014-01-01

The use of an Intra-Vehicular Activity (IVA) suit for a spacewalk or Extra-Vehicular Activity (EVA) was evaluated for mobility and usability in the Neutral Buoyancy Lab (NBL) environment. The Space Shuttle Advanced Crew Escape Suit (ACES) has been modified (MACES) to integrate with the Orion spacecraft. The first several missions of the Orion MPCV spacecraft will not have mass available to carry an EVA specific suit so any EVA required will have to be performed by the MACES. Since the MACES was not designed with EVA in mind, it was unknown what mobility the suit would be able to provide for an EVA or if a person could perform useful tasks for an extended time inside the pressurized suit. The suit was evaluated in multiple NBL runs by a variety of subjects including crewmembers with significant EVA experience. Various functional mobility tasks performed included: translation, body positioning, carrying tools, body stabilization, equipment handling, and use of tools. Hardware configurations included with and without TMG, suit with IVA gloves and suit with EVA gloves. Most tasks were completed on ISS mockups with existing EVA tools. Some limited tasks were completed with prototype tools on a simulated rocky surface. Major findings include: demonstration of the ability to weigh-out the suit, understanding the need to have subjects perform multiple runs prior to getting feedback, determination of critical sizing factors, and need for adjustment of suit work envelop. The early testing has demonstrated the feasibility of EVA's limited duration and limited scope. Further testing is required with more flight like tasking and constraints to validate these early results. If the suit is used for EVA, it will require mission specific modifications for umbilical management or PLSS integration, safety tether attachment, and tool interfaces. These evaluations are continuing through calendar year 2014.

Morphing: A Novel Approach to Astronaut Suit Sizing

Science.gov (United States)

Margerum, Sarah; Clowers, Kurt; Rajulu, Sudhakar

2006-01-01

The fitting of a spacesuit to an astronaut is an iterative process consisting of two parts. The first uses anthropometric data to provide an approximation of the suit components that will fit the astronaut. The second part is the subjective fitting, where small adjustments are made based on the astronaut s preference. By providing a better approximation of the correct suit components, the entire fit process time can be reduced significantly. The goals of this project are twofold: (1) To evaluate the effectiveness of the existing sizing algorithm for the Mark III Hybrid suit and (2) to determine what additional components are needed in order to provide adequate sizing for the existing astronaut population. A single subject was scanned using a 3D whole-body scanner (VITUS 3D) in the Mark III suit in eight different poses and four subjects in minimal clothing were also scanned in similar poses. The 3D external body scans of the suit and the subject are overlaid and visually aligned in a customized MATLAB program. The suit components were contracted or expanded linearly along the subjects limbs to match the subjects segmental lengths. Two independent measures were obtained from the morphing program on four subjects and compared with the existing sizing information. Two of the four subjects were in correspondence with the sizing algorithm and morphing results. The morphing outcome for a third subject, incompatible with the suit, suggested that an additional arm element at least 6 inches smaller than the existing smallest suit component would need to be acquired. The morphing result of the fourth subject, deemed incompatible with the suit using the sizing algorithm, indicated a different suit configuration which would be compatible. This configuration matched with the existing suit fit check data.

Agaricus bisporus genome sequence: a commentary.

Science.gov (United States)

Kerrigan, Richard W; Challen, Michael P; Burton, Kerry S

2013-06-01

The genomes of two isolates of Agaricus bisporus have been sequenced recently. This soil-inhabiting fungus has a wide geographical distribution in nature and it is also cultivated in an industrialized indoor process ($4.7bn annual worldwide value) to produce edible mushrooms. Previously this lignocellulosic fungus has resisted precise econutritional classification, i.e. into white- or brown-rot decomposers. The generation of the genome sequence and transcriptomic analyses has revealed a new classification, 'humicolous', for species adapted to grow in humic-rich, partially decomposed leaf material. The Agaricus biporus genomes contain a collection of polysaccharide and lignin-degrading genes and more interestingly an expanded number of genes (relative to other lignocellulosic fungi) that enhance degradation of lignin derivatives, i.e. heme-thiolate peroxidases and β-etherases. A motif that is hypothesized to be a promoter element in the humicolous adaptation suite is present in a large number of genes specifically up-regulated when the mycelium is grown on humic-rich substrate. The genome sequence of A. bisporus offers a platform to explore fungal biology in carbon-rich soil environments and terrestrial cycling of carbon, nitrogen, phosphorus and potassium. Copyright © 2013 Elsevier Inc. All rights reserved.

Analytical Tools for Space Suit Design

Science.gov (United States)

Aitchison, Lindsay

2011-01-01

As indicated by the implementation of multiple small project teams within the agency, NASA is adopting a lean approach to hardware development that emphasizes quick product realization and rapid response to shifting program and agency goals. Over the past two decades, space suit design has been evolutionary in approach with emphasis on building prototypes then testing with the largest practical range of subjects possible. The results of these efforts show continuous improvement but make scaled design and performance predictions almost impossible with limited budgets and little time. Thus, in an effort to start changing the way NASA approaches space suit design and analysis, the Advanced Space Suit group has initiated the development of an integrated design and analysis tool. It is a multi-year-if not decadal-development effort that, when fully implemented, is envisioned to generate analysis of any given space suit architecture or, conversely, predictions of ideal space suit architectures given specific mission parameters. The master tool will exchange information to and from a set of five sub-tool groups in order to generate the desired output. The basic functions of each sub-tool group, the initial relationships between the sub-tools, and a comparison to state of the art software and tools are discussed.

Suited Contingency Ops Food - 2

Science.gov (United States)

Glass, J. W.; Leong, M. L.; Douglas, G. L.

2014-01-01

The contingency scenario for an emergency cabin depressurization event may require crewmembers to subsist in a pressurized suit for up to 144 hours. This scenario requires the capability for safe nutrition delivery through a helmet feed port against a 4 psi pressure differential to enable crewmembers to maintain strength and cognition to perform critical tasks. Two nutritional delivery prototypes were developed and analyzed for compatibility with the helmet feed port interface and for operational effectiveness against the pressure differential. The bag-in-bag (BiB) prototype, designed to equalize the suit pressure with the beverage pouch and enable a crewmember to drink normally, delivered water successfully to three different subjects in suits pressurized to 4 psi. The Boa restrainer pouch, designed to provide mechanical leverage to overcome the pressure differential, did not operate sufficiently. Guidelines were developed and compiled for contingency beverages that provide macro-nutritional requirements, a minimum one-year shelf life, and compatibility with the delivery hardware. Evaluation results and food product parameters have the potential to be used to improve future prototype designs and develop complete nutritional beverages for contingency events. These feeding capabilities would have additional use on extended surface mission EVAs, where the current in-suit drinking device may be insufficient.

Interoperative efficiency in minimally invasive surgery suites.

Science.gov (United States)

van Det, M J; Meijerink, W J H J; Hoff, C; Pierie, J P E N

2009-10-01

Performing minimally invasive surgery (MIS) in a conventional operating room (OR) requires additional specialized equipment otherwise stored outside the OR. Before the procedure, the OR team must collect, prepare, and connect the equipment, then take it away afterward. These extra tasks pose a thread to OR efficiency and may lengthen turnover times. The dedicated MIS suite has permanently installed laparoscopic equipment that is operational on demand. This study presents two experiments that quantify the superior efficiency of the MIS suite in the interoperative period. Preoperative setup and postoperative breakdown times in the conventional OR and the MIS suite in an experimental setting and in daily practice were analyzed. In the experimental setting, randomly chosen OR teams simulated the setup and breakdown for a standard laparoscopic cholecystectomy (LC) and a complex laparoscopic sigmoid resection (LS). In the clinical setting, the interoperative period for 66 LCs randomly assigned to the conventional OR or the MIS suite were analyzed. In the experimental setting, the setup and breakdown times were significantly shorter in the MIS suite. The difference between the two types of OR increased for the complex procedure: 2:41 min for the LC (p < 0.001) and 10:47 min for the LS (p < 0.001). In the clinical setting, the setup and breakdown times as a whole were not reduced in the MIS suite. Laparoscopic setup and breakdown times were significantly shorter in the MIS suite (mean difference, 5:39 min; p < 0.001). Efficiency during the interoperative period is significantly improved in the MIS suite. The OR nurses' tasks are relieved, which may reduce mental and physical workload and improve job satisfaction and patient safety. Due to simultaneous tasks of other disciplines, an overall turnover time reduction could not be achieved.

Improved Sleep in Military Personnel is Associated with Changes in the Expression of Inflammatory Genes and Improvement in Depression Symptoms

Directory of Open Access Journals (Sweden)

Whitney S. Livingston

2015-04-01

Full Text Available Study Objectives: Sleep disturbances are common in military personnel and are associated with increased risk for psychiatric morbidity, including posttraumatic stress disorder and depression, as well as inflammation. Improved sleep quality is linked to reductions in inflammatory bio-markers; however, the underlying mechanisms remain elusive. Methods: In this study we examine whole genome expression changes related to improved sleep in 68 military personnel diagnosed with insomnia. Subjects were classified into the following groups and then compared: improved sleep (n=46, or non-improved sleep (n=22 following three months of standard of care treatment for insomnia. Within subject differential expression was determined from microarray data using the Partek Genomics Suite analysis program and the interactive pathway analysis was used to determine key regulators of observed expression changes. Changes in symptoms of depression and posttraumatic stress disorder were also compared. Results: At baseline both groups were similar in demographics, clinical characteristics, and gene-expression profiles. The microarray data revealed that 217 coding genes were differentially expressed at the follow-up-period compared to baseline in the participants with improved sleep. Expression of inflammatory cytokines were reduced including IL-1β, IL-6, IL-8 and IL-13, with fold changes ranging from -3.19 to -2.1, and there were increases in the expression of inflammatory regulatory genes including toll-like receptors 1, 4, 7, and 8 in the improved sleep group. Interactive pathway analysis revealed 6 gene networks, including ubiquitin which was a major regulator in these gene-expression changes. The improved sleep group also had a significant reduction in the severity of depressive symptoms.Conclusions: Interventions that restore sleep likely reduce the expression of inflammatory genes, which relate to ubiquitin genes and relate to reductions in depressive symptoms.

Environmental genomics reveals a single species ecosystem deep within the Earth

Energy Technology Data Exchange (ETDEWEB)

Chivian, Dylan; Brodie, Eoin L.; Alm, Eric J.; Culley, David E.; Dehal, Paramvir S.; DeSantis, Todd Z.; Gihring, Thomas M.; Lapidus, Alla; Lin, Li-Hung; Lowry, Stephen R.; Moser, Duane P.; Richardson, Paul; Southam, Gordon; Wanger, Greg; Pratt, Lisa M.; Andersen, Gary L.; Hazen, Terry C.; Brockman, Fred J.; Arkin, Adam P.; Onstott, Tullis C.

2008-09-17

DNA from low biodiversity fracture water collected at 2.8 km depth in a South African gold mine was sequenced and assembled into a single, complete genome. This bacterium, Candidatus Desulforudis audaxviator, comprises>99.9percent of the microorganisms inhabiting the fluid phase of this particular fracture. Its genome indicates a motile, sporulating, sulfate reducing, chemoautotrophic thermophile that can fix its own nitrogen and carbon using machinery shared with archaea. Candidatus Desulforudis audaxviator is capable of an independent lifestyle well suited to long-term isolation from the photosphere deep within Earth?s crust, and offers the first example of a natural ecosystem that appears to have its biological component entirely encoded within a single genome.

The Variable Vector Countermeasure Suit (V2Suit for Space Habitation and Exploration

Directory of Open Access Journals (Sweden)

Kevin R Duda

2015-04-01

Full Text Available The Variable Vector Countermeasure Suit (V2Suit for Space Habitation and Exploration is a novel system concept that provides a platform for integrating sensors and actuators with daily astronaut intravehicular activities to improve health and performance, while reducing the mass and volume of the physiologic adaptation countermeasure systems, as well as the required exercise time during long-duration space exploration missions. The V2Suit system leverages wearable kinematic monitoring technology and uses inertial measurement units (IMUs and control moment gyroscopes (CMGs within miniaturized modules placed on body segments to provide a viscous resistance during movements against a specified direction of down – initially as a countermeasure to the sensorimotor adaptation performance decrements that manifest themselves while living and working in microgravity and during gravitational transitions during long-duration spaceflight, including post-flight recovery and rehabilitation. Several aspects of the V2Suit system concept were explored and simulated prior to developing a brassboard prototype for technology demonstration. This included a system architecture for identifying the key components and their interconnects, initial identification of key human-system integration challenges, development of a simulation architecture for CMG selection and parameter sizing, and the detailed mechanical design and fabrication of a module. The brassboard prototype demonstrates closed-loop control from down initialization through CMG actuation, and provides a research platform for human performance evaluations to mitigate sensorimotor adaptation, as well as a tool for determining the performance requirements when used as a musculoskeletal deconditioning countermeasure. This type of countermeasure system also has Earth benefits, particularly in gait or movement stabilization and rehabilitation.

Innovative technology summary report: Sealed-seam sack suits

International Nuclear Information System (INIS)

1998-09-01

Sealed-seam sack suits are an improved/innovative safety and industrial hygiene technology designed to protect workers from dermal exposure to contamination. Most of these disposable, synthetic-fabric suits are more protective than cotton suits, and are also water-resistant and gas permeable. Some fabrics provide a filter to aerosols, which is important to protection against contamination, while allowing air to pass, increasing comfort level of workers. It is easier to detect body-moisture breakthrough with the disposable suits than with cotton, which is also important to protecting workers from contamination. These suits present a safe and cost-effective (6% to 17% less expensive than the baseline) alternative to traditional protective clothing. This report covers the period from October 1996 to August 1997. During that time, sealed-seam sack suits were demonstrated during daily activities under normal working conditions at the C Reactor and under environmentally controlled conditions at the Los Alamos National Laboratory (LANL)

The ZPIC educational code suite

Science.gov (United States)

Calado, R.; Pardal, M.; Ninhos, P.; Helm, A.; Mori, W. B.; Decyk, V. K.; Vieira, J.; Silva, L. O.; Fonseca, R. A.

2017-10-01

Particle-in-Cell (PIC) codes are used in almost all areas of plasma physics, such as fusion energy research, plasma accelerators, space physics, ion propulsion, and plasma processing, and many other areas. In this work, we present the ZPIC educational code suite, a new initiative to foster training in plasma physics using computer simulations. Leveraging on our expertise and experience from the development and use of the OSIRIS PIC code, we have developed a suite of 1D/2D fully relativistic electromagnetic PIC codes, as well as 1D electrostatic. These codes are self-contained and require only a standard laptop/desktop computer with a C compiler to be run. The output files are written in a new file format called ZDF that can be easily read using the supplied routines in a number of languages, such as Python, and IDL. The code suite also includes a number of example problems that can be used to illustrate several textbook and advanced plasma mechanisms, including instructions for parameter space exploration. We also invite contributions to this repository of test problems that will be made freely available to the community provided the input files comply with the format defined by the ZPIC team. The code suite is freely available and hosted on GitHub at https://github.com/zambzamb/zpic. Work partially supported by PICKSC.

A novel genome-information content-based statistic for genome-wide association analysis designed for next-generation sequencing data.

Science.gov (United States)

Luo, Li; Zhu, Yun; Xiong, Momiao

2012-06-01

The genome-wide association studies (GWAS) designed for next-generation sequencing data involve testing association of genomic variants, including common, low frequency, and rare variants. The current strategies for association studies are well developed for identifying association of common variants with the common diseases, but may be ill-suited when large amounts of allelic heterogeneity are present in sequence data. Recently, group tests that analyze their collective frequency differences between cases and controls shift the current variant-by-variant analysis paradigm for GWAS of common variants to the collective test of multiple variants in the association analysis of rare variants. However, group tests ignore differences in genetic effects among SNPs at different genomic locations. As an alternative to group tests, we developed a novel genome-information content-based statistics for testing association of the entire allele frequency spectrum of genomic variation with the diseases. To evaluate the performance of the proposed statistics, we use large-scale simulations based on whole genome low coverage pilot data in the 1000 Genomes Project to calculate the type 1 error rates and power of seven alternative statistics: a genome-information content-based statistic, the generalized T(2), collapsing method, multivariate and collapsing (CMC) method, individual χ(2) test, weighted-sum statistic, and variable threshold statistic. Finally, we apply the seven statistics to published resequencing dataset from ANGPTL3, ANGPTL4, ANGPTL5, and ANGPTL6 genes in the Dallas Heart Study. We report that the genome-information content-based statistic has significantly improved type 1 error rates and higher power than the other six statistics in both simulated and empirical datasets.

Draft genome sequence of Microbacterium oleivorans strain Wellendorf implicates heterotrophic versatility and bioremediation potential

Directory of Open Access Journals (Sweden)

Anton P. Avramov

2016-12-01

Full Text Available Microbacterium oleivorans is a predominant member of hydrocarbon-contaminated environments. We here report on the genomic analysis of M. oleivorans strain Wellendorf that was isolated from an indoor door handle. The partial genome of M. oleivorans strain Wellendorf consists of 2,916,870 bp of DNA with 2831 protein-coding genes and 49 RNA genes. The organism appears to be a versatile mesophilic heterotroph potentially capable of hydrolysis a suite of carbohydrates and amino acids. Genomic analysis revealed metabolic versatility with genes involved in the metabolism and transport of glucose, fructose, rhamnose, galactose, xylose, arabinose, alanine, aspartate, asparagine, glutamate, serine, glycine, threonine and cysteine. This is the first detailed analysis of a Microbacterium oleivorans genome.

Cloud computing for genomic data analysis and collaboration.

Science.gov (United States)

Langmead, Ben; Nellore, Abhinav

2018-04-01

Next-generation sequencing has made major strides in the past decade. Studies based on large sequencing data sets are growing in number, and public archives for raw sequencing data have been doubling in size every 18 months. Leveraging these data requires researchers to use large-scale computational resources. Cloud computing, a model whereby users rent computers and storage from large data centres, is a solution that is gaining traction in genomics research. Here, we describe how cloud computing is used in genomics for research and large-scale collaborations, and argue that its elasticity, reproducibility and privacy features make it ideally suited for the large-scale reanalysis of publicly available archived data, including privacy-protected data.

[Antigravity suit used for neurosurgical operations in sitting position].

Science.gov (United States)

Szpiro-Zurkowska, A; Milczarek, Z; Marchel, A; Jagielski, J

1996-01-01

The aviator's antigravity suit (G-suit) was used for 40 operations on neurosurgical patients operated on in sitting position. The G-suit was filled with air to 0.2 atmosphere (20 kPa) pressure in 26 cases, and 0.3 atm. (30 kPa) in 14 cases. In all cases G-suit filling was followed by central venous pressure rise and mean arterial pressure rise. Venous air embolism was found in 5 (12.5%) patients. No other complications connected with the use of G-suit were observed.

Genotyping-by-sequencing for Populus population genomics: an assessment of genome sampling patterns and filtering approaches.

Directory of Open Access Journals (Sweden)

Martin P Schilling

Full Text Available Continuing advances in nucleotide sequencing technology are inspiring a suite of genomic approaches in studies of natural populations. Researchers are faced with data management and analytical scales that are increasing by orders of magnitude. With such dramatic advances comes a need to understand biases and error rates, which can be propagated and magnified in large-scale data acquisition and processing. Here we assess genomic sampling biases and the effects of various population-level data filtering strategies in a genotyping-by-sequencing (GBS protocol. We focus on data from two species of Populus, because this genus has a relatively small genome and is emerging as a target for population genomic studies. We estimate the proportions and patterns of genomic sampling by examining the Populus trichocarpa genome (Nisqually-1, and demonstrate a pronounced bias towards coding regions when using the methylation-sensitive ApeKI restriction enzyme in this species. Using population-level data from a closely related species (P. tremuloides, we also investigate various approaches for filtering GBS data to retain high-depth, informative SNPs that can be used for population genetic analyses. We find a data filter that includes the designation of ambiguous alleles resulted in metrics of population structure and Hardy-Weinberg equilibrium that were most consistent with previous studies of the same populations based on other genetic markers. Analyses of the filtered data (27,910 SNPs also resulted in patterns of heterozygosity and population structure similar to a previous study using microsatellites. Our application demonstrates that technically and analytically simple approaches can readily be developed for population genomics of natural populations.

Oracle SOA Suite 11g performance cookbook

CERN Document Server

Brasier, Matthew; Wright, Nicholas

2013-01-01

This is a Cookbook with interesting, hands-on recipes, giving detailed descriptions and lots of practical walkthroughs for boosting the performance of your Oracle SOA Suite.This book is for Oracle SOA Suite 11g administrators, developers, and architects who want to understand how they can maximise the performance of their SOA Suite infrastructure. The recipes contain easy to follow step-by-step instructions and include many helpful and practical tips. It is suitable for anyone with basic operating system and application server administration experience.

Safety in the use of pressurized suits

International Nuclear Information System (INIS)

1984-01-01

This Code of Practice describes the procedures relating to the safe operation of Pressurized Suit Areas and their supporting services. It is directed at personnel responsible for the design and/or operation of Pressurized Suit Areas. (author)

Suites of dwarfs around Nearby giant galaxies

International Nuclear Information System (INIS)

Karachentsev, Igor D.; Kaisina, Elena I.; Makarov, Dmitry I.

2014-01-01

The Updated Nearby Galaxy Catalog (UNGC) contains the most comprehensive summary of distances, radial velocities, and luminosities for 800 galaxies located within 11 Mpc from us. The high density of observables in the UNGC makes this sample indispensable for checking results of N-body simulations of cosmic structures on a ∼1 Mpc scale. The environment of each galaxy in the UNGC was characterized by a tidal index Θ 1 , depending on the separation and mass of the galaxy's main disturber (MD). We grouped UNGC galaxies with a common MD in suites, and ranked suite members according to their Θ 1 . All suite members with positive Θ 1 are assumed to be physical companions of the MD. About 58% of the sample are members of physical groups. The distribution of suites by the number of members, n, follows a relation N(n) ∼ n –2 . The 20 most populated suites contain 468 galaxies, i.e., 59% of the UNGC sample. The fraction of MDs among the brightest galaxies is almost 100% and drops to 50% at M B = –18 m . We discuss various properties of MDs, as well as galaxies belonging to their suites. The suite abundance practically does not depend on the morphological type, linear diameter, or hydrogen mass of the MD, the tightest correlation being with the MD dynamical mass. Dwarf galaxies around MDs exhibit well-known segregation effects: the population of the outskirts has later morphological types, richer H I contents, and higher rates of star formation activity. Nevertheless, there are some intriguing cases where dwarf spheroidal galaxies occur at the far periphery of the suites, as well as some late-type dwarfs residing close to MDs. Comparing simulation results with galaxy groups, most studies assume the Local Group is fairly typical. However, we recognize that the nearby groups significantly differ from each other and there is considerable variation in their properties. The suites of companions around the Milky Way and M31, consisting of the Local Group, do not

Space Suit Joint Torque Measurement Method Validation

Science.gov (United States)

Valish, Dana; Eversley, Karina

2012-01-01

In 2009 and early 2010, a test method was developed and performed to quantify the torque required to manipulate joints in several existing operational and prototype space suits. This was done in an effort to develop joint torque requirements appropriate for a new Constellation Program space suit system. The same test method was levied on the Constellation space suit contractors to verify that their suit design met the requirements. However, because the original test was set up and conducted by a single test operator there was some question as to whether this method was repeatable enough to be considered a standard verification method for Constellation or other future development programs. In order to validate the method itself, a representative subset of the previous test was repeated, using the same information that would be available to space suit contractors, but set up and conducted by someone not familiar with the previous test. The resultant data was compared using graphical and statistical analysis; the results indicated a significant variance in values reported for a subset of the re-tested joints. Potential variables that could have affected the data were identified and a third round of testing was conducted in an attempt to eliminate and/or quantify the effects of these variables. The results of the third test effort will be used to determine whether or not the proposed joint torque methodology can be applied to future space suit development contracts.

Sibelius. Karelia Suite, Op. 11 / Robert Layton

Index Scriptorium Estoniae

Layton, Robert

1996-01-01

Uuest heliplaadist "Sibelius. Karelia Suite, Op. 11. Luonnotar, Op. 70 a. Andante festivo. The Oceanides, Op. 73. King Christian II, Op. 27-Suite. Finlandia, Op. 26a. Gothenburg Symphony Orchester, Neeme Järvi" DG 447 760-2GH (72 minutes: DDD)

Advanced EVA Suit Camera System Development Project

Science.gov (United States)

Mock, Kyla

2016-01-01

The National Aeronautics and Space Administration (NASA) at the Johnson Space Center (JSC) is developing a new extra-vehicular activity (EVA) suit known as the Advanced EVA Z2 Suit. All of the improvements to the EVA Suit provide the opportunity to update the technology of the video imagery. My summer internship project involved improving the video streaming capabilities of the cameras that will be used on the Z2 Suit for data acquisition. To accomplish this, I familiarized myself with the architecture of the camera that is currently being tested to be able to make improvements on the design. Because there is a lot of benefit to saving space, power, and weight on the EVA suit, my job was to use Altium Design to start designing a much smaller and simplified interface board for the camera's microprocessor and external components. This involved checking datasheets of various components and checking signal connections to ensure that this architecture could be used for both the Z2 suit and potentially other future projects. The Orion spacecraft is a specific project that may benefit from this condensed camera interface design. The camera's physical placement on the suit also needed to be determined and tested so that image resolution can be maximized. Many of the options of the camera placement may be tested along with other future suit testing. There are multiple teams that work on different parts of the suit, so the camera's placement could directly affect their research or design. For this reason, a big part of my project was initiating contact with other branches and setting up multiple meetings to learn more about the pros and cons of the potential camera placements we are analyzing. Collaboration with the multiple teams working on the Advanced EVA Z2 Suit is absolutely necessary and these comparisons will be used as further progress is made for the overall suit design. This prototype will not be finished in time for the scheduled Z2 Suit testing, so my time was

Open architecture of smart sensor suites

Science.gov (United States)

Müller, Wilmuth; Kuwertz, Achim; Grönwall, Christina; Petersson, Henrik; Dekker, Rob; Reinert, Frank; Ditzel, Maarten

2017-10-01

Experiences from recent conflicts show the strong need for smart sensor suites comprising different multi-spectral imaging sensors as core elements as well as additional non-imaging sensors. Smart sensor suites should be part of a smart sensor network - a network of sensors, databases, evaluation stations and user terminals. Its goal is to optimize the use of various information sources for military operations such as situation assessment, intelligence, surveillance, reconnaissance, target recognition and tracking. Such a smart sensor network will enable commanders to achieve higher levels of situational awareness. Within the study at hand, an open system architecture was developed in order to increase the efficiency of sensor suites. The open system architecture for smart sensor suites, based on a system-of-systems approach, enables combining different sensors in multiple physical configurations, such as distributed sensors, co-located sensors combined in a single package, tower-mounted sensors, sensors integrated in a mobile platform, and trigger sensors. The architecture was derived from a set of system requirements and relevant scenarios. Its mode of operation is adaptable to a series of scenarios with respect to relevant objects of interest, activities to be observed, available transmission bandwidth, etc. The presented open architecture is designed in accordance with the NATO Architecture Framework (NAF). The architecture allows smart sensor suites to be part of a surveillance network, linked e.g. to a sensor planning system and a C4ISR center, and to be used in combination with future RPAS (Remotely Piloted Aircraft Systems) for supporting a more flexible dynamic configuration of RPAS payloads.

Advanced Sensor Platform to Evaluate Manloads For Exploration Suit Architectures

Science.gov (United States)

McFarland, Shane; Pierce, Gregory

2016-01-01

Space suit manloads are defined as the outer bounds of force that the human occupant of a suit is able to exert onto the suit during motion. They are defined on a suit-component basis as a unit of maximum force that the suit component in question must withstand without failure. Existing legacy manloads requirements are specific to the suit architecture of the EMU and were developed in an iterative fashion; however, future exploration needs dictate a new suit architecture with bearings, load paths, and entry capability not previously used in any flight suit. No capability currently exists to easily evaluate manloads imparted by a suited occupant, which would be required to develop requirements for a flight-rated design. However, sensor technology has now progressed to the point where an easily-deployable, repeatable and flexible manloads measuring technique could be developed leveraging recent advances in sensor technology. INNOVATION: This development positively impacts schedule, cost and safety risk associated with new suit exploration architectures. For a final flight design, a comprehensive and accurate man loads requirements set must be communicated to the contractor; failing that, a suit design which does not meet necessary manloads limits is prone to failure during testing or worse, during an EVA, which could cause catastrophic failure of the pressure garment posing risk to the crew. This work facilitates a viable means of developing manloads requirements using a range of human sizes & strengths. OUTCOME / RESULTS: Performed sensor market research. Highlighted three viable options (primary, secondary, and flexible packaging option). Designed/fabricated custom bracket to evaluate primary option on a single suit axial. Manned suited manload testing completed and general approach verified.

Correction factors for assessing immersion suits under harsh conditions.

Science.gov (United States)

Power, Jonathan; Tikuisis, Peter; Ré, António Simões; Barwood, Martin; Tipton, Michael

2016-03-01

Many immersion suit standards require testing of thermal protective properties in calm, circulating water while these suits are typically used in harsher environments where they often underperform. Yet it can be expensive and logistically challenging to test immersion suits in realistic conditions. The goal of this work was to develop a set of correction factors that would allow suits to be tested in calm water yet ensure they will offer sufficient protection in harsher conditions. Two immersion studies, one dry and the other with 500 mL of water within the suit, were conducted in wind and waves to measure the change in suit insulation. In both studies, wind and waves resulted in a significantly lower immersed insulation value compared to calm water. The minimum required thermal insulation for maintaining heat balance can be calculated for a given mean skin temperature, metabolic heat production, and water temperature. Combining the physiological limits of sustainable cold water immersion and actual suit insulation, correction factors can be deduced for harsh conditions compared to calm. The minimum in-situ suit insulation to maintain thermal balance is 1.553-0.0624·TW + 0.00018·TW(2) for a dry calm condition. Multiplicative correction factors to the above equation are 1.37, 1.25, and 1.72 for wind + waves, 500 mL suit wetness, and both combined, respectively. Calm water certification tests of suit insulation should meet or exceed the minimum in-situ requirements to maintain thermal balance, and correction factors should be applied for a more realistic determination of minimum insulation for harsh conditions. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Z-2 Prototype Space Suit Development

Science.gov (United States)

Ross, Amy; Rhodes, Richard; Graziosi, David; Jones, Bobby; Lee, Ryan; Haque, Bazle Z.; Gillespie, John W., Jr.

2014-01-01

NASA's Z-2 prototype space suit is the highest fidelity pressure garment from both hardware and systems design perspectives since the Space Shuttle Extravehicular Mobility Unit (EMU) was developed in the late 1970's. Upon completion the Z-2 will be tested in the 11 foot human-rated vacuum chamber and the Neutral Buoyancy Laboratory (NBL) at the NASA Johnson Space Center to assess the design and to determine applicability of the configuration to micro-, low- (asteroid), and planetary- (surface) gravity missions. This paper discusses the 'firsts' that the Z-2 represents. For example, the Z-2 sizes to the smallest suit scye bearing plane distance for at least the last 25 years and is being designed with the most intensive use of human models with the suit model.

Problem of Office Suite Training at the University

Directory of Open Access Journals (Sweden)

Natalia A. Nastashchuk

2013-01-01

Full Text Available Te paper considers the problem of office suite applications training, caused by a rapid change of their versions, variety of software developers and a rapid development of software and hardware platforms. The content of office suite applications training, based on the system of office suite notions, its basic functional and standards of information technologies development (OpenDocument Format Standard, ISO 26300-200Х is presented.

46 CFR 199.214 - Immersion suits and thermal protective aids.

Science.gov (United States)

2010-10-01

... 46 Shipping 7 2010-10-01 2010-10-01 false Immersion suits and thermal protective aids. 199.214... Passenger Vessels § 199.214 Immersion suits and thermal protective aids. (a) Each passenger vessel must... an immersion suit. (c) The immersion suits and thermal protective aids required under paragraphs (a...

PLEASE: The Python Low-energy Electron Analysis SuitE – Enabling Rapid Analysis of LEEM and LEED Data

Directory of Open Access Journals (Sweden)

Maxwell Grady

2018-02-01

Full Text Available PLEASE, the Python Low-energy Electron Analysis SuitE, provides an open source and cross-platform graphical user interface (GUI for rapid analysis and visualization of low energy electron microscopy (LEEM data sets. LEEM and the associated technique, selected area micro-spot low energy electron diffraction (μ-LEED, are powerful tools for analysis of the surface structure for many novel materials. Specifically, these tools are uniquely suited for the characterization of two-dimensional materials. PLEASE offers a user-friendly point-and-click method for extracting intensity-voltage curves from LEEM and LEED data sets. Analysis of these curves provides insight into the atomic structure of the target material surface with unparalleled resolution.

A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae).

Science.gov (United States)

Schoville, Sean D; Chen, Yolanda H; Andersson, Martin N; Benoit, Joshua B; Bhandari, Anita; Bowsher, Julia H; Brevik, Kristian; Cappelle, Kaat; Chen, Mei-Ju M; Childers, Anna K; Childers, Christopher; Christiaens, Olivier; Clements, Justin; Didion, Elise M; Elpidina, Elena N; Engsontia, Patamarerk; Friedrich, Markus; García-Robles, Inmaculada; Gibbs, Richard A; Goswami, Chandan; Grapputo, Alessandro; Gruden, Kristina; Grynberg, Marcin; Henrissat, Bernard; Jennings, Emily C; Jones, Jeffery W; Kalsi, Megha; Khan, Sher A; Kumar, Abhishek; Li, Fei; Lombard, Vincent; Ma, Xingzhou; Martynov, Alexander; Miller, Nicholas J; Mitchell, Robert F; Munoz-Torres, Monica; Muszewska, Anna; Oppert, Brenda; Palli, Subba Reddy; Panfilio, Kristen A; Pauchet, Yannick; Perkin, Lindsey C; Petek, Marko; Poelchau, Monica F; Record, Éric; Rinehart, Joseph P; Robertson, Hugh M; Rosendale, Andrew J; Ruiz-Arroyo, Victor M; Smagghe, Guy; Szendrei, Zsofia; Thomas, Gregg W C; Torson, Alex S; Vargas Jentzsch, Iris M; Weirauch, Matthew T; Yates, Ashley D; Yocum, George D; Yoon, June-Sun; Richards, Stephen

2018-01-31

The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain why Leptinotarsa decemlineata has high sensitivity to dsRNA. The L. decemlineata genome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest.

Phylogenomic, Pan-genomic, Pathogenomic and Evolutionary Genomic Insights into the Agronomically Relevant Enterobacteria Pantoea ananatis and Pantoea stewartii

Directory of Open Access Journals (Sweden)

Pieter De Maayer

2017-09-01

Full Text Available Pantoea ananatis is ubiquitously found in the environment and causes disease on a wide range of plant hosts. By contrast, its sister species, Pantoea stewartii subsp. stewartii is the host-specific causative agent of the devastating maize disease Stewart’s wilt. This pathogen has a restricted lifecycle, overwintering in an insect vector before being introduced into susceptible maize cultivars, causing disease and returning to overwinter in its vector. The other subspecies of P. stewartii subsp. indologenes, has been isolated from different plant hosts and is predicted to proliferate in different environmental niches. Here we have, by the use of comparative genomics and a comprehensive suite of bioinformatic tools, analyzed the genomes of ten P. stewartii and nineteen P. ananatis strains. Our phylogenomic analyses have revealed that there are two distinct clades within P. ananatis while far less phylogenetic diversity was observed among the P. stewartii subspecies. Pan-genome analyses revealed a large core genome comprising of 3,571 protein coding sequences is shared among the twenty-nine compared strains. Furthermore, we showed that an extensive accessory genome made up largely by a mobilome of plasmids, integrated prophages, integrative and conjugative elements and insertion elements has resulted in extensive diversification of P. stewartii and P. ananatis. While these organisms share many pathogenicity determinants, our comparative genomic analyses show that they differ in terms of the secretion systems they encode. The genomic differences identified in this study have allowed us to postulate on the divergent evolutionary histories of the analyzed P. ananatis and P. stewartii strains and on the molecular basis underlying their ecological success and host range.

Phylogenomic, Pan-genomic, Pathogenomic and Evolutionary Genomic Insights into the Agronomically Relevant Enterobacteria Pantoea ananatis and Pantoea stewartii.

Science.gov (United States)

De Maayer, Pieter; Aliyu, Habibu; Vikram, Surendra; Blom, Jochen; Duffy, Brion; Cowan, Don A; Smits, Theo H M; Venter, Stephanus N; Coutinho, Teresa A

2017-01-01

Pantoea ananatis is ubiquitously found in the environment and causes disease on a wide range of plant hosts. By contrast, its sister species, Pantoea stewartii subsp. stewartii is the host-specific causative agent of the devastating maize disease Stewart's wilt. This pathogen has a restricted lifecycle, overwintering in an insect vector before being introduced into susceptible maize cultivars, causing disease and returning to overwinter in its vector. The other subspecies of P. stewartii subsp. indologenes , has been isolated from different plant hosts and is predicted to proliferate in different environmental niches. Here we have, by the use of comparative genomics and a comprehensive suite of bioinformatic tools, analyzed the genomes of ten P. stewartii and nineteen P. ananatis strains. Our phylogenomic analyses have revealed that there are two distinct clades within P. ananatis while far less phylogenetic diversity was observed among the P. stewartii subspecies. Pan-genome analyses revealed a large core genome comprising of 3,571 protein coding sequences is shared among the twenty-nine compared strains. Furthermore, we showed that an extensive accessory genome made up largely by a mobilome of plasmids, integrated prophages, integrative and conjugative elements and insertion elements has resulted in extensive diversification of P. stewartii and P. ananatis . While these organisms share many pathogenicity determinants, our comparative genomic analyses show that they differ in terms of the secretion systems they encode. The genomic differences identified in this study have allowed us to postulate on the divergent evolutionary histories of the analyzed P. ananatis and P. stewartii strains and on the molecular basis underlying their ecological success and host range.

Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes

DEFF Research Database (Denmark)

Bohlin, J; Skjerve, E; Ussery, David

2008-01-01

with here are mainly used to examine similarities between archaeal and bacterial DNA from different genomes. These methods compare observed genomic frequencies of fixed-sized oligonucleotides with expected values, which can be determined by genomic nucleotide content, smaller oligonucleotide frequencies......, or be based on specific statistical distributions. Advantages with these statistical methods include measurements of phylogenetic relationship with relatively small pieces of DNA sampled from almost anywhere within genomes, detection of foreign/conserved DNA, and homology searches. Our aim was to explore...... the reliability and best suited applications for some popular methods, which include relative oligonucleotide frequencies (ROF), di- to hexanucleotide zero'th order Markov methods (ZOM) and 2.order Markov chain Method (MCM). Tests were performed on distant homology searches with large DNA sequences, detection...

A new device for the inflation of the antigravity suit.

Science.gov (United States)

Brodrick, P M

1986-02-01

The 'Schuco' orthopaedic tourniquet inflator can be simply converted into a suitable device for inflating an antigravity suit (G-suit). The antigravity suit may be used on neurosurgical patients undergoing procedures in the sitting position to help prevent hypotension and air embolism. The availability of this device may encourage the more widespread use of an antigravity suit in neuro-anaesthetic practice.

Development on smart suit for dairy work assistance.

Science.gov (United States)

Nara, Hiroyuki; Kusaka, Takashi; Tanaka, Takayuki; Yamagishi, Takayuki; Ogura, Shotaroh

2013-01-01

Our purpose in this study is to achieve an independent life and a social involvement for the elderly using KEIROKA Technology(fatigue-reduction) which makes it possible to improve the quality of chores and occupations by removing excessive strain and tiredness. The authors have developed power assist suits named "smart suit". The authors have evaluated the effect that the purpose of dairy work assistance, to measure EMG of the worker, compared to the potential of the surface of the non-wearing and wearing "smart suit".

Draft genome of the leopard gecko, Eublepharis macularius.

Science.gov (United States)

Xiong, Zijun; Li, Fang; Li, Qiye; Zhou, Long; Gamble, Tony; Zheng, Jiao; Kui, Ling; Li, Cai; Li, Shengbin; Yang, Huanming; Zhang, Guojie

2016-10-26

Geckos are among the most species-rich reptile groups and the sister clade to all other lizards and snakes. Geckos possess a suite of distinctive characteristics, including adhesive digits, nocturnal activity, hard, calcareous eggshells, and a lack of eyelids. However, one gecko clade, the Eublepharidae, appears to be the exception to most of these 'rules' and lacks adhesive toe pads, has eyelids, and lays eggs with soft, leathery eggshells. These differences make eublepharids an important component of any investigation into the underlying genomic innovations contributing to the distinctive phenotypes in 'typical' geckos. We report high-depth genome sequencing, assembly, and annotation for a male leopard gecko, Eublepharis macularius (Eublepharidae). Illumina sequence data were generated from seven insert libraries (ranging from 170 to 20 kb), representing a raw sequencing depth of 136X from 303 Gb of data, reduced to 84X and 187 Gb after filtering. The assembled genome of 2.02 Gb was close to the 2.23 Gb estimated by k-mer analysis. Scaffold and contig N50 sizes of 664 and 20 kb, respectively, were comparable to the previously published Gekko japonicus genome. Repetitive elements accounted for 42 % of the genome. Gene annotation yielded 24,755 protein-coding genes, of which 93 % were functionally annotated. CEGMA and BUSCO assessment showed that our assembly captured 91 % (225 of 248) of the core eukaryotic genes, and 76 % of vertebrate universal single-copy orthologs. Assembly of the leopard gecko genome provides a valuable resource for future comparative genomic studies of geckos and other squamate reptiles.

Immersion Suit Usage Within the RAAF

Science.gov (United States)

1992-01-01

IMMERSION SUIT USED UVIC QDIS HOLDINGS 202. in 12 Sizes, held by ALSS 492SQN REQUIREMENTS No comment USAGE POLICY REFERENCE DIRAF) AAP 7215.004-1 (P3C...held by ALSS 492SQN. REQUIREMENTS No comment ISACE POLICY REFERENCE DIIAF) AAP 7215.004-1 (P3C Flight Manual) RAAF Supplement No 92 USAGE POUICY UVIC...TYPE P3C REFERENCE Telecon FLTLT Toft I I SQNfRESO AVMED Dated 22 Mar 91 IMMERSION SUIT USED UVIC QDIS HOLDINGS No comment REQUIREMENTS No comment USAGE

Advanced Sensor Platform to Evaluate Manloads for Exploration Suit Architectures

Data.gov (United States)

National Aeronautics and Space Administration — Space suit manloads are defined as the outer bounds of force that the human occupant of a suit is able to exert onto the suit during motion. They are defined on a...

Alterations in MAST suit pressure with changes in ambient temperature.

Science.gov (United States)

Sanders, A B; Meislin, H W; Daub, E

1983-01-01

A study was undertaken to test the hypothesis that change in ambient air temperature has an effect on MAST suit pressure according to the ideal gas law. Two different MAST suits were tested on Resusci-Annie dummies. The MAST suits were applied in a cold room at 4.4 degrees C and warmed to 44 degrees C. Positive linear correlations were found in nine trials, but the two suits differed in their rate of increase in pressure. Three trials using humans were conducted showing increased pressure with temperature but at a lesser rate than with dummies. A correlation of 0.5 to 1.0 mm Hg increase in MAST suit pressure for each 1.0 degrees C increase in ambient temperature was found. Implications are discussed for the use of the MAST suit in environmental conditions where the temperature changes.

Safety Precautions and Operating Procedures in an (A)BSL-4 Laboratory: 1. Biosafety Level 4 Suit Laboratory Suite Entry and Exit Procedures.

Science.gov (United States)

Janosko, Krisztina; Holbrook, Michael R; Adams, Ricky; Barr, Jason; Bollinger, Laura; Newton, Je T'aime; Ntiforo, Corrie; Coe, Linda; Wada, Jiro; Pusl, Daniela; Jahrling, Peter B; Kuhn, Jens H; Lackemeyer, Matthew G

2016-10-03

Biosafety level 4 (BSL-4) suit laboratories are specifically designed to study high-consequence pathogens for which neither infection prophylaxes nor treatment options exist. The hallmarks of these laboratories are: custom-designed airtight doors, dedicated supply and exhaust airflow systems, a negative-pressure environment, and mandatory use of positive-pressure ("space") suits. The risk for laboratory specialists working with highly pathogenic agents is minimized through rigorous training and adherence to stringent safety protocols and standard operating procedures. Researchers perform the majority of their work in BSL-2 laboratories and switch to BSL-4 suit laboratories when work with a high-consequence pathogen is required. Collaborators and scientists considering BSL-4 projects should be aware of the challenges associated with BSL-4 research both in terms of experimental technical limitations in BSL-4 laboratory space and the increased duration of such experiments. Tasks such as entering and exiting the BSL-4 suit laboratories are considerably more complex and time-consuming compared to BSL-2 and BSL-3 laboratories. The focus of this particular article is to address basic biosafety concerns and describe the entrance and exit procedures for the BSL-4 laboratory at the NIH/NIAID Integrated Research Facility at Fort Detrick. Such procedures include checking external systems that support the BSL-4 laboratory, and inspecting and donning positive-pressure suits, entering the laboratory, moving through air pressure-resistant doors, and connecting to air-supply hoses. We will also discuss moving within and exiting the BSL-4 suit laboratories, including using the chemical shower and removing and storing positive-pressure suits.

Planetary Suit Hip Bearing Model for Predicting Design vs. Performance

Science.gov (United States)

Cowley, Matthew S.; Margerum, Sarah; Harvil, Lauren; Rajulu, Sudhakar

2011-01-01

Designing a planetary suit is very complex and often requires difficult trade-offs between performance, cost, mass, and system complexity. In order to verifying that new suit designs meet requirements, full prototypes must eventually be built and tested with human subjects. Using computer models early in the design phase of new hardware development can be advantageous, allowing virtual prototyping to take place. Having easily modifiable models of the suit hard sections may reduce the time it takes to make changes to the hardware designs and then to understand their impact on suit and human performance. A virtual design environment gives designers the ability to think outside the box and exhaust design possibilities before building and testing physical prototypes with human subjects. Reductions in prototyping and testing may eventually reduce development costs. This study is an attempt to develop computer models of the hard components of the suit with known physical characteristics, supplemented with human subject performance data. Objectives: The primary objective was to develop an articulating solid model of the Mark III hip bearings to be used for evaluating suit design performance of the hip joint. Methods: Solid models of a planetary prototype (Mark III) suit s hip bearings and brief section were reverse-engineered from the prototype. The performance of the models was then compared by evaluating the mobility performance differences between the nominal hardware configuration and hardware modifications. This was accomplished by gathering data from specific suited tasks. Subjects performed maximum flexion and abduction tasks while in a nominal suit bearing configuration and in three off-nominal configurations. Performance data for the hip were recorded using state-of-the-art motion capture technology. Results: The results demonstrate that solid models of planetary suit hard segments for use as a performance design tool is feasible. From a general trend perspective

Analysis of high-throughput sequencing and annotation strategies for phage genomes.

Directory of Open Access Journals (Sweden)

Matthew R Henn

Full Text Available BACKGROUND: Bacterial viruses (phages play a critical role in shaping microbial populations as they influence both host mortality and horizontal gene transfer. As such, they have a significant impact on local and global ecosystem function and human health. Despite their importance, little is known about the genomic diversity harbored in phages, as methods to capture complete phage genomes have been hampered by the lack of knowledge about the target genomes, and difficulties in generating sufficient quantities of genomic DNA for sequencing. Of the approximately 550 phage genomes currently available in the public domain, fewer than 5% are marine phage. METHODOLOGY/PRINCIPAL FINDINGS: To advance the study of phage biology through comparative genomic approaches we used marine cyanophage as a model system. We compared DNA preparation methodologies (DNA extraction directly from either phage lysates or CsCl purified phage particles, and sequencing strategies that utilize either Sanger sequencing of a linker amplification shotgun library (LASL or of a whole genome shotgun library (WGSL, or 454 pyrosequencing methods. We demonstrate that genomic DNA sample preparation directly from a phage lysate, combined with 454 pyrosequencing, is best suited for phage genome sequencing at scale, as this method is capable of capturing complete continuous genomes with high accuracy. In addition, we describe an automated annotation informatics pipeline that delivers high-quality annotation and yields few false positives and negatives in ORF calling. CONCLUSIONS/SIGNIFICANCE: These DNA preparation, sequencing and annotation strategies enable a high-throughput approach to the burgeoning field of phage genomics.

Satellite Ocean Heat Content Suite

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — This collection contains an operational Satellite Ocean Heat Content Suite (SOHCS) product generated by NOAA National Environmental Satellite, Data, and Information...

EVA Suit Microbial Leakage Investigation

Data.gov (United States)

National Aeronautics and Space Administration — The objective of this project is to collect microbial samples from various EVA suits to determine how much microbial contamination is typically released during...

Study of the suit inflation effect on crew safety during landing using a full-pressure IVA suit for new-generation reentry space vehicles

Science.gov (United States)

Wataru, Suzuki

Recently, manned space capsules have been recognized as beneficial and reasonable human space vehicles again. The Dragon capsule already achieved several significant successes. The Orion capsule is going to be sent to a high-apogee orbit without crews for experimental purposes in September 2014. For such human-rated space capsules, the study of acceleration impacts against the human body during splashdown is essential to ensure the safety of crews. Moreover, it is also known that wearing a full pressure rescue suit significantly increases safety of a crew, compared to wearing a partial pressure suit. This is mainly because it enables the use of a personal life support system independently in addition to that which installed in the space vehicle. However, it is unclear how the inflation of the full pressure suit due to pressurization affects the crew safety during splashdown, especially in the case of the new generation manned space vehicles. Therefore, the purpose of this work is to investigate the effect of the suit inflation on crew safety against acceleration impact during splashdown. For this objective, the displacements of the safety harness in relation with the suit, a human surrogate, and the crew seats during pressurizing the suit in order to determine if the safety and survivability of a crew can be improved by wearing a full pressure suit. For these tests, the DL/H-1 full pressure IVA suit, developed by Pablo de Leon and Gary L. Harris, will be used. These tests use image analysis techniques to determine the displacements. It is expected, as a result of these tests, that wearing a full pressure suit will help to mitigate the impacts and will increase the safety and survivability of a crew during landing since it works as a buffer to mitigate impact forces during splashdown. This work also proposes a future plan for sled test experiments using a sled facility such as the one in use by the Civil Aerospace Medical Institute (CAMI) for experimental validation

EVA Physiology and Medical Considerations Working in the Suit

Science.gov (United States)

Parazynski, Scott

2012-01-01

This "EVA Physiology and Medical Considerations Working in the Suit" presentation covers several topics related to the medical implications and physiological effects of suited operations in space from the perspective of a physician with considerable first-hand Extravehicular Activity (EVA) experience. Key themes include EVA physiology working in a pressure suit in the vacuum of space, basic EVA life support and work support, Thermal Protection System (TPS) inspections and repairs, and discussions of the physical challenges of an EVA. Parazynski covers the common injuries and significant risks during EVAs, as well as physical training required to prepare for EVAs. He also shares overall suit physiological and medical knowledge with the next generation of Extravehicular Mobility Unit (EMU) system designers.

Results from Carbon Dioxide Washout Testing Using a Suited Manikin Test Apparatus with a Space Suit Ventilation Test Loop

Science.gov (United States)

Chullen, Cinda; Conger, Bruce; McMillin, Summer; Vonau, Walt; Kanne, Bryan; Korona, Adam; Swickrath, Mike

2016-01-01

NASA is developing an advanced portable life support system (PLSS) to meet the needs of a new NASA advanced space suit. The PLSS is one of the most critical aspects of the space suit providing the necessary oxygen, ventilation, and thermal protection for an astronaut performing a spacewalk. The ventilation subsystem in the PLSS must provide sufficient carbon dioxide (CO2) removal and ensure that the CO2 is washed away from the oronasal region of the astronaut. CO2 washout is a term used to describe the mechanism by which CO2 levels are controlled within the helmet to limit the concentration of CO2 inhaled by the astronaut. Accumulation of CO2 in the helmet or throughout the ventilation loop could cause the suited astronaut to experience hypercapnia (excessive carbon dioxide in the blood). A suited manikin test apparatus (SMTA) integrated with a space suit ventilation test loop was designed, developed, and assembled at NASA in order to experimentally validate adequate CO2 removal throughout the PLSS ventilation subsystem and to quantify CO2 washout performance under various conditions. The test results from this integrated system will be used to validate analytical models and augment human testing. This paper presents the system integration of the PLSS ventilation test loop with the SMTA including the newly developed regenerative Rapid Cycle Amine component used for CO2 removal and tidal breathing capability to emulate the human. The testing and analytical results of the integrated system are presented along with future work.

Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

Energy Technology Data Exchange (ETDEWEB)

Condon, Bradford J.; Leng, Yueqiang; Wu, Dongliang; Bushley, Kathryn E.; Ohm, Robin A.; Otillar, Robert; Martin, Joel; Schackwitz, Wendy; Grimwood, Jane; MohdZainudin, NurAinlzzati; Xue, Chunsheng; Wang, Rui; Manning, Viola A.; Dhillon, Braham; Tu, Zheng Jin; Steffenson, Brian J.; Salamov, Asaf; Sun, Hui; Lowry, Steve; LaButti, Kurt; Han, James; Copeland, Alex; Lindquist, Erika; Barry, Kerrie; Schmutz, Jeremy; Baker, Scott E.; Ciuffetti, Lynda M.; Grigoriev, Igor V.; Zhong, Shaobin; Turgeon, B. Gillian

2013-01-24

The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25 higher than those between inbred lines and 50 lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.

The BRITNeY Suite: A Platfor for Experiments

DEFF Research Database (Denmark)

Westergaard, Michael

2006-01-01

This paper describes a platform, the BRITNeY Suite, for experimenting with Coloured Petri nets. The BRITNeY Suite provides access to data-structures and a simulator for Coloured Petri nets via a powerful scripting language and plug-in-mechanism, thereby making it easy to perform customized...

EDL Sensor Suite, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — Optical Air Data Systems (OADS) L.L.C. proposes a LIDAR based remote measurement sensor suite capable of satisfying a significant number of the desired sensing...

Integrated Suit Test 1 - A Study to Evaluate Effects of Suit Weight, Pressure, and Kinematics on Human Performance during Lunar Ambulation

Science.gov (United States)

Gernhardt, Michael L.; Norcross, Jason; Vos, Jessica R.

2008-01-01

In an effort to design the next generation Lunar suit, NASA has initiated a series of tests aimed at understanding the human physiological and biomechanical affects of space suits under a variety of conditions. The first of these tests was the EVA Walkback Test (ICES 2007-01-3133). NASA-JSC assembled a multi-disciplinary team to conduct the second test of the series, titled Integrated Suit Test 1 (IST-1), from March 6 through July 24, 2007. Similar to the Walkback Test, this study was performed with the Mark III (MKIII) EVA Technology Demonstrator suit, a treadmill, and the Partial Gravity Simulator in the Space Vehicle Mock-Up Facility at Johnson Space Center. The data collected for IST-1 included metabolic rates, ground reaction forces, biomechanics, and subjective workload and controllability feedback on both suited and unsuited (shirt-sleeve) astronaut subjects. For IST-1 the center of gravity was controlled to a nearly perfect position while the weight, pressure and biomechanics (waist locked vs. unlocked) were varied individually to evaluate the effects of each on the ability to perform level (0 degree incline) ambulation in simulated Lunar gravity. The detailed test methodology and preliminary key findings of IST-1 are summarized in this report.

Variable Vector Countermeasure Suit for Space Habitation and Exploration

Data.gov (United States)

National Aeronautics and Space Administration — The "Variable Vector Countermeasure Suit (V2Suit) for Space Habitation and Exploration" is a visionary system concept that will revolutionize space missions by...

NetSuite OneWorld Implementation 2011 R2

CERN Document Server

Foydel, Thomas

2011-01-01

This book is a focused, step-by step tutorial that shows you how to successfully implement NetSuite OneWorld into your organization. It is written in an easy-to-read style, with a strong emphasis on real-world, practical examples with step-by-step explanations. The book focuses on NetSuite OneWorld 2011 R1. If you are an application administrator, business analyst, project team member or business process owner who wants to implement NetSuite OneWorld into your organization, then this book is for you. This book might also be useful if you are a business manager considering a new system for your

Prokofieff: Krieg und Frieden (Sinfonische Suite), Die Verlobung im Kloster (Sommernacht-Suite), Russische Overtüre. Philharmonia Orchestra, Neeme Järvi / G. W.

Index Scriptorium Estoniae

G. W.

1993-01-01

Uuest heliplaadist "Prokofieff: Krieg und Frieden (Sinfonische Suite), Die Verlobung im Kloster (Sommernacht-Suite), Russische Overtüre. Philharmonia Orchestra, Neeme Järvi. (AD: 1991). Chandos/Koch CD 9096

Complete mitochondrial genome sequences from five Eimeria species (Apicomplexa; Coccidia; Eimeriidae) infecting domestic turkeys.

Science.gov (United States)

Ogedengbe, Mosun E; El-Sherry, Shiem; Whale, Julia; Barta, John R

2014-07-17

Clinical and subclinical coccidiosis is cosmopolitan and inflicts significant losses to the poultry industry globally. Seven named Eimeria species are responsible for coccidiosis in turkeys: Eimeria dispersa; Eimeria meleagrimitis; Eimeria gallopavonis; Eimeria meleagridis; Eimeria adenoeides; Eimeria innocua; and, Eimeria subrotunda. Although attempts have been made to characterize these parasites molecularly at the nuclear 18S rDNA and ITS loci, the maternally-derived and mitotically replicating mitochondrial genome may be more suited for species level molecular work; however, only limited sequence data are available for Eimeria spp. infecting turkeys. The purpose of this study was to sequence and annotate the complete mitochondrial genomes from 5 Eimeria species that commonly infect the domestic turkey (Meleagris gallopavo). Six single-oocyst derived cultures of five Eimeria species infecting turkeys were PCR-amplified and sequenced completely prior to detailed annotation. Resulting sequences were aligned and used in phylogenetic analyses (BI, ML, and MP) that included complete mitochondrial genomes from 16 Eimeria species or concatenated CDS sequences from each genome. Complete mitochondrial genome sequences were obtained for Eimeria adenoeides Guelph, 6211 bp; Eimeria dispersa Briston, 6238 bp; Eimeria meleagridis USAR97-01, 6212 bp; Eimeria meleagrimitis USMN08-01, 6165 bp; Eimeria gallopavonis Weybridge, 6215 bp; and Eimeria gallopavonis USKS06-01, 6215 bp). The order, orientation and CDS lengths of the three protein coding genes (COI, COIII and CytB) as well as rDNA fragments encoding ribosomal large and small subunit rRNA were conserved among all sequences. Pairwise sequence identities between species ranged from 88.1% to 98.2%; sequence variability was concentrated within CDS or between rDNA fragments (where indels were common). No phylogenetic reconstruction supported monophyly of Eimeria species infecting turkeys; Eimeria dispersa may have arisen

Metabolic and Subjective Results Review of the Integrated Suit Test Series

Science.gov (United States)

Norcross, J.R.; Stroud, L.C.; Klein, J.; Desantis, L.; Gernhardt, M.L.

2009-01-01

Crewmembers will perform a variety of exploration and construction activities on the lunar surface. These activities will be performed while inside an extravehicular activity (EVA) spacesuit. In most cases, human performance is compromised while inside an EVA suit as compared to a crewmember s unsuited performance baseline. Subjects completed different EVA type tasks, ranging from ambulation to geology and construction activities, in different lunar analog environments including overhead suspension, underwater and 1-g lunar-like terrain, in both suited and unsuited conditions. In the suited condition, the Mark III (MKIII) EVA technology demonstrator suit was used and suit pressure and suit weight were parameters tested. In the unsuited conditions, weight, mass, center of gravity (CG), terrain type and navigation were the parameters. To the extent possible, one parameter was varied while all others were held constant. Tests were not fully crossed, but rather one parameter was varied while all others were left in the most nominal setting. Oxygen consumption (VO2), modified Cooper-Harper (CH) ratings of operator compensation and ratings of perceived exertion (RPE) were measured for each trial. For each variable, a lower value correlates to more efficient task performance. Due to a low sample size, statistical significance was not attainable. Initial findings indicate that suit weight, CG and the operational environment can have a large impact on human performance during EVA. Systematic, prospective testing series such as those performed to date will enable a better understanding of the crucial interactions of the human and the EVA suit system and their environment. However, work remains to be done to confirm these findings. These data have been collected using only unsuited subjects and one EVA suit prototype that is known to fit poorly on a large demographic of the astronaut population. Key findings need to be retested using an EVA suit prototype better suited to a

Instrumented Suit Hard Upper Torso (HUT) for Ergonomic Assessment

Data.gov (United States)

National Aeronautics and Space Administration — It is well known that the EVA suit (EMU) has the potential to cause crew injury and decreased performance. Engineering data on the suit interaction of the human...

The Annotation, Mapping, Expression and Network (AMEN suite of tools for molecular systems biology

Directory of Open Access Journals (Sweden)

Primig Michael

2008-02-01

Full Text Available Abstract Background High-throughput genome biological experiments yield large and multifaceted datasets that require flexible and user-friendly analysis tools to facilitate their interpretation by life scientists. Many solutions currently exist, but they are often limited to specific steps in the complex process of data management and analysis and some require extensive informatics skills to be installed and run efficiently. Results We developed the Annotation, Mapping, Expression and Network (AMEN software as a stand-alone, unified suite of tools that enables biological and medical researchers with basic bioinformatics training to manage and explore genome annotation, chromosomal mapping, protein-protein interaction, expression profiling and proteomics data. The current version provides modules for (i uploading and pre-processing data from microarray expression profiling experiments, (ii detecting groups of significantly co-expressed genes, and (iii searching for enrichment of functional annotations within those groups. Moreover, the user interface is designed to simultaneously visualize several types of data such as protein-protein interaction networks in conjunction with expression profiles and cellular co-localization patterns. We have successfully applied the program to interpret expression profiling data from budding yeast, rodents and human. Conclusion AMEN is an innovative solution for molecular systems biological data analysis freely available under the GNU license. The program is available via a website at the Sourceforge portal which includes a user guide with concrete examples, links to external databases and helpful comments to implement additional functionalities. We emphasize that AMEN will continue to be developed and maintained by our laboratory because it has proven to be extremely useful for our genome biological research program.

Using Genomics for Natural Product Structure Elucidation.

Science.gov (United States)

Tietz, Jonathan I; Mitchell, Douglas A

2016-01-01

Natural products (NPs) are the most historically bountiful source of chemical matter for drug development-especially for anti-infectives. With insights gleaned from genome mining, interest in natural product discovery has been reinvigorated. An essential stage in NP discovery is structural elucidation, which sheds light not only on the chemical composition of a molecule but also its novelty, properties, and derivatization potential. The history of structure elucidation is replete with techniquebased revolutions: combustion analysis, crystallography, UV, IR, MS, and NMR have each provided game-changing advances; the latest such advance is genomics. All natural products have a genetic basis, and the ability to obtain and interpret genomic information for structure elucidation is increasingly available at low cost to non-specialists. In this review, we describe the value of genomics as a structural elucidation technique, especially from the perspective of the natural product chemist approaching an unknown metabolite. Herein we first introduce the databases and programs of interest to the natural products chemist, with an emphasis on those currently most suited for general usability. We describe strategies for linking observed natural product-linked phenotypes to their corresponding gene clusters. We then discuss techniques for extracting structural information from genes, illustrated with numerous case examples. We also provide an analysis of the biases and limitations of the field with recommendations for future development. Our overview is not only aimed at biologically-oriented researchers already at ease with bioinformatic techniques, but also, in particular, at natural product, organic, and/or medicinal chemists not previously familiar with genomic techniques.

Ultraviolet Testing of Space Suit Materials for Mars

Science.gov (United States)

Larson, Kristine; Fries, Marc

2017-01-01

Human missions to Mars may require radical changes in the approach to extra-vehicular (EVA) suit design. A major challenge is the balance of building a suit robust enough to complete multiple EVAs under intense ultraviolet (UV) light exposure without losing mechanical strength or compromising the suit's mobility. To study how the materials degrade on Mars in-situ, the Jet Propulsion Laboratory (JPL) invited the Advanced Space Suit team at NASA's Johnson Space Center (JSC) to place space suit materials on the Scanning Habitable Environments with Raman & Luminescence for Organics and Chemicals (SHERLOC) instrument's calibration target of the Mars 2020 rover. In order to select materials for the rover and understand the effects from Mars equivalent UV exposure, JSC conducted ground testing on both current and new space suit materials when exposed to 2500 hours of Mars mission equivalent UV. To complete this testing, JSC partnered with NASA's Marshall Space Flight Center to utilize their UV vacuum chambers. Materials tested were Orthofabric, polycarbonate, Teflon, Dacron, Vectran, spectra, bladder, nGimat coated Teflon, and nGimat coated Orthofabric. All samples were measured for mass, tensile strength, and chemical composition before and after radiation. Mass loss was insignificant (less than 0.5%) among the materials. Most materials loss tensile strength after radiation and became more brittle with a loss of elongation. Changes in chemical composition were seen in all radiated materials through Spectral Analysis. Results from this testing helped select the materials that will fly on the Mars 2020 rover. In addition, JSC can use this data to create a correlation to the chemical changes after radiation-which is what the rover will send back while on Mars-to the mechanical changes, such as tensile strength.

Genomic resources in mungbean for future breeding programs

Directory of Open Access Journals (Sweden)

Sue K Kim

2015-08-01

Full Text Available Among the legume family, mungbean (Vigna radiata has become one of the important crops in Asia, showing a steady increase in global production. It provides a good source of protein and contains most notably folate and iron. Beyond the nutritional value of mungbean, certain features make it a well-suited model organism among legume plants because of its small genome size, short life-cycle, self-pollinating, and close genetic relationship to other legumes. In the past, there have been several efforts to develop molecular markers and linkage maps associated with agronomic traits for the genetic improvement of mungbean and, ultimately, breeding for cultivar development to increase the average yields of mungbean. The recent release of a reference genome of the cultivated mungbean (V. radiata var. radiata VC1973A and an additional de novo sequencing of a wild relative mungbean (V. radiata var. sublobata has provided a framework for mungbean genetic and genome research, that can further be used for genome-wide association and functional studies to identify genes related to specific agronomic traits. Moreover, the diverse gene pool of wild mungbean comprises valuable genetic resources of beneficial genes that may be helpful in widening the genetic diversity of cultivated mungbean. This review paper covers the research progress on molecular and genomics approaches and the current status of breeding programs that have developed to move toward the ultimate goal of mungbean improvement.

M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species

Directory of Open Access Journals (Sweden)

Messeguer Xavier

2006-10-01

Full Text Available Abstract Background Due to recent advances in whole genome shotgun sequencing and assembly technologies, the financial cost of decoding an organism's DNA has been drastically reduced, resulting in a recent explosion of genomic sequencing projects. This increase in related genomic data will allow for in depth studies of evolution in closely related species through multiple whole genome comparisons. Results To facilitate such comparisons, we present an interactive multiple genome comparison and alignment tool, M-GCAT, that can efficiently construct multiple genome comparison frameworks in closely related species. M-GCAT is able to compare and identify highly conserved regions in up to 20 closely related bacterial species in minutes on a standard computer, and as many as 90 (containing 75 cloned genomes from a set of 15 published enterobacterial genomes in an hour. M-GCAT also incorporates a novel comparative genomics data visualization interface allowing the user to globally and locally examine and inspect the conserved regions and gene annotations. Conclusion M-GCAT is an interactive comparative genomics tool well suited for quickly generating multiple genome comparisons frameworks and alignments among closely related species. M-GCAT is freely available for download for academic and non-commercial use at: http://alggen.lsi.upc.es/recerca/align/mgcat/intro-mgcat.html.

Interaction of Space Suits with Windblown Soil: Preliminary Mars Wind Tunnel Results

Science.gov (United States)

Marshall, J.; Bratton, C.; Kosmo, J.; Trevino, R.

1999-09-01

Experiments in the Mars Wind Tunnel at NASA Ames Research Center show that under Mars conditions, spacesuit materials are highly susceptible to dust contamination when exposed to windblown soil. This effect was suspected from knowledge of the interaction of electrostatically adhesive dust with solid surfaces in general. However, it is important to evaluate the respective roles of materials, meteorological and radiation effects, and the character of the soil. The tunnel permits evaluation of dust contamination and sand abrasion of space suits by simulating both pressure and wind conditions on Mars. The long-term function of space suits on Mars will be primarily threatened by dust contamination. Lunar EVA activities caused heavy contamination of space suits, but the problem was never seriously manifest because of the brief utilization of the suits, and the suits were never reused. Electrostatically adhering dust grains have various detrimental effects: (1) penetration and subsequent wear of suit fabrics, (2) viewing obscuration through visors and scratching/pitting of visor surfaces, (3) penetration, wear, and subsequent seizing-up of mechanical suit joints, (4) changes in albedo and therefore of radiation properties of external heat-exchanger systems, (5) changes in electrical conductivity of suit surfaces which may affect tribocharging of suits and create spurious discharge effects detrimental to suit electronics/radio systems. Additional information is contained in the original.

Inertial motion capture system for biomechanical analysis in pressure suits

Science.gov (United States)

Di Capua, Massimiliano

A non-invasive system has been developed at the University of Maryland Space System Laboratory with the goal of providing a new capability for quantifying the motion of the human inside a space suit. Based on an array of six microprocessors and eighteen microelectromechanical (MEMS) inertial measurement units (IMUs), the Body Pose Measurement System (BPMS) allows the monitoring of the kinematics of the suit occupant in an unobtrusive, self-contained, lightweight and compact fashion, without requiring any external equipment such as those necessary with modern optical motion capture systems. BPMS measures and stores the accelerations, angular rates and magnetic fields acting upon each IMU, which are mounted on the head, torso, and each segment of each limb. In order to convert the raw data into a more useful form, such as a set of body segment angles quantifying pose and motion, a series of geometrical models and a non-linear complimentary filter were implemented. The first portion of this works focuses on assessing system performance, which was measured by comparing the BPMS filtered data against rigid body angles measured through an external VICON optical motion capture system. This type of system is the industry standard, and is used here for independent measurement of body pose angles. By comparing the two sets of data, performance metrics such as BPMS system operational conditions, accuracy, and drift were evaluated and correlated against VICON data. After the system and models were verified and their capabilities and limitations assessed, a series of pressure suit evaluations were conducted. Three different pressure suits were used to identify the relationship between usable range of motion and internal suit pressure. In addition to addressing range of motion, a series of exploration tasks were also performed, recorded, and analysed in order to identify different motion patterns and trajectories as suit pressure is increased and overall suit mobility is reduced

Nuclease Target Site Selection for Maximizing On-target Activity and Minimizing Off-target Effects in Genome Editing

Science.gov (United States)

Lee, Ciaran M; Cradick, Thomas J; Fine, Eli J; Bao, Gang

2016-01-01

The rapid advancement in targeted genome editing using engineered nucleases such as ZFNs, TALENs, and CRISPR/Cas9 systems has resulted in a suite of powerful methods that allows researchers to target any genomic locus of interest. A complementary set of design tools has been developed to aid researchers with nuclease design, target site selection, and experimental validation. Here, we review the various tools available for target selection in designing engineered nucleases, and for quantifying nuclease activity and specificity, including web-based search tools and experimental methods. We also elucidate challenges in target selection, especially in predicting off-target effects, and discuss future directions in precision genome editing and its applications. PMID:26750397

Microarray profiling shows distinct differences between primary tumors and commonly used preclinical models in hepatocellular carcinoma

International Nuclear Information System (INIS)

Wang, Weining; Iyer, N. Gopalakrishna; Tay, Hsien Ts’ung; Wu, Yonghui; Lim, Tony K. H.; Zheng, Lin; Song, In Chin; Kwoh, Chee Keong; Huynh, Hung; Tan, Patrick O. B.; Chow, Pierce K. H.

2015-01-01

Despite advances in therapeutics, outcomes for hepatocellular carcinoma (HCC) remain poor and there is an urgent need for efficacious systemic therapy. Unfortunately, drugs that are successful in preclinical studies often fail in the clinical setting, and we hypothesize that this is due to functional differences between primary tumors and commonly used preclinical models. In this study, we attempt to answer this question by comparing tumor morphology and gene expression profiles between primary tumors, xenografts and HCC cell lines. Hep G2 cell lines and tumor cells from patient tumor explants were subcutaneously (ectopically) injected into the flank and orthotopically into liver parenchyma of Mus Musculus SCID mice. The mice were euthanized after two weeks. RNA was extracted from the tumors, and gene expression profiling was performed using the Gene Chip Human Genome U133 Plus 2.0. Principal component analyses (PCA) and construction of dendrograms were conducted using Partek genomics suite. PCA showed that the commonly used HepG2 cell line model and its xenograft counterparts were vastly different from all fresh primary tumors. Expression profiles of primary tumors were also significantly divergent from their counterpart patient-derived xenograft (PDX) models, regardless of the site of implantation. Xenografts from the same primary tumors were more likely to cluster together regardless of site of implantation, although heat maps showed distinct differences in gene expression profiles between orthotopic and ectopic models. The data presented here challenges the utility of routinely used preclinical models. Models using HepG2 were vastly different from primary tumors and PDXs, suggesting that this is not clinically representative. Surprisingly, site of implantation (orthotopic versus ectopic) resulted in limited impact on gene expression profiles, and in both scenarios xenografts differed significantly from the original primary tumors, challenging the long

A Secure Communication Suite for Underwater Acoustic Sensor Networks

Directory of Open Access Journals (Sweden)

Angelica Lo Duca

2012-11-01

Full Text Available In this paper we describe a security suite for Underwater Acoustic Sensor Networks comprising both fixed and mobile nodes. The security suite is composed of a secure routing protocol and a set of cryptographic primitives aimed at protecting the confidentiality and the integrity of underwater communication while taking into account the unique characteristics and constraints of the acoustic channel. By means of experiments and simulations based on real data, we show that the suite is suitable for an underwater networking environment as it introduces limited, and sometimes negligible, communication and power consumption overhead.

HPC Benchmark Suite NMx, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — Intelligent Automation Inc., (IAI) and University of Central Florida (UCF) propose to develop a comprehensive numerical test suite for benchmarking current and...

Inherent work suit buoyancy distribution: effects on lifejacket self-righting performance.

Science.gov (United States)

Barwood, Martin J; Long, Geoffrey M; Lunt, Heather; Tipton, Michael J

2014-09-01

Accidental immersion in cold water is an occupational risk. Work suits and life jackets (LJ) should work effectively in combination to keep the airway clear of the water (freeboard) and enable self-righting. We hypothesized that inherent buoyancy, in the suit or LJ, would be beneficial for enabling freeboard, but its distribution may influence LJ self-righting. Six participants consented to complete nine immersions. Suits and LJ tested were: flotation suit (FLOAT; 85 N inherent buoyancy); oilskins 1 (OS-1) and 2 (OS-2), both with no inherent buoyancy; LJs (inherent buoyancy/buoyancy after inflation/total buoyancy), LJ-1 50/150/200 N, LJ-2 0/290/290 N, LJ-3 80/190/270 N. Once dressed, the subject entered an immersion pool where uninflated freeboard, self-righting performance, and inflated freeboard were measured. Data were compared using Friedman's test to the 0.05 alpha level. All suits and LJs enabled uninflated and inflated freeboard, but differences were seen between the suits and LJs. Self-righting was achieved on 43 of 54 occasions, irrespective of suit or LJ. On all occasions that self-righting was not achieved, this occurred in an LJ that included inherent buoyancy (11/54 occasions). Of these 11 failures, 8 occurred (73% of occasions) when the FLOAT suit was being worn. LJs that included inherent buoyancy, that are certified as effective on their own, worked less effectively from the perspective of self-righting in combination with a work suit that also included inherent buoyancy. Equipment that is approved for use in the workplace should be tested in combination to ensure adequate performance in an emergency scenario.

Oracle E-Business Suite Financials R12 A Functionality Guide

CERN Document Server

Iyer, Mohan

2012-01-01

This is a step-by-step functional guide to get you started easily with Oracle EBS Financials. If you are an Oracle E-Business Suite Financial consultant or an administrator looking to get a quick review on the capabilities of Oracle E-Business Suite and improve the use of the systems functionality, then this is the best guide for you. This book assumes that you have a fundamental knowledge of EBS Suite.

arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

Directory of Open Access Journals (Sweden)

Moreau Yves

2005-05-01

Full Text Available Abstract Background The availability of the human genome sequence as well as the large number of physically accessible oligonucleotides, cDNA, and BAC clones across the entire genome has triggered and accelerated the use of several platforms for analysis of DNA copy number changes, amongst others microarray comparative genomic hybridization (arrayCGH. One of the challenges inherent to this new technology is the management and analysis of large numbers of data points generated in each individual experiment. Results We have developed arrayCGHbase, a comprehensive analysis platform for arrayCGH experiments consisting of a MIAME (Minimal Information About a Microarray Experiment supportive database using MySQL underlying a data mining web tool, to store, analyze, interpret, compare, and visualize arrayCGH results in a uniform and user-friendly format. Following its flexible design, arrayCGHbase is compatible with all existing and forthcoming arrayCGH platforms. Data can be exported in a multitude of formats, including BED files to map copy number information on the genome using the Ensembl or UCSC genome browser. Conclusion ArrayCGHbase is a web based and platform independent arrayCGH data analysis tool, that allows users to access the analysis suite through the internet or a local intranet after installation on a private server. ArrayCGHbase is available at http://medgen.ugent.be/arrayCGHbase/.

eHive: An Artificial Intelligence workflow system for genomic analysis

Science.gov (United States)

2010-01-01

Background The Ensembl project produces updates to its comparative genomics resources with each of its several releases per year. During each release cycle approximately two weeks are allocated to generate all the genomic alignments and the protein homology predictions. The number of calculations required for this task grows approximately quadratically with the number of species. We currently support 50 species in Ensembl and we expect the number to continue to grow in the future. Results We present eHive, a new fault tolerant distributed processing system initially designed to support comparative genomic analysis, based on blackboard systems, network distributed autonomous agents, dataflow graphs and block-branch diagrams. In the eHive system a MySQL database serves as the central blackboard and the autonomous agent, a Perl script, queries the system and runs jobs as required. The system allows us to define dataflow and branching rules to suit all our production pipelines. We describe the implementation of three pipelines: (1) pairwise whole genome alignments, (2) multiple whole genome alignments and (3) gene trees with protein homology inference. Finally, we show the efficiency of the system in real case scenarios. Conclusions eHive allows us to produce computationally demanding results in a reliable and efficient way with minimal supervision and high throughput. Further documentation is available at: http://www.ensembl.org/info/docs/eHive/. PMID:20459813

eHive: An Artificial Intelligence workflow system for genomic analysis

Directory of Open Access Journals (Sweden)

Gordon Leo

2010-05-01

Full Text Available Abstract Background The Ensembl project produces updates to its comparative genomics resources with each of its several releases per year. During each release cycle approximately two weeks are allocated to generate all the genomic alignments and the protein homology predictions. The number of calculations required for this task grows approximately quadratically with the number of species. We currently support 50 species in Ensembl and we expect the number to continue to grow in the future. Results We present eHive, a new fault tolerant distributed processing system initially designed to support comparative genomic analysis, based on blackboard systems, network distributed autonomous agents, dataflow graphs and block-branch diagrams. In the eHive system a MySQL database serves as the central blackboard and the autonomous agent, a Perl script, queries the system and runs jobs as required. The system allows us to define dataflow and branching rules to suit all our production pipelines. We describe the implementation of three pipelines: (1 pairwise whole genome alignments, (2 multiple whole genome alignments and (3 gene trees with protein homology inference. Finally, we show the efficiency of the system in real case scenarios. Conclusions eHive allows us to produce computationally demanding results in a reliable and efficient way with minimal supervision and high throughput. Further documentation is available at: http://www.ensembl.org/info/docs/eHive/.

eHive: an artificial intelligence workflow system for genomic analysis.

Science.gov (United States)

Severin, Jessica; Beal, Kathryn; Vilella, Albert J; Fitzgerald, Stephen; Schuster, Michael; Gordon, Leo; Ureta-Vidal, Abel; Flicek, Paul; Herrero, Javier

2010-05-11

The Ensembl project produces updates to its comparative genomics resources with each of its several releases per year. During each release cycle approximately two weeks are allocated to generate all the genomic alignments and the protein homology predictions. The number of calculations required for this task grows approximately quadratically with the number of species. We currently support 50 species in Ensembl and we expect the number to continue to grow in the future. We present eHive, a new fault tolerant distributed processing system initially designed to support comparative genomic analysis, based on blackboard systems, network distributed autonomous agents, dataflow graphs and block-branch diagrams. In the eHive system a MySQL database serves as the central blackboard and the autonomous agent, a Perl script, queries the system and runs jobs as required. The system allows us to define dataflow and branching rules to suit all our production pipelines. We describe the implementation of three pipelines: (1) pairwise whole genome alignments, (2) multiple whole genome alignments and (3) gene trees with protein homology inference. Finally, we show the efficiency of the system in real case scenarios. eHive allows us to produce computationally demanding results in a reliable and efficient way with minimal supervision and high throughput. Further documentation is available at: http://www.ensembl.org/info/docs/eHive/.

Exploration Space Suit Architecture: Destination Environmental-Based Technology Development

Science.gov (United States)

Hill, Terry R.

2010-01-01

This paper picks up where EVA Space Suit Architecture: Low Earth Orbit Vs. Moon Vs. Mars (Hill, Johnson, IEEEAC paper #1209) left off in the development of a space suit architecture that is modular in design and interfaces and could be reconfigured to meet the mission or during any given mission depending on the tasks or destination. This paper will walk though the continued development of a space suit system architecture, and how it should evolve to meeting the future exploration EVA needs of the United States space program. In looking forward to future US space exploration and determining how the work performed to date in the CxP and how this would map to a future space suit architecture with maximum re-use of technology and functionality, a series of thought exercises and analysis have provided a strong indication that the CxP space suit architecture is well postured to provide a viable solution for future exploration missions. Through the destination environmental analysis that is presented in this paper, the modular architecture approach provides the lowest mass, lowest mission cost for the protection of the crew given any human mission outside of low Earth orbit. Some of the studies presented here provide a look and validation of the non-environmental design drivers that will become every-increasingly important the further away from Earth humans venture and the longer they are away. Additionally, the analysis demonstrates a logical clustering of design environments that allows a very focused approach to technology prioritization, development and design that will maximize the return on investment independent of any particular program and provide architecture and design solutions for space suit systems in time or ahead of being required for any particular manned flight program in the future. The new approach to space suit design and interface definition the discussion will show how the architecture is very adaptable to programmatic and funding changes with

HPC Benchmark Suite NMx, Phase II

Data.gov (United States)

National Aeronautics and Space Administration — In the phase II effort, Intelligent Automation Inc., (IAI) and University of Central Florida (UCF) propose to develop a comprehensive numerical test suite for...

Cosmonaut Sergei Krikalev receives assistance from suit technician

Science.gov (United States)

1994-01-01

Sergei Krikalev, alternative mission specialist for STS-63, gets help from Dawn Mays, a Boeing suit technician. The cosmonaut was about to participate in a training session at JSC's Weightless Environment Training Facility (WETF). Wearing the training version of the extravehicular mobility unit (EMU) space suit, weighted to allow neutral buoyancy in the 25 feet deep WETF pool, Krikalev minutes later was underwater simulating a contingency spacewalk, or extravehicular activity (EVA).

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

Science.gov (United States)

Agren, Rasmus; Liu, Liming; Shoaie, Saeed; Vongsangnak, Wanwipa; Nookaew, Intawat; Nielsen, Jens

2013-01-01

We present the RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox: a software suite that allows for semi-automated reconstruction of genome-scale models. It makes use of published models and/or the KEGG database, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology. The RAVEN Toolbox workflow was applied in order to reconstruct a genome-scale metabolic model for the important microbial cell factory Penicillium chrysogenum Wisconsin54-1255. The model was validated in a bibliomic study of in total 440 references, and it comprises 1471 unique biochemical reactions and 1006 ORFs. It was then used to study the roles of ATP and NADPH in the biosynthesis of penicillin, and to identify potential metabolic engineering targets for maximization of penicillin production. PMID:23555215

The BTeV Software Tutorial Suite

International Nuclear Information System (INIS)

Kutschke, Robert K.

2004-01-01

The BTeV Collaboration is starting to develop its C++ based offline software suite, an integral part of which is a series of tutorials. These tutorials are targeted at a diverse audience, including new graduate students, experienced physicists with little or no C++ experience, those with just enough C++ to be dangerous, and experts who need only an overview of the available tools. The tutorials must both teach C++ in general and the BTeV specific tools in particular. Finally, they must teach physicists how to find and use the detailed documentation. This report will review the status of the BTeV experiment, give an overview of the plans for and the state of the software and will then describe the plans for the tutorial suite

The antigravity suit in neurosurgery. Cardiovascular responses in seated neurosurgical patients.

Science.gov (United States)

Brodrick, P M; Ingram, G S

1988-09-01

The haemodynamic responses associated with inflation of the antigravity suit (G suit, aviation type) to 8.0 kPa were studied in a series of 40 patients who underwent neurosurgical operations in the sitting position. The study showed statistically significant increases in systolic arterial pressure (p less than 0.005) and mean central venous pressure (p less than 0.001) with inflation of the suit. The systolic arterial and mean central venous pressures remained significantly elevated immediately before deflation of the suit at the end of the operation (p less than 0.001 and p less than 0.005 respectively). The addition of 0.8-1.0 kPa positive end expiratory pressure during suit inflation was also investigated. A further increase in central venous pressure occurred but this did not achieve statistical significance.

Characterization of the Radiation Shielding Properties of US and Russian EVA Suits

International Nuclear Information System (INIS)

Benton, E.R.; Benton, E.V.; Frank, A.L.

2001-01-01

Reported herein are results from the Eril Research, Inc. (ERI) participation in the NASA Johnson Space Center sponsored study characterizing the radiation shielding properties of the two types of space suit that astronauts are wearing during the EVA on-orbit assembly of the International Space Station (ISS). Measurements using passive detectors were carried out to assess the shielding properties of the USEMU Suit and the Russian Orlan-M suit during irradiations of the suits and a tissue equivalent phantom to monoenergetic proton and electron beams at the Loma Linda University Medical Center (LLUMC). During irradiations of 6 MeV electrons and 60 MeV protons, absorbed dose as a function of depth was measured using TLDs exposed behind swatches of the two suit materials and inside the two EVA helmets. Considerable reduction in electron dose was measured behind all suit materials in exposures to 6MeV electrons. Slowing of the proton beam in the suit materials led to an increase in dose measured in exposures to 60 MeV protons. During 232 MeV proton irradiations, measurements were made with TLDs and CR-39 PNTDs at five organ locations inside a tissue equivalent phantom, exposed both with and without the two EVA suits. The EVA helmets produce a 13 to 27 percent reduction in total dose and a 0 to 25 percent reduction in dose equivalent when compared to measurements made in the phantom head alone. Differences in dose and dose equivalent between the suit and non-suit irradiations for the lower portions of the two EVA suits tended to be smaller. Proton-induced target fragmentation was found to be a significant source of increased dose equivalent, especially within the two EVA helmets, and average quality factor inside the EMU and Orlan-M helmets was 2 to 14 percent greater than that measured in the bare phantom head

Clinical Implications of Human Population Differences in Genome-wide Rates of Functional Genotypes

Directory of Open Access Journals (Sweden)

Ali eTorkamani

2012-11-01

Full Text Available There have been a number of recent successes in the use of whole genome sequencing and sophisticated bioinformatics techniques to identify pathogenic DNA sequence variants responsible for individual idiopathic congenital conditions. However, the success of this identification process is heavily influenced by the ancestry or genetic background of a patient with an idiopathic condition. This is so because potential pathogenic variants in a patient’s genome must be contrasted with variants in a reference set of genomes made up of other individuals’ genomes of the same ancestry as the patient. We explored the effect of ignoring the ancestries of both an individual patient and the individuals used to construct reference genomes. We pursued this exploration in two major steps. We first considered variation in the per-genome number and rates likely functional derived (i.e., non-ancestral, based on the chimp genome single nucleotide variants and small indels in 52 individual whole human genomes sampled from 10 different global populations. We took advantage of a suite of computational and bioinformatics techniques to predict the functional effect of over 24 million genomic variants, both coding and non-coding, across these genomes. We found that the typical human genome harbors ~5.5-6.1 million total derived variants, of which ~12,000 are likely to have a functional effect (~5000 coding and ~7000 non-coding. We also found that the rates of functional genotypes per the total number of genotypes in individual whole genomes differ dramatically between human populations. We then created tables showing how the use of comparator or reference genome panels comprised of genomes from individuals that do not have the same ancestral background as a patient can negatively impact pathogenic variant identification. Our results have important implications for clinical sequencing initiatives.

Extending the GI Brokering Suite to Support New Interoperability Specifications

Science.gov (United States)

Boldrini, E.; Papeschi, F.; Santoro, M.; Nativi, S.

2014-12-01

The GI brokering suite provides the discovery, access, and semantic Brokers (i.e. GI-cat, GI-axe, GI-sem) that empower a Brokering framework for multi-disciplinary and multi-organizational interoperability. GI suite has been successfully deployed in the framework of several programmes and initiatives, such as European Union funded projects, NSF BCube, and the intergovernmental coordinated effort Global Earth Observation System of Systems (GEOSS). Each GI suite Broker facilitates interoperability for a particular functionality (i.e. discovery, access, semantic extension) among a set of brokered resources published by autonomous providers (e.g. data repositories, web services, semantic assets) and a set of heterogeneous consumers (e.g. client applications, portals, apps). A wide set of data models, encoding formats, and service protocols are already supported by the GI suite, such as the ones defined by international standardizing organizations like OGC and ISO (e.g. WxS, CSW, SWE, GML, netCDF) and by Community specifications (e.g. THREDDS, OpenSearch, OPeNDAP, ESRI APIs). Using GI suite, resources published by a particular Community or organization through their specific technology (e.g. OPeNDAP/netCDF) can be transparently discovered, accessed, and used by different Communities utilizing their preferred tools (e.g. a GIS visualizing WMS layers). Since Information Technology is a moving target, new standards and technologies continuously emerge and are adopted in the Earth Science context too. Therefore, GI Brokering suite was conceived to be flexible and accommodate new interoperability protocols and data models. For example, GI suite has recently added support to well-used specifications, introduced to implement Linked data, Semantic Web and precise community needs. Amongst the others, they included: DCAT: a RDF vocabulary designed to facilitate interoperability between Web data catalogs. CKAN: a data management system for data distribution, particularly used by

ANALYSIS OF DESIGN ELEMENTS IN SKI SUITS

Directory of Open Access Journals (Sweden)

Birsen Çileroğlu

2014-06-01

Full Text Available Popularity of Ski Sport in 19th century necessitated a new perspective on protective skiing clothing ag ainst the mountain climates and excessive cold. Winter clothing were the basis of ski attire during this period. By the beginning of 20th century lining cloth were used to minimize the wind effect. The difference between the men and women’s ski attire of the time consisted of a knee - length skirts worn over the golf trousers. Subsequent to the First World War, skiing suit models were influenced by the period uniforms and the producers reflected the fashion trends to the ski clothing. In conformance with th e prevailing trends, ski trousers were designed and produced for the women thus leading to reduction in gender differences. Increases in the ski tourism and holding of the first winter olympics in 1924 resulted in variations in ski attires, development of design characteristics, growth in user numbers, and enlargement of production capacities. Designers emphasized in their collections combined presence of elegance and practicality in the skiing attire. In 1930s, the ski suits influenced by pilots’ uniforms included characteristics permitting freedom of motion, and the design elements exhibited changes in terms of style, material and aerodynamics. In time, the ski attires showed varying design features distinguishing professionals from the amateurs. While protective functionality was primary consideration for the amateurs, for professionals the aerodynamic design was also a leading factor. Eventually, the increased differences in design characteristics were exhibited in ski suit collections, World reknown brands were formed, production and sales volumes showed significant rise. During 20th century the ski suits influenced by fashion trends to acquire unique styles reached a position of dominance to impact current fashion trends, and apart from sports attir es they became a style determinant in the clothing of cold climates. Ski suits

IRscope: An online program to visualize the junction sites of chloroplast genomes.

Science.gov (United States)

Amiryousefi, Ali; Hyvönen, Jaakko; Poczai, Peter

2018-04-05

Genome plotting is performed using a wide range of visualizations tools each with emphasis on a different informative dimension of the genome. These tools can provide a deeper insight into the genomic structure of the organism. Here we announce a new visualization tool that is specifically designed for chloroplast genomes. It allows the users to depict the genetic architecture of up to ten chloroplast genomes in the vicinity of the sites connecting the inverted repeats to the short and long single copy regions. The software and its dependent libraries are fully coded in R and the reflected plot is scaled up to realistic size of nucleotide base pairs in the vicinity of the junction sites. We introduce a website for easier use of the program as well as R source code of the software to be used in case of preferences to be changed and integrated into personal pipelines. The input of the program is an annotation GenBank (.gb) file, the accession or GI number of the sequence or a DOGMA output file. The software was tested using over a hundred embryophyte chloroplast genomes and in all cases a reliable output was obtained. Source codes and the online suit available @ https://irscope.shinyapps.io/irapp/ or @ https://github.com/Limpfrog/irscope. ali.amiryousefi@helsinki.fi.

Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data

Directory of Open Access Journals (Sweden)

Merchant Sabeeha S

2011-07-01

Full Text Available Abstract Background Progress in genome sequencing is proceeding at an exponential pace, and several new algal genomes are becoming available every year. One of the challenges facing the community is the association of protein sequences encoded in the genomes with biological function. While most genome assembly projects generate annotations for predicted protein sequences, they are usually limited and integrate functional terms from a limited number of databases. Another challenge is the use of annotations to interpret large lists of 'interesting' genes generated by genome-scale datasets. Previously, these gene lists had to be analyzed across several independent biological databases, often on a gene-by-gene basis. In contrast, several annotation databases, such as DAVID, integrate data from multiple functional databases and reveal underlying biological themes of large gene lists. While several such databases have been constructed for animals, none is currently available for the study of algae. Due to renewed interest in algae as potential sources of biofuels and the emergence of multiple algal genome sequences, a significant need has arisen for such a database to process the growing compendiums of algal genomic data. Description The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of

DNA Microarray as Part of a Genomic-Assisted Breeding Approach

DEFF Research Database (Denmark)

Vincze, Éva; Bowra, Steve

2010-01-01

) is the ‘umbrella' term used to describe a suite of tools now being applied to plant breeding. In the context of genomic-assisted breeding, we will briefly discuss in the second section of this chapter the molecular genetic-based tools underpinning GAB (understanding gene expression, candidate gene selection......In the struggle to achieve global food security, crop breeding retains an important role in crop production. A current trend is the diversification of the aims of crop production, to include an increased awareness of aspects and consequences of food quality. The added emphasis on food and feed...... quality made crop breeding more challenging and required a combination of new tools. We illustrate these concepts by taking examples from barley, one of the most ancient of domesticated grains with a diverse profile of utilisation (feed, brewing, new nutritional uses). Genomic-assisted breeding (GAB...

Strauss: Der Rosenkavalier - Suite / Michael Kennedy

Index Scriptorium Estoniae

Kennedy, Michael

1990-01-01

Uuest heliplaadist "Strauss: Der Rosenkavalier - Suite, Salome-Dance of the seven veils, Capriccio-Prelude, Intermezzo, Morgen Mittag um elf! Felicity Lott, Scottish National Orchestra, Neeme Järvi" Chandos ABRD 1397. ABTD 1397. CHAN 8758

The Los Alamos suite of relativistic atomic physics codes

International Nuclear Information System (INIS)

Fontes, C J; Zhang, H L; Jr, J Abdallah; Clark, R E H; Kilcrease, D P; Colgan, J; Cunningham, R T; Hakel, P; Magee, N H; Sherrill, M E

2015-01-01

The Los Alamos suite of relativistic atomic physics codes is a robust, mature platform that has been used to model highly charged ions in a variety of ways. The suite includes capabilities for calculating data related to fundamental atomic structure, as well as the processes of photoexcitation, electron-impact excitation and ionization, photoionization and autoionization within a consistent framework. These data can be of a basic nature, such as cross sections and collision strengths, which are useful in making predictions that can be compared with experiments to test fundamental theories of highly charged ions, such as quantum electrodynamics. The suite can also be used to generate detailed models of energy levels and rate coefficients, and to apply them in the collisional-radiative modeling of plasmas over a wide range of conditions. Such modeling is useful, for example, in the interpretation of spectra generated by a variety of plasmas. In this work, we provide a brief overview of the capabilities within the Los Alamos relativistic suite along with some examples of its application to the modeling of highly charged ions. (paper)

Coupled Human-Space Suit Mobility Studies

Data.gov (United States)

National Aeronautics and Space Administration — Current EVA mobility studies only allow for comparisons of how the suit moves when actuated by a human and how the human moves when unsuited. There are now new...

Space Suit Performance: Methods for Changing the Quality of Quantitative Data

Science.gov (United States)

Cowley, Matthew; Benson, Elizabeth; Rajulu, Sudhakar

2014-01-01

NASA is currently designing a new space suit capable of working in deep space and on Mars. Designing a suit is very difficult and often requires trade-offs between performance, cost, mass, and system complexity. To verify that new suits will enable astronauts to perform to their maximum capacity, prototype suits must be built and tested with human subjects. However, engineers and flight surgeons often have difficulty understanding and applying traditional representations of human data without training. To overcome these challenges, NASA is developing modern simulation and analysis techniques that focus on 3D visualization. Early understanding of actual performance early on in the design cycle is extremely advantageous to increase performance capabilities, reduce the risk of injury, and reduce costs. The primary objective of this project was to test modern simulation and analysis techniques for evaluating the performance of a human operating in extra-vehicular space suits.

An improved air-supplied plastic suit for protection against tritium

International Nuclear Information System (INIS)

Wiernicki, C.

1987-01-01

A newly developed Saran/CPE plastic suit material is described which offers significantly better protection against HTO penetration and permeation than the 12-mil PVC currently used at SRP and most other DOE and commercial sites where tritium and HTO are exposure hazards. Tritium breakthrough time is an important parameter when evaluating the applicability of protective clothing; previously published tritium permeation tests did not measure this parameter. Future studies should quantify steady-state permeation rate and breakthrough time to more fully evaluate potential tritium protective clothing. Saran/CPE has successfully been fabricated into a plastic suit because, in addition to its superior tritium resistance, it has all the characteristics required to construct a rugged, dependable, and comfortable suit. The use of the Saran/CPE suit at SRP reactor and tritium production facilities should be a major contribution to the site As Low As Reasonably Achievable program. Both Saran/CPE have demonstrated excellent resistance to a wide range of chemical contaminants; therefore, this suit material may have applications in the general chemical industry and hazardous waste site cleanup operations. 4 refs., 3 figs., 1 tab

Philosophies Applied in the Selection of Space Suit Joint Range of Motion Requirements

Science.gov (United States)

Aitchison, Lindsway; Ross, Amy; Matty, Jennifer

2009-01-01

Space suits are the most important tool for astronauts working in harsh space and planetary environments; suits keep crewmembers alive and allow them to perform exploration, construction, and scientific tasks on a routine basis over a period of several months. The efficiency with which the tasks are performed is largely dictated by the mobility features of the space suit. For previous space suit development programs, the mobility requirements were written as pure functional mobility requirements that did not separate joint ranges of motion from the joint torques. The Constellation Space Suit Element has the goal to make more quantitative mobility requirements that focused on the individual components of mobility to enable future suit designers to build and test systems more effectively. This paper details the test planning and selection process for the Constellation space suit pressure garment range of motion requirements.

The Role of KREEP in the Production of Mg-Suite Magmas and Its Influence on the Extent of Mg-Suite Magmatism in the Lunar Crust

Science.gov (United States)

Elardo, S. M.; Shearer, C. K.; McCubbin, F. M.

2017-01-01

The lunar magnesian-suite, or Mg-suite, is a series of ancient plutonic rocks from the lunar crust. They have received a considerable amount of attention from lunar scientists since their discovery for three primary reasons: 1) their ages and geochemistry indicate they represent pristine magmatic samples that crystallized very soon after the formation of the Moon; 2) their ages often overlap with ages of the ferroan anorthosite (FAN) crust; and 3) planetary-scale processes are needed in formation models to account for their unique geochemical features. Taken as a whole, the Mg-suite samples, as magmatic cumulate rocks, approximate a fractional crystallization sequence in the low-pressure forsterite-anorthite-silica system, and thus these samples are generally thought to be derived from layered mafic intrusions which crystallized very slowly from magmas that intruded the anorthositic crust. However, no direct linkages have been established between different Mg-suite samples based either on field relationships or geochemistry.The model for the origin of the Mg-suite, which best fits the limited available data, is one where Mg-suite magmas form from melting of a hybrid cumulate package consisting of deep mantle dunite, crustal anorthosite, and KREEP (potassium-rare earth elements-phosphorus) at the base of the crust under the Procellarum KREEP Terrane (PKT). In this model, these three LMO (Lunar Magma Ocean) cumulate components are brought into close proximity by the cumulate overturn process. Deep mantle dunitic cumulates with an Mg number of approximately 90 rise to the base of the anorthositic crust due to their buoyancy relative to colder, more dense Fe- and Ti-rich cumulates. This hybridized source rock melts to form Mg-suite magmas, saturated in Mg-rich olivine and anorthitic plagioclase, that have a substantial KREEP component.

A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.

Directory of Open Access Journals (Sweden)

Wenyu Zhang

Full Text Available The advent of next-generation sequencing technologies is accompanied with the development of many whole-genome sequence assembly methods and software, especially for de novo fragment assembly. Due to the poor knowledge about the applicability and performance of these software tools, choosing a befitting assembler becomes a tough task. Here, we provide the information of adaptivity for each program, then above all, compare the performance of eight distinct tools against eight groups of simulated datasets from Solexa sequencing platform. Considering the computational time, maximum random access memory (RAM occupancy, assembly accuracy and integrity, our study indicate that string-based assemblers, overlap-layout-consensus (OLC assemblers are well-suited for very short reads and longer reads of small genomes respectively. For large datasets of more than hundred millions of short reads, De Bruijn graph-based assemblers would be more appropriate. In terms of software implementation, string-based assemblers are superior to graph-based ones, of which SOAPdenovo is complex for the creation of configuration file. Our comparison study will assist researchers in selecting a well-suited assembler and offer essential information for the improvement of existing assemblers or the developing of novel assemblers.

Comparison of phasing strategies for whole human genomes.

Science.gov (United States)

Choi, Yongwook; Chan, Agnes P; Kirkness, Ewen; Telenti, Amalio; Schork, Nicholas J

2018-04-01

Humans are a diploid species that inherit one set of chromosomes paternally and one homologous set of chromosomes maternally. Unfortunately, most human sequencing initiatives ignore this fact in that they do not directly delineate the nucleotide content of the maternal and paternal copies of the 23 chromosomes individuals possess (i.e., they do not 'phase' the genome) often because of the costs and complexities of doing so. We compared 11 different widely-used approaches to phasing human genomes using the publicly available 'Genome-In-A-Bottle' (GIAB) phased version of the NA12878 genome as a gold standard. The phasing strategies we compared included laboratory-based assays that prepare DNA in unique ways to facilitate phasing as well as purely computational approaches that seek to reconstruct phase information from general sequencing reads and constructs or population-level haplotype frequency information obtained through a reference panel of haplotypes. To assess the performance of the 11 approaches, we used metrics that included, among others, switch error rates, haplotype block lengths, the proportion of fully phase-resolved genes, phasing accuracy and yield between pairs of SNVs. Our comparisons suggest that a hybrid or combined approach that leverages: 1. population-based phasing using the SHAPEIT software suite, 2. either genome-wide sequencing read data or parental genotypes, and 3. a large reference panel of variant and haplotype frequencies, provides a fast and efficient way to produce highly accurate phase-resolved individual human genomes. We found that for population-based approaches, phasing performance is enhanced with the addition of genome-wide read data; e.g., whole genome shotgun and/or RNA sequencing reads. Further, we found that the inclusion of parental genotype data within a population-based phasing strategy can provide as much as a ten-fold reduction in phasing errors. We also considered a majority voting scheme for the construction of a

Corrections of the NIST Statistical Test Suite for Randomness

OpenAIRE

Kim, Song-Ju; Umeno, Ken; Hasegawa, Akio

2004-01-01

It is well known that the NIST statistical test suite was used for the evaluation of AES candidate algorithms. We have found that the test setting of Discrete Fourier Transform test and Lempel-Ziv test of this test suite are wrong. We give four corrections of mistakes in the test settings. This suggests that re-evaluation of the test results should be needed.

Reliability performance testing of totally encapsulating chemical protective suits

International Nuclear Information System (INIS)

Johnson, J.S.; Swearengen, P.M.

1991-01-01

The need to assure a high degree of reliability for totally encapsulating chemical protective (TECP) suits has been recognized by Lawrence Livermore National Laboratory's (LLNL) Hazards Control Department for some time. The following four tests were proposed as necessary to provide complete evaluation of TECP suit performance: 1. Quantitative leak test (ASTM draft), 2. Worst-case chemical exposure test (conceptual), 3. Pressure leak-rate test (complete, ASTM F1057-87), and 4. Chemical leak-rate test (ASTM draft). This paper reports on these tests which should be applied to measuring TECP suit performance in two stages: design qualification tests and field use tests. Test 1, 2, and 3 are used as design qualification tests, and tests 3 and 4 are used as field use tests

Suited versus unsuited analog astronaut performance using the Aouda.X space suit simulator: the DELTA experiment of MARS2013.

Science.gov (United States)

Soucek, Alexander; Ostkamp, Lutz; Paternesi, Roberta

2015-04-01

Space suit simulators are used for extravehicular activities (EVAs) during Mars analog missions. Flight planning and EVA productivity require accurate time estimates of activities to be performed with such simulators, such as experiment execution or traverse walking. We present a benchmarking methodology for the Aouda.X space suit simulator of the Austrian Space Forum. By measuring and comparing the times needed to perform a set of 10 test activities with and without Aouda.X, an average time delay was derived in the form of a multiplicative factor. This statistical value (a second-over-second time ratio) is 1.30 and shows that operations in Aouda.X take on average a third longer than the same operations without the suit. We also show that activities predominantly requiring fine motor skills are associated with larger time delays (between 1.17 and 1.59) than those requiring short-distance locomotion or short-term muscle strain (between 1.10 and 1.16). The results of the DELTA experiment performed during the MARS2013 field mission increase analog mission planning reliability and thus EVA efficiency and productivity when using Aouda.X.

Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing

DEFF Research Database (Denmark)

Hou, Yong; Wu, Kui; Shi, Xulian

2015-01-01

methods, focusing particularly on variations detection. Low-coverage whole-genome sequencing revealed that DOP-PCR had the highest duplication ratio, but an even read distribution and the best reproducibility and accuracy for detection of copy-number variations (CNVs). However, MDA had significantly...... performance using SCRS amplified by different WGA methods. It will guide researchers to determine which WGA method is best suited to individual experimental needs at single-cell level....

The Apollo Number: space suits, self-support, and the walk-run transition.

Directory of Open Access Journals (Sweden)

Christopher E Carr

Full Text Available BACKGROUND: How space suits affect the preferred walk-run transition is an open question with relevance to human biomechanics and planetary extravehicular activity. Walking and running energetics differ; in reduced gravity (<0.5 g, running, unlike on Earth, uses less energy per distance than walking. METHODOLOGY/PRINCIPAL FINDINGS: The walk-run transition (denoted * correlates with the Froude Number (Fr = v(2/gL, velocity v, gravitational acceleration g, leg length L. Human unsuited Fr* is relatively constant (approximately 0.5 with gravity but increases substantially with decreasing gravity below approximately 0.4 g, rising to 0.9 in 1/6 g; space suits appear to lower Fr*. Because of pressure forces, space suits partially (1 g or completely (lunar-g support their own weight. We define the Apollo Number (Ap = Fr/M as an expected invariant of locomotion under manipulations of M, the ratio of human-supported to total transported mass. We hypothesize that for lunar suited conditions Ap* but not Fr* will be near 0.9, because the Apollo Number captures the effect of space suit self-support. We used the Apollo Lunar Surface Journal and other sources to identify 38 gait events during lunar exploration for which we could determine gait type (walk/lope/run and calculate Ap. We estimated the binary transition between walk/lope (0 and run (1, yielding Fr* (0.36+/-0.11, mean+/-95% CI and Ap* (0.68+/-0.20. CONCLUSIONS/SIGNIFICANCE: The Apollo Number explains 60% of the difference between suited and unsuited Fr*, appears to capture in large part the effects of space suits on the walk-run transition, and provides several testable predictions for space suit locomotion and, of increasing relevance here on Earth, exoskeleton locomotion. The knowledge of how space suits affect gait transitions can be used to optimize space suits for use on the Moon and Mars.

Virtual reality simulation training in a high-fidelity procedure suite

DEFF Research Database (Denmark)

Lönn, Lars; Edmond, John J; Marco, Jean

2012-01-01

To assess the face and content validity of a novel, full physics, full procedural, virtual reality simulation housed in a hybrid procedure suite.......To assess the face and content validity of a novel, full physics, full procedural, virtual reality simulation housed in a hybrid procedure suite....

Corporation suit in administrative proceedings - BVerwG, NJW 1981, 362

International Nuclear Information System (INIS)

Skouris, W.

1982-01-01

The above mentioned decisions show that the repeated demand for an admission of the corporation suit has not had much impact on jurisdiction. Still the courts are examining whether the rights of corporations taking action against the executive measures are being infringed by them or not. They do not seem to be willing to admit the enforcement of members' rights or of public interests by means of a corporation suit except in those cases that are already embodied in the law. The latest statement of the administrative courts prove that the administrative procedural law (still) in force does not accept any general law on the conduct of a case on behalf of associations for the protection of their members' rights (egoistic corporation suit), nor does it acknowledge the legitimacy of corporations to see against objective illegalities in official decisions with the intention of reducing deficiencies in the execution (altruistic corporation suit). (orig.) [de

FRHAM-TEX trademark cool suit - OST reference No. 1854. Deactivation and decommissioning focus area

International Nuclear Information System (INIS)

1998-02-01

This paper describes a demonstration project for the FRHAM-TEX Cool Suit trademark manufactured by FRHAM Safety Products. It is a one-piece, disposable, breathable, waterproof coverall designed to permit moisture generated by the wearer to be transmitted outside the suit. The performance of this suit was compared to a Tyvek reg-sign suit as a baseline. The suit is proposed as safety ware for workers at decontamination and decommissioning projects

Software Application Profile: RVPedigree: a suite of family-based rare variant association tests for normally and non-normally distributed quantitative traits.

Science.gov (United States)

Oualkacha, Karim; Lakhal-Chaieb, Lajmi; Greenwood, Celia Mt

2016-04-01

RVPedigree (Rare Variant association tests in Pedigrees) implements a suite of programs facilitating genome-wide analysis of association between a quantitative trait and autosomal region-based genetic variation. The main features here are the ability to appropriately test for association of rare variants with non-normally distributed quantitative traits, and also to appropriately adjust for related individuals, either from families or from population structure and cryptic relatedness. RVPedigree is available as an R package. The package includes calculation of kinship matrices, various options for coping with non-normality, three different ways of estimating statistical significance incorporating triaging to enable efficient use of the most computationally-intensive calculations, and a parallelization option for genome-wide analysis. The software is available from the Comprehensive R Archive Network [CRAN.R-project.org] under the name 'RVPedigree' and at [https://github.com/GreenwoodLab]. It has been published under General Public License (GPL) version 3 or newer. © The Author 2016; all rights reserved. Published by Oxford University Press on behalf of the International Epidemiological Association.

Extreme-Environment Silicon-Carbide (SiC) Wireless Sensor Suite

Science.gov (United States)

Yang, Jie

2015-01-01

Phase II objectives: Develop an integrated silicon-carbide wireless sensor suite capable of in situ measurements of critical characteristics of NTP engine; Compose silicon-carbide wireless sensor suite of: Extreme-environment sensors center, Dedicated high-temperature (450 deg C) silicon-carbide electronics that provide power and signal conditioning capabilities as well as radio frequency modulation and wireless data transmission capabilities center, An onboard energy harvesting system as a power source.

Astronaut Neil Armstrong in Launch Complex 16 trailer during suiting up

Science.gov (United States)

1966-01-01

Astronaut Neil A. Armstrong, command pilot of the Gemini 8 space flight, sits in the Launch Complex 16 trailer during suiting up operations for the Gemini 8 mission. Suit technician Jim Garrepy assists.

snpTree - a web-server to identify and construct SNP trees from whole genome sequence data

DEFF Research Database (Denmark)

Leekitcharoenphon, Pimlapas; Kaas, Rolf Sommer; Thomsen, Martin Christen Frølund

2012-01-01

identify SNPs and construct phylogenetic trees from WGS as well as from assembled genomes or contigs. WGS data in fastq format are aligned to reference genomes by BWA while contigs in fasta format are processed by Nucmer. SNPs are concatenated based on position on reference genome and a tree is constructed...... to differentiate and classify isolates. One of the successfully and broadly used methods is analysis of single nucletide polymorphisms (SNPs). Currently, there are different tools and methods to identify SNPs including various options and cut-off values. Furthermore, all current methods require bioinformatic...... skills. Thus, we lack a standard and simple automatic tool to determine SNPs and construct phylogenetic tree from WGS data. Results Here we introduce snpTree, a server for online-automatic SNPs analysis. This tool is composed of different SNPs analysis suites, perl and python scripts. snpTree can...

Heat and mass transfer in air-fed pressurised suits

International Nuclear Information System (INIS)

Tesch, K.; Collins, M.W.; Karayiannis, T.G.; Atherton, M.A.; Edwards, P.

2009-01-01

Air-fed pressurised suits are used to protect workers against contamination and hazardous environments. The specific application here is the necessity for regular clean-up maintenance within the torus chamber of fusion reactors. The current design of suiting has been developed empirically. It is, therefore, very desirable to formulate a thermo-fluids model, which will be able to define optimum designs and operating parameters. Two factors indicate that the modelling should be as comprehensive as possible. Firstly, the overall thermo-fluids problem is three-dimensional and includes mass as well as heat transfer. The fluid field is complex, bounded on one side by the human body and on the other by what may be distensible, porous and multi-layer clothing. In this paper, we report firstly the modelling necessary for the additional mass and heat transport processes. This involves the use of Fick's and Fourier's laws and conjugate heat transfer. The results of an initial validation study are presented. Temperatures at the outlet of the suits were obtained experimentally and compared with those predicted by the overall CFD model. Realistic three-dimensional geometries were used for the suit and human body. Calculations were for turbulent flow with single- and two-component (species) models

The number of genes encoding repeat domain-containing proteins positively correlates with genome size in amoebal giant viruses

Science.gov (United States)

Shukla, Avi; Chatterjee, Anirvan

2018-01-01

Abstract Curiously, in viruses, the virion volume appears to be predominantly driven by genome length rather than the number of proteins it encodes or geometric constraints. With their large genome and giant particle size, amoebal viruses (AVs) are ideally suited to study the relationship between genome and virion size and explore the role of genome plasticity in their evolutionary success. Different genomic regions of AVs exhibit distinct genealogies. Although the vertically transferred core genes and their functions are universally conserved across the nucleocytoplasmic large DNA virus (NCLDV) families and are essential for their replication, the horizontally acquired genes are variable across families and are lineage-specific. When compared with other giant virus families, we observed a near–linear increase in the number of genes encoding repeat domain-containing proteins (RDCPs) with the increase in the genome size of AVs. From what is known about the functions of RDCPs in bacteria and eukaryotes and their prevalence in the AV genomes, we envisage important roles for RDCPs in the life cycle of AVs, their genome expansion, and plasticity. This observation also supports the evolution of AVs from a smaller viral ancestor by the acquisition of diverse gene families from the environment including RDCPs that might have helped in host adaption. PMID:29308275

STS-74 M.S. Jerry L. Ross suits up

Science.gov (United States)

1995-01-01

Spaceflight veteran Jerry L. Ross, Mission Specialist 2 on Shuttle Mission STS-74, is assisted by a suit technician as he finishes getting into his launch/entry suit in the Operations and Checkout Building. Ross and four fellow astronauts will depart shortly for Launch Pad 39A, where the Space Shuttle Atlantis awaits a second liftoff attempt during a seven-minute window scheduled to open at approximately 7:30 a.m. EST, Nov. 12.

Learning DHTMLX suite UI

CERN Document Server

Geske, Eli

2013-01-01

A fast-paced, example-based guide to learning DHTMLX.""Learning DHTMLX Suite UI"" is for web designers who have a basic knowledge of JavaScript and who are looking for powerful tools that will give them an extra edge in their own application development. This book is also useful for experienced developers who wish to get started with DHTMLX without going through the trouble of learning its quirks through trial and error. Readers are expected to have some knowledge of JavaScript, HTML, Document Object Model, and the ability to install a local web server.

Enhancing knowledge discovery from cancer genomics data with Galaxy.

Science.gov (United States)

Albuquerque, Marco A; Grande, Bruno M; Ritch, Elie J; Pararajalingam, Prasath; Jessa, Selin; Krzywinski, Martin; Grewal, Jasleen K; Shah, Sohrab P; Boutros, Paul C; Morin, Ryan D

2017-05-01

The field of cancer genomics has demonstrated the power of massively parallel sequencing techniques to inform on the genes and specific alterations that drive tumor onset and progression. Although large comprehensive sequence data sets continue to be made increasingly available, data analysis remains an ongoing challenge, particularly for laboratories lacking dedicated resources and bioinformatics expertise. To address this, we have produced a collection of Galaxy tools that represent many popular algorithms for detecting somatic genetic alterations from cancer genome and exome data. We developed new methods for parallelization of these tools within Galaxy to accelerate runtime and have demonstrated their usability and summarized their runtimes on multiple cloud service providers. Some tools represent extensions or refinement of existing toolkits to yield visualizations suited to cohort-wide cancer genomic analysis. For example, we present Oncocircos and Oncoprintplus, which generate data-rich summaries of exome-derived somatic mutation. Workflows that integrate these to achieve data integration and visualizations are demonstrated on a cohort of 96 diffuse large B-cell lymphomas and enabled the discovery of multiple candidate lymphoma-related genes. Our toolkit is available from our GitHub repository as Galaxy tool and dependency definitions and has been deployed using virtualization on multiple platforms including Docker. © The Author 2017. Published by Oxford University Press.

Effect of swimming suit design on the energy demands of swimming.

Science.gov (United States)

Starling, R D; Costill, D L; Trappe, T A; Jozsi, A C; Trappe, S W; Goodpaster, B H

1995-07-01

Eight competitive male swimmers completed a standardized 365.8 m (400 yd) freestyle swimming trial at a fixed pace (approximately 90% of maximal effort) while wearing a torso swim suit (TOR) or a standard racing suit (STD). Oxygen uptake (VO2), blood lactate, heart rate (HR), and distance per stroke (DPS) measurements were obtained. In addition, a video-computer system was used to collect velocity data during a prone underwater glide following a maximal leg push-off from the side of the pool while wearing the TOR and STD suits. These data were used to calculate the total distance covered during the glides. VO2 (3.76 +/- 0.16 vs 3.92 +/- 0.18 l.min-1) and lactate (8.08 +/- 0.53 vs, 9.66 +/- 0.66 mM) were significantly (P 0.05) between the TOR (170.1 +/- 5.1 b.min-1) and STD (173.5 +/- 5.7 b.min-1) trials. DPS was significantly greater during the TOR (2.70 +/- 0.066 m.stroke-1) versus STD (2.58 +/- 0.054 m.stroke-1) trial. A significantly greater total distance was covered during the prone glide while wearing the TOR (2.05 +/- 0.067 m) compared to the STD (2.00 +/- 0.080 m) suit. These findings demonstrate that a specially designed torso suit reduces the energy demand of swimming compared to a standard racing suit which may be due to a reduction in body drag.

Minimizing liability risks under the ACMG recommendations for reporting incidental findings in clinical exome and genome sequencing

Science.gov (United States)

Evans, Barbara J.

2014-01-01

Recent recommendations by the American College of Medical Genetics and Genomics (ACMG) for reporting incidental findings present novel ethical and legal issues. This article expresses no views on the ethical aspects of these recommendations and focuses strictly on liability risks and how to minimize them. The recommendations place labs and clinicians in a new liability environment that exposes them to intentional tort lawsuits as well to traditional suits for negligence. Intentional tort suits are especially troubling because of their potential to inflict ruinous personal financial losses on individual clinicians and laboratory personnel. This article surveys this new liability landscape and describes analytical approaches for minimizing tort liabilities. To a considerable degree, liability risks can be controlled by structuring activities in ways that make future lawsuits nonviable before the suits ever arise. Proactive liability analysis is an effective tool for minimizing tort liabilities in connection with the testing and reporting activities that the ACMG recommends. PMID:24030435

Minimizing liability risks under the ACMG recommendations for reporting incidental findings in clinical exome and genome sequencing.

Science.gov (United States)

Evans, Barbara J

2013-12-01

Recent recommendations by the American College of Medical Genetics and Genomics (ACMG) for reporting incidental findings present novel ethical and legal issues. This article expresses no views on the ethical aspects of these recommendations and focuses strictly on liability risks and how to minimize them. The recommendations place labs and clinicians in a new liability environment that exposes them to intentional tort lawsuits as well to traditional suits for negligence. Intentional tort suits are especially troubling because of their potential to inflict ruinous personal financial losses on individual clinicians and laboratory personnel. This article surveys this new liability landscape and describes analytical approaches for minimizing tort liabilities. To a considerable degree, liability risks can be controlled by structuring activities in ways that make future lawsuits nonviable before the suits ever arise. Proactive liability analysis is an effective tool for minimizing tort liabilities in connection with the testing and reporting activities that the ACMG recommends.

28 CFR 36.501 - Private suits.

Science.gov (United States)

2010-07-01

... ACCOMMODATIONS AND IN COMMERCIAL FACILITIES Enforcement § 36.501 Private suits. (a) General. Any person who is... order. Upon timely application, the court may, in its discretion, permit the Attorney General to... general public importance. Upon application by the complainant and in such circumstances as the court may...

Clementine sensor suite

Energy Technology Data Exchange (ETDEWEB)

Ledebuhr, A.G. [Lawrence Livermore National Lab., CA (United States)

1994-11-15

LLNL designed and built the suite of six miniaturized light-weight space-qualified sensors utilized in the Clementine mission. A major goal of the Clementine program was to demonstrate technologies originally developed for Ballistic Missile Defense Organization Programs. These sensors were modified to gather data from the moon. This overview presents each of these sensors and some preliminary on-orbit performance estimates. The basic subsystems of these sensors include optical baffles to reject off-axis stray light, light-weight ruggedized optical systems, filter wheel assemblies, radiation tolerant focal plane arrays, radiation hardened control and readout electronics and low mass and power mechanical cryogenic coolers for the infrared sensors. Descriptions of each sensor type are given along with design specifications, photographs and on-orbit data collected.

Results and Analysis from Space Suit Joint Torque Testing

Science.gov (United States)

Matty, Jennifer

2010-01-01

This joint mobility KC lecture included information from two papers, "A Method for and Issues Associated with the Determination of Space Suit Joint Requirements" and "Results and Analysis from Space Suit Joint Torque Testing," as presented for the International Conference on Environmental Systems in 2009 and 2010, respectively. The first paper discusses historical joint torque testing methodologies and approaches that were tested in 2008 and 2009. The second paper discusses the testing that was completed in 2009 and 2010.

A Test Suite for Safety-Critical Java using JML

DEFF Research Database (Denmark)

Ravn, Anders Peter; Søndergaard, Hans

2013-01-01

Development techniques are presented for a test suite for the draft specification of the Java profile for Safety-Critical Systems. Distinguishing features are: specification of conformance constraints in the Java Modeling Language, encoding of infrastructure concepts without implementation bias......, and corresponding specifications of implicitly stated behavioral and real-time properties. The test programs are auto-generated from the specification, while concrete values for test parameters are selected manually. The suite is open source and publicly accessible....

DEMON/ANGEL - A SUITE OF PROGRAMS TO CARRY OUT DENSITY MODIFICATION

NARCIS (Netherlands)

VELLIEUX, FMDAP; HUNT, JF; ROY, S; READ, RJ

1995-01-01

The DEMON/ANGEL suite of computer programs has been developed to carry out density modification by non-crystallographic symmetry-averaging, solvent-flattening and histogram-mapping techniques. This suite consists of programs that allow molecular envelopes to be defined and modified,

The functional genomic studies of curcumin.

Science.gov (United States)

Huminiecki, Lukasz; Horbańczuk, Jarosław; Atanasov, Atanas G

2017-10-01

Curcumin is a natural plant-derived compound that has attracted a lot of attention for its anti-cancer activities. Curcumin can slow proliferation of and induce apoptosis in cancer cell lines, but the precise mechanisms of these effects are not fully understood. However, many lines of evidence suggested that curcumin has a potent impact on gene expression profiles; thus, functional genomics should be the key to understanding how curcumin exerts its anti-cancer activities. Here, we review the published functional genomic studies of curcumin focusing on cancer. Typically, a cancer cell line or a grafted tumor were exposed to curcumin and profiled with microarrays, methylation assays, or RNA-seq. Crucially, these studies are in agreement that curcumin has a powerful effect on gene expression. In the majority of the studies, among differentially expressed genes we found genes involved in cell signaling, apoptosis, and the control of cell cycle. Curcumin can also induce specific methylation changes, and is a powerful regulator of the expression of microRNAs which control oncogenesis. We also reflect on how the broader technological progress in transcriptomics has been reflected on the field of curcumin. We conclude by discussing the areas where more functional genomic studies are highly desirable. Integrated OMICS approaches will clearly be the key to understanding curcumin's anticancer and chemopreventive effects. Such strategies may become a template for elucidating the mode of action of other natural products; many natural products have pleiotropic effects that are well suited for a systems-level analysis. Copyright © 2017 Elsevier Ltd. All rights reserved.

DYNA3D/ParaDyn Regression Test Suite Inventory

Energy Technology Data Exchange (ETDEWEB)

Lin, Jerry I. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2016-09-01

The following table constitutes an initial assessment of feature coverage across the regression test suite used for DYNA3D and ParaDyn. It documents the regression test suite at the time of preliminary release 16.1 in September 2016. The columns of the table represent groupings of functionalities, e.g., material models. Each problem in the test suite is represented by a row in the table. All features exercised by the problem are denoted by a check mark (√) in the corresponding column. The definition of “feature” has not been subdivided to its smallest unit of user input, e.g., algorithmic parameters specific to a particular type of contact surface. This represents a judgment to provide code developers and users a reasonable impression of feature coverage without expanding the width of the table by several multiples. All regression testing is run in parallel, typically with eight processors, except problems involving features only available in serial mode. Many are strictly regression tests acting as a check that the codes continue to produce adequately repeatable results as development unfolds; compilers change and platforms are replaced. A subset of the tests represents true verification problems that have been checked against analytical or other benchmark solutions. Users are welcomed to submit documented problems for inclusion in the test suite, especially if they are heavily exercising, and dependent upon, features that are currently underrepresented.

Extending and Enhancing SAS (Static Analysis Suite)

CERN Document Server

Ho, David

2016-01-01

The Static Analysis Suite (SAS) is an open-source software package used to perform static analysis on C and C++ code, helping to ensure safety, readability and maintainability. In this Summer Student project, SAS was enhanced to improve ease of use and user customisation. A straightforward method of integrating static analysis into a project at compilation time was provided using the automated build tool CMake. The process of adding checkers to the suite was streamlined and simplied by developing an automatic code generator. To make SAS more suitable for continuous integration, a reporting mechanism summarising results was added. This suitability has been demonstrated by inclusion of SAS in the Future Circular Collider Software nightly build system. Scalability of the improved package was demonstrated by using the tool to analyse the ROOT code base.

Statistical Evaluation of Causal Factors Associated with Astronaut Shoulder Injury in Space Suits.

Science.gov (United States)

Anderson, Allison P; Newman, Dava J; Welsch, Roy E

2015-07-01

Shoulder injuries due to working inside the space suit are some of the most serious and debilitating injuries astronauts encounter. Space suit injuries occur primarily in the Neutral Buoyancy Laboratory (NBL) underwater training facility due to accumulated musculoskeletal stress. We quantitatively explored the underlying causal mechanisms of injury. Logistic regression was used to identify relevant space suit components, training environment variables, and anthropometric dimensions related to an increased propensity for space-suited injury. Two groups of subjects were analyzed: those whose reported shoulder incident is attributable to the NBL or working in the space suit, and those whose shoulder incidence began in active duty, meaning working in the suit could be a contributing factor. For both groups, percent of training performed in the space suit planar hard upper torso (HUT) was the most important predictor variable for injury. Frequency of training and recovery between training were also significant metrics. The most relevant anthropometric dimensions were bideltoid breadth, expanded chest depth, and shoulder circumference. Finally, record of previous injury was found to be a relevant predictor for subsequent injury. The first statistical model correctly identifies 39% of injured subjects, while the second model correctly identifies 68% of injured subjects. A review of the literature suggests this is the first work to quantitatively evaluate the hypothesized causal mechanisms of all space-suited shoulder injuries. Although limited in predictive capability, each of the identified variables can be monitored and modified operationally to reduce future impacts on an astronaut's health.

A Method for and Issues Associated with the Determination of Space Suit Joint Requirements

Science.gov (United States)

Matty, Jennifer E.; Aitchison, Lindsay

2009-01-01

In the design of a new space suit it is necessary to have requirements that define what mobility space suit joints should be capable of achieving in both a system and at the component level. NASA elected to divide mobility into its constituent parts-range of motion (ROM) and torque- in an effort to develop clean design requirements that limit subject performance bias and are easily verified. Unfortunately, the measurement of mobility can be difficult to obtain. Current technologies, such as the Vicon motion capture system, allow for the relatively easy benchmarking of range of motion (ROM) for a wide array of space suit systems. The ROM evaluations require subjects in the suit to accurately evaluate the ranges humans can achieve in the suit. However, when it comes to torque, there are significant challenges for both benchmarking current performance and writing requirements for future suits. This is reflected in the fact that torque definitions have been applied to very few types of space suits and with limited success in defining all the joints accurately. This paper discussed the advantages and disadvantages to historical joint torque evaluation methods, describes more recent efforts directed at benchmarking joint torques of prototype space suits, and provides an outline for how NASA intends to address joint torque in design requirements for the Constellation Space Suit System (CSSS).

Walking a mile in another's shoes: The impact of wearing an Age Suit.

Science.gov (United States)

Lavallière, Martin; D'Ambrosio, Lisa; Gennis, Angelina; Burstein, Arielle; Godfrey, Kathryn M; Waerstad, Hilde; Puleo, Rozanne M; Lauenroth, Andreas; Coughlin, Joseph F

2017-01-01

The "Age Suit" described in this article was developed to enable future designers, business leaders, and engineers to experience navigating the world as many older adults must. Tools such as this Age Suit offer the opportunity to "walk a mile" in another's shoes to develop empathy that can result in better design of spaces, goods, and services to meet the needs of a rapidly growing older population. This work first examined, through a series of clinical tests, whether younger adults' physical capacities were reduced in a direction consistent with aging by wearing a suit developed by the MIT AgeLab. An experiential learning task was then completed with the suit to understand its impact on completion of an instrumental activity of daily living. Results showed that younger adults wearing the suit experienced changes in task performance consistent with expected changes associated with aging. Participants' self-reports from the experiential learning task indicated that they were able to empathize with older adults regarding some issues they face while completing a grocery shopping task. Future research with the suit should involve a wider range of individuals from the population and examine what effect participants' levels of fitness have on the experience of wearing the suit.

STS-76 Payload Cmdr Ronald Sega suits up

Science.gov (United States)

1996-01-01

STS-76 Payload Commander Ronald M. Sega is donning his launch/entry suit in the Operations and Checkout Building with assistance from a suit technician. The third docking between the Russian Space Station Mir and the U.S. Space Shuttle marks the second trip into space for Sega, who recently served a five-month assignment in Russia as operations director for NASA activities there. Once suitup activities are completed the six-member STS-76 flight crew will depart for Launch Pad 39B, where the Space Shuttle Atlantis is undergoing final preparations for liftoff during an approximately seven-minute launch window opening around 3:13 a.m. EST, March 22.

What's New with MS Office Suites

Science.gov (United States)

Goldsborough, Reid

2012-01-01

If one buys a new PC, laptop, or netbook computer today, it probably comes preloaded with Microsoft Office 2010 Starter Edition. This is a significantly limited, advertising-laden version of Microsoft's suite of productivity programs, Microsoft Office. This continues the trend of PC makers providing ever more crippled versions of Microsoft's…

Antigravity Suits For Studies Of Weightlessness

Science.gov (United States)

Kravik, Stein E.; Greenleaf, John

1992-01-01

Report presents results of research on use of "antigravity" suit, one applying positive pressure to lower body to simulate some effects of microgravity. Research suggests lower-body positive pressure is alternative to bed rest or immersion in water in terrestrial studies of cardioregulatory, renal, electrolyte, and hormonal changes induced in humans by microgravity.

The CMSSW benchmarking suite: Using HEP code to measure CPU performance

International Nuclear Information System (INIS)

Benelli, G

2010-01-01

The demanding computing needs of the CMS experiment require thoughtful planning and management of its computing infrastructure. A key factor in this process is the use of realistic benchmarks when assessing the computing power of the different architectures available. In recent years a discrepancy has been observed between the CPU performance estimates given by the reference benchmark for HEP computing (SPECint) and actual performances of HEP code. Making use of the CPU performance tools from the CMSSW performance suite, comparative CPU performance studies have been carried out on several architectures. A benchmarking suite has been developed and integrated in the CMSSW framework, to allow computing centers and interested third parties to benchmark architectures directly with CMSSW. The CMSSW benchmarking suite can be used out of the box, to test and compare several machines in terms of CPU performance and report with the wanted level of detail the different benchmarking scores (e.g. by processing step) and results. In this talk we describe briefly the CMSSW software performance suite, and in detail the CMSSW benchmarking suite client/server design, the performance data analysis and the available CMSSW benchmark scores. The experience in the use of HEP code for benchmarking will be discussed and CMSSW benchmark results presented.

33 CFR 144.20-5 - Exposure suits.

Science.gov (United States)

2010-07-01

... light that is approved under 46 CFR 161.012. Each light must be securely attached to the front shoulder... lanyard coiled and stopped off. (f) No stowage container for exposure suits may be capable of being locked...

Evaluation of Triathlon Suit Characteristics Relevant to Thermophysiology of an Athlete

Directory of Open Access Journals (Sweden)

Chris Watson

2018-02-01

Full Text Available The thermophysiological function of clothing influences athletic wellbeing and performance, particularly in outdoor endurance activities such as triathlon. However, there is very little existing research on the performance of triathlon suits relative to thermophysiological function of the wearer. This pilot study provides a benchmark for triathlon suit performance and insights into improving the suit design and material engineering. The study assessed the thermal and breathability attributes of 6 triathlon suits and concluded that while both of the attributes were similar overall, they varied in different body zones due to different design, construction and materials. Local thermal and evaporative performance were affected by fabric construction; double fabric layering in the stomach panel; the number, size, shape and material structure of rear pockets; cycle crotch pad size, shape and thickness; and panel design. The results of this study show the importance of garment design, construction and materials for the best thermal and evaporative resistance attributes of sportswear.

STS-82 Pilot Scott J. 'Doc' Horowitz Suit Up

Science.gov (United States)

1997-01-01

STS-82 Pilot Scott J. 'Doc' Horowitz puts on a glove of his launch and entry suit with assistance from a suit technician in the Operations and Checkout Building. This is Horowitz''';s second space flight. He and the six other crew members will depart shortly for Launch Pad 39A, where the Space Shuttle Discovery awaits liftoff on a 10-day mission to service the orbiting Hubble Space Telescope (HST). This will be the second HST servicing mission. Four back-to-back spacewalks are planned.

Surgical Space Suits Increase Particle and Microbiological Emission Rates in a Simulated Surgical Environment.

Science.gov (United States)

Vijaysegaran, Praveen; Knibbs, Luke D; Morawska, Lidia; Crawford, Ross W

2018-05-01

The role of space suits in the prevention of orthopedic prosthetic joint infection remains unclear. Recent evidence suggests that space suits may in fact contribute to increased infection rates, with bioaerosol emissions from space suits identified as a potential cause. This study aimed to compare the particle and microbiological emission rates (PER and MER) of space suits and standard surgical clothing. A comparison of emission rates between space suits and standard surgical clothing was performed in a simulated surgical environment during 5 separate experiments. Particle counts were analyzed with 2 separate particle counters capable of detecting particles between 0.1 and 20 μm. An Andersen impactor was used to sample bacteria, with culture counts performed at 24 and 48 hours. Four experiments consistently showed statistically significant increases in both PER and MER when space suits are used compared with standard surgical clothing. One experiment showed inconsistent results, with a trend toward increases in both PER and MER when space suits are used compared with standard surgical clothing. Space suits cause increased PER and MER compared with standard surgical clothing. This finding provides mechanistic evidence to support the increased prosthetic joint infection rates observed in clinical studies. Copyright © 2017 Elsevier Inc. All rights reserved.

Epigenetic Mechanisms of Genomic Imprinting: Common Themes in the Regulation of Imprinted Regions in Mammals, Plants, and Insects

Directory of Open Access Journals (Sweden)

William A. MacDonald

2012-01-01

Full Text Available Genomic imprinting is a form of epigenetic inheritance whereby the regulation of a gene or chromosomal region is dependent on the sex of the transmitting parent. During gametogenesis, imprinted regions of DNA are differentially marked in accordance to the sex of the parent, resulting in parent-specific expression. While mice are the primary research model used to study genomic imprinting, imprinted regions have been described in a broad variety of organisms, including other mammals, plants, and insects. Each of these organisms employs multiple, interrelated, epigenetic mechanisms to maintain parent-specific expression. While imprinted genes and imprint control regions are often species and locus-specific, the same suites of epigenetic mechanisms are often used to achieve imprinted expression. This review examines some examples of the epigenetic mechanisms responsible for genomic imprinting in mammals, plants, and insects.

The European space suit, a design for productivity and crew safety

Science.gov (United States)

Skoog, A. Ingemar; Berthier, S.; Ollivier, Y.

In order to fulfil the two major mission objectives, i.e. support planned and unplanned external servicing of the COLUMBUS FFL and support the HERMES vehicle for safety critical operations and emergencies, the European Space Suit System baseline configuration incorporates a number of design features, which shall enhance the productivity and the crew safety of EVA astronauts. The work in EVA is today - and will be for several years - a manual work. Consequently, to improve productivity, the first challenge is to design a suit enclosure which minimizes movement restrictions and crew fatigue. It is covered by the "ergonomic" aspect of the suit design. Furthermore, it is also necessary to help the EVA crewmember in his work, by giving him the right information at the right time. Many solutions exist in this field of Man-Machine Interface, from a very simple system, based on cuff check lists, up to advanced systems, including Head-Up Displays. The design concept for improved productivity encompasses following features: • easy donning/doffing thru rear entry, • suit ergonomy optimisation, • display of operational information in alpha-numerical and graphical from, and • voice processing for operations and safety critical information. Concerning crew safety the major design features are: • a lower R-factor for emergency EVA operations thru incressed suit pressure, • zero prebreath conditions for normal operations, • visual and voice processing of all safety critical functions, and • an autonomous life support system to permit unrestricted operations around HERMES and the CFFL. The paper analyses crew safety and productivity criteria and describes how these features are being built into the design of the European Space Suit System.

33 CFR 150.518 - What are the inspection requirements for work vests and immersion suits?

Science.gov (United States)

2010-07-01

... requirements for work vests and immersion suits? 150.518 Section 150.518 Navigation and Navigable Waters COAST... vests and immersion suits? (a) All work vests and immersion suits must be inspected by the owner or... a work vest or immersion suit is inspected and is in serviceable condition, then it may remain in...

FusionCharts Beginner's Guide The Official Guide for FusionCharts Suite

CERN Document Server

Nadhani, Sanket; Bhattacharya, Shamasis

2012-01-01

The book is written as a practical, step-by-step guide to using FusionCharts Suite. The book not only teaches you the fundamentals and implementation of FusionCharts Suite, but also makes you the data visualization guru among your friends and colleagues by teaching how to select the right chart type and usability tips. Filled with examples, code samples and practical tips in a no-nonsense way, the book is a breeze to read.This book is both for beginners and advanced web developers who need to create interactive charts for their web applications. No previous knowledge of FusionCharts Suite is a

Prokofiev. "Romeo and Juliet" - Suites / Iran March

Index Scriptorium Estoniae

March, Iran

1991-01-01

Uuest heliplaadist "Prokofiev. "Romeo and Juliet" - Suites: N 1 Op. 64 bis a; N 2 Op. 64 ter b; N 3 Op. 101 c. Royal Scottish National Orchestra /Neeme Järvi" Chandos cassette ABTD 1536; CD CHAN 8940 (78 minutes) etc

A comparison of two Shuttle launch and entry suits - Reach envelope, isokinetic strength, and treadmill tests

Science.gov (United States)

Schafer, Lauren E.; Rajulu, Sudhakar L.; Klute, Glenn K.

1992-01-01

A quantification has been conducted of any existing differences between the performance, in operational conditions, of the Space Shuttle crew Launch Entry Suit (LES) and the new Advanced Crew Escape Suit (ACES). While LES is a partial-pressure suit, the ACES system which is being considered as a replacement for LES is a full-pressure suit. Three tests have been conducted with six subjects to ascertain the suits' reach envelope, strength, and treadmill performance. No significant operational differences were found between the two suit designs.

A Parametric Model of Shoulder Articulation for Virtual Assessment of Space Suit Fit

Science.gov (United States)

Kim, K. Han; Young, Karen S.; Bernal, Yaritza; Boppana, Abhishektha; Vu, Linh Q.; Benson, Elizabeth A.; Jarvis, Sarah; Rajulu, Sudhakar L.

2016-01-01

Suboptimal suit fit is a known risk factor for crewmember shoulder injury. Suit fit assessment is however prohibitively time consuming and cannot be generalized across wide variations of body shapes and poses. In this work, we have developed a new design tool based on the statistical analysis of body shape scans. This tool is aimed at predicting the skin deformation and shape variations for any body size and shoulder pose for a target population. This new process, when incorporated with CAD software, will enable virtual suit fit assessments, predictively quantifying the contact volume, and clearance between the suit and body surface at reduced time and cost.

Comparison of Ion Personal Genome Machine Platforms for the Detection of Variants in BRCA1 and BRCA2.

Science.gov (United States)

Hwang, Sang Mee; Lee, Ki Chan; Lee, Min Seob; Park, Kyoung Un

2018-01-01

Transition to next generation sequencing (NGS) for BRCA1 / BRCA2 analysis in clinical laboratories is ongoing but different platforms and/or data analysis pipelines give different results resulting in difficulties in implementation. We have evaluated the Ion Personal Genome Machine (PGM) Platforms (Ion PGM, Ion PGM Dx, Thermo Fisher Scientific) for the analysis of BRCA1 /2. The results of Ion PGM with OTG-snpcaller, a pipeline based on Torrent mapping alignment program and Genome Analysis Toolkit, from 75 clinical samples and 14 reference DNA samples were compared with Sanger sequencing for BRCA1 / BRCA2 . Ten clinical samples and 14 reference DNA samples were additionally sequenced by Ion PGM Dx with Torrent Suite. Fifty types of variants including 18 pathogenic or variants of unknown significance were identified from 75 clinical samples and known variants of the reference samples were confirmed by Sanger sequencing and/or NGS. One false-negative results were present for Ion PGM/OTG-snpcaller for an indel variant misidentified as a single nucleotide variant. However, eight discordant results were present for Ion PGM Dx/Torrent Suite with both false-positive and -negative results. A 40-bp deletion, a 4-bp deletion and a 1-bp deletion variant was not called and a false-positive deletion was identified. Four other variants were misidentified as another variant. Ion PGM/OTG-snpcaller showed acceptable performance with good concordance with Sanger sequencing. However, Ion PGM Dx/Torrent Suite showed many discrepant results not suitable for use in a clinical laboratory, requiring further optimization of the data analysis for calling variants.

Enhancements to the opera-3d suite

International Nuclear Information System (INIS)

Riley, C.P.

1997-01-01

The OPERA-3D suite of programs has been enhanced to include 2 additional 3 dimensional finite element based solvers, with complimentary features in the pre- and postprocessing. SOPRANO computes electromagnetic fields at high frequency including displacement current effects. It has 2 modules emdash a deterministic solution at a user defined frequency and an eigenvalue solution for modal analysis. It is suitable for designing microwave structures and cavities found in particle accelerators. SCALA computes electrostatic fields in the presence of space charge from charged particle beams. The user may define the emission characteristics of electrodes or plasma surfaces and compute the resultant space charge limited beams, including the presence of magnetic fields. Typical applications in particle accelerators are electron guns and ion sources. Other enhancements to the suite include additional capabilities in TOSCA and ELEKTRA, the static and dynamic solvers. copyright 1997 American Institute of Physics

The Sample Analysis at Mars Investigation and Instrument Suite

Science.gov (United States)

Mahaffy, Paul; Webster, Christopher R.; Conrad, Pamela G.; Arvey, Robert; Bleacher, Lora; Brinckerhoff, William B.; Eigenbrode, Jennifer L.; Chalmers, Robert A.; Dworkin, Jason P.; Errigo, Therese;

Z-2 Space Suit: A Case Study in Human Spaceflight Public Outreach

Science.gov (United States)

McFarland, Shane M.

2016-01-01

NASA Johnson Space Center's Z-series of planetary space suit prototypes is an iterative development platform with a Mars-forward design philosophy, targeting a Mars surface mission in the mid-2030s. The first space suit assembly, called the Z-1, was delivered in 2012. While meeting the project's stated requirements and objectives, the general public's reception primarily focused on the color scheme, which vaguely invoked similarity to a certain animated cartoon character. The public at large has and continues to be exposed to varying space suit design aesthetics from popular culture and low TRL technology maturation efforts such as mechanical counterpressure. The lesson learned was that while the design aesthetic is not important from an engineering perspective, the perception of the public is important for NASA and human spaceflight in general. For the Z-2 space suit, an integrated public outreach strategy was employed to engage, excite and educate the public on the current technology of space suits and NASA's plans moving forward. The keystone of this strategy was a public vote on three different suit cover layer aesthetics, the winner of which would be used as inspiration in fabrication. Other components included social media, university collaboration, and select media appearances, the cumulative result of which, while intangible in its benefit, was ultimately a positive effect in terms of the image of NASA as well as the dissemination of information vital to dispelling public misconceptions.

The use of antigravity suits in the treatment of idiopathic orthostatic hypotension

Science.gov (United States)

Landmark, K.; Kravik, S.

1980-01-01

Idiopathic orthostatic hypotension is an uncommon disease characterized by a drop in blood pressure when going from a recumbent to a standing position. Treatment by medication generally produces poor results. Three patients at the Royal Hospital in Oslo were treated with antigravity suits and all were able to maintain adequate blood pressures in the standing position. One patient improved dramatically and was able to take short walks while wearing the suit. The two other patients, however, felt that wearing the suits eventually became uncomfortable. This treatment represents a useful treatment alternative for intractable cases.

Controlatron Neutron Tube Test Suite Software Manual - Operation Manual (V2.2)

CERN Document Server

Noel, W P; Hertrich, R J; Martinez, M L; Wallace, D L

2002-01-01

The Controlatron Software Suite is a custom built application to perform automated testing of Controlatron neutron tubes. The software package was designed to allowing users to design tests and to run a series of test suites on a tube. The data is output to ASCII files of a pre-defined format for data analysis and viewing with the Controlatron Data Viewer Application. This manual discusses the operation of the Controlatron Test Suite Software and a brief discussion of state machine theory, as state machine is the functional basis of the software.

Equation-of-State Test Suite for the DYNA3D Code

Energy Technology Data Exchange (ETDEWEB)

Benjamin, Russell D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2015-11-05

This document describes the creation and implementation of a test suite for the Equationof- State models in the DYNA3D code. A customized input deck has been created for each model, as well as a script that extracts the relevant data from the high-speed edit file created by DYNA3D. Each equation-of-state model is broken apart and individual elements of the model are tested, as well as testing the entire model. The input deck for each model is described and the results of the tests are discussed. The intent of this work is to add this test suite to the validation suite presently used for DYNA3D.

Complete mitochondrial DNA sequences of the Victoria tilapia (Oreochromis variabilis) and Redbelly Tilapia (Tilapia zilli): genome characterization and phylogeny analysis.

Science.gov (United States)

Kinaro, Zachary Omambia; Xue, Liangyi; Volatiana, Josies Ancella

2016-07-01

The Cichlid fishes have played an important role in evolutionary biology, population studies and aquaculture industry with East African species representing a model suited for studying adaptive radiation and speciation for cichlid genome projects in which closely related genomes are fast emerging presenting questions on phenotype-genotype relations. The complete mitochondrial genomes presented here are for two closely related but eco-morphologically distinct Lake Victoria basin cichlids, Oreochromis variabilis, an endangered native species and Tilapia zilli, an invasive species, both of which are important economic fishes in local areas. The complete mitochondrial genomes determined for O. variabilis and T. zilli are 16 626 and 16,619 bp, respectively. Both the mitogenomes contain 13 protein-coding genes, 22 tRNAs, 2 rRNAs and a non-coding control region, which are typical of vertebrate mitogenomes. Phylogenetic analyses of the two species revealed that though both lie within family Cichlidae, they are remotely related.

A transitional alkalic dolerite dike suite of Mesozoic age in Southeastern New England

Science.gov (United States)

Hermes, O. Don; Rao, J. M.; Dickenson, M. P.; Pierce, T. A.

1984-12-01

Dike rocks from the New England platform of Rhode Island and adjacent Massachusetts consist of premetamorphic and post-metamorphic suites. The older group includes metamorphosed dolerite, minette, and schistose dioritic rocks. Post-metamorphic dikes consist of dolerite and sparse monchiquite. The post-metamorphic dolerites are of comparable age to the Eastern North American dolerite suite associated with the Mesozoic basins along the eastern seaboard of North America. However, the southeastern New England dolerites exhibit mineralogy and chemistry more typical of a transitional alkalic suite compared to the more subalkalic tholeiitic dolerites of the Eastern North American suite. Both suites are compatible with a rift tectonic setting, but the more alkalic dolerites may represent a deeper source of small volume melts compared to the Eastern North American dolerites. These more alkaline melts may have concentrated at local centers, or they may be typical of flank dolerites as opposed to the less alkalic varieties that occur within the central axial rift.

Non-Venting Thermal and Humidity Control for EVA Suits

Science.gov (United States)

Izenson, Mike; Chen, Weibo; Bue, Grant

2011-01-01

Future EVA suits need processes and systems to control internal temperature and humidity without venting water to the environment. This paper describes an absorption-based cooling and dehumidification system as well as laboratory demonstrations of the key processes. There are two main components in the system: an evaporation cooling and dehumidification garment (ECDG) that removes both sensible heat and latent heat from the pressure garment, and an absorber radiator that absorbs moisture and rejects heat to space by thermal radiation. This paper discusses the overall design of both components, and presents recent data demonstrating their operation. We developed a design and fabrication approach to produce prototypical heat/water absorbing elements for the ECDG, and demonstrated by test that these elements could absorb heat and moisture at a high flux. Proof-of-concept tests showed that an ECDG prototype absorbs heat and moisture at a rate of 85 W/ft under conditions that simulate operation in an EVA suit. The heat absorption was primarily due to direct absorption of water vapor. It is possible to construct large, flexible, durable cooling patches that can be incorporated into a cooling garment with this system. The proof-of-concept test data was scaled to calculate area needed for full metabolic loads, thus showing that it is feasible to use this technology in an EVA suit. Full-scale, lightweight absorber/radiator modules have also been built and tested. They can reject heat at a flux of 33 W/ft while maintaining ECDG operation at conditions that will provide a cool and dry environment inside the EVA suit.

Compression under a mechanical counter pressure space suit glove

Science.gov (United States)

Waldie, James M A.; Tanaka, Kunihiko; Tourbier, Dietmar; Webb, Paul; Jarvis, Christine W.; Hargens, Alan R.

2002-01-01

Background: Current gas-pressurized space suits are bulky stiff shells severely limiting astronaut function and capability. A mechanical counter pressure (MCP) space suit in the form of a tight elastic garment could dramatically improve extravehicular activity (EVA) dexterity, but also be advantageous in safety, cost, mass and volume. The purpose of this study was to verify that a prototype MCP glove exerts the design compression of 200 mmHg, a pressure similar to the current NASA EVA suit. Methods: Seven male subjects donned a pressure measurement array and MCP glove on the right hand, which was placed into a partial vacuum chamber. Average compression was recorded on the palm, the bottom of the middle finger, the top of the middle finger and the dorsum of the hand at pressures of 760 (ambient), 660 and 580 mmHg. The vacuum chamber was used to simulate the pressure difference between the low breathing pressure of the current NASA space suits (approximately 200 mmHg) and an unprotected hand in space. Results: At ambient conditions, the MCP glove compressed the dorsum of the hand at 203.5 +/- 22.7 mmHg, the bottom of the middle finger at 179.4 +/- 16.0 mmHg, and the top of the middle finger at 183.8 +/- 22.6 mmHg. The palm compression was significantly lower (59.6 +/- 18.8 mmHg, pglove compression with the chamber pressure reductions. Conclusions: The MCP glove compressed the dorsum of the hand and middle finger at the design pressure.

A Suite of Tools for Technology Assessment

Science.gov (United States)

2007-09-01

Saden, Povinelli & Rosen, 1989). • This was a significant change in emphasis on the part of NASA, where technology had previously viewed as merely...Cost Analysis Symposium, April 13, 2005. A Suite of Tools for Technology Assessment 24 Bibliography - continued: • Sadin, Stanley T.; Povinelli

Evaluating Phylogenetic Congruence in the Post-Genomic Era

Science.gov (United States)

Leigh, Jessica W.; Lapointe, François-Joseph; Lopez, Philippe; Bapteste, Eric

2011-01-01

Congruence is a broadly applied notion in evolutionary biology used to justify multigene phylogeny or phylogenomics, as well as in studies of coevolution, lateral gene transfer, and as evidence for common descent. Existing methods for identifying incongruence or heterogeneity using character data were designed for data sets that are both small and expected to be rarely incongruent. At the same time, methods that assess incongruence using comparison of trees test a null hypothesis of uncorrelated tree structures, which may be inappropriate for phylogenomic studies. As such, they are ill-suited for the growing number of available genome sequences, most of which are from prokaryotes and viruses, either for phylogenomic analysis or for studies of the evolutionary forces and events that have shaped these genomes. Specifically, many existing methods scale poorly with large numbers of genes, cannot accommodate high levels of incongruence, and do not adequately model patterns of missing taxa for different markers. We propose the development of novel incongruence assessment methods suitable for the analysis of the molecular evolution of the vast majority of life and support the investigation of homogeneity of evolutionary process in cases where markers do not share identical tree structures. PMID:21712432

Mission Specialist Scott Parazynski checks his flight suit

Science.gov (United States)

1998-01-01

STS-95 Mission Specialist Scott E. Parazynski gets help with his flight suit in the Operations and Checkout Building from a suit technician George Brittingham. The final fitting takes place prior to the crew walkout and transport to Launch Pad 39B. Targeted for launch at 2 p.m. EST on Oct. 29, the mission is expected to last 8 days, 21 hours and 49 minutes, and return to KSC at 11:49 a.m. EST on Nov. 7. The STS-95 mission includes research payloads such as the Spartan solar-observing deployable spacecraft, the Hubble Space Telescope Orbital Systems Test Platform, the International Extreme Ultraviolet Hitchhiker, as well as the SPACEHAB single module with experiments on space flight and the aging process.

STS-87 Mission Specialist Winston E. Scott suits up

Science.gov (United States)

1997-01-01

STS-87 Mission Specialist Winston Scott dons his launch and entry suit with the assistance of a suit technician in the Operations and Checkout Building. This is Scotts second space flight. He and the five other crew members will depart shortly for Launch Pad 39B, where the Space Shuttle Columbia awaits liftoff on a 16-day mission to perform microgravity and solar research. Scott is scheduled to perform an extravehicular activity spacewalk with Mission Specialist Takao Doi, Ph.D., of the National Space Development Agency of Japan, during STS-87. He also performed a spacewalk on STS-72.

Genomic analysis of Xenopus organizer function

Directory of Open Access Journals (Sweden)

Suhai Sándor

2006-06-01

Full Text Available Abstract Background Studies of the Xenopus organizer have laid the foundation for our understanding of the conserved signaling pathways that pattern vertebrate embryos during gastrulation. The two primary activities of the organizer, BMP and Wnt inhibition, can regulate a spectrum of genes that pattern essentially all aspects of the embryo during gastrulation. As our knowledge of organizer signaling grows, it is imperative that we begin knitting together our gene-level knowledge into genome-level signaling models. The goal of this paper was to identify complete lists of genes regulated by different aspects of organizer signaling, thereby providing a deeper understanding of the genomic mechanisms that underlie these complex and fundamental signaling events. Results To this end, we ectopically overexpress Noggin and Dkk-1, inhibitors of the BMP and Wnt pathways, respectively, within ventral tissues. After isolating embryonic ventral halves at early and late gastrulation, we analyze the transcriptional response to these molecules within the generated ectopic organizers using oligonucleotide microarrays. An efficient statistical analysis scheme, combined with a new Gene Ontology biological process annotation of the Xenopus genome, allows reliable and faithful clustering of molecules based upon their roles during gastrulation. From this data, we identify new organizer-related expression patterns for 19 genes. Moreover, our data sub-divides organizer genes into separate head and trunk organizing groups, which each show distinct responses to Noggin and Dkk-1 activity during gastrulation. Conclusion Our data provides a genomic view of the cohorts of genes that respond to Noggin and Dkk-1 activity, allowing us to separate the role of each in organizer function. These patterns demonstrate a model where BMP inhibition plays a largely inductive role during early developmental stages, thereby initiating the suites of genes needed to pattern dorsal tissues

Virtual Suit Fit Assessment Using Body Shape Model

Data.gov (United States)

National Aeronautics and Space Administration — Shoulder injury is one of the most serious risks for crewmembers in long-duration spaceflight. While suboptimal suit fit and contact pressures between the shoulder...

What was uniform about the fin-de-siècle sailor suit?

Science.gov (United States)

Rose, Clare

2011-01-01

The sailor suits widely worn by children in late-nineteenth-century Britain have been interpreted at the time, and since, as expressions of an Imperial ethos. Yet, a closer examination of the ways that these garments were produced by mass manufacturers, mediated by advertisers and fashion advisors and consumed by families makes us question this characterization. Manufacturers interpreted sailor suits not as unchanging uniforms but as fashion items responding to seasonal changes. Consumers used them to assert social identities and social distinctions, selecting from the multiple variants available. Cultural commentators described sailor suits as emulating Royal practice—but also as ‘common’ and to be avoided. A close analysis of large samples of images and texts from the period 1870–1900 reveals how these different meanings overlapped, making the fin-de-siècle sailor suit a garment that undermines many of our assumptions.

A method of evaluating efficiency during space-suited work in a neutral buoyancy environment

Science.gov (United States)

Greenisen, Michael C.; West, Phillip; Newton, Frederick K.; Gilbert, John H.; Squires, William G.

1991-01-01

The purpose was to investigate efficiency as related to the work transmission and the metabolic cost of various extravehicular activity (EVA) tasks during simulated microgravity (whole body water immersion) using three space suits. Two new prototype space station suits, AX-5 and MKIII, are pressurized at 57.2 kPa and were tested concurrently with the operationally used 29.6 kPa shuttle suit. Four male astronauts were asked to perform a fatigue trial on four upper extremity exercises during which metabolic rate and work output were measured and efficiency was calculated in each suit. The activities were selected to simulate actual EVA tasks. The test article was an underwater dynamometry system to which the astronauts were secured by foot restraints. All metabolic data was acquired, calculated, and stored using a computerized indirect calorimetry system connected to the suit ventilation/gas supply control console. During the efficiency testing, steady state metabolic rate could be evaluated as well as work transmitted to the dynamometer. Mechanical efficiency could then be calculated for each astronaut in each suit performing each movement.

Specifications and test procedures for airline-type supplied-air suits

International Nuclear Information System (INIS)

Revoir, W.H.; Pritchard, J.A.; Davis, T.O.; Richards, C.P.; Wheat, L.D.

1975-05-01

Procedures and requirements have been established to permit airline-type supplied-air suits needed by contractors of the Energy Research and Development Administration to be tested for performance by the Respirator Research and Development Section, Industrial Hygiene Group, of the Los Alamos Scientific Laboratory, and to have the adequacy of the performance of these devices evaluated by the Los Alamos Scientific Laboratory Respirator Advisory Committee. Test equipment, test methods, and performance criteria for airline-type supplied-air suits are prescribed. (U.S.)

Fluid replacement advice during work in fully encapsulated impermeable chemical protective suits

NARCIS (Netherlands)

Rubenstein, C.D.; Hartog, E.A. den; Deaton, A.S.; Bogerd, C.P.; Kant, S. de

2017-01-01

A major concern for responders to hazardous materials (HazMat) incidents is the heat strain that is caused by fully encapsulated impermeable chemical protective suits. In a research project, funded by the US Department of Defense, the thermal strain experienced when wearing these suits was studied.

Optimizing the physical ergonomics indices for the use of partial pressure suits.

Science.gov (United States)

Ding, Li; Li, Xianxue; Hedge, Alan; Hu, Huimin; Feathers, David; Qin, Zhifeng; Xiao, Huajun; Xue, Lihao; Zhou, Qianxiang

2015-03-01

This study developed an ergonomic evaluation system for the design of high-altitude partial pressure suits (PPSs). A total of twenty-one Chinese males participated in the experiment which tested three types of ergonomics indices (manipulative mission, operational reach and operational strength) were studied using a three-dimensional video-based motion capture system, a target-pointing board, a hand dynamometer, and a step-tread apparatus. In total, 36 ergonomics indices were evaluated and optimized using regression and fitting analysis. Some indices that were found to be linearly related and redundant were removed from the study. An optimal ergonomics index system was established that can be used to conveniently and quickly evaluate the performance of different pressurized/non-pressurized suit designs. The resulting ergonomics index system will provide a theoretical basis and practical guidance for mission planners, suit designers and engineers to design equipment for human use, and to aid in assessing partial pressure suits. Copyright © 2014 Elsevier Ltd and The Ergonomics Society. All rights reserved.

Effect of fastskin suits on performance, drag, and energy cost of swimming.

Science.gov (United States)

Chatard, Jean-Claude; Wilson, Barry

2008-06-01

To investigate the effect of fastskin suits on 25- to 800-m performances, drag, and energy cost of swimming. The performances, stroke rate and distance per stroke, were measured for 14 competitive swimmers in a 25-m pool, when wearing a normal suit (N) and when wearing a full-body suit (FB) or a waist-to-ankle suit (L). Passive drag, oxygen uptake, blood lactate, and the perceived exertion were measured in a flume. There was a 3.2% +/- 2.4% performance benefit for all subjects over the six distances covered at maximal speed wearing FB and L when compared with N. When wearing L, the gain was significantly lower (1.8% +/- 2.5%, P energy cost of swimming was significantly reduced when wearing FB and L by 4.5% +/- 5.4% and 5.5% +/- 3.1%, respectively (P energy cost of submaximal swimming and an increased distance per stroke, at the same stroke rates, and reduced freestyle performance time.

Carbon Dioxide Washout Testing Using Various Inlet Vent Configurations in the Mark-III Space Suit

Science.gov (United States)

Korona, F. Adam; Norcross, Jason; Conger, Bruce; Navarro, Moses

2014-01-01

Requirements for using a space suit during ground testing include providing adequate carbon dioxide (CO2) washout for the suited subject. Acute CO2 exposure can lead to symptoms including headache, dyspnea, lethargy, and eventually unconsciousness or even death. Symptoms depend on several factors including inspired partial pressure of CO2 (ppCO2), duration of exposure, metabolic rate of the subject, and physiological differences between subjects. Computational Fluid Dynamics (CFD) analysis has predicted that the configuration of the suit inlet vent has a significant effect on oronasal CO2 concentrations. The main objective of this test was to characterize inspired oronasal ppCO2 for a variety of inlet vent configurations in the Mark-III suit across a range of workload and flow rates. Data and trends observed during testing along with refined CFD models will be used to help design an inlet vent configuration for the Z-2 space suit. The testing methodology used in this test builds upon past CO2 washout testing performed on the Z-1 suit, Rear Entry I-Suit, and the Enhanced Mobility Advanced Crew Escape Suit. Three subjects performed two test sessions each in the Mark-III suit to allow for comparison between tests. Six different helmet inlet vent configurations were evaluated during each test session. Suit pressure was maintained at 4.3 psid. Suited test subjects walked on a treadmill to generate metabolic workloads of approximately 2000 and 3000 BTU/hr. Supply airflow rates of 6 and 4 actual cubic feet per minute were tested at each workload. Subjects wore an oronasal mask with an open port in front of the mouth and were allowed to breathe freely. Oronasal ppCO2 was monitored real-time via gas analyzers with sampling tubes connected to the oronasal mask. Metabolic rate was calculated from the CO2 production measured by an additional gas analyzer at the air outlet from the suit. Real-time metabolic rate measurements were used to adjust the treadmill workload to meet

Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri

Energy Technology Data Exchange (ETDEWEB)

Prochnik, Simon E.; Umen, James; Nedelcu, Aurora; Hallmann, Armin; Miller, Stephen M.; Nishii, Ichiro; Ferris, Patrick; Kuo, Alan; Mitros, Therese; Fritz-Laylin, Lillian K.; Hellsten, Uffe; Chapman, Jarrod; Simakov, Oleg; Rensing, Stefan A.; Terry, Astrid; Pangilinan, Jasmyn; Kapitonov, Vladimir; Jurka, Jerzy; Salamov, Asaf; Shapiro, Harris; Schmutz, Jeremy; Grimwood, Jane; Lindquist, Erika; Lucas, Susan; Grigoriev, Igor V.; Schmitt, Rudiger; Kirk, David; Rokhsar, Daniel S.

2010-07-01

Analysis of the Volvox carteri genome reveals that this green alga's increased organismal complexity and multicellularity are associated with modifications in protein families shared with its unicellular ancestor, and not with large-scale innovations in protein coding capacity. The multicellular green alga Volvox carteri and its morphologically diverse close relatives (the volvocine algae) are uniquely suited for investigating the evolution of multicellularity and development. We sequenced the 138 Mb genome of V. carteri and compared its {approx}14,500 predicted proteins to those of its unicellular relative, Chlamydomonas reinhardtii. Despite fundamental differences in organismal complexity and life history, the two species have similar protein-coding potentials, and few species-specific protein-coding gene predictions. Interestingly, volvocine algal-specific proteins are enriched in Volvox, including those associated with an expanded and highly compartmentalized extracellular matrix. Our analysis shows that increases in organismal complexity can be associated with modifications of lineage-specific proteins rather than large-scale invention of protein-coding capacity.

Radiation Protection Studies of International Space Station Extravehicular Activity Space Suits

Science.gov (United States)

Cucinotta, Francis A. (Editor); Shavers, Mark R. (Editor); Saganti, Premkumar B. (Editor); Miller, Jack (Editor)

2003-01-01

This publication describes recent investigations that evaluate radiation shielding characteristics of NASA's and the Russian Space Agency's space suits. The introduction describes the suits and presents goals of several experiments performed with them. The first chapter provides background information about the dynamic radiation environment experienced at ISS and summarized radiation health and protection requirements for activities in low Earth orbit. Supporting studies report the development and application of a computer model of the EMU space suit and the difficulty of shielding EVA crewmembers from high-energy reentrant electrons, a previously unevaluated component of the space radiation environment. Chapters 2 through 6 describe experiments that evaluate the space suits' radiation shielding characteristics. Chapter 7 describes a study of the potential radiological health impact on EVA crewmembers of two virtually unexamined environmental sources of high-energy electrons-reentrant trapped electrons and atmospheric albedo or "splash" electrons. The radiological consequences of those sources have not been evaluated previously and, under closer scrutiny. A detailed computational model of the shielding distribution provided by components of the NASA astronauts' EMU is being developed for exposure evaluation studies. The model is introduced in Chapters 8 and 9 and used in Chapter 10 to investigate how trapped particle anisotropy impacts female organ doses during EVA. Chapter 11 presents a review of issues related to estimating skin cancer risk form space radiation. The final chapter contains conclusions about the protective qualities of the suit brought to light form these studies, as well as recommendations for future operational radiation protection.

U.S. Climate Normals Product Suite (1981-2010)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The NOAA Climate Normals are a large suite of data products that provide users with many tools to understand typical climate conditions for thousands of locations...

GABenchToB: a genome assembly benchmark tuned on bacteria and benchtop sequencers.

Directory of Open Access Journals (Sweden)

Sebastian Jünemann

Full Text Available De novo genome assembly is the process of reconstructing a complete genomic sequence from countless small sequencing reads. Due to the complexity of this task, numerous genome assemblers have been developed to cope with different requirements and the different kinds of data provided by sequencers within the fast evolving field of next-generation sequencing technologies. In particular, the recently introduced generation of benchtop sequencers, like Illumina's MiSeq and Ion Torrent's Personal Genome Machine (PGM, popularized the easy, fast, and cheap sequencing of bacterial organisms to a broad range of academic and clinical institutions. With a strong pragmatic focus, here, we give a novel insight into the line of assembly evaluation surveys as we benchmark popular de novo genome assemblers based on bacterial data generated by benchtop sequencers. Therefore, single-library assemblies were generated, assembled, and compared to each other by metrics describing assembly contiguity and accuracy, and also by practice-oriented criteria as for instance computing time. In addition, we extensively analyzed the effect of the depth of coverage on the genome assemblies within reasonable ranges and the k-mer optimization problem of de Bruijn Graph assemblers. Our results show that, although both MiSeq and PGM allow for good genome assemblies, they require different approaches. They not only pair with different assembler types, but also affect assemblies differently regarding the depth of coverage where oversampling can become problematic. Assemblies vary greatly with respect to contiguity and accuracy but also by the requirement on the computing power. Consequently, no assembler can be rated best for all preconditions. Instead, the given kind of data, the demands on assembly quality, and the available computing infrastructure determines which assembler suits best. The data sets, scripts and all additional information needed to replicate our results are freely

Ensembl Genomes 2016: more genomes, more complexity.

Science.gov (United States)

Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

2016-01-04

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Development of an online men’s suits customizing system using heuristic procedure for wheelchair users

NARCIS (Netherlands)

Jeong, Minseok; Yang, Chuneun; You, Heecheon; Park, Kwangae; Lee, W.

2016-01-01

An online suit-customizing system for the special accessibility needs of wheelchair users should be developed because the demand for business suits by wheelchair users involved in economic activities has increased. This study
develops a user interface an online customizing system for men's suits

Ventilation Transport Trade Study for Future Space Suit Life Support Systems

Science.gov (United States)

Kempf, Robert; Vogel, Matthew; Paul, Heather L.

2008-01-01

A new and advanced portable life support system (PLSS) for space suit surface exploration will require a durable, compact, and energy efficient system to transport the ventilation stream through the space suit. Current space suits used by NASA circulate the ventilation stream via a ball-bearing supported centrifugal fan. As NASA enters the design phase for the next generation PLSS, it is necessary to evaluate available technologies to determine what improvements can be made in mass, volume, power, and reliability for a ventilation transport system. Several air movement devices already designed for commercial, military, and space applications are optimized in these areas and could be adapted for EVA use. This paper summarizes the efforts to identify and compare the latest fan and bearing technologies to determine candidates for the next generation PLSS.

High Performance Electrical Modeling and Simulation Verification Test Suite - Tier I; TOPICAL

International Nuclear Information System (INIS)

SCHELLS, REGINA L.; BOGDAN, CAROLYN W.; WIX, STEVEN D.

2001-01-01

This document describes the High Performance Electrical Modeling and Simulation (HPEMS) Global Verification Test Suite (VERTS). The VERTS is a regression test suite used for verification of the electrical circuit simulation codes currently being developed by the HPEMS code development team. This document contains descriptions of the Tier I test cases

Telemetry Standards, IRIG Standard 106-17, Chapter 22, Network Based Protocol Suite

Science.gov (United States)

2017-07-01

requirements. 22.2 Network Access Layer 22.2.1 Physical Layer Connectors and cable media should meet the electrical or optical properties required by the...Telemetry Standards, IRIG Standard 106-17 Chapter 22, July 2017 i CHAPTER 22 Network -Based Protocol Suite Acronyms...iii Chapter 22. Network -Based Protocol Suite

phiGENOME: an integrative navigation throughout bacteriophage genomes.

Science.gov (United States)

Stano, Matej; Klucar, Lubos

2011-11-01

phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of phage genomes stored in the phiSITE, database of gene regulation in bacteriophages. phiGENOME is an integral part of the phiSITE web portal (http://www.phisite.org/phigenome) and it was optimised for visualisation of phage genomes with the emphasis on the gene regulatory elements. phiGENOME consists of three components: (i) genome map viewer built using Adobe Flash technology, providing dynamic and interactive graphical display of phage genomes; (ii) sequence browser based on precisely formatted HTML tags, providing detailed exploration of genome features on the sequence level and (iii) regulation illustrator, based on Scalable Vector Graphics (SVG) and designed for graphical representation of gene regulations. Bringing 542 complete genome sequences accompanied with their rich annotations and references, makes phiGENOME a unique information resource in the field of phage genomics. Copyright © 2011 Elsevier Inc. All rights reserved.

Exploration Space Suit Architecture and Destination Environmental-Based Technology Development

Science.gov (United States)

Hill, Terry R.; McFarland, Shane M.; Korona, F. Adam

2013-01-01

This paper continues forward where EVA Space Suit Architecture: Low Earth Orbit Vs. Moon Vs. Mars left off in the development of a space suit architecture that is modular in design and could be reconfigured prior to launch or during any given mission depending on the tasks or destination. This space suit system architecture and technologies required based on human exploration (EVA) destinations will be discussed, and how these systems should evolve to meet the future exploration EVA needs of the US human space flight program. A series of exercises and analyses provided a strong indication that the Constellation Program space suit architecture, with its maximum reuse of technology and functionality across a range of mission profiles and destinations, is postured to provide a viable solution for future space exploration missions. The destination environmental analysis demonstrates that the modular architecture approach could provide the lowest mass and mission cost for the protection of the crew, given any human mission outside of low-Earth orbit. Additionally, some of the high-level trades presented here provide a review of the environmental and nonenvironmental design drivers that will become increasingly important as humans venture farther from Earth. The presentation of destination environmental data demonstrates a logical clustering of destination design environments that allows a focused approach to technology prioritization, development, and design that will maximize the return on investment, largely independent of any particular design reference mission.

Consortium biology in immunology: the perspective from the Immunological Genome Project.

Science.gov (United States)

Benoist, Christophe; Lanier, Lewis; Merad, Miriam; Mathis, Diane

2012-10-01

Although the field has a long collaborative tradition, immunology has made less use than genetics of 'consortium biology', wherein groups of investigators together tackle large integrated questions or problems. However, immunology is naturally suited to large-scale integrative and systems-level approaches, owing to the multicellular and adaptive nature of the cells it encompasses. Here, we discuss the value and drawbacks of this organization of research, in the context of the long-running 'big science' debate, and consider the opportunities that may exist for the immunology community. We position this analysis in light of our own experience, both positive and negative, as participants of the Immunological Genome Project.

Genome Maps, a new generation genome browser.

Science.gov (United States)

Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

2013-07-01

Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

Adobe Creative Suite 6 Design and Web Premium all-in-one for dummies

CERN Document Server

Smith, Jennifer; Gerantabee, Fred

2012-01-01

The must-have book on the leading suite of software for graphic and web designers Fully revised and updated this hands-on resource offers a one-stop learning opportunity through eight mini-book dedicated to each product inside Adobe's Design & Web Premium Suite. The mini-books include Adobe Creative Suite Basics, InDesign, Illustrator, Photoshop, Acrobat, Dreamweaver, Flash, Fireworks. The book may contain new image enhancements to After Effects, 64-bit versions of Illustrator and Flash Professional, and a new tool, dubbed Helium, that will enable designers to create content using HTML5 and

Experimental Evaluation of Energy Efficiency for a Soft Wearable Robotic Suit.

Science.gov (United States)

Jin, Shanhai; Iwamoto, Noriyasu; Hashimoto, Kazunobu; Yamamoto, Motoji

2016-10-12

This paper presents a new soft wearable robotic suit for energy-efficient walking in daily activities for elderly persons. The presented robotic suit provides a small yet effective assistive force for hip flexion through winding belts that include elastic elements. In addition, it does not restrict the range of movement in the lower limbs. Moreover, its structure is simple and lightweight, and thus wearers can easily take the device on and off by themselves. Experimental results on nine elderly subjects (age = 74.23.7 years) show that the robotic suit worn and powered on (PON) significantly reduced energy expenditure by an average of 5.9 % compared with the condition of worn but powered off (POFF). Furthermore, compared with the POFF condition, there was a significant improvement in gait characteristics in the PON condition for all subjects.

Asteroid Redirect Crewed Mission Space Suit and EVA System Architecture Trade Study

Science.gov (United States)

Bowie, Jonathan; Buffington, Jesse; Hood, Drew; Kelly, Cody; Naids, Adam; Watson, Richard; Blanco, Raul; Sipila, Stephanie

2014-01-01

The Asteroid Redirect Crewed Mission (ARCM) requires a Launch/Entry/Abort (LEA) suit capability and short duration Extra Vehicular Activity (EVA) capability from the Orion spacecraft. For this mission, the pressure garment selected for both functions is the Modified Advanced Crew Escape Suit (MACES) with EVA enhancements and the life support option that was selected is the Exploration Portable Life Support System (PLSS) currently under development for Advanced Exploration Systems (AES). The proposed architecture meets the ARCM constraints, but much more work is required to determine the details of the suit upgrades, the integration with the PLSS, and the tools and equipment necessary to accomplish the mission. This work has continued over the last year to better define the operations and hardware maturation of these systems. EVA simulations were completed in the Neutral Buoyancy Lab (NBL) and interfacing options were prototyped and analyzed with testing planned for late 2014. This paper discusses the work done over the last year on the MACES enhancements, the use of tools while using the suit, and the integration of the PLSS with the MACES.

Robust Demographic Inference from Genomic and SNP Data

Science.gov (United States)

Excoffier, Laurent; Dupanloup, Isabelle; Huerta-Sánchez, Emilia; Sousa, Vitor C.; Foll, Matthieu

2013-01-01

We introduce a flexible and robust simulation-based framework to infer demographic parameters from the site frequency spectrum (SFS) computed on large genomic datasets. We show that our composite-likelihood approach allows one to study evolutionary models of arbitrary complexity, which cannot be tackled by other current likelihood-based methods. For simple scenarios, our approach compares favorably in terms of accuracy and speed with , the current reference in the field, while showing better convergence properties for complex models. We first apply our methodology to non-coding genomic SNP data from four human populations. To infer their demographic history, we compare neutral evolutionary models of increasing complexity, including unsampled populations. We further show the versatility of our framework by extending it to the inference of demographic parameters from SNP chips with known ascertainment, such as that recently released by Affymetrix to study human origins. Whereas previous ways of handling ascertained SNPs were either restricted to a single population or only allowed the inference of divergence time between a pair of populations, our framework can correctly infer parameters of more complex models including the divergence of several populations, bottlenecks and migration. We apply this approach to the reconstruction of African demography using two distinct ascertained human SNP panels studied under two evolutionary models. The two SNP panels lead to globally very similar estimates and confidence intervals, and suggest an ancient divergence (>110 Ky) between Yoruba and San populations. Our methodology appears well suited to the study of complex scenarios from large genomic data sets. PMID:24204310

Leveraging Active Knit Technologies for Aerospace Pressure Suit Applications

Data.gov (United States)

National Aeronautics and Space Administration — Anti-Gravity Suits (AGS) are garments used in astronautics to prevent crew from experiencing orthostatic intolerance (OI) and consequential blackouts while...

Safety Tips: Avoiding Negligence Suits in Chemistry Teaching.

Science.gov (United States)

Gerlovich, Jack A.

1983-01-01

Discusses various aspects related to negligence on the part of chemistry teachers. Areas addressed include negligence in tort law, avoiding negligence suits, proper instructions, proper supervision, equipment maintenance, and other considerations such as sovereign immunity, and contributory versus comparative negligence. (JN)

The genome and structural proteome of an ocean siphovirus: a new window into the cyanobacterial 'mobilome'.

Science.gov (United States)

Sullivan, Matthew B; Krastins, Bryan; Hughes, Jennifer L; Kelly, Libusha; Chase, Michael; Sarracino, David; Chisholm, Sallie W

2009-11-01

Prochlorococcus, an abundant phototroph in the oceans, are infected by members of three families of viruses: myo-, podo- and siphoviruses. Genomes of myo- and podoviruses isolated on Prochlorococcus contain DNA replication machinery and virion structural genes homologous to those from coliphages T4 and T7 respectively. They also contain a suite of genes of cyanobacterial origin, most notably photosynthesis genes, which are expressed during infection and appear integral to the evolutionary trajectory of both host and phage. Here we present the first genome of a cyanobacterial siphovirus, P-SS2, which was isolated from Atlantic slope waters using a Prochlorococcus host (MIT9313). The P-SS2 genome is larger than, and considerably divergent from, previously sequenced siphoviruses. It appears most closely related to lambdoid siphoviruses, with which it shares 13 functional homologues. The approximately 108 kb P-SS2 genome encodes 131 predicted proteins and notably lacks photosynthesis genes which have consistently been found in other marine cyanophage, but does contain 14 other cyanobacterial homologues. While only six structural proteins were identified from the genome sequence, 35 proteins were detected experimentally; these mapped onto capsid and tail structural modules in the genome. P-SS2 is potentially capable of integration into its host as inferred from bioinformatically identified genetic machinery int, bet, exo and a 53 bp attachment site. The host attachment site appears to be a genomic island that is tied to insertion sequence (IS) activity that could facilitate mobility of a gene involved in the nitrogen-stress response. The homologous region and a secondary IS-element hot-spot in Synechococcus RS9917 are further evidence of IS-mediated genome evolution coincident with a probable relic prophage integration event. This siphovirus genome provides a glimpse into the biology of a deep-photic zone phage as well as the ocean cyanobacterial prophage and IS element

Advanced Gas Sensing Technology for Space Suits, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — Advanced space suits require lightweight, low-power, durable sensors for monitoring critical life support materials. No current compact sensors have the tolerance...

Genomics using the Assembly of the Mink Genome

DEFF Research Database (Denmark)

Guldbrandtsen, Bernt; Cai, Zexi; Sahana, Goutam

2018-01-01

The American Mink’s (Neovison vison) genome has recently been sequenced. This opens numerous avenues of research both for studying the basic genetics and physiology of the mink as well as genetic improvement in mink. Using genotyping-by-sequencing (GBS) generated marker data for 2,352 Danish farm...... mink runs of homozygosity (ROH) were detect in mink genomes. Detectable ROH made up on average 1.7% of the genome indicating the presence of at most a moderate level of genomic inbreeding. The fraction of genome regions found in ROH varied. Ten percent of the included regions were never found in ROH....... The ability to detect ROH in the mink genome also demonstrates the general reliability of the new mink genome assembly. Keywords: american mink, run of homozygosity, genome, selection, genomic inbreeding...

The IMBA suite: integrated modules for bioassay analysis

Energy Technology Data Exchange (ETDEWEB)

Birchall, A.; Jarvis, N.S.; Peace, M.S.; Riddell, A.E.; Battersby, W.P

1998-07-01

The increasing complexity of models representing the biokinetic behaviour of radionuclides in the body following intake poses problems for people who are required to implement these models. The problem is exacerbated by the current paucity of suitable software. In order to remedy this situation, a collaboration between British Nuclear Fuels, Westlakes Research Institute and the National Radiological Protection Board has started with the aim of producing a suite of modules for estimating intakes and doses from bioassay measurements using the new ICRP models. Each module will have a single purpose (e.g. to calculate respiratory tract deposition) and will interface with other software using data files. The elements to be implemented initially are plutonium, uranium, caesium, iodine and tritium. It is intended to make the software available to other parties under terms yet to be decided. This paper describes the proposed suite of integrated modules for bioassay analysis, IMBA. (author)

Visualization for genomics: the Microbial Genome Viewer.

NARCIS (Netherlands)

Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D; Siezen, R.J.

2004-01-01

SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a

Isotopic variation in the Tuolumne Intrusive Suite, central Sierra Nevada, California

Science.gov (United States)

Kistler, R.W.; Chappell, B.W.; Peck, D.L.; Bateman, P.C.

1986-01-01

Granitoid rocks of the compositionally zoned Late Cretaceous Toulumne Intrusive Suite in the central Sierra Nevada, California, have initial87Sr/86Sr values (Sri) and143Nd/144Nd values (Ndi) that vary from 0.7057 to 0.7067 and from 0.51239 to 0.51211 respectively. The observed variation of both Sri and Ndi and of chemical composition in rocks of the suite cannot be due to crystal fractionation of magma solely under closed system conditons. The largest variation in chemistry, Ndi, and Sri is present in the outer-most equigranular units of the Tuolumne Intrusive Suite. Sri varies positively with SiO2, Na2O, K2O, and Rb concentrations, and negatively with Ndi, Al2O3, Fe2O3, MgO, FeO, CaO, MnO, P2O5, TiO2, and Sr concentrations. This covariation of Sri, Ndi and chemistry can be modeled by a process of simple mixing of basaltic and granitic magmas having weight percent SiO2 of 48.0 and 73.3 respectively. Isotopic characteristic of the mafic magma are Sri=0.7047, Ndi=0.51269 and ??18O=6.0, and of the felsic magma are Sri=0.7068, Ndi=0.51212 and ??18O=8.9. The rocks sampled contain from 50 to 80% of the felsic component. An aplite in the outer equigranular unit of the Tuolumne Intrusive Suite apparently was derived by fractional crystallization of plagioclase and hornblende from magma with granudiorite composition that was a product of mixing of the magmas described above. Siliceous magmas derived from the lower crust, having a maximum of 15 percent mantle-derived mafic component, are represented by the inner prophyritic units of the Tuolumne Intrusive Suite. ?? 1986 Springer-Verlag.

Segane saksa-eesti kirjakeel ja eesti lauluraamat / Gustav Suits

Index Scriptorium Estoniae

Suits, Gustav, 1883-1956

1999-01-01

Varem ilmunud: Suits, Gustav. Eesti kirjanduslugu I. Lund : Eesti Kirjanike Kooperatiiv, 1953. Heinrich Stahli käsiraamatu Hand-, Hausz- und Kirchenbuch (1654-1656) osana ilmunud lauluraamatust Neu Ehstnisches Gesangbuch (1656)

Assuring Condition and Inventory Accountability of Chemical Protective Suits

National Research Council Canada - National Science Library

2000-01-01

.... As part of the Defense Logistics Agency's efforts to consolidate depot operations and improve inventory accuracy, chemical protective suits were transferred to the Defense Depot, Albany, Georgia, during FY 1991.

Space Suit Simulator (S3) for Partial Gravity EVA Experimentation and Training, Phase II

Data.gov (United States)

National Aeronautics and Space Administration — Pressurized space suits impose high joint torques on the wearer, reducing mobility for upper and lower body motions. Using actual space suits in training or...

Modular Algorithm Testbed Suite (MATS): A Software Framework for Automatic Target Recognition

Science.gov (United States)

2017-01-01

NAVAL SURFACE WARFARE CENTER PANAMA CITY DIVISION PANAMA CITY, FL 32407-7001 TECHNICAL REPORT NSWC PCD TR-2017-004 MODULAR ...31-01-2017 Technical Modular Algorithm Testbed Suite (MATS): A Software Framework for Automatic Target Recognition DR...flexible platform to facilitate the development and testing of ATR algorithms. To that end, NSWC PCD has created the Modular Algorithm Testbed Suite

The audio and visual communication systems for suited engineering activities on JET

International Nuclear Information System (INIS)

Pearce, R.J.H.; Bruce, J.; Callaghan, C.; Hart, M.; Martin, P.; Middleton, R.; Tait, J.

2001-01-01

The beryllium and/or tritium contamination of the JET tokamak and auxiliary systems necessitates that many activities are carried out in air line fed pressurised suits. To enable often complex engineering activities to be performed, a number of novel audio and visual and communications systems have been designed. The paper describes these systems which give freedom of visual and audio communication between suited personnel, supervisors, operators and engineers. The system enhances the safety of the working environment as well as helping to minimise the radiation dose to personnel. It is concluded, from a number of years experience of using the audio and visual communications systems for suited operations, that safety and the progress of complex engineering tasks have been significantly enhanced

The audio and visual communication systems for suited engineering activities on JET

Energy Technology Data Exchange (ETDEWEB)

Pearce, R.J.H. E-mail: robert.pearce@jet.uk; Bruce, J.; Callaghan, C.; Hart, M.; Martin, P.; Middleton, R.; Tait, J

2001-11-01

The beryllium and/or tritium contamination of the JET tokamak and auxiliary systems necessitates that many activities are carried out in air line fed pressurised suits. To enable often complex engineering activities to be performed, a number of novel audio and visual and communications systems have been designed. The paper describes these systems which give freedom of visual and audio communication between suited personnel, supervisors, operators and engineers. The system enhances the safety of the working environment as well as helping to minimise the radiation dose to personnel. It is concluded, from a number of years experience of using the audio and visual communications systems for suited operations, that safety and the progress of complex engineering tasks have been significantly enhanced.

Touring the Tomato: A Suite of Chemistry Laboratory Experiments

Science.gov (United States)

Sarkar, Sayantani; Chatterjee, Subhasish; Medina, Nancy; Stark, Ruth E.

2013-01-01

An eight-session interdisciplinary laboratory curriculum has been designed using a suite of analytical chemistry techniques to study biomaterials derived from an inexpensive source such as the tomato fruit. A logical

Improved airline-type supplied-air plastic suit. [For personnel protection against inhalation of airborne plutonium and tritium

Energy Technology Data Exchange (ETDEWEB)

Jolley, L. Jr.; Zippler, D.B.; Cofer, C.H.; Harper, J.A.

1978-06-01

Two piece supplied-air plastic suits are used extensively at the Savannah River Plant for personnel protection against inhalation of airborne plutonium and tritium. Worker comfort and noise level problems gave impetus to development of an improved suit and aid distribution system. The resulting plastic suit and development work are discussed. The plastic suit unit cost is less than $20, the hearing zone noise level is less than 75 dBA, protection factors exceed 10,000, and user comfort is approved. This suit is expected to meet performance requirements for unrestricted use.

The GenABEL Project for statistical genomics.

Science.gov (United States)

Karssen, Lennart C; van Duijn, Cornelia M; Aulchenko, Yurii S

2016-01-01

Development of free/libre open source software is usually done by a community of people with an interest in the tool. For scientific software, however, this is less often the case. Most scientific software is written by only a few authors, often a student working on a thesis. Once the paper describing the tool has been published, the tool is no longer developed further and is left to its own device. Here we describe the broad, multidisciplinary community we formed around a set of tools for statistical genomics. The GenABEL project for statistical omics actively promotes open interdisciplinary development of statistical methodology and its implementation in efficient and user-friendly software under an open source licence. The software tools developed withing the project collectively make up the GenABEL suite, which currently consists of eleven tools. The open framework of the project actively encourages involvement of the community in all stages, from formulation of methodological ideas to application of software to specific data sets. A web forum is used to channel user questions and discussions, further promoting the use of the GenABEL suite. Developer discussions take place on a dedicated mailing list, and development is further supported by robust development practices including use of public version control, code review and continuous integration. Use of this open science model attracts contributions from users and developers outside the "core team", facilitating agile statistical omics methodology development and fast dissemination.

The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics.

Science.gov (United States)

Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F X; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

2013-02-01

Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species.

The genome and structural proteome of an ocean siphovirus: a new window into the cyanobacterial ‘mobilome’

Science.gov (United States)

Sullivan, Matthew B; Krastins, Bryan; Hughes, Jennifer L; Kelly, Libusha; Chase, Michael; Sarracino, David; Chisholm, Sallie W

2009-01-01

Prochlorococcus, an abundant phototroph in the oceans, are infected by members of three families of viruses: myo-, podo- and siphoviruses. Genomes of myo- and podoviruses isolated on Prochlorococcus contain DNA replication machinery and virion structural genes homologous to those from coliphages T4 and T7 respectively. They also contain a suite of genes of cyanobacterial origin, most notably photosynthesis genes, which are expressed during infection and appear integral to the evolutionary trajectory of both host and phage. Here we present the first genome of a cyanobacterial siphovirus, P-SS2, which was isolated from Atlantic slope waters using a Prochlorococcus host (MIT9313). The P-SS2 genome is larger than, and considerably divergent from, previously sequenced siphoviruses. It appears most closely related to lambdoid siphoviruses, with which it shares 13 functional homologues. The ∼108 kb P-SS2 genome encodes 131 predicted proteins and notably lacks photosynthesis genes which have consistently been found in other marine cyanophage, but does contain 14 other cyanobacterial homologues. While only six structural proteins were identified from the genome sequence, 35 proteins were detected experimentally; these mapped onto capsid and tail structural modules in the genome. P-SS2 is potentially capable of integration into its host as inferred from bioinformatically identified genetic machinery int, bet, exo and a 53 bp attachment site. The host attachment site appears to be a genomic island that is tied to insertion sequence (IS) activity that could facilitate mobility of a gene involved in the nitrogen-stress response. The homologous region and a secondary IS-element hot-spot in Synechococcus RS9917 are further evidence of IS-mediated genome evolution coincident with a probable relic prophage integration event. This siphovirus genome provides a glimpse into the biology of a deep-photic zone phage as well as the ocean cyanobacterial prophage and IS element �

Monitoring Human Performance During Suited Operations: A Technology Feasibility Study Using EMU Gloves

Science.gov (United States)

Bekdash, Omar; Norcross, Jason; McFarland, Shane

2015-01-01

Mobility tracking of human subjects while conducting suited operations still remains focused on the external movement of the suit and little is known about the human movement within it. For this study, accelerometers and bend sensitive resistors were integrated into a custom carrier glove to quantify range of motion and dexterity from within the pressurized glove environment as a first stage feasibility study of sensor hardware, integration, and reporting capabilities. Sensors were also placed on the exterior of the pressurized glove to determine if it was possible to compare a glove joint angle to the anatomical joint angle of the subject during tasks. Quantifying human movement within the suit was feasible, with accelerometers clearly detecting movements in the wrist and reporting expected joint angles at maximum flexion or extension postures with repeatability of plus or minus 5 degrees between trials. Bend sensors placed on the proximal interphalangeal and distal interphalangeal joints performed less well. It was not possible to accurately determine the actual joint angle using these bend sensors, but these sensors could be used to determine when the joint was flexed to its maximum and provide a general range of mobility needed to complete a task. Further work includes additional testing with accelerometers and the possible inclusion of hardware such as magnetometers or gyroscopes to more precisely locate the joint in 3D space. We hope to eventually expand beyond the hand and glove and develop a more comprehensive suit sensor suite to characterize motion across more joints (knee, elbow, shoulder, etc.) and fully monitor the human body operating within the suit environment.

Whole genome sequencing of the monomorphic pathogen Mycobacterium bovis reveals local differentiation of cattle clinical isolates.

Science.gov (United States)

Lasserre, Moira; Fresia, Pablo; Greif, Gonzalo; Iraola, Gregorio; Castro-Ramos, Miguel; Juambeltz, Arturo; Nuñez, Álvaro; Naya, Hugo; Robello, Carlos; Berná, Luisa

2018-01-02

Bovine tuberculosis (bTB) poses serious risks to animal welfare and economy, as well as to public health as a zoonosis. Its etiological agent, Mycobacterium bovis, belongs to the Mycobacterium tuberculosis complex (MTBC), a group of genetically monomorphic organisms featured by a remarkably high overall nucleotide identity (99.9%). Indeed, this characteristic is of major concern for correct typing and determination of strain-specific traits based on sequence diversity. Due to its historical economic dependence on cattle production, Uruguay is deeply affected by the prevailing incidence of Mycobacterium bovis. With the world's highest number of cattle per human, and its intensive cattle production, Uruguay represents a particularly suited setting to evaluate genomic variability among isolates, and the diversity traits associated to this pathogen. We compared 186 genomes from MTBC strains isolated worldwide, and found a highly structured population in M. bovis. The analysis of 23 new M. bovis genomes, belonging to strains isolated in Uruguay evidenced three groups present in the country. Despite presenting an expected highly conserved genomic structure and sequence, these strains segregate into a clustered manner within the worldwide phylogeny. Analysis of the non-pe/ppe differential areas against a reference genome defined four main sources of variability, namely: regions of difference (RD), variable genes, duplications and novel genes. RDs and variant analysis segregated the strains into clusters that are concordant with their spoligotype identities. Due to its high homoplasy rate, spoligotyping failed to reflect the true genomic diversity among worldwide representative strains, however, it remains a good indicator for closely related populations. This study introduces a comprehensive population structure analysis of worldwide M. bovis isolates. The incorporation and analysis of 23 novel Uruguayan M. bovis genomes, sheds light onto the genomic diversity of this

Family genome browser: visualizing genomes with pedigree information.

Science.gov (United States)

Juan, Liran; Liu, Yongzhuang; Wang, Yongtian; Teng, Mingxiang; Zang, Tianyi; Wang, Yadong

2015-07-15

Families with inherited diseases are widely used in Mendelian/complex disease studies. Owing to the advances in high-throughput sequencing technologies, family genome sequencing becomes more and more prevalent. Visualizing family genomes can greatly facilitate human genetics studies and personalized medicine. However, due to the complex genetic relationships and high similarities among genomes of consanguineous family members, family genomes are difficult to be visualized in traditional genome visualization framework. How to visualize the family genome variants and their functions with integrated pedigree information remains a critical challenge. We developed the Family Genome Browser (FGB) to provide comprehensive analysis and visualization for family genomes. The FGB can visualize family genomes in both individual level and variant level effectively, through integrating genome data with pedigree information. Family genome analysis, including determination of parental origin of the variants, detection of de novo mutations, identification of potential recombination events and identical-by-decent segments, etc., can be performed flexibly. Diverse annotations for the family genome variants, such as dbSNP memberships, linkage disequilibriums, genes, variant effects, potential phenotypes, etc., are illustrated as well. Moreover, the FGB can automatically search de novo mutations and compound heterozygous variants for a selected individual, and guide investigators to find high-risk genes with flexible navigation options. These features enable users to investigate and understand family genomes intuitively and systematically. The FGB is available at http://mlg.hit.edu.cn/FGB/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Prokofiev: Romeo and Juliet - Suite N1 / Ivan March

Index Scriptorium Estoniae

March, Ivan

1990-01-01

Uuest heliplaadist "Prokofiev: Romeo and Juliet - Suite N1, Op.64b, N2, Op.64c. Philharmonia Orchestra, Barry Wordsworth" Collins Classics cassette 1116-4. CD. Võrreldud Neeme Järvi plaadistustega 1116-2

eGenomics: Cataloguing Our Complete Genome Collection III

Directory of Open Access Journals (Sweden)

Dawn Field

2007-01-01

Full Text Available This meeting report summarizes the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection III” workshop held September 11–13, 2006, at the National Institute for Environmental eScience (NIEeS, Cambridge, United Kingdom. This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The first half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised “Minimum Information about a Genome Sequence” (MIGS specification (v1.1, consensus on a variety of features to be added to the Genome Catalogue (GCat, agreement by several researchers to adopt MIGS for imminent genome publications, and an agreement by the EBI and NCBI to input their genome collections into GCat for the purpose of quantifying the amount of optional data already available (e.g., for geographic location coordinates and working towards a single, global list of all public genomes and metagenomes.

Failure to exercise due diligence costs plaintiff her suit.

Science.gov (United States)

1997-11-28

The Mississippi State Supreme Court affirmed a lower court ruling dismissing a last-minute suit filed by a plaintiff against United Blood Services of Mississippi and the American Association of Blood Banks. A woman known as D. Doe was a recipient of a tainted transfusion. She contracted HIV in 1983 and died of AIDS-related causes in 1991. Her daughter, the plaintiff, filed a contaminated blood transfusion lawsuit just five days before the statute of limitations ran out but failed to ascertain the correct identity of the blood bank. She named two blood banks in her suit because she was unable to determine the source of the blood. The Supreme Court ruled that waiting until five days before the statute elapsed indicated that the plaintiff did not exercise reasonable diligence within a specific time frame.

Genomic Prediction from Whole Genome Sequence in Livestock: The 1000 Bull Genomes Project

DEFF Research Database (Denmark)

Hayes, Benjamin J; MacLeod, Iona M; Daetwyler, Hans D

Advantages of using whole genome sequence data to predict genomic estimated breeding values (GEBV) include better persistence of accuracy of GEBV across generations and more accurate GEBV across breeds. The 1000 Bull Genomes Project provides a database of whole genome sequenced key ancestor bulls....... In a dairy data set, predictions using BayesRC and imputed sequence data from 1000 Bull Genomes were 2% more accurate than with 800k data. We could demonstrate the method identified causal mutations in some cases. Further improvements will come from more accurate imputation of sequence variant genotypes...

Tools for Accurate and Efficient Analysis of Complex Evolutionary Mechanisms in Microbial Genomes. Final Report

Energy Technology Data Exchange (ETDEWEB)

Nakhleh, Luay

2014-03-12

I proposed to develop computationally efficient tools for accurate detection and reconstruction of microbes' complex evolutionary mechanisms, thus enabling rapid and accurate annotation, analysis and understanding of their genomes. To achieve this goal, I proposed to address three aspects. (1) Mathematical modeling. A major challenge facing the accurate detection of HGT is that of distinguishing between these two events on the one hand and other events that have similar "effects." I proposed to develop a novel mathematical approach for distinguishing among these events. Further, I proposed to develop a set of novel optimization criteria for the evolutionary analysis of microbial genomes in the presence of these complex evolutionary events. (2) Algorithm design. In this aspect of the project, I proposed to develop an array of e cient and accurate algorithms for analyzing microbial genomes based on the formulated optimization criteria. Further, I proposed to test the viability of the criteria and the accuracy of the algorithms in an experimental setting using both synthetic as well as biological data. (3) Software development. I proposed the nal outcome to be a suite of software tools which implements the mathematical models as well as the algorithms developed.

Time Management in the Operating Room: An Analysis of the Dedicated Minimally Invasive Surgery Suite

Science.gov (United States)

Hsiao, Kenneth C.; Machaidze, Zurab

2004-01-01

Background: Dedicated minimally invasive surgery suites are available that contain specialized equipment to facilitate endoscopic surgery. Laparoscopy performed in a general operating room is hampered by the multitude of additional equipment that must be transported into the room. The objective of this study was to compare the preparation times between procedures performed in traditional operating rooms versus dedicated minimally invasive surgery suites to see whether operating room efficiency is improved in the specialized room. Methods: The records of 50 patients who underwent laparoscopic procedures between September 2000 and April 2002 were retrospectively reviewed. Twenty-three patients underwent surgery in a general operating room and 18 patients in an minimally invasive surgery suite. Nine patients were excluded because of cystoscopic procedures undergone prior to laparoscopy. Various time points were recorded from which various time intervals were derived, such as preanesthesia time, anesthesia induction time, and total preparation time. A 2-tailed, unpaired Student t test was used for statistical analysis. Results: The mean preanesthesia time was significantly faster in the minimally invasive surgery suite (12.2 minutes) compared with that in the traditional operating room (17.8 minutes) (P=0.013). Mean anesthesia induction time in the minimally invasive surgery suite (47.5 minutes) was similar to time in the traditional operating room (45.7 minutes) (P=0.734). The average total preparation time for the minimally invasive surgery suite (59.6 minutes) was not significantly faster than that in the general operating room (63.5 minutes) (P=0.481). Conclusion: The amount of time that elapses between the patient entering the room and anesthesia induction is statically shorter in a dedicated minimally invasive surgery suite. Laparoscopic surgery is performed more efficiently in a dedicated minimally invasive surgery suite versus a traditional operating room. PMID

Vibrotactile perception assessment for a haptic interface on an antigravity suit.

Science.gov (United States)

Ko, Sang Min; Lee, Kwangil; Kim, Daeho; Ji, Yong Gu

2017-01-01

Haptic technology is used in various fields to transmit information to the user with or without visual and auditory cues. This study aimed to provide preliminary data for use in developing a haptic interface for an antigravity (anti-G) suit. With the structural characteristics of the anti-G suit in mind, we determined five areas on the body (lower back, outer thighs, inner thighs, outer calves, and inner calves) on which to install ten bar-type eccentric rotating mass (ERM) motors as vibration actuators. To determine the design factors of the haptic anti-G suit, we conducted three experiments to find the absolute threshold, moderate intensity, and subjective assessments of vibrotactile stimuli. Twenty-six fighter pilots participated in the experiments, which were conducted in a fixed-based flight simulator. From the results of our study, we recommend 1) absolute thresholds of ∼11.98-15.84 Hz and 102.01-104.06 dB, 2) moderate intensities of 74.36 Hz and 126.98 dB for the lower back and 58.65 Hz and 122.37 dB for either side of the thighs and calves, and 3) subjective assessments of vibrotactile stimuli (displeasure, easy to perceive, and level of comfort). The results of this study will be useful for the design of a haptic anti-G suit. Copyright © 2016 Elsevier Ltd. All rights reserved.

HelmCoP: an online resource for helminth functional genomics and drug and vaccine targets prioritization.

Directory of Open Access Journals (Sweden)

Sahar Abubucker

Full Text Available A vast majority of the burden from neglected tropical diseases result from helminth infections (nematodes and platyhelminthes. Parasitic helminthes infect over 2 billion, exerting a high collective burden that rivals high-mortality conditions such as AIDS or malaria, and cause devastation to crops and livestock. The challenges to improve control of parasitic helminth infections are multi-fold and no single category of approaches will meet them all. New information such as helminth genomics, functional genomics and proteomics coupled with innovative bioinformatic approaches provide fundamental molecular information about these parasites, accelerating both basic research as well as development of effective diagnostics, vaccines and new drugs. To facilitate such studies we have developed an online resource, HelmCoP (Helminth Control and Prevention, built by integrating functional, structural and comparative genomic data from plant, animal and human helminthes, to enable researchers to develop strategies for drug, vaccine and pesticide prioritization, while also providing a useful comparative genomics platform. HelmCoP encompasses genomic data from several hosts, including model organisms, along with a comprehensive suite of structural and functional annotations, to assist in comparative analyses and to study host-parasite interactions. The HelmCoP interface, with a sophisticated query engine as a backbone, allows users to search for multi-factorial combinations of properties and serves readily accessible information that will assist in the identification of various genes of interest. HelmCoP is publicly available at: http://www.nematode.net/helmcop.html.

Metabolic Diet App Suite for inborn errors of amino acid metabolism.

Science.gov (United States)

Ho, Gloria; Ueda, Keiko; Houben, Roderick F A; Joa, Jeff; Giezen, Alette; Cheng, Barbara; van Karnebeek, Clara D M

2016-03-01

An increasing number of rare inborn errors of metabolism (IEMs) are amenable to targeted metabolic nutrition therapy. Daily adherence is important to attain metabolic control and prevent organ damage. This is challenging however, given the lack of information of disorder specific nutrient content of foods, the limited availability and cost of specialty products as well as difficulties in reliable calculation and tracking of dietary intake and targets. To develop apps for all inborn errors of amino acid metabolism for which the mainstay of treatment is a medical diet, and obtain patient and family feedback throughout the process to incorporate this into subsequent versions. The Metabolic Diet App Suite was created with input from health care professionals as a free, user-friendly, online tool for both mobile devices and desktop computers (http://www.metabolicdietapp.org) for 15 different IEMs. General information is provided for each IEM with links to useful online resources. Nutrient information is based on the MetabolicPro™, a North American food database compiled by the Genetic Metabolic Dietitians International (GMDI) Technology committee. After user registration, a personalized dashboard and management plan including specific nutrient goals are created. Each Diet App has a user-friendly interface and the functions include: nutrient intake counts, adding your own foods and homemade recipes and, managing a daily food diary. Patient and family feedback was overall positive and specific suggestions were used to further improve the App Suite. The Metabolic Diet App Suite aids individuals affected by IEMs to track and plan their meals. Future research should evaluate its impact on patient adherence, metabolic control, quality of life and health-related outcomes. The Suite will be updated and expanded to Apps for other categories of IEMs. Finally, this Suite is a support tool only, and does not replace medical/metabolic nutrition professional advice. Copyright �

Geophysical characterization from Itu intrusive suite

International Nuclear Information System (INIS)

Pascholati, M.E.

1989-01-01

The integrated use of geophysical, geological, geochemical, petrographical and remote sensing data resulted in a substantial increase in the knowledge of the Itu Intrusive Suite. The main geophysical method was gamma-ray spectrometry together with fluorimetry and autoradiography. Three methods were used for calculation of laboratory gamma-ray spectrometry data. For U, the regression method was the best one. For K and Th, equations system and absolute calibration presented the best results. Surface gamma-ray spectrometry allowed comparison with laboratory data and permitted important contribution to the study of environmental radiation. (author)

Statutes of limitations: the special problem of DES suits

International Nuclear Information System (INIS)

Feigin, C.A.

1981-01-01

In 1971, medical studies determined that DES causes a rare type of vaginal cancer in a small number of daughters of mothers who took DES during pregnancy. Subsequently, medical studies determined that exposure to DES can cause other vaginal abnormalities in the daughters, some of which may be precancerous. As a result of these discoveries, many lawsuits have been filed by these daughters against DES manufacturers. Many DES suits may be barred by statutes of limitations, both because the number of years between the daughters' exposure to DES in utero and the discovery that DES can cause injuries exceeds the statutory period, and because the cancer or other injuries caused by DES may not develop for many additional years. This Note discusses two methods that DES plaintiffs may be able to use to overcome the potential statutes of limitations bar: the discovery rule, and state provisions which toll the statute of limitations for minors. The Note contends that courts should apply an expanded discovery rule to DES suits to avoid the unfair result of barring a claim before the plaintiff could have known that she had a cause of action. In addition, the Note argues that the injury which causes the statute of limitations to begin to run in DES suits should not be rigidly defined. Finally, the Note urges that courts allow eligible DES plaintiffs to take advantage of applicable state provisions that toll the statute of limitations for minors

Genome U-Plot: a whole genome visualization.

Science.gov (United States)

Gaitatzes, Athanasios; Johnson, Sarah H; Smadbeck, James B; Vasmatzis, George

2018-05-15

The ability to produce and analyze whole genome sequencing (WGS) data from samples with structural variations (SV) generated the need to visualize such abnormalities in simplified plots. Conventional two-dimensional representations of WGS data frequently use either circular or linear layouts. There are several diverse advantages regarding both these representations, but their major disadvantage is that they do not use the two-dimensional space very efficiently. We propose a layout, termed the Genome U-Plot, which spreads the chromosomes on a two-dimensional surface and essentially quadruples the spatial resolution. We present the Genome U-Plot for producing clear and intuitive graphs that allows researchers to generate novel insights and hypotheses by visualizing SVs such as deletions, amplifications, and chromoanagenesis events. The main features of the Genome U-Plot are its layered layout, its high spatial resolution and its improved aesthetic qualities. We compare conventional visualization schemas with the Genome U-Plot using visualization metrics such as number of line crossings and crossing angle resolution measures. Based on our metrics, we improve the readability of the resulting graph by at least 2-fold, making apparent important features and making it easy to identify important genomic changes. A whole genome visualization tool with high spatial resolution and improved aesthetic qualities. An implementation and documentation of the Genome U-Plot is publicly available at https://github.com/gaitat/GenomeUPlot. vasmatzis.george@mayo.edu. Supplementary data are available at Bioinformatics online.

Miniature Flexible Humidity Sensitive Patches for Space Suits, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — Advanced space suit technologies demand improved, simplified, long-life regenerative sensing technologies, including humidity sensors, that exceed the performance of...

CAMEO (Computer-Aided Management of Emergency Operations) Software Suite

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — CAMEO is the umbrella name for a system of software applications used widely to plan for and respond to chemical emergencies. All of the programs in the suite work...

Arensky. Silhouettes (Suite N 2), Op. 23 / Jonathan Swain

Index Scriptorium Estoniae

Swain, Jonathan

1991-01-01

Uuest heliplaadist "Arensky. Silhouettes (Suite N 2), Op. 23. Scrjabin. Symphony N 3 in C minor, Op. 43 "Le divin poeme". Danish National Radio Symphony Orchestra. Neeme Järvi. Chandos cassette ABTD 1509; CD CHAN 8898 (66 minutes)

Rimsky-Korsakov: Symphony N2 (Symphonic Suite) / Warrack, John

Index Scriptorium Estoniae

Warrack, John

1990-01-01

Uuest heliplaadist "Rimsky-Korsakov: Symphony N2 (Symphonic Suite), Op. 9, "Antar" Russian Easter Festival Overture, Op.36. Philharmonia Orchestra, Evgeni Svetlanov. Hyperion KA 66399. CDA 66399. Teise sümfoonia esitust võrreldud Neeme Järvi plaadistusega

A Thousand Fly Genomes: An Expanded Drosophila Genome Nexus.

Science.gov (United States)

Lack, Justin B; Lange, Jeremy D; Tang, Alison D; Corbett-Detig, Russell B; Pool, John E

2016-12-01

The Drosophila Genome Nexus is a population genomic resource that provides D. melanogaster genomes from multiple sources. To facilitate comparisons across data sets, genomes are aligned using a common reference alignment pipeline which involves two rounds of mapping. Regions of residual heterozygosity, identity-by-descent, and recent population admixture are annotated to enable data filtering based on the user's needs. Here, we present a significant expansion of the Drosophila Genome Nexus, which brings the current data object to a total of 1,121 wild-derived genomes. New additions include 305 previously unpublished genomes from inbred lines representing six population samples in Egypt, Ethiopia, France, and South Africa, along with another 193 genomes added from recently-published data sets. We also provide an aligned D. simulans genome to facilitate divergence comparisons. This improved resource will broaden the range of population genomic questions that can addressed from multi-population allele frequencies and haplotypes in this model species. The larger set of genomes will also enhance the discovery of functionally relevant natural variation that exists within and between populations. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Visualization for genomics: the Microbial Genome Viewer.

Science.gov (United States)

Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

2004-07-22

A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

STS-90 Pilot Scott Altman is suited up for launch

Science.gov (United States)

1998-01-01

STS-90 Pilot Scott Altman is assisted during suit-up activities by Lockheed Suit Technician Valerie McNeil from Johnson Space Center in KSC's Operations and Checkout Building. Altman and the rest of the STS-90 crew will shortly depart for Launch Pad 39B, where the Space Shuttle Columbia awaits a second liftoff attempt at 2:19 p.m. EDT. His first trip into space, Altman is participating in a life sciences research flight that will focus on the most complex and least understood part of the human body - - the nervous system. Neurolab will examine the effects of spaceflight on the brain, spinal cord, peripheral nerves and sensory organs in the human body.

Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud.

Directory of Open Access Journals (Sweden)

Enis Afgan

Full Text Available Analyzing high throughput genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation. A computational platform enabling best practice genomics analysis ideally meets a number of requirements, including: a wide range of analysis and visualisation tools, closely linked to large user and reference data sets; workflow platform(s enabling accessible, reproducible, portable analyses, through a flexible set of interfaces; highly available, scalable computational resources; and flexibility and versatility in the use of these resources to meet demands and expertise of a variety of users. Access to an appropriate computational platform can be a significant barrier to researchers, as establishing such a platform requires a large upfront investment in hardware, experience, and expertise.We designed and implemented the Genomics Virtual Laboratory (GVL as a middleware layer of machine images, cloud management tools, and online services that enable researchers to build arbitrarily sized compute clusters on demand, pre-populated with fully configured bioinformatics tools, reference datasets and workflow and visualisation options. The platform is flexible in that users can conduct analyses through web-based (Galaxy, RStudio, IPython Notebook or command-line interfaces, and add/remove compute nodes and data resources as required. Best-practice tutorials and protocols provide a path from introductory training to practice. The GVL is available on the OpenStack-based Australian Research Cloud (http://nectar.org.au and the Amazon Web Services cloud. The principles, implementation and build process are designed to be cloud-agnostic.This paper provides a blueprint for the design and implementation of a cloud-based Genomics Virtual Laboratory. We discuss scope, design considerations and technical and logistical constraints

Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud.

Science.gov (United States)

Afgan, Enis; Sloggett, Clare; Goonasekera, Nuwan; Makunin, Igor; Benson, Derek; Crowe, Mark; Gladman, Simon; Kowsar, Yousef; Pheasant, Michael; Horst, Ron; Lonie, Andrew

2015-01-01

Analyzing high throughput genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation. A computational platform enabling best practice genomics analysis ideally meets a number of requirements, including: a wide range of analysis and visualisation tools, closely linked to large user and reference data sets; workflow platform(s) enabling accessible, reproducible, portable analyses, through a flexible set of interfaces; highly available, scalable computational resources; and flexibility and versatility in the use of these resources to meet demands and expertise of a variety of users. Access to an appropriate computational platform can be a significant barrier to researchers, as establishing such a platform requires a large upfront investment in hardware, experience, and expertise. We designed and implemented the Genomics Virtual Laboratory (GVL) as a middleware layer of machine images, cloud management tools, and online services that enable researchers to build arbitrarily sized compute clusters on demand, pre-populated with fully configured bioinformatics tools, reference datasets and workflow and visualisation options. The platform is flexible in that users can conduct analyses through web-based (Galaxy, RStudio, IPython Notebook) or command-line interfaces, and add/remove compute nodes and data resources as required. Best-practice tutorials and protocols provide a path from introductory training to practice. The GVL is available on the OpenStack-based Australian Research Cloud (http://nectar.org.au) and the Amazon Web Services cloud. The principles, implementation and build process are designed to be cloud-agnostic. This paper provides a blueprint for the design and implementation of a cloud-based Genomics Virtual Laboratory. We discuss scope, design considerations and technical and logistical constraints, and explore the

Development of Advanced Suite of Deterministic Codes for VHTR Physics Analysis

Energy Technology Data Exchange (ETDEWEB)

Kim, Kang Seog; Cho, J. Y.; Lee, K. H. (and others)

2007-07-15

Advanced Suites of deterministic codes for VHTR physics analysis has been developed for detailed analysis of current and advanced reactor designs as part of a US-ROK collaborative I-NERI project. These code suites include the conventional 2-step procedure in which a few group constants are generated by a transport lattice calculation, and the reactor physics analysis is performed by a 3-dimensional diffusion calculation, and a whole core transport code that can model local heterogeneities directly at the core level. Particular modeling issues in physics analysis of the gas-cooled VHTRs were resolved, which include a double heterogeneity of the coated fuel particles, a neutron streaming in the coolant channels, a strong core-reflector interaction, and large spectrum shifts due to changes of the surrounding environment, temperature and burnup. And the geometry handling capability of the DeCART code were extended to deal with the hexagonal fuel elements of the VHTR core. The developed code suites were validated and verified by comparing the computational results with those of the Monte Carlo calculations for the benchmark problems.

Integrated Instrument Simulator Suites for Earth Science

Science.gov (United States)

Tanelli, Simone; Tao, Wei-Kuo; Matsui, Toshihisa; Hostetler, Chris; Hair, John; Butler, Carolyn; Kuo, Kwo-Sen; Niamsuwan, Noppasin; Johnson, Michael P.; Jacob, Joseph C.;

Ergonomic assessment of neck posture in the minimally invasive surgery suite during laparoscopic cholecystectomy.

Science.gov (United States)

van Det, M J; Meijerink, W J H J; Hoff, C; van Veelen, M A; Pierie, J P E N

2008-11-01

With the expanding implementation of minimally invasive surgery, the operating team is confronted with challenges in the field of ergonomics. Visual feedback is derived from a monitor placed outside the operating field. This crossover trial was conducted to evaluate and compare neck posture in relation to monitor position in a dedicated minimally invasive surgery (MIS) suite and a conventional operating room. Assessment of the neck was conducted for 16 surgeons, assisting surgeons, and scrub nurses performing a laparoscopic cholecystectomy in both types of operating room. Flexion and rotation of the cervical spine were measured intraoperatively using a video analysis system. A two-question visual analog scale (VAS) questionnaire was used to evaluate posture in relation to the monitor position. Neck rotation was significantly reduced in the MIS suite for the surgeon (p = 0.018) and the assisting surgeon (p < 0.001). Neck flexion was significantly improved in the MIS suite for the surgeon (p < 0.001) and the scrub nurse (p = 0.018). On the questionnaire, the operating room team scored their posture significantly higher in the MIS suite and also indicated fewer musculoskeletal complaints. The ergonomic quality of the neck posture is significantly improved in the MIS suite for the entire operating room team.

The PAUL Suit(©) : an experience of ageing.

Science.gov (United States)

Bennett, Paul; Moore, Malcolm; Wenham, John

2016-04-01

An ageing population worldwide makes it increasingly important that health students understand issues that elderly people face and can provide empathic care to them. This teaching department in an isolated rural setting developed an interprofessional learning session to assist health students to understand issues of functional loss and social isolation that can affect elderly people. The Premature Ageing Unisex Leisure (PAUL) Suit(©) was developed as part of a 1-day learning session for undergraduate health students - including students of medicine, nursing and allied health - attending clinical placement in far-west New South Wales. The suit was developed locally and can be adjusted to simulate a wide range of functional losses in the wearer. Students undertake a range of daily tasks in the community while wearing the suit in the company of a student 'carer'. Over the past 4 years, approximately 140 students have participated in the simulation. Post-simulation evaluations report that students gain a greater understanding of some functional issues associated with ageing, and of the social isolation that can be associated with these. The experiential nature of the activity leads to some powerful insights. This activity is an innovative, experiential tool to deepen students understanding of issues related to ageing This activity is an innovative, experiential tool to deepen students understanding of issues relating to ageing. The interprofessional nature of the activity is an important factor in the success of the day, and produces a wide range of shared insights. The activity also enhances the partnerships between the university, the health service and the local community. Our experience supports the value of simulation in providing a deep learning opportunity in the area of ageing and disability. © 2015 John Wiley & Sons Ltd.

G SUIT FOR EDUCATION AS AN ENVIRONMENT FOR STUDENTS OF EDUCATIONAL PRACTICES

OpenAIRE

Olena Glazunova; Olena Kuzminska; Tetyana Voloshyna; Taisia Sayapina; Valentyna Korolchuk

2017-01-01

Materials article analyzes the opportunities and benefits of using cloud services G Suite (Google Apps) during the practical training of students. In the course of the study, an e-environment based on G Suit for Education was developed and its use for effective organization of information technology practice training. A model of e-learning environment for organizing group project work in Google Classroom-based training has been built. The design methodology is grounded as one of the most effe...

Development of the DL/H-1 full pressure suit for private spaceflight

Science.gov (United States)

León, Pablo de; Harris, Gary L.

2010-06-01

The objective of this paper is to detail the need for full pressure suits to protect spaceflight participants during the experimental phases of flight testing of new space vehicles. It also details the objectives, historical background, basis for design, problems encountered by the designers and final development of the DL/H-1 full pressure suit. It will include justification for its use and results of the initial tests in the high altitude chamber and spacecraft simulator at the J.D. Odegard School of Aerospace Sciences at the University of North Dakota. For the test flights of early commercial space vehicles and tourist suborbital spacecrafts, emergency protection from the rarified air of the upper atmosphere and the vacuum of low Earth orbit almost certainly will be a requirement. Suborbital vehicles could be operating in "space equivalent conditions" for as long as 30 min to as much as several hours. In the case of cabin pressure loss, without personal protection, catastrophic loss of crew and vehicle could result. This paper explains the different steps taken by the authors who designed and built a preflight hardware pressure suit that can meet the physiological and comfort requirements of the tourist suborbital industry and the early commercial private spaceflight community. The suborbital tourist and commercial spaceflight industry have unique problems confronting the pressure suit builder such as unpressurized comfort, reasonable expense, unique sizing of the general population, decompression complications of persons not fitting a past military physiology profile and equipment weight issues. In addition, the lack of a certifying agency or guidance from international or national aviation authorities has created the opportunity for the emerging civilian pressure suit industry to create a new safety standard by which it can regulate itself in the same way the recreational SCUBA diving industry has since the late 1950s.

Human skin in vitro permeation of bentazon and isoproturon formulations with or without protective clothing suit.

Science.gov (United States)

Berthet, Aurélie; Hopf, Nancy B; Miles, Alexandra; Spring, Philipp; Charrière, Nicole; Garrigou, Alain; Baldi, Isabelle; Vernez, David

2014-01-01

Skin exposures to chemicals may lead, through percutaneous permeation, to a significant increase in systemic circulation. Skin is the primary route of entry during some occupational activities, especially in agriculture. To reduce skin exposures, the use of personal protective equipment (PPE) is recommended. PPE efficiency is characterized as the time until products permeate through material (lag time, Tlag). Both skin and PPE permeations are assessed using similar in vitro methods; the diffusion cell system. Flow-through diffusion cells were used in this study to assess the permeation of two herbicides, bentazon and isoproturon, as well as four related commercial formulations (Basagran(®), Basamais(®), Arelon(®) and Matara(®)). Permeation was measured through fresh excised human skin, protective clothing suits (suits) (Microchem(®) 3000, AgriSafe Pro(®), Proshield(®) and Microgard(®) 2000 Plus Green), and a combination of skin and suits. Both herbicides, tested by itself or as an active ingredient in formulations, permeated readily through human skin and tested suits (Tlag < 2 h). High permeation coefficients were obtained regardless of formulations or tested membranes, except for Microchem(®) 3000. Short Tlag, were observed even when skin was covered with suits, except for Microchem(®) 3000. Kp values tended to decrease when suits covered the skin (except when Arelon(®) was applied to skin covered with AgriSafe Pro and Microgard(®) 2000), suggesting that Tlag alone is insufficient in characterizing suits. To better estimate human skin permeations, in vitro experiments should not only use human skin but also consider the intended use of the suit, i.e., the active ingredient concentrations and type of formulations, which significantly affect skin permeation.

The Sequenced Angiosperm Genomes and Genome Databases.

Science.gov (United States)

Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

2018-01-01

Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.

Identification and structural characterization of serobactins, a suite of lipopeptide siderophores produced by the grass endophyte Herbaspirillum seropedicae.

Science.gov (United States)

Rosconi, Federico; Davyt, Danilo; Martínez, Verónica; Martínez, Marcela; Abin-Carriquiry, Juan Andrés; Zane, Hannah; Butler, Alison; de Souza, Emanuel M; Fabiano, Elena

2013-03-01

Herbaspirillum seropedicae Z67 is a diazotrophic endophyte able to colonize the interior of many economically relevant crops such as rice, wheat, corn and sorghum. Structures of siderophores produced by bacterial endophytes have not yet been elucidated. The aim of this work was to identify and characterize the siderophores produced by this bacterium. In a screening for mutants unable to produce siderophores we found a mutant that had a transposon insertion in a non-ribosomal peptide synthase (NRPS) gene coding for a putative siderophore biosynthetic enzyme. The chemical structure of the siderophore was predicted using computational genomic tools. The predicted structure was confirmed by chemical analysis. We found that siderophores produced by H. seropedicae Z67 are a suite of amphiphilic lipopeptides, named serobactin A, B and C, which vary by the length of the fatty acid chain. We also demonstrated the biological activity of serobactins as nutritional iron sources for H. seropedicae. These are the first structurally described siderophores produced by endophytic bacteria. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

COMBO-FISH Enables High Precision Localization Microscopy as a Prerequisite for Nanostructure Analysis of Genome Loci

Directory of Open Access Journals (Sweden)

Rainer Kaufmann

2010-10-01

Full Text Available With the completeness of genome databases, it has become possible to develop a novel FISH (Fluorescence in Situ Hybridization technique called COMBO-FISH (COMBinatorial Oligo FISH. In contrast to other FISH techniques, COMBO-FISH makes use of a bioinformatics approach for probe set design. By means of computer genome database searching, several oligonucleotide stretches of typical lengths of 15–30 nucleotides are selected in such a way that all uniquely colocalize at the given genome target. The probes applied here were Peptide Nucleic Acids (PNAs—synthetic DNA analogues with a neutral backbone—which were synthesized under high purity conditions. For a probe repetitively highlighted in centromere 9, PNAs labeled with different dyes were tested, among which Alexa 488Ò showed reversible photobleaching (blinking between dark and bright state a prerequisite for the application of SPDM (Spectral Precision Distance/Position Determination Microscopy a novel technique of high resolution fluorescence localization microscopy. Although COMBO-FISH labeled cell nuclei under SPDM conditions sometimes revealed fluorescent background, the specific locus was clearly discriminated by the signal intensity and the resulting localization accuracy in the range of 10–20 nm for a detected oligonucleotide stretch. The results indicate that COMBO-FISH probes with blinking dyes are well suited for SPDM, which will open new perspectives on molecular nanostructural analysis of the genome.

GenColors-based comparative genome databases for small eukaryotic genomes.

Science.gov (United States)

Felder, Marius; Romualdi, Alessandro; Petzold, Andreas; Platzer, Matthias; Sühnel, Jürgen; Glöckner, Gernot

2013-01-01

Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources.

Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute's genomic medicine portfolio.

Science.gov (United States)

Manolio, Teri A

2016-10-01

Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual's genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of "Genomic Medicine Meetings," under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and difficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI's genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so. Published by Elsevier Ireland Ltd.

Nonventing Thermal and Humidity Control for EVA Suits, Phase II

Data.gov (United States)

National Aeronautics and Space Administration — Future manned space exploration missions will require space suits with capabilities beyond the current state of the art. Portable Life Support Systems for these...

Dynamic Human-Centered Suit Design: A Computational and Experimental Method

Data.gov (United States)

National Aeronautics and Space Administration — Introduction: Manned space flight necessitates an ability to provide life support to crewmembers during multiple mission stages, in the form of space suits. With...

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

Science.gov (United States)

Machado, Henrique; Gram, Lone

2017-01-01

Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur , amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.

Rodent malaria parasites : genome organization & comparative genomics

NARCIS (Netherlands)

Kooij, Taco W.A.

2006-01-01

The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P.

Genome size analyses of Pucciniales reveal the largest fungal genomes.

Science.gov (United States)

Tavares, Sílvia; Ramos, Ana Paula; Pires, Ana Sofia; Azinheira, Helena G; Caldeirinha, Patrícia; Link, Tobias; Abranches, Rita; Silva, Maria do Céu; Voegele, Ralf T; Loureiro, João; Talhinhas, Pedro

2014-01-01

Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.

Asteroid Redirect Crewed Mission Space Suit and EVA System Architecture Trade Study

Science.gov (United States)

Blanco, Raul A.; Bowie, Jonathan T.; Watson, Richard D.; Sipila, Stephanie A.

2014-01-01

The Asteroid Redirect Crewed Mission (ARCM) requires a Launch/Entry/Abort (LEA) suit capability and short duration Extra Vehicular Activity (EVA) capability for Orion. The EVAs will involve a two-person crew for approximately four hours. Currently, two EVAs are planned with one contingency EVA in reserve. Providing this EVA capability is very challenging due to system level constraints and a new and unknown environment. The goal of the EVA architecture for ARCM is one that builds upon previously developed technologies and lessons learned, and that accomplishes the ARCM mission while providing a stepping stone to future missions and destinations. The primary system level constraints are to 1) minimize system mass and volume and 2) minimize the interfacing impacts to the baseline Orion design. In order to minimize the interfacing impacts and to not perturb the baseline Orion schedule, the concept of adding "kits" to the baseline system is proposed. These kits consist of: an EVA kit (converts LEA suit to EVA suit), EVA Servicing and Recharge Kit (provides suit consumables), the EVA Tools, Translation Aids & Sample Container Kit (the tools and mobility aids to complete the tasks), the EVA Communications Kit (interface between the EVA radio and the MPCV), and the Cabin Repress Kit (represses the MPCV between EVAs). This paper will focus on the trade space, analysis, and testing regarding the space suit (pressure garment and life support system). Historical approaches and lessons learned from all past EVA operations were researched. Previous and current, successfully operated EVA hardware and high technology readiness level (TRL) hardware were evaluated, and a trade study was conducted for all possible pressure garment and life support options. Testing and analysis was conducted and a recommended EVA system architecture was proposed. Pressure garment options that were considered for this mission include the currently in-use ISS EVA Mobility Unit (EMU), all variations of

Sibelius: Karelia Suite, Op. 11. Luonnotar, Op. 70 a. Andante festivo. The Oceanides, Op. 73. King Christian II, Op. 27-Suite. Finlandia, Op. 26a. Gothenburg Symphony Orchester, Neeme Järvi / Michael Scott Rohan

Index Scriptorium Estoniae

Rohan, Michael Scott

1996-01-01

Sibelius: Karelia Suite, Op. 11. Luonnotar, Op. 70 a. Andante festivo. The Oceanides, Op. 73. King Christian II, Op. 27-Suite. Finlandia, Op. 26a. Gothenburg Symphony Orchester, Neeme Järvi. 1 CD Deutsche Grammophon 447 760-2GH (72 minutes: DDD)

ASIM - an Instrument Suite for the International Space Station

DEFF Research Database (Denmark)

Neubert, Torsten; Crosby, B.; Huang, T.-Y.

2009-01-01

ASIM (Atmosphere-Space Interactions Monitor) is an instrument suite for studies of severe thunderstorms and their effects on the atmosphere and ionosphere. The instruments are designed to observe transient luminous events (TLEs)—sprites, blue jets and elves—and terrestrial gamma-ray flashes (TGFs...

Geochemical fingerprinting of ∼2.5 Ga forearc-arc-backarc related magmatic suites in the Bastar Craton, central India

Science.gov (United States)

Asthana, Deepanker; Kumar, Sirish; Vind, Aditya Kumar; Zehra, Fatima; Kumar, Harshavardhan; Pophare, Anil M.

2018-05-01

The Pitepani volcanic suite of the Dongargarh Supergroup, central India comprises of a calc-alkaline suite and a tholeiitic suite, respectively. The rare earth element (REE) patterns, mantle normalized plots and relict clinopyroxene chemistry of the Pitepani calc-alkaline suite are akin to high-Mg andesites (HMA) and reveal remarkable similarity to the Cenozoic Setouchi HMA from Japan. The Pitepani HMAs are geochemically correlated with similar rocks in the Kotri-Dongargarh mobile belt (KDMB) and in the mafic dykes of the Bastar Craton. The rationale behind lithogeochemical correlations are that sanukitic HMAs represent fore-arc volcanism over a very limited period of time, under abnormally high temperature conditions and are excellent regional and tectonic time markers. Furthermore, the tholeiitic suites that are temporally and spatially associated with the HMAs in the KDMB and in the mafic dykes of the Bastar Craton are classified into: (a) a continental back-arc suite that are depleted in incompatible elements, and (b) a continental arc suite that are more depleted in incompatible elements, respectively. The HMA suite, the continental back-arc and continental arc suites are lithogeochemically correlated in the KDMB and in the mafic dykes of the Bastar Craton. The three geochemically distinct Neoarchaean magmatic suites are temporally and spatially related to each other and to an active continental margin. The identification of three active continental margin magmatic suites for the first time, provides a robust conceptual framework to unravel the Neoarchaean geodynamic evolution of the Bastar Craton. We propose an active continental margin along the Neoarchaen KDMB with eastward subduction coupled with slab roll back or preferably, ridge-subduction along the Central Indian Tectonic Zone (CITZ) to account for the three distinct magmatic suites and the Neoarchean geodynamic evolution of the Bastar Craton.

RPAN: rice pan-genome browser for ∼3000 rice genomes.

Science.gov (United States)

Sun, Chen; Hu, Zhiqiang; Zheng, Tianqing; Lu, Kuangchen; Zhao, Yue; Wang, Wensheng; Shi, Jianxin; Wang, Chunchao; Lu, Jinyuan; Zhang, Dabing; Li, Zhikang; Wei, Chaochun

2017-01-25

A pan-genome is the union of the gene sets of all the individuals of a clade or a species and it provides a new dimension of genome complexity with the presence/absence variations (PAVs) of genes among these genomes. With the progress of sequencing technologies, pan-genome study is becoming affordable for eukaryotes with large-sized genomes. The Asian cultivated rice, Oryza sativa L., is one of the major food sources for the world and a model organism in plant biology. Recently, the 3000 Rice Genome Project (3K RGP) sequenced more than 3000 rice genomes with a mean sequencing depth of 14.3×, which provided a tremendous resource for rice research. In this paper, we present a genome browser, Rice Pan-genome Browser (RPAN), as a tool to search and visualize the rice pan-genome derived from 3K RGP. RPAN contains a database of the basic information of 3010 rice accessions, including genomic sequences, gene annotations, PAV information and gene expression data of the rice pan-genome. At least 12 000 novel genes absent in the reference genome were included. RPAN also provides multiple search and visualization functions. RPAN can be a rich resource for rice biology and rice breeding. It is available at http://cgm.sjtu.edu.cn/3kricedb/ or http://www.rmbreeding.cn/pan3k. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome

Science.gov (United States)

CRISPR/Cas9 has been recently demonstrated as an effective and popular genome editing tool for modifying genomes of human, animals, microorganisms, and plants. Success of such genome editing is highly dependent on the availability of suitable target sites in the genomes to be edited. Many specific t...

Anesthesia and the pediatric cardiac catheterization suite: a review.

Science.gov (United States)

Lam, Jennifer E; Lin, Erica P; Alexy, Ryan; Aronson, Lori A

2015-02-01

Advances in technology over the last couple of decades have caused a shift in pediatric cardiac catheterization from a primary focus on diagnostics to innovative therapeutic interventions. These improvements allow patients a wider range of nonsurgical options for treatment of congenital heart disease. However, these therapeutic modalities can entail higher risk in an already complex patient population, compounded by the added challenges inherent to the environment of the cardiac catheterization suite. Anesthesiologists caring for children with congenital heart disease must understand not only the pathophysiology of the disease but also the effects the anesthetics and interventions have on the patient in order to provide a safe perioperative course. It is the aim of this article to review the latest catheterization modalities offered to patients with congenital heart disease, describe the unique challenges presented in the cardiac catheterization suite, list the most common complications encountered during catheterization and finally, to review the literature regarding different anesthetic drugs used in the catheterization lab. © 2014 John Wiley & Sons Ltd.

Modeling the Impact of Space Suit Components and Anthropometry on the Center of Mass of a Seated Crewmember

Science.gov (United States)

Blackledge, Christopher; Margerum, Sarah; Ferrer, Mike; Morency, Richard; Rajulu, Sudhakar

2010-01-01

The Crew Impact Attenuation System (CIAS) is the energy-absorbing strut concept that dampens Orion Crew Exploration Vehicle (CEV) landing loads to levels sustainable by the crew. Significant COM variations across suited crew configurations would amplify the inertial effects of the pallet and potentially create unacceptable crew loading during launch and landing. The objective of this study was to obtain data needed for dynamic simulation models by quantifying the effects of posture, suit components, and the expected range of anthropometry on the COM of a seated individual. Several elements are required for the COM calculation of a suited human in a seated position: anthropometry, body segment mass, suit component mass, suit component location relative to the body, and joint angles defining the seated posture. Three-dimensional (3D) human body models, suit mass data, and vector calculus were utilized to compute the COM positions for 12 boundary manikins in two different seated postures. The analysis focused on two objectives: (1) quantify how much the wholebody COM varied from the smallest to largest subject and (2) quantify the effects of the suit components on the overall COM in each seat configuration. The location of the anterior-posterior COM varied across all boundary manikins by about 7 cm, and the vertical COM varied by approximately 9 to 10 cm. The mediolateral COM varied by 1.2 cm from the midline sagittal plane for both seat configurations. The suit components caused an anterior shift of the total COM by approximately 2 cm and a shift to the right along the mediolateral axis of 0.4 cm for both seat configurations. When the seat configuration was in the standard posture the suited vertical COM shifted inferiorly by as much as 1 cm, whereas in the CEV posture the vertical COM had no appreciable change. These general differences were due to the high proportion of suit mass located in the boots and lower legs and their corresponding distance from the body COM

Prokofiev: War and Peace - Symphonic Suite (arr. Palmer) / Ivan March

Index Scriptorium Estoniae

March, Ivan

1993-01-01

Uuest heliplaadist "Prokofiev: War and Peace - Symphonic Suite (arr. Palmer), Summer Night, Op. 123. Russian Overture, Op. 72. Philharmonia Orchestra / Neeme Järvi. Chandos ABTD 1598 CHAN9096 (64 minutes:DDD) Igor - Polovtsian Dances

Genomics Portals: integrative web-platform for mining genomics data.

Science.gov (United States)

Shinde, Kaustubh; Phatak, Mukta; Johannes, Freudenberg M; Chen, Jing; Li, Qian; Vineet, Joshi K; Hu, Zhen; Ghosh, Krishnendu; Meller, Jaroslaw; Medvedovic, Mario

2010-01-13

A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

i-Genome: A database to summarize oligonucleotide data in genomes

Directory of Open Access Journals (Sweden)

Chang Yu-Chung

2004-10-01

Full Text Available Abstract Background Information on the occurrence of sequence features in genomes is crucial to comparative genomics, evolutionary analysis, the analyses of regulatory sequences and the quantitative evaluation of sequences. Computing the frequencies and the occurrences of a pattern in complete genomes is time-consuming. Results The proposed database provides information about sequence features generated by exhaustively computing the sequences of the complete genome. The repetitive elements in the eukaryotic genomes, such as LINEs, SINEs, Alu and LTR, are obtained from Repbase. The database supports various complete genomes including human, yeast, worm, and 128 microbial genomes. Conclusions This investigation presents and implements an efficiently computational approach to accumulate the occurrences of the oligonucleotides or patterns in complete genomes. A database is established to maintain the information of the sequence features, including the distributions of oligonucleotide, the gene distribution, the distribution of repetitive elements in genomes and the occurrences of the oligonucleotides. The database can provide more effective and efficient way to access the repetitive features in genomes.

Integrative Functional Genomics for Systems Genetics in GeneWeaver.org.

Science.gov (United States)

Bubier, Jason A; Langston, Michael A; Baker, Erich J; Chesler, Elissa J

2017-01-01

The abundance of existing functional genomics studies permits an integrative approach to interpreting and resolving the results of diverse systems genetics studies. However, a major challenge lies in assembling and harmonizing heterogeneous data sets across species for facile comparison to the positional candidate genes and coexpression networks that come from systems genetic studies. GeneWeaver is an online database and suite of tools at www.geneweaver.org that allows for fast aggregation and analysis of gene set-centric data. GeneWeaver contains curated experimental data together with resource-level data such as GO annotations, MP annotations, and KEGG pathways, along with persistent stores of user entered data sets. These can be entered directly into GeneWeaver or transferred from widely used resources such as GeneNetwork.org. Data are analyzed using statistical tools and advanced graph algorithms to discover new relations, prioritize candidate genes, and generate function hypotheses. Here we use GeneWeaver to find genes common to multiple gene sets, prioritize candidate genes from a quantitative trait locus, and characterize a set of differentially expressed genes. Coupling a large multispecies repository curated and empirical functional genomics data to fast computational tools allows for the rapid integrative analysis of heterogeneous data for interpreting and extrapolating systems genetics results.

STS-95 Mission Specialist Pedro Duque suits up for launch

Science.gov (United States)

1998-01-01

STS-95 Mission Specialist Pedro Duque of Spain, with the European Space Agency, is helped with his flight suit by suit tech Tommy McDonald in the Operations and Checkout Building. The final fitting takes place prior to the crew walkout and transport to Launch Pad 39B. Targeted for launch at 2 p.m. EST on Oct. 29, the mission is expected to last 8 days, 21 hours and 49 minutes, and return to KSC at 11:49 a.m. EST on Nov. 7. The STS-95 mission includes research payloads such as the Spartan solar-observing deployable spacecraft, the Hubble Space Telescope Orbital Systems Test Platform, the International Extreme Ultraviolet Hitchhiker, as well as the SPACEHAB single module with experiments on space flight and the aging process.

Differential gene expression by 1,25(OH)2D3 in an endometriosis stromal cell line.

Science.gov (United States)

Ingles, Sue Ann; Wu, Liang; Liu, Benjamin T; Chen, Yibu; Wang, Chun-Yeh; Templeman, Claire; Brueggmann, Doerthe

2017-10-01

Endometriosis is a common female reproductive disease characterized by invasion of endometrial cells into other organs, frequently causing pelvic pain and infertility. Alterations of the vitamin D system have been linked to endometriosis incidence and severity. To shed light on the potential mechanism for these associations, we examined the effects of 1,25(OH) 2 D 3 on gene expression in endometriosis cells. Stromal cell lines derived from endometriosis tissue were treated with 1,25(OH) 2 D 3 , and RNA-seq was used to identify genes differentially expressed between treated and untreated cells. Gene ontology and pathway analyses were carried out using Partek Flow and Ingenuity software suites, respectively. We identified 1627 genes that were differentially expressed (886 down-regulated and 741 up-regulated) by 1,25(OH) 2 D 3 . Only one gene, CYP24A1, was strongly up-regulated (369-fold). Many genes were strongly down-regulated. 1,25(OH) 2 D 3 treatment down-regulated several genetic pathways related to neuroangiogenesis, cellular motility, and invasion, including pathways for axonal guidance, Rho GDP signaling, and matrix metalloprotease inhibition. These findings support a role for vitamin D in the pathophysiology of endometriosis, and provide new targets for investigation into possible causes and treatments. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Perennial Ryegrass GenomeZipper: Targeted Use of Genome Resources for Comparative Grass Genomics1[C][W

Science.gov (United States)

Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F.X.; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

2013-01-01

Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species. PMID:23184232

Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute’s genomic medicine portfolio

Science.gov (United States)

Manolio, Teri A.

2016-01-01

Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual’s genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of “Genomic Medicine Meetings,” under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and diffficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI’s genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so. PMID:27612677

GenomeCAT: a versatile tool for the analysis and integrative visualization of DNA copy number variants.

Science.gov (United States)

Tebel, Katrin; Boldt, Vivien; Steininger, Anne; Port, Matthias; Ebert, Grit; Ullmann, Reinhard

2017-01-06

The analysis of DNA copy number variants (CNV) has increasing impact in the field of genetic diagnostics and research. However, the interpretation of CNV data derived from high resolution array CGH or NGS platforms is complicated by the considerable variability of the human genome. Therefore, tools for multidimensional data analysis and comparison of patient cohorts are needed to assist in the discrimination of clinically relevant CNVs from others. We developed GenomeCAT, a standalone Java application for the analysis and integrative visualization of CNVs. GenomeCAT is composed of three modules dedicated to the inspection of single cases, comparative analysis of multidimensional data and group comparisons aiming at the identification of recurrent aberrations in patients sharing the same phenotype, respectively. Its flexible import options ease the comparative analysis of own results derived from microarray or NGS platforms with data from literature or public depositories. Multidimensional data obtained from different experiment types can be merged into a common data matrix to enable common visualization and analysis. All results are stored in the integrated MySQL database, but can also be exported as tab delimited files for further statistical calculations in external programs. GenomeCAT offers a broad spectrum of visualization and analysis tools that assist in the evaluation of CNVs in the context of other experiment data and annotations. The use of GenomeCAT does not require any specialized computer skills. The various R packages implemented for data analysis are fully integrated into GenomeCATs graphical user interface and the installation process is supported by a wizard. The flexibility in terms of data import and export in combination with the ability to create a common data matrix makes the program also well suited as an interface between genomic data from heterogeneous sources and external software tools. Due to the modular architecture the functionality of

STS-93 Pilot Ashby suits up before launch

Science.gov (United States)

1999-01-01

In the Operations and Checkout Building during final launch preparations for the second time, STS-93 Pilot Jeffrey S. Ashby waves after donning his launch and entry suit while a suit tech adjusts his boot. After Space Shuttle Columbia's July 20 launch attempt was scrubbed at the T-7 second mark in the countdown, the launch was rescheduled for Thursday, July 22, at 12:28 a.m. EDT. The target landing date is July 26, 1999, at 11:24 p.m. EDT. STS- 93 is a five-day mission primarily to release the Chandra X-ray Observatory, which will allow scientists from around the world to study some of the most distant, powerful and dynamic objects in the universe. The new telescope is 20 to 50 times more sensitive than any previous X-ray telescope and is expected unlock the secrets of supernovae, quasars and black holes. The STS-93 crew numbers five: Commander Eileen M. Collins, Ashby, and Mission Specialists Stephen A. Hawley (Ph.D.), Catherine G. Coleman (Ph.D.) and Michel Tognini of France, with the Centre National d'Etudes Spatiales (CNES). Collins is the first woman to serve as commander of a shuttle mission.

Comparing Mycobacterium tuberculosis genomes using genome topology networks.

Science.gov (United States)

Jiang, Jianping; Gu, Jianlei; Zhang, Liang; Zhang, Chenyi; Deng, Xiao; Dou, Tonghai; Zhao, Guoping; Zhou, Yan

2015-02-14

Over the last decade, emerging research methods, such as comparative genomic analysis and phylogenetic study, have yielded new insights into genotypes and phenotypes of closely related bacterial strains. Several findings have revealed that genomic structural variations (SVs), including gene gain/loss, gene duplication and genome rearrangement, can lead to different phenotypes among strains, and an investigation of genes affected by SVs may extend our knowledge of the relationships between SVs and phenotypes in microbes, especially in pathogenic bacteria. In this work, we introduce a 'Genome Topology Network' (GTN) method based on gene homology and gene locations to analyze genomic SVs and perform phylogenetic analysis. Furthermore, the concept of 'unfixed ortholog' has been proposed, whose members are affected by SVs in genome topology among close species. To improve the precision of 'unfixed ortholog' recognition, a strategy to detect annotation differences and complete gene annotation was applied. To assess the GTN method, a set of thirteen complete M. tuberculosis genomes was analyzed as a case study. GTNs with two different gene homology-assigning methods were built, the Clusters of Orthologous Groups (COG) method and the orthoMCL clustering method, and two phylogenetic trees were constructed accordingly, which may provide additional insights into whole genome-based phylogenetic analysis. We obtained 24 unfixable COG groups, of which most members were related to immunogenicity and drug resistance, such as PPE-repeat proteins (COG5651) and transcriptional regulator TetR gene family members (COG1309). The GTN method has been implemented in PERL and released on our website. The tool can be downloaded from http://homepage.fudan.edu.cn/zhouyan/gtn/ , and allows re-annotating the 'lost' genes among closely related genomes, analyzing genes affected by SVs, and performing phylogenetic analysis. With this tool, many immunogenic-related and drug resistance-related genes

A universal genomic coordinate translator for comparative genomics.

Science.gov (United States)

Zamani, Neda; Sundström, Görel; Meadows, Jennifer R S; Höppner, Marc P; Dainat, Jacques; Lantz, Henrik; Haas, Brian J; Grabherr, Manfred G

2014-06-30

Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic sequences. However, a comprehensive analysis of duplication events and their contributions to evolution would require all-to-all genome alignments, which increases at N2 with the number of available genomes, N. Here, we introduce Kraken, software that omits the all-to-all requirement by recursively traversing a graph of pairwise alignments and dynamically re-computing orthology. Kraken scales linearly with the number of targeted genomes, N, which allows for including large numbers of genomes in analyses. We first evaluated the method on the set of 12 Drosophila genomes, finding that orthologous correspondence computed indirectly through a graph of multiple synteny maps comes at minimal cost in terms of sensitivity, but reduces overall computational runtime by an order of magnitude. We then used the method on three well-annotated mammalian genomes, human, mouse, and rat, and show that up to 93% of protein coding transcripts have unambiguous pairwise orthologous relationships across the genomes. On a nucleotide level, 70 to 83% of exons match exactly at both splice junctions, and up to 97% on at least one junction. We last applied Kraken to an RNA-sequencing dataset from multiple vertebrates and diverse tissues, where we confirmed that brain-specific gene family members, i.e. one-to-many or many-to-many homologs, are more highly correlated across species than single-copy (i.e. one-to-one homologous) genes. Not limited to protein coding genes, Kraken also identifies thousands of newly identified transcribed loci, likely non-coding RNAs that are consistently transcribed in human, chimpanzee and gorilla, and maintain significant correlation of expression levels across

Measuring Test Case Similarity to Support Test Suite Understanding

NARCIS (Netherlands)

Greiler, M.S.; Van Deursen, A.; Zaidman, A.E.

2012-01-01

Preprint of paper published in: TOOLS 2012 - Proceedings of the 50th International Conference, Prague, Czech Republic, May 29-31, 2012; doi:10.1007/978-3-642-30561-0_8 In order to support test suite understanding, we investigate whether we can automatically derive relations between test cases. In

Automated integration of lidar into the LANDFIRE product suite

Science.gov (United States)

Birgit Peterson; Kurtis J. Nelson; Carl Seielstad; Jason Stoker; W. Matt Jolly; Russell Parsons

2015-01-01

Accurate information about three-dimensional canopy structure and wildland fuel across the landscape is necessary for fire behaviour modelling system predictions. Remotely sensed data are invaluable for assessing these canopy characteristics over large areas; lidar data, in particular, are uniquely suited for quantifying three-dimensional canopy structure. Although...

Post-collisional magmatism in the central East African Orogen: The Maevarano Suite of north Madagascar

Science.gov (United States)

Goodenough, K.M.; Thomas, Ronald J.; De Waele, B.; Key, R.M.; Schofield, D.I.; Bauer, W.; Tucker, R.D.; Rafahatelo, J.-M.; Rabarimanana, M.; Ralison, A.V.; Randriamananjara, T.

2010-01-01

Late tectonic, post-collisional granite suites are a feature of many parts of the Late Neoproterozoic to Cambrian East African Orogen (EAO), where they are generally attributed to late extensional collapse of the orogen, accompanied by high heat flow and asthenospheric uprise. The Maevarano Suite comprises voluminous plutons which were emplaced in some of the tectonostratigraphic terranes of northern Madagascar, in the central part of the EAO, following collision and assembly during a major orogeny at ca. 550 Ma. The suite comprises three main magmatic phases: a minor early phase of foliated gabbros, quartz diorites, and granodiorites; a main phase of large batholiths of porphyritic granitoids and charnockites; and a late phase of small-scale plutons and sheets of monzonite, syenite, leucogranite and microgranite. The main phase intrusions tend to be massive, but with variably foliated margins. New U-Pb SHRIMP zircon data show that the whole suite was emplaced between ca. 537 and 522 Ma. Geochemically, all the rocks of the suite are enriched in the LILE, especially K, and the LREE, but are relatively depleted in Nb, Ta and the HREE. These characteristics are typical of post-collisional granitoids in the EAO and many other orogenic belts. It is proposed that the Maevarano Suite magmas were derived by melting of sub-continental lithospheric mantle that had been enriched in the LILE during earlier subduction events. The melting occurred during lithospheric delamination, which was associated with extensional collapse of the East African Orogen. ?? 2009 Natural Environment Research Council.

Tchaikovsky, P.: Orchestral Suite no. 3 op. 55 / Terry Williams

Index Scriptorium Estoniae

Williams, Terry

1996-01-01

Uuest heliplaadist "Tchaikovsky, P.: Orchestral Suite no. 3 op. 55. Francesca di Rimini op. 32. Detroit Symphony Orchestra, Neeme Järvi". Chandos CHAN 9 419, distribution Media 7 (CD: 160F). TT: 1h 09'20"

Enhanced verification test suite for physics simulation codes

Energy Technology Data Exchange (ETDEWEB)

Kamm, James R.; Brock, Jerry S.; Brandon, Scott T.; Cotrell, David L.; Johnson, Bryan; Knupp, Patrick; Rider, William J.; Trucano, Timothy G.; Weirs, V. Gregory

2008-09-01

This document discusses problems with which to augment, in quantity and in quality, the existing tri-laboratory suite of verification problems used by Los Alamos National Laboratory (LANL), Lawrence Livermore National Laboratory (LLNL), and Sandia National Laboratories (SNL). The purpose of verification analysis is demonstrate whether the numerical results of the discretization algorithms in physics and engineering simulation codes provide correct solutions of the corresponding continuum equations.

Genomics Portals: integrative web-platform for mining genomics data

Directory of Open Access Journals (Sweden)

Ghosh Krishnendu

2010-01-01

Full Text Available Abstract Background A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Results Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc, and the integration with an extensive knowledge base that can be used in such analysis. Conclusion The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis.

Science.gov (United States)

Koo, Byoung-Mo; Kritikos, George; Farelli, Jeremiah D; Todor, Horia; Tong, Kenneth; Kimsey, Harvey; Wapinski, Ilan; Galardini, Marco; Cabal, Angelo; Peters, Jason M; Hachmann, Anna-Barbara; Rudner, David Z; Allen, Karen N; Typas, Athanasios; Gross, Carol A

2017-03-22

A systems-level understanding of Gram-positive bacteria is important from both an environmental and health perspective and is most easily obtained when high-quality, validated genomic resources are available. To this end, we constructed two ordered, barcoded, erythromycin-resistance- and kanamycin-resistance-marked single-gene deletion libraries of the Gram-positive model organism, Bacillus subtilis. The libraries comprise 3,968 and 3,970 genes, respectively, and overlap in all but four genes. Using these libraries, we update the set of essential genes known for this organism, provide a comprehensive compendium of B. subtilis auxotrophic genes, and identify genes required for utilizing specific carbon and nitrogen sources, as well as those required for growth at low temperature. We report the identification of enzymes catalyzing several missing steps in amino acid biosynthesis. Finally, we describe a suite of high-throughput phenotyping methodologies and apply them to provide a genome-wide analysis of competence and sporulation. Altogether, we provide versatile resources for studying gene function and pathway and network architecture in Gram-positive bacteria. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

[The antigravity suit, chamberless type, as a means of increasing orthostatic tolerance after water immersion hypokinesis and acceleration].

Science.gov (United States)

Shul'zhenko, E B; Kozlova, V G; Kurdin, K A; Iarov, A S; Plokhova, V G

1983-01-01

Orthostatic tolerance after 7-day dry immersion and head-to-feet acceleration was investigated on test subjects with and without an antigravity suit of bladderless type. With the suit on, the 20 min tilt test at 70 degrees prior to immersion induced less marked changes than without the suit. When the suit was on, cardiovascular reactions to tilt tests after immersion and acceleration improved. The maximum heart rate decreased from 135 +/- 4 to 101 +/- 5 beats/min (p less than 0.01), minimum stroke volume increased from 29 +/- 2 to 41 +/- 3 ml (p less than 0.05), and pulse pressure grew. Thus, an antigravity suit may help increase initial orthostatic tolerance and maintain it after the combined effect of simulated hypogravity and acceleration.

Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative.

Science.gov (United States)

Wang, Jun; Kurilshikov, Alexander; Radjabzadeh, Djawad; Turpin, Williams; Croitoru, Kenneth; Bonder, Marc Jan; Jackson, Matthew A; Medina-Gomez, Carolina; Frost, Fabian; Homuth, Georg; Rühlemann, Malte; Hughes, David; Kim, Han-Na; Spector, Tim D; Bell, Jordana T; Steves, Claire J; Timpson, Nicolas; Franke, Andre; Wijmenga, Cisca; Meyer, Katie; Kacprowski, Tim; Franke, Lude; Paterson, Andrew D; Raes, Jeroen; Kraaij, Robert; Zhernakova, Alexandra

2018-06-08

In recent years, human microbiota, especially gut microbiota, have emerged as an important yet complex trait influencing human metabolism, immunology, and diseases. Many studies are investigating the forces underlying the observed variation, including the human genetic variants that shape human microbiota. Several preliminary genome-wide association studies (GWAS) have been completed, but more are necessary to achieve a fuller picture. Here, we announce the MiBioGen consortium initiative, which has assembled 18 population-level cohorts and some 19,000 participants. Its aim is to generate new knowledge for the rapidly developing field of microbiota research. Each cohort has surveyed the gut microbiome via 16S rRNA sequencing and genotyped their participants with full-genome SNP arrays. We have standardized the analytical pipelines for both the microbiota phenotypes and genotypes, and all the data have been processed using identical approaches. Our analysis of microbiome composition shows that we can reduce the potential artifacts introduced by technical differences in generating microbiota data. We are now in the process of benchmarking the association tests and performing meta-analyses of genome-wide associations. All pipeline and summary statistics results will be shared using public data repositories. We present the largest consortium to date devoted to microbiota-GWAS. We have adapted our analytical pipelines to suit multi-cohort analyses and expect to gain insight into host-microbiota cross-talk at the genome-wide level. And, as an open consortium, we invite more cohorts to join us (by contacting one of the corresponding authors) and to follow the analytical pipeline we have developed.

Implementing Sentinels in the TARGIT BI Suite

DEFF Research Database (Denmark)

Middelfart, Morten; Pedersen, Torben Bach

2011-01-01

This paper describes the implementation of socalled sentinels in the TARGIT BI Suite. Sentinels are a novel type of rules that can warn a user if one or more measure changes in a multi-dimensional data cube are expected to cause a change to another measure critical to the user. Sentinels notify u...... pattern mining or correlation techniques. We demonstrate, through extensive experiments, that mining and usage of sentinels is feasible with good performance for the typical users on a real, operational data warehouse....

ANALYSIS OF DESIGN ELEMENTS IN SKI SUITS

OpenAIRE

Çileroğlu, Birsen; Kelleci Özeren, Figen; Kıvılcımlar, İnci Seda

2015-01-01

Popularity of Ski Sport in 19th century necessitated a new perspective on protective skiing clothing against the mountain climates and excessive cold. Winter clothing were the basis of ski attire during this period.  By the beginning of 20th century lining cloth were used to minimize the wind effect. The difference between the men and women’s ski attire of the time consisted of a knee-length skirts worn over the golf trousers.  Subsequent to the First World War, skiing suit models were influe...

Genomic selection: genome-wide prediction in plant improvement.

Science.gov (United States)

Desta, Zeratsion Abera; Ortiz, Rodomiro

2014-09-01

Association analysis is used to measure relations between markers and quantitative trait loci (QTL). Their estimation ignores genes with small effects that trigger underpinning quantitative traits. By contrast, genome-wide selection estimates marker effects across the whole genome on the target population based on a prediction model developed in the training population (TP). Whole-genome prediction models estimate all marker effects in all loci and capture small QTL effects. Here, we review several genomic selection (GS) models with respect to both the prediction accuracy and genetic gain from selection. Phenotypic selection or marker-assisted breeding protocols can be replaced by selection, based on whole-genome predictions in which phenotyping updates the model to build up the prediction accuracy. Copyright © 2014 Elsevier Ltd. All rights reserved.

Modeling the Impact of Space Suit Components and Anthropometry on the Center of Mass of a Seated Crewmember

Science.gov (United States)

Rajulu, Sudhakar; Blackledge, Christopher; Ferrer, Mike; Margerum, Sarah

2009-01-01

The designers of the Orion Crew Exploration Vehicle (CEV) utilize an intensive simulation program in order to predict the launch and landing characteristics of the Crew Impact Attenuation System (CIAS). The CIAS is the energy absorbing strut concept that dampens loads to levels sustainable by the crew during landing and consists of the crew module seat pallet that accommodates four to six seated astronauts. An important parameter required for proper dynamic modeling of the CIAS is knowledge of the suited center of mass (COM) variations within the crew population. Significant center of mass variations across suited crew configurations would amplify the inertial effects of the pallet and potentially create unacceptable crew loading during launch and landing. Established suited, whole-body, and posture-based mass properties were not available due to the uncertainty of the final CEV seat posture and suit hardware configurations. While unsuited segmental center of mass values can be obtained via regression equations from previous studies, building them into a model that was posture dependent with custom anthropometry and integrated suit components proved cumbersome and time consuming. Therefore, the objective of this study was to quantify the effects of posture, suit components, and the expected range of anthropometry on the center of mass of a seated individual. Several elements are required for the COM calculation of a suited human in a seated position: anthropometry; body segment mass; suit component mass; suit component location relative to the body; and joint angles defining the seated posture. Anthropometry and body segment masses used in this study were taken from a selection of three-dimensional human body models, called boundary manikins, which were developed in a previous project. These boundary manikins represent the critical anthropometric dimension extremes for the anticipated astronaut population. Six male manikins and 6 female manikins, representing a

Technical Reference Suite Addressing Challenges of Providing Assurance for Fault Management Architectural Design

Science.gov (United States)

Fitz, Rhonda; Whitman, Gerek

2016-01-01

Research into complexities of software systems Fault Management (FM) and how architectural design decisions affect safety, preservation of assets, and maintenance of desired system functionality has coalesced into a technical reference (TR) suite that advances the provision of safety and mission assurance. The NASA Independent Verification and Validation (IV&V) Program, with Software Assurance Research Program support, extracted FM architectures across the IV&V portfolio to evaluate robustness, assess visibility for validation and test, and define software assurance methods applied to the architectures and designs. This investigation spanned IV&V projects with seven different primary developers, a wide range of sizes and complexities, and encompassed Deep Space Robotic, Human Spaceflight, and Earth Orbiter mission FM architectures. The initiative continues with an expansion of the TR suite to include Launch Vehicles, adding the benefit of investigating differences intrinsic to model-based FM architectures and insight into complexities of FM within an Agile software development environment, in order to improve awareness of how nontraditional processes affect FM architectural design and system health management. The identification of particular FM architectures, visibility, and associated IV&V techniques provides a TR suite that enables greater assurance that critical software systems will adequately protect against faults and respond to adverse conditions. Additionally, the role FM has with regard to strengthened security requirements, with potential to advance overall asset protection of flight software systems, is being addressed with the development of an adverse conditions database encompassing flight software vulnerabilities. Capitalizing on the established framework, this TR suite provides assurance capability for a variety of FM architectures and varied development approaches. Research results are being disseminated across NASA, other agencies, and the

Hollow Fiber Space Suit Water Membrane Evaporator Development for Lunar Missions

Science.gov (United States)

Bue, Grant C.; Trevino, Luis A.; Hanford, Anthony J.; Mitchell, Keith

2009-01-01

The Space Suit Water Membrane Evaporator (SWME) is the baseline heat rejection technology selected for development for the Constellation lunar suit. The Hollow Fiber (HoFi) SWME is being considered for service in the Constellation Space Suit Element (CSSE) Portable Life Support Subsystem (PLSS) to provide cooling to the thermal loop through water evaporation to the vacuum of space. Previous work described the test methodology and planning to compare the test performance of three commercially available hollow fiber materials as alternatives to the sheet membrane prototype for SWME: 1) porous hydrophobic polypropylene, 2) porous hydrophobic polysulfone, and 3) ion exchange through nonporous hydrophilic modified Nafion. Contamination tests were performed to probe for sensitivities of the candidate SWME elements to organics and non-volative inorganics expected to be found in the target feedwater source, i.e., potable water provided by the vehicle. The resulting presence of precipitate in the coolant water could plug pores and tube channels and affect the SWME performance. From this prior work, a commercial porous hydrophobic hollow fiber was selected to satisfy both the sensitivity question and the need to provide 800 W of heat rejection. This paper describes the trade studies, the design methodology, and the hollow fiber test data used to design a full

Functional Mobility Testing: A Novel Method to Create Suit Design Requirements

Science.gov (United States)

England, Scott A.; Benson, Elizabeth A.; Rajulu, Sudhakar L.

2008-01-01

This study was performed to aide in the creation of design requirements for the next generation of space suits that more accurately describe the level of mobility necessary for a suited crewmember through the use of an innovative methodology utilizing functional mobility. A novel method was utilized involving the collection of kinematic data while 20 subjects (10 male, 10 female) performed pertinent functional tasks that will be required of a suited crewmember during various phases of a lunar mission. These tasks were selected based on relevance and criticality from a larger list of tasks that may be carried out by the crew. Kinematic data was processed through Vicon BodyBuilder software to calculate joint angles for the ankle, knee, hip, torso, shoulder, elbow, and wrist. Maximum functional mobility was consistently lower than maximum isolated mobility. This study suggests that conventional methods for establishing design requirements for human-systems interfaces based on maximal isolated joint capabilities may overestimate the required mobility. Additionally, this method provides a valuable means of evaluating systems created from these requirements by comparing the mobility available in a new spacesuit, or the mobility required to use a new piece of hardware, to this newly established database of functional mobility.

OryzaGenome: Genome Diversity Database of Wild Oryza Species

KAUST Repository

Ohyanagi, Hajime

2015-11-18

The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of next-generation sequencing (NGS) technology, a flood of Oryza species reference genomes and genomic variation information has become available in recent years. This genomic information, combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype-phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions derived by imputation and of 17 accessions derived by imputation-free deep sequencing. Two variant viewers are implemented: SNP Viewer as a conventional genome browser interface and Variant Table as a textbased browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tabdelimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/ scaffolds/contigs and genome-wide variation information for almost all of the closely and distantly related wild Oryza species from the NIG Wild Rice Collection will be available in future releases. All of the resources can be accessed through http://viewer.shigen.info/oryzagenome/.

Using Partial Genomic Fosmid Libraries for Sequencing CompleteOrganellar Genomes

Energy Technology Data Exchange (ETDEWEB)

McNeal, Joel R.; Leebens-Mack, James H.; Arumuganathan, K.; Kuehl, Jennifer V.; Boore, Jeffrey L.; dePamphilis, Claude W.

2005-08-26

Organellar genome sequences provide numerous phylogenetic markers and yield insight into organellar function and molecular evolution. These genomes are much smaller in size than their nuclear counterparts; thus, their complete sequencing is much less expensive than total nuclear genome sequencing, making broader phylogenetic sampling feasible. However, for some organisms it is challenging to isolate plastid DNA for sequencing using standard methods. To overcome these difficulties, we constructed partial genomic libraries from total DNA preparations of two heterotrophic and two autotrophic angiosperm species using fosmid vectors. We then used macroarray screening to isolate clones containing large fragments of plastid DNA. A minimum tiling path of clones comprising the entire genome sequence of each plastid was selected, and these clones were shotgun-sequenced and assembled into complete genomes. Although this method worked well for both heterotrophic and autotrophic plants, nuclear genome size had a dramatic effect on the proportion of screened clones containing plastid DNA and, consequently, the overall number of clones that must be screened to ensure full plastid genome coverage. This technique makes it possible to determine complete plastid genome sequences for organisms that defy other available organellar genome sequencing methods, especially those for which limited amounts of tissue are available.

28 CFR 36.503 - Suit by the Attorney General.

Science.gov (United States)

2010-07-01

... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Suit by the Attorney General. 36.503... discretion, the Attorney General may commence a civil action in any appropriate United States district court if the Attorney General has reasonable cause to believe that— (a) Any person or group of persons is...

Nielsen: Aladdin-Suite, FS89. Maskarade-Overture / Robert Layton

Index Scriptorium Estoniae

Layton, Robert

1996-01-01

Uuest heliplaadist "Nielsen: Aladdin-Suite, FS89. Maskarade-Overture, Prelude, Act 2. The Cockerels' Dance. Rhapsody Overture: An imaginary journey to the Faroe Islands, FS123. Helios Overture, FS32. Saga-Drom, FS46. Pan and Syrinx, FS87. Gothenburg Symphony Orchestra, Neeme Järvi" DG 447 757-2GH (72 minutes: DDD)

Tailoring Vantage 5 (fuel) to suit each operator's need

Energy Technology Data Exchange (ETDEWEB)

Chapin, D L; Secker, J R [Westinghouse Electric Corp., Philadelphia, PA (USA)

1990-03-01

By the end of 1989, Westinghouse Vantage 5 fuel had been reloaded into 36 nuclear power plants. The fuel offers a number of features operators can choose from to suit their own particular needs. Experience so far has shown the fuel to have performed well, with coolant activity levels remaining low. (author).

Precise detection of de novo single nucleotide variants in human genomes.

Science.gov (United States)

Gómez-Romero, Laura; Palacios-Flores, Kim; Reyes, José; García, Delfino; Boege, Margareta; Dávila, Guillermo; Flores, Margarita; Schatz, Michael C; Palacios, Rafael

2018-05-07

The precise determination of de novo genetic variants has enormous implications across different fields of biology and medicine, particularly personalized medicine. Currently, de novo variations are identified by mapping sample reads from a parent-offspring trio to a reference genome, allowing for a certain degree of differences. While widely used, this approach often introduces false-positive (FP) results due to misaligned reads and mischaracterized sequencing errors. In a previous study, we developed an alternative approach to accurately identify single nucleotide variants (SNVs) using only perfect matches. However, this approach could be applied only to haploid regions of the genome and was computationally intensive. In this study, we present a unique approach, coverage-based single nucleotide variant identification (COBASI), which allows the exploration of the entire genome using second-generation short sequence reads without extensive computing requirements. COBASI identifies SNVs using changes in coverage of exactly matching unique substrings, and is particularly suited for pinpointing de novo SNVs. Unlike other approaches that require population frequencies across hundreds of samples to filter out any methodological biases, COBASI can be applied to detect de novo SNVs within isolated families. We demonstrate this capability through extensive simulation studies and by studying a parent-offspring trio we sequenced using short reads. Experimental validation of all 58 candidate de novo SNVs and a selection of non-de novo SNVs found in the trio confirmed zero FP calls. COBASI is available as open source at https://github.com/Laura-Gomez/COBASI for any researcher to use. Copyright © 2018 the Author(s). Published by PNAS.

Malpractice suits in chest radiology: an evaluation of the histories of 8265 radiologists.

Science.gov (United States)

Baker, Stephen R; Patel, Ronak H; Yang, Lily; Lelkes, Valdis M; Castro, Alejandro

2013-11-01

The aim of this study was to present rates of claims, causes of error, percentage of cases resulting in a judgment, and average payments made by radiologists in chest-related malpractice cases in a survey of 8265 radiologists. The malpractice histories of 8265 radiologists were evaluated from the credentialing files of One-Call Medical Inc., a preferred provider organization for computed tomography/magnetic resonance imaging in workers' compensation cases. Of the 8265 radiologists, 2680 (32.4%) had at least 1 malpractice suit. Of those who were sued, the rate of claims was 55.1 per 1000 person years. The rate of thorax-related suits was 6.6 claims per 1000 radiology practice years (95% confidence interval, 6.0-7.2). There were 496 suits encompassing 48 different causes. Errors in diagnosis comprised 78.0% of the causes. Failure to diagnose lung cancer was by far the most frequent diagnostic error, representing 211 cases or 42.5%. Of the 496 cases, an outcome was known in 417. Sixty-one percent of these were settled in favor of the plaintiff, with a mean payment of $277,230 (95% confidence interval, 226,967-338,614). Errors in diagnosis, and among them failure to diagnose lung cancer, were by far the most common reasons for initiating a malpractice suit against radiologists related to the thorax and its contents.

Grass genomes

OpenAIRE

Bennetzen, Jeffrey L.; SanMiguel, Phillip; Chen, Mingsheng; Tikhonov, Alexander; Francki, Michael; Avramova, Zoya

1998-01-01

For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that in...

Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies.

Directory of Open Access Journals (Sweden)

Clive J Hoggart

2008-07-01

Full Text Available Testing one SNP at a time does not fully realise the potential of genome-wide association studies to identify multiple causal variants, which is a plausible scenario for many complex diseases. We show that simultaneous analysis of the entire set of SNPs from a genome-wide study to identify the subset that best predicts disease outcome is now feasible, thanks to developments in stochastic search methods. We used a Bayesian-inspired penalised maximum likelihood approach in which every SNP can be considered for additive, dominant, and recessive contributions to disease risk. Posterior mode estimates were obtained for regression coefficients that were each assigned a prior with a sharp mode at zero. A non-zero coefficient estimate was interpreted as corresponding to a significant SNP. We investigated two prior distributions and show that the normal-exponential-gamma prior leads to improved SNP selection in comparison with single-SNP tests. We also derived an explicit approximation for type-I error that avoids the need to use permutation procedures. As well as genome-wide analyses, our method is well-suited to fine mapping with very dense SNP sets obtained from re-sequencing and/or imputation. It can accommodate quantitative as well as case-control phenotypes, covariate adjustment, and can be extended to search for interactions. Here, we demonstrate the power and empirical type-I error of our approach using simulated case-control data sets of up to 500 K SNPs, a real genome-wide data set of 300 K SNPs, and a sequence-based dataset, each of which can be analysed in a few hours on a desktop workstation.

Knowledge Architect : A Tool Suite for Managing Software Architecture Knowledge

NARCIS (Netherlands)

Liang, Peng; Jansen, Anton; Avgeriou, Paris

2009-01-01

Management of software architecture knowledge (AK) is vital for improving an organization’s architectural capabilities. To support the architecting process within our industrial partner: Astron, the Dutch radio astronomy institute, we implemented the Knowledge Architect (KA): a tool suite for

UKRmol: a low-energy electron- and positron-molecule scattering suite

Science.gov (United States)

Carr, J. M.; Galiatsatos, P. G.; Gorfinkiel, J. D.; Harvey, A. G.; Lysaght, M. A.; Madden, D.; Mašín, Z.; Plummer, M.; Tennyson, J.; Varambhia, H. N.

2012-03-01

We describe the UK computational implementation of the R-matrix method for the treatment of electron and positron scattering from molecules. Recent developments in the UKRmol suite are detailed together with the collision processes it is enabling us to treat.

Goodbye genome paper, hello genome report: the increasing popularity of 'genome announcements' and their impact on science.

Science.gov (United States)

Smith, David Roy

2017-05-01

Next-generation sequencing technologies have revolutionized genomics and altered the scientific publication landscape. Life-science journals abound with genome papers-peer-reviewed descriptions of newly sequenced chromosomes. Although they once filled the pages of Nature and Science, genome papers are now mostly relegated to journals with low-impact factors. Some have forecast the death of the genome paper and argued that they are using up valuable resources and not advancing science. However, the publication rate of genome papers is on the rise. This increase is largely because some journals have created a new category of manuscript called genome reports, which are short, fast-tracked papers describing a chromosome sequence(s), its GenBank accession number and little else. In 2015, for example, more than 2000 genome reports were published, and 2016 is poised to bring even more. Here, I highlight the growing popularity of genome reports and discuss their merits, drawbacks and impact on science and the academic publication infrastructure. Genome reports can be excellent assets for the research community, but they are also being used as quick and easy routes to a publication, and in some instances they are not peer reviewed. One of the best arguments for genome reports is that they are a citable, user-generated genomic resource providing essential methodological and biological information, which may not be present in the sequence database. But they are expensive and time-consuming avenues for achieving such a goal. © The Author 2016. Published by Oxford University Press.

A suite of models to support the quantitative assessment of spread in pest risk analysis

NARCIS (Netherlands)

Robinet, C.; Kehlenbeck, H.; Werf, van der W.

2012-01-01

In the frame of the EU project PRATIQUE (KBBE-2007-212459 Enhancements of pest risk analysis techniques) a suite of models was developed to support the quantitative assessment of spread in pest risk analysis. This dataset contains the model codes (R language) for the four models in the suite. Three

Compact, Efficient, and Reliable Ventilation Fan for EVA Suits, Phase II

Data.gov (United States)

National Aeronautics and Space Administration — Advanced EVA suits for space exploration will need a portable life support system (PLSS) that is compact, lightweight, highly reliable, and meets stringent...

Complete Sequence and Analysis of the Mitochondrial Genome of Hemiselmis andersenii CCMP644 (Cryptophyceae

Directory of Open Access Journals (Sweden)

Bowman Sharen

2008-05-01

Full Text Available Abstract Background Cryptophytes are an enigmatic group of unicellular eukaryotes with plastids derived by secondary (i.e., eukaryote-eukaryote endosymbiosis. Cryptophytes are unusual in that they possess four genomes–a host cell-derived nuclear and mitochondrial genome and an endosymbiont-derived plastid and 'nucleomorph' genome. The evolutionary origins of the host and endosymbiont components of cryptophyte algae are at present poorly understood. Thus far, a single complete mitochondrial genome sequence has been determined for the cryptophyte Rhodomonas salina. Here, the second complete mitochondrial genome of the cryptophyte alga Hemiselmis andersenii CCMP644 is presented. Results The H. andersenii mtDNA is 60,553 bp in size and encodes 30 structural RNAs and 36 protein-coding genes, all located on the same strand. A prominent feature of the genome is the presence of a ~20 Kbp long intergenic region comprised of numerous tandem and dispersed repeat units of between 22–336 bp. Adjacent to these repeats are 27 copies of palindromic sequences predicted to form stable DNA stem-loop structures. One such stem-loop is located near a GC-rich and GC-poor region and may have a regulatory function in replication or transcription. The H. andersenii mtDNA shares a number of features in common with the genome of the cryptophyte Rhodomonas salina, including general architecture, gene content, and the presence of a large repeat region. However, the H. andersenii mtDNA is devoid of inverted repeats and introns, which are present in R. salina. Comparative analyses of the suite of tRNAs encoded in the two genomes reveal that the H. andersenii mtDNA has lost or converted its original trnK(uuu gene and possesses a trnS-derived 'trnK(uuu', which appears unable to produce a functional tRNA. Mitochondrial protein coding gene phylogenies strongly support a variety of previously established eukaryotic groups, but fail to resolve the relationships among higher

Predicting genome-wide redundancy using machine learning

Directory of Open Access Journals (Sweden)

Shasha Dennis E

2010-11-01

Full Text Available Abstract Background Gene duplication can lead to genetic redundancy, which masks the function of mutated genes in genetic analyses. Methods to increase sensitivity in identifying genetic redundancy can improve the efficiency of reverse genetics and lend insights into the evolutionary outcomes of gene duplication. Machine learning techniques are well suited to classifying gene family members into redundant and non-redundant gene pairs in model species where sufficient genetic and genomic data is available, such as Arabidopsis thaliana, the test case used here. Results Machine learning techniques that combine multiple attributes led to a dramatic improvement in predicting genetic redundancy over single trait classifiers alone, such as BLAST E-values or expression correlation. In withholding analysis, one of the methods used here, Support Vector Machines, was two-fold more precise than single attribute classifiers, reaching a level where the majority of redundant calls were correctly labeled. Using this higher confidence in identifying redundancy, machine learning predicts that about half of all genes in Arabidopsis showed the signature of predicted redundancy with at least one but typically less than three other family members. Interestingly, a large proportion of predicted redundant gene pairs were relatively old duplications (e.g., Ks > 1, suggesting that redundancy is stable over long evolutionary periods. Conclusions Machine learning predicts that most genes will have a functionally redundant paralog but will exhibit redundancy with relatively few genes within a family. The predictions and gene pair attributes for Arabidopsis provide a new resource for research in genetics and genome evolution. These techniques can now be applied to other organisms.

Tier-3 Monitoring Software Suite (T3MON) proposal

CERN Document Server

Andreeva, J; The ATLAS collaboration; Klimentov, A; Korenkov, V; Oleynik, D; Panitkin, S; Petrosyan, A

2011-01-01

The ATLAS Distributed Computing activities concentrated so far in the “central” part of the computing system of the experiment, namely the first 3 tiers (CERN Tier0, the 10 Tier1s centres and the 60+ Tier2s). This is a coherent system to perform data processing and management on a global scale and host (re)processing, simulation activities down to group and user analysis. Many ATLAS Institutes and National Communities built (or have plans to build) Tier-3 facilities. The definition of Tier-3 concept has been outlined (REFERENCE). Tier-3 centres consist of non-pledged resources mostly dedicated for the data analysis by the geographically close or local scientific groups. Tier-3 sites comprise a range of architectures and many do not possess Grid middleware, which would render application of Tier-2 monitoring systems useless. This document describes a strategy to develop a software suite for monitoring of the Tier3 sites. This software suite will enable local monitoring of the Tier3 sites and the global vie...

Genome update: the 1000th genome - a cautionary tale

DEFF Research Database (Denmark)

Lagesen, Karin; Ussery, David; Wassenaar, Gertrude Maria

2010-01-01

conclusions for example about the largest bacterial genome sequenced. Biological diversity is far greater than many have thought. For example, analysis of multiple Escherichia coli genomes has led to an estimate of around 45 000 gene families more genes than are recognized in the human genome. Moreover......There are now more than 1000 sequenced prokaryotic genomes deposited in public databases and available for analysis. Currently, although the sequence databases GenBank, DNA Database of Japan and EMBL are synchronized continually, there are slight differences in content at the genomes level...... for a variety of logistical reasons, including differences in format and loading errors, such as those caused by file transfer protocol interruptions. This means that the 1000th genome will be different in the various databases. Some of the data on the highly accessed web pages are inaccurate, leading to false...

Pre-genomic, genomic and post-genomic study of microbial communities involved in bioenergy.

Science.gov (United States)

Rittmann, Bruce E; Krajmalnik-Brown, Rosa; Halden, Rolf U

2008-08-01

Microorganisms can produce renewable energy in large quantities and without damaging the environment or disrupting food supply. The microbial communities must be robust and self-stabilizing, and their essential syntrophies must be managed. Pre-genomic, genomic and post-genomic tools can provide crucial information about the structure and function of these microbial communities. Applying these tools will help accelerate the rate at which microbial bioenergy processes move from intriguing science to real-world practice.

Multipurpose Cooling Garment for Improved Space Suit Environmental Control, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — Future manned space exploration missions will require space suits with capabilities beyond the current state of the art. Portable Life Support Systems for these...

Fabrication and performance analysis of a DEA cuff designed for dry-suit applications

International Nuclear Information System (INIS)

Ahmadi, S; Camacho Mattos, A; Barbazza, A; Soleimani, M; Boscariol, P; Menon, C

2013-01-01

A method for manufacturing a cylindrical dielectric elastomer actuator (DEA) is presented. The cylindrical DEA can be used in fabricating the cuff area of dry-suits where the garment is very tight and wearing the suit is difficult. When electrically actuated, the DEA expands radially and the suit can be worn more comfortably. In order to study the performance of the DEA, a customized testing setup was designed, and silicone-made cuff samples with different material stiffnesses were tested. Analytical and FEM modeling were considered to evaluate the experimental output. The results revealed that although the stiffness of the DEA material has a direct relationship with the radial constrictive pressure caused by mechanically stretching the DEA, it has a minor effect on the actuation pressure. It was also found that stacking multiple layers of the DEA to fabricate a laminated structure enabled the attainment of a desired variation of pressure required for the implementation of an electrically tunable cuff. (paper)

UniPOPS: Unified data reduction suite

Science.gov (United States)

Maddalena, Ronald J.; Garwood, Robert W.; Salter, Christopher J.; Stobie, Elizabeth B.; Cram, Thomas R.; Morgan, Lorrie; Vance, Bob; Hudson, Jerome

2015-03-01

UniPOPS, a suite of programs and utilities developed at the National Radio Astronomy Observatory (NRAO), reduced data from the observatory's single-dish telescopes: the Tucson 12-m, the Green Bank 140-ft, and archived data from the Green Bank 300-ft. The primary reduction programs, 'line' (for spectral-line reduction) and 'condar' (for continuum reduction), used the People-Oriented Parsing Service (POPS) as the command line interpreter. UniPOPS unified previous analysis packages and provided new capabilities; development of UniPOPS continued within the NRAO until 2004 when the 12-m was turned over to the Arizona Radio Observatory (ARO). The submitted code is version 3.5 from 2004, the last supported by the NRAO.

Genome Surfing As Driver of Microbial Genomic Diversity.

Science.gov (United States)

Choudoir, Mallory J; Panke-Buisse, Kevin; Andam, Cheryl P; Buckley, Daniel H

2017-08-01

Historical changes in population size, such as those caused by demographic range expansions, can produce nonadaptive changes in genomic diversity through mechanisms such as gene surfing. We propose that demographic range expansion of a microbial population capable of horizontal gene exchange can result in genome surfing, a mechanism that can cause widespread increase in the pan-genome frequency of genes acquired by horizontal gene exchange. We explain that patterns of genetic diversity within Streptomyces are consistent with genome surfing, and we describe several predictions for testing this hypothesis both in Streptomyces and in other microorganisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

Tartumurdelise kirjanduse ettejõudmine ; Parandatud kirikukeele ja rahvaraamatute poole / Gustav Suits

Index Scriptorium Estoniae

Suits, Gustav, 1883-1956

1999-01-01

Varem ilmunud: Suits, Gustav. Eesti kirjanduslugu I. Lund : Eesti Kirjanike Kooperatiiv, 1953. Lõunaeestikeelne "Meie Issanda Jesusse Kristusse Wastne Testament" (Riia, 1686). Eeltöödest põhjaeestikeelse piibli väljaandmiseks

Deep whole-genome sequencing of 90 Han Chinese genomes.

Science.gov (United States)

Lan, Tianming; Lin, Haoxiang; Zhu, Wenjuan; Laurent, Tellier Christian Asker Melchior; Yang, Mengcheng; Liu, Xin; Wang, Jun; Wang, Jian; Yang, Huanming; Xu, Xun; Guo, Xiaosen

2017-09-01

Next-generation sequencing provides a high-resolution insight into human genetic information. However, the focus of previous studies has primarily been on low-coverage data due to the high cost of sequencing. Although the 1000 Genomes Project and the Haplotype Reference Consortium have both provided powerful reference panels for imputation, low-frequency and novel variants remain difficult to discover and call with accuracy on the basis of low-coverage data. Deep sequencing provides an optimal solution for the problem of these low-frequency and novel variants. Although whole-exome sequencing is also a viable choice for exome regions, it cannot account for noncoding regions, sometimes resulting in the absence of important, causal variants. For Han Chinese populations, the majority of variants have been discovered based upon low-coverage data from the 1000 Genomes Project. However, high-coverage, whole-genome sequencing data are limited for any population, and a large amount of low-frequency, population-specific variants remain uncharacterized. We have performed whole-genome sequencing at a high depth (∼×80) of 90 unrelated individuals of Chinese ancestry, collected from the 1000 Genomes Project samples, including 45 Northern Han Chinese and 45 Southern Han Chinese samples. Eighty-three of these 90 have been sequenced by the 1000 Genomes Project. We have identified 12 568 804 single nucleotide polymorphisms, 2 074 210 short InDels, and 26 142 structural variations from these 90 samples. Compared to the Han Chinese data from the 1000 Genomes Project, we have found 7 000 629 novel variants with low frequency (defined as minor allele frequency genome. Compared to the 1000 Genomes Project, these Han Chinese deep sequencing data enhance the characterization of a large number of low-frequency, novel variants. This will be a valuable resource for promoting Chinese genetics research and medical development. Additionally, it will provide a valuable supplement to the 1000

Fungal Genomics Program

Energy Technology Data Exchange (ETDEWEB)

Grigoriev, Igor

2012-03-12

The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

Comparative Genome Analysis and Genome Evolution

NARCIS (Netherlands)

Snel, Berend

2002-01-01

This thesis described a collection of bioinformatic analyses on complete genome sequence data. We have studied the evolution of gene content and find that vertical inheritance dominates over horizontal gene trasnfer, even to the extent that we can use the gene content to make genome phylogenies.

Genome projects and the functional-genomic era.

Science.gov (United States)

Sauer, Sascha; Konthur, Zoltán; Lehrach, Hans

2005-12-01

The problems we face today in public health as a result of the -- fortunately -- increasing age of people and the requirements of developing countries create an urgent need for new and innovative approaches in medicine and in agronomics. Genomic and functional genomic approaches have a great potential to at least partially solve these problems in the future. Important progress has been made by procedures to decode genomic information of humans, but also of other key organisms. The basic comprehension of genomic information (and its transfer) should now give us the possibility to pursue the next important step in life science eventually leading to a basic understanding of biological information flow; the elucidation of the function of all genes and correlative products encoded in the genome, as well as the discovery of their interactions in a molecular context and the response to environmental factors. As a result of the sequencing projects, we are now able to ask important questions about sequence variation and can start to comprehensively study the function of expressed genes on different levels such as RNA, protein or the cell in a systematic context including underlying networks. In this article we review and comment on current trends in large-scale systematic biological research. A particular emphasis is put on technology developments that can provide means to accomplish the tasks of future lines of functional genomics.

GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes.

Science.gov (United States)

Yuan, Lina; Yu, Yang; Zhu, Yanmin; Li, Yulai; Li, Changqing; Li, Rujiao; Ma, Qin; Siu, Gilman Kit-Hang; Yu, Jun; Jiang, Taijiao; Xiao, Jingfa; Kang, Yu

2017-01-25

Next-generation sequencing (NGS) technologies have greatly promoted the genomic study of prokaryotes. However, highly fragmented assemblies due to short reads from NGS are still a limiting factor in gaining insights into the genome biology. Reference-assisted tools are promising in genome assembly, but tend to result in false assembly when the assigned reference has extensive rearrangements. Herein, we present GAAP, a genome assembly pipeline for scaffolding based on core-gene-defined Genome Organizational Framework (cGOF) described in our previous study. Instead of assigning references, we use the multiple-reference-derived cGOFs as indexes to assist in order and orientation of the scaffolds and build a skeleton structure, and then use read pairs to extend scaffolds, called local scaffolding, and distinguish between true and chimeric adjacencies in the scaffolds. In our performance tests using both empirical and simulated data of 15 genomes in six species with diverse genome size, complexity, and all three categories of cGOFs, GAAP outcompetes or achieves comparable results when compared to three other reference-assisted programs, AlignGraph, Ragout and MeDuSa. GAAP uses both cGOF and pair-end reads to create assemblies in genomic scale, and performs better than the currently available reference-assisted assembly tools as it recovers more assemblies and makes fewer false locations, especially for species with extensive rearranged genomes. Our method is a promising solution for reconstruction of genome sequence from short reads of NGS.

Compact, Efficient, and Reliable Ventilation Fan for EVA Suits, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — Advanced EVA suits for space exploration will need a portable life support system (PLSS) that is compact, lightweight, and highly reliable. A key component is a...

The Perennial Ryegrass GenomeZipper – Targeted Use of Genome Resources for Comparative Grass Genomics

DEFF Research Database (Denmark)

Pfeiffer, Matthias; Martis, Mihaela; Asp, Torben

2013-01-01

(Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold......Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass...... to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous...

Population Genomics of Infectious and Integrated Wolbachia pipientis Genomes in Drosophila ananassae

Science.gov (United States)

Choi, Jae Young; Bubnell, Jaclyn E.; Aquadro, Charles F.

2015-01-01

Coevolution between Drosophila and its endosymbiont Wolbachia pipientis has many intriguing aspects. For example, Drosophila ananassae hosts two forms of W. pipientis genomes: One being the infectious bacterial genome and the other integrated into the host nuclear genome. Here, we characterize the infectious and integrated genomes of W. pipientis infecting D. ananassae (wAna), by genome sequencing 15 strains of D. ananassae that have either the infectious or integrated wAna genomes. Results indicate evolutionarily stable maternal transmission for the infectious wAna genome suggesting a relatively long-term coevolution with its host. In contrast, the integrated wAna genome showed pseudogene-like characteristics accumulating many variants that are predicted to have deleterious effects if present in an infectious bacterial genome. Phylogenomic analysis of sequence variation together with genotyping by polymerase chain reaction of large structural variations indicated several wAna variants among the eight infectious wAna genomes. In contrast, only a single wAna variant was found among the seven integrated wAna genomes examined in lines from Africa, south Asia, and south Pacific islands suggesting that the integration occurred once from a single infectious wAna genome and then spread geographically. Further analysis revealed that for all D. ananassae we examined with the integrated wAna genomes, the majority of the integrated wAna genomic regions is represented in at least two copies suggesting a double integration or single integration followed by an integrated genome duplication. The possible evolutionary mechanism underlying the widespread geographical presence of the duplicate integration of the wAna genome is an intriguing question remaining to be answered. PMID:26254486

Dramatic improvement in genome assembly achieved using doubled-haploid genomes.

Science.gov (United States)

Zhang, Hong; Tan, Engkong; Suzuki, Yutaka; Hirose, Yusuke; Kinoshita, Shigeharu; Okano, Hideyuki; Kudoh, Jun; Shimizu, Atsushi; Saito, Kazuyoshi; Watabe, Shugo; Asakawa, Shuichi

2014-10-27

Improvement in de novo assembly of large genomes is still to be desired. Here, we improved draft genome sequence quality by employing doubled-haploid individuals. We sequenced wildtype and doubled-haploid Takifugu rubripes genomes, under the same conditions, using the Illumina platform and assembled contigs with SOAPdenovo2. We observed 5.4-fold and 2.6-fold improvement in the sizes of the N50 contig and scaffold of doubled-haploid individuals, respectively, compared to the wildtype, indicating that the use of a doubled-haploid genome aids in accurate genome analysis.

The Aouda.X space suit simulator and its applications to astrobiology.

Science.gov (United States)

Groemer, Gernot E; Hauth, Stefan; Luger, Ulrich; Bickert, Klaus; Sattler, Birgit; Hauth, Eva; Föger, Daniel; Schildhammer, Daniel; Agerer, Christian; Ragonig, Christoph; Sams, Sebastian; Kaineder, Felix; Knoflach, Martin

2012-02-01

We have developed the space suit simulator Aouda.X, which is capable of reproducing the physical and sensory limitations a flight-worthy suit would have on Mars. Based upon a Hard-Upper-Torso design, it has an advanced human-machine interface and a sensory network connected to an On-Board Data Handling system to increase the situational awareness in the field. Although the suit simulator is not pressurized, the physical forces that lead to a reduced working envelope and physical performance are reproduced with a calibrated exoskeleton. This allows us to simulate various pressure regimes from 0.3-1 bar. Aouda.X has been tested in several laboratory and field settings, including sterile sampling at 2800 m altitude inside a glacial ice cave and a cryochamber at -110°C, and subsurface tests in connection with geophysical instrumentation relevant to astrobiology, including ground-penetrating radar, geoacoustics, and drilling. The communication subsystem allows for a direct interaction with remote science teams via telemetry from a mission control center. Aouda.X as such is a versatile experimental platform for studying Mars exploration activities in a high-fidelity Mars analog environment with a focus on astrobiology and operations research that has been optimized to reduce the amount of biological cross contamination. We report on the performance envelope of the Aouda.X system and its operational limitations.

Genetic gatekeepers: regulating direct-to-consumer genomic services in an era of participatory medicine.

Science.gov (United States)

Palmer, Jessica Elizabeth

2012-01-01

Should consumers be able to obtain information about their own bodies, even if it has no proven medical value? Direct-to-consumer ("DTC") genomic companies offer consumers two services: generation of the consumer's personal genetic sequence, and interpretation of that sequence in light of current research. Concerned that consumers will misunderstand genomic information and make ill-advised health decisions, regulators, legislators and scholars have advocated restricted access to DTC genomic services. The Food and Drug Administration, which has historically refrained from regulating most genetic tests, has announced its intent to treat DTC genomic services as medical devices because they make "medical claims." This Article argues that FDA regulation of genomic services as medical devices would be counterproductive. Clinical laboratories conducting genetic tests are already overseen by a federal regime administered by the Centers for Medicare and Medicaid Services. While consumers and clinicians would benefit from clearer communication of test results and their health implications, FDA's gatekeeping framework is ill-suited to weigh the safety and efficacy of genomic information that is not medically actionable in traditional ways. Playing gatekeeper would burden FDA's resources, conflict with the patient-empowering policies promoted by personalized medicine initiatives, impair individuals' access to information in which they have powerful autonomy interests, weaken novel participatory research infrastructures, and set a poor precedent for the future regulation of medical information. Rather than applying its risk-based regulatory framework to genetic information, FDA should ameliorate regulatory uncertainty by working with the Federal Trade Commission and Centers for Medicare and Medicaid Services to ensure that DTC genomic services deliver analytically valid data, market and implement their services in a truthful manner, and fully disclose the limitations of their

Cancer genomics

DEFF Research Database (Denmark)

Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

2007-01-01

Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

A Laser-Based Diagnostic Suite for Hypersonic Test Facilities, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — In this SBIR effort, Los Gatos Research (LGR) proposes to develop a suite of laser-based diagnostics for the study of reactive and non-reactive hypersonic flows....

Heart Rhythm Monitoring in the Constellation Lunar and Launch/Landing EVA Suit: Recommendations from an Expert Panel

Science.gov (United States)

Scheuring, Richard A.; Hamilton, Doug; Jones, Jeffrey A.; Alexander, David

2009-01-01

There are currently several physiological monitoring requirements for EVA in the Human-Systems Interface Requirements (HSIR) document. There are questions as to whether the capability to monitor heart rhythm in the lunar surface space suit is a necessary capability for lunar surface operations. Similarly, there are questions as to whether the capability to monitor heart rhythm during a cabin depressurization scenario in the launch/landing space suit is necessary. This presentation seeks to inform space medicine personnel of recommendations made by an expert panel of cardiovascular medicine specialists regarding in-suit ECG heart rhythm monitoring requirements during lunar surface operations. After a review of demographic information and clinical cases and panel discussion, the panel recommended that ECG monitoring capability as a clinical tool was not essential in the lunar space suit; ECG monitoring was not essential in the launch/landing space suit for contingency scenarios; the current hear rate monitoring capability requirement for both launch/landing and lunar space suits should be maintained; lunar vehicles should be required to have ECG monitoring capability with a minimum of 5-lead ECG for IVA medical assessments; and, exercise stress testing for astronaut selection and retention should be changed from the current 85% maximum heart rate limit to maximal, exhaustive 'symptom-limited' testing to maximize diagnostic utility as a screening tool for evaluating the functional capacity of astronauts and their cardiovascular health.

Personal genomics services: whose genomes?

Science.gov (United States)

Gurwitz, David; Bregman-Eschet, Yael

2009-07-01

New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below.

Enhanced Verification Test Suite for Physics Simulation Codes

Energy Technology Data Exchange (ETDEWEB)

Kamm, J R; Brock, J S; Brandon, S T; Cotrell, D L; Johnson, B; Knupp, P; Rider, W; Trucano, T; Weirs, V G

2008-10-10

This document discusses problems with which to augment, in quantity and in quality, the existing tri-laboratory suite of verification problems used by Los Alamos National Laboratory (LANL), Lawrence Livermore National Laboratory (LLNL), and Sandia National Laboratories (SNL). The purpose of verification analysis is demonstrate whether the numerical results of the discretization algorithms in physics and engineering simulation codes provide correct solutions of the corresponding continuum equations. The key points of this document are: (1) Verification deals with mathematical correctness of the numerical algorithms in a code, while validation deals with physical correctness of a simulation in a regime of interest. This document is about verification. (2) The current seven-problem Tri-Laboratory Verification Test Suite, which has been used for approximately five years at the DOE WP laboratories, is limited. (3) Both the methodology for and technology used in verification analysis have evolved and been improved since the original test suite was proposed. (4) The proposed test problems are in three basic areas: (a) Hydrodynamics; (b) Transport processes; and (c) Dynamic strength-of-materials. (5) For several of the proposed problems we provide a 'strong sense verification benchmark', consisting of (i) a clear mathematical statement of the problem with sufficient information to run a computer simulation, (ii) an explanation of how the code result and benchmark solution are to be evaluated, and (iii) a description of the acceptance criterion for simulation code results. (6) It is proposed that the set of verification test problems with which any particular code be evaluated include some of the problems described in this document. Analysis of the proposed verification test problems constitutes part of a necessary--but not sufficient--step that builds confidence in physics and engineering simulation codes. More complicated test cases, including physics models of

Microbial contamination determination of Cream suit,Traditional Ice Cream and Olovia in Yasuj City

OpenAIRE

SS Khoramrooz; M Sarikhani; SA Khosravani; M Farhang Falah; Y Mahmoudi; A Sharifi

2015-01-01

Background & aim: Prevalence of diseases caused by consumption of contaminated food has always been a problem all over the world, and every year spent on improving the disease is costly.Cream suit, Ice cream & olowye for ingredient substance and manufacture & preservation conditional have very high possibility for contamination.The aim of this study is Microbial contamination determination of Cream suit, Traditional Ice Cream and Olovia in Yasuj City Methods: This study is randomized cros...

A geological investigation of the Proterozoic T'Oubep Suite, northwestern Cape Province, South Africa

International Nuclear Information System (INIS)

Agenbacht, A.L.D.; Schoch, A.E.; Van der Merwe, S.W.

1990-01-01

The T'Oubep Suite occurs in the central part of the Namaqua mobile belt approximately 80km southwest of Kakamas. The Suite comprises seven different rock types with compositions ranging from betabasite through granodiorite and tonalite to granite. The igneous rocks were extensively metamorphosed during the Namaqua tectogenesis. The comagmatic origin for the granitic rocks suggested by the field relations is corroborated by whole rock, trace element and REE chemistry. 5 refs., 3 figs

Insights into structural variations and genome rearrangements in prokaryotic genomes.

Science.gov (United States)

Periwal, Vinita; Scaria, Vinod

2015-01-01

Structural variations (SVs) are genomic rearrangements that affect fairly large fragments of DNA. Most of the SVs such as inversions, deletions and translocations have been largely studied in context of genetic diseases in eukaryotes. However, recent studies demonstrate that genome rearrangements can also have profound impact on prokaryotic genomes, leading to altered cell phenotype. In contrast to single-nucleotide variations, SVs provide a much deeper insight into organization of bacterial genomes at a much better resolution. SVs can confer change in gene copy number, creation of new genes, altered gene expression and many other functional consequences. High-throughput technologies have now made it possible to explore SVs at a much refined resolution in bacterial genomes. Through this review, we aim to highlight the importance of the less explored field of SVs in prokaryotic genomes and their impact. We also discuss its potential applicability in the emerging fields of synthetic biology and genome engineering where targeted SVs could serve to create sophisticated and accurate genome editing. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Parasite Genome Projects and the Trypanosoma cruzi Genome Initiative

Directory of Open Access Journals (Sweden)

Wim Degrave

1997-11-01

Full Text Available Since the start of the human genome project, a great number of genome projects on other "model" organism have been initiated, some of them already completed. Several initiatives have also been started on parasite genomes, mainly through support from WHO/TDR, involving North-South and South-South collaborations, and great hopes are vested in that these initiatives will lead to new tools for disease control and prevention, as well as to the establishment of genomic research technology in developing countries. The Trypanosoma cruzi genome project, using the clone CL-Brener as starting point, has made considerable progress through the concerted action of more than 20 laboratories, most of them in the South. A brief overview of the current state of the project is given

DEALed : A tool suite for distributed real-time systems development

NARCIS (Netherlands)

Bolshakov, K.; Karpov, Y.; Sintotski, A.; Malyshkin, V.

1999-01-01

DEALed is a tool suite for development of distributed systems using DEAL language. DEAL is being developed at Eindhoven University of Technology as a part of DEDOS project. Area of application of the DEALed is the development of the distributed real- time safety-critical control systems.

Short and long-term genome stability analysis of prokaryotic genomes.

Science.gov (United States)

Brilli, Matteo; Liò, Pietro; Lacroix, Vincent; Sagot, Marie-France

2013-05-08

Gene organization dynamics is actively studied because it provides useful evolutionary information, makes functional annotation easier and often enables to characterize pathogens. There is therefore a strong interest in understanding the variability of this trait and the possible correlations with life-style. Two kinds of events affect genome organization: on one hand translocations and recombinations change the relative position of genes shared by two genomes (i.e. the backbone gene order); on the other, insertions and deletions leave the backbone gene order unchanged but they alter the gene neighborhoods by breaking the syntenic regions. A complete picture about genome organization evolution therefore requires to account for both kinds of events. We developed an approach where we model chromosomes as graphs on which we compute different stability estimators; we consider genome rearrangements as well as the effect of gene insertions and deletions. In a first part of the paper, we fit a measure of backbone gene order conservation (hereinafter called backbone stability) against phylogenetic distance for over 3000 genome comparisons, improving existing models for the divergence in time of backbone stability. Intra- and inter-specific comparisons were treated separately to focus on different time-scales. The use of multiple genomes of a same species allowed to identify genomes with diverging gene order with respect to their conspecific. The inter-species analysis indicates that pathogens are more often unstable with respect to non-pathogens. In a second part of the text, we show that in pathogens, gene content dynamics (insertions and deletions) have a much more dramatic effect on genome organization stability than backbone rearrangements. In this work, we studied genome organization divergence taking into account the contribution of both genome order rearrangements and genome content dynamics. By studying species with multiple sequenced genomes available, we were

NIH bows to part of Rifkin suit.

Science.gov (United States)

Sun, M

1984-11-30

Having lost a round in its legal battle with Jeremy Rifkin over field tests of genetically engineered bacteria, the National Institutes of Health will conduct the simpler of two ecological analyses required by the National Environmental Policy Act on three proposed experiments. In May 1984 a federal district court ruling halted a University of California field test pending a decision on Rifkin's 1983 suit, which alleged that NIH had violated the Act by approving experiments without studying the ecological consequences. Still to be decided by the U.S. Court of Appeals is whether NIH must also issue full-scale environmental impact statements.

Genomic Data Commons and Genomic Cloud Pilots - Google Hangout

Science.gov (United States)

Join us for a live, moderated discussion about two NCI efforts to expand access to cancer genomics data: the Genomic Data Commons and Genomic Cloud Pilots. NCI subject matters experts will include Louis M. Staudt, M.D., Ph.D., Director Center for Cancer Genomics, Warren Kibbe, Ph.D., Director, NCI Center for Biomedical Informatics and Information Technology, and moderated by Anthony Kerlavage, Ph.D., Chief, Cancer Informatics Branch, Center for Biomedical Informatics and Information Technology. We welcome your questions before and during the Hangout on Twitter using the hashtag #AskNCI.

The genomes and comparative genomics of Lactobacillus delbrueckii phages.

Science.gov (United States)

Riipinen, Katja-Anneli; Forsman, Päivi; Alatossava, Tapani

2011-07-01

Lactobacillus delbrueckii phages are a great source of genetic diversity. Here, the genome sequences of Lb. delbrueckii phages LL-Ku, c5 and JCL1032 were analyzed in detail, and the genetic diversity of Lb. delbrueckii phages belonging to different taxonomic groups was explored. The lytic isometric group b phages LL-Ku (31,080 bp) and c5 (31,841 bp) showed a minimum nucleotide sequence identity of 90% over about three-fourths of their genomes. The genomic locations of their lysis modules were unique, and the genomes featured several putative overlapping transcription units of genes. LL-Ku and c5 virions displayed peptidoglycan hydrolytic activity associated with a ~36-kDa protein similar in size to the endolysin. Unexpectedly, the 49,433-bp genome of the prolate phage JCL1032 (temperate, group c) revealed a conserved gene order within its structural genes. Lb. delbrueckii phages representing groups a (a phage LL-H), b and c possessed only limited protein sequence homology. Genomic comparison of LL-Ku and c5 suggested that diversification of Lb. delbrueckii phages is mainly due to insertions, deletions and recombination. For the first time, the complete genome sequences of group b and c Lb. delbrueckii phages are reported.

Astronaut John Young during final suiting operations for Apollo 10 mission

Science.gov (United States)

1969-01-01

A technician attaches hose from test stand to spacesuit of Astronaut John W. Young, Apollo 10 command module pilot, during final suiting operations for the Apollo 10 lunar orbit mission. Another technician makes adjustment behind Young.

SSAGES: Software Suite for Advanced General Ensemble Simulations

Energy Technology Data Exchange (ETDEWEB)

Sidky, Hythem [Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA; Colón, Yamil J. [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA; Institute for Molecular Engineering and Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA; Helfferich, Julian [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA; Steinbuch Center for Computing, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; Sikora, Benjamin J. [Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA; Bezik, Cody [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA; Chu, Weiwei [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA; Giberti, Federico [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA; Guo, Ashley Z. [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA; Jiang, Xikai [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA; Lequieu, Joshua [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA; Li, Jiyuan [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA; Moller, Joshua [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA; Quevillon, Michael J. [Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA; Rahimi, Mohammad [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA; Ramezani-Dakhel, Hadi [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA; Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA; Rathee, Vikramjit S. [Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA; Reid, Daniel R. [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA; Sevgen, Emre [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA; Thapar, Vikram [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA; Webb, Michael A. [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA; Institute for Molecular Engineering and Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA; Whitmer, Jonathan K. [Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA; de Pablo, Juan J. [Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA; Institute for Molecular Engineering and Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA

2018-01-28

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods, and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite.

Wireless hydrotherapy smart suit for monitoring handicapped people

Science.gov (United States)

Correia, Jose H.; Mendes, Paulo M.

2005-02-01

This paper presents a smart suit, water impermeable, containing sensors and electronics for monitoring handicapped people at hydrotherapy sessions in swimming-pools. For integration into textiles, electronic components should be designed in a functional, robust and inexpensive way. Therefore, small-size electronics microsystems are a promising approach. The smart suit allows the monitoring of individual biometric data, such as heart rate, temperature and movement of the body. Two solutions for transmitting the data wirelessly are presented: through a low-voltage (3.0 V), low-power, CMOS RF IC (1.6 mm x 1.5 mm size dimensions) operating at 433 MHz, with ASK modulation and a patch antenna built on lossy substrates compatible with integrated circuits fabrication. Two different substrates were used for antenna implementation: high-resistivity silicon (HRS) and Corning Pyrex #7740 glass. The antenna prototypes were built to operate close to the 5 GHz ISM band. They operate at a center frequency of 5.705 GHz (HRS) and 5.995 GHz (Pyrex). The studied parameters were: substrate thickness, substrate losses, oxide thickness, metal conductivity and thickness. The antenna on HRS uses an area of 8 mm2, providing a 90 MHz bandwidth and ~0.3 dBi of gain. On a glass substrate, the antenna uses 12 mm2, provides 100 MHz bandwidth and ~3 dBi of gain.

Generating an Automated Test Suite by Variable Strength Combinatorial Testing for Web Services

Directory of Open Access Journals (Sweden)

Yin Li

2016-09-01

Full Text Available Testing Web Services has become the spotlight of software engineering as an important means to assure the quality of Web application. Due to lacking of graphic interface and source code, Web services need an automated testing method, which is an important part in efficiently designing and generating test suite. However, the existing testing methods may lead to the redundancy of test suite and the decrease of fault-detecting ability since it cannot handle scenarios where the strengths of the different interactions are not uniform. With the purpose of solving this problem, firstly the formal tree model based on WSDL is constructed and the actual interaction relationship of each node is made sufficient consideration into, then the combinatorial testing is proposed to generate variable strength combinatorial test suite based on One-test-at-a-time strategy. At last test cases are minimized according to constraint rules. The results show that compared with conventional random testing, the proposed approach can detect more errors with the same amount of test cases which turning out to be more ideal than existing ones in size.

STS-93 M.S. Hawley suits up for launch

Science.gov (United States)

1999-01-01

During final launch preparations in the Operations and Checkout Building, STS-93 Mission Specialist Steven A. Hawley (Ph.D.)gets help donning his launch and entry suit from a suit tech. After Space Shuttle Columbia's July 20 launch attempt was scrubbed at the T-7 second mark in the countdown, the launch was rescheduled for Thursday, July 22, at 12:28 a.m. EDT. The target landing date is July 26, 1999, at 11:24 p.m. EDT. STS-93 is a five-day mission primarily to release the Chandra X-ray Observatory, which will allow scientists from around the world to study some of the most distant, powerful and dynamic objects in the universe. The new telescope is 20 to 50 times more sensitive than any previous X- ray telescope and is expected unlock the secrets of supernovae, quasars and black holes. The STS-93 crew numbers five: Commander Eileen M. Collins, Pilot Jeffrey S. Ashby, and Mission Specialists Hawley, Catherine G. Coleman (Ph.D.) and Michel Tognini of France, with the Centre National d'Etudes Spatiales (CNES). Collins is the first woman to serve as commander of a shuttle mission.

Cost and Morbidity Analysis of Chest Port Insertion: Interventional Radiology Suite Versus Operating Room.

Science.gov (United States)

LaRoy, Jennifer R; White, Sarah B; Jayakrishnan, Thejus; Dybul, Stephanie; Ungerer, Dirk; Turaga, Kiran; Patel, Parag J

2015-06-01

To compare complications and cost, from a hospital perspective, of chest port insertions performed in an interventional radiology (IR) suite versus in surgery in an operating room (OR). This study was approved by an institutional review board and is HIPAA compliant. Medical records were retrospectively searched on consecutive chest port placement procedures, in the IR suite and the OR, between October 22, 2010 and February 26, 2013, to determine patients' demographic information and chest port-related complications and/or infections. A total of 478 charts were reviewed (age range: 21-85 years; 309 women, 169 men). Univariate and bivariate analyses were performed to identify risk factors associated with an increased complication rate. Cost data on 149 consecutive Medicare outpatients (100 treated in the IR suite; 49 treated in the OR) who had isolated chest port insertions between March 2012 and February 2013 were obtained for both the operative services and pharmacy. Nonparametric tests for heterogeneity were performed using the Kruskal-Wallis method. Early complications occurred in 9.2% (22 of 239) of the IR patients versus 13.4% (32 of 239) of the OR patients. Of the 478 implanted chest ports, 9 placed in IR and 18 placed in surgery required early removal. Infections from the ports placed in IR versus the OR were 0.25 versus 0.18 infections per 1000 catheters, respectively. Overall mean costs for chest port insertion were significantly higher in the OR, for both room and pharmacy costs (P chest ports in an OR setting was almost twice that of placement in the IR suite. Hospital costs to place a chest port were significantly lower in the IR suite than in the OR, whereas radiology and surgery patients did not show a significantly different rate of complications and/or infections. Copyright © 2015 American College of Radiology. Published by Elsevier Inc. All rights reserved.

Genome-wide characterization of centromeric satellites from multiple mammalian genomes.

Science.gov (United States)

Alkan, Can; Cardone, Maria Francesca; Catacchio, Claudia Rita; Antonacci, Francesca; O'Brien, Stephen J; Ryder, Oliver A; Purgato, Stefania; Zoli, Monica; Della Valle, Giuliano; Eichler, Evan E; Ventura, Mario

2011-01-01

Despite its importance in cell biology and evolution, the centromere has remained the final frontier in genome assembly and annotation due to its complex repeat structure. However, isolation and characterization of the centromeric repeats from newly sequenced species are necessary for a complete understanding of genome evolution and function. In recent years, various genomes have been sequenced, but the characterization of the corresponding centromeric DNA has lagged behind. Here, we present a computational method (RepeatNet) to systematically identify higher-order repeat structures from unassembled whole-genome shotgun sequence and test whether these sequence elements correspond to functional centromeric sequences. We analyzed genome datasets from six species of mammals representing the diversity of the mammalian lineage, namely, horse, dog, elephant, armadillo, opossum, and platypus. We define candidate monomer satellite repeats and demonstrate centromeric localization for five of the six genomes. Our analysis revealed the greatest diversity of centromeric sequences in horse and dog in contrast to elephant and armadillo, which showed high-centromeric sequence homogeneity. We could not isolate centromeric sequences within the platypus genome, suggesting that centromeres in platypus are not enriched in satellite DNA. Our method can be applied to the characterization of thousands of other vertebrate genomes anticipated for sequencing in the near future, providing an important tool for annotation of centromeres.

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

DEFF Research Database (Denmark)

Machado, Henrique; Gram, Lone

2017-01-01

was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.......Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand...... the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two...

BrainStorm: a psychosocial game suite design for non-invasive cross-generational cognitive capabilities data collection

Science.gov (United States)

Ahmad, Faizan; Chen, Yiqiang; Hu, Lisha; Wang, Shuangquan; Wang, Jindong; Chen, Zhenyu; Jiang, Xinlong; Shen, Jianfei

2017-11-01

Currently available traditional as well as videogame-based cognitive assessment techniques are inappropriate due to several reasons. This paper presents a novel psychosocial game suite, BrainStorm, for non-invasive cross-generational cognitive capabilities data collection, which additionally provides cross-generational social support. A motivation behind the development of presented game suite is to provide an entertaining and exciting platform for its target users in order to collect gameplay-based cognitive capabilities data in a non-invasive manner. An extensive evaluation of the presented game suite demonstrated high acceptability and attraction for its target users. Besides, the data collection process is successfully reported as transparent and non-invasive.

75 FR 24946 - Proposed Consent Decree, Clean Air Act Citizen Suit

Science.gov (United States)

2010-05-06

..., South Carolina, Wisconsin, Indiana, Michigan, Ohio, Louisiana, Kansas, Nebraska, Missouri, Colorado..., Wisconsin, Indiana, Michigan, Ohio, Louisiana, Kansas, Nebraska, Missouri, Colorado, Montana, South Dakota... ENVIRONMENTAL PROTECTION AGENCY [FRL-9146-3] Proposed Consent Decree, Clean Air Act Citizen Suit...

SNUGB: a versatile genome browser supporting comparative and functional fungal genomics

Directory of Open Access Journals (Sweden)

Kim Seungill

2008-12-01

Full Text Available Abstract Background Since the full genome sequences of Saccharomyces cerevisiae were released in 1996, genome sequences of over 90 fungal species have become publicly available. The heterogeneous formats of genome sequences archived in different sequencing centers hampered the integration of the data for efficient and comprehensive comparative analyses. The Comparative Fungal Genomics Platform (CFGP was developed to archive these data via a single standardized format that can support multifaceted and integrated analyses of the data. To facilitate efficient data visualization and utilization within and across species based on the architecture of CFGP and associated databases, a new genome browser was needed. Results The Seoul National University Genome Browser (SNUGB integrates various types of genomic information derived from 98 fungal/oomycete (137 datasets and 34 plant and animal (38 datasets species, graphically presents germane features and properties of each genome, and supports comparison between genomes. The SNUGB provides three different forms of the data presentation interface, including diagram, table, and text, and six different display options to support visualization and utilization of the stored information. Information for individual species can be quickly accessed via a new tool named the taxonomy browser. In addition, SNUGB offers four useful data annotation/analysis functions, including 'BLAST annotation.' The modular design of SNUGB makes its adoption to support other comparative genomic platforms easy and facilitates continuous expansion. Conclusion The SNUGB serves as a powerful platform supporting comparative and functional genomics within the fungal kingdom and also across other kingdoms. All data and functions are available at the web site http://genomebrowser.snu.ac.kr/.

Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

Energy Technology Data Exchange (ETDEWEB)

Kuo, Alan; Grigoriev, Igor

2009-04-17

Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.

BuddySuite: Command-Line Toolkits for Manipulating Sequences, Alignments, and Phylogenetic Trees.

Science.gov (United States)

Bond, Stephen R; Keat, Karl E; Barreira, Sofia N; Baxevanis, Andreas D

2017-06-01

The ability to manipulate sequence, alignment, and phylogenetic tree files has become an increasingly important skill in the life sciences, whether to generate summary information or to prepare data for further downstream analysis. The command line can be an extremely powerful environment for interacting with these resources, but only if the user has the appropriate general-purpose tools on hand. BuddySuite is a collection of four independent yet interrelated command-line toolkits that facilitate each step in the workflow of sequence discovery, curation, alignment, and phylogenetic reconstruction. Most common sequence, alignment, and tree file formats are automatically detected and parsed, and over 100 tools have been implemented for manipulating these data. The project has been engineered to easily accommodate the addition of new tools, is written in the popular programming language Python, and is hosted on the Python Package Index and GitHub to maximize accessibility. Documentation for each BuddySuite tool, including usage examples, is available at http://tiny.cc/buddysuite_wiki. All software is open source and freely available through http://research.nhgri.nih.gov/software/BuddySuite. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution 2017. This work is written by US Government employees and is in the public domain in the US.

G SUIT FOR EDUCATION AS AN ENVIRONMENT FOR STUDENTS OF EDUCATIONAL PRACTICES

Directory of Open Access Journals (Sweden)

Olena Glazunova

2017-04-01

Full Text Available Materials article analyzes the opportunities and benefits of using cloud services G Suite (Google Apps during the practical training of students. In the course of the study, an e-environment based on G Suit for Education was developed and its use for effective organization of information technology practice training. A model of e-learning environment for organizing group project work in Google Classroom-based training has been built. The design methodology is grounded as one of the most effective for the organization of educational practice in information technologies. The stages of realization of the project task during the educational practice, as well as the tools, the achieved competence, features of the activity of teachers and students at each stage are researched. Examples of tasks, resources and services that were used to achieve project results are given.The implementation of individual project implementation phases in the Google Classroom-based electronic environment has been demonstrated, in particular, project planning, adding new services in the electronic environment, collaborative work with documents, portfolio elements, student reflection. The results of the survey of students on the organization of educational practice using the method of projects and the e-environment based on the use of cloud services G Suite (Google Apps are analyzed.

Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite

Energy Technology Data Exchange (ETDEWEB)

Jurrus, Elizabeth [Pacific Northwest National Laboratory, Richland Washington; Engel, Dave [Pacific Northwest National Laboratory, Richland Washington; Star, Keith [Pacific Northwest National Laboratory, Richland Washington; Monson, Kyle [Pacific Northwest National Laboratory, Richland Washington; Brandi, Juan [Pacific Northwest National Laboratory, Richland Washington; Felberg, Lisa E. [University of California, Berkeley California; Brookes, David H. [University of California, Berkeley California; Wilson, Leighton [University of Michigan, Ann Arbor Michigan; Chen, Jiahui [Southern Methodist University, Dallas Texas; Liles, Karina [Pacific Northwest National Laboratory, Richland Washington; Chun, Minju [Pacific Northwest National Laboratory, Richland Washington; Li, Peter [Pacific Northwest National Laboratory, Richland Washington; Gohara, David W. [St. Louis University, St. Louis Missouri; Dolinsky, Todd [FoodLogiQ, Durham North Carolina; Konecny, Robert [University of California San Diego, San Diego California; Koes, David R. [University of Pittsburgh, Pittsburgh Pennsylvania; Nielsen, Jens Erik [Protein Engineering, Novozymes A/S, Copenhagen Denmark; Head-Gordon, Teresa [University of California, Berkeley California; Geng, Weihua [Southern Methodist University, Dallas Texas; Krasny, Robert [University of Michigan, Ann Arbor Michigan; Wei, Guo-Wei [Michigan State University, East Lansing Michigan; Holst, Michael J. [University of California San Diego, San Diego California; McCammon, J. Andrew [University of California San Diego, San Diego California; Baker, Nathan A. [Pacific Northwest National Laboratory, Richland Washington; Brown University, Providence Rhode Island

2017-10-24

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining pKa values, and an improved web-based visualization tool for viewing electrostatics.

New Lithium-ion Polymer Battery for the Extravehicular Mobility Unit Suit

Science.gov (United States)

Jeevarajan, J. A.; Darcy, E. C.

2004-01-01

The Extravehicular Mobility Unit (EMU) suit currently has a silver-zinc battery that is 20.5 V and 45 Ah capacity. The EMU's portable life support system (PLSS) will draw power from the battery during the entire period of an EVA. Due to the disadvantages of using the silver-zinc battery in terms of cost and performance, a new high energy density battery is being developed for future use, The new battery (Lithium-ion battery or LIB) will consist of Li-ion polymer cells that will provide power to the EMU suit. The battery design consists of five 8 Ah cells in parallel to form a single module of 40 Ah and five such modules will be placed in series to give a 20.5 V, 40 Ah battery. Charging will be accomplished on the Shuttle or Station using the new LIB charger or the existing ALPS (Air Lock Power Supply) charger. The LIB delivers a maximum of 3.8 A on the average, for seven continuous hours, at voltages ranging from 20.5 V to 16.0 V and it should be capable of supporting transient pulses during start up and once every hour to support PLSS fan and pump operation. Figure 1 shows the placement of the battery in the backpack area of the EMU suit. The battery and cells will undergo testing under different conditions to understand its performance and safety characteristics.

Rimsky-Korsakov: Symphony N2 (Symphonic Suite), Op. 9 / John Warrack

Index Scriptorium Estoniae

Warrack, John

1990-01-01

Uuest heliplaadist "Rimsky-Korsakov: Symphony N2 (Symphonic Suite), Op. 9, "Antar" Russian Easter Festival Overture, Op.36. Philharmonia Orchestra, Evgeni Svetlanov" Hyperion KA 66399. CDA 66399. Teise sümfoonia esitust võrreldud Neeme Järvi plaadistusega

Novel genomes and genome constitutions identified by GISH and 5S rDNA and knotted1 genomic sequences in the genus Setaria.

Science.gov (United States)

Zhao, Meicheng; Zhi, Hui; Doust, Andrew N; Li, Wei; Wang, Yongfang; Li, Haiquan; Jia, Guanqing; Wang, Yongqiang; Zhang, Ning; Diao, Xianmin

2013-04-11

The Setaria genus is increasingly of interest to researchers, as its two species, S. viridis and S. italica, are being developed as models for understanding C4 photosynthesis and plant functional genomics. The genome constitution of Setaria species has been studied in the diploid species S. viridis, S. adhaerans and S. grisebachii, where three genomes A, B and C were identified respectively. Two allotetraploid species, S. verticillata and S. faberi, were found to have AABB genomes, and one autotetraploid species, S. queenslandica, with an AAAA genome, has also been identified. The genomes and genome constitutions of most other species remain unknown, even though it was thought there are approximately 125 species in the genus distributed world-wide. GISH was performed to detect the genome constitutions of Eurasia species of S. glauca, S. plicata, and S. arenaria, with the known A, B and C genomes as probes. No or very poor hybridization signal was detected indicating that their genomes are different from those already described. GISH was also performed reciprocally between S. glauca, S. plicata, and S. arenaria genomes, but no hybridization signals between each other were found. The two sets of chromosomes of S. lachnea both hybridized strong signals with only the known C genome of S. grisebachii. Chromosomes of Qing 9, an accession formerly considered as S. viridis, hybridized strong signal only to B genome of S. adherans. Phylogenetic trees constructed with 5S rDNA and knotted1 markers, clearly classify the samples in this study into six clusters, matching the GISH results, and suggesting that the F genome of S. arenaria is basal in the genus. Three novel genomes in the Setaria genus were identified and designated as genome D (S. glauca), E (S. plicata) and F (S. arenaria) respectively. The genome constitution of tetraploid S. lachnea is putatively CCC'C'. Qing 9 is a B genome species indigenous to China and is hypothesized to be a newly identified species. The

[Pitfalls in informed consent: a statistical analysis of malpractice law suits].

Science.gov (United States)

Echigo, Junko

2014-05-01

In medical malpractice law suits, the notion of informed consent is often relevant in assessing whether negligence can be attributed to the medical practitioner who has caused injury to a patient. Furthermore, it is not rare that courts award damages for a lack of appropriate informed consent alone. In this study, two results were arrived at from a statistical analysis of medical malpractice law suits. One, unexpectedly, was that the severity of a patient's illness made no significant difference to whether damages were awarded. The other was that cases of typical medical treatment that national medical insurance does not cover were involved significantly more often than insured treatment cases. In cases where damages were awarded, the courts required more disclosure and written documents of information by medical practitioners, especially about complications and adverse effects that the patient might suffer.

Personnel protective equipment total-encapsulating suit decontamination study using shower systems

International Nuclear Information System (INIS)

Menkhaus, D.E.

1991-01-01

This report documents an experimental evaluation, conducted at the Idaho National Engineering Laboratory, of a shower-based decontamination station for personnel wearing a Level A, total- encapsulating, chemical-protective suit. The decontamination station is used by personnel when egressing a dry, dusty environment contaminated with transuranic radionuclides. This system has the potential to minimize the risk of spreading the contaminants to clean areas. Two types of shower systems were evaluated, a drench shower and a multi-nozzle shower. A total-encapsulating suit, worn by personnel. was contaminated with soil containing 239 Pu. Pre- shower and post-shower contamination samples were collected and visual observations were made to evaluate the ability of the shower system to remove the contaminated dust and to obtain baseline data useful in designing a shower-based personnel decontamination system. 12 figs., 7 tabs

Genome-derived vaccines.

Science.gov (United States)

De Groot, Anne S; Rappuoli, Rino

2004-02-01

Vaccine research entered a new era when the complete genome of a pathogenic bacterium was published in 1995. Since then, more than 97 bacterial pathogens have been sequenced and at least 110 additional projects are now in progress. Genome sequencing has also dramatically accelerated: high-throughput facilities can draft the sequence of an entire microbe (two to four megabases) in 1 to 2 days. Vaccine developers are using microarrays, immunoinformatics, proteomics and high-throughput immunology assays to reduce the truly unmanageable volume of information available in genome databases to a manageable size. Vaccines composed by novel antigens discovered from genome mining are already in clinical trials. Within 5 years we can expect to see a novel class of vaccines composed by genome-predicted, assembled and engineered T- and Bcell epitopes. This article addresses the convergence of three forces--microbial genome sequencing, computational immunology and new vaccine technologies--that are shifting genome mining for vaccines onto the forefront of immunology research.

JGI Fungal Genomics Program

Energy Technology Data Exchange (ETDEWEB)

Grigoriev, Igor V.

2011-03-14

Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

Genomic Encyclopedia of Fungi

Energy Technology Data Exchange (ETDEWEB)

Grigoriev, Igor

2012-08-10

Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

The Genomic Code: Genome Evolution and Potential Applications

KAUST Repository

Bernardi, Giorgio

2016-01-25

The genome of metazoans is organized according to a genomic code which comprises three laws: 1) Compositional correlations hold between contiguous coding and non-coding sequences, as well as among the three codon positions of protein-coding genes; these correlations are the consequence of the fact that the genomes under consideration consist of fairly homogeneous, long (≥200Kb) sequences, the isochores; 2) Although isochores are defined on the basis of purely compositional properties, GC levels of isochores are correlated with all tested structural and functional properties of the genome; 3) GC levels of isochores are correlated with chromosome architecture from interphase to metaphase; in the case of interphase the correlation concerns isochores and the three-dimensional “topological associated domains” (TADs); in the case of mitotic chromosomes, the correlation concerns isochores and chromosomal bands. Finally, the genomic code is the fourth and last pillar of molecular biology, the first three pillars being 1) the double helix structure of DNA; 2) the regulation of gene expression in prokaryotes; and 3) the genetic code.

Vadose zone flow convergence test suite

Energy Technology Data Exchange (ETDEWEB)

Butcher, B. T. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

2017-06-05

Performance Assessment (PA) simulations for engineered disposal systems at the Savannah River Site involve highly contrasting materials and moisture conditions at and near saturation. These conditions cause severe convergence difficulties that typically result in unacceptable convergence or long simulation times or excessive analyst effort. Adequate convergence is usually achieved in a trial-anderror manner by applying under-relaxation to the Saturation or Pressure variable, in a series of everdecreasing RELAxation values. SRNL would like a more efficient scheme implemented inside PORFLOW to achieve flow convergence in a more reliable and efficient manner. To this end, a suite of test problems that illustrate these convergence problems is provided to facilitate diagnosis and development of an improved convergence strategy. The attached files are being transmitted to you describing the test problem and proposed resolution.

PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes

Directory of Open Access Journals (Sweden)

Wasnick Michael

2008-03-01

Full Text Available Abstract Background The conservation of gene order among prokaryotic genomes can provide valuable insight into gene function, protein interactions, or events by which genomes have evolved. Although some tools are available for visualizing and comparing the order of genes between genomes of study, few support an efficient and organized analysis between large numbers of genomes. The Prokaryotic Sequence homology Analysis Tool (PSAT is a web tool for comparing gene neighborhoods among multiple prokaryotic genomes. Results PSAT utilizes a database that is preloaded with gene annotation, BLAST hit results, and gene-clustering scores designed to help identify regions of conserved gene order. Researchers use the PSAT web interface to find a gene of interest in a reference genome and efficiently retrieve the sequence homologs found in other bacterial genomes. The tool generates a graphic of the genomic neighborhood surrounding the selected gene and the corresponding regions for its homologs in each comparison genome. Homologs in each region are color coded to assist users with analyzing gene order among various genomes. In contrast to common comparative analysis methods that filter sequence homolog data based on alignment score cutoffs, PSAT leverages gene context information for homologs, including those with weak alignment scores, enabling a more sensitive analysis. Features for constraining or ordering results are designed to help researchers browse results from large numbers of comparison genomes in an organized manner. PSAT has been demonstrated to be useful for helping to identify gene orthologs and potential functional gene clusters, and detecting genome modifications that may result in loss of function. Conclusion PSAT allows researchers to investigate the order of genes within local genomic neighborhoods of multiple genomes. A PSAT web server for public use is available for performing analyses on a growing set of reference genomes through any

The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes.

Science.gov (United States)

Mao, Qing; Ciotlos, Serban; Zhang, Rebecca Yu; Ball, Madeleine P; Chin, Robert; Carnevali, Paolo; Barua, Nina; Nguyen, Staci; Agarwal, Misha R; Clegg, Tom; Connelly, Abram; Vandewege, Ward; Zaranek, Alexander Wait; Estep, Preston W; Church, George M; Drmanac, Radoje; Peters, Brock A

2016-10-11

Since the completion of the Human Genome Project in 2003, it is estimated that more than 200,000 individual whole human genomes have been sequenced. A stunning accomplishment in such a short period of time. However, most of these were sequenced without experimental haplotype data and are therefore missing an important aspect of genome biology. In addition, much of the genomic data is not available to the public and lacks phenotypic information. As part of the Personal Genome Project, blood samples from 184 participants were collected and processed using Complete Genomics' Long Fragment Read technology. Here, we present the experimental whole genome haplotyping and sequencing of these samples to an average read coverage depth of 100X. This is approximately three-fold higher than the read coverage applied to most whole human genome assemblies and ensures the highest quality results. Currently, 114 genomes from this dataset are freely available in the GigaDB repository and are associated with rich phenotypic data; the remaining 70 should be added in the near future as they are approved through the PGP data release process. For reproducibility analyses, 20 genomes were sequenced at least twice using independent LFR barcoded libraries. Seven genomes were also sequenced using Complete Genomics' standard non-barcoded library process. In addition, we report 2.6 million high-quality, rare variants not previously identified in the Single Nucleotide Polymorphisms database or the 1000 Genomes Project Phase 3 data. These genomes represent a unique source of haplotype and phenotype data for the scientific community and should help to expand our understanding of human genome evolution and function.

A novel Sulfolobus non-conjugative extrachromosomal genetic element capable of integration into the host genome and spreading in the presence of a fusellovirus

DEFF Research Database (Denmark)

Wang, Ying; Duan, Zhenhong; Zhu, Haojun

2007-01-01

An integrative non-conjugative extrachromosomal genetic element, denoted as pSSVi, has been isolated from a Sulfolobus solfataricus P2 strain and was characterized. This genetic element is a double-stranded DNA of 5740 bp in size and contains eight open reading frames (ORFs). It resembles members....... Interestingly, pSSVi encodes an SSV-type integrase which probably catalyzes the integration of its genome into a specific site (a tRNA(Arg) gene) in the S. solfataricus P2 genome. Like pSSVx, pSSVi can be packaged into a spindle-like viral particle and spread with the help of SSV1 or SSV2. In addition, both SSV......1 and SSV2 appeared to replicate more efficiently in the presence of pSSVi. Given the versatile genetic abilities, pSSVi appears to be well suited for a role in horizontal gene transfer....

Brief Guide to Genomics: DNA, Genes and Genomes

Science.gov (United States)

... clinic. Most new drugs based on genome-based research are estimated to be at least 10 to 15 years away, though recent genome-driven efforts in lipid-lowering therapy have considerably shortened that interval. According ...

An Effective Strategy to Build Up a Balanced Test Suite for Spectrum-Based Fault Localization

Directory of Open Access Journals (Sweden)

Ning Li

2016-01-01

Full Text Available During past decades, many automated software faults diagnosis techniques including Spectrum-Based Fault Localization (SBFL have been proposed to improve the efficiency of software debugging activity. In the field of SBFL, suspiciousness calculation is closely related to the number of failed and passed test cases. Studies have shown that the ratio of the number of failed and passed test case has more significant impact on the accuracy of SBFL than the total number of test cases, and a balanced test suite is more beneficial to improving the accuracy of SBFL. Based on theoretical analysis, we proposed an PNF (Passed test cases, Not execute Faulty statement strategy to reduce test suite and build up a more balanced one for SBFL, which can be used in regression testing. We evaluated the strategy making experiments using the Siemens program and Space program. Experiments indicated that our PNF strategy can be used to construct a new test suite effectively. Compared with the original test suite, the new one has smaller size (average 90% test case was reduced in experiments and more balanced ratio of failed test cases to passed test cases, while it has the same statement coverage and fault localization accuracy.

MIPS plant genome information resources.

Science.gov (United States)

Spannagl, Manuel; Haberer, Georg; Ernst, Rebecca; Schoof, Heiko; Mayer, Klaus F X

2007-01-01

The Munich Institute for Protein Sequences (MIPS) has been involved in maintaining plant genome databases since the Arabidopsis thaliana genome project. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable data sets for model plant genomes as a backbone against which experimental data, for example from high-throughput functional genomics, can be organized and evaluated. In addition, model genomes also form a scaffold for comparative genomics, and much can be learned from genome-wide evolutionary studies.

SSAGES: Software Suite for Advanced General Ensemble Simulations

Science.gov (United States)

Sidky, Hythem; Colón, Yamil J.; Helfferich, Julian; Sikora, Benjamin J.; Bezik, Cody; Chu, Weiwei; Giberti, Federico; Guo, Ashley Z.; Jiang, Xikai; Lequieu, Joshua; Li, Jiyuan; Moller, Joshua; Quevillon, Michael J.; Rahimi, Mohammad; Ramezani-Dakhel, Hadi; Rathee, Vikramjit S.; Reid, Daniel R.; Sevgen, Emre; Thapar, Vikram; Webb, Michael A.; Whitmer, Jonathan K.; de Pablo, Juan J.

2018-01-01

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse-grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite. The code may be found at: https://github.com/MICCoM/SSAGES-public.

Defining Constellation Suit Helmet Field of View Requirements Employing a Mission Segment Based Reduction Process

Science.gov (United States)

McFarland, Shane

2009-01-01

Field of view has always been a design feature paramount to helmets, and in particular space suits, where the helmet must provide an adequate field of view for a large range of activities, environments, and body positions. For Project Constellation, a different approach to helmet requirement maturation was utilized; one that was less a direct function of body position and suit pressure and more a function of the mission segment in which the field of view will be required. Through taxonimization of various parameters that affect suited field of view, as well as consideration for possible nominal and contingency operations during that mission segment, a reduction process was employed to condense the large number of possible outcomes to only six unique field of view angle requirements that still captured all necessary variables while sacrificing minimal fidelity.

Effect of STS space suit on astronaut dominant upper limb EVA work performance

Science.gov (United States)

Greenisen, Michael C.

1987-01-01

The STS Space Suited and unsuited dominant upper limb performance was evaluated in order to quantify future EVA astronaut skeletal muscle upper limb performance expectations. Testing was performed with subjects standing in EVA STS foot restraints. Data was collected with a CYBEX Dynamometer enclosed in a waterproof container. Control data was taken in one g. During one g testing, weight of the Space Suit was relieved from the subject via an overhead crane with a special connection to the PLSS of the suit. Experimental data was acquired during simulated zero g, accomplished by neutral buoyancy in the Weightless Environment Training Facility. Unsuited subjects became neutrally buoyant via SCUBA BC vests. Actual zero g experimental data was collected during parabolic arc flights on board NASA's modified KC-135 aircraft. During all test conditions, subjects performed five EVA work tasks requiring dominant upper limb performance and ten individual joint articulation movements. Dynamometer velocities for each tested movement were 0 deg/sec, 30 or 60 deg/sec and 120 or 180 deg/sec, depending on the test, with three repetitions per test. Performance was measured in foot pounds of torque.

Great Lakes Hyperspectral Water Quality Instrument Suite for Airborne Monitoring of Algal Blooms

Science.gov (United States)

Lekki, John; Leshkevich, George; Nguyen, Quang-Viet; Flatico, Joseph; Prokop, Norman; Kojima, Jun; Anderson, Robert; Demers, James; Krasowski, Michael

2007-01-01

NASA Glenn Research Center and NOAA Great Lakes Environmental Research Lab are collaborating to utilize an airborne hyperspectral imaging sensor suite to monitor Harmful Algal Blooms (HABs) in the western basin of Lake Erie. The HABs are very dynamic events as they form, spread and then disappear within a 4 to 8 week time period in late summer. They are a concern for human health, fish and wildlife because they can contain blue green toxic algae. Because of this toxicity there is a need for the blooms to be continually monitored. This situation is well suited for aircraft based monitoring because the blooms are a very dynamic event and they can spread over a large area. High resolution satellite data is not suitable by itself because it will not give the temporal resolution due to the infrequent overpasses of the quickly changing blooms. A custom designed hyperspectral imager and a point spectrometer mounted on aT 34 aircraft have been used to obtain data on an algal bloom that formed in the western basin of Lake Erie during September 2006. The sensor suite and operations will be described and preliminary hyperspectral data of this event will be presented

Effectiveness comparison of partially executed t-way test suite based generated by existing strategies

Science.gov (United States)

Othman, Rozmie R.; Ahmad, Mohd Zamri Zahir; Ali, Mohd Shaiful Aziz Rashid; Zakaria, Hasneeza Liza; Rahman, Md. Mostafijur

2015-05-01

Consuming 40 to 50 percent of software development cost, software testing is one of the most resource consuming activities in software development lifecycle. To ensure an acceptable level of quality and reliability of a typical software product, it is desirable to test every possible combination of input data under various configurations. Due to combinatorial explosion problem, considering all exhaustive testing is practically impossible. Resource constraints, costing factors as well as strict time-to-market deadlines are amongst the main factors that inhibit such consideration. Earlier work suggests that sampling strategy (i.e. based on t-way parameter interaction or called as t-way testing) can be effective to reduce number of test cases without effecting the fault detection capability. However, for a very large system, even t-way strategy will produce a large test suite that need to be executed. In the end, only part of the planned test suite can be executed in order to meet the aforementioned constraints. Here, there is a need for test engineers to measure the effectiveness of partially executed test suite in order for them to assess the risk they have to take. Motivated by the abovementioned problem, this paper presents the effectiveness comparison of partially executed t-way test suite generated by existing strategies using tuples coverage method. Here, test engineers can predict the effectiveness of the testing process if only part of the original test cases is executed.

20 CFR 423.1 - Suits against the Social Security Administration and its employees in their official capacities.

Science.gov (United States)

2010-04-01

... Federal Register, and are available on-line at the Social Security Administration's Internet site, http... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Suits against the Social Security... SECURITY ADMINISTRATION SERVICE OF PROCESS § 423.1 Suits against the Social Security Administration and its...

Variability in heat strain in fully encapsulated impermeable suits in different climates and at different work loads

NARCIS (Netherlands)

Hartog, E.A. den; Rubenstein, C.D.; Deaton, A.S.; Bogerd, C.P.

2017-01-01

A major concern for responders to hazardous materials (HazMat) incidents is the heat strain that is caused by fully encapsulated impermeable (NFPA 1991) suits. In a research project, funded by the US Department of Defense, the thermal strain experienced when wearing these suits was studied. Forty

Airport Gate Activity Monitoring Tool Suite for Improved Turnaround Prediction, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — The objective of this research is to create a suite of tools for monitoring airport gate activities with the objective of improving aircraft turnaround. Airport ramp...

Ensembl Genomes 2013: scaling up access to genome-wide data.

Science.gov (United States)

Kersey, Paul Julian; Allen, James E; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Hughes, Daniel Seth Toney; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Langridge, Nicholas; McDowall, Mark D; Maheswari, Uma; Maslen, Gareth; Nuhn, Michael; Ong, Chuang Kee; Paulini, Michael; Pedro, Helder; Toneva, Iliana; Tuli, Mary Ann; Walts, Brandon; Williams, Gareth; Wilson, Derek; Youens-Clark, Ken; Monaco, Marcela K; Stein, Joshua; Wei, Xuehong; Ware, Doreen; Bolser, Daniel M; Howe, Kevin Lee; Kulesha, Eugene; Lawson, Daniel; Staines, Daniel Michael

2014-01-01

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. This article provides an update to the previous publications about the resource, with a focus on recent developments. These include the addition of important new genomes (and related data sets) including crop plants, vectors of human disease and eukaryotic pathogens. In addition, the resource has scaled up its representation of bacterial genomes, and now includes the genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely to become increasingly important in future as the number of available genomes increases within all domains of life, and some of the challenges faced in representing bacterial data are likely to become commonplace for eukaryotes in future.

The Zoot Suit Riots: Exploring Social Issues in American History

Science.gov (United States)

Chiodo, John J.

2013-01-01

The Zoot Suit Riots provide students with a case study of social unrest in American history. The influx of Latinos into the Los Angeles area prior to World War II created high levels of social unrest between Mexican Americans, military servicemen, and local residences. With large numbers of soldiers stationed in the area during the Second World…

Toward genome-enabled mycology.

Science.gov (United States)

Hibbett, David S; Stajich, Jason E; Spatafora, Joseph W

2013-01-01

Genome-enabled mycology is a rapidly expanding field that is characterized by the pervasive use of genome-scale data and associated computational tools in all aspects of fungal biology. Genome-enabled mycology is integrative and often requires teams of researchers with diverse skills in organismal mycology, bioinformatics and molecular biology. This issue of Mycologia presents the first complete fungal genomes in the history of the journal, reflecting the ongoing transformation of mycology into a genome-enabled science. Here, we consider the prospects for genome-enabled mycology and the technical and social challenges that will need to be overcome to grow the database of complete fungal genomes and enable all fungal biologists to make use of the new data.

DelPhi: a comprehensive suite for DelPhi software and associated resources

Directory of Open Access Journals (Sweden)

Li Lin

2012-05-01

Full Text Available Abstract Background Accurate modeling of electrostatic potential and corresponding energies becomes increasingly important for understanding properties of biological macromolecules and their complexes. However, this is not an easy task due to the irregular shape of biological entities and the presence of water and mobile ions. Results Here we report a comprehensive suite for the well-known Poisson-Boltzmann solver, DelPhi, enriched with additional features to facilitate DelPhi usage. The suite allows for easy download of both DelPhi executable files and source code along with a makefile for local installations. The users can obtain the DelPhi manual and parameter files required for the corresponding investigation. Non-experienced researchers can download examples containing all necessary data to carry out DelPhi runs on a set of selected examples illustrating various DelPhi features and demonstrating DelPhi’s accuracy against analytical solutions. Conclusions DelPhi suite offers not only the DelPhi executable and sources files, examples and parameter files, but also provides links to third party developed resources either utilizing DelPhi or providing plugins for DelPhi. In addition, the users and developers are offered a forum to share ideas, resolve issues, report bugs and seek help with respect to the DelPhi package. The resource is available free of charge for academic users from URL: http://compbio.clemson.edu/DelPhi.php.

New isotope data from the Koperberg Suite and some associated rocks, Okiep district, Namaqualand, South Africa

International Nuclear Information System (INIS)

Clifford, T.N.; Barton, E.S.; Retief, E.A.; Rex, D.C.

1990-01-01

The Koperberg Suite is an anorthosite-charnockite kindred and 1500 bodies of these rocks have been recognised in the Okiep district and 30 of them have been mined for copper since 1852. The suite is intrusive into country rocks. New isotope data presented includes U-Pb zircon and whole-rock Pb-Pb, Rb-Sr, Sm-Nd and Ar-Ar analyses. 10 refs

Plantagora: modeling whole genome sequencing and assembly of plant genomes.

Directory of Open Access Journals (Sweden)

Roger Barthelson

Full Text Available BACKGROUND: Genomics studies are being revolutionized by the next generation sequencing technologies, which have made whole genome sequencing much more accessible to the average researcher. Whole genome sequencing with the new technologies is a developing art that, despite the large volumes of data that can be produced, may still fail to provide a clear and thorough map of a genome. The Plantagora project was conceived to address specifically the gap between having the technical tools for genome sequencing and knowing precisely the best way to use them. METHODOLOGY/PRINCIPAL FINDINGS: For Plantagora, a platform was created for generating simulated reads from several different plant genomes of different sizes. The resulting read files mimicked either 454 or Illumina reads, with varying paired end spacing. Thousands of datasets of reads were created, most derived from our primary model genome, rice chromosome one. All reads were assembled with different software assemblers, including Newbler, Abyss, and SOAPdenovo, and the resulting assemblies were evaluated by an extensive battery of metrics chosen for these studies. The metrics included both statistics of the assembly sequences and fidelity-related measures derived by alignment of the assemblies to the original genome source for the reads. The results were presented in a website, which includes a data graphing tool, all created to help the user compare rapidly the feasibility and effectiveness of different sequencing and assembly strategies prior to testing an approach in the lab. Some of our own conclusions regarding the different strategies were also recorded on the website. CONCLUSIONS/SIGNIFICANCE: Plantagora provides a substantial body of information for comparing different approaches to sequencing a plant genome, and some conclusions regarding some of the specific approaches. Plantagora also provides a platform of metrics and tools for studying the process of sequencing and assembly

Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes.

Science.gov (United States)

Puigbò, Pere; Lobkovsky, Alexander E; Kristensen, David M; Wolf, Yuri I; Koonin, Eugene V

2014-08-21

Genomes of bacteria and archaea (collectively, prokaryotes) appear to exist in incessant flux, expanding via horizontal gene transfer and gene duplication, and contracting via gene loss. However, the actual rates of genome dynamics and relative contributions of different types of event across the diversity of prokaryotes are largely unknown, as are the sizes of microbial supergenomes, i.e. pools of genes that are accessible to the given microbial species. We performed a comprehensive analysis of the genome dynamics in 35 groups (34 bacterial and one archaeal) of closely related microbial genomes using a phylogenetic birth-and-death maximum likelihood model to quantify the rates of gene family gain and loss, as well as expansion and reduction. The results show that loss of gene families dominates the evolution of prokaryotes, occurring at approximately three times the rate of gain. The rates of gene family expansion and reduction are typically seven and twenty times less than the gain and loss rates, respectively. Thus, the prevailing mode of evolution in bacteria and archaea is genome contraction, which is partially compensated by the gain of new gene families via horizontal gene transfer. However, the rates of gene family gain, loss, expansion and reduction vary within wide ranges, with the most stable genomes showing rates about 25 times lower than the most dynamic genomes. For many groups, the supergenome estimated from the fraction of repetitive gene family gains includes about tenfold more gene families than the typical genome in the group although some groups appear to have vast, 'open' supergenomes. Reconstruction of evolution for groups of closely related bacteria and archaea reveals an extremely rapid and highly variable flux of genes in evolving microbial genomes, demonstrates that extensive gene loss and horizontal gene transfer leading to innovation are the two dominant evolutionary processes, and yields robust estimates of the supergenome size.

Closed-Loop, Non-Venting Thermal Control for Mars EVA Suits, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — NASA seeks new thermal control technology for EVA suits on Mars. The system must be closed-loop and non-venting, have negligible impact on the Martian environment,...

Uptake and usage of IntelliCare: A publicly available suite of mental health and well-being apps

Directory of Open Access Journals (Sweden)

Emily G. Lattie

2016-05-01

Conclusions: The use rate of the IntelliCare suite of apps is higher than public deployments of other comparable digital resources. Our findings suggest that people will use multiple apps and provides support for the concept of app suites as a useful strategy for providing diverse behavioral strategies.

A Web-Based Comparative Genomics Tutorial for Investigating Microbial Genomes

Directory of Open Access Journals (Sweden)

Michael Strong

2009-12-01

Full Text Available As the number of completely sequenced microbial genomes continues to rise at an impressive rate, it is important to prepare students with the skills necessary to investigate microorganisms at the genomic level. As a part of the core curriculum for first-year graduate students in the biological sciences, we have implemented a web-based tutorial to introduce students to the fields of comparative and functional genomics. The tutorial focuses on recent computational methods for identifying functionally linked genes and proteins on a genome-wide scale and was used to introduce students to the Rosetta Stone, Phylogenetic Profile, conserved Gene Neighbor, and Operon computational methods. Students learned to use a number of publicly available web servers and databases to identify functionally linked genes in the Escherichia coli genome, with emphasis on genome organization and operon structure. The overall effectiveness of the tutorial was assessed based on student evaluations and homework assignments. The tutorial is available to other educators at http://www.doe-mbi.ucla.edu/~strong/m253.php.

Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus.

Directory of Open Access Journals (Sweden)

Fabian Staubach

Full Text Available General parameters of selection, such as the frequency and strength of positive selection in natural populations or the role of introgression, are still insufficiently understood. The house mouse (Mus musculus is a particularly well-suited model system to approach such questions, since it has a defined history of splits into subspecies and populations and since extensive genome information is available. We have used high-density single-nucleotide polymorphism (SNP typing arrays to assess genomic patterns of positive selection and introgression of alleles in two natural populations of each of the subspecies M. m. domesticus and M. m. musculus. Applying different statistical procedures, we find a large number of regions subject to apparent selective sweeps, indicating frequent positive selection on rare alleles or novel mutations. Genes in the regions include well-studied imprinted loci (e.g. Plagl1/Zac1, homologues of human genes involved in adaptations (e.g. alpha-amylase genes or in genetic diseases (e.g. Huntingtin and Parkin. Haplotype matching between the two subspecies reveals a large number of haplotypes that show patterns of introgression from specific populations of the respective other subspecies, with at least 10% of the genome being affected by partial or full introgression. Using neutral simulations for comparison, we find that the size and the fraction of introgressed haplotypes are not compatible with a pure migration or incomplete lineage sorting model. Hence, it appears that introgressed haplotypes can rise in frequency due to positive selection and thus can contribute to the adaptive genomic landscape of natural populations. Our data support the notion that natural genomes are subject to complex adaptive processes, including the introgression of haplotypes from other differentiated populations or species at a larger scale than previously assumed for animals. This implies that some of the admixture found in inbred strains of mice

Metallogenic aspects of Itu intrusive suite

International Nuclear Information System (INIS)

Amaral, G.; Pascholati, E.M.

1990-01-01

The integrated use of geological, geochemical, geophysical and remote sensing data is providing interesting new information on the metallogenic characteristics of the Itu Intrusive Suite. During World War II, up to 1959, a wolframite deposit was mined near the border of the northernmost body (Itupeva Granite). This deposit is formed by greisen veins associated with cassiterite and topaz, clearly linked with later phases of magmatic differentiation. Generally those veins are related to hydrothermal alteration of the granites and the above mentioned shear zone. U, Th and K determinations by field and laboratory gammaspectrometry were used for regional distribution analysis of those elements and its ratios and calculation of radioactivity heat production. In this aspects, the Itupeva Granite is the hottest and presents several anomalies in the Th/U ratio, indicative of late or post magmatic oxidation processes. (author)

Astronaut Ronald Evans is suited up for EVA training

Science.gov (United States)

1972-01-01

Astronaut Ronald E. Evans, command module pilot of the Apollo 17 lunar landing mission, is assisted by technicians in suiting up for extravehicular activity (EVA) training in a water tank in bldg 5 at the Manned Spacecraft Center (49970); Evans participates in EVA training in a water tank in bldg 5 at the Manned Spacecraft Center. The structure in the picture simulates the Scientific Instrument Module (SIM) bay of the Apollo 17 Service Module (49971).

Apollo 11 astronaut Neil Armstrong suits up before launch

Science.gov (United States)

1969-01-01

Apollo 11 Commander Neil Armstrong prepares to put on his helmet with the assistance of a spacesuit technician during suiting operations in the Manned Spacecraft Operations Building (MSOB) prior to the astronauts' departure to Launch Pad 39A. The three astronauts, Edwin E. Aldrin Jr., Neil A Armstrong and Michael Collins, will then board the Saturn V launch vehicle, scheduled for a 9:32 a.m. EDT liftoff, for the first manned lunar landing mission.

Reduced representation approaches to interrogate genome diversity in large repetitive plant genomes.

Science.gov (United States)

Hirsch, Cory D; Evans, Joseph; Buell, C Robin; Hirsch, Candice N

2014-07-01

Technology and software improvements in the last decade now provide methodologies to access the genome sequence of not only a single accession, but also multiple accessions of plant species. This provides a means to interrogate species diversity at the genome level. Ample diversity among accessions in a collection of species can be found, including single-nucleotide polymorphisms, insertions and deletions, copy number variation and presence/absence variation. For species with small, non-repetitive rich genomes, re-sequencing of query accessions is robust, highly informative, and economically feasible. However, for species with moderate to large sized repetitive-rich genomes, technical and economic barriers prevent en masse genome re-sequencing of accessions. Multiple approaches to access a focused subset of loci in species with larger genomes have been developed, including reduced representation sequencing, exome capture and transcriptome sequencing. Collectively, these approaches have enabled interrogation of diversity on a genome scale for large plant genomes, including crop species important to worldwide food security. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Between Two Fern Genomes

Science.gov (United States)

2014-01-01

Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves. PMID:25324969

Exploring Other Genomes: Bacteria.

Science.gov (United States)

Flannery, Maura C.

2001-01-01

Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)

Comparative Pan-Genome Analysis of Piscirickettsia salmonis Reveals Genomic Divergences within Genogroups

Directory of Open Access Journals (Sweden)

Guillermo Nourdin-Galindo

2017-10-01

Full Text Available Piscirickettsia salmonis is the etiological agent of salmonid rickettsial septicemia, a disease that seriously affects the salmonid industry. Despite efforts to genomically characterize P. salmonis, functional information on the life cycle, pathogenesis mechanisms, diagnosis, treatment, and control of this fish pathogen remain lacking. To address this knowledge gap, the present study conducted an in silico pan-genome analysis of 19 P. salmonis strains from distinct geographic locations and genogroups. Results revealed an expected open pan-genome of 3,463 genes and a core-genome of 1,732 genes. Two marked genogroups were identified, as confirmed by phylogenetic and phylogenomic relationships to the LF-89 and EM-90 reference strains, as well as by assessments of genomic structures. Different structural configurations were found for the six identified copies of the ribosomal operon in the P. salmonis genome, indicating translocation throughout the genetic material. Chromosomal divergences in genomic localization and quantity of genetic cassettes were also found for the Dot/Icm type IVB secretion system. To determine divergences between core-genomes, additional pan-genome descriptions were compiled for the so-termed LF and EM genogroups. Open pan-genomes composed of 2,924 and 2,778 genes and core-genomes composed of 2,170 and 2,228 genes were respectively found for the LF and EM genogroups. The core-genomes were functionally annotated using the Gene Ontology, KEGG, and Virulence Factor databases, revealing the presence of several shared groups of genes related to basic function of intracellular survival and bacterial pathogenesis. Additionally, the specific pan-genomes for the LF and EM genogroups were defined, resulting in the identification of 148 and 273 exclusive proteins, respectively. Notably, specific virulence factors linked to adherence, colonization, invasion factors, and endotoxins were established. The obtained data suggest that these

Carbohydrate-active enzymes from pigmented Bacilli: a genomic approach to assess carbohydrate utilization and degradation

Directory of Open Access Journals (Sweden)

Henrissat Bernard

2011-09-01

Full Text Available Abstract Background Spore-forming Bacilli are Gram-positive bacteria commonly found in a variety of natural habitats, including soil, water and the gastro-intestinal (GI-tract of animals. Isolates of various Bacillus species produce pigments, mostly carotenoids, with a putative protective role against UV irradiation and oxygen-reactive forms. Results We report the annotation of carbohydrate active enzymes (CAZymes of two pigmented Bacilli isolated from the human GI-tract and belonging to the Bacillus indicus and B. firmus species. A high number of glycoside hydrolases (GHs and carbohydrate binding modules (CBMs were found in both isolates. A detailed analysis of CAZyme families, was performed and supported by growth data. Carbohydrates able to support growth as the sole carbon source negatively effected carotenoid formation in rich medium, suggesting that a catabolite repression-like mechanism controls carotenoid biosynthesis in both Bacilli. Experimental results on biofilm formation confirmed genomic data on the potentials of B. indicus HU36 to produce a levan-based biofilm, while mucin-binding and -degradation experiments supported genomic data suggesting the ability of both Bacilli to degrade mammalian glycans. Conclusions CAZy analyses of the genomes of the two pigmented Bacilli, compared to other Bacillus species and validated by experimental data on carbohydrate utilization, biofilm formation and mucin degradation, suggests that the two pigmented Bacilli are adapted to the intestinal environment and are suited to grow in and colonize the human gut.

A Genome-Wide Landscape of Retrocopies in Primate Genomes.

Science.gov (United States)

Navarro, Fábio C P; Galante, Pedro A F

2015-07-29

Gene duplication is a key factor contributing to phenotype diversity across and within species. Although the availability of complete genomes has led to the extensive study of genomic duplications, the dynamics and variability of gene duplications mediated by retrotransposition are not well understood. Here, we predict mRNA retrotransposition and use comparative genomics to investigate their origin and variability across primates. Analyzing seven anthropoid primate genomes, we found a similar number of mRNA retrotranspositions (∼7,500 retrocopies) in Catarrhini (Old Word Monkeys, including humans), but a surprising large number of retrocopies (∼10,000) in Platyrrhini (New World Monkeys), which may be a by-product of higher long interspersed nuclear element 1 activity in these genomes. By inferring retrocopy orthology, we dated most of the primate retrocopy origins, and estimated a decrease in the fixation rate in recent primate history, implying a smaller number of species-specific retrocopies. Moreover, using RNA-Seq data, we identified approximately 3,600 expressed retrocopies. As expected, most of these retrocopies are located near or within known genes, present tissue-specific and even species-specific expression patterns, and no expression correlation to their parental genes. Taken together, our results provide further evidence that mRNA retrotransposition is an active mechanism in primate evolution and suggest that retrocopies may not only introduce great genetic variability between lineages but also create a large reservoir of potentially functional new genomic loci in primate genomes. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Effect of antigravity suit inflation on cardiovascular, PRA, and PVP responses in humans. [Plasma Renin Activity and Plasma VasoPressin

Science.gov (United States)

Kravik, S. E.; Keil, L. C.; Geelen, G.; Wade, C. E.; Barnes, P. R.

1986-01-01

The effects of lower body and abdominal pressure, produced by antigravity suit inflation, on blood pressure, pulse rate, fluid and electrolyte shift, plasma vasopressin and plasma renin activity in humans in upright postures were studied. Five men and two women stood upright for 3 hr with the suit being either inflated or uninflated. In the control tests, the suit was inflated only during the latter part of the trials. Monitoring was carried out with a sphygnomanometer, with sensors for pulse rates, and using a photometer and osmometer to measure blood serum characteristics. The tests confirmed earlier findings that the anti-g suit eliminates increases in plasma renin activity. Also, the headward redistribution of blood obtained in the tests commends the anti-g suit as an alternative to water immersion or bed rest for initial weightlessness studies.

Comparative genomics of the marine bacterial genus Glaciecola reveals the high degree of genomic diversity and genomic characteristic for cold adaptation.

Science.gov (United States)

Qin, Qi-Long; Xie, Bin-Bin; Yu, Yong; Shu, Yan-Li; Rong, Jin-Cheng; Zhang, Yan-Jiao; Zhao, Dian-Li; Chen, Xiu-Lan; Zhang, Xi-Ying; Chen, Bo; Zhou, Bai-Cheng; Zhang, Yu-Zhong

2014-06-01

To what extent the genomes of different species belonging to one genus can be diverse and the relationship between genomic differentiation and environmental factor remain unclear for oceanic bacteria. With many new bacterial genera and species being isolated from marine environments, this question warrants attention. In this study, we sequenced all the type strains of the published species of Glaciecola, a recently defined cold-adapted genus with species from diverse marine locations, to study the genomic diversity and cold-adaptation strategy in this genus.The genome size diverged widely from 3.08 to 5.96 Mb, which can be explained by massive gene gain and loss events. Horizontal gene transfer and new gene emergence contributed substantially to the genome size expansion. The genus Glaciecola had an open pan-genome. Comparative genomic research indicated that species of the genus Glaciecola had high diversity in genome size, gene content and genetic relatedness. This may be prevalent in marine bacterial genera considering the dynamic and complex environments of the ocean. Species of Glaciecola had some common genomic features related to cold adaptation, which enable them to thrive and play a role in biogeochemical cycle in the cold marine environments.

Funding Opportunity: Genomic Data Centers

Science.gov (United States)

Funding Opportunity CCG, Funding Opportunity Center for Cancer Genomics, CCG, Center for Cancer Genomics, CCG RFA, Center for cancer genomics rfa, genomic data analysis network, genomic data analysis network centers,

Solid-solid phase change thermal storage application to space-suit battery pack

Science.gov (United States)

Son, Chang H.; Morehouse, Jeffrey H.

1989-01-01

High cell temperatures are seen as the primary safety problem in the Li-BCX space battery. The exothermic heat from the chemical reactions could raise the temperature of the lithium electrode above the melting temperature. Also, high temperature causes the cell efficiency to decrease. Solid-solid phase-change materials were used as a thermal storage medium to lower this battery cell temperature by utilizing their phase-change (latent heat storage) characteristics. Solid-solid phase-change materials focused on in this study are neopentyl glycol and pentaglycerine. Because of their favorable phase-change characteristics, these materials appear appropriate for space-suit battery pack use. The results of testing various materials are reported as thermophysical property values, and the space-suit battery operating temperature is discussed in terms of these property results.

MicroScope: a platform for microbial genome annotation and comparative genomics.

Science.gov (United States)

Vallenet, D; Engelen, S; Mornico, D; Cruveiller, S; Fleury, L; Lajus, A; Rouy, Z; Roche, D; Salvignol, G; Scarpelli, C; Médigue, C

2009-01-01

The initial outcome of genome sequencing is the creation of long text strings written in a four letter alphabet. The role of in silico sequence analysis is to assist biologists in the act of associating biological knowledge with these sequences, allowing investigators to make inferences and predictions that can be tested experimentally. A wide variety of software is available to the scientific community, and can be used to identify genomic objects, before predicting their biological functions. However, only a limited number of biologically interesting features can be revealed from an isolated sequence. Comparative genomics tools, on the other hand, by bringing together the information contained in numerous genomes simultaneously, allow annotators to make inferences based on the idea that evolution and natural selection are central to the definition of all biological processes. We have developed the MicroScope platform in order to offer a web-based framework for the systematic and efficient revision of microbial genome annotation and comparative analysis (http://www.genoscope.cns.fr/agc/microscope). Starting with the description of the flow chart of the annotation processes implemented in the MicroScope pipeline, and the development of traditional and novel microbial annotation and comparative analysis tools, this article emphasizes the essential role of expert annotation as a complement of automatic annotation. Several examples illustrate the use of implemented tools for the review and curation of annotations of both new and publicly available microbial genomes within MicroScope's rich integrated genome framework. The platform is used as a viewer in order to browse updated annotation information of available microbial genomes (more than 440 organisms to date), and in the context of new annotation projects (117 bacterial genomes). The human expertise gathered in the MicroScope database (about 280,000 independent annotations) contributes to improve the quality of

Ebolavirus comparative genomics

DEFF Research Database (Denmark)

Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat

2015-01-01

The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms...

78 FR 43200 - Proposed Settlement Agreement, Clean Air Act Citizen Suit

Science.gov (United States)

2013-07-19

... Social Responsibility--Los Angeles v. EPA, No. 12-56175, upon receipt of written notice from EPA that the... ENVIRONMENTAL PROTECTION AGENCY [EPA-HQ-OGC-2013-0484; FRL-9835-6] Proposed Settlement Agreement, Clean Air Act Citizen Suit AGENCY: Environmental Protection Agency (EPA). ACTION: Notice of proposed...

SIGMA: A System for Integrative Genomic Microarray Analysis of Cancer Genomes

Directory of Open Access Journals (Sweden)

Davies Jonathan J

2006-12-01

Full Text Available Abstract Background The prevalence of high resolution profiling of genomes has created a need for the integrative analysis of information generated from multiple methodologies and platforms. Although the majority of data in the public domain are gene expression profiles, and expression analysis software are available, the increase of array CGH studies has enabled integration of high throughput genomic and gene expression datasets. However, tools for direct mining and analysis of array CGH data are limited. Hence, there is a great need for analytical and display software tailored to cross platform integrative analysis of cancer genomes. Results We have created a user-friendly java application to facilitate sophisticated visualization and analysis such as cross-tumor and cross-platform comparisons. To demonstrate the utility of this software, we assembled array CGH data representing Affymetrix SNP chip, Stanford cDNA arrays and whole genome tiling path array platforms for cross comparison. This cancer genome database contains 267 profiles from commonly used cancer cell lines representing 14 different tissue types. Conclusion In this study we have developed an application for the visualization and analysis of data from high resolution array CGH platforms that can be adapted for analysis of multiple types of high throughput genomic datasets. Furthermore, we invite researchers using array CGH technology to deposit both their raw and processed data, as this will be a continually expanding database of cancer genomes. This publicly available resource, the System for Integrative Genomic Microarray Analysis (SIGMA of cancer genomes, can be accessed at http://sigma.bccrc.ca.

Genomics With Cloud Computing

OpenAIRE

Sukhamrit Kaur; Sandeep Kaur

2015-01-01

Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computin...

Genomics technologies to study structural variations in the grapevine genome

Directory of Open Access Journals (Sweden)

Cardone Maria Francesca

2016-01-01

Full Text Available Grapevine is one of the most important crop plants in the world. Recently there was great expansion of genomics resources about grapevine genome, thus providing increasing efforts for molecular breeding. Current cultivars display a great level of inter-specific differentiation that needs to be investigated to reach a comprehensive understanding of the genetic basis of phenotypic differences, and to find responsible genes selected by cross breeding programs. While there have been significant advances in resolving the pattern and nature of single nucleotide polymorphisms (SNPs on plant genomes, few data are available on copy number variation (CNV. Furthermore association between structural variations and phenotypes has been described in only a few cases. We combined high throughput biotechnologies and bioinformatics tools, to reveal the first inter-varietal atlas of structural variation (SV for the grapevine genome. We sequenced and compared four table grape cultivars with the Pinot noir inbred line PN40024 genome as the reference. We detected roughly 8% of the grapevine genome affected by genomic variations. Taken into account phenotypic differences existing among the studied varieties we performed comparison of SVs among them and the reference and next we performed an in-depth analysis of gene content of polymorphic regions. This allowed us to identify genes showing differences in copy number as putative functional candidates for important traits in grapevine cultivation.

The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

Energy Technology Data Exchange (ETDEWEB)

Nordberg, Henrik [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Cantor, Michael [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Dusheyko, Serge [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Hua, Susan [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Poliakov, Alexander [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Shabalov, Igor [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Smirnova, Tatyana [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Grigoriev, Igor V. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Dubchak, Inna [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

2013-11-12

The U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a national user facility, serves the diverse scientific community by providing integrated high-throughput sequencing and computational analysis to enable system-based scientific approaches in support of DOE missions related to clean energy generation and environmental characterization. The JGI Genome Portal (http://genome.jgi.doe.gov) provides unified access to all JGI genomic databases and analytical tools. The JGI maintains extensive data management systems and specialized analytical capabilities to manage and interpret complex genomic data. A user can search, download and explore multiple data sets available for all DOE JGI sequencing projects including their status, assemblies and annotations of sequenced genomes. In this paper, we describe major updates of the Genome Portal in the past 2 years with a specific emphasis on efficient handling of the rapidly growing amount of diverse genomic data accumulated in JGI.

MRI-guided stereotactic neurosurgical procedures in a diagnostic MRI suite: Background and safe practice recommendations.

Science.gov (United States)

Larson, Paul S; Willie, Jon T; Vadivelu, Sudhakar; Azmi-Ghadimi, Hooman; Nichols, Amy; Fauerbach, Loretta Litz; Johnson, Helen Boehm; Graham, Denise

2017-07-01

The development of navigation technology facilitating MRI-guided stereotactic neurosurgery has enabled neurosurgeons to perform a variety of procedures ranging from deep brain stimulation to laser ablation entirely within an intraoperative or diagnostic MRI suite while having real-time visualization of brain anatomy. Prior to this technology, some of these procedures required multisite workflow patterns that presented significant risk to the patient during transport. For those facilities with access to this technology, safe practice guidelines exist only for procedures performed within an intraoperative MRI. There are currently no safe practice guidelines or parameters available for facilities looking to integrate this technology into practice in conventional MRI suites. Performing neurosurgical procedures in a diagnostic MRI suite does require precautionary measures. The relative novelty of technology and workflows for direct MRI-guided procedures requires consideration of safe practice recommendations, including those pertaining to infection control and magnet safety issues. This article proposes a framework of safe practice recommendations designed for assessing readiness and optimization of MRI-guided neurosurgical interventions in the diagnostic MRI suite in an effort to mitigate patient risk. The framework is based on existing clinical evidence, recommendations, and guidelines related to infection control and prevention, health care-associated infections, and magnet safety, as well as the clinical and practical experience of neurosurgeons utilizing this technology. © 2017 American Society for Healthcare Risk Management of the American Hospital Association.

Effects of sample treatments on genome recovery via single-cell genomics

Energy Technology Data Exchange (ETDEWEB)

Clingenpeel, Scott [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Schwientek, Patrick [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Hugenholtz, Philip [Univ. of Queensland, Brisbane (Australia); Woyke, Tanja [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

2014-06-13

It is known that single-cell genomics is a powerful tool for accessing genetic information from uncultivated microorganisms. Methods of handling samples before single-cell genomic amplification may affect the quality of the genomes obtained. Using three bacterial strains we demonstrate that, compared to cryopreservation, lower-quality single-cell genomes are recovered when the sample is preserved in ethanol or if the sample undergoes fluorescence in situ hybridization, while sample preservation in paraformaldehyde renders it completely unsuitable for sequencing.

In-silico human genomics with GeneCards

Directory of Open Access Journals (Sweden)

Stelzer Gil

2011-10-01

Full Text Available Abstract Since 1998, the bioinformatics, systems biology, genomics and medical communities have enjoyed a synergistic relationship with the GeneCards database of human genes (http://www.genecards.org. This human gene compendium was created to help to introduce order into the increasing chaos of information flow. As a consequence of viewing details and deep links related to specific genes, users have often requested enhanced capabilities, such that, over time, GeneCards has blossomed into a suite of tools (including GeneDecks, GeneALaCart, GeneLoc, GeneNote and GeneAnnot for a variety of analyses of both single human genes and sets thereof. In this paper, we focus on inhouse and external research activities which have been enabled, enhanced, complemented and, in some cases, motivated by GeneCards. In turn, such interactions have often inspired and propelled improvements in GeneCards. We describe here the evolution and architecture of this project, including examples of synergistic applications in diverse areas such as synthetic lethality in cancer, the annotation of genetic variations in disease, omics integration in a systems biology approach to kidney disease, and bioinformatics tools.

Even at a Board Meeting, Your Immunity to Defamation Suits Is Limited.

Science.gov (United States)

Henderson, Donald H.

1986-01-01

Common law grants immunity for defamatory statements to administrative bodies such as boards. The limitations under which board participants function in relation to immunity from defamation suits are outlined. Includes discussion of specific court cases. (MD)

Higher Order Thinking in the Australian Army Suite of Logistic Officer Courses

National Research Council Canada - National Science Library

Bradford, Scott R

2006-01-01

.... The current Suite of Logistic Officer Courses (SOLOC) has been recently criticized for failing to meet this requirement, with the general perception that there is a distinct lack of higher-order thinking competencies within this continuum...

Microbial contamination determination of Cream suit,Traditional Ice Cream and Olovia in Yasuj City

Directory of Open Access Journals (Sweden)

SS Khoramrooz

2015-09-01

Full Text Available Background & aim: Prevalence of diseases caused by consumption of contaminated food has always been a problem all over the world, and every year spent on improving the disease is costly.Cream suit, Ice cream & olowye for ingredient substance and manufacture & preservation conditional have very high possibility for contamination.The aim of this study is Microbial contamination determination of Cream suit, Traditional Ice Cream and Olovia in Yasuj City Methods: This study is randomized cross sectional study was performed on 64 samples.The samples were taken from the ice cream and confectionery shops in Yasuj city and keep on cold box then the samples were transported in sterile conditions, to the department of medical microbiology laboratory in medical university of yasuj and  microbial contamination rate evaluated by national standard method. Collected data analysed with SPSS software for data description,from central dispersion and table frequency and draw chart.  RESULTS: The survey results showed that 40% o traditional ice cream,cream suit were infected by Staph aurous, Escherichia coli and salmonella respectly (6.7,87 and 0,(50,30 and 0.(0,0 and0 present, and no seen any bacteria on olowye. Conclusion: Due to our research contamination rate traditional ice cream,cream suit and olowye were by Staph aurous, Escherichia coli and salmonella were very high . therefore using different ways to control bacterial growth especaly E.coli the mostly transmited by fecal oral including the use of healthly and safe raw material for promoting health awareness of people involved in the food preparation and production is essential.

A Deterministic Electron, Photon, Proton and Heavy Ion Radiation Transport Suite for the Study of the Jovian System

Science.gov (United States)

Norman, Ryan B.; Badavi, Francis F.; Blattnig, Steve R.; Atwell, William

2011-01-01

A deterministic suite of radiation transport codes, developed at NASA Langley Research Center (LaRC), which describe the transport of electrons, photons, protons, and heavy ions in condensed media is used to simulate exposures from spectral distributions typical of electrons, protons and carbon-oxygen-sulfur (C-O-S) trapped heavy ions in the Jovian radiation environment. The particle transport suite consists of a coupled electron and photon deterministic transport algorithm (CEPTRN) and a coupled light particle and heavy ion deterministic transport algorithm (HZETRN). The primary purpose for the development of the transport suite is to provide a means for the spacecraft design community to rapidly perform numerous repetitive calculations essential for electron, proton and heavy ion radiation exposure assessments in complex space structures. In this paper, the radiation environment of the Galilean satellite Europa is used as a representative boundary condition to show the capabilities of the transport suite. While the transport suite can directly access the output electron spectra of the Jovian environment as generated by the Jet Propulsion Laboratory (JPL) Galileo Interim Radiation Electron (GIRE) model of 2003; for the sake of relevance to the upcoming Europa Jupiter System Mission (EJSM), the 105 days at Europa mission fluence energy spectra provided by JPL is used to produce the corresponding dose-depth curve in silicon behind an aluminum shield of 100 mils ( 0.7 g/sq cm). The transport suite can also accept ray-traced thickness files from a computer-aided design (CAD) package and calculate the total ionizing dose (TID) at a specific target point. In that regard, using a low-fidelity CAD model of the Galileo probe, the transport suite was verified by comparing with Monte Carlo (MC) simulations for orbits JOI--J35 of the Galileo extended mission (1996-2001). For the upcoming EJSM mission with a potential launch date of 2020, the transport suite is used to compute

Informational laws of genome structures

Science.gov (United States)

Bonnici, Vincenzo; Manca, Vincenzo

2016-06-01

In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined.

How genome complexity can explain the difficulty of aligning reads to genomes.

Science.gov (United States)

Phan, Vinhthuy; Gao, Shanshan; Tran, Quang; Vo, Nam S

2015-01-01

Although it is frequently observed that aligning short reads to genomes becomes harder if they contain complex repeat patterns, there has not been much effort to quantify the relationship between complexity of genomes and difficulty of short-read alignment. Existing measures of sequence complexity seem unsuitable for the understanding and quantification of this relationship. We investigated several measures of complexity and found that length-sensitive measures of complexity had the highest correlation to accuracy of alignment. In particular, the rate of distinct substrings of length k, where k is similar to the read length, correlated very highly to alignment performance in terms of precision and recall. We showed how to compute this measure efficiently in linear time, making it useful in practice to estimate quickly the difficulty of alignment for new genomes without having to align reads to them first. We showed how the length-sensitive measures could provide additional information for choosing aligners that would align consistently accurately on new genomes. We formally established a connection between genome complexity and the accuracy of short-read aligners. The relationship between genome complexity and alignment accuracy provides additional useful information for selecting suitable aligners for new genomes. Further, this work suggests that the complexity of genomes sometimes should be thought of in terms of specific computational problems, such as the alignment of short reads to genomes.

Phytozome Comparative Plant Genomics Portal

Energy Technology Data Exchange (ETDEWEB)